C. Arighi

发表

An improved ontological representation of dendritic cells as a paradigm for all cell types

Barry Smith, Alexander D. Diehl, Richard H. Scheuermann, 2009, BMC Bioinformatics.

The representation of protein complexes in the Protein Ontology (PRO)

Cathy H. Wu, Barry Smith, Alan Ruttenberg, 2011, BMC Bioinformatics.

Framework for a Protein Ontology

Cathy H. Wu, W. C. Barker, J. Blake, 2006, TMBIO '06.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

André L. M. Santos, Yifan Peng, Sophia Ananiadou, 2016, Database J. Biol. Databases Curation.

BioCreative IV Interactive Task

Catalina O. Tudor, C. Arighi, P. Roberts, 2013 .

The Gene Ontology Resource: 20 years and still GOing strong

James C. Hu, Benjamin M. Good, Steven J. Marygold, 2019 .

The Gene Ontology Task at BioCreative IV

C. Arighi, K. V. Auken, Zhiyong Lu, 2013 .

Corpus Construction for the BioCreative IV GO Task

Zhiyong Lu, Kimberly Van Auken, Paul W. Sternberg, 2013 .

The eFIP system for text mining of protein interaction networks of phosphorylated proteins

Cathy H. Wu, Cecilia N. Arighi, K. Vijay-Shanker, 2012, Database J. Biol. Databases Curation.

RLIMS-P : Literature-based curation of protein phosphorylation information

Cathy H. Wu, C. Arighi, K. Vijay-Shanker, 2013 .

eFIP: a tool for mining functional impact of phosphorylation from literature.

Cathy H. Wu, Catalina O. Tudor, Vijay K. Shanker, 2011, Methods in molecular biology.

Temperature-induced conformational switch in intestinal fatty acid binding protein (IFABP) revealing an alternative mode for ligand binding.

C. Arighi, J. M. Delfino, J. Rossi, 2003, Biochemistry.

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

Zhiyong Lu, Alex Bateman, Cecilia N. Arighi, 2016, bioRxiv.

Murine Oviductosomes (OVS) microRNA profiling during the estrous cycle: Delivery of OVS-borne microRNAs to sperm where miR-34c-5p localizes at the centrosome

C. Arighi, P. Green, M. Accerbi, 2018, Scientific Reports.

Protein ontology on the semantic web for knowledge discovery

Cathy H. Wu, Karen E. Ross, Darren A. Natale, 2020, Scientific data.

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

Cathy H. Wu, Cecilia Arighi, Liang-Chin Huang, 2018, Scientific Reports.

PIRSF Family Classification System for Protein Functional and Evolutionary Analysis

Cathy H. Wu, Hongzhan Huang, Cecilia N. Arighi, 2006, Evolutionary bioinformatics online.

A crowdsourcing open platform for literature curation in UniProt

Cathy H. Wu, C. Arighi, Hongzhan Huang, 2021, PLoS biology.

Divalent interaction of the GGAs with the Rabaptin‐5–Rabex‐5 complex

C. Arighi, J. Bonifacino, M. Zerial, 2003, The EMBO journal.

Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, gamma-ear-containing, ADP-ribosylation-factor-binding proteins.

C. Arighi, J. Bonifacino, J. Hurley, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system

Cathy H. Wu, Karen E. Ross, Cecilia N. Arighi, 2015, Database J. Biol. Databases Curation.

2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012, Philadelphia, PA, USA, October 4-7, 2012

Xiaohua Hu, Yunming Ye, Majid Sarrafzadeh, 2012, IEEE International Conference on Bioinformatics and Biomedicine.

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature

Manabu Torii, Cathy H. Wu, Cecilia N. Arighi, 2013, BCB.

The Universal Protein Resource (UniProt) in 2010

María Martín, Peter B. McGarvey, Cathy H. Wu, 2010 .

UniProt: the Universal Protein knowledgebase

Cathy H. Wu, Jerven T. Bolleman, Béatrice A. Cuche, 2004, Nucleic Acids Res..

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Eric P. Nawrocki, Anton I. Petrov, Joshua B. Singer, 2020, Briefings Bioinform..

UniProt: the universal protein knowledgebase

Cathy H. Wu, Christian J. A. Sigrist, Jerven T. Bolleman, 2016, Nucleic Acids Research.

BioRED: a rich biomedical relation extraction dataset

C. Arighi, Zhiyong Lu, Chih-Hsuan Wei, 2022, Briefings Bioinform..

A roadmap for the functional annotation of protein families: a community perspective

Benjamin M. Gyori, Lucy J. Colwell, Ian K. Blaby, 2022, Database J. Biol. Databases Curation.

Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework

Cathy H. Wu, Barry Smith, Alan Ruttenberg, 2015, PloS one.

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework

Cathy H. Wu, Barry Smith, A. Masci, 2015, PloS one.

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Robert D. Finn, Alex Bateman, Niko Beerenwinkel, 2020, Briefings Bioinform..

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII

K. Dolinski, T. Korves, M. Tyers, 2022, Database J. Biol. Databases Curation.

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

Claire O'Donovan, Elisabeth Coudert, Hongzhan Huang, 2020, Bioinform..

SPARQL-Powered search engine and RESTful APIs for protein ontology

Cathy H. Wu, Xiang Li, Darren A. Natale, 2019 .

Protein Bioinformatics From Protein Modifications and Networks to Proteomics

Cathy H. Wu, Cecilia N. Arighi, C. Arighi, 2017 .

Building a text mining pipeline to retrieve literature to study stress response in Arabidopsis

Cathy H. Wu, Cecilia N. Arighi, Rita Hayford, 2020 .

Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer

Cathy H. Wu, Karen E. Ross, Cecilia N. Arighi, 2015, PloS one.

Mining Protein Interactions of Phosphorylated Proteins from the Literature using eFIP

Cathy H. Wu, Catalina O. Tudor, C. Arighi, 2012 .

Framework for a Protein Ontology

Cathy H. Wu, W. C. Barker, J. Blake, 2006, TMBIO '06.

Original Text mining for the biocuration workflow

Thomas C. Wiegers, Cathy H. Wu, Karen G. Dowell, 2012 .

BioCreative-IV virtual issue

Thomas C. Wiegers, Cathy H. Wu, A. Valencia, 2014, Database J. Biol. Databases Curation.

The Gene Ontology resource: enriching a GOld mine

Anushya Muruganujan, Cathy H. Wu, Alex Bateman, 2020, Nucleic Acids Res..

UniProt: the universal protein knowledgebase in 2021

Peter B. McGarvey, Cathy H. Wu, Alex Bateman, 2020, Nucleic Acids Res..

UniProt: A hub for protein information

María Martín, Peter B. McGarvey, Y Wang, 2015 .

Activities at the Universal Protein Resource (UniProt)

María Martín, Peter B. McGarvey, Y Wang, 2013, Nucleic Acids Res..

An effective biomedical document classification scheme in support of biocuration: addressing class imbalance

Hagit Shatkay, Judith A. Blake, Cecilia N. Arighi, 2019, Database J. Biol. Databases Curation.

Micellar lipoproteins as the possible storage and translocation form of intracellular diacylglycerol.

C. Arighi, J. M. Delfino, J. Caramelo, 1998, Biochemical and biophysical research communications.

Integration of bioinformatics resources for functional analysis of gene expression and proteomic data.

Zhang-Zhi Hu, Cathy H. Wu, Cecilia N Arighi, 2007, Frontiers in bioscience : a journal and virtual library.

UniProt: the Universal Protein Knowledgebase in 2023

Cathy H. Wu, Jerven T. Bolleman, The UniProt Consortium, 2022, Nucleic acids research.

Robust segmentation of biomedical figures for image-based document retrieval

Cathy H. Wu, Cecilia N. Arighi, Hongzhan Huang, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine.

miRTex: A Text Mining System for miRNA-Gene Relation Extraction

Yifan Peng, Cathy H. Wu, Karen E. Ross, 2015, PLoS Comput. Biol..

A framework for biomedical figure segmentation towards image-based document retrieval

Manabu Torii, Cathy H. Wu, Cecilia N. Arighi, 2013, BMC Systems Biology.

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Zhiyong Lu, Cecilia N. Arighi, Alex Bateman, 2017, Bioinform..

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

Anne Morgat, Alan Bridge, Damien Lieberherr, 2020, Bioinformatics.

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

Jian Zhang, Cathy H. Wu, William D. Duncan, 2016, Nucleic Acids Res..

iPTMnet: an integrated resource for protein post-translational modification network discovery

Cathy H. Wu, Karen E. Ross, Cecilia N. Arighi, 2017, Nucleic Acids Res..

Overview of the gene ontology task at BioCreative IV

Jung-Hsien Chiang, Zhiyong Lu, Hongfang Liu, 2014, Database J. Biol. Databases Curation.

Role of the mammalian retromer in sorting of the cation-independent mannose 6-phosphate receptor

C. Arighi, J. Bonifacino, C. Haft, 2004, The Journal of cell biology.

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

Cathy H. Wu, Hongzhan Huang, Cecilia N. Arighi, 2012, Database J. Biol. Databases Curation.

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information

Manabu Torii, Cathy H. Wu, Cecilia N. Arighi, 2014, Database J. Biol. Databases Curation.

Activities at the Universal Protein Resource (UniProt)

Cathy H. Wu, Tony Sawford, Michel Schneider, 2014, Nucleic Acids Research.

BC4GO: a full-text corpus for the BioCreative IV GO task

Zhiyong Lu, Kimberly Van Auken, Hans-Michael Müller, 2014, Database J. Biol. Databases Curation.

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information

Cathy H. Wu, Cecilia N. Arighi, K. Vijay-Shanker, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Open Peer Review Invited Referee Responses

Karin M. Verspoor, Karin Verspoor, Philippe Thomas, 2022 .

BioCreative-IV virtual issue

Zhiyong Lu, K. Bretonnel Cohen, Alfonso Valencia, 2014, Database J. Biol. Databases Curation.

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer’s Disease Through Expert Curation of Key Protein Targets

Livia Perfetto, Sandra Orchard, Michele Magrane, 2020, Journal of Alzheimer's disease : JAD.

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

Claire O'Donovan, Alan Bridge, Cecilia N. Arighi, 2014, Database J. Biol. Databases Curation.

Utilizing image and caption information for biomedical document classification

G. E. Marai, M. Ringwald, C. Arighi, 2021, Bioinform..

UPCLASS: a deep learning-based classifier for UniProtKB entry publications

Patrick Ruch, Julien Gobeill, Douglas Teodoro, 2019, bioRxiv.

BioCreative-2012 Virtual Issue

Zhiyong Lu, K. Bretonnel Cohen, Alfonso Valencia, 2012, Database J. Biol. Databases Curation.

The Protein Ontology: a structured representation of protein forms and complexes

Jian Zhang, Cathy H. Wu, Barry Smith, 2010, Nucleic Acids Res..

RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

Cathy H. Wu, Cecilia Arighi, Chuming Chen, 2020, Database : the journal of biological databases and curation.

PIRSitePredict for protein functional site prediction using position-specific rules

Cathy H. Wu, Hongzhan Huang, Darren A. Natale, 2019, Database J. Biol. Databases Curation.

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality

Cathy H. Wu, Michel Schneider, Damien Lieberherr, 2017, Database J. Biol. Databases Curation.

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature

Subha Madhavan, Shruti Rao, Peter B. McGarvey, 2018, Database J. Biol. Databases Curation.

emiRIT: a text-mining-based resource for microRNA information

Cecilia N. Arighi, K. Vijay-Shanker, Samir Gupta, 2020, bioRxiv.

Overview of the interactive task in BioCreative V

Jeyakumar Natarajan, Shruti Rao, Zhiyong Lu, 2015, Database J. Biol. Databases Curation.

TGF-beta signaling proteins and the Protein Ontology

Hongfang Liu, Cathy H. Wu, Barry Smith, 2009, BMC Bioinformatics.

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents

Hagit Shatkay, Cathy H. Wu, Hongzhan Huang, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Jeyakumar Natarajan, Zhiyong Lu, K. Bretonnel Cohen, 2013, Database J. Biol. Databases Curation.

Text mining for the biocuration workflow

K. Bretonnel Cohen, Alfonso Valencia, Thomas C. Wiegers, 2012, Database J. Biol. Databases Curation.

Corrigendum to: Utilizing image and caption information for biomedical document classification

Hagit Shatkay, Cecilia Arighi, Xiangying Jiang, 2021, Bioinform..

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach

Cathy H. Wu, Cecilia N. Arighi, K. Vijay-Shanker, 2013, BCB.

BioCreative III interactive task: an overview

Zhiyong Lu, Fabio Rinaldi, Simon Clematide, 2011, BMC Bioinformatics.

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Zhiyong Lu, Ioannis Xenarios, Johanna R. McEntyre, 2016, Database J. Biol. Databases Curation.

Tutorial on Protein Ontology Resources.

Karen R Christie, Karen E Ross, Cecilia N Arighi, 2017, Methods in molecular biology.

Protein Ontology: a controlled structured network of protein entities

Jian Zhang, Cathy H. Wu, Olivia Helfer, 2013, Nucleic Acids Res..

pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

Cathy H. Wu, Cecilia N. Arighi, K. Vijay-Shanker, 2015, PloS one.

Modality-Classification of Microscopy Images Using Shallow Variants of Deep Networks

G. Elisabeta Marai, Cecilia Arighi, Pengyuan Li, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Overview of the COVID-19 Text Mining Tool Interactive Demo Track in BioCreative VII

K. Dolinski, T. Korves, M. Tyers, 2021 .

Temperature-induced conformational transition of intestinal fatty acid binding protein enhancing ligand binding: a functional, spectroscopic, and molecular modeling study.

C. Arighi, J. M. Delfino, J. Rossi, 1998, Biochemistry.

Overview of the BioCreative III Workshop

Zhiyong Lu, K. Bretonnel Cohen, Alfonso Valencia, 2011, BMC Bioinformatics.

Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.

Cathy H. Wu, Gang Li, Karen E Ross, 2017, Methods in molecular biology.

UniProt: the Universal Protein Knowledgebase in 2023

Cathy H. Wu, Christian J. A. Sigrist, Jerven T. Bolleman, 2022, Nucleic Acids Res..

THE PURIFICATION AND CHARACTERIZATION OF USP30 by Jason Cargill A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Master of Science in Chemistry and Biochemistry

C. Arighi, M. Johnston, Zhihao Zhuang, 2017 .

An evolutionarily conserved motif is required for Plasmodesmata-located protein 5 to regulate cell-to-cell movement

C. Arighi, Jung-Youn Lee, Gabriel Robles Luna, 2020, Communications Biology.

Original article Text mining for the biocuration workflow

K. Bretonnel Cohen, Alfonso Valencia, Thomas C. Wiegers, 2012 .

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P

Manabu Torii, Cathy H. Wu, Peter D'Eustachio, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops.

iPTMnet: Integrative Bioinformatics for Studying PTM Networks.

Cathy H. Wu, Hongzhan Huang, Sheng-Chih Chen, 2017, Methods in molecular biology.

An evolutionarily conserved motif is required for Plasmodesmata-located protein 5 to regulate cell-to-cell movement

C. Arighi, Jung-Youn Lee, Gabriel Robles Luna, 2020, Communications Biology.

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint

Cathy H. Wu, Hongzhan Huang, Karen E. Ross, 2013, Database J. Biol. Databases Curation.

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis

Cathy H. Wu, Gang Li, Karen E. Ross, 2014, ICBO.

Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus

Haibin Liu, Thomas C. Wiegers, W. John Wilbur, 2014, Database J. Biol. Databases Curation.

The Universal Protein Resource (UniProt) in 2010

Baris E. Suzek, Christian J. A. Sigrist, Petra S. Langendijk-Genevaux, 2009, Nucleic Acids Res..