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Weisheng Wu, Ph.D. - Publications

Affiliations: 
2011 Pennsylvania State University, State College, PA, United States 
Area:
Bioinformatics Biology, Genetics, Human Development
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52 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 Cao YL, Chen YY, Li YL, Li CI, Lin ST, Lee BR, Hsieh CL, Hsiao YY, Fan YF, Luo Q, Zhao JH, Yin Y, An W, Shi ZG, Chow CN, ... ... Wu WS, et al. Wolfberry genome database: integrated genomic datasets for studying molecular biology. Frontiers in Plant Science. 15: 1310346. PMID 38444537 DOI: 10.3389/fpls.2024.1310346  0.398
2022 Sharma SB, Melvin WJ, Audu CO, Bame M, Rhoads NM, Wu W, Kanthi Y, Knight J, Adili R, Holinstat M, Wakefield TW, Henke P, Moore BB, Gallagher KA, Obi AT. The Histone Methyltransferase MLL1/KMT2A in Monocytes Drives Coronavirus-Associated Coagulopathy and Inflammation. Blood. PMID 36493338 DOI: 10.1182/blood.2022015917  0.302
2020 Du Z, Regan J, Bartom E, Wu WS, Zhang L, Goncharoff DK, Li L. Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses. Scientific Reports. 10: 21838. PMID 33318504 DOI: 10.1038/s41598-020-77993-0  0.397
2019 Vincenz C, Lovett JL, Wu W, Shedden K, Strassmann BI. Loss of imprinting in human placentas is widespread, coordinated, and predicts birth phenotypes. Molecular Biology and Evolution. PMID 31639821 DOI: 10.1093/Molbev/Msz226  0.308
2019 Zafar MA, Hammond AJ, Hamaguchi S, Wu W, Kono M, Zhao L, Weiser JN. Identification of Pneumococcal Factors Affecting Pneumococcal Shedding Shows that the Locus Promotes Inflammation and Transmission. Mbio. 10. PMID 31213554 DOI: 10.1128/Mbio.01032-19  0.303
2019 Armbruster CE, Forsyth VS, Johnson AO, Smith SN, White AN, Brauer AL, Learman BS, Zhao L, Wu W, Anderson MT, Bachman MA, Mobley HLT. Twin arginine translocation, ammonia incorporation, and polyamine biosynthesis are crucial for Proteus mirabilis fitness during bloodstream infection. Plos Pathogens. 15: e1007653. PMID 31009518 DOI: 10.1371/Journal.Ppat.1007653  0.412
2018 Wu WS, Tu HP, Chu YH, Nordling TEM, Tseng YY, Liaw HJ. YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. Database : the Journal of Biological Databases and Curation. 2018. PMID 30371756 DOI: 10.1093/database/bay116  0.345
2018 Wu WS, Jiang YX, Chang JW, Chu YH, Chiu YH, Tsao YH, Nordling TEM, Tseng YY, Tseng JT. HRPDviewer: human ribosome profiling data viewer. Database : the Journal of Biological Databases and Curation. 2018. PMID 30010738 DOI: 10.1093/database/bay074  0.374
2018 Gensterblum-Miller E, Wu W, Sawalha AH. Novel Transcriptional Activity and Extensive Allelic Imbalance in the Human MHC Region. Journal of Immunology (Baltimore, Md. : 1950). PMID 29311362 DOI: 10.4049/Jimmunol.1701061  0.452
2017 Wu WS, Chen PH, Chen TT, Tseng YY. YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. Database : the Journal of Biological Databases and Curation. 2017. PMID 29220473 DOI: 10.1093/Database/Bax085  0.356
2017 Zhao L, Anderson MT, Wu W, T Mobley HL, Bachman MA. TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. Bmc Bioinformatics. 18: 326. PMID 28683752 DOI: 10.1186/S12859-017-1745-2  0.386
2017 Su WP, Ho YC, Wu CK, Hsu SH, Shiu JL, Huang JC, Chang SB, Chiu WT, Hung JJ, Liu TL, Wu WS, Wu PY, Su WC, Chang JY, Liaw H. Chronic treatment with cisplatin induces chemoresistance through the TIP60-mediated Fanconi anemia and homologous recombination repair pathways. Scientific Reports. 7: 3879. PMID 28634400 DOI: 10.1038/s41598-017-04223-5  0.323
2017 Armbruster CE, Forsyth-DeOrnellas V, Johnson AO, Smith SN, Zhao L, Wu W, Mobley HLT. Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements. Plos Pathogens. 13: e1006434. PMID 28614382 DOI: 10.1371/Journal.Ppat.1006434  0.363
2016 Wu WS, Hsieh YC, Lai FJ. YCRD: Yeast Combinatorial Regulation Database. Plos One. 11: e0159213. PMID 27392072 DOI: 10.1371/journal.pone.0159213  0.383
2016 Wu WS, Lai FJ, Tu BW, Chang DT. CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. Database : the Journal of Biological Databases and Curation. 2016. PMID 27242036 DOI: 10.1093/Database/Baw092  0.368
2016 Wu WS. A Computational Method for Identifying Yeast Cell Cycle Transcription Factors. Methods in Molecular Biology (Clifton, N.J.). 1342: 209-19. PMID 26254926 DOI: 10.1007/978-1-4939-2957-3_12  0.348
2015 Wu WS, Lai FJ. Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. Bmc Genomics. 16: S10. PMID 26679776 DOI: 10.1186/1471-2164-16-S12-S10  0.32
2015 Wu WS, Lai FJ. Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out. Bmc Systems Biology. 9: S2. PMID 26678747 DOI: 10.1186/1752-0509-9-S6-S2  0.427
2015 Su WP, Hsu SH, Chia LC, Lin JY, Chang SB, Jiang ZD, Lin YJ, Shih MY, Chen YC, Chang MS, Yang WB, Hung JJ, Hung PC, Wu WS, Myung K, et al. Combined Interactions of Plant Homeodomain and Chromodomain Regulate NuA4 Activity at DNA Double-Strand Breaks. Genetics. PMID 26564157 DOI: 10.1534/Genetics.115.184432  0.311
2015 Bachman MA, Breen P, Deornellas V, Mu Q, Zhao L, Wu W, Cavalcoli JD, Mobley HL. Genome-Wide Identification of Klebsiella pneumoniae Fitness Genes during Lung Infection. Mbio. 6. PMID 26060277 DOI: 10.1128/Mbio.00775-15  0.371
2015 Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics & Chromatin. 8: 16. PMID 25984238 DOI: 10.1186/S13072-015-0009-5  0.766
2014 Wu WS, Wei ML, Yeh CM, Chang DT. A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae. Bmc Systems Biology. 8: S9. PMID 25560196 DOI: 10.1186/1752-0509-8-S5-S9  0.387
2014 Lai FJ, Jhu MH, Chiu CC, Huang YM, Wu WS. Identifying cooperative transcription factors in yeast using multiple data sources. Bmc Systems Biology. 8: S2. PMID 25559499 DOI: 10.1186/1752-0509-8-S5-S2  0.374
2014 Hung PC, Yang TH, Liaw HJ, Wu WS. The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast. Bmc Genomics. 15: S5. PMID 25522035 DOI: 10.1186/1471-2164-15-S9-S5  0.4
2014 Yang TH, Wang CC, Hung PC, Wu WS. cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. Bmc Systems Biology. 8: S8. PMID 25521507 DOI: 10.1186/1752-0509-8-S4-S8  0.428
2014 Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 515: 402-5. PMID 25409831 DOI: 10.1038/Nature13986  0.626
2014 Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, et al. Principles of regulatory information conservation between mouse and human. Nature. 515: 371-5. PMID 25409826 DOI: 10.1038/Nature13985  0.846
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.763
2014 Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Research. 24: 1932-44. PMID 25319996 DOI: 10.1101/Gr.164178.113  0.781
2014 Wu W, Morrissey CS, Keller CA, Mishra T, Pimkin M, Blobel GA, Weiss MJ, Hardison RC. Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. Genome Research. 24: 1945-62. PMID 25319994 DOI: 10.1101/Gr.164830.113  0.77
2014 Yang TH, Wang CC, Wang YC, Wu WS. YTRP: a repository for yeast transcriptional regulatory pathways. Database : the Journal of Biological Databases and Curation. 2014: bau014. PMID 24608172 DOI: 10.1093/database/bau014  0.388
2013 Yang TH, Wu WS. Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. Bmc Systems Biology. 7: S13. PMID 24565265 DOI: 10.1186/1752-0509-7-S6-S13  0.391
2013 Lai FJ, Chiu CC, Yang TH, Huang YM, Wu WS. Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. Plos One. 8: e83791. PMID 24386279 DOI: 10.1371/journal.pone.0083791  0.392
2013 Chang DT, Li WS, Bai YH, Wu WS. YGA: identifying distinct biological features between yeast gene sets. Gene. 518: 26-34. PMID 23266802 DOI: 10.1016/j.gene.2012.11.089  0.326
2012 Yang TH, Wu WS. Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. Bmc Systems Biology. 6: 102. PMID 22898448 DOI: 10.1186/1752-0509-6-102  0.371
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Wu W, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.652
2011 Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Research. 21: 1659-71. PMID 21795386 DOI: 10.1101/Gr.125088.111  0.791
2011 Wu WS. Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites. Bioinformatics and Biology Insights. 5: 1-11. PMID 21423404 DOI: 10.4137/BBI.S6362  0.371
2011 Chang DT, Huang CY, Wu CY, Wu WS. YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucleic Acids Research. 39: D647-52. PMID 21045055 DOI: 10.1093/nar/gkq1086  0.481
2010 Lai F, Chang JS, Wu WS. Identifying a Transcription Factor's Regulatory Targets from its Binding Targets. Gene Regulation and Systems Biology. 4: 125-33. PMID 21245946 DOI: 10.4137/GRSB.S6458  0.32
2010 Lin Z, Wu WS, Liang H, Woo Y, Li WH. The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. Bmc Genomics. 11: 581. PMID 20958978 DOI: 10.1186/1471-2164-11-581  0.304
2009 Cheng Y, Wu W, Kumar SA, Yu D, Deng W, Tripic T, King DC, Chen KB, Zhang Y, Drautz D, Giardine B, Schuster SC, Miller W, Chiaromonte F, Zhang Y, et al. Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Research. 19: 2172-84. PMID 19887574 DOI: 10.1101/Gr.098921.109  0.837
2009 Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J, Chiaromonte F, Hardison RC. Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Research. 37: 7024-38. PMID 19767611 DOI: 10.1093/Nar/Gkp747  0.768
2008 Wu WS, Li WH. Systematic identification of yeast cell cycle transcription factors using multiple data sources. Bmc Bioinformatics. 9: 522. PMID 19061501 DOI: 10.1186/1471-2105-9-522  0.338
2008 Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW, Yu D, Klein AM, Dorman C, Wu W, Hardison RC, Paw BH, Weiss MJ. A GATA-1-regulated microRNA locus essential for erythropoiesis. Proceedings of the National Academy of Sciences of the United States of America. 105: 3333-8. PMID 18303114 DOI: 10.1073/Pnas.0712312105  0.525
2007 Wu WS, Li WH, Chen BS. Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. Bmc Bioinformatics. 8: 188. PMID 17559637 DOI: 10.1186/1471-2105-8-188  0.411
2007 Dore LC, dos Santos CO, Amigo J, Dorman C, Wu W, Hardison RC, Paw BH, Weiss MJ. A GATA-1-Regulated microRNA Cluster That Is Essential for Erythropoiesis. Blood. 110: 378-378. DOI: 10.1182/Blood.V110.11.378.378  0.557
2006 Wu WS, Li WH, Chen BS. Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. Bmc Bioinformatics. 7: 421. PMID 17010188 DOI: 10.1186/1471-2105-7-421  0.422
2006 Wu W, Lu J, Wei Y, Wang J, Lin J, Cao S, Sun X, Tang K. Isolation and characterization of the first putative peroxidase gene from oilseed rape (Brassica napus) which is highly homologous to HRPC. Bioscience Reports. 26: 263-80. PMID 16855866 DOI: 10.1007/S10540-006-9021-0  0.353
2006 Deng Z, Wang Y, Jiang K, Liu X, Wu W, Gao S, Lin J, Sun X, Tang K. Molecular cloning and characterization of a novel dehydrin gene from Ginkgo biloba. Bioscience Reports. 26: 203-15. PMID 16850253 DOI: 10.1007/s10540-006-9016-x  0.308
2006 Shen G, Pang Y, Wu W, Deng Z, Zhao L, Cao Y, Sun X, Tang K. Cloning and characterization of a flavanone 3-hydroxylase gene from Ginkgo biloba. Bioscience Reports. 26: 19-29. PMID 16779664 DOI: 10.1007/S10540-006-9007-Y  0.36
2005 Pang Y, Shen G, Wu W, Liu X, Lin J, Tan F, Sun X, Tang K. Characterization and expression of chalcone synthase gene from Ginkgo biloba Plant Science. 168: 1525-1531. DOI: 10.1016/J.Plantsci.2005.02.003  0.337
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