Publications of WH. Chen

Publications of WH. Chen

The individual publication lists here have to be considered only in the context of the Bork Group.
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2024 1 publication(s).
22.
Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing.
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
2024 Jan 19; : e2305818. PubMed: 38240578.
Abstract + PDF
2023 2 publication(s).
21.
Enterotypes of the human gut mycobiome.
Lai S, Yan Y, Pu Y, Lin S, Qiu JG, Jiang BH, Keller MI, Wang M, Bork P, Chen WH, Zheng Y, Zhao XM
2023 Aug 11; 11(1): 179. PubMed: 37563687.
Abstract + PDF
20.
Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.
Sun C, Chen J, Jin M, Zhao X, Li Y, Dong Y, Gao N, Liu Z, Bork P, Zhao XM, Chen WH
2023 Sep 29; 10(25): e2302159. PubMed: 37382405.
Abstract + PDF
2021 1 publication(s).
19.
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.
Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH
2021 Jan 8; 49(D1): D998-D1003. PubMed: 33084874.
Abstract + PDF
2018 1 publication(s).
18.
MVP: a microbe-phage interaction database.
Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH
2018 Jan 4; 46: D700-D707. PubMed: 29177508.
Abstract + PDF
2017 2 publication(s).
17.
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.
Chen WH, Lu G, Chen X, Zhao XM, Bork P
2017 Jan 4; 45(D1): D940-D944. PubMed: 27799467.
Abstract + PDF
16.
GEAR: A database of Genomic Elements Associated with drug Resistance.
Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM
2017 Mar 15; 7: 44085. PubMed: 28294141.
Abstract + PDF
2016 3 publication(s).
15.
Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
Chen WH, Lu G, Bork P, Hu S, Lercher MJ
2016 Apr 21; 7: 11334. PubMed: 27098217.
Abstract + PDF
14.
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.
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
2016 Feb 18; 44(3): 1192-202. Epub 2016 Jan 14; PubMed: 26773059.
Abstract + PDF
13.
Bacterial antisense RNAs are mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M
2016 Mar; 2(3): e1501363. PubMed: 26973873.
Abstract + PDF
2015 1 publication(s).
12.
Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
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, Gavin AC, Bork P, Serrano L
2015 Jan 21; 11(1): 780. PubMed: 25609650.
Abstract + PDF
2014 2 publication(s).
11.
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.
Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell S, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P
2014 Dec 16; 42(22): 13525-33. Epub 2014 Nov 14; PubMed: 25398899.
Abstract + PDF
10.
Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
2014 Jul; 10(7): e1003758. PubMed: 25077479.
PDF
2013 2 publication(s).
9.
Human monogenic disease genes have frequently functionally redundant paralogs.
2013 May; 9(5): e1003073. PubMed: 23696728.
Abstract + PDF
8.
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.
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, Oesterhelt C, Lercher MJ, Weber AP
2013 Mar 8; 339(6124): 1207-10. PubMed: 23471408.
Abstract
2012 3 publication(s).
7.
OGEE: an online gene essentiality database.
2012 Jan 10; 40(Database issue): D901-6. Epub 2011 Nov 10; PubMed: 22075992.
Abstract + PDF
6.
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.
2012 Jul 7; 29(7): 1703-6. Epub 2012 Mar 7; PubMed: 22319151.
Abstract + PDF
5.
Transcription start site associated RNAs in bacteria.
Yus E, Güell M, Vivancos AP, Chen WH, Lluch-Senar M, Delgado J, Claude Gavin A, Bork P, Serrano L
2012 May 22; 8: 585. PubMed: 22617959.
Abstract + PDF
2011 1 publication(s).
4.
Orthology prediction methods: A quality assessment using curated protein families.
2011 Oct 19; 33(10): 769-80. Epub 2011 Aug 19; PubMed: 21853451.
Abstract + PDF
2009 3 publication(s).
3.
Transcriptome complexity in a genome-reduced bacterium.
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, Serrano L
2009 Nov 27; 326(5957): 1268-71. PubMed: 19965477.
Abstract + PDF
2.
Proteome organization in a genome-reduced bacterium.
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 DP, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC
2009 Nov 27; 326(5957): 1235-40. PubMed: 19965468.
Abstract + PDF
1.
Impact of genome reduction on bacterial metabolism and its regulation.
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, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L
2009 Nov 27; 326(5957): 1263-8. PubMed: 19965476.
Abstract + PDF