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Lawrence Hunter

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TOP 3
K Bretonnel Cohen; Lawrence Hunter
Chapter 16: text mining for translational bioinformatics.
Lawrence Hunter
Computational challenges of mass phenotyping.
Charles W Rehrer; Nicole R Stob; Teri L Hernandez; Lawrence Hunter; Anis Karimpour-Fard; Christopher K Law; Robert H Eckel
Regional differences in subcutaneous adipose tissue gene expression.

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All Publications

2013: K Bretonnel Cohen; Lawrence Hunter
Chapter 16: text mining for translational bioinformatics.
PLoS computational biology 2013;9(4):e1003044.
2013: Lawrence Hunter
Computational challenges of mass phenotyping.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2013;():454-5.
2012: Charles W Rehrer; Nicole R Stob; Teri L Hernandez; Lawrence Hunter; Anis Karimpour-Fard; Christopher K Law; Robert H Eckel
Regional differences in subcutaneous adipose tissue gene expression.
Obesity (Silver Spring, Md.) 2012;20(11):2168-73.
2012: Suparna A Sarkar; Hannah Tipney; Jay A Walters; Jason D Dinella; John C Hutton; Kirstine Juhl; Anis Karimpour-Fard; Catherine E Lee; Lawrence Hunter
Synergizing genomic analysis with biological knowledge to identify and validate novel genes in pancreatic development.
Pancreas 2012;41(6):962-9.
2012: James J Galligan; Lawrence Hunter; L. Elaine Epperson; Kristofer S Fritz; Rebecca L Smathers; Dennis R Petersen
Protein carbonylation in a murine model for early alcoholic liver disease.
Chemical research in toxicology 2012;25(5):1012-21.
2012: Karin Verspoor; Colin Warner; Nianwen Xue; Michael Bada; William A Baumgartner; Jinho D Choi; K Bretonnel Cohen; Miriam Eckert; Christopher Funk; Helen L Johnson; Arrick Lanfranchi; Yuriy Malenkiy; Martha Palmer; Christophe Roeder; Lawrence Hunter
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.
BMC bioinformatics 2012;13():207.
2012: Michael Bada; William A Baumgartner; Judith A Blake; K Bretonnel Cohen; Miriam Eckert; Donald Evans; Kristin Garcia; Krista Shipley; Dmitry Sitnikov; Karin Verspoor; Lawrence Hunter
Concept annotation in the CRAFT corpus.
BMC bioinformatics 2012;13():161.
2011: Allyson G Hindle; Lawrence Hunter; Anis Karimpour-Fard; L. Elaine Epperson; Sandra L Martin
Skeletal muscle proteomics: carbohydrate metabolism oscillates with seasonal and torpor-arousal physiology of hibernation.
American journal of physiology. Regulatory, integrative and comparative physiology 2011;301(5):R1440-52.
2011: James J Galligan; Kristofer S Fritz; Hannah Tipney; Rebecca L Smathers; James R Roede; Colin T Shearn; Lawrence Hunter; Dennis R Petersen
Profiling impaired hepatic endoplasmic reticulum glycosylation as a consequence of ethanol ingestion.
Journal of proteome research 2011;10(4):1837-47.
2011: Michael Bada; Lawrence Hunter
Desiderata for ontologies to be used in semantic annotation of biomedical documents.
Journal of biomedical informatics 2011;44(1):94-101.
2011: Yoshinobu Kano; Halil Kilicoglu; Jin-Dong Kim; Makoto Miwa; Mariana Neves; Tomoko Ohta; Alberto Pascual-Montano; Sampo Pyysalo; Dragomir R Radev; Sebastian Riedel; Christophe Roeder; Rune Sætre; Tapio Salakoski; Sophia Ananiadou; Sabine Bergler; Jari Björne; Ekaterina Buyko; Hong-Woo Chun; K Bretonnel Cohen; Filip Ginter; Udo Hahn; Lawrence Hunter; Yves Van de Peer; Sofie Van Landeghem; Thomas Van Parys; Karin Verspoor; Arzucan Özgür; Jun'ichi Tsujii
U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC bioinformatics 2011;12():481.
2010: Anis Karimpour-Fard; Laura Dumas; Tzu Lip Phang; James M Sikela; Lawrence Hunter
A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation.
Human genomics 2010;4(6):421-7.
2010: Christophe Roeder; Clement Jonquet; Nigam Shah; William A Baumgartner; Karin Verspoor; Lawrence Hunter
A UIMA wrapper for the NCBO annotator.
Bioinformatics (Oxford, England) 2010;26(14):1800-1.
2010: Hannah Tipney; Lawrence Hunter
An introduction to effective use of enrichment analysis software.
Human genomics 2010;4(3):202-6.
2010: K Bretonnel Cohen; Helen L Johnson; Karin Verspoor; Christophe Roeder; Lawrence Hunter
The structural and content aspects of abstracts versus bodies of full text journal articles are different.
BMC bioinformatics 2010;11():492.
2009: Yoshinobu Kano; William A Baumgartner; Luke McCrohon; Sophia Ananiadou; K Bretonnel Cohen; Lawrence Hunter; Jun'ichi Tsujii
U-Compare: share and compare text mining tools with UIMA.
Bioinformatics (Oxford, England) 2009;25(15):1997-8.
2009: Karin Verspoor; Daniel Dvorkin; K Bretonnel Cohen; Lawrence Hunter
Ontology quality assurance through analysis of term transformations.
Bioinformatics (Oxford, England) 2009;25(12):i77-84.
2009: Chia-Yu Yen; Karen Meyer-Arendt; Brian Eichelberger; Shaojun Sun; Stephane Houel; William M Old; Rob Knight; Natalie G Ahn; Lawrence Hunter; Katheryn A Resing
A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins.
Molecular & cellular proteomics : MCP 2009;8(4):857-69.
2009: Sonia M Leach; Hannah Tipney; Weiguo Feng; William A Baumgartner; Priyanka Kasliwal; Ronald P Schuyler; Trevor Williams; Richard A Spritz; Lawrence Hunter
Biomedical discovery acceleration, with applications to craniofacial development.
PLoS computational biology 2009;5(3):e1000215.
2009: Hannah J Tipney; Ronald P Schuyler; Lawrence Hunter
Consistent visualizations of changing knowledge.
Summit on translational bioinformatics 2009;2009():129-32.
2009: Weiguo Feng; Sonia M Leach; Hannah Tipney; Tzulip Phang; Mark Geraci; Richard A Spritz; Lawrence Hunter; Trevor Williams
Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences.
PloS one 2009;4(12):e8066.
2009: Karin Verspoor; K Bretonnel Cohen; Lawrence Hunter
The textual characteristics of traditional and Open Access scientific journals are similar.
BMC bioinformatics 2009;10():183.
2009: Beth Tamburini; Susan Trapp; Tzu Lip Phang; Jill T Schappa; Lawrence Hunter; Jaime F Modiano
Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed.
PloS one 2009;4(5):e5549.
2009: Hannah J Tipney; Sonia M Leach; Weiguo Feng; Richard Spritz; Trevor Williams; Lawrence Hunter
Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology.
BMC bioinformatics 2009;10 Suppl 2():S12.
2008: Djuana M E Harvell; Nicole S Spoelstra; Meenakshi Singh; James L McManaman; Christina Finlayson; Tzu Phang; Susan Trapp; Lawrence Hunter; Wendy W Dye; Virginia F Borges; Anthony Elias; Kathryn B Horwitz; Jennifer K Richer
Molecular signatures of neoadjuvant endocrine therapy for breast cancer: characteristics of response or intrinsic resistance.
Breast cancer research and treatment 2008;112(3):475-88.
2008: Michael Bada; Lawrence Hunter
Identification of OBO nonalignments and its implications for OBO enrichment.
Bioinformatics (Oxford, England) 2008;24(12):1448-55.
2008: Deborah H Glueck; Lawrence Hunter; Anis Karimpour-Fard; Jan Mandel; Keith E Muller
Exact calculations of average power for the Benjamini-Hochberg procedure.
The international journal of biostatistics 2008;4(1):Article 11.
2008: J Gregory Caporaso; Sandra Smit; Brett C Easton; Lawrence Hunter; Gavin A Huttley; Rob Knight
Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics.
BMC evolutionary biology 2008;8():327.
2008: William A Baumgartner; Zhiyong Lu; Helen L Johnson; J Gregory Caporaso; Jesse Paquette; Anna Lindemann; EK White; Olga Medvedeva; K Bretonnel Cohen; Lawrence Hunter
Concept recognition for extracting protein interaction relations from biomedical text.
Genome biology 2008;9 Suppl 2():S9.
2008: Anis Karimpour-Fard; Sonia M Leach; Ryan T Gill; Lawrence Hunter
Predicting protein linkages in bacteria: which method is best depends on task.
BMC bioinformatics 2008;9():397.
2008: K Bretonnel Cohen; Martha Palmer; Lawrence Hunter
Nominalization and alternations in biomedical language.
PloS one 2008;3(9):e3158.
2008: Anis Karimpour-Fard; Sonia M Leach; Lawrence Hunter; Ryan T Gill
The topology of the bacterial co-conserved protein network and its implications for predicting protein function.
BMC genomics 2008;9():313.
2008: Steven Bethard; Zhiyong Lu; James H Martin; Lawrence Hunter
Semantic role labeling for protein transport predicates.
BMC bioinformatics 2008;9():277.
2008: Aaron P Gabow; Sonia M Leach; William A Baumgartner; Lawrence Hunter; Debra S Goldberg
Improving protein function prediction methods with integrated literature data.
BMC bioinformatics 2008;9():198.
2008: Lawrence Hunter; Zhiyong Lu; James Firby; William A Baumgartner; Helen L Johnson; Philip V Ogren; K Bretonnel Cohen
OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.
BMC bioinformatics 2008;9():78.
2008: William A Baumgartner; K Bretonnel Cohen; Lawrence Hunter
An open-source framework for large-scale, flexible evaluation of biomedical text mining systems.
Journal of biomedical discovery and collaboration 2008;3():1.
2008: J Gregory Caporaso; Nita Deshpande; J Lynn Fink; Philip Bourne; K Bretonnel Cohen; Lawrence Hunter
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2008;():640-51.
2008: K Bretonnel Cohen; Lawrence Hunter
Getting started in text mining.
PLoS computational biology 2008;4(1):e20.
2007: J Gregory Caporaso; William A Baumgartner; David A Randolph; K Bretonnel Cohen; Lawrence Hunter
Rapid pattern development for concept recognition systems: application to point mutations.
Journal of bioinformatics and computational biology 2007;5(6):1233-59.
2007: J Gregory Caporaso; William A Baumgartner; David A Randolph; K Bretonnel Cohen; Lawrence Hunter
MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinformatics (Oxford, England) 2007;23(14):1862-5.
2007: William A Baumgartner; K Bretonnel Cohen; Lynne M Fox; George K Acquaah-Mensah; Lawrence Hunter
Manual curation is not sufficient for annotation of genomic databases.
Bioinformatics (Oxford, England) 2007;23(13):i41-8.
2007: Michael Bada; Lawrence Hunter
Enrichment of OBO ontologies.
Journal of biomedical informatics 2007;40(3):300-15.
2007: Natalie J Serkova; Yu Zhang; John L Coatney; Lawrence Hunter; Michael Wachs; Claus U Niemann; M Susan Mandell
Early detection of graft failure using the blood metabolic profile of a liver recipient.
Transplantation 2007;83(4):517-21.
2007: Sonia Leach; Aaron Gabow; Lawrence Hunter; Debra S Goldberg
Assessing and combining reliability of protein interaction sources.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():433-44.
2007: Zhiyong Lu; K Bretonnel Cohen; Lawrence Hunter
GeneRIF quality assurance as summary revision.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():269-80.
2007: Helen L Johnson; K Bretonnel Cohen; Lawrence Hunter
A fault model for ontology mapping, alignment, and linking systems.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2007;():233-44.
2007: Anis Karimpour-Fard; Lawrence Hunter; Ryan T Gill
Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling.
BMC genomics 2007;8():393.
2007: Helen L Johnson; William A Baumgartner; Martin Krallinger; K Bretonnel Cohen; Lawrence Hunter
Corpus refactoring: a feasibility study.
Journal of biomedical discovery and collaboration 2007;2():4.
2007: Anis Karimpour-Fard; Corrella Detweiler; Kimberly D Erickson; Lawrence Hunter; Ryan T Gill
Cross-species cluster co-conservation: a new method for generating protein interaction networks.
Genome biology 2007;8(9):R185.
2007: Sanjiv Bhave; Cheryl Hornbaker; Tzu Lip Phang; Laura Saba; Razvan Lapadat; Katherina Kechris; Jeanette Gaydos; Daniel McGoldrick; Andrew Dolbey; Sonia Leach; Brian Soriano; Allison Ellington; Eric Ellington; Kendra Jones; Jonathan Mangion; John K Belknap; Robert Williams; Lawrence Hunter; Paula L Hoffman; Boris Tabakoff
The PhenoGen informatics website: tools for analyses of complex traits.
BMC genetics 2007;8():59.
2006: Jeffrey Guzelian; Joyce L Barwick; Lawrence Hunter; Tzu Lip Phang; Linda C Quattrochi; Philip S Guzelian
Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats.
Toxicological sciences : an official journal of the Society of Toxicology 2006;94(2):379-87.
2006: Brian D Lowes; Ronald Zolty; Wayne A Minobe; Alastair D Robertson; Sonia Leach; Lawrence Hunter; Michael R Bristow
Serial gene expression profiling in the intact human heart.
The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation 2006;25(5):579-88.
2006: Lawrence Hunter; K Bretonnel Cohen
Biomedical language processing: what's beyond PubMed?
Molecular cell 2006;21(5):589-94.
2006: K Bretonnel Cohen; Lawrence Hunter
A critical review of PASBio's argument structures for biomedical verbs.
BMC bioinformatics 2006;7 Suppl 3():S5.
2006: Zhiyong Lu; K Bretonnel Cohen; Lawrence Hunter
Finding GeneRIFs via gene ontology annotations.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():52-63.
2006: Helen L Johnson; K Bretonnel Cohen; William A Baumgartner; Zhiyong Lu; Michael Bada; Todd Kester; Hyunmin Kim; Lawrence Hunter
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2006;():28-39.
2005: K Bretonnel Cohen; Lynne Fox; Philip V Ogren; Lawrence Hunter
Empirical data on corpus design and usage in biomedical natural language processing.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2005;():156-60.
2005: Marilyn E Coors; Lawrence Hunter
Evaluation of genetic enhancement: will human wisdom properly acknowledge the value of evolution?
The American journal of bioethics : AJOB 2005;5(3):21-2; discussion W4-9.
2005: Shuhei Kinoshita; K Bretonnel Cohen; Philip V Ogren; Lawrence Hunter
BioCreAtIvE task1A: entity identification with a stochastic tagger.
BMC bioinformatics 2005;6 Suppl 1():S4.
2005: Philip V Ogren; K Bretonnel Cohen; Lawrence Hunter
Implications of compositionality in the gene ontology for its curation and usage.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():174-85.
2005: Zhiyong Lu; Lawrence Hunter
Go molecular function terms are predictive of subcellular localization.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005;():151-61.
2004: Steven A Russell; William Old; Katheryn A Resing; Lawrence Hunter
Proteomic informatics.
International review of neurobiology 2004;61():127-57.
2004: Philip V Ogren; K Bretonnel Cohen; George K Acquaah-Mensah; J Eberlein; Lawrence Hunter
The compositional structure of Gene Ontology terms.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():214-25.
2003: Michael C Rudolph; James L McManaman; Lawrence Hunter; Tzu Lip Phang; Margaret C. Neville
Functional development of the mammary gland: use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution.
Journal of mammary gland biology and neoplasia 2003;8(3):287-307.
2003: Robert Shenkar; J Paul Elliott; Katrina Diener; Judith Gault; Ling-Jia Hu; randall cohrs; Tzu Lip Phang; Lawrence Hunter; Robert E Breeze; Issam A Awad
Differential gene expression in human cerebrovascular malformations.
Neurosurgery 2003;52(2):465-77; discussion 477-8.
2003: Tzu Lip Phang; Margaret C. Neville; M Rudolph; Lawrence Hunter
Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():351-62.
2002: Lawrence Hunter
Ontologies for programs, not people.
Genome biology 2002;3(6):INTERACTIONS1002.
2001: Lawrence Hunter; R C Taylor; S M Leach; R Simon
GEST: a gene expression search tool based on a novel Bayesian similarity metric.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S115-22.
2000: Thomas C Rindflesch; Lorraine Tanabe; John N Weinstein; Lawrence Hunter
EDGAR: extraction of drugs, genes and relations from the biomedical literature.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():517-28.
1999: Lorraine Tanabe; Uwe Scherf; Lawrence H Smith; Jae K Lee; Lawrence Hunter; John N Weinstein
MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.
BioTechniques 1999;27(6):1210-4, 1216-7.
1999: Thomas C Rindflesch; Lawrence Hunter; Alan R Aronson
Mining molecular binding terminology from biomedical text.
Proceedings / AMIA ... Annual Symposium. AMIA Symposium 1999;():127-31.