Publications

Home Publications

2022

  • Updating…

2021

  • Updating…

2020

2019

  • Zou, X., Gao, X., & Chen, W. (2019). Deep Learning Deepens the Analysis of Alternative Splicing. Genomics Proteomics Bioinformatics, 17(2), 219-221. doi:10.1016/j.gpb.2019.05.001
  • Zhang, H., Liao, L., Cai, Y., Hu, Y., & Wang, H. (2019). IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques. Methods, 166, 57-65. doi:10.1016/j.ymeth.2019.03.012
  • Wang, X., You, X., Langer, J. D., Hou, J., Rupprecht, F., Vlatkovic, I., . . . Chen, W. (2019). Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus. Nat Commun, 10(1), 5009. doi:10.1038/s41467-019-13037-0
  • Wang, M., Hou, J., Muller-McNicoll, M., Chen, W., & Schuman, E. M. (2019). Long and Repeat-Rich Intronic Sequences Favor Circular RNA Formation under Conditions of Reduced Spliceosome Activity. iScience, 20, 237-247. doi:10.1016/j.isci.2019.08.058
  • Mai, K., Li, L. N., Wiegand, S., Brachs, M., Leupelt, V., Ernert, A., . . . Spranger, J. (2019). An Integrated Understanding of the Molecular Mechanisms of How Adipose Tissue Metabolism Affects Long-term Body Weight Maintenance. Diabetes, 68(1), 57-65. doi:10.2337/db18-0440
  • Leisegang, M. S., Gu, L., Preussner, J., Gunther, S., Hitzel, J., Ratiu, C., . . . Brandes, R. P. (2019). The histone demethylase PHF8 facilitates alternative splicing of the histocompatibility antigen HLA-G. FEBS Lett, 593(5), 487-498. doi:10.1002/1873-3468.13337
  • Lam, J. H., Li, Y., Zhu, L., Umarov, R., Jiang, H., Heliou, A., . . . Gao, X. (2019). A deep learning framework to predict binding preference of RNA constituents on protein surface. Nat Commun, 10(1), 4941. doi:10.1038/s41467-019-12920-0
  • Hu, H., Kahrizi, K., Musante, L., Fattahi, Z., Herwig, R., Hosseini, M., . . . Najmabadi, H. (2019). Genetics of intellectual disability in consanguineous families. Mol Psychiatry, 24(7), 1027-1039. doi:10.1038/s41380-017-0012-2
  • Gong, M., Yu, Y., Liang, L., Vuralli, D., Froehler, S., Kuehnen, P., . . . Raile, K. (2019). HDAC4 mutations cause diabetes and induce beta-cell FoxO1 nuclear exclusion. Mol Genet Genomic Med, 7(5), e602. doi:10.1002/mgg3.602
  • Chen, T., Zhang, B., Ziegenhals, T., Prusty, A. B., Frohler, S., Grimm, C., . . . Chen, W. (2019). A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing. PLoS Genet, 15(10), e1008460. doi:10.1371/journal.pgen.1008460

2018

  • Boeckel JN, Perret MF, Glaser SF, Seeger T, Heumüller AW, Chen W, John D, Kokot KE, Katus HA, Haas J, Lackner MK, Kayvanpour E, Grabe N, Dieterich C, von Haehling S, Ebner N, Hünecke S, Leuschner F, Fichtlscherer S, Meder B, Zeiher AM, Dimmeler S, Keller T. Identification and regulation of the long non-coding RNA Heat2 in heart failure. J Mol Cell Cardiol. 2018 Nov 13;126:13-22. doi: 10.1016/j.yjmcc.2018.11.004. [Epub ahead of print]
  • Mai K, Li L, Wiegand S, Brachs M, Leupelt V, Ernert A, Kühnen P, Hübner N, Robinson P, Chen W, Krude H, Spranger J. An Integrated Understanding of the Molecular Mechanisms of How Adipose Tissue Metabolism Affects Long-term Body Weight Maintenance.  Diabetes. 2019 Jan;68(1):57-65. doi: 10.2337/db18-0440. Epub 2018 Nov 2.
  • Mikuda N, Kolesnichenko M, Beaudette P, Popp O, Uyar B, Sun W, Tufan AB, Perder B, Akalin A,Chen W, Mertins P, Dittmar G, Hinz M, Scheidereit C.The IκB kinase complex is a regulator of mRNA stability. EMBO J. 2018 Nov 22. pii: e98658. doi: 10.15252/embj.201798658. [Epub ahead of print]
  • Löber U, Hobbs M, Dayaram A, Tsangaras K, Jones K, Alquezar-Planas DE, Ishida Y, Meers J, Mayer J, Quedenau C, Chen W, Johnson RN, Timms P, Young PR, Roca AL, Greenwood AD. Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. Proc Natl Acad Sci U S A. 2018 Aug 6. pii: 201807598. doi: 10.1073/pnas.1807598115.
  • Josipovic I, Pflüger B, Fork C, Vasconez AE, Oo JA, Hitzel J, Seredinski S, Gamen E, Heringdorf DMZ, Chen W, Looso M, Pullamsetti SS, Brandes RP, Leisegang MS. Long noncoding RNALISPR1 is required for S1P signaling and endothelial cell function. J Mol Cell Cardiol. 2018 Mar;116:57-68. doi: 10.1016/j.yjmcc.2018.01.015. Epub 2018 Feb 3
  • Yang JY, Deng XY, Li YS, Ma XC, Feng JX, Yu B, Chen Y, Luo YL, Wang X, Chen ML, Fang ZX, Zheng FX, Li YP, Zhong Q, Kang TB, Song LB, Xu RH, Zeng MS, Chen W, Zhang H, Xie W, Gao S. Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control. Nat Commun. 2018 Mar 21;9(1):1165. doi: 10.1038/s41467-018-03544-x.
  • Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry. 2018 Jan 4. doi: 10.1038/s41380-017-0012-2. [Epub ahead of print]

2017

  • Pei W, Feyerabend TB, Rössler J, Wang X, Postrach D, Busch K, Rode I, Klapproth K, Dietlein N, Quedenau C, Chen W, Sauer S, Wolf S, Höfer T, Rodewald HR. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature. 2017 Aug 16. doi: 10.1038/nature23653. [Epub ahead of print]
  • Bischoff FC, Werner A, John D, Boeckel JN, Melissari MT, Grote P, Glaser SF, Demolli S, Uchida S, Michalik KM, Meder B, Katus HA, Haas J, Chen W, Pullamsetti SS, Seeger W, Zeiher AM, Dimmeler S, Zehendner CM. Identification and Functional Characterization of Hypoxia-Induced Endoplasmic ReticulumStress Regulating lncRNA (HypERlnc)in Pericytes. Circ Res. 2017 Jun 13. pii: CIRCRESAHA.116.310531. doi: 10.1161/CIRCRESAHA.116.310531. [Epub ahead of print]
  • Natale F, Rapp A, Yu W, Maiser A, Harz H, Scholl A, Grulich S, Anton T, Hörl D, Chen W, Durante M , Taucher-Scholz G, Leonhardt H, Cardoso MC Identification of the elementary structural units of the DNA damage response. Nat Commun. 2017 Jun 12;8:15760. doi: 10.1038/ncomms15760.
  • Sun Y, Bao Y, Han W, Song F, Shen X, Zhao J, Zuo J, Saffen D, Chen W, Wang Z, You X, Wang Y. Autoregulation ofRBM10and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated d Nucleic Acids Res. 2017 Jun 6. doi: 10.1093/nar/gkx508. [Epub ahead of print]
  • Buonocore F, Kühnen P, Suntharalingham JP, Del Valle I, Digweed M, Stachelscheid H, Khajavi N, Didi M, Brady AF, Blankenstein O, Procter AM, Dimitri P, Wales JK, Ghirri P, Knöbl D, Strahm B, Erlacher M, Wlodarski MW, Chen W, Kokai GK, Anderson G, Morrogh D, Moulding DA, McKee SA, Niemeyer CM, Grüters A, Achermann JC. Somatic mutations and progressive monosomy modify SAMD9-related phenotypes in humans J Clin Invest. 2017 Mar 27. pii: 91913. doi: 10.1172/JCI91913. [Epub ahead of print]

2016

  • Stunnenberg HG; International Human Epigenome Consortium., Hirst M. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 2016 Nov 17;167(5):1145-1149. doi: 10.1016/j.cell.2016.11.007.
  • Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Amirabad AD, Ardakani FB, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch CD, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Richter AS, Sieverling L; DEEP Consortium., Chang HD, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schulz MH, Schultze JL, Radbruch A, Walter J, Hamann A, Polansky JK. Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity. 2016 Nov 15;45(5):1148-1161. doi: 10.1016/j.immuni.2016.10.022.
  • Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dehghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler JG, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz MH. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. Nucleic Acids Res. 2016 Nov 29. pii: gkw1061. [Epub ahead of print]
  • Grunert M, Dorn C, Cui H, Dunkel I, Schulz K, Schoenhals S, Sun W, Berger F, Chen W, Sperling SR. Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases. Cardiovasc Res. 2016 Oct;112(1):464-77. doi: 10.1093/cvr/cvw195.
  • McShane E, Sin C, Zauber H, Wells JN, Donnelly N, Wang X, Hou J, Chen W, Storchova Z, Marsh JA, Valleriani A, Selbach M. Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation. Cell. 2016 Oct 5. pii: S0092-8674(16)31248-X. doi: 10.1016/j.cell.2016.09.015.
  • Stutika C, Mietzsch M, Gogol-Döring A, Weger S, Sohn M, Chen W, Heilbronn R. Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation. PLoS One. 2016 Sep 9;11(9):e0161454. doi: 10.1371/journal.pone.0161454. eCollection 2016.
  • Pink M, Ratsch BA, Mardahl M, Durek P, Polansky JK, Karl M, Baumgrass R, Wallner S, Cadenas C, Gianmoena K, Floess S, Chen W, Nordstroem K, Tierling S, Olek S, Walter J, Hamann A, Syrbe U. Imprinting of Skin/Inflammation Homing in CD4+ T Cells Is Controlled by DNA Methylation within the Fucosyltransferase 7 Gene. J Immunol. 2016 Sep 2. pii: 1502434. [Epub ahead of print]
  • Müller R, Weirick T, John D, Militello G, Chen W, Dimmeler S, Uchida S. ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. Sci Rep. 2016 Sep 1;6:32475. doi: 10.1038/srep32475.
  • Kinkley S, Helmuth J, Polansky JK, Dunkel I, Gasparoni G, Fröhler S, Chen W, Walter J, Hamann A, Chung HR. reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells. Nat Commun. 2016 Aug 17;7:12514. doi: 10.1038/ncomms12514.
  • Stellos K, Gatsiou A, Stamatelopoulos K, Perisic Matic L, John D, Lunella FF, Jaé N, Rossbach O, Amrhein C, Sigala F, Boon RA, Fürtig B, Manavski Y, You X, Uchida S, Keller T, Boeckel JN, Franco-Cereceda A, Maegdefessel L, Chen W, Schwalbe H, Bindereif A, Eriksson P, Hedin U, Zeiher AM, Dimmeler. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation. Nat Med. 2016 Sep 5. doi: 10.1038/nm.4172. [Epub ahead of print]
  • Wallner S, Schröder C, Leitão E, Berulava T, Haak C, Beißer D, Rahmann S, Richter AS, Manke T, Bönisch U, Arrigoni L, Fröhler S, Klironomos F, Chen W, Rajewsky N, Müller F, Ebert P, Lengauer T, Barann M, Rosenstiel P, Gasparoni G, Nordström K, Walter J, Brors B, Zipprich G, Felder B, Klein-Hitpass L, Attenberger C, Schmitz G, Horsthemke B. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016 Jul 29;9:33. doi: 10.1186/s13072-016-0079-z. eCollection 2016.
  • M. Jargosch, S. Kröger, E. Gralinska, U. Klotz, Z. Fang, W. Chen, U. Leser, J. Selbig, D. Groth, R. Baumgrass. Data integration for identification of important transcription factors of STAT6-mediated cell fate decisions Genet. Mol. Res. 15 (2 ): – DOI: 10.4238/gmr.15028493

2015 and earlier

  • Xu X, Meng Q, Erben U, Wang P, Glauben R, Kühl AA, Wu H, Ma CW, Hu M, Wang Y, Sun W, Jia J, Wu X, Chen W, Siegmund B, Qin Z. Myeloid-derived suppressor cells promote B-cell production of IgA in a TNFR2-dependent manner. Cell Mol Immunol. 2016 May 2. doi: 10.1038/cmi.2015.103. [Epub ahead of print]
  • Gogol-Döring A, Ammar I, Gupta S, Bunse M, Miskey C, Chen W, Uckert W, Schulz TF, Izsvák Z, Ivics Z. Genome-Wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4+ T Cells.  Mol Ther. 2016 Jan 12. doi: 10.1038/mt.2016.11. [Epub ahead of print]
  • Stutika C, Gogol-Döring A, Botschen L, Mietzsch M, Weger S, Feldkamp M, Chen W, Heilbronn R. A Comprehensive RNA-Seq Analysis of the Adeno-Associated Virus type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins. J Virol. 2015 Nov 11. pii: JVI.02750-15. [Epub ahead of print]
  • Shen SQ, Wei HX, Fu YH, Zhang H, Mo QY, Wang XJ, Deng SQ, Zhao W, Liu Y, Feng XS, Chen W, Peng HJ. Multiple Sources of Infection and Potential Endemic Characteristics of the Large Outbreak of Dengue in Guangdong in 2014. Sci Rep. 2015 Nov 23;5:16913. doi: 10.1038/srep16913.
  • Boeckel JN, Jaé N, Heumüller AW, Chen W, Boon RA, Stellos K, Zeiher AM, John D, Uchida S, Dimmeler S. Identification and Characterization of Hypoxia-Regulated Endothelial Circular RNA. Circ Res. 2015 Sep 16. pii: CIRCRESAHA.115.306319. [Epub ahead of print]
  • Kraemer N, Picker-Minh S, Abbasi AA, Fröhler S, Ninnemann O, Khan MN, Ali G, Chen W, Kaindl AM. Genetic causes of MCPH in consanguineous Pakistani families. Clin Genet. 2015 Nov 8. doi: 10.1111/cge.12685.
  • Bertelsen B, Nazaryan-Petersen L, Sun W, Mehrjouy MM, Xie G, Chen W, Hjermind LE, Taschner PE, Tümer Z. A germline chromothripsis event stably segregating in 11 individuals through three generations. Genet Med. 2015 Aug 27. doi: 10.1038/gim.2015.112. [Epub ahead of print]
  • Zaniewska M, Alenina N, Wydra K, Fröhler S, Kuśmider M, McCreary AC, Chen W, Bader M, Filip MDiscovering the mechanisms underlying serotonin (5-HT)2A and 5-HT2C receptor regulation following nicotine withdrawal in rats J Neurochem. 2015 May 30. doi: 10.1111/jnc.13192. [Epub ahead of print]
  • Winkelmann A, You X, Grünewald N, Häussler U, Krestel H, Haas CA, Schwarz G, Chen W, Meier JC. Identification of a New Genomic Hot Spot of Evolutionary Diversification of Protein Function. PLoS One. 2015 May 8;10(5):e0125413. doi: 0.1371/journal.pone.0125413. eCollection 2015.
  • Zhang B, Calado DP, Wang Z, Fröhler S, Köchert K, Qian Y, Koralov SB, Schmidt-Supprian M, Sasaki Y, Unitt C, Rodig S, Chen W, Dalla-Favera R, Alt FW, Pasqualucci L, Rajewsky K. An Oncogenic Role for Alternative NF-κB Signaling in DLBCL Revealed upon Deregulated BCL6 Expression. Cell Rep. 2015 May 5;11(5):715-26. doi: 10.1016/j.celrep.2015.03.059. Epub 2015 Apr 23.
  • Jia S, Ivanov A, Blasevic D, Müller T, Purfürst B, Sun W, Chen W, Poy MN, Rajewsky N, Birchmeier C. Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function. EMBO J. 2015 Mar 31. pii: e201490819. [Epub ahead of print]
  • Aue A, Hinze C, Walentin K, Ruffert J, Yurtdas Y, Werth M, Chen W, Rabien A, Kilic E, Schulzke JD, Schumann M, Schmidt-Ott KM. A Grainyhead-Like 2/Ovo-Like 2 Pathway Regulates Renal Epithelial Barrier Function and Lumen Expansion.. J Am Soc Nephrol. 2015 Mar 18. pii: ASN.2014080759. [Epub ahead of print]
  • Bertelsen B, Melchior L, Jensen LR, Groth C, Nazaryan L, Debes NM, Skov L, Xie G, Sun W, Brøndum-Nielsen K, Kuss AW, Chen W, Tümer Z. A t(3;9)(q25.1;q34.3) translocation leading to OLFM1 fusion transcripts in Gilles de la Tourette syndrome, OCD and ADHD Psychiatry Res. 2015 Feb 28;225(3):268-75.
  • Hu H, Haas SA, Chelly J, Van Esch H, Raynaud M, de Brouwer AP, Weinert S, Froyen G, Frints SG, Laumonnier F, Zemojtel T, Love MI, Richard H, Emde AK, Bienek M, Jensen C, Hambrock M, Fischer U, Langnick C, Feldkamp M, Wissink-Lindhout W, Lebrun N, Castelnau L, Rucci J, Montjean R, Dorseuil O, Billuart P, Stuhlmann T, Shaw M, Corbett MA, Gardner A, Willis-Owen S, Tan C, Friend KL, Belet S, van Roozendaal KE, Jimenez-Pocquet M, Moizard MP, Ronce N, Sun R, O’Keeffe S, Chenna R, van Bömmel A, Göke J, Hackett A, Field M, Christie L, Boyle J, Haan E, Nelson J, Turner G, Baynam G, Gillessen-Kaesbach G, Müller U, Steinberger D, Budny B, Badura-Stronka M, Latos-Bieleńska A, Ousager LB, Wieacker P, Rodríguez Criado G, Bondeson ML, Annerén G, Dufke A, Cohen M, Van Maldergem L, Vincent-Delorme C, Echenne B, Simon-Bouy B, Kleefstra T, Willemsen M, Fryns JP, Devriendt K, Ullmann R, Vingron M, Wrogemann K, Wienker TF, Tzschach A, van Bokhoven H, Gecz J, Jentsch TJ, Chen W, Ropers HH, Kalscheuer VM. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Mol Psychiatry. 2015 Feb 3. doi: 10.1038/mp.2014.193. [Epub ahead of print]
  • Doddaballapur A, Michalik KM, Manavski Y, Lucas T, Houtkooper RH, You X, Chen W, Zeiher AM, Potente M, Dimmeler S, Boon RA. Laminar Shear Stress Inhibits Endothelial Cell Metabolism via KLF2-Mediated Repression of PFKFB3. Arterioscler Thromb Vasc Biol. 2015 Jan;35(1):137-45.
  • Haftmann C, Stittrich AB, Zimmermann J, Fang Z, Hradilkova K, Bardua M, Westendorf K, Heinz GA, Riedel R, Siede J, Lehmann K, Weinberger EE, Zimmel D, Lauer U, Häupl T, Sieper J, Backhaus M, Neumann C, Hoffmann U, Porstner M, Chen W, Grün JR, Baumgrass R, Matz M, Löhning M, Scheffold A, Wittmann J, Chang HD, Rajewsky N, Jäck HM, Radbruch A, Mashreghi MF. (2014) miR-148a is upregulated by Twist1 and T-bet and promotes Th1-cell survival by regulating the proapoptotic gene Bim. Eur J Immunol. 2014 Dec 8. doi: 10.1002/eji.201444633. [Epub ahead of print]
  • Weyrich A, Schüllermann T, Heeger F, Jeschek M, Mazzoni CJ, Chen W, Schumann K, Fickel J. (2014) Whole genome sequencing and methylome analysis of the wild guinea pig. BMC Genomics. 2014 Nov 28;15(1):1036. [Epub ahead of print]
  • Wang J, Xie G, Singh M, Ghanbarian AT, Raskó T, Szvetnik A, Cai H, Besser D, Prigione A, Fuchs NV, Schumann GG, Chen W, Lorincz MC, Ivics Z, Hurst LD, Izsvák Z  (2014): Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature. 2014 Oct 15. doi: 10.1038/nature13804. [Epub ahead of print]
  • Peter S, Borkowska E, Drayton RM, Rakhit CP, Noon AP, Chen W, Catto JW. (2014): Identification of differentially expressed long non-coding RNAs in bladder cancer.Clin Cancer Res. 2014 Aug 27. pii: clincanres.0706.2014. [Epub ahead of print]
  • Hüser D, Gogol-Döring A, Chen W, Heilbronn R (2014): AAV Type 2 Wild-Type and Vector-Mediated Genomic Integration Profiles in Human Diploid Fibroblasts Analyzed by 3rd Generation PacBio DNA Sequencing.J Virol. 2014 Jul 16. pii: JVI.01356-14
  • Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N. (2014) Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res. 2014 Jun;24(6):942-53. doi: 10.1101/gr.169029.113. Epub 2014 May 2.
  • Gregersen LH, Schueler M, Munschauer M, Mastrobuoni G, Chen W, Kempa S, Dieterich C, Landthaler M.  (2014) MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs. Mol Cell. 2014 Apr 8. pii: S1097-2765(14)00222-6. doi: 10.1016/j.molcel.2014.03.017. [Epub ahead of print]
  • Michalik KM, You X, Manavski Y, Doddaballapur A, Zörnig M, Braun T, John D, Ponomareva Y, Chen W, Uchida S, Boon RA, Dimmeler S. (2014) The Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth. Circ Res. 2014 Mar 6. [Epub ahead of print]
  • Szentiks CA, Tsangaras K, Abendroth B, Scheuch M, Stenglein MD, Wohlsein P, Heeger F, Höveler R, Chen W, Sun W, Damiani A, Nikolin V,Gruber AD, Grobbel M, Kalthoff D, Höper D, Czirják GÁ, DeRisi J, Mazzoni CJ, Schüle A, Aue A, East ML, Hofer H, Beer M, Osterrieder K, Greenwood AD (2013): Polar bear encephalitis: Establishment of a comprehensive next-generation pathogen analysis pipeline for captive and free-living wildlife. Journal of Comparative Pathology, doi: 10.1016/j.jcpa.2013.12.005.
  • Schueler M.; Munschauer M.; Gregersen L.H.; Finzel A.; Loewer A.; Chen W.; Landthaler M.; Dieterich C. 
Differential protein occupancy profiling of the mRNA transcriptome 
Genome Biology 15 (1): R15 (2014-01-13)
  • Tattikota SG, Rathjen T, McAnulty SJ, Wessels HH, Akerman I, van de Bunt M, Hausser J, Esguerra JL, Musahl A, Pandey AK, You X, Chen W, Herrera PL, Johnson PR, O’Carroll D, Eliasson L, Zavolan M, Gloyn AL, Ferrer J, Shalom-Feuerstein R, Aberdam D, Poy MN: Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell. Cell Metab. 2013 Dec 18. pii: S1550-4131(13)00464-6. doi: 10.1016/j.cmet.2013.11.015. [Epub ahead of print]:
  • Kühnen P, Turan S, Fröhler S, Güran T, Abali S, Biebermann H, Bereket A, Grüters A, Chen W, Krude H: Identification of PENDRIN (SLC26A4) mutations in patients with congenital hypothyroidism and “apparent” thyroid dysgenesis. JCEM jc.2013-2619; doi:10.1210/jc.2013-2619
  • Robinson DG, Chen W, Storey JD, Gresham D. Design and Analysis of Bar-seq Experiments. G3 (Bethesda). 2013 Nov 5. doi:pii: g3.113.008565v1. 10.1534/g3.113.008565. [Epub ahead of print]
  • Rodríguez-Seguel E, Mah N, Naumann H, Pongrac IM, Cerdá-Esteban N, Fontaine JF, Wang Y, Chen W, Andrade-Navarro MA, Spagnoli FM. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence. Genes Dev. (2013 )Sep 1;27(17):1932-46. doi: 10.1101/gad.220244.113
  • de Brouwer AP, Nabuurs SB, Verhaart IE, Oudakker AR, Hordijk R, Yntema HG, Hordijk-Hos JM, Voesenek K, de Vries BB, van Essen T, Chen W, Hu H, Chelly J, den Dunnen JT, Kalscheuer VM, Aartsma-Rus AM, Hamel BC, van Bokhoven H, Kleefstra T. A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy. Eur J Hum Genet. 2013 Jul 31. doi: 10.1038/ejhg.2013.169. [Epub ahead of print]
  • Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, John Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, Gopalakrishnan K, Garrett MR, Joe B, Citterio L, Bianchi G, McBride M, Dominiczak A, Adams DJ, Serikawa T, Flicek P, Cuppen E, Hubner N, Petretto E, Gauguier D, Kwitek A, Jacob H, Aitman TJ. Genome Sequencing Reveals Loci under Artificial Selection that Underlie Disease Phenotypes in the Laboratory Rat. Cell. 2013 Jul 23. doi:pii: S0092-8674(13)00779-4. 10.1016/j.cell.2013.06.040. [Epub ahead of print]
  • Ahmed R, Chang Z, Younis AE, Langnick C, Li N, Chen W, Brattig N, Dieterich C. Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes. Genome Biol Evol. 2013 May 31
  • Mayer J, Tsangaras K, Heeger F, Avila-Arcos M, Stenglein MD, Chen W, Sun W, Mazzoni CJ, Osterrieder N, Greenwood AD. A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca). Virology. 2013 May 29. doi:pii: S0042-6822(13)00267-5. 10.1016/j.virol.2013.05.008. [Epub ahead of print]
  • Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W, Längst G, Benner C, Rehli M. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. 2013 May 8. [Epub ahead of print]
  • Bainbridge MN, Hu H, Muzny DM, Musante L, Lupski JR, Graham BH, Chen W, Gripp KW, Jenny K, Wienker TF, Yang Y, Sutton VR, Gibbs RA, Ropers HH. (2013) De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome. Genome Med. 2013 Feb 5;5(2):11.
  • Tattikota SG, Sury MD, Rathjen T, Wessels HH, Pandey AK, You X, Becker C, Chen W, Selbach M, Poy MN. (2013) Argonaute2 regulates the pancreatic β-cell secretome. Mol Cell Proteomics. 2013 Jan 28. [Epub ahead of print]
  • Samuel Marguerat, Alexander Schmidt, Sandra Codlin, Wei Chen, Ruedi Aebersold, and Jurg Bahler (2012) Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cell. Cell 151(3):671-683.
  • Peng C, Li N, Ng YK, Zhang J, Meier F, Theis FJ, Merkenschlager M, Chen W, Wurst W, Prakash N.A (2012) Unilateral Negative Feedback Loop Between miR-200 microRNAs and Sox2/E2F3 Controls Neural Progenitor Cell-Cycle Exit and Differentiation. J Neurosci. 32(38):13292-13308
  • Pham TH, Benner C, Lichtinger M, Schwarzfischer L, Hu Y, Andreesen R, Chen W, Rehli M. (2012) Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. Blood. 2012 May 1. [Epub ahead of print]
  • Voigt K, Gogol-Döring A, Miskey C, Chen W, Cathomen T, Izsvák Z, Ivics Z. (2012) Retargeting Sleeping Beauty Transposon Insertions by Engineered Zinc Finger DNA-binding Domains. Mol Ther. 2012 Jul 10. doi: 10.1038/mt.2012.126. [Epub ahead of print]
  • Ammar I, Gogol-Döring A, Miskey C, Chen W, Cathomen T, Izsvák Z, Ivics Z. (2012) Retargeting transposon insertions by the adeno-associated virus Rep protein. Nucleic Acids Res (14):6693-712.
  • Onal P, Grün D, Adamidi C, Rybak A, Solana J, Mastrobuoni G, Wang Y, Rahn HP, Chen W, Kempa S, Ziebold U, Rajewsky N. (2012) Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. EMBO J. (12):2755-69
  • Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 40(1):37-52
  • Liu X, Somel M, Tang L, Yan Z, Jiang X, Guo S, Yuan Y, He L, Oleksiak A, Zhang Y, Li N, Hu Y, Chen W, Qiu Z, Pääbo S,Khaitovich P. (2012) Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. Genome Res. 22(4):611-22
  • 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. (2011) MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates. PLoS Biol. 9(12):e1001214
  • 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. (2011) MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains. PLoS Genet. 7(10):e1002327
  • 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 (2011) Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature. 478(7367):57-63.
  • Hu H, Eggers K, Chen W, Garshasbi M, Motazacker MM, Wrogemann K, Kahrizi K, Tzschach A, Hosseini M, Bahman I, Hucho T, Mühlenhoff M, Gerardy-Schahn R, Najmabadi H, Ropers HH, Kuss AW. (2011) ST3GAL3 Mutations Impair the Development of Higher Cognitive Functions Am J Hum Genet 9;89(3):407-14
  • Moldt B, Miskey C, Staunstrup NH, Gogol-Döring A, Bak RO, Sharma N, Mátés L, Izsvák Z, Chen W, Ivics Z, Mikkelsen JG (2011) Comparative Genomic Integration Profiling of Sleeping Beauty Transposons Mobilized With High Efficacy From Integrase-defective Lentiviral Vectors in Primary Human Cells. Mol Ther. 19(8):1499-510
  • 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 (2011) Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells Blood 117(10):2827-38
  • 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 (2011)The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes Nature Immunology 11 (11): 1057-1062
  • Kahrizi K, Hu CH, Garshasbi M, Abedini SS, Ghadami S, Kariminejad R, Ullmann R, Chen W, Ropers HH, Kuss AW, Najmabadi H, Tzschach A. (2011) Next generation sequencing in a family with autosomal recessive Kahrizi syndrome (OMIM 612713) reveals a homozygous frameshift mutation in SRD5A3. Eur J Hum Genet. 19(1):115-7
  • Peleg S, Sananbenesi F, Zovoilis A, Burkhardt S, Bahari-Javan S, Agis-Balboa RC, Cota P, Wittnam JL, Gogol-Doering A, Opitz L, Salinas-Riester G, Dettenhofer M, Kang H, Farinelli L, Chen W, Fischer A.(2010) Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice Science. 328(5979):753-6.
  • Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler PF, Rajewsky N, Einspanier R. (2010) Deciphering the porcine intestinal microRNA transcriptome. BMC Genomics.11(1):275.
  • 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. (2010) Genomic Analysis of miRNAs in an Extreme Mammalian Hibernator, the Arctic Ground Squirrel. Physiol Genomics. 42A(1):39-51
  • Qiu W, Hu Y, Andersen TE, Jafari A, Li N, Chen W, Kassem M. (2010) Tumor necrosis factor receptor superfamily member 19 (TNFRSF19) regulates differentiation fate of human mesenchymal (stromal) stem cells through canonical Wnt signaling and C/EBP.J Biol Chem.285(19):14438-49.
  • Grabundzija I, Irgang M, Mátés L, Belay E, Matrai J, Gogol-Döring A, awakami K, Chen W, Ruiz P, Chuah MK, Vandendriessche T, Izsvák Z, Ivics Z (2010) Comparative Analysis of Transposable Element Vector Systems in Human Cells. Mol Ther. 18(6):1200-9
  • Stoeckius M, Maaskola J, Colombo T, Rahn HP, Friedländer MR, Li N, Chen W, Piano F, Rajewsky N. (2009) Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat Methods 6(10):745-51
  • Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G.(2008) Human snoRNA with MicroRNA-Like Functions Mol Cell. 32(4):519-28.
  • Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 26(4):407-15.
  • Scheffer IE, Turner SJ, Dibbens LM, Bayly MA, Friend K, Hodgson B, Burrows L, Shaw M, Wei Chen, 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. (2008) Epilepsy and mental retardation limited to females: an under-recognized disorder. Brain 131(Pt 4):918-27
  • Kirov G, Gumus D, Chen W, Norton N, Georgieva L, Sari M, O’Donovan MC, Erdogan F, Owen MJ, Ropers HH, Ullmann R (2008) Comparative genome hybridisation analysis suggests a role for NRXN1 and APBA2 in schizophrenia. Hum Mol Genet. 17(3):458-65
  • Erdogan F, Larsen LA, Zhang L, Tümer Z, Tommerup N, Chen W, Jacobsen JR, Schubert M, Jurkatis J, Tzschach A, Ropers HH, Ullmann R. (2008) High frequency of submicroscopic genomic aberrations detected by tiling path array comparative genome hybridisation in patients with isolated congenital heart disease. J Med Genet. 2008 Nov;45(11):704-9.
  • 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. (2007) Array CGH identifies reciprocal 16p13.1 duplications and deletions that predispose to autism and/or mental retardation. Hum Mutat. 28(7):674-82.
  • 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. (2007) Homozygosity mapping in consanguineous families reveals extreme heterogeneity of non-syndromic autosomal recessive mental retardation and identifies 8 novel gene loci. Hum Genet. 121(1):43-8.
  • Jensen LR, Lenzner S, Moser B, Freude K, Tzschach A, Wei Chen, Fryns JP, Chelly J, Turner G, Moraine C, Hamel B, Ropers HH, Kuss AW. (2007) X-linked mental retardation: a comprehensive molecular screen of 47 candidate genes from a 7.4 Mb interval in Xp11 Eur J Hum Genet. 15(1):68-75
  • Erdogan F, Ullmann R, Chen W, Schubert M, Adolph S, Hultschig C, Kalscheuer V, Ropers HH, Spaich C, Tzschach A. (2007) 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 143(2):172-8.
  • 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 (2006) A novel X-linked recessive syndrome characterized by mental retardation and primary ciliary dyskinesia is allelic to OFD1. Human Genetics 120(2):171-8
  • Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG (2001) Go!Poly: A gene-oriented polymorphism database. Hum Mutat. 18(5):382-7.

Book Chapters

  • Doering A & Chen W (2010) Finding Optimal Sets of Enriched Regions in ChIP-Seq Data Proceedings of the German Conference on Bioinformatics
  • Sun W, Chen W. Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcriptionand Decay. Methods Mol Biol. 2018;1720:25-34. doi: 10.1007/978-1-4939-7540-2_3.