Cathy Wu

Cathy Wu

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Beyond communication training: The MaRIS model for developing medical students' human capabilities and personal resilience.

Med Teach 2019 Oct 13:1-9. Epub 2019 Oct 13.

Griffith Health Institute for the Development of Education And Scholarship (Health IDEAS), Griffith University , Gold Coast , Australia.

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http://dx.doi.org/10.1080/0142159X.2019.1670340DOI Listing
October 2019

Using distant supervision to augment manually annotated data for relation extraction.

PLoS One 2019 30;14(7):e0216913. Epub 2019 Jul 30.

Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0216913PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667146PMC
July 2019

UniProt genomic mapping for deciphering functional effects of missense variants.

Hum Mutat 2019 Jun 3;40(6):694-705. Epub 2019 Apr 3.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.

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http://doi.wiley.com/10.1002/humu.23738
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http://dx.doi.org/10.1002/humu.23738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563471PMC
June 2019

Tunable synthetic extracellular matrices to investigate breast cancer response to biophysical and biochemical cues.

APL Bioeng 2019 Mar 8;3(1):016101. Epub 2019 Feb 8.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA.

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http://dx.doi.org/10.1063/1.5064596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481819PMC
March 2019

Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition.

Epigenetics Chromatin 2019 02 8;12(1):11. Epub 2019 Feb 8.

Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

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https://epigeneticsandchromatin.biomedcentral.com/articles/1
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http://dx.doi.org/10.1186/s13072-019-0256-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368739PMC
February 2019

Automatic gene annotation using GO terms from cellular component domain.

BMC Med Inform Decis Mak 2018 12 7;18(Suppl 5):119. Epub 2018 Dec 7.

Department of Computer and Information Science, University of Delaware, Newark, DE, 19716, USA.

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http://dx.doi.org/10.1186/s12911-018-0694-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284271PMC
December 2018

Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking.

IEEE/ACM Trans Comput Biol Bioinform 2017 Sep-Oct;14(5):1082-1093. Epub 2016 Jan 22.

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http://dx.doi.org/10.1109/TCBB.2016.2520931DOI Listing
May 2018

Completing sparse and disconnected protein-protein network by deep learning.

BMC Bioinformatics 2018 03 22;19(1):103. Epub 2018 Mar 22.

Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716, Delaware, USA.

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http://dx.doi.org/10.1186/s12859-018-2112-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863833PMC
March 2018

Protein Bioinformatics Databases and Resources.

Methods Mol Biol 2017 ;1558:3-39

Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.

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http://dx.doi.org/10.1007/978-1-4939-6783-4_1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5506686PMC
February 2018

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

Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA.

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http://dx.doi.org/10.1007/978-1-4939-6783-4_10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446092PMC
February 2018

iPTMnet: Integrative Bioinformatics for Studying PTM Networks.

Methods Mol Biol 2017 ;1558:333-353

Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20057, USA.

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http://link.springer.com/10.1007/978-1-4939-6783-4_16
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http://dx.doi.org/10.1007/978-1-4939-6783-4_16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436273PMC
February 2018

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

Nucleic Acids Res 2018 01;46(D1):D542-D550

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/nar/gkx1104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753337PMC
January 2018

eGARD: Extracting associations between genomic anomalies and drug responses from text.

PLoS One 2017 20;12(12):e0189663. Epub 2017 Dec 20.

Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189663PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738129PMC
January 2018

DEXTER: Disease-Expression Relation Extraction from Text.

Database (Oxford) 2018 01;2018

Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, DE 19716, USA.

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http://dx.doi.org/10.1093/database/bay045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007211PMC
January 2018

Evolutionary analysis and interaction prediction for protein-protein interaction network in geometric space.

PLoS One 2017 8;12(9):e0183495. Epub 2017 Sep 8.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183495PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590856PMC
October 2017

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.

Database (Oxford) 2016 11;2016. Epub 2016 May 11.

Computer & Information Sciences, University of Delaware and.

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http://dx.doi.org/10.1093/database/baw072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915133PMC
January 2017

Inference of protein-protein interaction networks from multiple heterogeneous data.

EURASIP J Bioinform Syst Biol 2016 Dec 19;2016(1). Epub 2016 Feb 19.

Department of Computer and Information Sciences, University of Delaware, 18 Amstel Avenue, Newark, 19716 DE USA ; Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, 19711 DE USA.

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http://dx.doi.org/10.1186/s13637-016-0040-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761017PMC
December 2016

Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction.

EURASIP J Bioinform Syst Biol 2016 Dec 22;2016(1):17. Epub 2016 Oct 22.

Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716 USA.

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http://dx.doi.org/10.1186/s13637-016-0051-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075339PMC
December 2016

Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

Methods 2016 11 6;110:97-105. Epub 2016 Jun 6.

Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.06.001DOI Listing
November 2016

Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology.

CEUR Workshop Proc 2016 Aug 29;1747. Epub 2016 Nov 29.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504912PMC
August 2016

Computational clustering for viral reference proteomes.

Bioinformatics 2016 07 26;32(13):2041-3. Epub 2016 Feb 26.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920120PMC
July 2016

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

PLoS One 2015 28;10(10):e0141773. Epub 2015 Oct 28.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141773PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624812PMC
June 2016

pGenN, a gene normalization tool for plant genes and proteins in scientific literature.

PLoS One 2015 10;10(8):e0135305. Epub 2015 Aug 10.

Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135305PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530884PMC
May 2016

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

J Biomed Semantics 2016 04 29;7(1). Epub 2016 Apr 29.

Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA.

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http://dx.doi.org/10.1186/s13326-015-0044-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877743PMC
April 2016

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

PLoS Comput Biol 2015 25;11(9):e1004391. Epub 2015 Sep 25.

Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583433PMC
March 2016

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

Database (Oxford) 2015 31;2015. Epub 2015 Mar 31.

Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA Department of Computer and Information Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.

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http://dx.doi.org/10.1093/database/bav020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381107PMC
September 2015

Development of Bioinformatics Pipeline for Analyzing Clinical Pediatric NGS Data.

AMIA Jt Summits Transl Sci Proc 2015 23;2015:207-11. Epub 2015 Mar 23.

Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525226PMC
August 2015

An integrated approach for analyzing clinical genomic variant data from next-generation sequencing.

J Biomol Tech 2015 Apr;26(1):19-28

1 Center for Bioinformatics and Computational Biology, and 2 Biomolecular Core Laboratory, Nemours Alfred I. duPont Hospital for Children Wilmington, Delaware 19803, USA; and 3 Department of Biological Sciences, University of Delaware, Newark, Delaware 19711, USA.

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http://dx.doi.org/10.7171/jbt.15-2601-002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310222PMC
April 2015

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.

Bioinformatics 2015 Mar 13;31(6):926-32. Epub 2014 Nov 13.

Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla 48000, Turkey, Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btu739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375400PMC
March 2015

BioC interoperability track overview.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/database/bau053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074764PMC
February 2015

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

Database (Oxford) 2014 13;2014. Epub 2014 Aug 13.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.

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http://dx.doi.org/10.1093/database/bau081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131691PMC
February 2015

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes.

F1000Res 2014 12;3:191. Epub 2014 Aug 12.

Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.

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http://dx.doi.org/10.12688/f1000research.4996.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184313PMC
October 2014

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.

Database (Oxford) 2014 21;2014. Epub 2014 May 21.

Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, USA and Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/database/bau038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028706PMC
August 2014

BioCreative-IV virtual issue.

Database (Oxford) 2014 22;2014. Epub 2014 May 22.

Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.

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http://dx.doi.org/10.1093/database/bau039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030502PMC
August 2014

A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems.

BMC Bioinformatics 2014 Aug 23;15:285. Epub 2014 Aug 23.

Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, USA.

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http://dx.doi.org/10.1186/1471-2105-15-285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262219PMC
August 2014

Software for pre-processing Illumina next-generation sequencing short read sequences.

Source Code Biol Med 2014 3;9. Epub 2014 May 3.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA.

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http://dx.doi.org/10.1186/1751-0473-9-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064128PMC
June 2014

BioC: a minimalist approach to interoperability for biomedical text processing.

Database (Oxford) 2013 18;2013:bat064. Epub 2013 Sep 18.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, Harvard Medical School, Harvard University, Boston, MA 02115 USA, Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA, Structural and Computational Biology Group, Spanish National Cancer Research Centre, Madrid E-28029, Spain, Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, National ICT Australia (NICTA), Victoria Research Laboratory, The University of Melbourne, Parkville VIC 3010, Australia and Department of Biology, North Carolina State University, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1093/database/bat064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889917PMC
March 2014

Integrative computational and experimental approaches to establish a post-myocardial infarction knowledge map.

PLoS Comput Biol 2014 Mar 20;10(3):e1003472. Epub 2014 Mar 20.

Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America; San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1003472
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http://dx.doi.org/10.1371/journal.pcbi.1003472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961365PMC
March 2014

Protein Ontology: a controlled structured network of protein entities.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D415-21. Epub 2013 Nov 21.

Protein Information Resource, Georgetown University Medical Center, WA 20007, USA, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Bioinformatics and Computational Biology, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, NY 10016, USA, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA, Department of Immunology, Duke University Medical Center, Durham, NC 27705, USA and Department of Oral Diagnostic Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY 14214, USA.

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http://dx.doi.org/10.1093/nar/gkt1173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964965PMC
January 2014

A fast Peptide Match service for UniProt Knowledgebase.

Bioinformatics 2013 Nov 19;29(21):2808-9. Epub 2013 Aug 19.

Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799477PMC
November 2013

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

Database (Oxford) 2013 7;2013:bat038. Epub 2013 Jun 7.

Center for Bioinformatics and Computational Biology, 15 Innovation Way, Suite 205, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/database/bat038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675891PMC
October 2013

Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint.

Front Genet 2013 26;4:62. Epub 2013 Apr 26.

Center for Bioinformatics and Computational Biology, University of Delaware Newark, DE, USA.

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http://dx.doi.org/10.3389/fgene.2013.00062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636526PMC
May 2013

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

Database (Oxford) 2012 5;2012:bas044. Epub 2012 Dec 5.

Department of Computer and Information Sciences, University of Delaware, Newark, USA.

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http://dx.doi.org/10.1093/database/bas044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514748PMC
April 2013

Prediction of contact matrix for protein-protein interaction.

Bioinformatics 2013 Apr 15;29(8):1018-25. Epub 2013 Feb 15.

Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3624801PMC
April 2013

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach.

BMC Struct Biol 2013 Apr 25;13. Epub 2013 Apr 25.

Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, DC 20007, USA.

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http://dx.doi.org/10.1186/1472-6807-13-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662625PMC
April 2013

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

Computer and Information Sciences Department, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA.

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http://dx.doi.org/10.1109/TCBB.2011.136DOI Listing
October 2012

Validity of self-reported eye disease and treatment in a population-based study: the Los Angeles Latino Eye Study.

Ophthalmology 2012 Sep 25;119(9):1725-30. Epub 2012 Apr 25.

Doheny Eye Institute and Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.

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http://dx.doi.org/10.1016/j.ophtha.2012.02.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413787PMC
September 2012

Four-year incidence of open-angle glaucoma and ocular hypertension: the Los Angeles Latino Eye Study.

Am J Ophthalmol 2012 Aug 27;154(2):315-325.e1. Epub 2012 Apr 27.

Doheny Eye Institute and the Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1016/j.ajo.2012.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401311PMC
August 2012

Overview of the BioCreative III Workshop.

BMC Bioinformatics 2011 Oct 3;12 Suppl 8:S1. Epub 2011 Oct 3.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.

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http://link.springer.com/content/pdf/10.1186%2F1471-2105-12-
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http://www.biomedcentral.com/1471-2105/12/S8/S1
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http://dx.doi.org/10.1186/1471-2105-12-S8-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269932PMC
October 2011

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data.

Adv Bioinformatics 2010 29:423589. Epub 2010 Mar 29.

Department of Computer & Information Sciences, Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://www.hindawi.com/journals/abi/aip/423589.pdf
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http://www.hindawi.com/journals/abi/2010/423589/
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http://dx.doi.org/10.1155/2010/423589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847380PMC
July 2011

Omics-based molecular target and biomarker identification.

Methods Mol Biol 2011 ;719:547-71

Lombardi Cancer Center, Georgetown University, Washington, DC, USA.

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http://dx.doi.org/10.1007/978-1-61779-027-0_26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742302PMC
June 2011

A comprehensive protein-centric ID mapping service for molecular data integration.

Bioinformatics 2011 Apr;27(8):1190-1

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072559PMC
April 2011

Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

PLoS One 2011 Apr 27;6(4):e18910. Epub 2011 Apr 27.

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018910PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083393PMC
April 2011

Protein bioinformatics databases and resources.

Methods Mol Biol 2011 ;694:3-24

Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1007/978-1-60761-977-2_1DOI Listing
February 2011

Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase.

Methods Mol Biol 2011 ;694:91-105

Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.

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http://dx.doi.org/10.1007/978-1-60761-977-2_7DOI Listing
February 2011

Protein-centric data integration for functional analysis of comparative proteomics data.

Methods Mol Biol 2011 ;694:323-39

Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA.

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http://dx.doi.org/10.1007/978-1-60761-977-2_20DOI Listing
February 2011

Molecular mechanisms mediating the effect of mono-(2-ethylhexyl) phthalate on hormone-stimulated steroidogenesis in MA-10 mouse tumor Leydig cells.

Endocrinology 2010 Jul 12;151(7):3348-62. Epub 2010 May 12.

The Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Avenue, Room C10-148, Montreal, Quebec, Canada H3G 1A4.

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http://dx.doi.org/10.1210/en.2010-0010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903930PMC
July 2010

Document classification for mining host pathogen protein-protein interactions.

Artif Intell Med 2010 Jul 15;49(3):155-60. Epub 2010 May 15.

Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, USA.

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http://dx.doi.org/10.1016/j.artmed.2010.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902599PMC
July 2010

Phylogenomic analysis of marine Roseobacters.

PLoS One 2010 Jul 15;5(7):e11604. Epub 2010 Jul 15.

State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011604PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904699PMC
July 2010

Community annotation in biology.

Biol Direct 2010 Feb 18;5:12. Epub 2010 Feb 18.

Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA.

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http://dx.doi.org/10.1186/1745-6150-5-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834641PMC
February 2010

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

PLoS One 2009 Sep 25;4(9):e7162. Epub 2009 Sep 25.

Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007162PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745575PMC
September 2009

Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes.

Virus Genes 2009 Aug 13;39(1):1-9. Epub 2009 Mar 13.

Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA.

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http://link.springer.com/10.1007/s11262-009-0343-4
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http://dx.doi.org/10.1007/s11262-009-0343-4DOI Listing
August 2009

BioTagger-GM: a gene/protein name recognition system.

J Am Med Inform Assoc 2009 Mar-Apr;16(2):247-55. Epub 2008 Dec 11.

The Imaging Science and Information Systems Center, Department of Oncology, Georgetown University Medical Center, 2115 Wisconsin Avenue NW, Washington, DC 20057, USA.

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http://dx.doi.org/10.1197/jamia.M2844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2649315PMC
April 2009

Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data.

J Proteomics Bioinform 2008 May;1(2):47-60

Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603135PMC
May 2008

Challenges and solutions in proteomics.

Curr Genomics 2007 Mar;8(1):21-8

Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington DC, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474689PMC
March 2007