Search Results

Runx1+ vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo

Gonzalez Galofre ZN, Kilpatrick AM, Marques M, Sá da Bandeira D, Ventura T, Gomez Salazar M, Bouilleau L, Marc Y, Barbosa AB, Rossi F, Beltran M, van de Werken HJG, van IJcken WFJ, Henderson NC, Forbes SJ, Crisan M.Nat Commun. 2024 Feb 23PubMed

Cell-free DNA methylation

Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC.Ann Clin Transl Neurol. 2024 Mar 13PubMed

Liquid Biopsies for Colorectal Cancer and Advanced Adenoma Screening and Surveillance: What to Measure?

Eikenboom EL, Wilting SM, Deger T, Srebniak MI, Van Veghel-Plandsoen M, Boers RG, Boers JB, van IJcken WFJ, Gribnau JH, Atmodimedjo P, Dubbink HJ, Martens JWM, Spaander MCW, Wagner A.Cancers (Basel). 2023 Sep 17PubMed

Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men

Hornung, B.V.H.; Azmani, Z.; den Dekker, A.T.; Oole, E.; Ozgur, Z.; Brouwer, R.W.W.; van den Hout, M.C.G.N.; van IJcken, W.F.J.Genes 2023 Dec 16.PubMed

Single-Cell RNA Sequencing

Single-Cell RNA Sequencing of Donor-Reactive T Cells Reveals Role of Apoptosis in Donor-Specific Hyporesponsiveness of Kidney Transplant Recipients van der List ACJ, Litjens NHR, Brouwer RWW, Klepper M, den Dekker AT, van Ijcken WFJ, Betjes MGH.Int J Mol Sci. 2023 Sep 23PubMed

Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men

Hornung, B.V.H.; Azmani, Z.; den Dekker, A.T.; Oole, E.; Ozgur, Z.; Brouwer, R.W.W.; van den Hout, M.C.G.N.; van IJcken, W.F.J.Genes 2023 Dec 16.PubMed

scRNA Sequencing

PD-L1 checkpoint blockade promotes regulatory T cell activity that underlies therapy resistance van Gulijk M, van Krimpen A, Schetters S, Eterman M, van Elsas M, Mankor J, Klaase L, de Bruijn M, van Nimwegen M, van Tienhoven T, van Ijcken W, Boon L, van der Schoot J, Verdoes M, Scheeren F, van der Burg SH, […]

Center for Biomics will be closed on December 24th till January 2nd.

On behalf of all the staff at the Center for Biomics, we would like to thank you for your continued support during 2023. The Center for Biomics has been bringing you the sequencing solutions you rely on, and our team is proud to have been able to support your team throughout the past year. We’d […]

DNA

Mutation Analysis of Pancreatic Juice and Plasma for the Detection of Pancreatic Cancer Levink IJM, Jansen MPHM, Azmani Z, van IJcken W, van Marion R, Peppelenbosch MP, Cahen DL, Fuhler GM, Bruno MJ. Int J Mol Sci. 2023 Aug 23. PubMed

RNA

3D chromatin reprogramming primes human memory TH2 cells for rapid recall and pathogenic dysfunction Onrust-van Schoonhoven A, de Bruijn MJW, Stikker B, Brouwer RWW, Braunstahl GJ, van IJcken WFJ, Graf T, Huylebroeck D, Hendriks RW, Stik G, Stadhouders R. Sci Immunol. 2023 Jul 14. PubMed

cfDNA

Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels Jongbloed EM, Jansen MPHM, de Weerd V, Helmijr JA, Beaufort CM, Reinders MJT, van Marion R, van IJcken WFJ, Sonke GS, Konings IR, Jager A, Martens JWM, Wilting SM, Makrodimitris S. Sci Rep. 2023 Jun 27. PubMed

RNA

PD-L1 checkpoint blockade promotes regulatory T cell activity that underlies therapy resistance van Gulijk M, van Krimpen A, Schetters S, Eterman M, van Elsas M, Mankor J, Klaase L, de Bruijn M, van Nimwegen M, van Tienhoven T, van Ijcken W, Boon L, van der Schoot J, Verdoes M, Scheeren F, van der Burg SH, […]

RNA

Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis Tyc O, Kulkarni P, Ossowicki A, Tracanna V, Medema MH, van Baarlen P, van IJcken WFJ, Verhoeven KJF, Garbeva P. mSystems. 2023 Feb 23. PubMed

RNA

Rabies virus uniquely reprograms the transcriptome of human monocyte-derived macrophages Embregts CWE, Wentzel AS, den Dekker AT, van IJcken WFJ, Stadhouders R, GeurtsvanKessel CH. Front Cell Infect Microbiol. 2023 Jan 31. PubMed

MeD-seq

Retrospective analysis of enhancer activity and transcriptome history Boers R, Boers J, Tan B, van Leeuwen ME, Wassenaar E, Sanchez EG, Sleddens E, Tenhagen Y, Mulugeta E, Laven J, Creyghton M, Baarends W, van IJcken WFJ, Gribnau J. Nat Biotechnol. 2023 Feb 23. PubMed

RNA sequencing

Zeb2 DNA-Binding Sites in Neuroprogenitor Cells Reveal Autoregulation and Affirm Neurodevelopmental Defects, Including in Mowat-Wilson Syndrome Birkhoff JC, Korporaal AL, Brouwer RWW, Nowosad K, Milazzo C, Mouratidou L, van den Hout MCGN, van IJcken WFJ, Huylebroeck D, Conidi A. Genes (Basel). 2023 Mar 2. PubMed

Med-seq

Genome-wide analysis toward the epigenetic aetiology of myelodysplastic syndrome disease progression and pharmacoepigenomic basis of hypomethylating agents drug treatment response Siamoglou S, Boers R, Koromina M, Boers J, Tsironi A, Chatzilygeroudi T, Lazaris V, Verigou E, Kourakli A, van IJcken WFJ, Gribnau J, Symeonidis A, Patrinos GP. Hum Genomics. 2023 Apr 25. PubMed

MGC courses open for registration

You can (pre-)register for the following MGC course (see website: http://www.medgencentre.com/MGC-courses/): Next Generation Sequencing data analysis: 28-30 August, 2023 Location: LUMC, building 1, lecture room 4 and others Organizers: Susan Kloet, Judith de Boer, Wilfred van IJcken, Saskia Hiltermann en Leon Mei The aim of the course is to give a broad overview of the […]

RNA Sequencing

USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3. Sijm A, Atlasi Y, van der Knaap JA, Wolf van der Meer J, Chalkley GE, Bezstarosti K, Dekkers DHW, Doff WAS, Ozgur Z, van IJcken WFJ, Demmers JAA, Verrijzer CP. Sci Adv. 2022 Nov 4. PubMed

DNA Sequencing

CABA-V7: a prospective biomarker selected trial of cabazitaxel treatment in AR-V7 positive prostate cancer patients. Isebia KT, Mostert B, Belderbos BPS, Buck SAJ, Helmijr JCA, Kraan J, Beaufort CM, Van MN, Oomen-de Hoop E, Sieuwerts AM, van IJcken WFJ, van den Hout-van Vroonhoven MCGN, Brouwer RWW, Oole E, Hamberg P, Haberkorn BCM, Helgason HH, de […]

Center for Biomics will be closed on December 26th till January 3rd.

On behalf of all the staff at the Center for Biomics, we would like to thank you for your continued support during 2022. The Center for Biomics has been bringing you the sequencing solutions you rely on, and our team is proud to have been able to support your team throughout the past year. We’d […]

RNA Sequencing

Molecular and behavioral consequences of Ube3a gene overdosage in mice. Punt AM, Judson MC, Sidorov MS, Williams BN, Johnson NS, Belder S, den Hertog D, Davis CR, Feygin MS, Lang PF, Jolfaei MA, Curran PJ, van IJcken WF, Elgersma Y, Philpot BD. JCI Insight. 2022 Sep. PubMed

Presentations

Please check video for The Genomics Core Facility Tour

RNA Sequencing

Bio-distribution and longevity of mesenchymal stromal cell derived membrane particles Vos J, Tejeda-Mora H, Merino A, Wu L, Woud WW, Demmers JAA, van IJcken WFJ, Reinders MEJ, Hoogduijn MJ. J Control Release. 2022 Sep 7. PubMed

RNA Sequencing

A kinase inhibitor screen reveals MEK1/2 as a novel therapeutic target to antagonize IGF1R-mediated antiestrogen resistance in ERα-positive luminal breast cancer Wester L, Venneker S, Hazenoot M, Pont C, Koedoot E, Timmermans AM, Martens JWM, Jansen MPHM, Kockx CEM, van IJcken WFJ, Meerman JHN, Zhang Y, van de Water B. Biochem Pharmacol. 2022 Aug 28. […]

DNA Sequencing

Effect of bovine milk fat-based infant formulae on microbiota, metabolites and stool parameters in healthy term infants in a randomized, crossover, placebo-controlled trial Looijesteijn E, Brouwer RWW, Schoemaker RJW, Ulfman LH, Ham SL, Jeurink P, Karaglani E, van IJcken WFJ, Manios Y. BMC Nutr. 2022 Aug 29. PubMed

RNA Sequencing

Dominant-acting CSF1R variants cause microglial depletion and altered astrocytic phenotype in zebrafish and adult-onset leukodystrophy Berdowski WM, van der Linde HC, Breur M, Oosterhof N, Beerepoot S, Sanderson L, Wijnands LI, de Jong P, Tsai-Meu-Chong E, de Valk W, de Witte M, van IJcken WFJ, Demmers J, van der Knaap MS, Bugiani M, Wolf NI, […]

RNA Sequencing

Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints. Nowosad K, Brouwer RWW, Odrzywolski A, Korporaal AL, Gielniewski B, Wojtaś B, van IJcken WFJ, Grosveld F, Huylebroeck D, Tylzanowski P. Sci Rep. 2022 Jul 27. PubMed

single-cell RNA-sequencing

PDGFRβ + cells play a dual role as hematopoietic precursors and niche cells during mouse ontogeny. Sá da Bandeira D, Kilpatrick AM, Marques M, Gomez-Salazar M, Ventura T, Gonzalez ZN, Stefancova D, Rossi F, Vermeren M, Vink CS, Beltran M, Henderson NC, Jung B, van der Linden R, van de Werken HJG, van Ijcken WFJ, […]

Whole exome sequencing

A multiplex pedigree with pathologically confirmed multiple system atrophy and Parkinson’s disease with dementia. Fanciulli A, Leys F, Lehner F, Sidoroff V, Ruf VC, Raccagni C, Mahlknecht P, Kuipers DJS, van IJcken WFJ, Stockner H, Musacchio T, Volkmann J, Monoranu CM, Stankovic I, Breedveld G, Ferraro F, Fevga C, Windl O, Herms J, Kiechl S, […]

RNA sequencing

Dominant-acting CSF1R variants cause microglial depletion and altered astrocytic phenotype in zebrafish and adult-onset leukodystrophy. Berdowski WM, van der Linde HC, Breur M, Oosterhof N, Beerepoot S, Sanderson L, Wijnands LI, de Jong P, Tsai-Meu-Chong E, de Valk W, de Witte M, van IJcken WFJ, Demmers J, van der Knaap MS, Bugiani M, Wolf NI, […]

4C-seq assay

JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation. Vicioso-Mantis M, Fueyo R, Navarro C, Cruz-Molina S, van IJcken WFJ, Rebollo E, Rada-Iglesias Á, Martínez-Balbás MA. Nat Commun. 2022 Jun 7. PubMed

single-cell RNA-sequencing

Comparative single-cell RNA-sequencing profiling of BMP4-treated primary glioma cultures reveals therapeutic markers. Verploegh ISC, Conidi A, Brouwer RWW, Balcioglu HE, Karras P, Makhzami S, Korporaal A, Marine JC, Lamfers M, van IJcken WFJ, Leenstra S, Huylebroeck D. Neuro Oncol. 2022 May 26. PubMed

Single-Cell

Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level. Litjens NHR, Langerak AW, Azmani Z, den Dekker X, Betjes MGH, Brouwer RWW, van IJcken WFJ.. Methods Mol Biol. 2022. PubMed

single-cell RNA sequencing

Kidney Organoids Are Capable of Forming Tumors, but Not Teratomas. Shankar AS, Du Z, Tejeda Mora H, Boers R, Cao W, van den Bosch TPP, Korevaar SS, Boers J, van IJcken WFJ, Bindels EMJ, Eussen B, de Klein A, Pan Q, Oudijk L, Clahsen-van Groningen MC, Hoorn EJ, Baan CC, Gribnau J, Hoogduijn MJ. Stem […]

CRISPRs

CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. van Riet J, Saha C, Strepis N, Brouwer RWW, Martens-Uzunova ES, van de Geer WS, Swagemakers SMA, Stubbs A, Halimi Y, Voogd S, Tanmoy AM, Komor MA, Hoogstrate Y, Janssen B, Fijneman RJA, Niknafs YS, Chinnaiyan AM, van IJcken […]

DNA methylation

Temozolomide and Radiotherapy versus Radiotherapy Alone in Patients with Glioblastoma, IDH-wildtype: Post Hoc Analysis of the EORTC Randomized Phase III CATNON Trial. Tesileanu CMS, Sanson M, Wick W, Brandes AA, Clement PM, Erridge SC, Vogelbaum MA, Nowak AK, Baurain JF, Mason WP, Wheeler H, Chinot OL, Gill S, Griffin M, Rogers L, Taal W, Rudà […]

RNA Sequencing

NOXA expression drives synthetic lethality to RUNX1 inhibition in pancreatic cancer. Doffo J, Bamopoulos SA, Köse H, Orben F, Zang C, Pons M, den Dekker AT, Brouwer RWW, Baluapuri A, Habringer S, Reichert M, Illendula A, Krämer OH, Schick M, Wolf E, van IJcken WFJ, Esposito I, Keller U, Schneider G, Wirth M. Proc Natl […]

SNP-array

Unraveling the Genetics of Congenital Diaphragmatic Hernia: An Ongoing Challenge. Brosens E, Peters NCJ, van Weelden KS, Bendixen C, Brouwer RWW, Sleutels F, Bruggenwirth HT, van Ijcken WFJ, Veenma DCM, Otter SCMC, Wijnen RMH, Eggink AJ, van Dooren MF, Reutter HM, Rottier RJ, Schnater JM, Tibboel D, de Klein A. Front Pediatr. 2022 Feb 3. […]

DNA methylation

Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells. Mira-Bontenbal H, Tan B, Gontan C, Goossens S, Boers RG, Boers JB, Dupont C, van Royen ME, IJcken WFJ, French P, Bedalov A, Gribnau J. Stem Cell Reports. 2022 Mar 8. PubMed

Biomics will be closed on 26-07-2022 and 29-07-2022

Biomics will be closed on Tuesday July 26th and Friday 29th. There will not be courier services to BaseClear at Thuesday 26th. Apologies for the inconvenience.

Biomics will be closed on 26-05-2022 and 27-05-2022

We are closed on Ascension. Biomics will be closed on Thursday May 26th and Friday 27th. There will not be courier services to BaseClear at Thursday 26th. Apologies for the inconvenience.

CellenOne

blabla

Public holidays

Every year in April we have some public holidays. We will be open on Good Friday 15 April. During Easter Monday (April 18) and Kings day we will be closed (April 27). Warmest wises!

RNA Sequencing

Epigenomic analysis of KLF1 haploinsufficiency in primary human erythroblasts. Heshusius S, Grech L, Gillemans N, Brouwer RWW, den Dekker XT, van IJcken WFJ, Nota B, Felice AE, van Dijk TB, von Lindern M, Borg J, van den Akker E, Philipsen S. Sci Rep. 2022 Jan 10. PubMed

SNP-array

Unraveling the Genetics of Congenital Diaphragmatic Hernia: An Ongoing Challenge. Brosens E, Peters NCJ, van Weelden KS, Bendixen C, Brouwer RWW, Sleutels F, Bruggenwirth HT, van Ijcken WFJ, Veenma DCM, Otter SCMC, Wijnen RMH, Eggink AJ, van Dooren MF, Reutter HM, Rottier RJ, Schnater JM, Tibboel D, de Klein A. Front Pediatr. 2022 Feb 3. […]

DNA methylation

Genome-wide aberrant methylation in primary metastatic UM and their matched metastases. Smit KN, Boers R, Vaarwater J, Boers J, Brands T, Mensink H, Verdijk RM, van IJcken WFJ, Gribnau J, de Klein A, Kilic E. Sci Rep. 2022 Jan 7. PubMed

ATAC-seq

NOXA expression drives synthetic lethality to RUNX1 inhibition in pancreatic cancer. Doffo J, Bamopoulos SA, Köse H, Orben F, Zang C, Pons M, den Dekker AT, Brouwer RWW, Baluapuri A, Habringer S, Reichert M, Illendula A, Krämer OH, Schick M, Wolf E, van IJcken WFJ, Esposito I, Keller U, Schneider G, Wirth M. Proc Natl […]

RNA Sequencing

Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells. Mira-Bontenbal H, Tan B, Gontan C, Goossens S, Boers RG, Boers JB, Dupont C, van Royen ME, IJcken WFJ, French P, Bedalov A, Gribnau J. Stem Cell Reports. 2022 Mar 8. PubMed

RNA Sequencing

Endothelial Zeb2 preserves the hepatic angioarchitecture and protects against liver fibrosis. de Haan W, Dheedene W, Apelt K, Décombas-Deschamps S, Vinckier S, Verhulst S, Conidi A, Deffieux T, Staring MW, Vandervoort P, Caluwé E, Lox M, Mannaerts I, Takagi T, Jaekers J, Berx G, Haigh J, Topal B, Zwijsen A, Higashi Y, van Grunsven LA, […]

DNA methylation

Temozolomide and radiotherapy versus radiotherapy alone in patients with glioblastoma, IDH-wildtype: post-hoc analysis of the EORTC randomized phase 3 CATNON trial. Tesileanu CMS, Sanson M, Wick W, Brandes AA, Clement PM, Erridge SC, Vogelbaum MA, Nowak AK, Baurain JF, Mason WP, Wheeler H, Chinot OL, Gill S, Griffin M, Rogers L, Taal W, Rudà R, […]

ICELL8 Single Cell customer studies

ICELL8 Single Cell customer studies This brochure was made by Takara Bio to highlight customer studies using the the iCell8 amongst them a succesful collaboration between the labs of Nicolle Litjens, Ton Langerak, Michel Betjens and the Center for Biomics. The results were published in Litjens paper et al. PubMed

NGS Intake Extern

NGS Intake for extern Customers Dear Customer If you wish to send in samples for Next Generation Sequencing, please contact us via email at ecb@erasmusmc.nl before sending your samples. We will discuss your project and needs, and send you a quotation for your project. If you have submitted samples previously, and know already what you […]

Delayed Bioanalyzer Chips

Bioanalyzer RNA Nano chips are currently out of stock. New chips have been ordered but unfortunately there is a delay in delivery by Agilent. Sorry for the inconvenience.

Biomics is closed from December 30th to January 5th.

Biomics is closed from December 30th to January 5th. During the holidays there will not be courier services to BaseClear. Wishing you a Merry Christmas and a Happy New Year.

Stavast

The tumor suppressor MIR139 is silenced by POLR2M to promote AML oncogenesis. Stavast CJ, van Zuijen I, Karkoulia E, Özçelik A, van Hoven-Beijen A, Leon LG, Voerman JSA, Janssen GMC, van Veelen PA, Burocziova M, Brouwer RWW, van IJcken WFJ, Maas A, Bindels EM, van der Velden VHJ, Schliehe C, Katsikis PD, Alberich-Jorda M, Erkeland […]

Brosens

Heritability and De Novo Mutations in Oesophageal Atresia and Tracheoesophageal Fistula Aetiology. Brosens E, Brouwer RWW, Douben H, van Bever Y, Brooks AS, Wijnen RMH, van IJcken WFJ, Tibboel D, Rottier RJ, de Klein A. Genes (Basel). 2021 Oct 10. PubMed

MacKenzie

The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model. MacKenzie KC, Garritsen R, Chauhan RK, Sribudiani Y, de Graaf BM, Rugenbrink T, Brouwer R, van Ijcken WFJ, de Blaauw I, Brooks AS, Sloots CEJ, Meeuwsen CJHM, Wijnen RM, Newgreen DF, Burns AJ, Hofstra RMW, Alves MM, Brosens E. Int J Mol Sci. […]

Deger

High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments. Deger T, Boers RG, de Weerd V, Angus L, van der Put MMJ, Boers JB, Azmani Z, van IJcken WFJ, Grünhagen DJ, van Dessel LF, Lolkema MPJK, Verhoef C, Sleijfer S, Martens JWM, Gribnau J, Wilting […]

Bleckwehl

Enhancer-associated H3K4 methylation safeguards in vitro germline competence. Bleckwehl T, Crispatzu G, Schaaf K, Respuela P, Bartusel M, Benson L, Clark SJ, Dorighi KM, Barral A, Laugsch M, van IJcken WFJ, Manzanares M, Wysocka J, Reik W, Rada-Iglesias Á. Nat Commun. 2021 Oct 1. PubMed

DNA Methylation

CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. Soochit W, Sleutels F, Stik G, Bartkuhn M, Basu S, Hernandez SC, Merzouk S, Vidal E, Boers R, Boers J, van der Reijden M, Geverts B, van Cappellen WA, van den Hout M, Ozgur Z, van IJcken WFJ, Gribnau […]

van der Sijde

Circulating TP53 mutations are associated with early tumor progression and poor survival in pancreatic cancer patients treated with FOLFIRINOX. van der Sijde F, Azmani Z, Besselink MG, Bonsing BA, de Groot JWB, Groot Koerkamp B, Haberkorn BCM, Homs MYV, van IJcken WFJ, Janssen QP, Lolkema MP, Luelmo SAC, Mekenkamp LJM, Mustafa DAM, van Schaik RHN, […]

Ralf

RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates. Ralf A, Zandstra D, Weiler N, van Ijcken WFJ, Sijen T, Kayser M. Forensic Sci Int Genet. 2021 Sep 11. PubMed

Boltsis

Low Input Targeted Chromatin Capture (Low-T2C). Boltsis I, Nowosad K, Brouwer RWW, Tylzanowski P, van IJcken WFJ, Huylebroeck D, Grosveld F, Kolovos P. Methods Mol Biol. 2021. PubMed

Wessels

Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S. Blood […]

Haan

Endothelial Zeb2 preserves the hepatic angioarchitecture and protects against liver fibrosis. de Haan W, Dheedene W, Apelt K, Décombas-Deschamps S, Vinckier S, Verhulst S, Conidi A, Deffieux T, Staring MW, Vandervoort P, Caluwé E, Lox M, Mannaerts I, Takagi T, Jaekers J, Berx G, Haigh J, Topal B, Zwijsen A, Higashi Y, van Grunsven LA, […]

Giraud

Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis. Giraud G, Kolovos P, Boltsis I, van Staalduinen J, Guyot B, Weiss-Gayet M, IJcken WV, Morlé F, Grosveld F. iScience. 2021 Feb 20. PubMed

Pachano

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. Pachano T, Sánchez-Gaya V, Ealo T, Mariner-Faulí M, Bleckwehl T, Asenjo HG, Respuela P, Cruz-Molina S, Muñoz-San Martín M, Haro E, van IJcken WFJ, Landeira D, Rada-Iglesias A. Nat Genet. 2021 Jul. PubMed

Marques

Identification of SPRY4 as a Novel Candidate Susceptibility Gene for Familial Nonmedullary Thyroid Cancer. Marques IJ, Gomes I, Pojo M, Pires C, Moura MM, Cabrera R, Santos C, van IJcken WFJ, Teixeira MR, Ramalho JS, Leite V, Cavaco BM. Thyroid. 2021 Jun 3. PubMed

Slot

Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus. Slot E, Boers R, Boers J, van IJcken WFJ, Tibboel D, Gribnau J, Rottier R, de Klein A. Clin Epigenetics. 2021 Jul 29. PubMed

Rao

Selective cell death in HIV-1-infected cells by DDX3 inhibitors leads to depletion of the inducible reservoir. Rao S, Lungu C, Crespo R, Steijaert TH, Gorska A, Palstra RJ, Prins HAB, van Ijcken W, Mueller YM, van Kampen JJA, Verbon A, Katsikis PD, Boucher CAB, Rokx C, Gruters RA, Mahmoudi T. Nat Commun. 2021 Apr 30. […]

Tesileanu

Prognostic significance of genome-wide DNA methylation profiles within the randomised, phase 3, EORTC CATNON trial on non-1p/19q deleted anaplastic glioma. Tesileanu CMS, van den Bent MJ, Sanson M, Wick W, Brandes AA, Clement PM, Erridge SC, Vogelbaum MA, Nowak AK, Baurain JF, Mason WP, Wheeler H, Chinot OL, Gill S, Griffin M, Rogers L, Taal […]

Biomics will be closed on 26-04-2021 and 14-05-2021

Biomics will be closed on Monday April 26th and on Friday May 14th. There will not be courier services to BaseClear on Monday April 26th. Apologies for the inconvenience.

Biomics logins are currently not available

It is not possible at this moment to login at the Biomics website. If you want to do an NGS intake or book an apparatus please send us an email to ecb@erasmusmc.nl. We don’t know when this issue is fixed. Sorry for the inconvenience

Ploeg van der

Steroid-resistant human inflammatory ILC2s are marked by CD45RO and elevated in type 2 respiratory diseases. van der Ploeg EK, Golebski K, van Nimwegen M, Fergusson JR, Heesters BA, Martinez-Gonzalez I, Kradolfer CMA, van Tol S, Scicluna BP, de Bruijn MJW, de Boer GM, Tramper-Stranders GA, Braunstahl GJ, van IJcken WFJ, Nagtegaal AP, van Drunen CM, […]

Groeneveldt

The Bone-Forming Properties of Periosteum-Derived Cells Differ Between Harvest Sites. Groeneveldt LC, Herpelinck T, Maréchal M, Politis C, van IJcken WFJ, Huylebroeck D, Geris L, Mulugeta E, Luyten FP. Front Cell Dev Biol. 2020 Nov 25. PubMed

Scheenstra

Comparison of the PU.1 transcriptional regulome and interactome in human and mouse inflammatory dendritic cells. Scheenstra MR, Martínez-Botía P, Acebes-Huerta A, Brouwer RWW, Caballero-Sánchez N, Gillemans N, De Bleser P, Nota B, De Cuyper IM, Salunkhe V, Woltman AM, van de Laar L, Rijkers E, Demmers JAA, van IJcken WFJ, Philipsen S, van den Berg […]

Brosens

Histological, immunohistochemical and transcriptomic characterization of human tracheoesophageal fistulas. Brosens E, Felix JF, Boerema-de Munck A, de Jong EM, Lodder EM, Swagemakers S, Buscop-van Kempen M, de Krijger RR, Wijnen RMH, van IJcken WFJ, van der Spek P, de Klein A, Tibboel D, Rottier RJ. PLoS One. 2020 Nov 17. PubMed

Timbergen

Differentially Methylated Regions in Desmoid-Type Fibromatosis: A Comparison Between CTNNB1 S45F and T41A Tumors. Timbergen MJM, Boers R, Vriends ALM, Boers J, van IJcken WFJ, Lavrijsen M, Grünhagen DJ, Verhoef C, Sleijfer S, Smits R, Gribnau J, Wiemer EAC. Front Oncol. 2020 Oct 29. PubMed

Nextera DNA Flex

Background:   The Nextera DNA Flex Library Preparation uses On-Bead Tagmentation and subsequent PCR to create an Illumina sequencing library from a genomic DNA sample. This has enabled major improvements in library preparation performance. The Nextera DNA Flex Library Preparation Kit produces highly uniform and consistent insert sizes (300–350 bp), across a wide DNA input range (1-500 ng). […]

CRISPR sequencing

Background For CRISPR sequencing the customer performs a CRISPR Cas9 screen in which guide RNAs are built into the Sample DNA (https://pubmed.ncbi.nlm.nih.gov/25075903/). We prepare this sample for Illumina sequencing by performing a PCR reaction to amplify the lentiCRISPR sgRNAs and a second PCR reaction to attach adaptors and indexes. After cleanup, the library is ready […]

ChIPThruPLEX Sequencing

Map Chromatin associated proteins with Chip Sequencing ChIPThruPLEX Sequencing   Background: A ChIP DNA sample will be handed in by the customer. From this, we prepare the ChIP sequence library using the Thruplex DNA seq kit. ChIP experiments have usually a very low yield of ChIP DNA. The The Thruplex DNA seq kit is very […]

Omni-ATAC sequencing

  Map Chromatin Accessibility Genome-wide with ATAC Sequencing ATAC-Sequencing   Background: Omni-ATAC is an improved ATAC-seq protocol(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/) for chromatin accessibility profiling that works universally across multiple cell types and cell contexts with significant improvement of signal-to-background ratio and information content. The Omni-ATAC protocol enables chromatin accessibility profiling from material that was previously deemed intractable including […]

Next Generation Sequencing old

Next Generation Sequencing Platforms   Biomics operates a fexible NGS pipeline with HiSeq2500, HiSeq4000 and Miseq sequencers. Please check our overview comparing the sequencers. The Illumina NGS platforms are superior due to the large number of short sequence reads and the speed of production Omni-ATAC Sequencing ChIPThruplex V2 Sequencing (from: Buenrostro et al) Assay for […]

Biomics is closed from December 24th to January 4th.

Biomics is closed from December 24th to January 4th. During the holidays there will not be courier services to BaseClear. Wishing you a Merry Christmas and a Happy New Year.

Single Cell Dispensing & Sequencing

Single Cell Dispensing & Sequencing https://www.takarabio.com/learning-centers/automation-systems/icell8-introduction/icell8-technology-overview ICELL8 Single-Cell System (Takara) The ICELL8 Single Cell System is an advanced, integrated automation platform that combines the power of dispensing a single cell suspension into a 5,184-nanowell chip followed by imaging. This allows us to perform a rapid dispense of 8 samples simultaneously into a nanowell chip. Before […]

Ouwendijk

Alveolar barrier disruption in varicella pneumonia is associated with neutrophil extracellular trap formation. Ouwendijk WJ, van den Ham HJ, Delany MW, van Kampen JJ, van Nierop GP, Mehraban T, Zaaraoui-Boutahar F, van IJcken WF, van den Brand JM, de Vries RD, Andeweg AC, Verjans GM. JCI Insight. 2020 Nov 5. PubMed

Litjens

Validation of a Combined Transcriptome and T Cell Receptor Alpha/Beta (TRA/TRB) Repertoire Assay at the Single Cell Level for Paucicellular Samples. Litjens NHR, Langerak AW, van der List ACJ, Klepper M, de Bie M, Azmani Z, den Dekker AT, Brouwer RWW, Betjes MGH, Van IJcken WFJ. Front Immunol. 2020 Aug 28. PubMed

CHANGED: BaseClear Sample intake

From November 16th onwards, samples are sent to Baseclear every Monday, Tuesday, Wednesday and Thursday. Sample delivery time has not changed. Deliver your samples before 12h and they will arrive at Baseclear the next day. Please make sure that you deliver your samples before 12h at Biomics!

Stoszko

Gliotoxin, identified from a screen of fungal metabolites, disrupts 7SK snRNP, releases P-TEFb, and reverses HIV-1 latency. Stoszko M, Al-Hatmi AMS, Skriba A, Roling M, Ne E, Crespo R, Mueller YM, Najafzadeh MJ, Kang J, Ptackova R, LeMasters E, Biswas P, Bertoldi A, Kan TW, de Crignis E, Sulc M, Lebbink JHG, Rokx C, Verbon […]

Klei

Hemolysis in the spleen drives erythrocyte turnover. Klei TRL, Dalimot JJ, Nota B, Veldthuis M, Mul E, Rademakers T, Hoogenboezem M, Nagelkerke SQ, van IJcken WFJ, Oole E, Svendsen P, Moestrup SK, van Alphen F, Meijer AB, Kuijpers TW, Zwieten RV, van Bruggen R. Blood. 2020 Aug 10. PubMed

Birkhoff

Targeted Chromatin Conformation (T2C) analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation. Birkhoff JC, Brouwer RWW, Kolovos P, Korporaal AL, Bermejo-Santos A, Boltsis I, Nowosad K, Hout MCGN, Grosveld FG, van IJcken WFJ, Huylebroeck D, Conidi A. Hum Mol Genet. 2020 Jul 6. PubMed

Zhao

Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation. Zhao M, Kiernan CH, Stairiker CJ, Hope JL, Leon LG, van Meurs M, Brouwers-Haspels I, Boers R, Boers J, Gribnau J, van IJcken WFJ, Bindels EM, Hoogenboezem RM, Erkeland SJ, Mueller YM, Katsikis PD. PLoS Pathog. 2020 Jun […]

Parenti

MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia De Lange Syndrome. Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, van Staveren T, van IJcken WFJ, Strom TM, Pié […]

van der Spek

Exome Sequencing Analysis Identifies Rare Variants in ATM and RPL8 That Are Associated With Shorter Telomere Length. van der Spek A, Warner SC, Broer L, Nelson CP, Vojinovic D, Ahmad S, Arp PP, Brouwer RWW, Denniff M, van den Hout MCGN, van Rooij JGJ, Kraaij R, van IJcken WFJ, Samani NJ, Ikram MA, Uitterlinden AG, […]

Neagu

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states. Neagu A, van Genderen E, Escudero I, Verwegen L, Kurek D, Lehmann J, Stel J, Dirks RAM, van Mierlo G, Maas A, Eleveld C, Ge Y, den Dekker AT, Brouwer RWW, van IJcken WFJ, Modic M, Drukker M, Jansen JH, Rivron […]

Access to general equipment on the 6th floor

From Saturday September 25th access to the general equipment room will not be limited anymore. We advice you to maintain a proper distance. Equipment such as the Bioanalyzer, Tapestation, Sonicator, Femto Pulse and Covaris still needs to be booked.

Restart Laboratory Activities

From May 6th onwards the Genomics core facility will restart our laboratory services. Laboratory project delivery times may be affected due to the Corona pandemic and temporarily closure of the laboratory. We are glad that we can continue to contribute to the progress of science using Genomics and Bioinformatics. Weekly on Tuesday and Thursday samples […]

Robotics

Robotics Bravo Liquid Handling System Janus Liquid Handling System Biomics has a Bravo Liquid Handling System for automated sample preparation e.g. Agilent SureSelect Whole Exome Capturing Please contact us for details Biomics has a Janus Liquid Handling System Please contact us for details Mosquito Liquid Handling System I.DOT Liquid Handling System Biomics has a Mosquito […]

Imaging

  Imaging (multiplex western blot on Odyssey) Biomics has a number of imaging options available. (quantification on Typhoon) Odyssey Typhoon Li-cor Odyssey CLx & Odyssey Classic Direct fluorescence detection Typhoon 5 & Typhoon FLA 9500 PhosphorImaging Fluorescence Chemiluminescence Detection Amersham Imager 600 Amersham Imager 600 CCD camera to acquire images from protein and DNA samples […]

Ten Kate

Infantile hypertrophic pyloric stenosis in patients with esophageal atresia. Ten Kate CA, Brouwer RWW, van Bever Y, Martens VK, Brands T, van Beelen NWG, Brooks AS, Huigh D, van der Helm RM, Eussen BHFMM, van IJcken WFJ, IJsselstijn H, Tibboel D, Wijnen RMH, de Klein A, Hofstra RMW, Brosens E. Birth Defects Res. 2020 Apr […]

Tindemans

Notch signaling licenses allergic airway inflammation by promoting Th2 cell lymph node egress. Tindemans I, van Schoonhoven A, KleinJan A, de Bruijn MJ, Lukkes M, van Nimwegen M, van den Branden A, Bergen IM, Corneth OBJ, van IJcken WF, Stadhouders R, Hendriks RW. J Clin Invest. 2020 Apr 7. PubMed

Casa

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control. Casa V, Moronta Gines M, Gade Gusmao E, Slotman JA, Zirkel A, Josipovic N, Edwin O, van IJcken WFJ, Houtsmuller AB, Papantonis A, Wendt KS. Genome Res. 2020 Apr 6. PubMed

Deryckere

Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb. Deryckere A, Stappers E, Dries R, Peyre E, van den Berghe V, Conidi A, Zampeta FI, Francis A, Bresseleers M, Stryjewska A, Vanlaer R, Maas E, Smal IV, van IJcken WFJ, Grosveld FG, Nguyen L, Huylebroeck D, Seuntjens E. Development. […]

Folkerts

Butyrate inhibits human mast cell activation via epigenetic regulation of FcεRI-mediated signaling. Folkerts J, Redegeld F, Folkerts G, Blokhuis B, van den Berg MPM, de Bruijn MJW, van IJcken WFJ, Junt T, Tam SY, Galli SJ, Hendriks RW, Stadhouders R, Maurer M. Allergy. 2020 Feb 28. PubMed

Kenter

Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients. Kenter AT, Rentmeester E, van Riet J, Boers R, Boers J, Ghazvini M, Xavier VJ, van Leenders GJLH, Verhagen PCMS, van Til ME, Eussen B, Losekoot M, de Klein A, Peters DJM, van IJcken WFJ, van de Werken HJG, Zietse R, Hoorn EJ, […]

The ECB personal will stay at home due to the Corona measures of the Dutch government until further notice.

The ECB personal will stay at home due to the Corona measures of the Dutch government until further notice. In case you need assistance please email ecb@erasmusmc.nl Please anticipate a delayed response. This new measure is necessary in view of the risk of infection, the importance of continuity of care, continuity of business operations and […]

Vos

MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma. Vos M, Boers R, Vriends ALM, Boers J, van Kuijk PF, van Houdt WJ, van Leenders GJLH, Wagrodzki M, van IJcken WFJ, Gribnau J, Grünhagen DJ, Verhoef C, Sleijfer S, Wiemer EAC. PLos One., 2020 Jan 23 PubMed

Liu

CREPT Promotes Melanoma Progression Through Accelerated Proliferation and Enhanced Migration by RhoA-Mediated Actin Filaments and Focal Adhesion Formation. Liu H, Seynhaeve ALB, Brouwer RWW, van IJcken WFJ, Yang L, Wang Y, Chang Z, Ten Hagen TLM. Cancers (Basel)., 2019 Dec 20 PubMed

Wisnumurti

G6PD genetic variations in neonatal Hyperbilirubinemia in Indonesian Deutromalay population. Wisnumurti DA, Sribudiani Y, Porsch RM, Maskoen AM, Rahayuningsih SE, Asni EK, Sleutels F, van Ijcken WFJ, Sukadi A, Achmad TH. BMC Pediatr., 2019 Dec 20 PubMed

Perenthaler

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases. Perenthaler E, Nikoncuk A, Yousefi S, Berdowski WM, Alsagob M, Capo I, van der Linde HC, van den Berg P, Jacobs EH, Putar D, Ghazvini M, Aronica E, van IJcken WFJ, […]

Gerritsen

Characterization of the ferret TRB locus guided by V, D, J, and C gene expression analysis. Gerritsen B, Pandit A, Zaaraoui-Boutahar F, van den Hout MCGN, van IJcken WFJ, de Boer RJ, Andeweg AC. Immunogenetics, 2019 Dec 3 PubMed

Biomics will be closed on December 23rd till January 5th.

Biomics will be closed on December 23rd till January 5th. Wishing you a Merry Christmas and a Happy New Year.

Weiterer

Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner. Weiterer SS, Meier-Soelch J, Georgomanolis T, Mizi A, Beyerlein A, Weiser H, Brant L, Mayr-Buro C, Jurida L, Beuerlein K, Müller H, Weber A, Tenekeci U, Dittrich-Breiholz O, Bartkuhn M, Nist A, Stiewe T, van IJcken WF, Riedlinger T, Schmitz […]

Introduction to Western Blotting on Odyssey

You will learn about the science, best practices, and mechanics behind each step in the Western blot workflow from preparing your samples through collecting your data. Includes 8 courses, 64 lessons, Lifetime access and Certificate of completion. 8 steps to better Western blots: Check out the “Introduction to Western Blotting” learning path on the Lambda […]

Carrión

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Víctor J. Carrión, Juan Perez-Jaramillo, Viviane Cordovez, Vittorio Tracanna, Mattias de Hollander, Daniel Ruiz-Buck, Lucas W. Mendes, Wilfred F.J. van Ijcken, Ruth Gomez-Exposito, Somayah S. Elsayed, Prarthana Mohanraju, Adini Arifah, John van der Oost, Joseph N. Paulson, Rodrigo Mendes, Gilles P. van Wezel, Marnix H. […]

Muggen

The presence of CLL-associated stereotypic B cell receptors in the normal BCR repertoire from healthy individuals increases with age. Muggen AF, de Jong M, Wolvers-Tettero ILM, Kallemeijn MJ, Teodósio C, Darzentas N, Stadhouders R, IJspeert H, van der Burg M, van IJcken WF, Verhaar JAN, Abdulahad WH, Brouwer E, Boots AMH, Hendriks RW, van Dongen […]

Kuipers

Late-onset phenotype associated with a homozygous GJC2 missense mutation in a Turkish family. Kuipers DJS, Tufekcioglu Z, Bilgiç B, Olgiati S, Dremmen MHG, van IJcken WFJ, Breedveld GJ, Mancini GMS, Hanagasi HA, Emre M, Bonifati V. Parkinsonism Relat Disord., 2019 Jul 31 PubMed

Shahmoradian

Lewy pathology in Parkinson’s disease consists of crowded organelles and lipid membranes. Shahmoradian SH, Lewis AJ, Genoud C, Hench J, Moors TE, Navarro PP, Castaño-Díez D, Schweighauser G, Graff-Meyer A, Goldie KN, Sütterlin R, Huisman E, Ingrassia A, Gier Y, Rozemuller AJM, Wang J, Paepe A, Erny J, Staempfli A, Hoernschemeyer J, Großerüschkamp F, Niedieker […]

Quevedo

Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. Quevedo M, Meert L, Dekker MR, Dekkers DHW, Brandsma JH, van den Berg DLC, Ozgür Z, IJcken WFJV, Demmers J, Fornerod M, Poot RA. Nat Commun., 2019 Jun 17 PubMed PDF

Rao-Ruiz

Engram-specific transcriptome profiling of contextual memory consolidation. Rao-Ruiz P, Couey JJ, Marcelo IM, Bouwkamp CG, Slump DE, Matos MR, van der Loo RJ, Martins GJ, van den Hout M, van IJcken WF, Costa RM, van den Oever MC, Kushner SA. Nat Commun., 2019 May 20

Laugsch

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šarić T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Cell Stem Cell., 2019 May 2

Cantú

The mouse KLF1 Nan variant impairs nuclear condensation and erythroid maturation. Cantú I, van de Werken HJG, Gillemans N, Stadhouders R, Heshusius S, Maas A, Esteghamat F, Ozgur Z, van IJcken WFJ, Grosveld F, von Lindern M, Philipsen S, van Dijk TB. PLoS One., 2019 Mar 28

Sayas

Distinct Functions for Mammalian CLASP1 and -2 During Neurite and Axon Elongation. Sayas CL, Basu S, van der Reijden M, Bustos-Morán E, Liz M, Sousa M, van IJcken WFJ, Avila J, Galjart N. Front Cell Neurosci., 2019 Jan 29

Biomics will be closed on 30-05-2019 and 31-05-2019

Biomics will be closed on Thursday May 30th and Friday 31th. There will not be courier services to BaseClear at Thursday 30th. Apologies for the inconvenience.

Biomics closed on December 24th till January 4th

Biomics will be closed on December 24th till January 4th. Wishing you a Merry Christmas and a Happy New Year.

Kuipers

PTRHD1 Loss-of-function mutation in an african family with juvenile-onset Parkinsonism and intellectual disability. Kuipers DJS, Carr J, Bardien S, Thomas P, Sebate B, Breedveld GJ, van Minkelen R, Brouwer RWW, van Ijcken WFJ, van Slegtenhorst MA, Bonifati V, Quadri M. Mov Disord., 2018 Nov 6

Vojinovic

Whole-Genome Linkage Scan Combined With Exome Sequencing Identifies Novel Candidate Genes for Carotid Intima-Media Thickness. Vojinovic D, Kavousi M, Ghanbari M, Brouwer RWW, van Rooij JGJ, van den Hout MCGN, Kraaij R, van Ijcken WFJ, Uitterlinden AG, van Duijn CM, Amin N. Front Genet., 2018 Oct 9

Doebar

Progression of ductal carcinoma in situ to invasive breast cancer: comparative genomic sequencing. Doebar SC, Krol NM, van Marion R, Brouwer RWW, van Ijcken WFJ, Martens JM, Dinjens WNM, van Deurzen CHM. Virchows Arch., 2018 Oct 4

Novalis-Cruz

Mitotic progression, arrest, exit or death relies on centromere structural integrity, rather than de novo transcription. Novais-Cruz M, Alba Abad M, van IJcken WF, Galjart N, Jeyaprakash AA, Maiato H, Ferrás C. Elife., 2018 Aug 6

Oosterhof

Colony-Stimulating Factor 1 Receptor (CSF1R) Regulates Microglia Density and Distribution, but Not Microglia Differentiation In Vivo. Oosterhof N, Kuil LE, van der Linde HC, Burm SM, Berdowski W, van Ijcken WFJ, van Swieten JC, Hol EM, Verheijen MHG, van Ham TJ. Cell Rep., 2018 Jul 31

Quadri

LRP10 genetic variants in familial Parkinson’s disease and dementia with Lewy bodies: a genome-wide linkage and sequencing study. Quadri M, Mandemakers W, Grochowska MM, Masius R, Geut H, Fabrizio E, Breedveld GJ, Kuipers D, Minneboo M, Vergouw LJM, Carreras Mascaro A, Yonova-Doing E, Simons E, Zhao T, Di Fonzo AB, Chang HC, Parchi P, Melis […]

van der Wal

Large-Scale Expansion of Human iPSC-Derived Skeletal Muscle Cells for Disease Modeling and Cell-Based Therapeutic Strategies. van der Wal E, Herrero-Hernandez P, Wan R, Broeders M, In ‘t Groen SLM, van Gestel TJM, van IJcken WFJ, Cheung TH, van der Ploeg AT, Schaaf GJ, Pijnappel WWMP. Stem Cell Reports., 2018 Jun 5

Amin

Employed family-based genetic discovery combining linkage analysis and exome sequencing to identify RCL1 as a novel candidate gene for depression, with independent replication in a population-based cohort. Amin N, de Vrij FMS, Baghdadi M, Brouwer RWW, van Rooij JGJ, Jovanova O, Uitterlinden AG, Hofman A, Janssen HLA, Murad SD, Kraaij R, Stedehouder J, van den […]

Koraka

Analysis of Mouse Brain Transcriptome After Experimental Duvenhage Virus Infection Shows Activation of Innate Immune Response and Pyroptotic Cell Death Pathway. Koraka P, Martina BEE, van den Ham HJ, Zaaraoui-Boutahar F, van IJcken W, Roose J, van Amerongen G, Andeweg A, Osterhaus ADME. Front Microbiol., 2018 Mar 20

Wisnumurti

UGT1A1 Genetic Variations and a Haplotype Associated with Neonatal Hyperbilirubinemia in Indonesian Population. Wisnumurti DA, Sribudiani Y, Porsch RM, Maskoen AM, Abdulhamied LI, Rahayuningsih SE, Asni EK, Sleutels F, Kockx CEM, van Ijcken WFJ, Sukadi A, Achmad TH. Biomed Res Int., 2018 Jan 23

Sribudiani

Identification of Variants in RET and IHH Pathway Members in a Large Family With History of Hirschsprung Disease. Sribudiani Y, Chauhan RK, Alves MM, Petrova L, Brosens E, Harrison C, Wabbersen T, de Graaf BM, Rügenbrink T, Burzynski G, Brouwer RWW, van IJcken WFJ, Maas SM, de Klein A, Osinga J, Eggen BJL, Burns AJ, […]

Bouwkamp

ACO2 homozygous missense mutation associated with complicated hereditary spastic paraplegia. Bouwkamp CG, Afawi Z, Fattal-Valevski A, Krabbendam IE, Rivetti S, Masalha R, Quadri M, Breedveld GJ, Mandel H, Tailakh MA, Beverloo HB, Stevanin G, Brice A, van IJcken WFJ, Vernooij MW, Dolga AM, de Vrij FMS, Bonifati V, Kushner SA. Neurol Genet., 2018 Mar 21

Welcome at Biomics

Erasmus Center for Biomics develops Applications & Services for Fundamental Research, Clinical Research and Clinical Diagnostics using Next Generation Sequencing & Micro-Array technology. Our NGS pipelines cover genetic analyses such as genome & exome sequencing and mutation & variant analyses and epigenetic analyses including RNA sequencing & expression analyses, ChIP sequencing and Chromatin Conformation Capture […]

Brouwer

Nimbus: A design-driven analyses suite for amplicon based NGS data. Brouwer RWW, van den Hout MCGN, Kockx CEM, Brosens E, Eussen B, de Klein A, Sleutels F, van IJcken WFJ. Bioinformatics., 2018 Mar 10

Palstra

Allele-specific long-distance regulation dictates IL-32 isoform switching and mediates susceptibility to HIV-1. Palstra RJ, de Crignis E, Röling MD, van Staveren T, Kan TW, van Ijcken W, Mueller YM, Katsikis PD, Mahmoudi T. Sci Adv., 2018 Feb 4

Stadhouders

Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes to asthma susceptibility. Stadhouders R, Li BWS, de Bruijn MJW, Gomez A, Rao TN, Fehling HJ, van IJcken WFJ, Lim AI, Di Santo JP, Graf T, Hendriks RW. J Allergy Clin Immunol., 2018 Feb 24

Kolovos

Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C. Kolovos P, Brouwer RWW, Kockx CEM, Lesnussa M, Kepper N, Zuin J, Imam AMA, van de Werken HJG, Wendt KS, Knoch TA, van IJcken WFJ, Grosveld F. Nat Protoc., 2018 Feb 8

Weerts

Sensitive detection of mitochondrial DNA variants for analysis of mitochondrial DNA-enriched extracts from frozen tumor tissue. Weerts MJA, Timmermans EC, Vossen RHAM, van Strijp D, Van den Hout-van Vroonhoven MCGN, van IJcken WFJ, van der Zaag PJ, Anvar SY, Sleijfer S, Martens JWM. Sci Rep., 2018 Feb 2

Kievit

Variants in members of the cadherin-catenin complex, CDH1 and CTNND1, cause blepharocheilodontic syndrome. Kievit A, Tessadori F, Douben H, Jordens I, Maurice M, Hoogeboom J, Hennekam R, Nampoothiri S, Kayserili H, Castori M, Whiteford M, Motter C, Melver C, Cunningham M, Hing A, Kokitsu-Nakata NM, Vendramini-Pittoli S, Richieri-Costa A, Baas AF, Breugem CC, Duran K, […]

CRISPR sequencing

Background For CRISPR sequencing the customer performs a CRISPR Cas9 screen in which guide RNAs are built into the Sample DNA (https://pubmed.ncbi.nlm.nih.gov/25075903/). We prepare this sample for Illumina sequencing by performing a PCR reaction to amplify the lentiCRISPR sgRNAs and a second PCR reaction to attach adaptors and indexes. After cleanup, the library is ready […]

Omni-ATAC sequencing

  Map Chromatin Accessibility Genome-wide with ATAC Sequencing ATAC-Sequencing   Background: Omni-ATAC is an improved ATAC-seq protocol(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/) for chromatin accessibility profiling that works universally across multiple cell types and cell contexts with significant improvement of signal-to-background ratio and information content. The Omni-ATAC protocol enables chromatin accessibility profiling from material that was previously deemed intractable including […]

Typhoon Old

Typhoon Trio and Typhoon FLA 9500 Applications: PhosphorImaging Important Notice: Please do NOT use the metal covered Phosphorimaging screens on the Typhoon FLA9500. The thin Phosphorimager Screens, without the metal support, are for use with the Typhoon FLA9500. You will need to change the Fluo stage (“the drawer”) for the Phosphor stage to scan your […]

Quantification old

Quantification & Imaging (quantification on Tapestation)   Biomics has a number of imaging and quantification options available (multiplex western blot on Odyssey) Nanodrop Typhoon   Nanodrop 2000 & 8000 DNA & RNA quantification from a 1 ul drop   Typhoon Trio, Typhoon FLA 9500 & Typhoon RGB PhosphorImaging Fluorescence Chemiluminescence Detection Bioanalyzer Odyssey Agilent 2100 […]

Services NEW

Overview Of Our Biomics Services Next Generation Sequencing Single Cell Sequencing Genome Exome Chip-Seq 3C-Seq/HiC RNA-Seq Cells Nuclei Micro Array Bioinformatics & Software Expression Array Tiling Array Promoter Array Protein Array Data management Interpretation & analysesDemultiplexing Alignment & Coverage Peak& Variant Calling Plots & figures Licenses, Tools, Software Quantification and Imaging Sonication, Size Selection and […]

Amersham Imager 600 RGB

Amersham Imager 600 RGB The Amersham Imager 600 RGB is an CCD-based imaging system for the capture and analysis of high resolution protein and DNA samples in gels and membranes. The system is equipped with a dark sample cabinet, a camera system, filter wheel, light sources, and a built-in computer with control and analysis software. The […]

DeNovix

DeNovix DS-11 The DeNovix DS-11 Stand-Alone spectrophotometer delivers full spectrum UV-Vis analysis and is ideal for rapid nucleic acid and protein quantification. Simply pipette and measure. The DS-11 is always calibrated. SmartPath Technology controls the pathlength in real time to ensure accurate and precise measurement. BridgeTesting is the proprietary process to compress and monitor a […]

old Nulcei

UNDER CONSTRUCTION

Cells

UNDER CONSTRUCTION

Single Cell Sequencing

Sonication & Size Selection

Sonication & Size selection Ultrasound Sonicator Covaris Ultrasonicator Biomics has a MSE Soniprep 150 plus Available in room Ee6.86 for disruption of DNA/cells/bacteria. Book the Soniprep yourself Biomics has a Covaris S220 Ultrasonicator for the disruption of DNA/RNA/etc. Please contact us for details Pippin HT Biomics has a Pippin HT for size selection of DNA […]

Femto Pulse

FEMTO Pulse The FEMTO Pulse is an automated Pulsed-Field Capillary Electrophoresis (PFCE) instrument to quantify, qualify and size DNA and RNA samples with accuracy and precision. By using the pulsed-filed power supply on the FEMTO Pulse, DNA smears as large as 165 kbp and DNA fragments as large as 200 kbp can be separated. Applications […]

Quantification

Quantification (quantification on Femto Pulse) Biomics has a number of quantification options available. (quantification on Tapestation) Femto Pulse DeNovix Femto Pulse For accurate RNA & DNA quantification in a multisample format DeNovix DNA & RNA & protein quantification from a 1 ul droplet Bioanalyzer Tapestation Agilent 2100 Bioanalyzer For accurate RNA & DNA & protein […]

Next Generation Sequencing

Next Generation Sequencing Platforms   Biomics operates a fexible NGS pipeline with HiSeq2500, HiSeq4000 and Miseq sequencers. Please check our overview comparing the sequencers. The Illumina NGS platforms are superior due to the large number of short sequence reads and the speed of production Omni-ATAC sequencing ChIPThruplex V2 Sequencing (from: Buenrostro et al) Assay for […]

van Riet

SNPitty: An intuitive web-application for interactive B-allele frequency and copy-number visualization of next-generation sequencing data. van Riet J, Krol NMG, Atmodimedjo PN, Brosens E, van IJcken WFJ, Jansen MPHM, Martens JWM, Looijenga LH, Jenster G, Dubbink HJ, Dinjens WNM, van de Werken HJG.J Mol Diagn., 2018 Jan 2

Odyssey CLx is installed

Center for Biomics is proud to announce that we have bought a new Odyssey CLx system. The odyssey CLx is installed in room Ee-675 and is ready for use. Please be aware that the old odyssey software is not compatible with the new odyssey CLx. You need to install Image Studio on your own computer […]

Zuin

Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element. Zuin J, Casa V, Pozojevic J, Kolovos P, van den Hout MCGN, van Ijcken WFJ, Parenti I, Braunholz D, Baron Y, Watrin E, Kaiser FJ, Wendt KS. PLoS Genet., 2017 Dec 20

Li

Group 2 Innate Lymphoid Cells Exhibit a Dynamic Phenotype in Allergic Airway Inflammation. Li BWS, Stadhouders R, de Bruijn MJW, Lukkes M, Beerens DMJM, Brem MD, KleinJan A, Bergen I, Vroman H, Kool M, van IJcken WFJ, Rao TN, Fehling HJ, Hendriks RW. Front Immunol., 2017 Dec 1

Biomics closed on December 25th till January 5th

Biomics will be closed on December 25th till January 5th. Wishing you a Merry Christmas and a Happy New Year.

Boers

Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI. Boers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, van IJcken W, Laven J, Gribnau J.Genome Res., 2017 Dec 8

van Nistelrooij

Germline variant in MSX1 identified in a Dutch family with clustering of Barrett’s esophagus and esophageal adenocarcinoma. van Nistelrooij AMJ, van Marion R, van Ijcken WFJ, de Klein A, Wagner A, Biermann K, Spaander MCW, van Lanschot JJB, Dinjens WNM, Wijnhoven BPL.Fam Cancer., 2017 Nov 13

The Biomics data export server biomics-sftp.erasmusmc.nl will be unavailable

The Biomics data export server biomics-sftp.erasmusmc.nl will be unavailable for system maintenance starting Wednesday November 15, 14:00. We expect the server to be back online Thursday November 16, end of the day. Your data will be available again when the server is back online.  

Biomics closed on November 16th and 17th

Biomics will be closed on Thursday November 16th and Friday 17th. Apologies for the inconvenience.  

van der Spek

Exome-Wide Meta-Analysis Identifies Rare 3′-UTR Variant in ERCC1/CD3EAP Associated with Symptoms of Sleep Apnea. van der Spek A, Luik AI, Kocevska D, Liu C, Brouwer RWW, van Rooij JGJ, van den Hout MCGN, Kraaij R, Hofman A, Uitterlinden AG, van IJcken WFJ, Gottlieb DJ, Tiemeier H, van Duijn CM, Amin N.Front Genet., 2017 Oct 18

VanDuijn

Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. VanDuijn MM, Dekker LJ, van IJcken WFJ, Sillevis Smitt PAE, Luider TM.Front Immunol., 2017 Oct 16

Singh

Cell lines generated from a chronic lymphocytic leukemia mouse model exhibit constitutive Btk and Akt signaling. Singh SP, Pillai SY, de Bruijn MJW, Stadhouders R, Corneth OBJ, van den Ham HJ, Muggen A, van IJcken W, Slinger E, Kuil A, Spaargaren M, Kater AP, Langerak AW, Hendriks RW.Oncotarget., 2017 May 26

Massolt

Thyroid State Regulates Gene Expression in Human Whole Blood. Massolt ET, Meima ME, Swagemakers SMA, Leeuwenburgh S, van den Hout-van Vroonhoven MCGM, Brigante G, Kam BLR, van der Spek PJ, van IJcken WFJ, Visser TJ, Peeters RP, Visser WE.J Clin Endocrinol Metab., 2017 Oct 23

Lim

Transcriptomic Analyses Reveal Differential Gene Expression of Immune and Cell Death Pathways in the Brains of Mice Infected with West Nile Virus and Chikungunya Virus. Lim SM, van den Ham HJ, Oduber M, Martina E, Zaaraoui-Boutahar F, Roose JM, van IJcken WFJ, Osterhaus ADME, Andeweg AC, Koraka P, Martina BEE.Front Microbiol., 2017 Aug 17

Mohd-Sarip

DOC1-Dependent Recruitment of NURD Reveals Antagonism with SWI/SNF during Epithelial-Mesenchymal Transition in Oral Cancer Cells. Mohd-Sarip A, Teeuwssen M, Bot AG, De Herdt MJ, Willems SM, Baatenburg de Jong RJ, Looijenga LHJ, Zatreanu D, Bezstarosti K, van Riet J, Oole E, van Ijcken WFJ, van de Werken HJG, Demmers JA, Fodde R, Verrijzer CP.Cell Rep., […]

Halim

Loss-of-Function Variants in MYLK Cause Recessive Megacystis Microcolon Intestinal Hypoperistalsis Syndrome. Halim D, Brosens E, Muller F, Wangler MF, Beaudet AL, Lupski JR, Akdemir ZHC, Doukas M, Stoop HJ, de Graaf BM, Brouwer RWW, van Ijcken WFJ, Oury JF, Rosenblatt J, Burns AJ, Tibboel D, Hofstra RMW, Alves MM.Am j Hum Genet., 2017 Jul 6

Srebniak

The influence of SNP-based chromosomal microarray and NIPT on the diagnostic yield in 10,000 fetuses with and without fetal ultrasound anomalies. Srebniak MI, Knapen MFCM, Polak M, Joosten M, Diderich KEM, Govaerts LCP, Boter M, Kromosoeto JNR, van Hassel DACM, Huijbregts G, van IJcken WFJ, Heydanus R, Dijkman A, Toolenaar T, de Vries FAT, Knijnenburg […]

Schmidt

Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. Schmidt R, Jager V, Zühlke D, Wolff C, Bernhardt J, Cankar K, Beekwilder J, Ijcken WV, Sleutels F, Boer W, Riedel K, Garbeva P. Sci Rep., 2017 Apr 13

MinION sequencing technology

MinION sequencing technology MinION Sequencing   Background: The new MinION sequencing technology from Oxford Nanopore is currently available! The MinION is a portable, real-time device for single molecule DNA/RNA sequencing. The flowcell contains Nanopore channels, allowing to sequence ultra-long reads (hundreds of kb). Each flowcell can generate upto 2-5 Gb of DNA sequence data (sample […]

Moen

An interaction network of mental disorder proteins in neural stem cells. Moen MJ, Adams HH, Brandsma JH, Dekkers DH, Akinci U, Karkampouna S, Quevedo M, Kockx CE, Ozgür Z, van IJcken WF, Demmers J, Poot RA. Transl Psychiatry, 2017 Apr 4

Baar

Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging. Baar MP, Brandt RM, Putavet DA, Klein JD, Derks KW, Bourgeois BR, Stryeck S, Rijksen Y, van Willigenburg H, Feijtel DA, van der Pluijm I, Essers J, van Cappellen WA, van IJcken WF, Houtsmuller AB, Pothof J, de Bruin RW, Madl […]

Amin

A rare missense variant in RCL1 segregates with depression in extended families. Amin N, de Vrij FM, Baghdadi M, Brouwer RW, van Rooij JG, Jovanova O, Uitterlinden AG, Hofman A, Janssen HL, Darwish Murad S, Kraaij R, Stedehouder J, van den Hout MC, Kros JM, van IJcken WF, Tiemeier H, Kushner SA, van Duijn CM. […]

Halim

Loss of LMOD1 impairs smooth muscle cytocontractility and causes megacystis microcolon intestinal hypoperistalsis syndrome in humans and mice. Halim D, Wilson MP, Oliver D, Brosens E, Verheij JB, Han Y, Nanda V, Lyu Q, Doukas M, Stoop H, Brouwer RW, van IJcken WF, Slivano OJ, Burns AJ, Christie CK, de Mesy Bentley KL, Brooks AS, […]

Cruz-Molina

PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation. Cruz-Molina S, Respuela P, Tebartz C, Kolovos P, Nikolic M, Fueyo R, van Ijcken WF, Grosveld F, Frommolt P, Bazzi H, Rada-Iglesias A. Cell Stem Cell, 2017 Feb 28

Gui

Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RW, Burns AJ, Cherny SS, Dopazo J, Eggen BJ, Griseri P, Jalloh B, Le TL, Lui VC, Luzón-Toro B, Matera I, Ngan ES, Pelet A, […]

Knoch

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes. Knoch TA, Wachsmuth M, Kepper N, Lesnussa M, Abuseiris A, Ali Imam AM, Kolovos P, Zuin J, Kockx CE, Brouwer RW, van de Werken HJ, van IJcken WF, Wendt KS, Grosveld FG. Epigenetics Chromatin., 2016 Dec 24

Brant

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A. Mol Syst Biol., 2016 Dec 9

CHANGED: BaseClear Sample intake

From 1-1-2018 all orders need to be placed via https://orders.baseclear.com. Click here for detailed ordering instructions. Deliver your samples bundled together with the sample sheet in an envelope to the Erasmus Center for Biomics in Ee-675 (same location as before) on Tuesday and Thursday before 12:00 a.m.

Instruments moved from room Ee678 to room Ee675

The Typhoons, Las4000 imager, Odyssey systems and the BaseClear intake computer/freezer are moved from room Ee678 to room Ee675.

Spuesens

Comparison of Mycoplasma pneumoniae Genome Sequences from Strains Isolated from Symptomatic and Asymptomatic Patients. Spuesens EB, Brouwer RW, Mol KH, Hoogenboezem T, Kockx CE, Jansen R, Van IJcken WF, Van Rossum AM, Vink C. Front Microbiol, 2016 Oct 27

Jong

Transcriptome assists prognosis of disease severity in respiratory syncytial virus infected infants. Jong VL, Ahout IM, van den Ham HJ, Jans J, Zaaraoui-Boutahar F, Zomer A, Simonetti E, Bijl MA, Brand HK, van IJcken WF, de Jonge MI, Fraaij PL, de Groot R, Osterhaus AD, Eijkemans MJ, Ferwerda G, Andeweg AC. Sci Rep, 2016 Nov […]

Scheenstra

GATA1-Deficient Dendritic Cells Display Impaired CCL21-Dependent Migration toward Lymph Nodes Due to Reduced Levels of Polysialic Acid. Scheenstra MR, De Cuyper IM, Branco-Madeira F, de Bleser P, Kool M, Meinders M, Hoogenboezem M, Mul E, Wolkers MC, Salerno F, Nota B, Saeys Y, Klarenbeek S, van IJcken WF, Hammad H, Philipsen S, van den Berg […]

Amin

Nonsynonymous Variation in NKPD1 Increases Depressive Symptoms in the European Populations. Amin N, Belonogova NM, Jovanova O, Brouwer RW, van Rooij JG, van den Hout MC, Svishcheva GR, Kraaij R, Zorkoltseva IV, Kirichenko AV, Hofman A, Uitterlinden AG, van IJcken WF, Tiemeier H, Axenovich TI, van Duijn CM. Biol Psychiatry, 2016 Aug 11

Stryjewska

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells. Stryjewska A, Dries R, Pieters T, Verstappen G, Conidi A, Coddens K, Francis A, Umans L, van IJcken WF, Berx G, van Grunsven LA, Grosveld F, Goossens S, Haigh JJ, Huylebroeck D. Stem Cells, 2016 Oct 14

Rother

Decreased IL7Rα and TdT expression underlie the skewed immunoglobulin repertoire of human B-cell precursors from fetal origin. Rother MB, Jensen K, van der Burg M, van de Bovenkamp FS, Kroek R, van IJcken WF, van der Velden VH, Cupedo T, Olstad OK, van Dongen JJ, van Zelm MC. Sci Rep., 2016 Sep 23

Kolovos

Binding of nuclear factor kappa B to non-canonical consensus sites reveals its multimodal role during the early inflammatory response. Kolovos P, Georgomanolis T, Koeferle A, Larkin JD, Brant L, Nikolic M, Gusmao EG, Zirkel A, Knoch TA, Costa IG, van Ijcken WF, Cook PR, Grosveld FG, Papantonis A. Genome Res., 2016 Sep 15

Biomics closed on Wednesday October 5th

Biomics will be closed Wednesday October 5th. Apologies for the inconvenience.  

Mulugeta

Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes. Mulugeta E, Wassenaar E, Sleddens-Linkels E, van IJcken WF, Heard E, Grootegoed JA, Just W, Gribnau J, Baarends WM. Genome Res., 2016 Aug 10

Amin

Exome-sequencing in a large population-based study reveals a rare Asn396Ser variant in the LIPG gene associated with depressive symptoms. Amin N, Jovanova O, Adams HH, Dehghan A, Kavousi M, Vernooij MW, Peeters RP, de Vrij FM, van der Lee SJ, van Rooij JG, van Leeuwen EM, Chaker L, Demirkan A, Hofman A, Brouwer RW, Kraaij […]

Meuwissen

Human USP18 deficiency underlies type 1 interferonopathy leading to severe pseudo-TORCH syndrome. Meuwissen ME, Schot R, Buta S, Oudesluijs G, Tinschert S, Speer SD, Li Z, van Unen L, Heijsman D, Goldmann T, Lequin MH, Kros JM, Stam W, Hermann M, Willemsen R, Brouwer RW, Van IJcken WF, Martin-Fernandez M, de Coo I, Dudink J, […]

Wiekmeijer

Overexpression of LMO2 causes aberrant human T-Cell development in vivo by three potentially distinct cellular mechanisms. Wiekmeijer AS, Pike-Overzet K, Brugman MH, van Eggermond MC, Cordes M, de Haas EF, Li Y, Oole E, van IJcken WF, Egeler RM, Meijerink JP, Staal FJ. Exp Hematol. 2016 Jun 11

Zubakov

Human age estimation from blood using mRNA, DNA methylation, DNA rearrangement, and telomere length. Zubakov D, Liu F, Kokmeijer I, Choi Y, van Meurs JB, van IJcken WF, Uitterlinden AG, Hofman A, Broer L, van Duijn CM, Lewin J, Kayser M. Forensic Sci Int Genet., 2016 May 24

Sepe

Inefficient DNA Repair Is an Aging-Related Modifier of Parkinson’s Disease. Sepe S, Milanese C, Gabriels S, Derks KW, Payan-Gomez C, van IJcken WF, Rijksen YM, Nigg AL, Moreno S, Cerri S, Blandini F, Hoeijmakers JH, Mastroberardino PG. Cell Rep., 2016 May 31

Amin

Genetic variants in RBFOX3 are associated with sleep latency. Amin N, Allebrandt KV, van der Spek A, Müller-Myhsok B, Hek K, Teder-Laving M, Hayward C, Esko T, van Mill JG, Mbarek H, Watson NF, Melville SA, Del Greco FM, Byrne EM, Oole E, Kolcic I, Chen TH, Evans DS, Coresh J, Vogelzangs N, Karjalainen J, […]

HiSeq 4000 installed

We have recently installed the Illumina HiSeq4000 system at Biomics. Unique to this system above the HiSeq 2500 is its patterned flow cell technology. The HiSeq 4000 generates up to 10 billion sequences of 150 bp in 3.5 days allowing you to sequence 12 complete human genomes within 3.5 days! Check out the overview of […]

Olgiati

Paroxysmal exercise-induced dystonia within the phenotypic spectrum of ECHS1 deficiency. Olgiati S, Skorvanek M, Quadri M, Minneboo M, Graafland J, Breedveld GJ, Bonte R, Ozgur Z, van den Hout MC, Schoonderwoerd K, Verheijen FW, van IJcken WF, Chien HF, Barbosa ER, Chang HC, Lai SC, Yeh TH, Lu CS, Wu-Chou YH, Kievit AJ, Han V, […]

Hoogduijn

Effects of freeze-thawing and intravenous infusion on mesenchymal stromal cell gene expression. Hoogduijn MJ, de Witte S, Luk F, van den Hout-van Vroonhoven MC, Ignatowicz L, Catar R, Strini T, Korevaar SS, van IJcken WF, Betjes MG, Franquesa M, Moll G, Baan CC. Stem Cells Dev. 2016 Feb 25

Crisan

BMP and Hedgehog Regulate Distinct AGM Hematopoietic Stem Cells Ex Vivo. Crisan M, Solaimani Kartalaei P, Neagu A, Karkanpouna S, Yamada-Inagawa T, Purini C, Vink CS, van der Linden R, van Ijcken W, Chuva de Sousa Lopes SM, Monteiro R, Mummery C, Dzierzak E. Stem Cell Reports 2016 Feb 17

Korpershoek

Complex MAX Rearrangement in a Family With Malignant Pheochromocytoma, Renal Oncocytoma, and Erythrocytosis. Korpershoek E, Koffy D, Eussen BH, Oudijk L, Papathomas TG, van Nederveen FH, Belt EJ, Franssen GJ, Restuccia DF, Krol NM, van der Luijt RB, Feelders RA, Oldenburg RA, van Ijcken WF, de Klein A, de Herder WW, de Krijger RR, Dinjens […]

Almomani

Biallelic Truncating Mutations in ALPK3 Cause Severe Pediatric Cardiomyopathy. Almomani R, Verhagen JM, Herkert JC, Brosens E, van Spaendonck-Zwarts KY, Asimaki A, van der Zwaag PA, Frohn-Mulder IM, Bertoli-Avella AM, Boven LG, van Slegtenhorst MA, van der Smagt JJ, van IJcken WF, Timmer B, van Stuijvenberg M, Verdijk RM, Saffitz JE, du Plessis FA, Michels […]

Halim

ACTG2 variants impair actin polymerization in sporadic Megacystis Microcolon Intestinal Hypoperistalsis Syndrome. Halim D, Hofstra RM, Signorile L, Verdijk RM, van der Werf CS, Sribudiani Y, Brouwer RW, van IJcken WF, Dahl N, Verheij JB, Baumann C, Kerner J, van Bever Y, Galjart N, Wijnen RM, Tibboel D, Burns AJ, Muller F, Brooks AS, Alves […]

Rother

Nuclear positioning rather than contraction controls ordered rearrangements of immunoglobulin loci. Rother MB, Palstra RJ, Jhunjhunwala S, van Kester KA, van IJcken WF, Hendriks RW, van Dongen JJ, Murre C, van Zelm MC. Nucleic acid Res. 2016 Jan 8

Stadhouders

Control of developmentally primed erythroid genes by combinatorial co-repressor actions. Stadhouders R, Cico A, Stephen T, Thongjuea S, Kolovos P, Baymaz HI, Yu X, Demmers J, Bezstarosti K, Maas A, Barroca V, Kockx C, Ozgur Z, van Ijcken W, Arcangeli ML, Andrieu-Soler C, Lenhard B, Grosveld F, Soler E. Nat Commun 2015 Nov 23

van Jaarsveld

miR-634 restores drug sensitivity in resistant ovarian cancer cells by targeting the Ras-MAPK pathway. van Jaarsveld MT, van Kuijk PF, Boersma AW, Helleman J, van IJcken WF, Mathijssen RH, Pothof J, Berns EM, Verweij J, Wiemer EA. Mol Cancer 2015 Nov 17

Caputo

The Isl1/Ldb1 Complex Orchestrates Genome-wide Chromatin Organization to Instruct Differentiation of Multipotent Cardiac Progenitors. Caputo L, Witzel HR, Kolovos P, Cheedipudi S, Looso M, Mylona A, van IJcken WF, Laugwitz KL, Evans SM, Braun T, Soler E, Grosveld F, Dobreva G. Cell Stem Cell 2015 Sep 3

Nanodrop ND-2000

  The single channel Nanodrop ND-2000 in room Ee-693 is missing. Please use the other single channel Nanodrop or the 8-channel Nanodrop ND-8000.  

Crisan

BMP signalling differentially regulates distinct haematopoietic stem cell types. Crisan M, Kartalaei PS, Vink CS, Yamada-Inagawa T, Bollerot K, van IJcken W, van der Linden R, de Sousa Lopes SM, Monteiro R, Mummery C, Dzierzak E. Nat Commun. 2015 Oct 29 Erratum for Nat Commun. 2015 Aug 18

Tresini

The Core spliceosome as target and effector of non-canonical ATM signalling. Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JA, van IJcken WF, Grosveld FG, Medema RH, Hoeijmakers JH, Mullenders LH, Vermeulen W, Marteijn JA. Nature 2015 Jul 2  

Engelen

Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Engelen E, Brandsma JH, Moen MJ, Signorile L, Dekkers DH, Demmers J, Kockx CE, Ozgür Z, van IJcken WF, van den Berg DL, Poot RA. Nat Commun. 2015 May 20  

Liu

Genetics of skin color variation in Earopeans: genome-wide association studies with functional follow-up. Liu F, Visser M, Duffy DL, Hysi PG, Jacobs LC, Lao O, Zhong K, Walsh S, Chaitanya L, Wollstein A, Zhu G, Montgomery GW, Henders AK, Mangino M, Glass D, Bataille V, Sturm RA, Rivadeneira F, Hofman A, van IJcken WF, Uitterlinden […]

hAwk 3 release

The "NGS in DNA Diagnostics Course" will be organized by the ErasmusMC at 22-24 September. During one of the workshops in the course, hAwk 3 will be demonstrated. hAwk is a tool, developend by Biomics and Clinical Genetics, to perform QC and analysis on NGS data from e.g. gene panels and Whole Exome Sequencing. The manual […]

Typhoon out of order

Wednesday July 8th, our Typhoon TRIO will be out of order. Apologies for the inconvenience.

Nellist

Targeted Next Generation Sequencing reveals previously unidentified TSC1 and TSC2 mutations. Nellist M, Brouwer RW, Kockx CE, van Veghel-Plandsoen M, Withagen-Hermans C, Prins-Bakker L, Hoogeveen-Westerveld M, Mrsic A, van den Berg MM, Koopmans AE, de Wit MC, Jansen FE, Maat-Kievit AJ, van den Ouweland A, Halley D, de Klein A, van IJcken WF. BMC Med […]

Litjens

Allogeneic Mature Human Dendritic Cells Generate Superior Alloreactive Regulatory T Cells in the Presence of IL-15. Litjens NH, Boer K, Zuijderwijk JM, Klepper M, Peeters AM, Prens EP, Verschoor W, Kraaijeveld R, Ozgur Z, van den Hout-van Vroonhoven MC, van IJcken WF, Baan CC, Betjes MG. J Immunol. 2015 Apr 27.

de Goede et al

DC immunotherapy in HIV-1 infection induces a major blood transcriptome shift. de Goede AL, Andeweg AC, van den Ham HJ, Bijl MA, Zaaraoui-Boutahar F, van IJcken WF, Wilgenhof S, Aerts JL, Gruters RA, Osterhaus AD; DC-TRN trial investigators, Allard SD, van Baalen CA, De Keersmaecker B, van der Ende ME, Thielemans K, Lacor P. Vaccine. […]

Federici

Incomplete meiotic sex chromosome inactivation in the domestic dog. Federici F, Mulugeta E, Schoenmakers S, Wassenaar E, Hoogerbrugge JW, van der Heijden GW, van Cappellen WA, Slotman JA, van IJcken WF, Laven JS, Grootegoed JA, Baarends WM. BMC Genomics. 2015 Apr 12.

Zhao

A New CRB1 Rat Mutation Links Müller Glial Cells to Retinal Telangiectasia. Zhao M, Andrieu-Soler C, Kowalczuk L, Paz Cortés M, Berdugo M, Dernigoghossian M, Halili F, Jeanny JC, Goldenberg B, Savoldelli M, El Sanharawi M, Naud MC, van Ijcken W, Pescini-Gobert R, Martinet D, Maass A, Wijnholds J, Crisanti P, Rivolta C, Behar-Cohen F. […]

van der Lee

PLD3 variants in population studies. van der Lee SJ, Holstege H, Wong TH, Jakobsdottir J, Bis JC, Chouraki V, van Rooij JG, Grove ML, Smith AV, Amin N, Choi SH, Beiser AS, Garcia ME, van IJcken WF, Pijnenburg YA, Louwersheimer E, Brouwer RW, van den Hout MC, Oole E, Eirkisdottir G, Levy D, Rotter JI, […]

Derks

Deciphering the RNA landscape by RNAome sequencing. Derks KW, Misovic B, van den Hout MC, Kockx CE, Gomez CP, Brouwer RW, Vrieling H, Hoeijmakers JH, van IJcken WF, Pothof J. RNA Biol. 2015 Jan 2

van de Weg

Time since onset of disease and individual clinical markers associate with transcriptional changes in uncomplicated dengue. van de Weg CA, van den Ham HJ, Bijl MA, Anfasa F, Zaaraoui-Boutahar F, Dewi BE, Nainggolan L, van IJcken WF, Osterhaus AD, Martina BE, van Gorp EC, Andeweg AC. PLoS Negl Trop Dis. 2015 Mar 3  

Haloplex: Powerful Targeted Capture

Haloplex targeted capture shows off its sunny side. Agilent Haloplex offers a fast capture protocol for targeted enrichment. It employs restriction enzymes to fragment genomic DNA followed by a smart circularization and capture of favourable DNA fragments before they get PCR amplified and sequencing. The structure of the Haloplex NGS data facilitates fast and accurate […]

Vrijenhoek

Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects. Vrijenhoek T, Kraaijeveld K, Elferink M, de Ligt J, Kranendonk E, Santen G, Nijman IJ, Butler D, Claes G, Costessi A, Dorlijn W, van Eyndhoven W, Halley DJ, van den Hout MC, van Hove S, Johansson LF, Jongbloed JD, Kamps R, Kockx […]

Solaimani Kartalaei

Whole-transcriptome analysis of endothelial to hematopoietic stem cell transition reveals a requirement for Gpr56 in HSC generation. Solaimani Kartalaei P, Yamada-Inagawa T, Vink CS, de Pater E, van der Linden R, Marks-Bluth J, van der Sloot A, van den Hout M, Yokomizo T, van Schaick-Solernó ML, Delwel R, Pimanda JE, van IJcken WF, Dzierzak E. […]

Kurek

Endogenous WNT signals mediate BMP-induced and spontaneous differentiation of epiblast stem cells and human embryonic stem cells. Kurek D, Neagu A, Tastemel M, Tüysüz N, Lehmann J, van de Werken HJ, Philipsen S, van der Linden R, Maas A, van IJcken WF, Drukker M, ten Berge D. Stem Cell Reports. 2015 Jan 13

Meinders

Sp1/Sp3 transcription factors regulate hallmarks of megakaryocyte maturation and platelet formation and function. Meinders M, Kulu DI, van de Werken HJ, Hoogenboezem M, Janssen H, Brouwer RW, van Ijcken WF, Rijkers EJ, Demmers JA, Krüger I, van den Berg TK, Suske G, Gutiérrez L, Philipsen S Blood. 2015 Mar 19;125

Kuster

Gene reprogramming in exercise-induced cardiac hypertrophy in swine: A transcriptional genomics approach. Kuster DW, Merkus D, Blonden LA, Kremer A, van IJcken WF, Verhoeven AJ, Duncker DJ. J Mol Cell Cardiol. 2014 Dec

Sap

Global quantitative proteomics reveals novel factors in the ecdysone signaling pathway in Drosophila melanogaster. Sap KA, Bezstarosti K, Dekkers DH, van den Hout M, van Ijcken W, Rijkers E, Demmers JA. Proteomics. 2015 Feb;15

van der eerden

Identification of microRNAs in human plasma. van der Eerden BC, Alves RD, Kockx CE, Ozgur Z, Schreuders-Koedam M, van de Peppel J, van Ijcken WF, van Leeuwen JP. Methods Mol Biol. 2015;1226.

Beaufort

Ovarian cancer cell line panel (OCCP): clinical importance of in vitro morphological subtypes. Beaufort CM, Helmijr JC, Piskorz AM, Hoogstraat M, Ruigrok-Ritstier K, Besselink N, Murtaza M, van IJcken WF, Heine AA, Smid M, Koudijs MJ, Brenton JD, Berns EM, Helleman J. PLoS One. 2014 Sep 17.

Vojinovic

The dystrophin gene and cognitive function in the general population. Vojinovic D, Adams HH, van der Lee SJ, Ibrahim-Verbaas CA, Brouwer R, van den Hout MC, Oole E, van Rooij J, Uitterlinden A, Hofman A, van IJcken WF, Aartsma-Rus A, van Ommen GB, Ikram MA, van Duijn CM, Amin N. Eur J Hum Genet. 2014 […]

Hou

Gene expression profiling to predict and assess the consequences of therapy-induced virus eradication in chronic hepatitis C virus infection. Hou J, van Oord G, Groothuismink ZM, Claassen MA, Kreefft K, Zaaraoui-Boutahar F, van IJcken WF, Osterhaus AD, Janssen HL, Andeweg AC, de Knegt RJ, Boonstra A. J Virol. 2014 Nov;88

Kolovos

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Kolovos P, van de Werken HJ, Kepper N, Zuin J, Brouwer RW, Kockx CE, Wendt KS, van IJcken WF, Grosveld F, Knoch TA. Epigenetics Chromatin. 2014 Jun 16

Hou

Analysis of the transcriptome and immune function of monocytes during IFNα-based therapy in chronic HCV revealed induction of TLR7 responsiveness. Hou J, Groothuismink ZM, Koning L, Roomer R, van IJcken WF, Kreefft K, Liu BS, Janssen HL, de Knegt RJ, Boonstra A. Antiviral Res. 2014 Sep;109

Gits

MicroRNA response to hypoxic stress in soft tissue sarcoma cells: microRNA mediated regulation of HIF3α. Gits CM, van Kuijk PF, de Rijck JC, Muskens N, Jonkers MB, van IJcken WF, Mathijssen RH, Verweij J, Sleijfer S, Wiemer EA. BMC Cancer. 2014 Jun 13

Onderdijk

Regulated genes in psoriatic skin during treatment with fumaric acid esters. Onderdijk AJ1, Balak DM, Baerveldt EM, Florencia EF, Kant M, Laman JD, van IJcken WF, Racz E, de Ridder D, Thio HB, Prens EP. Br J Dermatol. 2014 Oct;171

Spiegelberg

Gene expression analysis reveals inhibition of radiation-induced TGFβ-signaling by hyperbaric oxygen therapy in mouse salivary glands. Spiegelberg L1, Swagemakers SM2, Van Ijcken WF3, Oole E3, Wolvius EB1, Essers J4, Braks JA1. Mol Med. 2014 Jul 10

2015!

Center for Biomics will be closed from Monday December 22 to Friday January 2nd. We would like to take this opportunity to thank you for your continuous support and hope to serve you even better in 2015. Wishing you a Merry Christmas and a Happy New Year. Last courier services to BaseClear in 2014 will […]

Speedvac

Our SpeedVac is out of order until further notice, Apologies for the inconvenience.    

Cryostat out of order

The Cryostat in room JNI BE-250 is out of order. Maintenance will be performed asap.   Marcel Kap, Weefselbank

Biomics closed on May 29th

Thursday May 29th is Ascension. Biomics will be closed that day. Samples for Baseclear will not be couriered on May 29th. Apologies for the inconvenience.  

Koopmans et al

Clinical significance of immunohistochemistry for detection of BAP1 mutations in uveal melanoma. Koopmans AE, Verdijk RM, Brouwer RW, van den Bosch TP, van den Berg MM, Vaarwater J, Kockx CE, Paridaens D, Naus NC, Nellist M, van Ijcken WF, Kiliç E, de Klein A. Mod Pathol. 2014 Mar 14.

Stadhouders et al

HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. Stadhouders R, Aktuna S, Thongjuea S, Aghajanirefah A, Pourfarzad F, van Ijcken W, Lenhard B, Rooks H, Best S, Menzel S, Grosveld F, Thein SL, Soler E. J Clin Invest. 2014 Apr 1;124(4)

Stadhouders et al

Pre-B cell receptor signaling induces immunoglobulin κ locus accessibility by functional redistribution of enhancer-mediated chromatin interactions. Stadhouders R, de Bruijn MJ, Rother MB, Yuvaraj S, Ribeiro de Almeida C, Kolovos P, Van Zelm MC, van Ijcken W, Grosveld F, Soler E, Hendriks RW. PLoS Biol. 2014 Feb 18;12

Haberle et al

Two independent transcription initiation codes overlap on vertebrate core promoters. Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. Nature. 2014 Mar 20;507

Zuin et al

A cohesin-independent role for NIPBL at promoters provides insights in CdLS. Zuin J, Franke V, van Ijcken WF, van der Sloot A, Krantz ID, van der Reijden MI, Nakato R, Lenhard B, Wendt KS. PLoS Genet. 2014 Feb 13;10(2)

Jaarsveld et al

DNA damage responsive microRNAs misexpressed in human cancer modulate therapy sensitivity. van Jaarsveld MT, Wouters MD, Boersma AW, Smid M, van Ijcken WF, Mathijssen RH, Hoeijmakers JH, Martens JW, van Laere S, Wiemer EA, Pothof J. Mol Oncol. 2014 May;8(3)

Melis et al

In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Melis JP, Derks KW, Pronk TE, Wackers P, Schaap MM, Zwart E, van Ijcken WF, Jonker MJ, Breit TM, Pothof J, van Steeg H, Luijten M. Arch Toxicol. 2014 Apr;88(4):1023-34

Blauw Bloed, DNA Code VIDEO

Biomics is devoted to unleash the possibilities genomics can offer for medicine. We run a number of genomics services including Next Generation Sequencing and DNA Profiling of individuals in order to detect and discover DNA variants contributing to disease. Commissioned by NWO, Frank Sleutels from Biomics and media artist Teresa van Twuijver made the video […]

Typhoon Repaired

Our Typhoon Trio has been repaired and is up and running. Sorry for the inconvenience    

Gits et al

Microrna expression profiles distinguish liposarcoma subtypes and implicate MIR-145 AND MIR-451 as tumor suppressors. Gits CM, van Kuijk PF, Jonkers MB, Boersma AW, Smid M, van Ijcken WF, Coindre JM, Chibon F, Verhoef C, Mathijssen RH, den Bakker MA, Verweij J, Sleijfer S, Wiemer EA. Int J Cancer. 2013 Dec 21

Zuin et al

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, Brouwer RW, van de Corput MP, van de Werken HJ, Knoch TA, van Ijcken WF, Grosveld FG, Ren B, Wendt KS. Proc Natl Acad Sci U S A. 2013 Dec […]

Van Lierop et al

Gene expression analysis of peripheral cells for subclassification of pediatric inflammatory bowel disease in remission. van Lierop PP, Swagemakers SM, de Bie CI, Middendorp S, van Baarlen P, Samsom JN, van Ijcken WF, Escher JC, van der Spek PJ, Nieuwenhuis EE. PLoS One. 2013 Nov 18;8(11)

All the best for 2014

At Biomics, we would like to wish everone a year with many data, papers, discoveries and success.

Riepsaame et al

MicroRNA-Mediated Down-Regulation of M-CSF Receptor Contributes to Maturation of Mouse Monocyte-Derived Dendritic Cells. Riepsaame J, van Oudenaren A, den Broeder BJ, van Ijcken WF, Pothof J, Leenen PJ. Front Immunol. 2013 Oct 30

Iglesias et al

Exome sequencing and functional analyses suggest that SIX6 is a gene involved in an altered proliferation-differentiation balance early in life and optic nerve degeneration at old age. Iglesias AI, Springelkamp H, Linde HV, Severijnen LA, Amin N, Oostra B, Kockx CE, van den Hout MC, van Ijcken WF, Hofman A, Uitterlinden AG, Verdijk RM, Klaver […]

Spronsen et al

Developmental and Activity-Dependent miRNA Expression Profiling in Primary Hippocampal Neuron Cultures. van Spronsen M, van Battum EY, Kuijpers M, Vangoor VR, Rietman ML, Pothof J, Gumy LF, van Ijcken WF, Akhmanova A, Pasterkamp RJ, Hoogenraad CC. PLoS One. 2013 Oct 3;8(10)

Moshkin et al

Histone chaperone NAP1 mediates sister chromatid resolution by counteracting protein phosphatase 2A. Moshkin YM, Doyen CM, Kan TW, Chalkley GE, Sap K, Bezstarosti K, Demmers JA, Ozgur Z, van Ijcken WF, Verrijzer CP. PLoS Genet. 2013 Sep;9(9)

Christmas and New Year

The Center for Biomics will be closed from Monday December 23rd till Thursday January 2nd. We would like to take this opportunity to thank you for your continuous support and hope to serve you even better in 2014. Wishing you a Merry Christmas and a Happy New Year. During the festive season Genomics support and […]

No data transfer

Friday morning, November 29th, our sftp server will be down for maintenance. You will not be able to download data from our server. Sorry for the inconvenience.

FLA repaired again

The Typhoon FLA 9500 imager has been repaired and is fully functional.    

Uittenboogaard et al

BACH2: A marker of DNA damage and ageing. Uittenboogaard LM, Payan-Gomez C, Pothof J, van Ijcken W, Mastroberardino PG, van der Pluijm I, Hoeijmakers JH, Tresini M. DNA Repair (Amst). 2013 Nov;12(11)  

Digital/Droplet PCR

Digital/Droplet PCR product & application seminar by Bio-Rad, RainDance Technologies and Fluidigm. Copy Number Detection, Rare mutation detection, SNP genotyping, Ultra precise concentration determination. Applications in Next Generation Sequencing, Tumor Biology, Oncogenesis, Non Invasive Prenatal Diagnostics, Clinical Diagnostics and many more. November 20th, Download the program    

Nepal et al

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S, Gehrig J, Akalin A, Kockx CE, van der Sloot AA, van Ijcken WF, Armant O, Rastegar S, Watson C, Strähle U, […]

Gits et al

MiR-17-92 and miR-221/222 cluster members target KIT and ETV1 in human gastrointestinal stromal tumours. Gits CM, van Kuijk PF, Jonkers MB, Boersma AW, van Ijcken WF, Wozniak A, Sciot R, Rutkowski P, Schöffski P, Taguchi T, Mathijssen RH, Verweij J, Sleijfer S, Debiec-Rychter M, Wiemer EA. Br J Cancer. 2013 Sep 17

Introducing the ImageQuant LAS 4000

Sensitive ECL detection for your Western, Northern or Southern with our New ImageQuant LAS 4000. Hands on training for this imager, installed in Ee 6.78, will be on Thursday September 5th. Please see the flyer for details. Are you looking for a sensitive chemiluminescence imager or for an alternative to the Utitec Cambridge Alliance 2.7 […]

NGS course Data Analysis 7th edition

Registration is open for the 7th NGS course in Data Analysis. Please visit http://www.medgencentre.nl/ for registration details. The program is available   A PDF file with the course exercises is available here The zip file for the workshop exercise C can be downloaded here

NGS course Data Analysis

August 28-30 2013 @ UMC Utrecht. The program is available. You can register at the MGC website.  

New Imagers

Introduction of the new chemiluminescent, fluorescent and autoradiography scanners. Replacing the Typhoons and Kodak Imaging station.   June 11th: 14:30-16:00h Ae406 See the flyer.     This seminar is organized by the Center for Biomics because we purchased recently the FLA9500 imager as replacement for the Tyfoon. The FLA 9500 is a variable mode laser […]

Alves et al

Contribution of rare and common variants determine complex diseases – Hirschsprung disease as a model Alves MM, Sribudiani Y, Brouwer RW, Amiel J, Antiñolo G, Borrego S, Ceccherini I, Chakravarti A, Fernández RM, Garcia-Barcelo MM, Griseri P, Lyonnet S, Tam PK, van Ijcken WF, Eggen BJ, Te Meerman GJ, Hofstra RM Dev Biol. 2013 May […]

FLA repaired

The Typhoon FLA 9500 imager is up and running again. The glass tray (The Fluo Stage) got broken. Please handle the Stages with care when removing, changing or inserting a Stage. Note that while you pull a Stage out of the machine it dislocates promptly.    

Armant et al

Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos Armant O, März M, Schmidt R, Ferg M, Diotel N, Ertzer R, Bryne JC, Yang L, Baader I, Reischl M, Legradi J, Mikut R, Stemple D, Ijcken WV, van der Sloot A, Lenhard B, Strähle U, Rastegar S Dev Biol. 2013 May 14

Outchkourov et al

Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT Cell Rep. 2013 Apr 25;3

Sigma Mission

New Tools for Functional Genetics: Mission shRNA. The new Sigma Mission shRNA TRC2 is available at Biomics. Read more

Papasavva et al

Next generation sequencing of SNPs for non-invasive prenatal diagnosis: challenges and feasibility as illustrated by an application to β-thalassaemia. Papasavva T, van Ijcken WF, Kockx CE, van den Hout MC, Kountouris P, Kythreotis L, Kalogirou E, Grosveld FG, Kleanthous M Eur J Hum Genet. 2013 Apr 10

Ghamari et al

In vivo live imaging of RNA polymerase II transcription factories in primary cells Ghamari A, van de Corput MP, Thongjuea S, van Cappellen WA, van Ijcken W, van Haren J, Soler E, Eick D, Lenhard B, Grosveld FG Genes Dev. 2013 Apr 1;27

Sigma Mission TRC2

New Tools for Functional Genetics: Mission shRNA The new Sigma Mission shRNA TRC2 is available at Biomics. TRC2 contains over 127,000 clones targeting over 15,000 human genes and almost 13,000 mouse genes. There are more than 4,000 genes covered exclusively in TRC2! The TRC2 vector can be used for both transient or stable RNAi and […]

de Graaf et al

Small Hydrophobic Protein of Human Metapneumovirus Does Not Affect Virus Replication and Host Gene Expression In Vitro. de Graaf M, Herfst S, Aarbiou J, Burgers PC, Zaaraoui-Boutahar F, Bijl M, van Ijcken W, Schrauwen EJ, Osterhaus AD, Luider TM, Scholte BJ, Fouchier RA, Andeweg AC. PLoS One. 2013

Stadhouders et al

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Stadhouders R, Kolovos P, Brouwer R, Zuin J, van den Heuvel A, Kockx C, Palstra RJ, Wendt KS, Grosveld F, van Ijcken W, Soler E. Nat Protoc. 2013 Feb 14;8(3):509-24

Huang et al

Hypoxia Inducible Factor 3α Plays a Critical Role in Alveolarization and Distal Epithelial Cell Differentiation during Mouse Lung Development. Huang Y, Kapere Ochieng J, Kempen MB, Munck AB, Swagemakers S, van Ijcken W, Grosveld F, Tibboel D, Rottier RJ. PLoS One. 2013;8(2)

Van den Ham et al

Early divergence of Th1 and Th2 transcriptomes involves a small core response and sets of transiently expressed genes. van den Ham HJ, de Waal L, Zaaraoui-Boutahar F, Bijl M, van Ijcken WF, Osterhaus AD, de Boer RJ, Andeweg AC. Eur J Immunol. 2013 Feb 22

Agilent Haloplex Exome Release

“Agilent is pleased to announce a number of products to simplify sequencing of clinical research samples,” said Olle Ericsson, Agilent director of marketing, DNA Sequencing. “The HaloPlex Exome delivers streamlined capture of all coding exons, with low input sample requirements, on all Illumina sequencing platforms. Together with SureDesign, and the SureCall software, these products constitute […]

Presenting Haloplex Exome at AGBT

Agilents introduces the new HaloPlex exome. Dr. Wilfred van IJcken from ErasmusMC, one of the first in the world to test it, has presented his results at the annual AGBT (Advances in Genome Biology and Technology) conference. read more

HiSeq2500

Choose between speed and output: Recently installed and already running at Biomics is our Illumina HiSeq 2500 system! Get more speed and read length in Rapid Run mode or obtain more sequences in High Output mode. The choice is yours….   Check out the comparison between the HiSeq 2000 and the Hiseq 2500 system.

Mylona et al

Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis. Mylona A, Andrieu-Soler C, Thongjuea S, Martella A, Soler E, Jorna R, Hou J, Kockx C, van Ijcken W, Lenhard B, Grosveld F. Blood. 2013 Feb 6.

Yin et al

MicroRNA-133 Controls Brown Adipose Determination in Skeletal Muscle Satellite Cells by Targeting Prdm16. Yin H, Pasut A, Soleimani VD, Bentzinger CF, Antoun G, Thorn S, Seale P, Fernando P, van Ijcken W, Grosveld F, Dekemp RA, Boushel R, Harper ME, Rudnicki MA. Cell Metab. 2013 Feb 5

Sybesma et al

Genome instability in Lactobacillus rhamnosus GG. Sybesma W, Molenaar D, van Ijcken W, Venema K, Kort R. Appl Environ Microbiol. 2013 Jan 25  

van den Berghe et al

Directed migration of cortical interneurons depends on the cell-autonomous action of sip1. van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, Goossens S, Haigh JJ, Fishell G, Goffinet A, Aerts S, […]

Price et al

Canonical Wnt signaling induces a primitive endoderm metastable state in mouse embryonic stem cells. Price FD, Yin H, Jones A, van Ijcken W, Grosveld F, Rudnicki MA. Stem Cells. 2013 Jan 10.  

HiSeq 2500 installed

We have recently installed the Illumina HiSeq2500 system at Biomics. Unique to this system above the HiSeq 2000 is its dual mode operation: Mode 1 is High Output mode with a maximum production of 6 billion sequences of 100 bp in 11 days. Sequence a complete human genome within 11 days! Mode 2 is Rapid […]

Biomics closed with Xmas and New Year

Biomics will be closed from Monday 24th of December 2012 until Tuesday January 1st 2013. During the holidays there will be neither Baseclear nor In House Sequencing Service. Enjoy your Christmas and New Year!  

Pourfarzad et al

Hydroxyurea responsiveness in β-thalassemic patients is determined by the stress response adaptation of erythroid progenitors and their differentiation propensity. Pourfarzad F, von Lindern M, Azarkeivan A, Hou J, Kheradmand Kia S, Esteghamat F, van Ijcken W, Philipsen S, Najmabadi H, Grosveld F. Haematologica. 2012 Oct 25.

Exome data presented at the American Society of Human Genetics

For the Erasmus Rucphen Family (ERF) project, researchers at Erasmus and their collaborators sequenced the whole exomes of 1,300 individuals from the Rucphen population, using Agilent kits to capture coding sequences that were subsequently sequenced on Illumina's HiSeq 2000 instrument. At the American Society of Human Genetics annual meeting, Erasmus Medical Center Rotterdam researcher Cornelia […]

Multiplex ChIP-Seq

At popular demand! We now offer multiplexing for ChIP-Seq. Chromatin Immunoprecipitated (ChIP) of multiple samples within one single sequence run reduces the costs for ChIP-Seq. Depending on your needed coverage, we can sequence up to 96 samples within one lane. Moreover, with our new ChIP-sequencing pipeline, mapping, peak calling, vizualization and sample comparision are ready […]

Password Lost?

diag intake

diag status

Drabek et al

The Microtubule Plus-End Tracking Protein CLASP2 Is Required for Hematopoiesis and Hematopoietic Stem Cell Maintenance. Drabek K, Gutiérrez L, Vermeij M, Clapes T, Patel SR, Boisset JC, van Haren J, Pereira AL, Liu Z, Akinci U, Nikolic T, van Ijcken W, van den Hout M, Meinders M, Melo C, Sambade C, Drabek D, Hendriks RW, […]

Problem deciding between Arrays and NGS?

Do you face difficulties deciding whether to use MicroArrays or Next Generation Sequencing for your transcriptome analyses? Affymetrix, lead developer in Array solutions, facilitates in making your decision on their page on Arrays versus NGS. They also provide an in depth document with figures, numbers and arguments when to use which technology.       […]

Borg et al

KLF10 gene expression is associated with high fetal hemoglobin levels and with response to hydroxyurea treatment in β-hemoglobinopathy patients. Borg J, Phylactides M, Bartsakoulia M, Tafrali C, Lederer C, Felice AE, Papachatzopoulou A, Kourakli A, Stavrou EF, Christou S, Hou J, Karkabouna S, Lappa-Manakou C, Ozgur Z, van Ijcken W, von Lindern M, Grosveld FG, […]

van Jaarsveld et al

miR-141 regulates KEAP1 and modulates cisplatin sensitivity in ovarian cancer cells. van Jaarsveld MT, Helleman J, Boersma AW, van Kuijk PF, van Ijcken WF, Despierre E, Vergote I, Mathijssen RH, Berns EM, Verweij J, Pothof J, Wiemer EA. Oncogene. 2012 Oct 8.

lims

lims

beheer

Typhoon Specs

  Thyphoon Techincal specifications   Imaging modes PhosphorImaging Green excited fluorescence (532 nm) Red excited fluorescence (633 nm) Chemiluminescence Scan area 35 × 43 cm Sensitivity (limit of detection) Storage Phosphor: Storage phosphor screens retain energy from beta particles, X-rays, and gamma rays. The lower limit of detection for a 1 h exposure is > 2 dpm/mm2 for 14C […]

Biomics Website

The Biomics website has been completely updated! New are the applications and the services that deal with Next Generation Sequencing. You ask, We sequence.    

Borg et al

Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal hemoglobin. Borg J, Papadopoulos P, Georgitsi M, Gutierrez L, Grech G, Fanis P, Phylactides M, Verkerk AJ, van der Spek PJ, Scerri CA, Cassar W, Galdies R, van IJcken W, Ozgur Z, Gillemans N, Hou J, Bugeja M, Grosveld FG, von Lindern M, […]

Octet

  Protein and Small Molecule Label-free ForteBio’s Octet family of instruments provide scientists with label-free, real-time information about biomolecular interactions (ka, kd, and KD) in microplate format — particularly for proteins, peptides, DNA, RNA, and small molecules. Complement your Biacore system with faster throughput and solve your data acquisition bottle neck challenge in bio-therapeutic discovery. […]

Tecan HS 4800

  The Tecan HS4800 delivers fully automated hybridization of microarrays, from pre-hybridization and denaturation up to slide drying. The system is easy to use and improves reproducibility and sensitivity. Up to 12 slides can be processed in parallel on the system. Per 4 slides different hybridization temperatures can be set between 4 and 85°C. Denaturation […]

Tecan LS Reloaded

  The Tecan LS Reloaded is an extremely sensitive and flexible microarray laser scanner. The scanner has green (532nm) and red (633nm) lasers and specific filters for Cy3, Cy5 and OD detection. Some special features are listed: Different formats (with adapter) can be scanned: slides, microplates, petidishes LS 4-slide adapter provides seamless integration with HS4800 […]

Nimblegen Hyb Station

NimbleGen Systems Inc. provides a complete line of instrumentation, kits and consumables specifically designed to facilitate hybridization, washing and drying of NimbleChip™ DNA microarrays. NimbleGen's 4-Bay System is designed for highly reproducible hybridization conditions with precision controlled temperature and active mixing to provide high sensitivity and specificity hybridization results. The Hybridization Systems are used with […]

Nimblegen

Roche Nimblegen   Nimblegen     Background: Although Affymetrix is Biomics' primary array platform Nimblegen array infrastructure is up and running as well.   Our Service: Biomics can facilitate hybridization, washing and drying on the Nimblegen 4-bay HS4800 Arrays are scanned on the Tecan Laser scanner We have extensive experience exploiting Nimblegen producst as capture platforms. […]

Software

Software Biomics offers access to software packages & licenses, analyses tools and software       Agilent Bioanalyzer 2100 Expert Software Integrative Genomics Viewer The profiles acquired by the Bioanalyzer can be analyzed with the Expert Software version B.02.08 Or check the user guide Please visit the Biomics Bioanalyzer section for info on the machine […]

DNA Isolation

Automated DNA Isolation   DNA Isolation   Background: Automated and High throughout DNA Isolation Our Service: Biomics offers a DNA isolation service for Plasmid DNA from E. coli BAC DNA from E. coli Cosmid DNA from E. coli How to deliver and retrieve your samples? Email Center for Biomics to request DNA isolation of your […]

publicationtest2

test2

Publicationtest

test1

From Colony to DNA and Sanger Sequencing

From Colony to DNA and Sanger Sequence Biomics operates a workflow that can start from automated colony picking via high throughput DNA isolation to outsourced Sanger Sequencing Baseclear Sanger Sequencing Sanger Sequencing Service In collaboration with Baseclear Ultrasound Sonicator Covaris Ultrasonicator Biomics has a MSE Soniprep 150 plus Available in room Ee6.86 for disruption of […]

In House Sequencing Service

In House Sequencing Service   Sanger Sequencing     Background: The Center for Biomics offers a Sanger Sequencing Service for fast, single shot, in house sequencing.   Our Service: Biomics offers a flexible workflow for In House Sanger Sequencing in collaboration with Erasmus Clinical Genetics. Please see below for details on the workflow. Biomics collects the […]

BaseClear sequencing

BaseClear Sanger Sequencing Service Sanger Sequencing     Background: The Center for Biomics collaborates with Baseclear, Leiden in a Sanger Sequencing Service. For fast, single shot sequencing to complete Sanger sequencing projects. Our Service: Biomics offers a flexible workflow for Sanger Sequencing In collaboration with Baseclear, Leiden. Please see below for details on the workflow. Biomics […]

In house Sequencing Order

Baseclear SangerSeq Order

Illumina Status

Affymetrix Status

Custom Arrays

Custom Arrays   Custom Array Service     Biomics is fully equiped for Custom Array production and analyses.   Biomics can print barcoded arrays for customers Arrays are printed in a class 10.000 cleanroom using an airconditioned Chipwriter Pro Print, hybridisation and QC of batches up to 126 slides Arrays are hybridized and washed on […]

NGS Data Analyses Course

Next Generation Sequencing (NGS) Data analysis Course 11 September 2012 – 13 September 2012 Location: Erasmus MC   The course aims at PhD students, postdocs and senior researchers who are interested in, planning, or already working with next-generation sequencing. Currently available technologies as well as hardware and software solutions will be presented and discussed. The […]

Affymetrix Array

Affymetrix Array Service GeneChip/GeneAtlas                             Background: Affymetrix offers sensitive Arrays for a number of applications: expression analyses, copy number variation, variant detection, linkage analyses and more. Depending on the application, the starting point can be either DNA or RNA. Most commonly Affymetrix […]

Typhoon out of order

The Tyfoon scanner in room Ee-678 cannot be used. Repair is scheduled for Monday November 12th. We hope that at least one of the two scanners can be used again that Monday.                   

Chromatin Analyses

Chromatin Analyses   Chromatin Analyses Service     Biomics offers bioinformatics solutions to analyze the complete spectrum of Chromatin and Chromatome features. From DNA (hydroxy) methylation, histone compositions and modification, protein binding e.g. transcription factor complexes to chromatin accessibility, DNAse hypersensitivity and inter and intra chromosomal interactions.   Biomics can produce both NGS and Micro-Array data for most […]

Expression Analyses

Expression Analyses   Expression Analyses Service     Biomics offers bioinformatic solutions for RNA & Expression analyses. We have developed an Expression Analyses Service for automated expression value profiling, sample comparison and filtering of responding genes.   Biomics developed the "Expression Analyses Service" that directly accepts output from the Narwhal pipeline. For mapping we use […]

Narwhal

Narwhal   Primary NGS Pipeline     Once the sequencer finishes, the produced data (the raw sequences) will need demultiplexing & mapping for the majority of projects. For automated and flexible processing of these raw sequences, Biomics has written and published Narwhal: Our primary pipeline for NGS processing.   The raw sequence reads will be […]

mutation & variant analyses

Mutation & Variants Analyses   Applications     NGS technology revolutionized the systematic identification, screening and analyses of Variants & Mutations causing & contributing to disease. Biomics offers bioinformatic solutions aiding the analyses of mutations & variants. We have developed pipelines for automated variant calling & risc annotation, de novo mutation discovery and dominant or recessive […]

Biomics Illumina Infrastructure

  Biomics Illumina Infrastructure Illumina NextSeq 2000 Biomics operates 2 Illumina NextSeq 2000 1 flowcell per run Flow Cell Type P1 P2 P3 Single-end Reads 100 M 400 M 1.2 B Paired-end Reads 200 M 800 M 2.4 B   For detailed information visit Illumina Illumina HiSeq 2500 Biomics operates 2 Illumina HiSeq 2500 including […]

Gene regulation & Epigenetics

Epigenetics Applications         With the draft release of the human genome in 2000, the focus in fundamental & medical research has shifted from genetics to epigenetics. Epigenetics describes how the DNA sequences are read and interpreted by the machinery of the cell. Epigenetics includes DNA modifications e.g DNA (hydroxy)methylation, the histone code […]

Genomics & Genetics

Genomics & Genetics Applications   Biomics offers solutions for Genomics & Genetics questions including phylogenetics and comparative applications, ploidy & copy number variation (CNV), variant/mutation/haplotype/species identification, detection and analyses and more. For these purposes we can sequence, assemble and analyze from a single locus to genes, contigs and even whole genomes. Please check our application options below which […]

Odyssey

Odyssey CLx and Odyssey Classic 8 steps to better Western blots: Check out the “Introduction to Western Blotting” learning path on the Lambda U® Education Portal. We’ve enhanced the Lambda U Introduction to Western Blotting learning path for you! Expand your knowledge with digestible content and the latest in best practices – all in one […]

typhoon

Amersham Typhoon 5 & Typhoon FLA9500 Imaging System   The Amersham Typhoon 5 and the Typhoon FLA9500 Imaging System are the next generation scanners. These new lasers scanner are designed for versatile imaging and precise quantification of RGB fluorescent, near infrared fluorescent (only available Amersham Typhoon 5), colorimetric, and radiolabeled proteins and nucleic acid.   […]

van Riel et al

A novel complex, RUNX1- MYEF2, represses hematopoietic genes in erythroid cells. van Riel B, Pakozdi T, Brouwer R, Monteiro R, Tuladhar K, Franke V, Bryne JC, Jorna R, Rijkers EJ, van IJcken W, Andrieu-Soler C, Demmers J, Patient R, Soler E,Lenhard B,Grosveld F Mol Cell Biol. 2012 Jul 16

TapeStation

Agilent 2200 TapeStation The Agilent 2200 TapeStation offers automated sample processing and scalable throughput (2-96 samples per run). It is with the ready-to-use ScreenTape technology a fast and flexible system for quality control, sizing and quantification of RNA, DNA and proteins with zero carry-over. Agilent offers a wide range of ScreenTapes for the analysis of […]

Bioanalyzer

Agilent 2100 BioAnalyzer The Agilent 2100 BioAnalyzer is an automated analysis tool capable of handling nucleic acids, proteins and cells on one platform. It is usefull for quality control, sizing and quantitation of RNA, DNA and proteins. Agilent offers a wide range of LabChip kits for the analysis of RNA, DNA and proteins. The software […]

Nanodrop

Nanodrop The NanoDrop ND-2000 UV-VIS spectrophotometer enables highly accurate analyses of small samples. Recommended for fast calculation of incorporation efficiency of Cy3 and Cy5 labeled samples, DNA, RNA, protein and cell cultures. Only 1 µl of sample required (2 µl for protein and high-dye solutions) No cuvette needed Only 30 seconds to load your sample, […]

Variants & Mutations

NGS technology has revolutionized the systematic identification and analyses of Variants & Mutations and provided valuable insight into their effect and risk. Biomics produces both the NGS data and the bioinformatic analyses for the identification and risk assessment of the causative and contributing variants and mutations, crucial for understanding and treating diseases.

Soleimani et al

Snail Regulates MyoD Binding-Site Occupancy to Direct Enhancer Switching and Differentiation-Specific Transcription in Myogenesis. Soleimani VD, Yin H, Jahani-Asl A, Ming H, Kockx CE, van IJcken WF, Grosveld F, Rudnicki MA. Mol Cell. 2012 Jul 3

email list

user administration

sample validation

Restricted

pagina voor ecb

fantom Orderform

shRNAi orderform

More information on Mission shRNAi libraries

Affymetrix Intake

Hughes Carvalho et al

Genome-wide DNA methylation profiling of non-small cell lung carcinomas Hughes Carvalho R, Haberle V, Hou J, van Gent T, Thongjuea S, van IJcken W, Kockx C, Brouwer RW, Rijkers E, Sieuwerts A, Foekens J, van Vroonhoven M, Aerts J, Grosveld F, Lenhard B, Philipsen S. Epigenetics Chromatin. 2012 Jun 22;5(1):9

Chromatin Conformation Sequencing

  3D view on the chromosomes: Chromatin Interactome Chromatin Conformation Sequencing   Background: With Chromatin Conformation Sequencing, genome-wide chromatin interactions can be generated and integrated to build a 3D view of the genome.   Our Service: We offer a Chromatin Conformation Capture Sequencing workflow that can accept from different protocols (for details: see below): 3C-Seq: Chromatin […]

ChIPThruPLEX Sequencing

Map Chromatin associated proteins with Chip Sequencing ChIPThruPLEX Sequencing   Background: A ChIP DNA sample will be handed in by the customer. From this, we prepare the ChIP sequence library using the Thruplex DNA seq kit. ChIP experiments have usually a very low yield of ChIP DNA. The The Thruplex DNA seq kit is very […]

RNA Sequencing

Sensitive & Flexible analyses of gene activity RNA Sequencing       Background: With RNA Sequencing one can detect, monitor and analyse all species of RNAs. From mRNA to lincRNAs. From gene activity to whole transcriptome analyses. From viral genomes to rRNA based phylogenetics. From alternative splicing to splice variants.   Our Service: Biomics offers […]

Exome Sequencing

Cost Effective Sequencing of Genome Coding Regions Exome Sequencing     Background: The coding parts of the genome (the exons) are captured in an optimized application followed by high throughput sequencing. Goal is to sequence the exons of the entire exome or selected gene strands at high coverage at a competitive price to allow mutation or variant […]

Genome Sequencing

Smart Tools for Whole Genome Sequencing Genome Sequencing     Background: Whole genomes, including de novo can be sequenced for many purposes: Variant comparison, mutation discovery, phylogenetics or for other scientific or medical objectives.     Our Service: We offer a flexible workflow for whole genome sequencing (see below for details) that consists of two parts: […]

template 5 columns overview

Overview Of Our Biomics Services       Next Generation Sequencing Micro Array Genome Exome Chip-Seq 3C-Seq RNA-Seq Expression Array SNP Array Tiling Array Promoter Array Protein Array Custom Arrays       Bioinformatics Libraries Data management Interpretation & analyses Demultiplexing, Aligning Peak Calling Plotting Coverages Variant Calling Sigma mission shRNAi library functional analyses RNAi […]

template 2 column details

Biomics Libraries   Sigma shRNA Mission Library         Fast and Functional test of your Favourite gene(s) with our shRNA (RNAi, knock-down) library for human and mouse   Our Service: Sigma Mission human and mouse shRNAi clones are available as bacterial glycerol stocks (in 1.5ml tube with 10 ul of LB) to ErasmusMc researchers […]

Terms & Conditions

  Erasmus Center for Biomics Terms and Conditions General The Erasmus Center for Biomics is a core facility of Erasmus MC. After acceptance of a project the term will be determined in which the project can be finished. We will do our utmost best to perform the tests with maximum accuracy in the predicted term. […]

Variants & Mutations

  Variants & Mutations Applications   Crucial for understanding and treating diseases are the identification and risk assessment of the causative and contributing variants and mutations. NGS technology has revolutionized the systematic identification, screening and analyses of these Variants & Mutations and provided valuable insight into their effect and risk. Variants and Mutations can be analyzed for […]

Sleutels et al

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner. Sleutels F, Soochit W, Bartkuhn M, Heath H, Dienstbach S, Bergmaier P, Franke V, Rosa-Garrido M, van de Nobelen S, Caesar L, van der Reijden M, Bryne JC, van IJcken W, Grootegoed JA, […]

Kozhevnikova et al

Metabolic Enzyme IMPDH Is Also a Transcription Factor Regulated by Cellular State. Kozhevnikova EN, van der Knaap JA, Pindyurin AV, Ozgur Z, van IJcken WF, Moshkin YM, Verrijzer CP. Mol Cell. 2012 May 31

Soleimani et al

Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs. Soleimani VD, Punch VG, Kawabe YI, Jones AE, Palidwor GA, Porter CJ, Cross JW, Carvajal JJ, Kockx CE, van IJcken WF, Perkins TJ, Rigby PW, Grosveld F, Rudnicki MA. Dev Cell. 2012 May 16

Mission Statement

Our Mission Mission Statement The Erasmus Center for Biomics was initiated in 2002 as a central Dutch facility at Erasmus MC as a concerted action of all Departments. The Center aims to contribute to the progress of science using Genomics, Proteomics and Bioinformatics. Its mission is to design and deliver reliable and innovative services to […]

Profile

  please wait

Illumina Intake

Illumina

Information and Ordering     * Register as Erasmus MC customer. This enables access to all information of all available services, and will help us to advise you properly.     * You can contact us. We can tell you what the possibilities are. Please check first the information on our website.     * Make a plan […]

Logout

please wait

Register

please wait

Booking

Login

Login

Website Functionality for Biomics Clients Biomics Clients Diagnostics / Clinical Genetics Logout Register Intake Status NGS: Next Generation Sequencing Micro Array Intake Status Intake Status Functional Libraries Sanger Sequencing (for ErasmusMC clients only) cDNA Fantom shRNA Mission BaseClear Booking (for ErasmusMC clients only) Booking of Equipment www.biomics.nl please wait

Feedback

Feedback   For feedback, remarks, ideas, suggestions and advise on our center, applications or services, we invite you to drop by at the Erasmus Center for Biomics and talk to Dr. Ir. Wilfred van IJcken or email: : w.vanijcken@erasmusmc.nl or phone: +31 10 70 44 454   Your feedback is highly appreciated www.biomics.nl

Contact

Contact Dr. Ir. Wilfred van IJcken Erasmus MC, Center for Biomics Building Ee, Room Ee6.79b Wytemaweg 80, 3015 CN Rotterdam the Netherlands Tel: +31 10 70 44 454 Fax: +31 10 70 44 743 email: w.vanijcken@erasmusmc.nl Directions Postal Address & Sample Sending information How to reach Erasmus MC Packages and Sample Sending: ErasmusMC Center for […]

News

Nieuwe pagina!!

Group Members

Genomics Members Dr. Ir. Wilfred van IJcken, Head Center for Biomics and PI Cell Biology department Ing. Zeliha Ozgur, Technician Ing. Edwin Oole, Technician Ing. Xander den Dekker, Technician Ing. Zakia Azmani, Technician MSc. Kayleigh Hiscock, Bioinformatician Dr. Mirjam van den Hout, Bioinformatician    

Support

Biomics Support       Contact People contact information How to reach Biomics In Rotterdam, The Netherlands The people at Biomics       Publications News Publications & Papers published by or in collaboration with Biomics   News Overview       Feedback Jobs We do appreciate feedback Check our job opportunities       […]

Imaging

  Imaging (multiplex western blot on Odyssey) Biomics has a number of imaging options available. (quantification on Typhoon) Odyssey Typhoon Li-cor Odyssey CLx & Odyssey Classic Direct fluorescence detection Typhoon 5 & Typhoon FLA 9500 PhosphorImaging Fluorescence Chemiluminescence Detection Amersham Imager 600 Amersham Imager 600 CCD camera to acquire images from protein and DNA samples […]

Libraries

Biomics Libraries Sigma shRNA Mission Library             Fast and Functional test of your Favourite gene(s) with our shRNA (RNAi, knock-down) library   Our Service: Providing human and mouse shRNAi clones as bacterial glycerol stocks (in 1.5ml tube with 10 ul of LB) to Erasmus MC researchers Providing control clones as […]

Bioinformatics

BioInformatics The unmatched research and diagnostic opportunities that Next Generation Sequencing offer elicited an explosion in projects exploiting NGS. Together with the increasing number of sequences outputted by the Mass Parallel Sequencers, the demand on the downstream analyses of these sequences AND their projects has exploded accordingly. Storing, Handeling, Mapping, Processing, Interpreting, Visualizing and Analyzing […]

Micro and Custom Array

Micro Array Platforms Biomics operates both Affymetrix and Nimblegen platforms. Our pipelines include labelling, hybridization, washing and scanning and plotting. Our chips are used for a number of analyses including expression, splicing, SNP, chromatin conformation capture chip (4c) and more. Affymetrix Nimblegen Biomics used Affymetrix GeneAtlas and GeneChip Arrays Nimblegen Array for Expression Analysis and […]

OOLLDDEERR Next Generation Sequencing older

Next Generation Sequencing Platforms Biomics operates a fexible NGS pipeline with HiSeq2500, HiSeq4000 and Miseq sequencers Please check our overview comparing the sequencersThe Illumina NGS platforms are superior due to the large number of short sequence reads and the speed of production Genome Sequencing Exome Sequencing (De Novo) genome sequencing e.g. bacteria, viruses, animal models […]

Services

Overview Of Our Biomics Services Next Generation Sequencing Micro Array Genome Exome Chip-Seq 3C-Seq/HiC RNA-Seq Expression Array SNP Array Tiling Array Promoter Array Protein Array Custom Arrays Bioinformatics & Software Libraries Data management Interpretation & analysesDemultiplexing Alignment & Coverage Peak & Variant Calling Plots & figures Licenses, Tools, Software Sigma mission shRNAi library functional analyses […]

Diagnostics

Diagnostics   Applications     Biomics partners with clinics and research centra in developing pipelines for clinical diagnostics. Our pipelines flow from patient sample processing to data generation, analysis and interpretation. Our goal is to support researchers, clinical geneticists and physicians in understanding, diagnosing and treating the condition. Biomics uses Next Generation Sequencing technology to identify, screen and analyse variants […]

Chromatin Conformation

Chromatin Conformation Biomics operates an automated NGS pipeline with 2 Illumina Hiseq 2000 platforms including cBot cluster stations 1 MiSeq Personal sequencer The Illumina NGS platforms are superior due to the large number of short sequence reads and the speed of production       Genome Sequencing Exome Sequencing (De Novo) genome sequencing e.g. bacteria, […]

template adding a video

hier staat een link naar services  

Applications

Overview Of Our Biomics Applications       Genomics & Genetics Variants & Mutations Whole Genome/Locus/Gene Sequencing & Screening Assembly & Annotation Exome capture & sequencing Variant & Mutation Calling Detection & Screening Effect & Risc analyses        Epigenetics Diagnostics (from: Stadhouders et al) RNA profiling & Expression Analyses Chromatin Modifications DNA Methylation […]

Brazão et al

A new function of ROD1 in nonsense-mediated mRNA decay. Brazão TF, Demmers J, van IJcken W, Strouboulis J, Fornerod M, Romão L, Grosveld FG. FEBS Lett. 2012 Apr 24;586(8):1101-10.

Huang et al

Hypoxia-inducible factor 2a plays a critical role in the formation of alveoli and surfactant. Huang Y, Kempen MB, Munck AB, Swagemakers S, Driegen S, Mahavadi P, Meijer D, van IJcken W, van der Spek P, Grosveld F, Günther A, Tibboel D, Rottier RJ. Am J Respir Cell Mol Biol. 2012 Feb;46(2):224-32. 

van der Horst et al

Progesterone Inhibits Epithelial-to-Mesenchymal Transition in Endometrial Cancer. van der Horst PH, Wang Y, Vandenput I, Kühne LC, Ewing PC, van IJcken WF, van der Zee M, Amant F, Burger CW, Blok LJ. PLoS One. 2012;7(1):e30840.

Stadhouders et al

Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra RJ, Bryne JC, van den Heuvel A, Stevens M, de Boer E, Kockx C, van der Sloot A, van den Hout M, van IJcken W, Eick D, Lenhard B, Grosveld F, Soler E. EMBO J. 2011 Dec […]

Kuster et al

Left ventricular remodeling in swine after myocardial infarction: a transcriptional genomics approach. Kuster DW, Merkus D, Kremer A, van IJcken WF, de Beer VJ, Verhoeven AJ, Duncker DJ. Basic Res Cardiol. 2011 Nov 5.

Brouwer et al

NARWHAL, a primary analysis pipeline for NGS data. Brouwer RW, van den Hout MC, Grosveld FG, van IJcken WF. Bioinformatics. 2011 Nov 8.

Moshkin et al

Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner. Moshkin YM, Chalkley GE, Kan TW, Reddy BA, Ozgur Z, van IJcken WF, Dekkers DH, Demmers JA, Travers AA, Verrijzer CP. Mol Cell Biol. 2011 Nov 28.

Ribeiro de Almeida et al

The DNA-Binding Protein CTCF Limits Proximal Vk Recombination and Restricts k Enhancer Interactions to the Immunoglobulin k Light Chain Locus. Ribeiro de Almeida C, Stadhouders R, de Bruijn MJ, Bergen IM, Thongjuea S, Lenhard B, van IJcken W, Grosveld F, Galjart N, Soler E, Hendriks RW. Immunity. 2011 Oct 28;35(4):501-13.

Marques et al

Modulation of androgen receptor signaling in hormonal therapy-resistant prostate cancer cell lines. Marques RB, Dits NF, Erkens-Schulze S, van IJcken WF, van Weerden WM, Jenster G. PLoS One. 2011;6(8):e23144

Splinter et al

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJ, Zhu Y, Kaaij LJ, van IJcken W, Gribnau J, Heard E, de Laat W. Genes Dev. 2011 Jul 1;25(13):1371-83

Libregts et al

Chronic IFN{gamma} production in mice induces anemia by reducing erythrocyte lifespan and inhibiting erythropoiesis through an IRF-1/PU.1-axis. Libregts SF, Gutierrez L, de Bruin AM, Wensveen FM, Papadopoulos P, van IJcken W, Ozgur Z, Philipsen S, Nolte MA. Blood. 2011 Jul 1

Bralten et al

Absence of common somatic alterations in genes on 1p and 19q in oligodendrogliomas. Bralten LB, Nouwens S, Kockx C, Erdem L, Hoogenraad CC, Kros JM, Moorhouse MJ, Sillevis Smitt PA, van der Spek P, van IJcken W, Stubbs A, French PJ. PLoS One. 2011;6(7):e22000.

Pan et al

Mobilization of hepatic mesenchymal stem cells from human liver grafts. Pan Q, Fouraschen SM, Kaya FS, Verstegen MM, Pescatori M, Stubbs AP, van IJcken W, van der Sloot A, Smits R, Kwekkeboom J, Metselaar HJ, Kazemier G, de Jonge J, Tilanus HW, Wagemaker G, Janssen HL, van der Laan LJ. Liver Transpl. 2011 May;17(5):596-609

Engelen et al

Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes. Engelen E, Akinci U, Bryne JC, Hou J, Gontan C, Moen M, Szumska D, Kockx C, van IJcken W, Dekkers DH, Demmers J, Rijkers EJ, Bhattacharya S, Philipsen S, Pevny LH, Grosveld FG, Rottier RJ, Lenhard B, Poot RA. Nat Genet. 2011 […]

Esteghamat et al

The DNA binding factor Hmg20b is a repressor of erythroid differentiation. Esteghamat F, van Dijk TB, Braun H, Dekker S, van der Linden R, Hou J, Fanis P, Demmers J, van IJcken W, Ozgur Z, Horos R, Pourfarzad F, von Lindern M, Philipsen S. The DNA binding factor Haematologica. 2011 May 23

Schotte et al

Discovery of new microRNAs by small RNAome deep sequencing in childhood acute lymphoblastic leukemia. Schotte D, Moqadam FA, Lange-Turenhout EA, Chen C, van IJcken WF, Pieters R, den Boer ML. Leukemia. 2011 May 24

Nagel et al

Gene expression profiling assigns CHEK2 1100delC breast cancers to the luminal intrinsic subtypes. Nagel JH, Peeters JK, Smid M, Sieuwerts AM, Wasielewski M, de Weerd V, Trapman-Jansen AM, van den Ouweland A, Bruggenwirth H, van IJcken WF, Klijn JG, van der Spek PJ, Foekens JA, Martens JW, Schutte M, Meijers-Heijboer H. Breast Cancer Res Treat. […]

Gontan et al

RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation. Gontan C, Achame EM, Demmers J, Barakat TS, Rentmeester E, van IJcken W, Grootegoed JA, Gribnau J. Nature. 2012 Apr 29;485(7398):386-90

Racz et al

Effective Treatment of Psoriasis with Narrow-Band UVB Phototherapy Is Linked to Suppression of the IFN and Th17 Pathways. Racz E, Prens EP, Kurek D, Kant M, de Ridder D, Mourits S, Baerveldt EM, Ozgur Z, van IJcken WF, Laman JD, Staal FJ, van der Fits L. J Invest Dermatol. 2011 Mar 17.

Smits et al

Distinct SARS-Coronavirus Induced Acute Lung Injury Pathways in Two Different Non-Human Primate Species. Smits SL, van den Brand JM, de Lang A, Leijten LM, van IJcken WF, van Amerongen G, Osterhaus AD, Andeweg AC, Haagmans BL. J Virol. 2011 Feb 16.

Soler et al

A systems approach to analyze transcription factors in mammalian cells. Soler E, Andrieu-Soler C, Boer E, Bryne JC, Thongjuea S, Rijkers E, Demmers J, IJcken W, Grosveld F. Methods. 2011 Feb;53(2):151-62.

Martianov et al

Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells. Martianov I, Choukrallah MA, Krebs A, Ye T, Legras S, Rijkers E, van IJcken W, Jost B, Sassone-Corsi P, Davidson I. BMC Genomics. 2010 Sep 29;11:530.

Crop et al

Inflammatory conditions affect gene expression and function of human adipose tissue-derived mesenchymal stem cells. Crop MJ, Baan CC, Korevaar SS, IJzermans JNM, Pescatori M, Stubbs AP, van IJcken WFJ, Dahlke MH, Eggenhofer E, Weimar W, Hoogduijn MJ. Clin Exp Immunol. 2010 Sep 15. doi: 10.1111/j.1365-2249.2010.04256.x.

Mulugeta Achame et al

The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids. Mulugeta Achame E, Wassenaar E, Hoogerbrugge JW, Sleddens-Linkels E, Ooms M, Sun Z-W, van IJcken WFJ, Grootegoed JA and Baarends WM. BMC Genomics 2010, 11:367.

Visser et al

Transcriptional profiling of fibroblasts from patients with mutations in MCT8 and comparative analysis with the human brain transcriptome. Visser WE, Swagemakers SMA, Ozgur Z, Schot R, Verheyen FW, van IJcken WFJ, van der Spek PJ and Visser TJ. Human Molecular Genetics, 2010 Aug 12. 

Lao et al

Correlation between Genetic and Geographic Structure in Europe. Lao O, Lu TT, Nothnagel M, Junge O, Freitag-Wolf S, Caliebe A, Balascakova M, Bertranpetit J, Bindoff LA, Comas D, Holmlund G, Kouvatsi A, Macek M, Mollet I, Parson W, Palo J, Ploski R, Sajantila A, Tagliabracci A, Gether U, Werge T, Rivadeneira F, Hofman A, Uitterlinden […]

Delhanty et al

Unacylated ghrelin rapidly modulates lipogenic and insulin signaling pathway gene expression in metabolically active tissues of GHSR deleted mice. Delhanty PJ, Sun Y, Visser JA, van Kerkwijk A, Huisman M, van IJcken WF, Swagemakers S, Smith RG, Themmen AP, van der Lely AJ. PLoS One. 2010 Jul 26;5(7):e11749. 

Herfst et al

Pandemic 2009 H1N1 influenza virus causes diffuse alveolar damage in cynomolgus macaques. Herfst S, van den Brand JM, Schrauwen EJA, de Wit E, Munster VJ, van Amerongen G, Linster M, Zaaraoui F, van IJcken WFJ, Rimmelzwaan GF, Osterhaus ADME, Fouchier RAM, Andeweg AC, and Kuiken T. Vet Pathol. 2010 Jul 20.

Kassouf et al

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells. Kassouf MT, Hughes JR, Taylor S, McGowan SJ, Soneji S, Green AL, Vyas P, Porcher C. Genome Res. 2010 Jun 21.

Hou et al

Gene expression-based classification of non-small cell lung carcinomas and survival prediction. Hou J, Aerts J, den Hamer B, van IJcken W, den Bakker M, Riegman P, van der Leest C, van der Spek P, Foekens J, Hoogsteden H, Grosveld F, Philipsen S. PLoS ONE, 2010 Apr 22;5(4):e10312.

Mitchell et al

Short-term dietary restriction and fasting precondition against ischemia reperfusion injury in mice. Mitchell JR, Verweij M, Brand K, van de Ven M, Goemaere N, van den Engel S, Chu T, Forrer F, M.ller C, de Jong M, van IJcken W, IJzermans JN, Hoeijmakers JH, de Bruin RW. Aging Cell. 2010 Feb;9(1):40-53.

Saskia et al

Exacerbated Innate Host Response to SARS-CoV in Aged Non-human Primates. Saskia L. Smits, Anna De Lang, Judith M. A. van den Brand, Lonneke M. E. Leijten, Wilfred F. van IJcken, Geert van Amerongen, Thijs Kuiken, Arno Andeweg, Albert D. M. E. Osterhaus, and Bart L. Haagmans. PLoS Pathog. 2010 Feb 5;6(2):e1000756. 

Soler et al

The Genome-Wide Dynamics of the Binding of Ldb1 Complexes during Erythroid Differentiation. Soler E, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, Palstra R-J, Kockx C, van IJcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B and Grosveld F. Genes Dev. 2010 Feb 1;24(3):277-89.

van Agthoven et al

CITED2 and NCOR2 in anti-estrogen resistance and progression of breast cancer. van Agthoven T, Sieuwerts AM, Veldscholte J, Meijer-van Gelder ME, Smid M, Brinkman A, den Dekker AT, Leroy IM, van IJcken WFJ, Sleijfer S, Foekens JA, and Dorssers LCJ. British Journal of Cancer, 2009 Dec 1;101(11):1824-32.

Quaedackers et al

Monitoring of the immunomodulatory effect of CP-690,550 by analysis of the JAK/STAT pathway in kidney transplant patients. Quaedackers ME, Mol W, Korevaar SS, van Gurp EAFJ, van IJcken WFJ, Chan G, Weimar W and Baan CC. Transplantation. 2009 Oct 27;88(8):1002-9. 

de Jong et al

Molecular cytogenetics of congenital disorders. de Jong EM, Eussen B, Douben H, van IJcken W. and de Klein A In: W.B. van Leeuwen and C.Vink (editors), Molecular Diagnostics: Techniques and applications. IVA Groep BV, p139-147., 2009.  

Heul-Nieuwenhuijsen et al

The FOXF2 pathway in the human prostate stroma. Heul-Nieuwenhuijsen LV, Dits N, van IJcken W, de Lange D, Jenster G. Prostate. 2009 Oct 1;69(14):1538-47. 

Pothof et al

MicroRNA-mediated gene silencing modulates the UV-induced DNA-damage response. Pothof J, Verkaik NS, van IJcken W, Wiemer EA, Ta VT, van der Horst GT, Jaspers NG, van Gent DC, Hoeijmakers JH, Persengiev SP. EMBO J. 2009 Jul 22;28(14):2090-9.

Visser et al

Physiological thyroid hormone levels regulate numerous skeletal muscle transcripts. Visser WE, Heemstra KA, Swagemakers SM, Ozgur Z, Corssmit EP, Burggraaf J, van IJcken WF, van der Spek PJ, Smit JW, Visser TJ. J Clin Endocrinol Metab. 2009 Sep;94(9):3487-96.

Garinis et al

Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Garinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van IJcken W, Breit TM, van Steeg H, Mullenders LH, van der Horst GT, Brüning JC, Niessen CM, Hoeijmakers JH, Schumacher B. Nat Cell Biol. 2009 May;11(5):604-15.

Meester-Smoor et al

MN1 affects expression of genes involved in hematopoiesis and can enhance as well as inhibit RAR/RXR induced gene expression. Meester-Smoor MA, Janssen MJ, Grosveld GC, de Klein A, van IJcken WF, Douben H, Zwarthoff EC. Carcinogenesis. 2008 Oct;29(10):2025-34.

van Gils et al

Expression profiling in uveal melanoma provides a strong marker for survival and reveals two regions on chromosome 3p related to prognosis. van Gils W, Lodder EM, Mensink HW, Kilic E, Naus NC, Bruggenwirth H, van IJcken W, Paridaens D, Luyten GP, De Klein A. Invest Ophthalmol Vis Sci. 2008 Oct;49(10):4254-62.

Schumacher et al

Delayed and accelerated aging share common longevity assurance mechanisms. Schumacher B, van der Pluijm I, Moorhouse MJ, Kosteas T, Robinson AR, Suh Y, Breit TM, van Steeg H, Niedernhofer LJ, van Ijcken W, Bartke A, Spindler SR, Hoeijmakers JH, van der Horst GT, Garinis GA. PLoS Genet. 2008 Aug 15;4(8):e1000161.

Noordermeer et al

Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region. Noordermeer D, Branco MR, Splinter E, Klous P, van IJcken W, Swagemakers S, Koutsourakis M, van der Spek P, Pombo A, de Laat W. PLoS Genet. 2008 Mar 7;4(3):e1000016. 

Zubakov et al

Stable RNA markers for identification of blood and saliva stains revealed from whole genome expression analysis of time-wise degraded samples. Zubakov D, Hanekamp E, Kokshoorn M, van IJcken W, Kayser M. Int J Legal Med. 2008 Mar;122(2):135-42.

Kayser et al

Three Genome-wide Association Studies and a Linkage Analysis Identify HERC2 as a Human Iris Color Gene. Kayser M, Liu F, Janssens AC, Rivadeneira F, Lao O, van Duijn K, Vermeulen M, Arp P, Jhamai MM, van IJcken WF, den Dunnen JT, Heath S, Zelenika D, Despriet DD, Klaver CC, Vingerling JR, de Jong PT, Hofman […]

Hanifi-Moghaddam et al

Difference in signalling between various hormone therapies in endometrium, myometrium and upper part of the vagina. Hanifi-Moghaddam P, Boers-Sijmons B, Klaassens AH, van Wijk FH, van IJcken WF, Van der Spek P, Verheul HA, Kloosterboer HJ, Burger CW, Blok LJ. Hum Reprod. 2008 Feb;23(2):298-305.

van Loo et al

Transcription factor Sp3 knockout mice display serious cardiac malformations. van Loo PF, Mahtab EA, Wisse LJ, Hou J, Grosveld F, Suske G, Philipsen S, Gittenberger-de Groot AC. Mol Cell Biol. 2007 Dec;27(24):8571-82. 

Gielen et al

Genomic and nongenomic effects of estrogen signaling in human endometrial cells: involvement of the growth factor receptor signaling downstream AKT pathway. Gielen SC, Santegoets LA, K.hne LC, van IJcken WF, Boers-Sijmons B, Hanifi-Moghaddam P, Helmerhorst TJ, Blok LJ, Burger CW. Reprod Sci. 2007 Oct;14(7):646-54. 

Santegoets et al

HPV related VIN: highly proliferative and diminished responsiveness to extracellular signals. Santegoets LA, Seters M, Helmerhorst TJ, Heijmans-Antonissen C, Hanifi-Moghaddam P, Ewing PC, van IJcken WF, van der Spek PJ, van der Meijden WI, Blok LJ. Int J Cancer. 2007 Aug 15;121(4):759-66. 

Moshkin et al

Functional differentiation of SWI/SNF remodelers in transcription and cell cycle control. Moshkin YM, Mohrmann L, van IJcken WF, Verrijzer CP. Mol Cell Biol. 2007 Jan;27(2):651-61.

Kurek et al

Transcriptome and phenotypic analysis reveals Gata3-dependent signalling pathways in murine hair follicles. Kurek D, Garinis GA, van Doorninck JH, van der Wees J, Grosveld FG. Development. 2007 Jan;134(2):261-72. 

van der Heul-Nieuwenhuijsen et al

Gene expression profiling of the human prostate zones. van der Heul-Nieuwenhuijsen L, Hendriksen PJ, van der Kwast TH, Jenster G. BJU Int. 2006 Oct;98(4):886-97. 

Hanifi-Moghaddam et al

The hormone replacement therapy drug tibolone acts very similar to medroxyprogesterone acetate in an estrogen-and progesterone-responsive endometrial cancer cell line. Hanifi-Moghaddam P, Sijmons B, Ott MC, van IJcken WF, Nowzari D, Kuhne EC, van der Spek P, Kloosterboer HJ, Burger CW, Blok LJ. J Mol Endocrinol. 2006 Dec;37(3):405-13. 

Gielen et al

Tamoxifen treatment for breast cancer enforces a distinct gene-expression profile on the human endometrium: an exploratory study. Gielen SC, Kuhne LC, Ewing PC, Blok LJ, Burger CW. Endocr Relat Cancer. 2005 Dec;12(4):1037-49. 

Biomics.nl, The Erasmus Center for Biomics in Rotterdam, managed by Wifred van IJcken, Ph.D.