• • Clegg BA, Shepherd JA
  Benchmarking natural-language parsers for biological applications using dependency graphs
  BMC Bioinformatics. 8:24. 2007.
  



• • Feldman R, Sanger J
  The Text Mining Handbook: Advanced Approaches in Analyzing Unstructured Data, Cambridge University Press
  Cambridge University Press. 1-424. 2007.
  



• • Shatkay H, Höglund A, Brady S, Blum T, Dönnes P, Kohlbacher O
  SherLoc : High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data.
  Bioinformatics. 23(11):1410-1417. 2007.
  PMID: 17392328



• • Ananiadou S, Kell BD, Tsujii J
  Text Mining and its Potential Applications in Systems Biology
  Trends in Biotechnology. 24(12):571-579. 2006.
  



• • Ananiadou S, McNaught J
  Text Mining for Biology and Biomedicine
  Edited Book. Publisher: Artech House, Norwood, MA. ISBN 1-58053-984-X.. 2006.
  



• • Baker JOC, Witte R
  Mutation Mining : A Prospectors Tale
  Information Systems Frontiers. 8(1):47-57. 2006.
  



• • Blei MD
  Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span
  BMC Bioinformatics. 7. 2006.
  



• • Chagoyen M, Carmona-Saez P, Gil C, Carazo MJ, Pascual-Montano A
  A literature-based similarity metric for biological processes
  BMC Bioinformatics. 7:363. 2006.
  PMID: 16872502



• • Chagoyen M, Carmona-Saez P, Shatkay H, Carazo MJ, Pascual-Montano A
  Discovering semantic features in the literature: a foundation for building functional associations
  BMC Bioinformatics. 7:41. 2006.
  PMID: 16438716



• • Chun HW, Tsuruoka Y, Kim JD, Shiba R, Nagata N, Hishiki T, et al.
  Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine Learning
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Fan W, Wallace L, Rich S, Zhang Z
  Tapping the power of Text Mining
  Communications of the ACM. 49(9):76-82. 2006.
  



• • Good MB, Tranfield ME, Tan CP, Shehata M, Singhera KG, Gosselink J, et al.
  Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Hoeglund A, Blum T, Brady S, Doennes P, San-Miguel J, Rocheford M, et al.
  Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data
  Proceedings of the 11th Pacific Symposium on Biocomputing. 16-27. 2006.
  



• • Jensen JL, Saric J, Bork P
  Literature mining for the biologist: from information retrieval to biological discovery
  Nature Reviews Genetics. 7:119-129. 2006.
  PMID: 16418747



• • Johnson LH, Cohen KB, Baumgartner JAW, Lu Z, Bada M, Kester T, et al.
  Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Kushida T, Takagi T, Fukuda IK
  Event Ontology: A Pathway-Centric Ontology for Biological Processes
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B
  Automatically Generating Gene Summaries from Biomedical Literature
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Lu Z, Cohen KB, Hunter L
  Finding GeneRIFs via Gene Ontology Annotations
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C
  PhenoGO: Assigning Phenotypic Context to Gene Ontology Annotations with Natural Language Processing
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Maguitman GA, Rechtsteiner A, Verspoor K, Strauss EC, Rocha ML
  Large-Scale Testing of Bibliome Informatics Using Pfam Protein Families
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Mukherjea S, Sahay S
  Discovering Biomedical Relations Utilizing the World-Wide Web
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Stoica E, Hearst M
  Predicting Gene Functions from Text Using a Cross-Species Approach
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Vlachos A, Gasperin C, Lewin I, Briscoe T
  Bootstrapping the Recognition and Anaphoric Linking of Named Entities in Drosophila Articles
  Proceedings of the 11th Pacific Symposium on Biocomputing. 2006.
  



• • Wilbur JW, Rzhetsky A, Shatkay H
  New Directions in Biomedical Text Annotations: Deifinitions, Guidelines and Corpus Construction.
  BMC Bioinformatics. 7:356. 2006.
  PMID: 16867190



• • Yetisgen-Yildiz M, Pratt W
  Using Statistical and Knowledge-Based Approaches for Literature Based Discovery
  Journal of Biomedical Informatics (in press). 39(6):600-611. 2006.
  



• • Zhou D, He Y, Kwoh CK
  Extracting Protein-Protein Interactions from the Literature using the Hidden Vector State Model
  International Workshop on Bioinformatics Research and Applications 2006 . 2006.
  



• •
  Get ready to GO! A biologist's guide to the Gene Ontology
  Briefings in Bioinformatics. 6(3):298-304. 2005.
  PMID: 16212777



• • Afantenos DS, Karkaletsis V, Stamatopoulos P
  Summarization from Medical Documents: A Survey
  Artificial Intelligence in Medicine. 33(2):157-177. 2005.
  PMID: 15811783



• • Ahmed ST, Chidambaram D, Davalcu H, Baral C
  IntEx: A Syntactic Role Driven Protein-Protein Interaction Extractor for Bio-Medical Text
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Baker C, Witte R
  Combining Biological Databases and Text Mining to support New Bioinformatics Applications
  Proc. of the 10th International Workshop on Applications of Natural Language to Information Systems. 2005.
  



• • Bechhofer SK, Stevens RD, Lord PW
  Ontology Driven Dynamic Linking of Biology Resources
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Blaschke C, Leon AE, Krallinger M, Valencia A
  Evaluation of BioCreAtIvE assessment of task 2
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960828



• • Bodenreider O, Aubry M, Burgun A
  Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Bodenreider O, Mitchell JA, McCray AT
  Session Introduction
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Camon BE, Barrell GD, Dimmer CE, Lee V, Magrane M, Maslen J, et al.
  An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960829



• • Cantor MN, Sarkar IN, Bodenreider O, Lussier YA
  GenesTrace: Phenomic Knowledge Discovery via Structured Terminology
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Clegg AB, Shepherd AJ
  Evaluating and Integrating Treebank Parsers on a Biomedical Corpus
  Association for Computational Linguistics, Workshop on Software05. 2005.
  



• • Cohen A
  Unsupervised Gene/Protein Named Entity Normalization Using Automatically Extracted Dictionaries
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Cohen AM, Hersh WR
  A Survey of Current Work in Biomedical Text Mining
  BRIEFINGS IN BIOINFORMATICS. 6(1):57-71. 2005.
  PMID: 15826357



• • Cohen AM, Hersh WR, Dubay C, Spackman K
  Using Co-Occurrence Network Structure to Extract Synonymous Gene and Protein Names from MEDLINE Abstracts
  BMC Bioinformatics. 6(1):103. 2005.
  PMID: 15847682



• • Cohen KB, Fox L, Ogren PV, Hunger L
  Corpus Design for Biomedical Natural Language Processing
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Cohen KB, Hunter L
  Natural Language Processing and Systems Biology
  Artificial Intelligence and Systems Biology, Springer Series on Computational Biology. Dubitzky W. and Azuaje F. (Eds.). 2005.
  



• • Colosimo ME, Morgan AA, Yeh AS, Colombe JB, Hirschman L
  Data preparation and interannotator agreement: BioCreAtIvE Task 1B
  BMC Bioinformatics. 6(Suppl 1):S12. 2005.
  



• • Couto FM, Silva JM, Coutinho MP
  Finding genomic ontology terms in text using evidence content
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960834



• • Crim J, McDonald R, Pereira F
  Automatically annotating documents with normalized gene lists
  BMC Bioinformatics. 6(Suppl 1):S13. 2005.
  PMID: 15960825



• • Ding J, Viswanathan K, Berleant D, Hughes L, Wurtele SE, Ashlock D, et al.
  Using the biological taxonomy to access biological literature with PathBinderH
  Bioinformatics. 21(10):2560-2562. 2005.
  PMID: 15769838



• • Divoli A, Attwood KT
  BioIE: extracting informative sentences from the biomedical literature
  Bioinformatics. 21:2138-2139. 2005.
  PMID: 15691860



• • Doms A, Schroeder M
  GoPubMed: exploring PubMed with the Gene Ontology
  Nucleic Acids Research. 33(Web server issue). 2005.
  PMID: 15980585



• • Ehrler F, Geissbühler A, Jimeno A, Ruch P
  Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960836



• • Finkel J, Dingare S, Manning CD, Nissim M, Alex B, Grover C
  Exploring the boundaries: gene and protein identification in biomedical text
  BMC Bioinformatics. 6(Suppl 1):S5. 2005.
  PMID: 1590839



• • Fundel K, Güttler D, Zimmer R, Apostolakis J
  A simple approach for protein name identification: prospects and limits
  BMC Bioinformatics. 2005.
  PMID: 15960827



• • Gennari JH, Silberfein A, Wiley JC
  Integrating Genomic Knowledge Sources Through an Anatomy Ontology
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Hakenberg J, Plake C, Leser U
  Optimizing Syntax Patterns for Discovering Protein-Protein Interactions
  ACM Symposium on Applied Computing (SAC), Bioinformatics Track. 2005. 2005.
  



• • Hakenberg J, Rutsch J, Leser U
  Tuning text classification for hereditary diseases with section weighting
  First International Symposium on Semantic Mining in Biomedicine (SMBM). 2005.
  



• • Hakenberg J, Bickel S, Plake C, Brefeld U, Zahn H, Faulstich L, et al.
  Systematic feature evaluation for gene name recognition
  BMC Bioinformatics. 6(Suppl 1):S9. 2005.
  PMID: 15960843



• • Hayete B, Bienkowska JR
  GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Hirschman L, Colosimo M, Morgan A, Yeh A
  Overview of BioCreAtIvE task 1B: normalized gene lists
  BMC Bioinformatics. 6(Suppl 1):S11. 2005.
  PMID: 15960823



• • Hirschman L, Yeh A, Blaschke C, Valencia A
  Overview of BioCreAtIvE: critical assessment of information extraction for biology
  BMC Bioinformatics. 6(Suppl 1):S1. 2005.
  PMID: 15960821



• • Hoffman M, Arnoldi C, Chuang I
  The Clinical Bioinformatics Ontology: A Curated Semantic Network Utilizing RefSeq Information
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Hoffman R, Valencia A
  Implementing the iHOP Concept for Navigation of Biomedical Literature
  Bioinformatics (ECCB Suppl). 21(suppl 2). 2005.
  



• • Hoffmann R, Krallinger M, Andres E, Tamames J, Blaschke C, Valencia A
  Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks
  Sci STKE. 283:21. 2005.
  PMID: 15886388



• • Hofmann O, Schomburg D
  Concept-based annotation of enzyme classes
  Bioinformatics. 21:2059-2066. 2005.
  PMID: 15661799



• • Homayouni R, Heinrich K, Wei L, Berry MW
  Gene Clustering by Latent Semantic Indexing of MEDLINE Abstracts
  Bioinformatics. 21(1):104-115. 2005.
  PMID: 15308538



• • Hong M, Kairmpour-fard A, Russell S, Hunter L
  Integrated Term Weighting, Visualization, and User Interface Development for Bioinformation Retrieval
  Lecture Notes in Computer Science, Springer-Verlag. (Proc. of AIS, Artificial Intelligence and Simulation, 2004). 3397:673. 2005.
  



• • Jelier R, Jenster G, Dorssers CJL, van der Eijk CC, van Mulligan ME, Mons B, et al.
  Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
  Bioinformatics. 21(9):2049-2058. 2005.
  PMID: 15657104



• • Kinoshita S, Cohen KB, Ogren VP, Hunter L
  BioCreative Task1A: entity identification with a stochastic tagger
  BMC Bioinformatics. 2005.
  



• • Korbel OJ, Doerks T, Jensen JL, Perex-Iratxeta C, Kaczanowski S, Hooper DS, et al.
  Systematic Association of Genes to Phenotypes by Genome and Literature
  PLoS Biology. 3, No. 5:134. 2005.
  PMID: 15799710



• • Krallinger M, Valencia A
  Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps (Chapter 4)
  Data Analysis and Visualization in Genomics and Proteomics. 2005.
  



• • Krallinger M, Erhardt RA, Valencia A
  Text-mining approaches in molecular biology and biomedicine
  Drug Discovery Today. 10(6):439-445. 2005.
  PMID: 15808823



• • Krallinger M, Padron M, Valencia A
  A sentence sliding window approach to extract protein annotations from biomedical articles
  BMC Bioinformatics. 6(Suppl 1). 2005.
  



• • Krallinger M, Valencia A
  Text-Mining and Information-Retrieval Services for Molecular Biology
  Genome Biology. 6:224. 2005.
  



• • Kuffner R, Fundel K, Zimmer R
  Expert Knowledge Without the Expert: Integrated Analysis of Gene Expression and Literature to Derive Active Functional Contexts
  Bioinformatics (ECCB Suppl). 21(Suppl 2). 2005.
  



• • Lease M, Charniak E
  Parsing Biomedical Literature
  Second International Joint Conference on Natural Language Processing (IJCNLP05). 2005.
  



• • Leser U, Hakenberg J
  What makes a gene name? Named entity recognition in the biomedical literature
  Briefings in Bioinformatics. 6(4):357-369. 2005.
  PMID: 16420734



• • Liu M, Grigoriev A
  Fast parsers for Entrez Gene
  Bioinformatics 2005. 21:3189-3190. 2005.
  PMID: 1587945



• • Lu Z, Hunter L
  GO Molecular Function Terms Are Predictive of Subcellular Localization
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  PMID: 15759622



• • Marshall B, Su H, McDonald D, Chen H
  Linking Ontological Resources Using Aggregatable Substance Identifiers to Organize Extracted Relations
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • McDonald R, Pereira F
  Identifying gene and protein mentions in text using conditional random fields
  BMC Bioinformatics. 6(Suppl 1):S6. 2005.
  PMID: 159060840



• • Mitsumori T, Fation S, Murata M, Doi K, Doi H
  Gene/protein name recognition based on support vector machine using dictionary as features
  BMC Bioinformatics. 6(Suppl 1):S8. 2005.
  PMID: 15960842



• • Mooney RJ, Bunescu R
  Mining Knowledge from Text Using Information Extraction
  SIGKDD Explorations. 7(1):3-10. 2005.
  



• • Mukherjea S
  Information retrieval and knowledge discovery utilising a biomedical Semantic Web
  Briefings in Bioinformatics. 6(3):252-262. 2005.
  PMID: 16212773



• • Mullen T, Mizuta Y, Collier N
  A baseline feature set for learning rhetorical zones using full articles in the biomedical domain
  SIGKDD. 7(1):52-58. 2005.
  



• • Ogren PV, Cohen KB, Hunter L
  Implications of Compositionality in the Gene Ontology for Its Curation and Usage
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  PMID: 15759624



• • Orchard S, Montecchi-Palazzi L, Hermjakob H, Apweiler R
  The Use of Common Ontologies and Controlled Vocabularies to Enable Data Exchange and Deposition for Complex Proteomic Experiments
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Polavarapu N, Navathe SB, Ramnarayanan R, ul HA, Sahay S, Liu Y
  Investigation into Biomedical Literature Classification using Support Vector Machines
  Proceedings of the IEEE Conference on Computational Systems in Bioinformatics (CSB2005, to appear). 2005.
  



• • Ramani A, Bunescu R, Mooney R, Marcotte E
  Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Ray S, Craven M
  Learning Statistical Models for Annotating Proteins with Function Information using Biomedical Text
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960830



• • Rebholz-Schuhmann D, Kirsch H, Couto F
  Facts from Text—Is Text Mining Ready to Deliver?
  PLoS Biology. 3(2):188-191. 2005.
  



• • Rice BS, Nenadic G, Stapley JB
  Mining protein function from text using term-based support vector machines
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960835



• • Ruch P
  Automatic Assignment of Biomedical Categories: Toward a Generic Approach
  Bioinformatics (Advance Access published online). 2005.
  PMID: 16287934



• • Saric J, Jensen JL, Rossitza O, Isabel R, Peer B
  Extraction of regulatory gene/protein networks from Medline
  Bioinformatics. 2005.
  PMID: 16046493



• • Scherf M, Epple A, Werner T
  The next generation of literature analysis: Integration of genomic analysis into text mining
  Briefings in Bioinformatics. 6(3):287-297. 2005.
  PMID: 16212776



• • Schmeier S
  Automated Recognition and Extraction of Entities Related to Enzyme Kinetics from Text
  MSc Thesis, Dept. of Mathematics and Computer Science, Free University of Berlin. 2005.
  



• • Settles B
  ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text
  Bioinformatics. 21:3191-3192. 2005.
  PMID: 15860559



• • Shatkay H
  Hairpins in bookstacks: Information retrieval from biomedical text
  Briefings in Bioinformatics. 6(3):222-238. 2005.
  PMID: 16212771



• • Skusa A, Ruegg A, Koehler J
  Extraction of biological interaction networks from scientific literature
  Breifings in Bioinformatics. 6(3):263-276. 2005.
  PMID: 16212774



• • Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, et al.
  Relations in Biomedical Ontologies
  Genome Biology. 6(5). 2005.
  



• • Smith LH, Tanabe L, Rindlesch T, Wilbur WJ
  MedTag: A Collection of Biomedical Annotations
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Spasic I, Ananiadou S
  A Flexible Measure of Contextual Similarity for Biomedical Terms
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Spasic I, Ananiadou S, McNaught J, Kumar A
  Text mining and ontologies in biomedicine: Making sense of raw text
  Briefings in Bioinformatics. 6(3):239-251. 2005.
  PMID: 16212772



• • Suomela PB, Andrade AM
  Ranking the whole MEDLINE database according to a large training set using text indexing
  BMC Bioinformatics. 6:75. 2005.
  



• • Szugat M, Guttler D, Fundel K, Sohler F, Zimmer R
  Web Servicing the Biological Office
  Bioinformatics. 21(Suppl 2). 2005.
  



• • Tamames J
  Text Detective: a rule-based system for gene annotation in biomedical texts
  BMC Bioinformatics. 6(Suppl 1):S10. 2005.
  PMID: 15960822



• • Tanabe L, Xie N, Thom LH, Matten W, Wilbur WJ
  GENETAG: a tagged corpus for gene/protein named entity recognition
  BMC Bioinformatics. 6(Suppl 1):S5. 2005.
  PMID: 15960837



• • Tari L, Baral C, Dasgupta P
  Understanding the Global Properties of Functionally-Related Gene Networks Using the Gene Ontology
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Toldo L, Rippmann F
  Integrated Bioinformatics Application for Automated Target Discovery
  Journal of the American Society for Information Science and Technology. 56:483-492. 2005.
  



• • Tsuruoka Y, Ananiadou S, Tsujii J
  A Machine Learning Approach to Acryonym Generation
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Verspoor K
  Towards a Semantic Lexicon for Biological Language Processing
  Comparative and Functional Genomics. 6(1-2):61-66. 2005.
  



• • Verspoor K, Cohn J, Joslyn C, Mniszewski S, Rechtsteiner A, Rocha ML, et al.
  Protein annotation as term categorization in the gene ontology using word proximity networks
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960833



• • Weeber M, Kors AJ, Mons B
  Online tools to support literature-based discovery in the life sciences
  Briefings in Bioinformatics. 6(3):277-286. 2005.
  PMID: 16212775



• • Wellner B
  Weakly Supervised Learning Methods for Improving the Quality of Gene Name Normalization Data
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Wellner B, Castaño J, Pustejovsky J
  Adaptive String Similarity Metrics for Biomedical Reference Resolution
  Proceedings of the Joint ACL Workshop and BioLINK SIG (ISMB) on Linking Biological Literature Ontologies and Databases, 2005. 2005.
  



• • Wren DJ
  Automating Literature-based Lead Discovery
  Frontieres in Drug Design & Discovery. 1:267-286. 2005.
  



• • Wren DJ, Chang TJ, Pustejovsky J, Adar E, Garner RH, Altman BR
  Biomedical Term Mapping Databases
  Nucleic Acids Research (Database Issue). 33:289-293. 2005.
  PMID: 15608198



• • Xiong H, He X, Ding C, Zhang Y, Kumar V, Holbrook SR
  Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Yamakawa H, Maruhashi K, Nakao Y
  Multi-Aspect Gene Relation Analysis
  Proceedings of the Pacific Symposium on Biocomputing (PSB). 2005.
  



• • Yang C, Zeng E, Li T, Narasimhan G
  Clustering Genes using Gene Expression and Text Literature Data
  Proceedings of the IEEE Conference on Computational Systems in Bioinformatics (CSB2005, to appear). 2005.
  



• • Yeh A, Morgan A, Colosimo M, Hirschman L
  BioCreAtIvE Task 1A: gene mention finding evaluation
  BMC Bioinformatics. 6(Suppl 1):S2. 2005.
  PMID: 15960832



• • Yetisgen-Yildiz M, Pratt W
  The Effect of Feature Representation on MEDLINE Document Classification
  American Medical Informatics Association Fall Symposium (AMIA05). 2005.
  



• • Zhou GD, Shen D, Zhang J, Su J, Tan SH
  Recognition of protein/gene names from text using an ensemble of classifiers
  BMC Bioinformatics. 6(Suppl 1). 2005.
  PMID: 15960841



• • Zhu S, Okuno Y, Tsujimoto G, Mamitsuka H
  A Probabilistic Model for Mining Implicit ‘Chemical Compound–Gene’ Relations from Literature
  Bioinformatics (ECCB Suppl). 21(suppl 2). 2005.
  



• • Adar E
  SaRAD: A Simple and Robust Abbreviation Dictionary
  Bioinformatics. 20(4):527-533. 2004.
  PMID: 14990448



• • Aitken JS, Webber BL, Bard JBL
  Part-of Relations in Anatomy Ontologies: A Proposal for RDFS and OWL Formalisations
  Proceedings of the 9th Pacific Symposium on Biocomputing. 166-177. 2004.
  



• • Alphonse E, Aubin S, Bessieres P, Bisson G, Hamon T, Lagarrigue S
  Event-Based Information Extraction for the Biomedical Domain: the Caderige Project
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 43-49. 2004.
  



• • Amrani A, Kodratoff Y, Matte-Tailliez O
  A Semi-automatic System for Tagging Specialized Corpora
  Lecture Notes in Artificial Intelligence (PAKDD'04). 3056:670-681. 2004.
  



• • Ananiadou S, Friedman C, Tsujii J
  Introduction: named entity recognition in biomedicine
  Journal of Biomedical Informatics. 37(6):393-395. 2004.
  PMID: 15542013



• • Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Malsen J, et al.
  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
  Nucleic Acids Res.. 32D262-D266. 2004.
  PMID: 14681408



• • Carpenter B
  Phrasal Queries with LingPipe and Lucene
  Proceedings of the 13th Text Retrieval Conference (TREC). Genomics Track.. 2004.
  



• • Chang JT, Altman RB
  Extracting and Characterizing Gene-Drug Relationships from the Literature
  Pharmacogenetics. 14(9):577-586. 2004.
  PMID: 15475731



• • Chang JT, Schutze H, Altman RB
  GAPSCORE: Finding Gene and Protein Names One Word at a Time
  Bioinformatics. 20(2):216-225. 2004.
  PMID: 14734313



• • Chen H, Sharp BM
  Content-Rich Biological Network Constructed by Mining PubMed Abstracts
  BMC Bioinformatics. 5(1):147. 2004.
  PMID: 15473905



• • Chen L, Liu H, Friedman C
  Gene name ambiguity of eukaryotic nomenclatures
  Bioinformatics. 2004.
  PMID: 15333458



• • Chiang JH, Yu HC, Hsu HJ
  GIS: A Biomedical Text-Mining System for Gene Information Discovery
  Bioinformatics. 20(1):120-121. 2004.
  PMID: 14693818



• • Cohen KB, Tanabe L, Kinoshita S, Hunter L
  A Resource for Constructing Customized Test Suites for Molecular Biology Entity Identification Systems
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 1-8. 2004.
  



• • Collier N, Takeuchi K
  Comparison of character-level and part of speech features for name recognition in biomedical texts
  Journal of Biomedical Informatics. 37(6):423-435. 2004.
  PMID: 15542016



• • Corney DP, Buxton BF, Langdon WB, Jones DT
  BioRAT: Extracting Bilogica Information from Full-Length Papers
  Bioinformatics. 20(17):3206-3213. 2004.
  PMID: 15231534



• • Couto FM, Martins B, Silva JM
  Classifying Biomedical Articles using Web Resources
  19th ACM Symposium on Applied Computing (SAC), Bioinformatics Track, Nicosia, Cyprus. 2004.
  



• • Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I
  Extracting human protein interactions from MEDLINE using a full-sentence parser.
  Bioinformatics. 20(5):604-11. 2004.
  PMID: 15033866



• • Daraselia N, Egorov S, Yazhuk A, Novichkova S, Yuryev A, Mazo I
  Extracting human protein interactions from MEDLINE using a full-sentence parser
  Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics. 11-17. 2004.
  PMID: 15033866



• • Egorov S, Yuryev A, Daraselia N
  A Simple and Practical Dictionary-Based Approach for Identification of Proteins in MEDLINE Abstracts.
  J Am Med Inform Assoc. 2004.
  PMID: 14764613



• • Eom JH, Zhang BT
  PubMiner: Machine Learning Based Text Mining for Biomedical Information Analysis
  Genomics & Informatics. 2(2):99-106. 2004.
  



• • Eskin E, Agichtein E
  Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions
  Proceedings of the 9th Pacific Symposium on Biocomputing. 288-299. 2004.
  PMID: 14992511



• • Finkel J, Dingare S, Nguyen H, Nissim M, Manning C, Sinclair G
  Exploiting Context for Biomedical Entity Recognition: From Syntax to the Web
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 88-91. 2004.
  



• • Ginter F, Boberg J, Jarvinen J, Salakoski T
  New Techniques for Disambiguation in Natural Language and Their Application to Biological Text
  Journal of Machine Learning Research (JMLR). 5:605-621. 2004.
  



• • Glenisson P
  Integrating scientific literature with large scale gene expression analysis
  PhD Thesis, Katholieke Universiteit Leuven, Belgium. 2004.
  



• • Glenisson P, Coessens B, Van Vooren S, Mathys J, Moreau Y, De Moor B
  TXTGate : Profiling gene groups with text-based information
  Genome Biology. 5(6). 2004.
  



• • GuoDong Z, Jian S
  Exploring Deep Knowledge Resources in Biomedical Name Recognition
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 96-99. 2004.
  



• • Hakenberg J, Schmeier S, Kowald A, Klipp E, Leser U
  Finding Kinetic Parameters Using Text Mining
  OMICS: A Journal of Integrative Biology. 8(2):131-152. 2004.
  PMID: 15268772



• • Harkema H, Gaizauskas R, Hepple M, Roberts A, Roberts I, Davis N, et al.
  A Large Scale Terminology Resource for Biomedical Text Processing
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 53-60. 2004.
  



• • Hersh W, Bhupatiraju TR, Corley S
  Enhancing Access to the Bibliome: The TREC Genomics Track
  MedInfo 2004. 773-777. 2004.
  PMID: 15360917



• • Hou WJ, Chen HH
  Enhancing performance of protein and gene name recognizers with filtering and integration strategies
  Journal of Biomedical Informatics. 37(6):448-460. 2004.
  PMID: 15542018



• • Huang M, Zhu X, Hao Y, Payan DG, Qu K, Li M
  Discovering Patterns to Extract Protein-Protein Interactions from Full Texts
  Bioinformatics. 2004.
  PMID: 15284092



• • Huang M, Zhu X, Payan DG, Qu K, Li M
  Discovering Patterns to Extract Protein-Protein Interactions from Full Biomedical Texts
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 22-28. 2004.
  



• • Kaneta Y, Munna MA, Ohkawa T
  A Method of Extracting Sentences Related to Protein Interaction from Literature using a Structure Database
  Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics. 18-25. 2004.
  



• • Karopka T, Scheel T, Bansemer S, Glass A
  Automatic construction of gene relation networks using text mining and gene expression data
  Medical Informatics and the Internet in Medicine. 29:169-183. 2004.
  PMID: 15370996



• • Karp PD, Paley S, Krieger CJ, Zhang P
  An Evidence Ontology for Use in Pathway/Genome Databases
  Pacific Symposium on Biocomputing. 9:190-201. 2004.
  



• • Kennedy PJ, Simoff SJ, Skillicorn D, Catchpoole D
  Extracting and Explaining Biological Knowledge in Microarray Data
  Lecture Notes in Artificial Intelligence (PAKDD'04). 3056:699-703. 2004.
  



• • Kiritchenko S, Matwin S, Famili AF
  Hierarchical Text Categorization as a Tool of Associating Genes with Gene Ontology Codes
  Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics. 26-30. 2004.
  



• • Koike A, Niwa Y, Takagi T
  Automatic Extraction of Gene/Protein Biological Functions from the Biomedical Text
  Bioinformatics. 2004.
  PMID: 15509601



• • Koike A, Takagi T
  Gene/Protein/Family Name Recognition in Biomedical Literature
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 9-16. 2004.
  



• • Krallinger M, Padron M, Blaschke C, Valencia A
  Assessing the Correlation between Contextual Patterns and Biological Entity Tagging
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 36-42. 2004.
  



• • Krauthammer M, Nenadic G
  Term identification in the biomedical literature
  Journal of Biomedical Informatics. 37(6):512-526. 2004.
  PMID: 15542023



• • Kulick S, Bies A, Liberman M, Mandel M, McDonald R, Palmer M, et al.
  Integrated Annotation for Biomedical Information Extraction
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 61-68. 2004.
  



• • Lee C, Hou WJ, Chen HH
  Annotating Multiple Types of Biomedical Entities: A Single Word Classification Approach
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 80-83. 2004.
  



• • Lee KJ, Hwang YS, Kim S, Rim HC
  Biomedical named entity recognition using two-phase model based on SVMs
  Journal of Biomedical Informatics. 37(6):436-447. 2004.
  PMID: 15542017



• • Leonard JE, Colombe JB, Levy JL
  Finding Relevant References to Genes and Proteins in Medline using a Bayesian Approach
  Bioinformatics. 18(11):1515-1522. 2004.
  PMID: 12424124



• • Libbus B, Kilicoglu H, Rindflesch TC, Mork JG, Aronson AR
  Using Natural Language Processing, LocusLink and the Gene Ontology to Compare OMIM to MEDLINE
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 69-76. 2004.
  



• • Light M, Qiu XY, Srinivasan P
  The Language of Bioscience: Facts, Speculations, and Statements In Between
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 17-24. 2004.
  



• • Liu H, Wu C
  A Study of Text Categorization for Model Organism Databases
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 25-32. 2004.
  



• • Lu X, Zhai C, Gopalakrishnan V, Buchanan GB
  Automatic annotation of protein motif function with Gene Ontology terms
  BMC Bioinformatics. 5:122. 2004.
  PMID: 15345032



• • Lussier YA, Li J
  Terminological Mapping for High Throughput Comparative Biology of Phenotypes
  Pacific Symposium on Biocomputing. 9:202-213. 2004.
  



• • Mack R, Mukherjea S, Soffer A, Uramoto N, Brown E, Coden A, et al.
  Text Analytics for Life Science using the Unstructured Information Management Architecture
  IBM Systems Journal. 43(3):490-525. 2004.
  



• • Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B
  GOToolBox: Functional Analysis of Gene Datasets based on Gene Ontology
  Genome Biology. 5(12). 2004.
  PMID: 15575967



• • Mathiak B, Eckstein S
  Five Steps to Text Mining in Biomedical Literature
  Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics. 43-46. 2004.
  



• • McDonald DM, Chen H, Su H, Marshall BB
  Extracting Gene Pathway Relations Using a Hybrid Grammar: the Arizona Relation Parser
  Bioinformatics. 2004.
  PMID: 15256411



• • McDonald TR, Winters SR, Mandel M, Jin Y, White SP, Pereira F
  An Entity Tagger for Recognizing Acquired Genomic Variations in Cancer Literature
  Bioinformatics. 20(17):3249-3251. 2004.
  PMID: 15180929



• • Mercer RE, Di Marco C
  A Design Methodology for a Biomedical Literature Indexing Tool Using the Rhetoric of Science
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 77-84. 2004.
  



• • Mika S, Rost B
  NLProt: Extracting Protein Names and Sequences from Papers.
  Nucleic Acids Res.. 32(Web Server issue). 2004.
  PMID: 15215466



• • Mika S, Rost B
  Protein Names Precisely Peeled Off Free Text
  ISMB/ECCB Glasgow 2004. 241-247. 2004.
  PMID: 15262805



• • Milward D, Bjareland M, Hayes W, Maxwell M, Oberg L, Tilford N, et al.
  Ontology-Based Interactive Information Extraction from Scientific Abstracts
  ISMB BioLING Text Data Mining SIG, ISMB/ECCB 2004. 2004.
  



• • Mizuta Y, Collier N
  Zone Identification in Biology Articles as a Basis for Information Extraction
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 29-35. 2004.
  



• • Morgan AA, Hirschman L, Colosimo M, Yeh AS, Colombe JB
  Gene name identification and normalization using a model organism database
  Journal of Biomedical Informatics. 37(6):396-410. 2004.
  PMID: 15542014



• • Mukherjea S, Subramaniam LV, Chanda G, Sankararaman S, Kothari R, Batra V, et al.
  Enhancing a Biomedical Information Extraction System with Dictionary Mining and Context Disambiguation
  IBM Journal of Research and Development. 48(5/6). 2004.
  



• • Muller HM, Kenny EE, Sternberg PW
  Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature
  PLoS Biol.. 2(11)E309. 2004.
  PMID: 15383839



• • Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L
  The Compositional Structure of Gene Ontology Terms
  Pacific Symposium on Biocomputing. 9:214-225. 2004.
  



• • Park KM, Kim SH, Lee KJ, Lee DG, Rim HC
  Incorporating Lexical Knowledge into Biomedical NE Recognition
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 76-79. 2004.
  



• • Pyysalo S, Ginter F, Pahikkala T, Boberg J, Jarvinen J, Salakoski T
  Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 15-21. 2004.
  



• • Rebholz-Schuhmann D, Marcel S, Albert S, Tolle R, Casari G, Kirsch H
  Automatic extraction of mutations from Medline and cross-validation with OMIM
  Nucleic Acids Research. 32(1):135-142. 2004.
  PMID: 14704350



• • Rector A
  Defaults, Context, and Knowledge: Alternatives for OWL-Indexed Knowledge Bases
  Pacific Symposium on Biocomputing. 9:226-237. 2004.
  



• • Rinaldi F, Schneider G, Kaljurand K, Dowdall J, Andronis C, Persidis A, et al.
  Mining relations in the GENIA corpus
  Proceedings of the Second European Workshop on Data Mining and Text Mining for Bioinformatics. 61-68. 2004.
  



• • Rossler M
  Adapting an NER-System for German to the Biomedical Domain
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 92-95. 2004.
  



• • Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, et al.
  GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.
  J Biomed Inform. 37(1):43-53. 2004.
  PMID: 15016385



• • Santos C, Eggle D, States D
  WNT Pathway Curation Using Automated Natural Language Processing: Combining Statistical Methods with Partial and Full Parse for Knowledge Extraction
  Bioinformatics. 21(8):1653-1658. 2004.
  PMID: 15564295



• • Saric J, Jensen JL, Ouzounova R, Rojas I, Bork P
  Extraction of Regulatory Gene Expression Networks from PubMed
  ACL 2004 Conference. 192-199. 2004.
  



• • Schuemie MJ, Weeber M, Schijvenaars BJ, van Mulligen EM, van der Eijk CC, Jelier R, et al.
  Distribution of Information in Biomedical Abstracts and Full-text Publications
  Bioinformatics. 20(16):2597-2604. 2004.
  PMID: 15130936



• • Semenova T, Hegland M, Graco W, Williams G
  Conceptual Mining of Large Administrative Health Data
  Lecture Notes in Artificial Intelligence (PAKDD'04). 3056:659-669. 2004.
  



• • Settles B
  Biomedical Named Entity Recognition using Conditional Random Fields and Rich Feature Sets
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 104-107. 2004.
  



• • Smith B, Rosse C
  The Role of Foundational Relations in the Alignment of Biomedical Ontologies
  Medinfo. 11:444-448. 2004.
  PMID: 15360852



• • Song Y, Kim E, Lee GG, Yi B
  POSBIOTM-NER in the Shared Task of BioNLP/NLPBA2004
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 100-103. 2004.
  



• • Spasic I, Ananiadou S
  Using automatically learnt verb selectional preferences for classification of biomedical terms
  Journal of Biomedical Informatics. 37(6):483-497. 2004.
  PMID: 15542021



• • Srinivasan P
  Text Mining: Generating Hypotheses from MEDLINE
  JASIST. 55(5):396-413. 2004.
  



• • Srinivasan P, Libbus B, Sehgal AK
  Mining MEDLINE: Postulating a Beneficial Role for Curcumin Longa in Retinal Diseases
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 33-40. 2004.
  



• • Struble CA, Dharmanolla C
  Clustering MeSH Representations of Biomedical Literature
  HLT-NAACL 2004 Workshop: BioLink 2004, Linking Biological Literature, Ontologies and Databases. 41-48. 2004.
  



• • Tbahriti I, Chichester C, Lisacek F, Ruch P
  Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 8-14. 2004.
  



• • Torii M, Kamboj S, Vijay-Shanker K
  Using name-internal and contextual features to classify biological terms
  Journal of Biomedical Informatics. 37(6):498-511. 2004.
  PMID: 15542022



• • Tsuruoka Y, Tsujii J
  Improving the performance of dictionary-based approaches in protein name recognition
  Journal of Biomedical Informatics. 37(6):461-470. 2004.
  PMID: 15542019



• • Tuason O, Chen L, Liu H, Blake JA, Friedman C
  Biological nomenclatures: a source of lexical knowledge and ambiguity.
  Pac Symp Biocomput. 238-249. 2004.
  PMID: 14992507



• • Uramoto N, Matsuzawa H, Nagano T, Murakami A, Takeuchi H, Takeda K
  A Text-Mining System for Knowledge Discovery from Biomedical Documents
  IBM Systems Journal. 43(3):516-533. 2004.
  



• • Wattarujeekrit T, Shah P, Collier N
  PASBio: predicate-argument structures for event extraction in molecular biology
  BMC Bioinformatics. 5(1):155. 2004.
  PMID: 15494078



• • Wren J
  Extending the mutual information measure to rank inferred literature relationships
  BMC Bioinformatics. 2004.
  PMID: 15471547



• • Wren JD
  The Emerging In-Silico Scientist: How Text-Based Bioinformatics is Bridging Biology and Artificial Intelligence
  IEEE Engineering in Medicine and Biology. 23(2):87-93. 2004.
  



• • Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR
  Knowledge Discovery by Automated Identification and Ranking of Implicit Relationships
  Bioinformatics. 20(3):389-98. 2004.
  



• • Wren JD, Garner HR
  Shared Relationship Analysis: Ranking Set Cohesion and Commonalities within a Literature-Derived Relationship Network
  Bioinformatics. 20(2):191-8. 2004.
  



• • Wu Z, Zhou X, Liu B, Chen J
  Text Mining for Finding Functional Community of Related Genes Using TCM Knowledge
  PKDD-04. LNAI 3202459-470. 2004.
  



• • Yamamoto K, Kudo T, Konagaya A, Matsumoto Y
  Use of morphological analysis in protein name recognition
  Journal of Biomedical Informatics. 37(6):471-482. 2004.
  PMID: 15542020



• • Zhang J, Shen D, Zhou G, Su J, Tan CL
  Enhancing HMM-based biomedical named entity recognition by studying special phenomena
  Journal of Biomedical Informatics. 37(6):411-422. 2004.
  PMID: 15542015



• • Zhang Z
  Weakly-Supervised Relation Classification for Information Extraction
  ACM Thirteenth Conference on Information and Knowledge Management (CIKM). 2004.
  



• • Zhao S
  Named Entity Recognition in Biomedical Texts using an HMM Model
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 84-87. 2004.
  



• • Zhou G, Zhang J, Su J, Shen D, Tan C
  Recognizing names in biomedical texts: a machine learning approach.
  Bioinformatics. 20(7):1178-1190. 2004.
  PMID: 14871877



• • Zhou GD
  Recognizing Names in Biomedical Texts using Hidden Markov Model and SVM plus Sigmoid
  Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA,COLING 2004). 1-7. 2004.
  



• • Albert S, Gaudan S, Knigge H, Raetsch A, Delgado A, Huhse B, et al.
  Computer-Assisted Generation of a Protein-Interaction Database for Nuclear Receptors
  Mol. Endocrinol.. 17(8):1555-1567. 2003.
  PMID: 12738764



• • Becker KG, Hosack DA, Dennis GJ, Lempicki RA, Bright TJ, Cheadle C, et al.
  PubMatrix: A Tool for Multiplex Literature Mining
  BMC Bioinformatics. 4(1):61. 2003.
  PMID: 14667255



• • Bodenreider O, Pakhomov SV
  Exploring Adjectival Modification in Biomedical Discourse Across Two Genres
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 105-112. 2003.
  



• • Brennan PF, Aronson AR
  Towards linking patients and clinical information: detecting UMLS concepts in e-mail.
  J Biomed Inform. 36(4-5):334-41. 2003.
  PMID: 14643729



• • Brown WE, Dolbey EA, Hunter L
  IBM Research and the University of Colorado TREC 2003 Genomics Track.
  Proceedings of the Twelfth Text Retrieval Conference (TREC 2003). 268-275. 2003.
  



• • Chiang JH, Yu HC
  MeKE: Discovering the Functions of Gene Products from Biomedical Literature via Sentence Alignment
  Bioinformatics. 19(11):1417-1422. 2003.
  PMID: 12874055



• • Crasto CJ, Morse TM, Migliore M, Nadkarni P, Hines M, Brash DE, et al.
  Creating Knowledgebases to Text-mine PUBMED Articles Using Clustering Techniques
  Proc. AMIA Symp.. 821. 2003.
  PMID: 14728326



• • Denny JC, Smithers JD, Miller RA, Spickard A
  "Understanding" medical school curriculum content using KnowledgeMap.
  J Am Med Inform Assoc. 10(4):351-62. 2003.
  PMID: 12668688



• • Dobrokhotov PB, Goutte C, Veuthey AL, Gaussier E
  A probabilistic information retrieval approach to medical annotation in SWISS-PROT.
  Stud Health Technol Inform. 95:421-6. 2003.
  PMID: 14664023



• • Dobrokhotov PB, Goutte C, Veuthey AL, Gaussier E
  Combining NLP and probabilistic categorisation for document and term selection for Swiss-Prot medical annotation
  Bioinformatics. 19 Suppl 1:191-194. 2003.
  PMID: 12855443



• • Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, et al.
  PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine.
  BMC Bioinformatics. 4(1):11. 2003.
  PMID: 12689350



• • Duclos-Cartolano C, Venot A
  Building and evaluation of a structured representation of pharmacokinetics information presented in SPCs: from existing conceptual views of pharmacokinetics associated with natural language processing to object-oriented design.
  J Am Med Inform Assoc. 10(3):271-80. 2003.
  PMID: 12626375



• • Erjavec T, Kim JD, Ohta T, Tateisi Y, Tsujii J
  Encoding Biomedical Resources in TEI: The Case of the GENIA Corpus
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 97-104. 2003.
  



• • Fiszman M, Rindflesch TC, Kilicoglu H
  Integrating a hypernymic proposition interpreter into a semantic processor for biomedical texts.
  Proc AMIA Symp. 2003.
  PMID: 14728170



• • Fiszman M, Rindflesch TC, Kilicoglu H
  Interpreting hypernymic propositions in an online medical encyclopedia.
  Proc AMIA Symp. 2003.
  PMID: 14728345



• • Friedman C, Liu H, Shagina L
  A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports.
  J Biomed Inform. 36(3):189-201. 2003.
  PMID: 14615228



• • Gaizauskas R, Demetriou G, Artymiuk PJ, Willett P
  Protein Structures and Information Extraction from Biological Texts: The PASTA System.
  Bioinformatics. 19(1):135-43. 2003.
  PMID: 12499303



• • Glenisson P, Antal P, Mathys J, Moreau Y, De Moor B
  Evaluation of the vector space representation in text-based gene clustering
  Pac Symp Biocomput. 391-402. 2003.
  PMID: 12603044



• • Glenisson P, Mathys J, De Moor B
  Meta-clustering of gene expression data and literature-extracted information
  ACM SIG KDD Explorations, Special Issue on Microarray Data Mining. 5(2). 2003.
  



• • Hanisch D, Fluck J, Mevissen HT, Zimmer R
  Playing biology's name game: identifying protein names in scientific text
  Pac Symp Biocomput. 403-414. 2003.
  PMID: 12603045



• • Happe A, Pouliquen B, Burgun A, Cuggia M, Le Beux P
  Automatic concept extraction from spoken medical reports.
  Int J Med Inf. 70(2-3):255-63. 2003.
  PMID: 12909177



• • Hirschman L, Friedman C, McEntire R, Wu C
  Linking Biological Language, Information and Knowledge
  Pacific Symposium on Biocomputing. 8:388-390. 2003.
  



• • Hou WJ, Chen HH
  Enhancing Performance of Protein Name Recognizers Using Collocation
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 25-32. 2003.
  



• • Huske-Kraus D
  Text generation in clinical medicine--a review.
  Methods Inf Med. 42(1):51-60. 2003.
  PMID: 12695796



• • Jacquemart P, Zweigenbaum P
  Towards a medical question-answering system: a feasibility study.
  Stud Health Technol Inform. 95:463-8. 2003.
  PMID: 14664030



• • Jelier R, Jenster G, Dorssers LC, Van Mulligen EM, Mons B, Kors JA
  Mining Microarray Datasets Aided by Knowledge Stored in Literature
  Proc. AMIA Symp.. 879. 2003.
  PMID: 14728384



• • Jiang G, Ogasawara K, Endoh A, Sakurai T
  Context-based ontology building support in clinical domains using formal concept analysis.
  Int J Med Inf. 71(1):71-81. 2003.
  PMID: 12909160



• • Kim JD, Ohta T, Tateisi Y, Tsujii J
  GENIA corpus-a semantically annotated corpus for bio-textmining.
  Bioinformatics. 19 Suppl 1I180-I182. 2003.
  PMID: 12855455



• • Koike A, Kobayashi Y, Takagi T
  Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource
  Genome Res. 13. 2003.
  PMID: 12799355



• • Kontos J, Malagardi I, Peros J
  The AROMA System for Intelligent Text Mining
  HERMIS International Journal of Computers mathematics and its Applications. 4:163-173. 2003.
  



• • Lee KJ, Hwang YS, Rim HC
  Two-Phase Biomedical NE Recognition based on SVMs
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 33-40. 2003.
  



• • Leroy G, Chen H, Martinez JD
  A shallow parser based on closed-class words to capture relations in biomedical text.
  J Biomed Inform. 36(3):145-58. 2003.
  PMID: 14615225



• • Liu H, Friedman C
  Mining terminological knowledge in large biomedical corpora
  Pac Symp Biocomput. 415-426. 2003.
  PMID: 12603046



• • Majoros WH, Subramanian GM, Yandell MD
  Identification of key concepts in biomedical literature using a modified Markov heuristic
  Bioinformatics. 19(3):402-407. 2003.
  PMID: 12584127



• • Mamlin BW, Heinze DT, McDonald CJ
  Automated Extraction and Normalization of Findings from Cancer-related Free-text Radiology Reports.
  Proc AMIA Symp. 420-4. 2003.
  PMID: 14728207



• • Mendonca EA, Haas J, Shagina L, Larson E, Friedman C
  Extracting Information on Pneumonia in Infants Using Natural Language Processing of Radiology Reports
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 81-88. 2003.
  



• • Meystre S, Haug PJ
  Medical problem and document model for natural language understanding.
  Proc AMIA Symp. 2003.
  PMID: 14728214



• • Mollah SA, Johnson SB
  Automatic learning of the morphology of medical language using information compression.
  Proc AMIA Symp. 2003.
  PMID: 14728443



• • Morgan A, Hirschman L, Yeh A, Colosimo M
  Gene Name Extraction Using FlyBase Resources
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 1-8. 2003.
  



• • Murff HJ, Forster AJ, Peterson JF, Fiskio JM, Heiman HL, Bates DW
  Electronically screening discharge summaries for adverse medical events.
  J Am Med Inform Assoc. 10(4):339-50. 2003.
  PMID: 12668691



• • Narayanaswamy M, Ravikumar KE, Vijay-Shanker K
  A biological named entity recognizer
  Pac Symp Biocomput. 427-438. 2003.
  PMID: 12603047



• • Nenadic G, Spasic I, Ananiadou S
  Terminology-driven mining of biomedical literature
  Bioinformatics. 19(8):938-943. 2003.
  PMID: 12761055



• • Nenadic G, Rice S, Spasic I, Ananiadou S, Stapley B
  Selecting Text Features for Gene Name Classification: from Documents to Terms
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 121-128. 2003.
  



• • Niu Y, Hirst G, McArthur G, Rodriguez-Gianolli P
  Answering Clinical Questions with Role Identification
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 73-80. 2003.
  



• • Novichkova S, Egorov S, Daraselia N
  MedScan, a natural language processing engine for MEDLINE abstracts.
  Bioinformatics. 19(13):1699-706. 2003.
  PMID: 12967967



• • Pakhomov SV, Buntrock J, Chute CG
  Identification of Patients with Congestive Heart Failure using a Binary Classifier: A Case Study.
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 89-96. 2003.
  



• • Pratt W, Yetisgen-Yildiz M
  LitLinker: Capturing Connections across the Biomedical Literature
  Proceedings of the 2nd International Conference on Knowledge Capture (KCap03). 105-112. 2003.
  



• • Raychaudhuri S, Altman R
  A Literature-Based Method for Assessing the Functional Coherence of a Gene Group
  Bioinformatics. 19(3):396-401. 2003.
  PMID: 12584126



• • Raychaudhuri S, Schütze H, Altman BR
  Inclusion of Textual Documentation in the Analysis of Multidimensional Data Sets: Application to Gene Expression Data
  Machine Learning. 52:119-145. 2003.
  



• • Rindflesch TC, Fiszman M
  The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text.
  J Biomed Inform. 36(6):462-77. 2003.
  PMID: 14759819



• • Ruch P, Baud R, Geissbuhler A
  Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record.
  Artif Intell Med. 29(1-2):169-84. 2003.
  PMID: 12957786



• • Samsonova M, Pisarev A, Blagov M
  Processing of natural language queries to a relational database.
  Bioinformatics. 19 Suppl 1i241-9. 2003.
  PMID: 12855465



• • Sarkar IN, Cantor MN, Gelman R, Hartel F, Lussier YA
  Linking biomedical language information and knowledge resources: GO and UMLS
  Pac Symp Biocomput. 439-450. 2003.
  PMID: 12603048



• • Schwartz AS, Hearst MA
  A simple algorithm for identifying abbreviation definitions in biomedical text
  Pac Symp Biocomput. 451-462. 2003.
  PMID: 12603049



• • Shah PK, Perez-Iratxeta C, Bork P, Andrade MA
  Information extraction from full text scientific articles: Where are the keywords?
  BMC Bioinformatics. 4(1):20. 2003.
  PMID: 12775220



• • Shatkay H, Feldman R
  Mining the biomedical literature in the genomic era: an overview.
  J Comput Biol. 10(6):821-855. 2003.
  PMID: 14980013



• • Shen D, Zhang J, Zhou G, Su J, Tan CL
  Effective Adaptation of Hidden Markov Model-based Named Entity Recognizer for Biomedical Domain
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 49-56. 2003.
  



• • Singh SB, Hull RD, Fluder EM
  Text Influenced Molecular Indexing (TIMI): a literature database mining approach that handles text and chemistry.
  J Chem Inf Comput Sci. 43(3):743-52. 2003.
  PMID: 12767132



• • Spasic I, Nenadic G, Ananiadou S
  Using Domain-Specific Verbs for Term Classification
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 17-24. 2003.
  



• • Subramaniam LV, Mukherjea S, Kankar P, Srivastava B, Batra VS, Kamesam PV, et al.
  Information Extraction from Biomedical Literature: Methodology, Evaluation and an Application
  ACM Thirteenth Conference on Information and Knowledge Management (CIKM. 2003.
  



• • Takeuchi K, Collier N
  Bio-Medical Entity Extraction using Support Vector Machines
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 57-64. 2003.
  



• • Temkin JM, Gilder MR
  Extraction of protein interaction information from unstructured text using a context-free grammar.
  Bioinformatics. 19(16):2046-53. 2003.
  PMID: 14594709



• • Torii M, Kamboj S, Vijay-Shanker K
  An Investigation of Various Information Sources for Classifying Biological names
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 113-120. 2003.
  



• • Tsuruoka Y, Tsujii J
  Boosting Precision and Recall of Dictionary-Based Protein Name Recognition
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 41-48. 2003.
  



• • Tsuruoka Y, Tsujii J
  Probabilistic Term Variant Generator for Biomedical Terms
  Proc. of the 26th Annual International ACM SIGIR Conference. 167-173. 2003.
  



• • Tsuruoka Y, Tsujii J
  Probabilistic Term Variant Generator for Biomedical Terms
  Proc. of the 26th Annual International ACM SIGIR Conference. 167-173. 2003.
  



• • Widdows D, Peters S, Cederberg S, Chan CK, Steffen D, Buitelaar P
  Unsupervised Monolingual and Bilingual Word-Sense Disambiguation of Medical Documents using UMLS
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 9-16. 2003.
  



• • Wilcox AB, Hripcsak G
  The role of domain knowledge in automating medical text report classification.
  J Am Med Inform Assoc. 10(4):330-8. 2003.
  PMID: 12668687



• • Wren JD
  The IRIDESCENT System: An Automated Data-Mining Method to Identify, Evaluate, and Analyze Sets of Relationships Within Textual Databases
  Ph.D. Dissertation, University of Texas Southwestern Medical Center. 2003.
  



• • Yamamoto K, Kudo T, Konagaya A, Matsumoto Y
  Protein Name Tagging for Biomedical Annotation in Text
  Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine. 65-72. 2003.
  



• • Yeh AS, Hirschman L, Morgan AA
  Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.
  Bioinformatics. 19 Suppl 1i331-9. 2003.
  PMID: 12855478



• • Yu H, Agichtein E
  Extracting synonymous gene and protein terms from biological literature.
  Bioinformatics. 19 Suppl 1i340-9. 2003.
  PMID: 12855479



• • Zou Q, Chu WW, Morioka C, Leazer GH, Kangarloo H
  IndexFinder: A Method of Extracting Key Concepts from Clinical Texts for Indexing.
  Proc AMIA Symp. 763-767. 2003.
  PMID: 14728276



• • Adamic AL, Wilkinson D, Huberman AB, Adar E
  A Literature Based Method for Identifying Gene-Disease Connections
  Proceedings of the IEEE Comput Soc Bioinform Conf (CSB), 2002. 1:109-117. 2002.
  PMID: 15838128



• • Baud R, Ruch P
  The future of natural language processing for biomedical applications.
  Int J Med Inf. 67(1-3):1-5. 2002.
  PMID: 12460627



• • Benedetto D, Caglioti E, Loreto V
  Language trees and zipping.
  Phys Rev Lett. 88(4):048702. 2002.
  PMID: 11801178



• • Berrios DC, Cucina RJ, Fagan LM
  Methods for semi-automated indexing for high precision information retrieval.
  J Am Med Inform Assoc. 9(6):637-52. 2002.
  PMID: 12386114



• • Blagosklonny MV, Pardee AB
  Conceptual biology: Unearthing the gems
  Nature. 416(6879):373. 2002.
  PMID: 11919607



• • Blaschke C, Hirschman L, Valencia A
  Information extraction in molecular biology.
  Brief Bioinform. 3(2):154-65. 2002.
  PMID: 12139435



• • Bodenreider O, Burgun A, Rindflesch TC
  Assessing the consistency of a biomedical terminology through lexical knowledge.
  Int J Med Inf. 67(1-3):85-95. 2002.
  PMID: 12460634



• • Bodenreider O, Rindflesch T, Burgun A
  Unsupervised, corpus-based method for extending a biomedical terminology
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 53-59. 2002.
  



• • Burgun A, Bodenreider O, Le DF, Moussouni F, Loreal O
  Representation of Roles in Biomedical Ontologies: A Case Study in Functional Genomics
  Proc. of the AMIA Symp. 2002. 86-90. 2002.
  



• • Campbell D, Johnson S
  A transformational-based learner for dependency grammars in discharge summaries
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 37-44. 2002.
  



• • Chang JT, Altman RB
  Promises of text processing: natural language processing meets AI
  Drug Discov Today. 7(19):992-993. 2002.
  PMID: 12546913



• • Chang JT, Schutze H, Altman RB
  Creating an online dictionary of abbreviations from MEDLINE
  J Am Med Inform Assoc. 9(6):612-620. 2002.
  PMID: 12386112



• • Chaussabel D, Sher A
  Mining microarray expression data by literature profiling.
  Genome Biol. 3(10):55. 2002.
  PMID: 12372143



• • Chiao YC, Zweigenbaum P
  Looking for French-English translations in comparable medical corpora.
  Proc AMIA Symp. 2002.
  PMID: 12463805



• • Christensen LM, Haug PJ, Fiszman M
  MPLUS: a probabilistic medical language understanding system
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 29-36. 2002.
  



• • Chuang JH, Friedman C, Hripcsak G
  A comparison of the Charlson comorbidities derived from medical language processing and administrative data.
  Proc AMIA Symp. 2002.
  PMID: 12463807



• • Chute CG
  The horizontal and vertical nature of patient phenotype retrieval: new directions for clinical text processing.
  Proc AMIA Symp. 2002.
  PMID: 12463808



• • Cohen KB, Dolbey AE, Acquaah-Mensah GK, Hunter L
  Contrast and variability in gene names
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 14-20. 2002.
  



• • de Bruijn B, Martin J
  Getting to the (c)ore of knowledge: mining biomedical literature.
  Int J Med Inf. 67(1-3):7-18. 2002.
  PMID: 12460628



• • Demetriou G, Gaizauskas. R
  Utilizing text mining results: The Pasta Web System
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 77-84. 2002.
  



• • Ding J, Berleant D, Nettleton D, Wurtele E
  Mining MEDLINE: abstracts, sentences, or phrases?
  Pac Symp Biocomput. 326-337. 2002.
  PMID: 11928487



• • Franzen K, Eriksson G, Olsson F, Asker L, Liden P, Coster J
  Protein names and how to find them
  Int J Med Inf. 67(1-3):49-61. 2002.
  PMID: 12460631



• • Friedman C, Kra P, Rzhetsky A
  Two biomedical sublanguages: a description based on the theories of Zellig Harris.
  J Biomed Inform. 35(4):222-35. 2002.
  PMID: 12755517



• • Ghanem MM, Guo Y, Lodhi H, Zhang Y
  Automatic Scientific Text Classification Using Local Patterns: KDD CUP 2002 (Task 1)
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:95-96. 2002.
  



• • Hahn U, Romacker M, Schulz S
  MEDSYNDIKATE-a natural language system for the extraction of medical information from findings reports.
  Int J Med Inf. 67(1-3):63-74. 2002.
  PMID: 12460632



• • Hahn U, Romacker M, Schultz S
  Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining System
  In Proceedings of the Pacific Symposium on Biocomputing. 338-349. 2002.
  PMID: 11928488



• • Hatzivassiloglou V, Weng W
  Learning anchor verbs for biological interaction patterns from published text articles.
  Int J Med Inf. 67(1-3):19-32. 2002.
  PMID: 12460629



• • Hirschman L, Morgan AA, Yeh AS
  Rutabaga by any other name: extracting biological names
  J Biomed Inform. 35(4):247-59. 2002.
  PMID: 12755519



• • Hirschman L, Park JC, Tsujii J, Wong L, Wu CH
  Accomplishments and challenges in literature data mining for biology
  Bioinformatics. 18(12):1553-1561. 2002.
  PMID: 12490438



• • Hobbs JR
  Information extraction from biomedical text.
  J Biomed Inform. 35(4):260-4. 2002.
  PMID: 12755520



• • Hripcsak G, Austin JH, Alderson PO, Friedman C
  Use of natural language processing to translate clinical information from a database of 889,921 chest radiographic reports.
  Radiology. 224(1):157-63. 2002.
  PMID: 12091676



• • Hunter L
  Ontologies for Programs, Not People
  Genome Biology. 3(6):1002.1-1002.2. 2002.
  PMID: 12093368



• • Karanikas H, Theodoulidis B
  Knowledge Discovery in Text and Text Mining Software
  Publication of CRIM. 2002.
  



• • Kazama J, Makino T, Ohta Y, Tsujii J
  Tuning support vector machines for biomedical named entity recognition
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 2002.
  



• • Keerthi SS, Ong CJ, Siah KB, Lim DBL, Chu W, Shi M, et al.
  A Machine Learning Approach for the Curation of Biomedical Literature - KDD Cup 2002 (Task 1)
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:93-94. 2002.
  



• • Kontos J, Elmaoglou A, Malagardi I
  ARISTA Causal Knowledge Discovery from Texts
  Proceedings of the 5th International Conference DS 2002. Luebeck, Germany, November 2002, Springer Verlag. 348-355. 2002.
  



• • Kontos J, Malagardi I, Peros J, Elmaoglou A
  System Modeling by Computer using Biomedical Texts
  Res Systemica. 2:1-8. 2002.
  



• • Kowalczyk A, Raskutti B
  One Class SVM for Yeast Regulation Prediction
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:99-100. 2002.
  



• • Krauthammer M, Johnson SB, Hripcsak G, Campbell DA, Friedman C
  Representing nested semantic information in a linear string of text using XML
  Proc AMIA Symp. 405-409. 2002.
  PMID: 12463856



• • Krauthammer M, Kra P, Iossifov I, Gomez SM, Hripcsak G, Hatzivassiloglou V, et al.
  Of truth and pathways: chasing bits of information through myriads of articles.
  Bioinformatics. 18 Suppl 1S249-57. 2002.
  PMID: 12169554



• • Krogel MA, Denecke M, Landwehr M, Scheffer T
  Combining Data and Text Mining Techniques for Yeast Gene Regulation Prediction: A Case Study
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:104-105. 2002.
  



• • Le Moigno S, Charlet J, Bourigault D, Degoulet P, Jaulent MC
  Terminology extraction from text to build an ontology in surgical intensive care.
  Proc AMIA Symp. 430-4. 2002.
  PMID: 12463860



• • Leroy G, Chen H
  Filling preposition-based templates to capture information from medical abstracts
  Pac Symp Biocomput. 350-361. 2002.
  PMID: 11928489



• • Libbus B, Rindflesch TC
  NLP-based information extraction for managing the molecular biology literature.
  Proc AMIA Symp. 2002.
  PMID: 12463863



• • Liu H, Aronson AR, Friedman C
  A study of abbreviations in MEDLINE abstracts
  Proc AMIA Symp. 464-468. 2002.
  PMID: 12463867



• • Liu H, Johnson SB, Friedman C
  Automatic resolution of ambiguous terms based on machine learning and conceptual relations in the UMLS
  J Am Med Inform Assoc. 9(6):621-636. 2002.
  PMID: 12386113



• • Mack R, Hehenberger M
  Text-based knowledge discovery: search and mining of life-sciences documents.
  Drug Discov Today. 7(11)S89. 2002.
  PMID: 12047886



• • Mao W, Chu WW
  Free-text medical document retrieval via phrase-based vector space model.
  Proc AMIA Symp. 489-93. 2002.
  PMID: 12463872



• • McCray AT, Browne AC, Bodenreider O
  The lexical properties of the gene ontology.
  Proc AMIA Symp. 2002.
  PMID: 12463875



• • Mendonca EA, Johnson SB, Seol YH, Cimino JJ
  Analyzing the Semantics of patient data to rank records of literature retrieval
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 69-76. 2002.
  



• • Morioka CA, Sinha U, Taira R, el-Saden S, Duckwiler G, Kangarloo H
  Structured reporting in neuroradiology.
  Ann N Y Acad Sci. 980:259-66. 2002.
  PMID: 12594095



• • Nair R, Rost B
  Inferring sub-cellular localization through automated lexical analysis
  Bioinformatics. 18. 2002.
  PMID: 12169534



• • Nenadic G, Mima H, Spasic I I, Ananiadou S, Tsujii J
  Terminology-driven literature mining and knowledge acquisition in biomedicine
  Int J Med Inf. 67(1-3):33-48. 2002.
  PMID: 12460630



• • Nenadic G, Spasic I, Ananiadou S
  Automatic acronym acquisition and management with domain specific texts
  Proceedings of LREC-3, 3rd International Conference on Language, Resources and Evaluation. 2155-2162. 2002.
  



• • Nenadic G, Spasic I, Ananiadou S
  Automatic discovery of term similarities using pattern mining
  Proceedings of International workshop of Computational Terminology, CompuTerm, Coling. 43-49. 2002.
  



• • Ohta T, Tateisi Y, Mima H, Tsujii J
  The GENIA Corpus: an Annotated Research Abstract Corpus in Molecular Biology Domain
  Proceedings of the Human Language Technology Conference. 2002.
  



• • Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB
  Ontology development for a pharmacogenetics knowledge base.
  Pac Symp Biocomput. 2002.
  PMID: 11928517



• • Pustejovsky J, Castano J, Zhang J, Kotecki M, Cochran B
  Robust relational parsing over biomedical literature: extracting inhibit relations
  Pac Symp Biocomput. 362-373. 2002.
  PMID: 11928490



• • Pustejovsky J, Castano J, Zhang J, Sauri R, Luo W
  Medstract: creating large-scale information servers from biomedical texts
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 85-92. 2002.
  



• • Raychaudhuri S, Chang JT, Sutphin PD, Altman RB
  Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature
  Genome Res. 12(1):203-214. 2002.
  PMID: 11779846



• • Raychaudhuri S, Schutze H, Altman RB
  Using text analysis to identify functionally coherent gene groups.
  Genome Res. 12(10):1582-90. 2002.
  PMID: 12368251



• • Regev Y, Finkelstein-Landau M, Feldman R, Gorodetsky M, Zheng X, Levy S, et al.
  Rule-based Extraction of Experimental Evidence in the Biomedical Domain - the KDD Cup (Task 1)
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:90-92. 2002.
  



• • Ruch P, Baud R, Geissbuhler A
  Evaluating and reducing the effect of data corruption when applying bag of words approaches to medical records.
  Int J Med Inf. 67(1-3):75-83. 2002.
  PMID: 12460633



• • Sarkar IN, Rindflesch TC
  Discovering protein similarity using natural language processing.
  Proc AMIA Symp. 2002.
  PMID: 12463910



• • Schultz S, Honeck M, Hahn U
  Biomedical text retrieval in languages with a complex morphology
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 61-68. 2002.
  



• • Sebastiani F
  Machine Learning in Automated Text Categorization
  ACM Computing Surveys. 34(1):1-47. 2002.
  



• • Shatkay H, Edward S, Boguski M
  Information Retrieval Meets Gene Analysis
  IEEE Intelligent Systems, Special Issue on Intelligent Systems in Biology. 17(2):45-53. 2002.
  



• • Sinclair G, Webber B, Davidson D
  Enhanced natural language access to anatomically-indexed data
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 45-52. 2002.
  



• • Stapley BJ, Kelley LA, Sternberg MJ
  Predicting the sub-cellular location of proteins from text using support vector machines
  Pac Symp Biocomput. 374-385. 2002.
  PMID: 11928491



• • Stetson PD, Johnson SB, Scotch M, Hripcsak G
  The sublanguage of cross-coverage.
  Proc AMIA Symp. 2002.
  PMID: 12463923



• • Tamames J, Clark D, Herrero J, Dopazo J, Blaschke C, Fernandez JM, et al.
  Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction.
  J Biotechnol. 98(2-3):269-83. 2002.
  PMID: 12141992



• • Tanabe L, Wilbur WJ
  Tagging gene and protein names in biomedical text.
  Bioinformatics. 18(8):1124-32. 2002.
  PMID: 12176836



• • Tanabe L, Wilbur WJ
  Tagging gene and protein names in full text articles
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 9-13. 2002.
  



• • Thomas SM, Mamlin B, Schadow G, McDonald C
  A successful technique for removing names in pathology reports using an augmented search and replace method.
  Proc AMIA Symp. 2002.
  PMID: 12463930



• • Vogel DS, Axelrod RC
  Predicting the Effects of Gene Deletion
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:101-103. 2002.
  



• • Volk M, Ripplinger B, Vintar S, Buitelaar P, Raileanu D, Sacaleanu B
  Semantic annotation for concept-based cross-language medical information retrieval.
  Int J Med Inf. 67(1-3):97-112. 2002.
  PMID: 12460635



• • Wilbur WJ
  A thematic analysis of the AIDS literature
  Pac Symp Biocomput. 386-397. 2002.
  PMID: 11928492



• • Wilcox AB, Narus SP, Bowes WA
  Using natural language processing to analyze physician modifications to data entry templates.
  Proc AMIA Symp. 2002.
  PMID: 12463955



• • Wren JD, Gamer HR
  Heuristics for Identification of Acronym-Definition Patterns Within Text: Towards an Automated Construction of Comprehensive Acronym-Definition Dictionaries
  Methods of Information in Medicine. 41(5):426-34. 2002.
  



• • Yandell MD, Majoros WH
  Genomics and natural language processing
  Nat Rev Genet. 3(8):601-610. 2002.
  PMID: 12154383



• • Yeh A, Hirschman L, Morgan A
  Background and Overview for KDD Cup 2002 Task 1: Information Extraction from Biomedical Articles
  SIGKDD Explorations: Newsletter of the ACM Special Interest Group on Knowledge Discovery and Data Mining. 4:87-89. 2002.
  



• • Yu H, Hatzivassiloglou V, Friedman C, Rzhetsky A, Wilbur WJ
  Automatic extraction of gene and protein synonyms from MEDLINE and journal articles
  Proc AMIA Symp. 919-923. 2002.
  PMID: 12463959



• • Yu H, Hripcsak G, Friedman C
  Mapping Abbreviations to Full Forms in Biomedical Articles
  Journal of the American Medical Informatics Association. 9:262-272. 2002.
  PMID: 11971887



• • Zweigenbaum P, Grabar N
  Restoring accents in unknown biomedical words: application to the French MeSH thesaurus.
  Int J Med Inf. 67(1-3):113-26. 2002.
  PMID: 12460636



• • Zweigenbaum P, Grabar N
  Accenting unknown words in a specialized language
  Proceedings of the ACL Workshop on Natural Language Processing in the Biomedical Domain. 2002.
  



• • Aronson AR
  Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.
  Proc AMIA Symp. 2001.
  PMID: 11825149



• • Baud RH, Lovis C, Ruch P, Rassinoux AM
  A light knowledge model for linguistic applications.
  Proc AMIA Symp. 2001.
  PMID: 11833480



• • Blaschke C, Oliveros JC, Valencia A
  Mining functional information associated with expression array
  Funct. Integrative Genomics. 1(4):256-268. 2001.
  PMID: 11793245



• • Blaschke C, Valencia A
  The potential use of SUISEKI as a protein interaction discovery tool.
  Genome Inform Ser Workshop Genome Inform. 12:123-34. 2001.
  PMID: 11791231



• • Boyer C, Baujard V, Scherrer JR
  HONselect: multilingual assistant search engine operated by a concept-based interface system to decentralized heterogeneous sources.
  Medinfo. 10(Pt 1):309-13. 2001.
  PMID: 11604753



• • Campbell DA, Johnson SB
  Comparing Syntactic Complexity in Medical and non-Medical Corpora.
  Proc AMIA Symp. 2001.
  PMID: 11825160



• • Chang JT, Raychaudhuri S, Altman RB
  Including Biological Literature Improves Homology Search
  In Proceedings of the Pacific Symposium on Biocomputing. (1)374-383. 2001.
  PMID: 11262956



• • Chapman WW, Fizman M, Chapman BE, Haug PJ
  A comparison of classification algorithms to automatically identify chest X-ray reports that support pneumonia.
  J Biomed Inform. 34(1):4-14. 2001.
  PMID: 11376542



• • Chu S, Cesnik B
  Knowledge representation and retrieval using conceptual graphs and free text document self-organisation techniques.
  Int J Med Inf. 62(2-3):121-33. 2001.
  PMID: 11470615



• • Friedman C, Friedman C, Liu H, Shagina L, Johnson S, Hripcsak G
  Evaluating the UMLS as a source of lexical knowledge for medical language processing.
  Proc AMIA Symp. 2001.
  PMID: 11825178



• • Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A
  GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.
  Bioinformatics. 17 Suppl 1S74-S82. 2001.
  PMID: 11472995



• • Hahn U, Honeck M, Piotrowski M, Schulz S
  Subword segmentation--leveling out morphological variations for medical document retrieval.
  Proc AMIA Symp. 229-33. 2001.
  PMID: 11825186



• • Hasman A, de Bruijn LM, Arends JW
  Evaluation of a method that supports pathology report coding.
  Methods Inf Med. 40(4):293-7. 2001.
  PMID: 11552341



• • Hatzivassiloglou V, Duboue PA, Rzhetsky A
  Disambiguating proteins, genes, and RNA in text: a machine learning approach.
  Bioinformatics. 17 Suppl 1S97-S106. 2001.
  PMID: 11472998



• • Heinze DT, Heinze DT, Morsch ML, Morsch ML
  Mining free-text medical records.
  Proc AMIA Symp. 2001.
  PMID: 11825190



• • Iliopoulos I, Enright AJ, Ouzounis CA
  Textquest: document clustering of Medline abstracts for concept discovery in molecular biology
  Pac Symp Biocomput. 384-395. 2001.
  PMID: 11262957



• • Jenssen TK, Laegreid A, Komorowski J, Hovig E
  A literature network of human genes for high-throughput analysis of gene expression
  Nature Genetics. 28(1):21-28. 2001.
  PMID: 11326270



• • Jordan DA, McKeown KR, Concepcion KJ, Feiner SK, Hatzivassiloglou V
  Generation and evaluation of intraoperative inferences for automated health care briefings on patient status after bypass surgery.
  J Am Med Inform Assoc. 8(3):267-80. 2001.
  PMID: 11320071



• • Kim W, Aronson AR, Wilbur WJ
  Automatic MeSH term assignment and quality assessment.
  Proc AMIA Symp. 2001.
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• • Krauthammer M, Hripcsak G
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