Publications

MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates.

Somel M, Liu X, Tang L, Yan Z, Hu H, Guo S, Jiang X, Zhang X, Xu G, Xie G, Li N, Hu Y, Chen W, Pääbo S, Khaitovich P.

PLoS Biol. 2011 Dec;9(12):e1001214. Epub 2011 Dec 6.

 

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains.

Hu HY, Guo S, Xi J, Yan Z, Fu N, Zhang X, Menzel C, Liang H, Yang H, Zhao M, Zeng R, Chen W, Pääbo S, Khaitovich P.

PLoS Genet. 2011 Oct;7(10):e1002327. Epub 2011 Oct 13.

 

Deep sequencing reveals 50 novel genes for recessive cognitive disorders.

Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P, Zecha A, Mohseni M, Püttmann L, Vahid LN, Jensen C, Moheb LA, Bienek M, Larti F, Mueller I, Weissmann R, Darvish H, Wrogemann K, Hadavi V, Lipkowitz B, Esmaeeli-Nieh S, Wieczorek D, Kariminejad R, Firouzabadi SG, Cohen M, Fattahi Z, Rost I, Mojahedi F, Hertzberg C, Dehghan A, Rajab A, Banavandi MJ, Hoffer J, Falah M, Musante L, Kalscheuer V, Ullmann R, Kuss AW, Tzschach A, Kahrizi K, Ropers HH.

Nature. 2011 Sep 21;478(7367):57-63.

 

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.

Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N.

Nucleic Acids Res. 2011 Sep 12. [Epub ahead of print]

 

ST3GAL3 Mutations Impair the Development of Higher Cognitive Functions

Hao Hu, Katinka Eggers, Wei Chen, Masoud Garshasbi, M. Mahdi Motazacker, Klaus Wrogemann, Kimia Kahrizi, Andreas Tzschach, Masoumeh Hosseini, Ideh Bahman, Tim Hucho, Martina Mühlenhoff, Rita Gerardy-Schahn, Hossein Najmabadi, H. Hilger Ropers, Andreas W. Kuss

The American Journal of Human Genetics - 9 September 2011 (Vol. 89, Issue 3, pp. 407-414)

 

Impact of novel sequencing technology on transcriptome analysis Wei Chen European Pharmaceutical Review 2011 Volume 16 Issue4 61-63

 

Global quantification of mammalian gene expression control

Schwanhäusser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J*, Chen W*, Selbach M*.

Nature. 2011 May 19;473(7347):337-42

*shared corresponding author

 

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.

Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Alvarado AS, Kempa S, Dieterich C, Rajewsky N, Chen W.

Genome Res. 2011 May 2. [Epub ahead of print]

 

Comparative Genomic Integration Profiling of Sleeping Beauty Transposons Mobilized With High Efficacy From Integrase-defective Lentiviral Vectors in Primary Human Cells.

Moldt B, Miskey C, Staunstrup NH, Gogol-Döring A, Bak RO, Sharma N, Mátés L, Izsvák Z, Chen W, Ivics Z, Mikkelsen JG.

Mol Ther. 2011 Apr 5. [Epub ahead of print]

 

Widespread expression of piRNA-like molecules in somatic tissues

Zheng Yan; Hai Yang Hu; Xi Jiang; Vera Maierhofer; Elena Neb; Liu He; Yuhui Hu; Hao Hu; Na Li; Wei Chen*; Philipp Khaitovich*

Nucleic Acids Research 2011; doi: 10.1093/nar/gkr298

*shared corresponding author

 

Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1.

Jensen LR, Chen W, Moser B, Lipkowitz B, Schroeder C, Musante L, Tzschach A, Kalscheuer VM, Meloni I, Raynaud M, van Esch H, Chelly J, de Brouwer AP, Hackett A, van der Haar S, Henn W, Gecz J, Riess O, Bonin M, Reinhardt R, Ropers HH, Kuss AW.

Eur J Hum Genet. 2011 Jan 26. [Epub ahead of print]

 

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells Leddin M; Perrod C; Hoogenkamp M; Ghani S; Assi S; Heinz S; Wilson NK; Follows G; Schoenheit J; Vockentanz L; Mosamam A; Chen W; Tenen DG; Westhead DR; Goettgens B; Bonifer C; Rosenbauer F Blood 2011 Jan 14. [Epub ahead of print]

 

The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes

Stittrich AB; Haftmann C; Sgouroudis E; Kuehl AA; Hegazy AN; Panse I; Riedel R; Flossdorf M; Dong J; Fuhrmann F; Heinz GA; Fang Z; Li N; Bissels U; Hatam F; Jahn A; Hammoud B; Matz M; Schulze FM; Baumgrass R; Bosio A; Mollenkopf HJ; Gruen J; Thiel A; Chen W; Hoefer T; Loddenkemper C; Loehning M; Chang HD; Rajewsky N; Radbruch A; Mashreghi MF


 

Nature Immunology 11 (11): 1057-1062 (2010-11)

 

Finding Optimal Sets of Enriched Regions in ChIP-Seq Data

Doering A & Chen W

Proceedings of the German Conference on Bioinformatics, GCB 2010

 

Next generation sequencing in a family with autosomal recessive Kahrizi syndrome (OMIM 612713) reveals a homozygous frameshift mutation in SRD5A3.

Kahrizi K, Hu CH, Garshasbi M, Abedini SS, Ghadami S, Kariminejad R, Ullmann R, Chen W, Ropers HH, Kuss AW, Najmabadi H, Tzschach A.

Eur J Hum Genet. 2010 Aug 11. [Epub ahead of print]

 

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain.

Somel M*, Guo S, Fu N, Yan Z, Hu HY, Xu Y, Yuan Y, Ning Z, Hu Y, Menzel C, Hu H, Lachmann M, Zeng R, Chen W*, Khaitovich P*.

Genome Res. 2010 Jul 20. [Epub ahead of print]

*shared corresponding author


Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

Xu AG, He L, Li Z, Xu Y, Li M, Fu X, Yan Z, Yuan Y, Menzel C, Li N, Somel M, Hu H, Chen W*, Pääbo S, Khaitovich P*.

PLoS Comput Biol. 2010 Jul 1;6:e1000843.

*shared corresponding author

 

Comprehensive survey of human brain microRNA by deep sequencing.

Shao NY, Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Li N, Chen W*, Khaitovich P*.

BMC Genomics. 2010 Jun 30;11(1):409. [Epub ahead of print] *shared corresponding author

 

Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice

Shahaf Peleg, Farahnaz Sananbenesi, Athanasios Zovoilis, Susanne Burkhardt, Sanaz Bahari-Javan, Roberto Carlos Agis-Balboa, Perla Cota, Jessica Lee Wittnam, Andreas Gogol-Doering, Lennart Opitz, Gabriella Salinas-Riester, Markus Dettenhofer, Hui Kang, Laurent Farinelli, Wei Chen, André Fischer

Science 7 May 2010: Vol. 328. no. 5979, pp. 753 - 756

 

Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing

Hao Hu, Klaus Wrogemann, Vera Kalscheuer, Andreas Tzschach, Hugues Richard, Stefan A. Haas, Corinna Menzel, Melanie Bienek, Guy Froyen, Martine Raynaud, Hans Van Bokhoven, Jamel Chelly, Hilger Ropers and Wei Chen

The HUGO Journal: Volume 3, Issue 1 (2010), Page 41.

 

Deciphering the porcine intestinal microRNA transcriptome.

Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler PF, Rajewsky N, Einspanier R.

BMC Genomics. 2010 Apr 30;11(1):275. [Epub ahead of print]

 

Genomic Analysis of miRNAs in an Extreme Mammalian Hibernator, the Arctic Ground Squirrel.

Liu Y, Hu W, Wang H, Lu M, Shao C, Menzel C, Yan Z, Li Y, Zhao S, Khaitovich P, Liu M, Chen W, Barnes BM, Yan J.

Physiol Genomics. 2010 May 4. [Epub ahead of print]

 

Tumor necrosis factor receptor superfamily member 19 (TNFRSF19) regulates differentiation fate of human mesenchymal (stromal) stem cells through canonical Wnt signaling and C/EBP.

Qiu W, Hu Y, Andersen TE, Jafari A, Li N, Chen W, Kassem M.

J Biol Chem. 2010 May 7;285(19):14438-49. Epub 2010 Mar 11.

 

Comparative Analysis of Transposable Element Vector Systems in Human Cells.

Grabundzija I, Irgang M, Mátés L, Belay E, Matrai J, Gogol-Döring A, Kawakami K, Chen W, Ruiz P, Chuah MK, Vandendriessche T, Izsvák Z, Ivics Z.

Mol Ther. 2010 Apr 6. [Epub ahead of print]

 

Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing.

Chen W, Ullmann R, Langnick C, Menzel C, Wotschofsky Z, Hu H, Döring A, Hu Y, Kang H, Tzschach A, Hoeltzenbein M, Neitzel H, Markus S,Wiedersberg E, Kistner G, van Ravenswaaij-Arts CM, Kleefstra T, Kalscheuer VM, Ropers HH.

Eur J Hum Genet. 2009 Dec 2. [Epub ahead of print]

 

Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.

Stoeckius M, Maaskola J, Colombo T, Rahn HP, Friedländer MR, Li N, Chen W, Piano F, Rajewsky N.

Nat Methods. 2009 Sep 6. [Epub ahead of print]

 

Sequence features associated with microRNA strand selection in humans and flies.

Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Zhou YH, Chen W*, Khaitovich P*.

BMC Genomics. 2009 Sep 4;10(1):413. [Epub ahead of print]

*shared corresponding author

 

Estimating accuracy of RNA-Seq and microarrays with proteomics.

Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W*, Li Y, Zeng R, Khaitovich P*.

BMC Genomics. 2009 Apr 16;10:161.

*shared corresponding author

 

A Human snoRNA with MicroRNA-Like Functions

Christine Ender, Azra Krek, Marc R. Friedländer, Michaela Beitzinger, Lasse Weinmann, Wei Chen, Sébastien Pfeffer, Nikolaus Rajewsky, Gunter Meister

Molecular Cell - 21 November 2008 (Vol. 32, Issue 4, pp. 519-528)

 

High frequency of submicroscopic genomic aberrations detected by tiling path array CGH in patients with isolated congenital heart disease

Fikret Erdogan, Lars Allen Larsen, Litu Zhang, Zeynep Tumer, Niels Tommerup, Wei Chen, Joes R Jacobsen, Marei Schubert, Jan Jurkatis, Andreas Tzschach, Hilger H Ropers, and Reinhard Ullmann

 

    J Med Genet Published Online First: 19 August 2008

 

MicroRNAs in Brain Function and Disease (Review)

Kuss AW &  Chen W

Current Neurology and Neuroscience Reports 2008, 8:190-197

 

Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N.

Discovering microRNAs from deep sequencing data using miRDeep.

Nat Biotechnol. 2008 Apr;26(4):407-15.

 

Chen W, Kalscheu V, Tzschach A, Menzel C, Ullmann R, Schulz M, Erdogan F, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U, Rost I, Dufke A, Grasshoff U, Glaeser BG, Vingron M, Ropers HH.

Mapping translocation breakpoints by next-generation sequencing.

Genome Res. 2008 Jul;18(7):1143-9

 

Scheffer IE, Turner SJ, Dibbens LM, Bayly MA, Friend K, Hodgson B, Burrows L, Shaw M, Wei C, Ullmann R, Ropers HH, Szepetowski P, Haan E, Mazarib A, Afawi Z, Neufeld MY, Andrews PI, Wallace G, Kivity S, Lev D, Lerman-Sagie T, Derry CP, Korczyn AD, Gecz J, Mulley JC, Berkovic SF.

Epilepsy and mental retardation limited to females: an under-recognized disorder.

Brain 2008 Jan 29; [Epub ahead of print]

 

Tzschach A*, Chen W*, Erdogan F, Hoeller A, Ropers HH, Castellan C, Ullmann R, Schinzel A.

Characterization of interstitial Xp duplications in two families by tiling path array CGH.

Am J Med Genet A. 2008 Jan 15;146(2):197-203.

*shared first author

 

Kirov G, Gumus D, Chen W, Norton N, Georgieva L, Sari M, O'Donovan MC, Erdogan F, Owen MJ, Ropers HH, Ullmann R

Comparative genome hybridisation analysis suggests a role for NRXN1 and APBA2 in schizophrenia. Hum Mol Genet. 2007 Nov 6; [Epub ahead of print]

 

Ullmann R, Turner G, Kirchhoff M, Chen W, Tonge B, Rosenberg C, Field M, Vianna-Morgante AM, Christie L, Krepischi-Santos AC, Banna L, Brereton AV, Hill A, Bisgaard AM, Muller I, Hultschig C, Erdogan F, Wieczorek G, Ropers HH.

Array CGH identifies reciprocal 16p13.1 duplications and deletions that predispose to autism and/or mental retardation.

Hum Mutat. 2007 Jul;28(7):674-82.

 

Chen W, Jensen LR, Gecz J, Fryns JP, Moraine C, de Brouwer A, Chelly J, Moser B, Ropers HH, Kuss AW: Mutation screening of brain-expressed X-chromosomal miRNA genes in 464 patients with nonsyndromic X-linked mental retardation. Eur J Hum Genet. 2007 Mar;15(3):375-8

 

Najmabadi H, Motazacker MM, Garshasbi M, Kahrizi K, Tzschach A, Chen W, Behjati F, Hadavi V, Nieh SE, Abedini SS, Vazifehmand R, Firouzabadi SG, Jamali P, Falah M, Seifati SM, Gruters A, Lenzner S, Jensen LR, Ruschendorf F, Kuss AW, Ropers HH.: Homozygosity mapping in consanguineous families reveals extreme heterogeneity of non-syndromic autosomal recessive mental retardation and identifies 8 novel gene loci. Hum Genet. 2007 Mar;121(1):43-8.

 

Jensen LR, Lenzner S, Moser B, Freude K, Tzschach A, Wei C, Fryns JP, Chelly J, Turner G, Moraine C, Hamel B, Ropers HH, Kuss AW.: X-linked mental retardation: a comprehensive molecular screen of 47 candidate genes from a 7.4 Mb interval in Xp11. Eur J Hum Genet. 2007 Jan;15(1):68-75

 

Erdogan F, Ullmann R, Chen W, Schubert M, Adolph S, Hultschig C, Kalscheuer V, Ropers HH, Spaich C, Tzschach A.: Characterization of a 5.3 Mb deletion in 15q14 by comparative genomic hybridization using a whole genome "tiling path" BAC array in a girl with heart defect, cleft palate, and developmental delay. Am J Med Genet A. 2007 Jan 15;143(2):172-8.

 

Erdogan F*, Chen W*, Kirchhoff M, Kalscheuer VM, Hultschig C, Muller I, Schulz R, Menzel C, Bryndorf T, Ropers HH, Ullmann R.: Impact of low copy repeats on the generation of balanced and unbalanced chromosomal aberrations in mental retardation. Cytogenetic and genome research. 2006;115(3-4):247-53.                                                                        

*Shared first author

 

Budny B, Chen W, Omran H, Fliegauf M, Tzschach A, Wisniewska M, Jensen LR, Raynaud M, Shoichet SA, Badura M, Lenzner S, Latos-Bielenska A, Ropers HH: A novel X-linked recessive syndrome characterized by mental retardation and primary ciliary dyskinesia is allelic to OFD1. Human Genetics 2006 Sep;120(2):171-8

Chen W, Erdogan F, Ropers HH, Lenzner S, Ullmann R: CGHPRO – A comprehensive data analysis tool for array CGH. BMC Bioinformatics 2005, 6:85

 

Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG: Go!Poly: A gene-oriented polymorphism database. Hum Mutat. 2001 Nov;18(5):382-7.

 

Chen W, Zhang G, Zhang S: Introduction to Go! Poly, a human genome polymorphism database.  Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2001 Dec;18(6):482-5.

 

Chen W, Zhang G, Zhang S:

Discovery of Candidate SNP by Bioinformatic Methods. Yi Chuan,2001,23(2):153-156.