Wei-Hua Chen - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/bork/members/index.php?s_personId=5333

43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen WH, Zhao XM. Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2305818. PMID 38240578 DOI: 10.1002/advs.202305818  0.482
2023 Lai S, Yan Y, Pu Y, Lin S, Qiu JG, Jiang BH, Keller MI, Wang M, Bork P, Chen WH, Zheng Y, Zhao XM. Enterotypes of the human gut mycobiome. Microbiome. 11: 179. PMID 37563687 DOI: 10.1186/s40168-023-01586-y  0.376
2023 Sun C, Chen J, Jin M, Zhao X, Li Y, Dong Y, Gao N, Liu Z, Bork P, Zhao XM, Chen WH. Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2302159. PMID 37382405 DOI: 10.1002/advs.202302159  0.407
2023 Jia L, Wu Y, Dong Y, Chen J, Chen WH, Zhao XM. A survey on computational strategies for genome-resolved gut metagenomics. Briefings in Bioinformatics. PMID 37114640 DOI: 10.1093/bib/bbad162  0.315
2022 Lai S, Pan S, Sun C, Coelho LP, Chen WH, Zhao XM. metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies. Genome Biology. 23: 242. PMID 36376928 DOI: 10.1186/s13059-022-02810-y  0.65
2022 Chong H, Zha Y, Yu Q, Cheng M, Xiong G, Wang N, Huang X, Huang S, Sun C, Wu S, Chen WH, Coelho LP, Ning K. EXPERT: transfer learning-enabled context-aware microbial community classification. Briefings in Bioinformatics. PMID 36124759 DOI: 10.1093/bib/bbac396  0.618
2020 Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH. OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Research. PMID 33084874 DOI: 10.1093/nar/gkaa884  0.507
2019 Gao NL, Chen J, Wang T, Lercher MJ, Chen WH. Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR. Frontiers in Microbiology. 10: 2254. PMID 31681190 DOI: 10.3389/Fmicb.2019.02254  0.424
2019 Wu S, Sun C, Li Y, Wang T, Jia L, Lai S, Yang Y, Luo P, Dai D, Yang YQ, Luo Q, Gao NL, Ning K, He LJ, Zhao XM, ... Chen WH, et al. GMrepo: a database of curated and consistently annotated human gut metagenomes. Nucleic Acids Research. PMID 31504765 DOI: 10.1093/Nar/Gkz764  0.317
2019 Dai D, Wang T, Wu S, Gao NL, Chen WH. Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis. Frontiers in Microbiology. 10: 1205. PMID 31214144 DOI: 10.3389/Fmicb.2019.01205  0.346
2018 Guzina J, Chen WH, Stankovic T, Djordjevic M, Zdobnov E, Djordjevic M. Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence. Frontiers in Genetics. 9: 474. PMID 30386377 DOI: 10.3389/Fgene.2018.00474  0.566
2018 Lu G, Hao X, Chen WH, Mu S. GAAD: A Gene and Autoimmiune Disease Association Database. Genomics, Proteomics & Bioinformatics. PMID 30268934 DOI: 10.1016/J.Gpb.2018.05.001  0.343
2017 He Z, Zhang C, Liu W, Lin Q, Wei T, Aljohi HA, Chen WH, Hu S. DRDB: An Online Date Palm Genomic Resource Database. Frontiers in Plant Science. 8: 1889. PMID 29209336 DOI: 10.3389/Fpls.2017.01889  0.396
2017 Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH. MVP: a microbe-phage interaction database. Nucleic Acids Research. PMID 29177508 DOI: 10.1093/Nar/Gkx1124  0.484
2017 Gao N, Lu G, Lercher MJ, Chen WH. Selection for energy efficiency drives strand-biased gene distribution in prokaryotes. Scientific Reports. 7: 10572. PMID 28874819 DOI: 10.1038/S41598-017-11159-3  0.444
2017 Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM. GEAR: A database of Genomic Elements Associated with drug Resistance. Scientific Reports. 7: 44085. PMID 28294141 DOI: 10.1038/Srep44085  0.46
2016 Chen WH, Lu G, Chen X, Zhao XM, Bork P. OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Research. PMID 27799467 DOI: 10.1093/Nar/Gkw1013  0.558
2016 Chen WH, Lu G, Bork P, Hu S, Lercher MJ. Energy efficiency trade-offs drive nucleotide usage in transcribed regions. Nature Communications. 7: 11334. PMID 27098217 DOI: 10.1038/Ncomms11334  0.495
2016 Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M. Bacterial antisense RNAs are mainly the product of transcriptional noise. Science Advances. 2: e1501363. PMID 26973873 DOI: 10.1126/Sciadv.1501363  0.52
2016 Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Research. PMID 26773059 DOI: 10.1093/Nar/Gkw004  0.777
2015 Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, et al. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Molecular Systems Biology. 11: 780. PMID 25609650 DOI: 10.15252/Msb.20145558  0.727
2014 Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, et al. An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum. Nucleic Acids Research. 42: 13525-33. PMID 25398899 DOI: 10.1093/Nar/Gku1147  0.776
2014 Chen WH, Zhao XM, van Noort V, Bork P. Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". Plos Computational Biology. 10: e1003758. PMID 25077479 DOI: 10.1371/Journal.Pcbi.1003758  0.734
2013 Chen WH, Zhao XM, van Noort V, Bork P. Human monogenic disease genes have frequently functionally redundant paralogs. Plos Computational Biology. 9: e1003073. PMID 23696728 DOI: 10.1371/Journal.Pcbi.1003073  0.693
2013 Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, et al. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science (New York, N.Y.). 339: 1207-10. PMID 23471408 DOI: 10.1126/Science.1231707  0.333
2012 Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Gavin AC, Bork P, Serrano L. Transcription start site associated RNAs in bacteria. Molecular Systems Biology. 8: 585. PMID 22617959 DOI: 10.1038/Msb.2012.16  0.49
2012 Chen WH, Trachana K, Lercher MJ, Bork P. Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. Molecular Biology and Evolution. 29: 1703-6. PMID 22319151 DOI: 10.1093/Molbev/Mss014  0.751
2012 Chen WH, Minguez P, Lercher MJ, Bork P. OGEE: an online gene essentiality database. Nucleic Acids Research. 40: D901-6. PMID 22075992 DOI: 10.1093/Nar/Gkr986  0.57
2011 Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P. Orthology prediction methods: a quality assessment using curated protein families. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 769-80. PMID 21853451 DOI: 10.1002/Bies.201100062  0.709
2011 Wang GZ, Chen WH, Lercher MJ. Coexpression of linked gene pairs persists long after their separation. Genome Biology and Evolution. 3: 565-70. PMID 21737396 DOI: 10.1093/Gbe/Evr049  0.403
2011 Chen WH, Wei W, Lercher MJ. Minimal regulatory spaces in yeast genomes. Bmc Genomics. 12: 320. PMID 21679449 DOI: 10.1186/1471-2164-12-320  0.34
2011 Wu G, Zhang H, Sun J, Liu F, Ge X, Chen WH, Yu J, Wang W. Diverse LEA (late embryogenesis abundant) and LEA-like genes and their responses to hypersaline stress in post-diapause embryonic development of Artemia franciscana. Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. 160: 32-9. PMID 21620991 DOI: 10.1016/J.Cbpb.2011.05.005  0.388
2010 Hao L, Ge X, Wan H, Hu S, Lercher MJ, Yu J, Chen WH. Human functional genetic studies are biased against the medically most relevant primate-specific genes. Bmc Evolutionary Biology. 10: 316. PMID 20961448 DOI: 10.1186/1471-2148-10-316  0.41
2010 He F, Chen WH, Collins S, Acquisti C, Goebel U, Ramos-Onsins S, Lercher MJ, de Meaux J. Assessing the influence of adjacent gene orientation on the evolution of gene upstream regions in Arabidopsis thaliana. Genetics. 185: 695-701. PMID 20233855 DOI: 10.1534/Genetics.110.114629  0.365
2010 Chen WH, de Meaux J, Lercher MJ. Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions. Bmc Genomics. 11: 178. PMID 20233415 DOI: 10.1186/1471-2164-11-178  0.41
2009 Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, et al. Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1268-71. PMID 19965477 DOI: 10.1126/Science.1176951  0.751
2009 Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, et al. Impact of genome reduction on bacterial metabolism and its regulation. Science (New York, N.Y.). 326: 1263-8. PMID 19965476 DOI: 10.1126/Science.1177263  0.749
2009 Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, et al. Proteome organization in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1235-40. PMID 19965468 DOI: 10.1126/Science.1176343  0.722
2009 Chen WH, Lercher MJ. ColorTree: a batch customization tool for phylogenic trees. Bmc Research Notes. 2: 155. PMID 19646243 DOI: 10.1186/1756-0500-2-155  0.331
2008 Ge X, Chen W, Song S, Wang W, Hu S, Yu J. Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines Bmc Plant Biology. 8. PMID 19000321 DOI: 10.1186/1471-2229-8-114  0.353
2008 Huang J, Jiang X, Zhang X, Chen W, Tian B, Shu Z, Hu S. Expressed sequence tag analysis of marine fungus Schizochytrium producing docosahexaenoic acid Journal of Biotechnology. 138: 9-16. PMID 18755227 DOI: 10.1016/J.Jbiotec.2008.07.1994  0.371
2007 Chen WH, Lv G, Lv C, Zeng C, Hu S. Systematic analysis of alternative first exons in plant genomes. Bmc Plant Biology. 7: 55. PMID 17941993 DOI: 10.1186/1471-2229-7-55  0.436
2007 Wang W, Meng B, Chen W, Ge X, Liu S, Yu J. A proteomic study on postdiapaused embryonic development of brine shrimp (Artemia franciscana) Proteomics. 7: 3580-3591. PMID 17907269 DOI: 10.1002/Pmic.200700259  0.321
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