OmicsEV: a tool for comprehensive quality evaluation of omics data tables.

Bing Zhang 0003 Baylor College of Medicine, Houston, TX, USA Vanderbilt University School of Medicine, Department of Biomedical Informatics, Nashville, TN, USA http://www.zhang-lab.org/ https://orcid.org/0000-0001-8676-2425 https://www.wikidata.org/entity/Q87787480 Bing Zhang Bing Zhang 0001 Chinese Academy of Sciences, Institute of Remote Sensing and Digital Earth, Beijing, China Chinese Academy of Sciences, Institute of Remote Sensing Applications, Beijing, China https://orcid.org/0000-0001-7311-9844 https://orcid.org/0000-0003-0319-7753 https://www.wikidata.org/entity/Q91308396 Bing Zhang 0002 National Institute of Information and Communications Technology (NICT), Wireless Network Research Institute, Kyoto, Japan Bing Zhang 0004 Raytheon BBN Technologies http://bbn.com/technology/speech/pubs Bing Zhang 0005 Kansai Advanced Research Center, Communications Research Laboratory Bing Zhang 0006 Shandong Water Polytechnic Bing Zhang 0007 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics Bing Zhang 0008 National Computer Network Emergency Response Technical Team, Coordination Center of China Bing Zhang 0009 National Engineering Laboratory for Offshore Oil Exploration, Wave and Information Institute, Xi'an Jiao Tong University Bing Zhang 0010 Xidian University, State Key Laboratory of Integrated Services Networks, Xi'an, China https://orcid.org/0000-0001-6457-3439 Bing Zhang 0011 Yanshan University, College of Information Science and Engineering, Qinhuangdao, China https://orcid.org/0000-0002-9867-8439 https://www.wikidata.org/entity/Q59189842 Bing Zhang 0012 Nanjing University Medical School Affiliated Drum Tower Hospital, Department of Radiology, China https://orcid.org/0000-0002-3953-0290 https://www.wikidata.org/entity/Q90181862 Bing Zhang 0013 Jilin University, State Key Laboratory of Automotive Simulation and Control, Changchun, China https://orcid.org/0000-0001-9008-855X Bing Zhang 0014 Shanghai University, School of Mechatronic Engineering and Automation, China Donghua University, College of Mechanical Engineering, Shanghai, China https://orcid.org/0000-0001-5650-2518 https://www.wikidata.org/entity/Q88471433 Bing Zhang 0015 https://orcid.org/0000-0001-5026-0255 Tianjin University of Commerce, Tianjin, China Bing Zhang 0016 https://orcid.org/0000-0002-9813-241X Hefei University of Technology, Hefei, China Bing Zhang 0017 https://orcid.org/0000-0003-0164-4193 https://www.wikidata.org/entity/Q137786573 Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu, China Bing Zhang 0018 https://orcid.org/0000-0002-5590-0001 University of Illinois at Urbana-Champaign, Champaign, IL, USA Bing Zhang 0019 https://orcid.org/0000-0002-9373-9976 Xi'an Jiaotong University, Xi'an, China Bing Zhang 0020 https://orcid.org/0000-0003-2093-2975 Liaoning Technical University, Fuxin, China Bing Zhang 0021 https://orcid.org/0000-0003-1911-8466 IBM Research - Almaden, San Jose, CA, USA Bing Zhang 0022 https://orcid.org/0000-0001-9077-7312 Guangzhou Medical University, Guangzhou, China Bing Zhang 0023 https://orcid.org/0009-0004-6495-7749 Beijing University of Technology, Beijing, China Bing Zhang 0024 https://orcid.org/0000-0002-4084-4705 Harbin Institute of Technology, Shenzhen, China

Bo Wen Eric J. Jaehnig Bing Zhang 0003 OmicsEV: a tool for comprehensive quality evaluation of omics data tables. 5463-5465 2022 December 38 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btac698 db/journals/bioinformatics/bioinformatics38.html#WenJZ22

Kuan Huang Yifei Cheng Qiang Gao Bing Zhang 0003 Weakly Unpaired Image Translation from Hematoxylin and Eosin Staining Image to Immunohistochemistry Staining Image. 1013-1019 2022 BIBM https://doi.org/10.1109/BIBM55620.2022.9995520 conf/bibm/2022 db/conf/bibm/bibm2022.html#HuangCGZ22

Seungyeul Yoo Zhiao Shi Bo Wen Soon Jye Kho Renke Pan Hanying Feng Hong Chen Anders Carlsson Patrik Edén Weiping Ma Michael L. Raymer Ezekiel J. Maier Zivana Tezak Elaine Johanson Denise Hinton Henry Rodriguez Jun Zhu Emily Boja Pei Wang Bing Zhang 0003 A community effort to identify and correct mislabeled samples in proteogenomic studies. 100245 2021 2 Patterns 5 https://doi.org/10.1016/j.patter.2021.100245 db/journals/patterns/patterns2.html#YooSWKPFCCEMRMT21

Junhui Shen Suhas V. Vasaikar Bing Zhang 0003 DLAD4U: deriving and prioritizing disease lists from PubMed literature. 29-37 2018 19-S BMC Bioinform. 17 https://doi.org/10.1186/s12859-018-2463-0 https://www.wikidata.org/entity/Q60927114 db/journals/bmcbi/bmcbi19S.html#ShenVZ18

Suhas V. Vasaikar Peter Straub Jing Wang Bing Zhang 0003 LinkedOmics: analyzing multi-omics data within and across 32 cancer types. D956-D963 2018 46 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkx1090 https://www.wikidata.org/entity/Q47106278 db/journals/nar/nar46.html#VasaikarSW018

Jing Wang Suhas V. Vasaikar Zhiao Shi Michael Greer Bing Zhang 0003 WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit. W130-W137 2017 45 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkx356 https://www.wikidata.org/entity/Q38377204 db/journals/nar/nar45.html#WangVSG017

Bo Wen Shaohang Xu Ruo Zhou Bing Zhang 0003 Xiaojing Wang Xin Liu 0007 Xun Xu Siqi Liu PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. 244 2016 17 BMC Bioinform. https://doi.org/10.1186/s12859-016-1133-3 https://www.wikidata.org/entity/Q36055712 db/journals/bmcbi/bmcbi17.html#WenXZZWLXL16

Jing Zhu Zhiao Shi Jing Wang Bing Zhang 0003 Empowering biologists with multi-omics data: colorectal cancer as a paradigm. 1436-1443 2015 31 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btu834 https://www.wikidata.org/entity/Q30643721 db/journals/bioinformatics/bioinformatics31.html#ZhuSWZ15

Xiaojing Wang Bing Zhang 0003 <i>customProDB</i>: an R package to generate customized protein databases from RNA-Seq data for proteomics search. 3235-3237 2013 29 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btt543 https://www.wikidata.org/entity/Q30668844 db/journals/bioinformatics/bioinformatics29.html#WangZ13a

Jing Wang Dexter T. Duncan Zhiao Shi Bing Zhang 0003 WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. 77-83 2013 41 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkt439 https://www.wikidata.org/entity/Q36954017 db/journals/nar/nar41.html#WangDS013

Yufei Huang 0001 Zhongming Zhao Hua Xu 0001 Yu Shyr Bing Zhang 0003 Advances in systems biology: computational algorithms and applications. S1 2012 6 BMC Syst. Biol. S-3 https://doi.org/10.1186/1752-0509-6-S3-S1 https://www.wikidata.org/entity/Q42413899 db/journals/bmcsb/bmcsb6S.html#HuangZXSZ12

Mingguang Shi Bing Zhang 0003 Semi-supervised learning improves gene expression-based prediction of cancer recurrence. 3017-3023 2011 27 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btr502 https://www.wikidata.org/entity/Q35411665 db/journals/bioinformatics/bioinformatics27.html#ShiZ11

Zhiao Shi Bing Zhang 0003 Fast network centrality analysis using GPUs. 149 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-149 https://www.wikidata.org/entity/Q33898898 db/journals/bmcbi/bmcbi12.html#ShiZ11

Bing Zhang 0003 Zhiao Shi Modules in Biological Networks: Identification and Application. 248-274 2011 Handbook of Research on Computational and Systems Biology https://doi.org/10.4018/978-1-60960-491-2.ch011 books/daglib/0025928 db/books/daglib/0025928.html#ZhangS11

Dexter T. Duncan Naresh Prodduturi Bing Zhang 0003 WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. P10 2010 11 BMC Bioinform. S-4 https://doi.org/10.1186/1471-2105-11-S4-P10 https://www.wikidata.org/entity/Q46782286 db/journals/bmcbi/bmcbi11S.html#DuncanPZ10

Jing Li Zeqiang Ma Robbert J. C. Slebos David L. Tabb Daniel C. Liebler Bing Zhang 0003 Enabling proteomics-based identification of human cancer variations. P29 2010 11 BMC Bioinform. S-4 https://doi.org/10.1186/1471-2105-11-S4-P29 https://www.wikidata.org/entity/Q46782615 db/journals/bmcbi/bmcbi11S.html#LiMSTLZ10

Zhiao Shi Catherine K. Derow Bing Zhang 0003 Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression. 74 2010 4 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-4-74 https://www.wikidata.org/entity/Q33589384 db/journals/bmcsb/bmcsb4.html#ShiD010

Bing Zhang 0003 Jing Li David L. Tabb Byung-Hoon Park Network Approaches for Shotgun Proteomics Data Analysis. 222 2009 IJCBS https://doi.org/10.1109/IJCBS.2009.74 https://doi.ieeecomputersociety.org/10.1109/IJCBS.2009.74 conf/ijcbs/2009 db/conf/ijcbs/ijcbs2009.html#ZhangLTP09

Bing Zhang 0003 Byung-Hoon Park Tatiana V. Karpinets Nagiza F. Samatova From pull-down data to protein interaction networks and complexes with biological relevance. 979-986 2008 24 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btn036 https://www.wikidata.org/entity/Q31147891 db/journals/bioinformatics/bioinformatics24.html#ZhangPKS08

Xi Chen Lily Wang 0001 Jonathan D. Smith Bing Zhang 0003 Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. 2474-2481 2008 24 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btn458 https://www.wikidata.org/entity/Q33364358 db/journals/bioinformatics/bioinformatics24.html#ChenWSZ08

Philip Gerlee Torbjörn Lundh Bing Zhang 0003 Alexander R. A. Anderson The gene-function relationship in the metabolism of yeast and digital organisms. 768 2008 ALIFE http://mitpress2.mit.edu/books/chapters/0262287196chap122.pdf conf/alife/2008 db/conf/alife/alife2008.html#GerleeLZA08 Byung-Hoon Park Bing Zhang 0003 Tatiana V. Karpinets Nagiza F. Samatova Multi-stage Framework to Infer Protein Functional Modules from Mass Spectrometry Pull-Down Data with Assessment of Biological Relevance. 223-229 2007 BIBM https://doi.org/10.1109/BIBM.2007.14 https://doi.ieeecomputersociety.org/10.1109/BIBM.2007.14 conf/bibm/2007 db/conf/bibm/bibm2007.html#ParkZKS07

S. A. Kirov Xinxia Peng E. Baker Denise Schmoyer Bing Zhang 0003 Jay Snoddy GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments. 72 2005 6 BMC Bioinform. https://doi.org/10.1186/1471-2105-6-72 https://www.wikidata.org/entity/Q24811591 db/journals/bmcbi/bmcbi6.html#KirovPBSZS05

Bing Zhang 0003 Stefan Kirov Jay Snoddy WebGestalt: an integrated system for exploring gene sets in various biological contexts. 741-748 2005 33 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gki475 https://www.wikidata.org/entity/Q24813284 db/journals/nar/nar33.html#ZhangKS05

Bing Zhang 0003 Denise Schmoyer Stefan Kirov Jay Snoddy GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. 16 2004 5 BMC Bioinform. https://doi.org/10.1186/1471-2105-5-16 https://www.wikidata.org/entity/Q24801173 db/journals/bmcbi/bmcbi5.html#ZhangSKS04

Alexander R. A. Anderson E. Baker Emily Boja Anders Carlsson Hong Chen Xi Chen Yifei Cheng Catherine K. Derow Dexter T. Duncan Patrik Edén Hanying Feng Qiang Gao Philip Gerlee Michael Greer Denise Hinton Kuan Huang Yufei Huang 0001 Eric J. Jaehnig Elaine Johanson Tatiana V. Karpinets Soon Jye Kho S. A. Kirov Stefan Kirov Jing Li Daniel C. Liebler Siqi Liu Xin Liu 0007 Torbjörn Lundh Weiping Ma Zeqiang Ma Ezekiel J. Maier Renke Pan Byung-Hoon Park Xinxia Peng Naresh Prodduturi Michael L. Raymer Henry Rodriguez Nagiza F. Samatova Denise Schmoyer Junhui Shen Mingguang Shi Zhiao Shi Robbert J. C. Slebos Jonathan D. Smith Jay Snoddy Peter Straub David L. Tabb Zivana Tezak Suhas V. Vasaikar Jing Wang Lily Wang 0001 Pei Wang Xiaojing Wang Bo Wen Hua Xu 0001 Shaohang Xu Xun Xu Seungyeul Yoo Shyr YuYu Shyr Zhongming Zhao Ruo Zhou Jing Zhu Jun Zhu