Gene Family Identification Network Design for Protein Sequence Analysis. - Cathy H. Wu; Hongzhan Huang; Jerry McLarty (Int. J. Artif. Intell. Tools, 1999)

ProClass Protein Family Database. - Cathy H. Wu; Sailaja Shivakumar; Hongzhan Huang (Nucleic Acids Res., 1999)

PIR: a new resource for bioinformatics. - Peter B. McGarvey; Hongzhan Huang; Winona C. Barker; Bruce C. Orcutt; John S. Garavelli; Geetha Y. Srinivasarao; Lai-Su L. Yeh; Chunlin Xiao; Cathy H. Wu (Bioinform., 2000)

The Protein Information Resource (PIR). - Winona C. Barker; John S. Garavelli; Hongzhan Huang; Peter B. McGarvey; Bruce C. Orcutt; Geetha Y. Srinivasarao; Chunlin Xiao; Lai-Su L. Yeh; Robert S. Ledley; Joseph F. Janda; Friedhelm Pfeiffer; Hans-Werner Mewes; et al. (Nucleic Acids Res., 2000)

ProClass protein family database. - Hongzhan Huang; Chunlin Xiao; Cathy H. Wu (Nucleic Acids Res., 2000)

Protein Information Resource: a community resource for expert annotation of protein data. - Winona C. Barker; John S. Garavelli; Zhenglin Hou; Hongzhan Huang; Robert S. Ledley; Peter B. McGarvey; Hans-Werner Mewes; Bruce C. Orcutt; Friedhelm Pfeiffer; Akira Tsugita; Cholanayakanahalli R. Vinayaka; Chunlin Xiao; et al. (Nucleic Acids Res., 2001)

iProClass: an integrated, comprehensive and annotated protein classification database. - Cathy H. Wu; Chunlin Xiao; Zhenglin Hou; Hongzhan Huang; Winona C. Barker (Nucleic Acids Res., 2001)

The Protein Information Resource: an integrated public resource of functional annotation of proteins. - Cathy H. Wu; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhang-Zhi Hu; Robert S. Ledley; Kali C. Lewis; Hans-Werner Mewes; Bruce C. Orcutt; Baris E. Suzek; Akira Tsugita; et al. (Nucleic Acids Res., 2002)

Protein family classification and functional annotation. - Cathy H. Wu; Hongzhan Huang; Lai-Su L. Yeh; Winona C. Barker (Comput. Biol. Chem., 2003)

iProClass: an integrated database of protein family, function and structure information. - Hongzhan Huang; Winona C. Barker; Yongxing Chen; Cathy H. Wu (Nucleic Acids Res., 2003)

The Protein Information Resource. - Cathy H. Wu; Lai-Su L. Yeh; Hongzhan Huang; Leslie Arminski; Jorge Castro-Alvear; Yongxing Chen; Zhang-Zhi Hu; Panagiotis Kourtesis; Robert S. Ledley; Baris E. Suzek; Cholanayakanahalli R. Vinayaka; Jian Zhang 051; et al. (Nucleic Acids Res., 2003)

The iProClass integrated database for protein functional analysis. - Cathy H. Wu; Hongzhan Huang; Anastasia N. Nikolskaya; Zhang-Zhi Hu; Winona C. Barker (Comput. Biol. Chem., 2004)

The PIR integrated protein databases and data retrieval system. - Hongzhan Huang; Zhang-Zhi Hu; Baris E. Suzek; Cathy H. Wu (Data Sci. J., 2004)

UniProt: the Universal Protein knowledgebase. - Rolf Apweiler; Amos Bairoch; Cathy H. Wu; Winona C. Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria Jesus Martin; Darren A. Natale; et al. (Nucleic Acids Res., 2004)

PIRSF: family classification system at the Protein Information Resource. - Cathy H. Wu; Anastasia N. Nikolskaya; Hongzhan Huang; Lai-Su L. Yeh; Darren A. Natale; Cholanayakanahalli R. Vinayaka; Zhang-Zhi Hu; Raja Mazumder; Sandeep Kumar; Panagiotis Kourtesis; Robert S. Ledley; Baris E. Suzek; et al. (Nucleic Acids Res., 2004)

The Universal Protein Resource (UniProt). - Amos Bairoch; Rolf Apweiler; Cathy H. Wu; Winona C. Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria Jesus Martin; Darren A. Natale; et al. (Nucleic Acids Res., 2005)

The Universal Protein Resource (UniProt): an expanding universe of protein information. - Cathy H. Wu; Rolf Apweiler; Amos Bairoch; Darren A. Natale; Winona C. Barker; Brigitte Boeckmann; Serenella Ferro; Elisabeth Gasteiger; Hongzhan Huang; Rodrigo Lopez; Michele Magrane; Maria Jesus Martin; et al. (Nucleic Acids Res., 2006)

UniRef: comprehensive and non-redundant UniProt reference clusters. - Baris E. Suzek; Hongzhan Huang; Peter B. McGarvey; Raja Mazumder; Cathy H. Wu (Bioinform., 2007)

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. - C. Zhang; Oswald Crasta; Stephen A. Cammer; Rebecca Will; Ron Kenyon; Daniel E. Sullivan; Q. Yu; W. Sun; R. Jha; D. Liu; Tian Xue; Y. Zhang; et al. (Nucleic Acids Res., 2008)

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. - Chuming Chen; Peter B. McGarvey; Hongzhan Huang; Cathy H. Wu (Adv. Bioinformatics, 2010)

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Hongzhan Huang; Hagit Shatkay; Cathy H. Wu (BIBM, 2011)

Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. - Cecilia N. Arighi; Darren A. Natale; Judith A. Blake; Carol J. Bult; Michael Caudy; Alexander D. Diehl; Harold J. Drabkin; Peter D'Eustachio; Alexei V. Evsikov; Hongzhan Huang; Natalia V. Roberts; Alan Ruttenberg; et al. (ICBO, 2011)

A comprehensive protein-centric ID mapping service for molecular data integration. - Hongzhan Huang; Peter B. McGarvey; Baris E. Suzek; Raja Mazumder; Jian Zhang 051; Yongxing Chen; Cathy H. Wu (Bioinform., 2011)

The Protein Ontology: a structured representation of protein forms and complexes. - Darren A. Natale; Cecilia N. Arighi; Winona C. Barker; Judith A. Blake; Carol J. Bult; Michael Caudy; Harold J. Drabkin; Peter D'Eustachio; Alexei V. Evsikov; Hongzhan Huang; Jules Nchoutmboube; Natalia V. Roberts; et al. (Nucleic Acids Res., 2011)

Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. - Xia Bi; Hongzhan Huang; Sherri Matis-Mitchell; Peter B. McGarvey; Manabu Torii; Hagit Shatkay; Cathy H. Wu (BIBM, 2012)

Robust segmentation of biomedical figures for image-based document retrieval. - Luis D. Lopez; Jingyi Yu; Catalina O. Tudor; Cecilia N. Arighi; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (BIBM, 2012)

Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees. - Qinghua Wang 003; Cecilia N. Arighi; Benjamin L. King; Shawn W. Polson; James Vincent; Chuming Chen; Hongzhan Huang; Brewster F. Kingham; Shallee T. Page; Marc Farnum Rendino; William Kelley Thomas; Daniel W. Udwary; et al. (Database J. Biol. Databases Curation, 2012)

An Integrated Approach for Interpretation of Clinical NGS Genomic Variant Data. - Erin L. Crowgey; Chuming Chen; Shawn W. Polson; Hongzhan Huang; Cathy H. Wu (AMIA, 2013)

ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome Assembly. - Chuming Chen; Sari S. Khaleel; Hongzhan Huang; Cathy H. Wu (BCB, 2013)

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Manabu Torii; K. Vijay-Shanker; Hongzhan Huang; Cathy H. Wu (BCB, 2013)

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. - Karen Ross; Cecilia N. Arighi; Jia Ren; Hongzhan Huang; Cathy H. Wu (Database J. Biol. Databases Curation, 2013)

A fast Peptide Match service for UniProt Knowledgebase. - Chuming Chen; Zhiwen Li; Hongzhan Huang; Baris E. Suzek; Cathy H. Wu (Bioinform., 2013)

A framework for biomedical figure segmentation towards image-based document retrieval. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Catalina O. Tudor; Manabu Torii; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (BMC Syst. Biol., 2013)

Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. - Qinghua Wang 003; Keerthi Venkataramanan; Hongzhan Huang; Eleftherios T. Papoutsakis; Cathy H. Wu (BMC Syst. Biol., 2013)

DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions. - Tianchuan Du; Alvaro J. González; Qinghua Wang 003; Hongzhan Huang; Li Liao; Cathy H. Wu (BCB, 2014)

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. - Manabu Torii; Gang Li 021; Zhiwen Li; Rose Oughtred; Francesca Diella; Irem Çelen; Cecilia N. Arighi; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (Database J. Biol. Databases Curation, 2014)

Protein Ontology: a controlled structured network of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Carol J. Bult; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; Olivia Helfer; Hongzhan Huang; Anna Maria Masci; et al. (Nucleic Acids Res., 2014)

Software for pre-processing Illumina next-generation sequencing short read sequences. - Chuming Chen; Sari S. Khaleel; Hongzhan Huang; Cathy H. Wu (Source Code Biol. Medicine, 2014)

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. - Baris E. Suzek; Yuqi Wang; Hongzhan Huang; Peter B. McGarvey; Cathy H. Wu (Bioinform., 2015)

The InterPro protein families database: the classification resource after 15 years. - Alex L. Mitchell; Hsin-Yu Chang; Louise C. Daugherty; Matthew Fraser; Sarah Hunter; Rodrigo Lopez; Craig McAnulla; Conor McMenamin; Gift Nuka; Sebastien Pesseat; Amaia Sangrador-Vegas; Maxim Scheremetjew; et al. (Nucleic Acids Res., 2015)

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. - Karen E. Ross; Darren A. Natale; Cecilia N. Arighi; Sheng-Chih Chen; Hongzhan Huang; Gang Li 021; Jia Ren; Michael Wang; K. Vijay-Shanker; Cathy H. Wu (ICBO/BioCreative, 2016)

Computational clustering for viral reference proteomes. - Chuming Chen; Hongzhan Huang; Raja Mazumder; Darren A. Natale; Peter B. McGarvey; Jian Zhang 051; Shawn W. Polson; Yuqi Wang; Cathy H. Wu (Bioinform., 2016)

InterPro in 2017 - beyond protein family and domain annotations. - Robert D. Finn; Teresa K. Attwood; Patricia C. Babbitt; Alex Bateman; Peer Bork; Alan J. Bridge; Hsin-Yu Chang; Zsuzsanna Dosztányi; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2017)

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Jonathan P. Bona; Chuming Chen; Sheng-Chih Chen; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; William D. Duncan; et al. (Nucleic Acids Res., 2017)

Cloud-based Semantic Integration and Knowledge Discovery Systems in Precision Medicine. - Chuming Chen; Julie E. Cowart; Jia Ren; Sachin Gavali; Yuqi Wang; Hongzhan Huang; Cathy H. Wu; Leslie Arminski; Jian Zhang 051; Peter B. McGarvey (BCB, 2018)

iPTMnet: an integrated resource for protein post-translational modification network discovery. - Hongzhan Huang; Cecilia N. Arighi; Karen E. Ross; Jia Ren; Gang Li 021; Sheng-Chih Chen; Qinghua Wang 003; Julie Cowart; K. Vijay-Shanker; Cathy H. Wu (Nucleic Acids Res., 2018)

iSyTE 2.0: a database for expression-based gene discovery in the eye. - Atul Kakrana; Andrian Yang; Deepti Anand; Djordje Djordjevic; S. Deepthi Ramachandruni; Abhyudai Singh; Hongzhan Huang; Joshua Wing Kei Ho; Salil A. Lachke (Nucleic Acids Res., 2018)

PIRSitePredict for protein functional site prediction using position-specific rules. - Chuming Chen; Qinghua Wang 003; Hongzhan Huang; Cholanayakanahalli R. Vinayaka; John S. Garavelli; Cecilia N. Arighi; Darren A. Natale; Cathy H. Wu (Database J. Biol. Databases Curation, 2019)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations. - Alex L. Mitchell; Teresa K. Attwood; Patricia C. Babbitt; Matthias Blum; Peer Bork; Alan J. Bridge; Shoshana D. Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2019)

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. - Alistair MacDougall; Vladimir Volynkin; Rabie Saidi; Diego Poggioli; Hermann Zellner; Emma Hatton-Ellis; Vishal Joshi; Claire O'Donovan; Sandra E. Orchard; Andrea H. Auchincloss; Delphine Baratin; Jerven T. Bolleman; et al. (Bioinform., 2021)

UniProt: the universal protein knowledgebase in 2021. - Alex Bateman; Maria Jesus Martin; Sandra E. Orchard; Michele Magrane; Rahat Agivetova; Shadab Ahmad; Emanuele Alpi; Emily H. Bowler-Barnett; Ramona Britto; Borisas Bursteinas; Hema Bye-A-Jee; Ray Coetzee; et al. (Nucleic Acids Res., 2021)

Hardware-friendly Scalable Image Super Resolution with Progressive Structured Sparsity. - Fangchen Ye; Jin Lin; Hongzhan Huang; Jianping Fan 007; Zhongchao Shi; Yuan Xie 006; Yanyun Qu (ACM Multimedia, 2023)

Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Elisabeth Coudert; Sebastien Gehant; Edouard De Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J. A. Sigrist; Nicole Redaschi; Alan J. Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H. Auchincloss; et al. (Bioinform., 2023)

Data-Free Learning for Lightweight Multi-Weather Image Restoration. - Pei Wang; Hongzhan Huang; Xiaotong Luo; Yanyun Qu (ISCAS, 2024)