Cathy Huey-Hwa Wu

TitleEdward G. Jefferson Endowed Professor
InstitutionUniversity of Delaware
DepartmentComputer & Information Sciences
Address18 Amstel Ave.
Newark DE 19716
Phone302-831-8869
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    Other Positions
    TitleProfessor
    InstitutionUniversity of Delaware
    DepartmentComputer & Information Sciences

    TitleProfessor
    InstitutionUniversity of Delaware
    DepartmentBiomedical Engineering


    Collapse Research 
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    R29LM005524     (WU, CATHY H)Jul 1, 1993 - Sep 30, 1999
    NIH
    CLASSIFICATION NEURAL NETWORKS FOR GENOME RESEARCH
    Role: Principal Investigator

    P41LM005798     (LEDLEY, ROBERT S)Mar 1, 1995 - Sep 30, 2002
    NIH
    PROTEIN INFORMATION RESOURCE
    Role: Co-Principal Investigator

    R01GM080646     (WU, CATHY H.)May 1, 2007 - Aug 31, 2020
    NIH
    PRO: A Protein Ontology in OBO Foundry for Scalable Integration of Biomedical Knowledge
    Role: Principal Investigator

    G08LM010720     (WU, CATHY H.)Aug 19, 2010 - Aug 18, 2014
    NIH
    Linking Text Mining and Data Mining for Biomedical Knowledge Discovery
    Role: Principal Investigator

    U01GM120953     (WU, CATHY H.)Aug 5, 2016 - Jul 31, 2020
    NIH
    Semantic Literature Annotation and Integrative Panomics Analysis for PTM-Disease Knowledge Network Discovery
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Zhang X, Maity TK, Ross KE, Qi Y, Cultraro CM, Bahta M, Pitts S, Keswani M, Gao S, Nguyen KDP, Cowart J, Kirkali F, Wu C, Guha U. Alterations in the global proteome and phosphoproteome in third-generation EGFR TKI resistance reveal drug targets to circumvent resistance. Cancer Res. 2021 Mar 16. PMID: 33727228.
      Citations:    
    2. Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354. PMID: 33156333.
      Citations:    
    3. Chitwood DG, Wang Q, Elliott K, Bullock A, Jordana D, Li Z, Wu C, Harcum SW, Saski CA. Characterization of metabolic responses, genetic variations, and microsatellite instability in ammonia-stressed CHO cells grown in fed-batch cultures. BMC Biotechnol. 2021 Jan 08; 21(1):4. PMID: 33419422.
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    4. Chen C, Huang H, Ross KE, Cowart JE, Arighi CN, Wu CH, Natale DA. Protein ontology on the semantic web for knowledge discovery. Sci Data. 2020 10 12; 7(1):337. PMID: 33046717.
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    5. Shamsaei B, Chojnacki S, Pilarczyk M, Najafabadi M, Niu W, Chen C, Ross K, Matlock A, Muhlich J, Chutipongtanate S, Zheng J, Turner J, Vidovic D, Jaffe J, MacCoss M, Wu C, Pillai A, Ma'ayan A, Schürer S, Kouril M, Medvedovic M, Meller J. piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 2020 Jul 02; 48(W1):W85-W93. PMID: 32469073.
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    6. Ovadia EM, Pradhan L, Sawicki LA, Cowart JE, Huber RE, Polson SW, Chen C, van Golen KL, Ross KE, Wu CH, Kloxin AM. Understanding ER+ Breast Cancer Dormancy Using Bioinspired Synthetic Matrices for Long-Term 3D Culture and Insights into Late Recurrence. Adv Biosyst. 2020 Jun 30; e2000119. PMID: 32603024.
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    7. Gavali S, Cowart J, Chen C, Ross KE, Arighi C, Wu CH. RESTful API for iPTMnet: a resource for protein post-translational modification network discovery. Database (Oxford). 2020 Jan 01; 2020. PMID: 32395768.
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    8. Su P, Li G, Wu C, Vijay-Shanker K. Using distant supervision to augment manually annotated data for relation extraction. PLoS One. 2019; 14(7):e0216913. PMID: 31361753.
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    9. McGarvey PB, Nightingale A, Luo J, Huang H, Martin MJ, Wu C. UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants. Hum Mutat. 2019 Mar 06. PMID: 30840782.
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    10. Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Coordination between TGF-ß cellular signaling and epigenetic regulation during epithelial to mesenchymal transition. Epigenetics Chromatin. 2019 02 08; 12(1):11. PMID: 30736855.
      Citations:    
    11. Sawicki LA, Ovadia EM, Pradhan L, Cowart JE, Ross KE, Wu CH, Kloxin AM. Tunable synthetic extracellular matrices to investigate breast cancer response to biophysical and biochemical cues. APL Bioeng. 2019 Mar; 3(1):016101. PMID: 31069334.
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    12. Chen C, Wang Q, Huang H, Vinayaka CR, Garavelli JS, Arighi CN, Natale DA, Wu CH. PIRSitePredict for protein functional site prediction using position-specific rules. Database (Oxford). 2019 Jan 01; 2019. PMID: 30805646.
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    13. Ding R, Qu Y, Wu CH, Vijay-Shanker K. Automatic gene annotation using GO terms from cellular component domain. BMC Med Inform Decis Mak. 2018 12 07; 18(Suppl 5):119. PMID: 30526566.
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    14. Cogburn LA, Trakooljul N, Chen C, Huang H, Wu CH, Carré W, Wang X, White HB. Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus). BMC Genomics. 2018 Sep 21; 19(1):695. PMID: 30241500.
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    15. Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep. 2018 Apr 25; 8(1):6518. PMID: 29695735.
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    16. Huang L, Liao L, Wu CH. Completing sparse and disconnected protein-protein network by deep learning. BMC Bioinformatics. 2018 Mar 22; 19(1):103. PMID: 29566671.
      Citations:    
    17. Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH. iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res. 2018 Jan 04; 46(D1):D542-D550. PMID: 29145615.
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    18. Gupta S, Dingerdissen H, Ross KE, Hu Y, Wu CH, Mazumder R, Vijay-Shanker K. DEXTER: Disease-Expression Relation Extraction from Text. Database (Oxford). 2018 01 01; 2018. PMID: 29860481.
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    19. Ren J, Li G, Ross K, Arighi C, McGarvey P, Rao S, Cowart J, Madhavan S, Vijay-Shanker K, Wu CH. iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. Database (Oxford). 2018 01 01; 2018. PMID: 30576489.
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    20. Mahmood ASMA, Rao S, McGarvey P, Wu C, Madhavan S, Vijay-Shanker K. eGARD: Extracting associations between genomic anomalies and drug responses from text. PLoS One. 2017; 12(12):e0189663. PMID: 29261751.
      Citations:    
    21. Huang L, Liao L, Wu CH. Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space. PLoS One. 2017; 12(9):e0183495. PMID: 28886027.
      Citations:    
    22. Ding R, Boutet E, Lieberherr D, Schneider M, Tognolli M, Wu CH, Vijay-Shanker K, Arighi CN. eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database (Oxford). 2017 Jan 01; 2017. PMID: 29220476.
      Citations:    
    23. Wang Q, Ross KE, Huang H, Ren J, Li G, Vijay-Shanker K, Wu CH, Arighi CN. Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature. Methods Mol Biol. 2017; 1558:213-232. PMID: 28150240.
      Citations:    
    24. Ross KE, Huang H, Ren J, Arighi CN, Li G, Tudor CO, Lv M, Lee JY, Chen SC, Vijay-Shanker K, Wu CH. iPTMnet: Integrative Bioinformatics for Studying PTM Networks. Methods Mol Biol. 2017; 1558:333-353. PMID: 28150246.
      Citations:    
    25. Chen C, Huang H, Wu CH. Protein Bioinformatics Databases and Resources. Methods Mol Biol. 2017; 1558:3-39. PMID: 28150231.
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    26. Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 04; 45(D1):D190-D199. PMID: 27899635.
      Citations:    
    27. Ross KE, Natale DA, Arighi C, Chen SC, Huang H, Li G, Ren J, Wang M, Vijay-Shanker K, Wu CH. Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology. CEUR Workshop Proc. 2016 Aug; 1747. PMID: 28706471.
      Citations:    
    28. Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 2017 Jan 04; 45(D1):D339-D346. PMID: 27899649.
      Citations:    
    29. Du T, Liao L, Wu CH. Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction. EURASIP J Bioinform Syst Biol. 2016 Dec; 2016(1):17. PMID: 27818677.
      Citations:    
    30. Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN. Overview of the interactive task in BioCreative V. Database (Oxford). 2016; 2016. PMID: 27589961.
      Citations:    
    31. Kim S, Islamaj Dogan R, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S, Santos A, Campos D, Oliveira JL, Singh O, Jonnagaddala J, Dai HJ, Su EC, Chang YC, Su YC, Chu CH, Chen CC, Hsu WL, Peng Y, Arighi C, Wu CH, Vijay-Shanker K, Aydin F, Hüsünbeyi ZM, Özgür A, Shin SY, Kwon D, Dolinski K, Tyers M, Wilbur WJ, Comeau DC. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016; 2016. PMID: 27589962.
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    32. Du T, Liao L, Wu CH, Sun B. Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning. Methods. 2016 Nov 1; 110:97-105. PMID: 27282356.
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    33. Peng Y, Arighi C, Wu CH, Vijay-Shanker K. BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database (Oxford). 2016; 2016. PMID: 27170286.
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    34. Gupta S, Ross KE, Tudor CO, Wu CH, Schmidt CJ, Vijay-Shanker K. miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases. J Biomed Semantics. 2016; 7(1):9. PMID: 27216254.
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    35. Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH. Computational clustering for viral reference proteomes. Bioinformatics. 2016 Jul 1; 32(13):2041-3. PMID: 27153712.
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    36. Huang L, Liao L, Wu CH. Inference of protein-protein interaction networks from multiple heterogeneous data. EURASIP J Bioinform Syst Biol. 2016 Dec; 2016(1):8. PMID: 26941784.
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    37. Goodacre N, Edwards N, Danielsen M, Uetz P, Wu C. Predicting nsSNPs the disrupt protein-protein interactions using docking. IEEE/ACM Trans Comput Biol Bioinform. 2016 Jan 22. PMID: 26812731.
      Citations:    
    38. Çelen I, Ross KE, Arighi CN, Wu CH. Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer. PLoS One. 2015; 10(10):e0141773. PMID: 26509276.
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    39. Resnyk CW, Chen C, Huang H, Wu CH, Simon J, Le Bihan-Duval E, Duclos MJ, Cogburn LA. RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism. PLoS One. 2015; 10(10):e0139549. PMID: 26445145.
      Citations:    
    40. Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K. miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput Biol. 2015 Sep; 11(9):e1004391. PMID: 26407127.
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    41. Ding R, Arighi CN, Lee JY, Wu CH, Vijay-Shanker K. pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature. PLoS One. 2015; 10(8):e0135305. PMID: 26258475.
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    42. Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm. IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun; 12(3):622-31. PMID: 26357273.
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    43. Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P. Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PLoS One. 2015; 10(3):e0122978. PMID: 25894391.
      Citations:    
    44. Crowgey EL, Stabley DL, Chen C, Huang H, Robbins KM, Polson SW, Sol-Church K, Wu CH. An integrated approach for analyzing clinical genomic variant data from next-generation sequencing. J Biomol Tech. 2015 Apr; 26(1):19-28. PMID: 25649353.
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    45. Tudor CO, Ross KE, Li G, Vijay-Shanker K, Wu CH, Arighi CN. Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database (Oxford). 2015; 2015. PMID: 25833953.
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    46. Crowgey EL, Kolb A, Wu CH. Development of Bioinformatics Pipeline for Analyzing Clinical Pediatric NGS Data. AMIA Jt Summits Transl Sci Proc. 2015; 2015:207-11. PMID: 26306272.
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    47. Selvanathan SP, Graham GT, Erkizan HV, Dirksen U, Natarajan TG, Dakic A, Yu S, Liu X, Paulsen MT, Ljungman ME, Wu CH, Lawlor ER, Üren A, Toretsky JA. Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing. Proc Natl Acad Sci U S A. 2015 Mar 17; 112(11):E1307-16. PMID: 25737553.
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    48. Torii M, Arighi CN. RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb; 12(1):17-29. PMID: 26357075.
      Citations:    
    49. Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2015 Jan 28; 43(Database issue):D213-21. PMID: 25428371.
      Citations:    
    50. Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics. 2015 Mar 15; 31(6):926-32. PMID: 25398609.
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    51. Peng Y, Torii M, Wu CH, Vijay-Shanker K. A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC Bioinformatics. 2014; 15:285. PMID: 25149151.
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    52. Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH. RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database (Oxford). 2014; 2014. PMID: 25122463.
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    53. Wyffels J, L King B, Vincent J, Chen C, Wu CH, Polson SW. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Res. 2014; 3:191. PMID: 25309735.
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    54. Comeau DC, Batista-Navarro RT, Dai HJ, Islamaj Dogan R, Jimeno Yepes A, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC interoperability track overview. Database (Oxford). 2014; 2014. PMID: 24980129.
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    55. Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, Lu Z, Wilbur JW, Wiegers TC. BioCreative-IV virtual issue. Database (Oxford). 2014; 2014. PMID: 24852177.
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    56. Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K. iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database (Oxford). 2014; 2014. PMID: 24850848.
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    57. Chen C, Khaleel SS, Huang H, Wu CH. Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol Med. 2014; 9:8. PMID: 24955109.
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    58. Nguyen NT, Zhang X, Wu C, Lange RA, Chilton RJ, Lindsey ML, Jin YF. Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map. PLoS Comput Biol. 2014 Mar; 10(3):e1003472. PMID: 24651374.
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    59. Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, Aljanahi A, Celen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 2014 Jan 1; 42(1):D415-21. PMID: 24270789.
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    60. Wang Q, Venkataramanan KP, Huang H, Papoutsakis ET, Wu CH. Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. BMC Syst Biol. 2013; 7:120. PMID: 24196194.
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    61. Lopez LD, Yu J, Arighi C, Tudor CO, Torii M, Huang H, Vijay-Shanker K, Wu C. A framework for biomedical figure segmentation towards image-based document retrieval. BMC Syst Biol. 2013; 7 Suppl 4:S8. PMID: 24565394.
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    62. Comeau DC, Islamaj Dogan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013; 2013:bat064. PMID: 24048470.
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    63. Chen C, Li Z, Huang H, Suzek BE, Wu CH. A fast Peptide Match service for UniProt Knowledgebase. Bioinformatics. 2013 Nov 1; 29(21):2808-9. PMID: 23958731.
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    64. Crooks DR, Natarajan TG, Jeong SY, Chen C, Park SY, Huang H, Ghosh MC, Tong WH, Haller RG, Wu C, Rouault TA. Elevated FGF21 secretion, PGC-1a and ketogenic enzyme expression are hallmarks of iron-sulfur cluster depletion in human skeletal muscle. Hum Mol Genet. 2014 Jan 1; 23(1):24-39. PMID: 23943793.
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    65. Ross KE, Arighi CN, Ren J, Huang H, Wu CH. Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. Database (Oxford). 2013; 2013(0):bat038. PMID: 23749465.
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    66. Ross KE, Arighi CN, Ren J, Natale DA, Huang H, Wu CH. Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. Front Genet. 2013; 4:62. PMID: 23637705.
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    67. Gana R, Rao S, Huang H, Wu C, Vasudevan S. Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. BMC Struct Biol. 2013; 13:6. PMID: 23617634.
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    68. González AJ, Liao L, Wu CH. Prediction of contact matrix for protein-protein interaction. Bioinformatics. 2013 Apr 15; 29(8):1018-25. PMID: 23418186.
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    69. Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-Aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford). 2013; 2013:bas056. PMID: 23327936.
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    70. Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K. The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database (Oxford). 2012; 2012:bas044. PMID: 23221174.
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    71. Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, John Wilbur W. BioCreative-2012 Virtual Issue. Database (Oxford). 2012; 2012:bas049. PMID: 23221175.
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    72. Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R. Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database (Oxford). 2012; 2012:bas036. PMID: 23110974.
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    73. González AJ, Liao L, Wu CH. Predicting ligand binding residues and functional sites using multipositional correlations with graph theoretic clustering and kernel CCA. IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug; 9(4):992-1001. PMID: 22025754.
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    74. Hirschman L, Burns GA, Krallinger M, Arighi C, Cohen KB, Valencia A, Wu CH, Chatr-Aryamontri A, Dowell KG, Huala E, Lourenço A, Nash R, Veuthey AL, Wiegers T, Winter AG. Text mining for the biocuration workflow. Database (Oxford). 2012; 2012:bas020. PMID: 22513129.
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    75. Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham BF, Page ST, Rendino MF, Thomas WK, Udwary DW, Wu CH. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford). 2012; 2012:bar064. PMID: 22434832.
      Citations:    
    76. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. PMID: 22096229.
      Citations:    
    77. Arighi CN, Lu Z, Krallinger M, Cohen KB, Wilbur WJ, Valencia A, Hirschman L, Wu CH. Overview of the BioCreative III Workshop. BMC Bioinformatics. 2011; 12 Suppl 8:S1. PMID: 22151647.
      Citations:    
    78. Arighi CN, Roberts PM, Agarwal S, Bhattacharya S, Cesareni G, Chatr-Aryamontri A, Clematide S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais LJ, Okazaki N, Perfetto L, Rinaldi F, Sætre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman L, Wu CH. BioCreative III interactive task: an overview. BMC Bioinformatics. 2011; 12 Suppl 8:S4. PMID: 22151968.
      Citations:    
    79. Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C. The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics. 2011; 12:371. PMID: 21929785.
      Citations:    
    80. Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He F, Hochstrasser D, Marko-Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlén M, Wu CH, Yamamoto T, Paik YK, Omenn GS. The human proteome project: current state and future direction. Mol Cell Proteomics. 2011 Jul; 10(7):M111.009993. PMID: 21742803.
      Citations:    
    81. Hu ZZ, Kagan BL, Ariazi EA, Rosenthal DS, Zhang L, Li JV, Huang H, Wu C, Jordan VC, Riegel AT, Wellstein A. Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells. PLoS One. 2011; 6(6):e20410. PMID: 21738574.
      Citations:    
    82. Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One. 2011; 6(4):e18910. PMID: 21556138.
      Citations:    
    83. Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, Wu CH. A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics. 2011 Apr 15; 27(8):1190-1. PMID: 21478197.
      Citations:    
    84. Chen C, Huang H, Wu CH. Protein bioinformatics databases and resources. Methods Mol Biol. 2011; 694:3-24. PMID: 21082424.
      Citations:    
    85. Arighi CN, Siu AY, Tudor CO, Nchoutmboube JA, Wu CH, Shanker VK. eFIP: a tool for mining functional impact of phosphorylation from literature. Methods Mol Biol. 2011; 694:63-75. PMID: 21082428.
      Citations:    
    86. Vasudevan S, Vinayaka CR, Natale DA, Huang H, Kahsay RY, Wu CH. Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase. Methods Mol Biol. 2011; 694:91-105. PMID: 21082430.
      Citations:    
    87. McGarvey PB, Zhang J, Natale DA, Wu CH, Huang H. Protein-centric data integration for functional analysis of comparative proteomics data. Methods Mol Biol. 2011; 694:323-39. PMID: 21082443.
      Citations:    
    88. Hu ZZ, Huang H, Wu CH, Jung M, Dritschilo A, Riegel AT, Wellstein A. Omics-based molecular target and biomarker identification. Methods Mol Biol. 2011; 719:547-71. PMID: 21370102.
      Citations:    
    89. Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH. The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res. 2011 Jan; 39(Database issue):D539-45. PMID: 20935045.
      Citations:    
    90. Tang K, Huang H, Jiao N, Wu CH. Phylogenomic analysis of marine Roseobacters. PLoS One. 2010; 5(7):e11604. PMID: 20657646.
      Citations:    
    91. Yin L, Xu G, Torii M, Niu Z, Maisog JM, Wu C, Hu Z, Liu H. Document classification for mining host pathogen protein-protein interactions. Artif Intell Med. 2010 Jul; 49(3):155-60. PMID: 20472411.
      Citations:    
    92. Fan J, Traore K, Li W, Amri H, Huang H, Wu C, Chen H, Zirkin B, Papadopoulos V. Molecular mechanisms mediating the effect of mono-(2-ethylhexyl) phthalate on hormone-stimulated steroidogenesis in MA-10 mouse tumor Leydig cells. Endocrinology. 2010 Jul; 151(7):3348-62. PMID: 20463053.
      Citations:    
    93. Chen C, McGarvey PB, Huang H, Wu CH. Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. Adv Bioinformatics. 2010; 423589. PMID: 20369061.
      Citations:    
    94. Mazumder R, Natale DA, Julio JA, Yeh LS, Wu CH. Community annotation in biology. Biol Direct. 2010; 5:12. PMID: 20167071.
      Citations:    
    95. McGarvey PB, Huang H, Mazumder R, Zhang J, Chen Y, Zhang C, Cammer S, Will R, Odle M, Sobral B, Moore M, Wu CH. Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PLoS One. 2009; 4(9):e7162. PMID: 19779614.
      Citations:    
    96. Prepublication data sharing. Nature. 2009 Sep 10; 461(7261):168-70. PMID: 19741685.
      Citations:    
    97. Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH. TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics. 2009; 10 Suppl 5:S3. PMID: 19426460.
      Citations:    
    98. Barker WC, Mazumder R, Vasudevan S, Sagripanti JL, Wu CH. Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes. Virus Genes. 2009 Aug; 39(1):1-9. PMID: 19283462.
      Citations:    
    99. Torii M, Hu Z, Wu CH, Liu H. BioTagger-GM: a gene/protein name recognition system. J Am Med Inform Assoc. 2009 Mar-Apr; 16(2):247-55. PMID: 19074302.
      Citations:    
    100. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009 Jan; 37(Database issue):D211-5. PMID: 18940856.
      Citations:    
    101. Hu ZZ, Huang H, Cheema A, Jung M, Dritschilo A, Wu CH. Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data. J Proteomics Bioinform. 2008 May; 1(2):47-60. PMID: 19088860.
      Citations:    
    102. Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH. Framework for a protein ontology. BMC Bioinformatics. 2007; 8 Suppl 9:S1. PMID: 18047702.
      Citations:    
    103. Torii M, Hu ZZ, Song M, Wu CH, Liu H. A comparison study on algorithms of detecting long forms for short forms in biomedical text. BMC Bioinformatics. 2007; 8 Suppl 9:S5. PMID: 18047706.
      Citations:    
    104. Huang H, Hu ZZ, Arighi CN, Wu CH. Integration of bioinformatics resources for functional analysis of gene expression and proteomic data. Front Biosci. 2007; 12:5071-88. PMID: 17569631.
      Citations:    
    105. Mazumder R, Hu ZZ, Vinayaka CR, Sagripanti JL, Frost SD, Kosakovsky Pond SL, Wu CH. Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. Virus Genes. 2007 Oct; 35(2):175-86. PMID: 17508277.
      Citations:    
    106. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007 May 15; 23(10):1282-8. PMID: 17379688.
      Citations:    
    107. Nikolskaya AN, Arighi CN, Huang H, Barker WC, Wu CH. PIRSF family classification system for protein functional and evolutionary analysis. Evol Bioinform Online. 2006; 2:197-209. PMID: 19455212.
      Citations:    
    108. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. New developments in the InterPro database. Nucleic Acids Res. 2007 Jan; 35(Database issue):D224-8. PMID: 17202162.
      Citations:    
    109. Hu ZZ, Valencia JC, Huang H, Chi A, Shabanowitz J, Hearing VJ, Appella E, Wu C. Comparative Bioinformatics Analyses and Profiling of Lysosome-Related Organelle Proteomes. Int J Mass Spectrom. 2007 Jan 01; 259(1-3):147-160. PMID: 17375895.
      Citations:    
    110. Chi A, Valencia JC, Hu ZZ, Watabe H, Yamaguchi H, Mangini NJ, Huang H, Canfield VA, Cheng KC, Yang F, Abe R, Yamagishi S, Shabanowitz J, Hearing VJ, Wu C, Appella E, Hunt DF. Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes. J Proteome Res. 2006 Nov; 5(11):3135-44. PMID: 17081065.
      Citations:    
    111. Qiu P, Wang ZJ, Liu KJ, Hu ZZ, Wu CH. Dependence network modeling for biomarker identification. Bioinformatics. 2007 Jan 15; 23(2):198-206. PMID: 17077095.
      Citations:    
    112. Han B, Obradovic Z, Hu ZZ, Wu CH, Vucetic S. Substring selection for biomedical document classification. Bioinformatics. 2006 Sep 1; 22(17):2136-42. PMID: 16837530.
      Citations:    
    113. Liu H, Hu ZZ, Torii M, Wu C, Friedman C. Quantitative assessment of dictionary-based protein named entity tagging. J Am Med Inform Assoc. 2006 Sep-Oct; 13(5):497-507. PMID: 16799122.
      Citations:    
    114. Petrova NV, Wu CH. Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinformatics. 2006; 7:312. PMID: 16790052.
      Citations:    
    115. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D187-91. PMID: 16381842.
      Citations:    
    116. Mazumder R, Natale DA, Murthy S, Thiagarajan R, Wu CH. Computational identification of strain-, species- and genus-specific proteins. BMC Bioinformatics. 2005; 6:279. PMID: 16305751.
      Citations:    
    117. Liu H, Hu ZZ, Zhang J, Wu C. BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics. 2006 Jan 1; 22(1):103-5. PMID: 16267085.
      Citations:    
    118. Liu H, Hu ZZ, Wu CH. DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinformatics. 2005; 6:201. PMID: 16091147.
      Citations:    
    119. Schneider M, Bairoch A, Wu CH, Apweiler R. Plant protein annotation in the UniProt Knowledgebase. Plant Physiol. 2005 May; 138(1):59-66. PMID: 15888679.
      Citations:    
    120. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. The Universal Protein Resource (UniProt). Nucleic Acids Res. 2005 Jan 1; 33(Database issue):D154-9. PMID: 15608167.
      Citations:    
    121. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH. InterPro, progress and status in 2005. Nucleic Acids Res. 2005 Jan 1; 33(Database issue):D201-5. PMID: 15608177.
      Citations:    
    122. Mani I, Hu Z, Jang SB, Samuel K, Krause M, Phillips J, Wu CH. Protein name tagging guidelines: lessons learned. Comp Funct Genomics. 2005; 6(1-2):72-6. PMID: 18629297.
      Citations:    
    123. Hu ZZ, Mani I, Hermoso V, Liu H, Wu CH. iProLINK: an integrated protein resource for literature mining. Comput Biol Chem. 2004 Dec; 28(5-6):409-16. PMID: 15556482.
      Citations:    
    124. Li W, Amri H, Huang H, Wu C, Papadopoulos V. Gene and protein profiling of the response of MA-10 Leydig tumor cells to human chorionic gonadotropin. J Androl. 2004 Nov-Dec; 25(6):900-13. PMID: 15477362.
      Citations:    
    125. Wu C, Nebert DW. Update on genome completion and annotations: Protein Information Resource. Hum Genomics. 2004 Mar; 1(3):229-33. PMID: 15588483.
      Citations:    
    126. Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC. The iProClass integrated database for protein functional analysis. Comput Biol Chem. 2004 Feb; 28(1):87-96. PMID: 15022647.
      Citations:    
    127. Apweiler R, Bairoch A, Wu CH. Protein sequence databases. Curr Opin Chem Biol. 2004 Feb; 8(1):76-80. PMID: 15036160.
      Citations:    
    128. Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC. PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D112-4. PMID: 14681371.
      Citations:    
    129. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D115-9. PMID: 14681372.
      Citations:    
    130. Wu CH, Huang H, Yeh LS, Barker WC. Protein family classification and functional annotation. Comput Biol Chem. 2003 Feb; 27(1):37-47. PMID: 12798038.
      Citations:    
    131. Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC. The Protein Information Resource. Nucleic Acids Res. 2003 Jan 1; 31(1):345-7. PMID: 12520019.
      Citations:    
    132. Huang H, Barker WC, Chen Y, Wu CH. iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res. 2003 Jan 1; 31(1):390-2. PMID: 12520030.
      Citations:    
    133. Hirschman L, Park JC, Tsujii J, Wong L, Wu CH. Accomplishments and challenges in literature data mining for biology. Bioinformatics. 2002 Dec; 18(12):1553-61. PMID: 12490438.
      Citations:    
    134. Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Lewis KC, Mewes HW, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh LS, Zhang J, Barker WC. The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res. 2002 Jan 1; 30(1):35-7. PMID: 11752247.
      Citations:    
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