Publications in Peer Reviewed Journals (Conferences; Other Venues)

• A. Wong and H. Shatkay. Protein Function Prediction using Text-based Features extracted from Biomedical Literature: The CAFA Challenge.
  BMC Bioinformatics 14(S3), S14. 2013.
  Selected for a highlight presentation at the ACM BCB 2012 Conference.

• P. Radivojac, W.T. Clark, T.R. Oron, et al. A Large-Scale Evaluation of Computational of Protein Function Prediction
  Nature Methods 10, 221-227. 2013.
  Selected for a highlight presentation at the ACM BCB 2012 Conference.

• A. Lourenco, M. Conover, A. Nematzadeh, F. Pan, A. Wong, H. Shatkay and L.M. Rocha. A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature.
  BMC Bioinformatics , 12(S8). 2011. S12.

• M. Krallinger , M. Vazquez, F. Leitner, D. Salgado, A. Chatr-aryamontri, A. Winter, L. Perfetto, L. Briganti, L. Licata, M. Iannuccelli, L. Castagnoli, G. Cesareni, M. Tyers, G. Schneider, F. Rinaldi, R. Leaman, G. Gonzalez, S. Matos, S. Kim, W.J. Wilbur, L. Rocha, H. Shatkay, A.V. Tendulkar, S. Agarwal, F. Liu, X. Wang, R. Rak, K. Noto, C. Elkan, Z. Lu, R. Islamaj Dogan, J.F. Fontaine, M.A. Andrade-Navarro and A. Valencia. The Protein-Protein Interaction tasks of BioCreative III: Classification/Ranking of Articles and Linking Bio-Ontology Concepts to Full Text.
  BMC Bioinformatics, 12(S8). 2011. S12.

• P. H. Lee and H. Shatkay. An Integrative Scoring System for Ranking SNPs by their Potential Deleterious Effects.
  Bioinformatics. 25(8). 2009. (pp. 1048-1055).

• A. Rzhetsky, H. Shatkay and W.J. Wilbur. How to Get the Most out of Your Curation Effort.
  PLoS Computational Biology. 5(5). 2009.

• S. Briesmeister, T. Blum, S. Brady, Y. Lam, O. Kohlbacher and H. Shatkay. SherLoc2: A High-Accuracy Hybrid Method for Predicting Subcellular Localization of Proteins.
  Journal of Proteome Research. 8(11), 2009. (pp. 5363-5366)

• P. H. Lee and H. Shatkay. F-SNP: Computationally Predicted Functional SNPs for Disease Association Studies.
  Nucleic Acids Research. 36, Database Issue, 2008. (pp. D820-D824)

• H. Shatkay, F. Pan, A. Rzhetsky and W.J. Wilbur. Multi-Dimensional Classification of Biomedical Text: Toward Automated, Practical Provision of High-Utility Text to Diverse Users.
  Bioinformatics. 24(18). 2008. (pp. 2086-2093).
  Selected for PLoS Highlight presentation at ISMB'09.

• R. Altman, C.M. Bergman,J. Blake, C. Blaschke, A. Cohen, F. Gannon, L. Grivell, U. Hahn, W. Hersh, L. Hirschman, L.J. Jensen, M. Krallinger, B. Mons, S. I. O'Donoghu, M.C. Peitsch, D. Rebholz-Schuhmann, H. Shatkay and A. Valencia. Text Mining for Biology - The Way Forward: Opinions from Leading Scientists.
  Genome Biology. 9(S2). 2008. S7.

• H. Shatkay, A. Höglund, S. Brady, T. Blum, P. Dönnes and O. Kohlbacher.
  SherLoc : High-Accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data.
  Bioinformatics. 23(11). March, 2007. (pp. 1410-1417).
  Selected for PLoS Highlight presentation at ISMB'08.

• P. H. Lee and H. Shatkay.
  BNTagger: Improved Tagging SNP Selection using Bayesian Networks.
  Bioinformatics. 22(11). Special issue: Proc. of the Int. Conf. on Intelligent Systems for Molecular Biology (ISMB'06). August, 2006. (pp. e211-e219)

• H. Shatkay, N. Chen and D. Blostein.
  Integrating Image Data into Biomedical Text Categorization.
  Bioinformatics. 22(11). Special issue: Proc. of the Int. Conf. on Intelligent Systems for Molecular Biology (ISMB'06). August, 2006. (pp. e446-e453).

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

• M. Yousef, M. Nebozhyn, H. Shatkay , S. Kanterakis, L.C. Showe, M.K. Showe.
  Combining Multi-Species Genomic Data for MicroRNA Identification Using a Naive Bayes Classifier. Bioinformatics. 22(11). March, 2006. (pp. 1325-1334)

• M. Chagoyen, P. Carmona-Saez, H. Shatkay , J.M. Carazo, A. Pascual-Montano.
  Discovering Semantic Features in the Literature: A Foundation for Building Functional Associations. BMC Bioinformatics. 7:41. January, 2006.

• H. Shatkay.
  Hairpins in Bookstacks: Information Retrieval from Biomedical Text. Briefings in Bioinformatics, V.6, #3, (pp. 222-238), September, 2005.

• H. Shatkay, J. Miller, C. Mobarry, M. Flanigan, S. Yooseph and G. Sutton.
  ThurGood: Evaluating Assembly-to-Assembly Mapping, Journal of Computational Biology (JCB), V.11, #5, (pp. 800-811), October, 2004.

• S. Istrail, G.G. Sutton, L. Florea, A.L. Halpern, C.M. Mobarry, R. Lippert, B. Walenz, H. Shatkay, I. Dew, J.R. Miller, M.J. Flanigan, N.J. Edwards, R. Bolanos, D. Fasulo, B.V. Halldorsson, S. Hannenhalli, R. Turner, S. Yooseph, F. Lu, D.R. Nusskern, B.C. Shue, X.H. Zheng, F. Zhong, A.L. Delcher, D.H. Huson, S.A. Kravitz, L. Mouchard, K. Reinert, K.A. Remington, A.G. Clark, M.S. Waterman, E.E. Eichler, M.D. Adams, M.W. Hunkapiller, E.W. Myers, and J.C. Venter.
  Whole-Genome Shotgun Assembly and Comparison of Human Genome Assemblies, PNAS, V.101, #7, (pp. 1916-1921), February, 2004.

• H. Shatkay and R. Feldman.
  Mining the Biomedical Literature in the Genomic Era: An Overview, Journal of Computational Biology (JCB), V.10, #6, (pp. 821-856), December, 2003.

• Y. Regev, Michal Finkelstein-Landau, Ronen Feldman, Maya Gorodetsky, Xin Zheng, Samuel Levy, Rosane Charlab, Charles Lawrence, Ross A. Lippert, Qing Zhang and Hagit Shatkay.
  Rule-Based Extraction of Experimental Evidence in the Biomedical Domain - the KDD Cup (Task 1). Invited report from KDD-2002. SIGKDD Explorations, V.4, #2, (pp. 90-91), December 2002.

• H. Shatkay, S. Edwards and M. Boguski,
  Information Retrieval Meets Gene Analysis; IEEE Intelligent Systems, Special Issue on Intelligent Systems in Biology, V.17, #2,(pp. 45-53), April-May 2002. A slightly modified version, Compressed Postscript, PDF.

• H. Shatkay and L.P. Kaelbling,
  Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Geometrical-Topological Gap, Journal of AI Research (JAIR), (pp. 167-207), April, 2002. PDF.

Publications in Peer Reviewed Conferences (Journals; Other Venues)

• H. Shatkay, R. Narayanaswamy, S. Nagaral, N. Harrington, R. Mv, G. Somanath, R. Tarpine, K. Schutter, T. Johnstone, D. Blostein, S. Istrail and C. Kambhamettu.
  OCR-based Image Features for Biomedical Image and Article Classification: Identifying Documents relevant to Cis-Regulatory Elements. Proc. of the ACM Conf. on Bioinformatics and Computional Biology (BCB). October, 2012.

• X. Bi, H. Huang, S. Matis-Mitchell, P. McGarvey, M. Torii, H. Shatkay and C. Wu.
  Building a Classifier for Identifying Sentences Pertaining to Disease-Drug Relationships in Tardive Dyskinesia.
  Proc. of the IEEE Int. Conf. on Bioinformatics and Biomedicine (BIBM). November, 2012.

• L.D. Lopez, J. Yu, C.N. Arighi, H. Huang, H. Shatkay and C. Wu.
  A System for Extracting Figures and Captions from Biomedical PDF Documents.
  Proc. of the IEEE Int. Conf. on Bioinformatics and Biomedicine (BIBM). November, 2011.

• A. Lorenco, M. Conover, A. Wong, F. Pan , A. Abi-Haidar, A. Nematzadeh, H. Shatkay and L.M. Rocha.
  Testing Extensive Use of NER Tools in Article Classifica- tion and a Statistical Approach for Method Interaction Extraction in the Protein-Protein Interaction Literature.
  Proc. of the BioCreative III workshop on Critical Evaluation of Information Extraction in Biology. September, 2010.

• R. Denroche, R. Madupu, S. Yooseph, G. Sutton and H. Shatkay.
  Toward Computer-Assisted Text Curation : Classification is Easy (Choosing Training Data can be Hard.)
  Proc. of the Workshop on Linking Literature, Information and Knowledge in Biology (BioLINK). Lecture Notes in Bioinformatics, 6004, Springer. 2010.

• C. Blaschke, L. Hirschman, H. Shatkay and A. Valencia.
  Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology.
  Proc. of the Workshop on Linking Literature, Information and Knowledge in Bi- ology (BioLINK). Lecture Notes in Bioinformatics, 6004, Springer. 2010.

• S. Kanagalingam, A. Pinheiro, H. Shatkay, Q.A. Rahman, V.L. Dimaano, M.S. Tomas, R. Thompson, J. Crosson, R. George, M. Corretti, J. Brenner and T. Abraham.
  Efficacy of the American Heart Association Questionnaire in Identifying Electrocardiographic and Echocardiographic Abnormalities in Young Athletes During Community-based Screening.
  Proc. of the Conf. of the American Heart Association. November, 2010.
  Selected for oral presentation at the AHA Conference.

• P. H. Lee and H. Shatkay.
  Ranking Single Nucleotide Polymorphisms by Potential Deleterious Effects.
  Proc. of the Annual Symp. of the American Medical Informatics Association (AMIA'08). November, 2008.

• S. Brady and H. Shatkay.
  EPILOC: A (Working) Text-Based System for Predicting Protein Subcellular Location
  Proc. of the Pacific Symposium on Biocomputing (PSB'08). January, 2008.

• J. Shen, P. H. Lee, J. J. A. Holden and H. Shatkay.
  Using Cluster Ensemble and Validation to Identify Subtypes of Pervasive Developmental Disorders
  Proc. of the Annual Symp. of the American Medical Informatics Association (AMIA'07). November, 2007.

• P. H. Lee and H. Shatkay.
  Two Birds One Stone : Selecting Functionally Informative Tag SNPs for Disease Association Studies
  Proc. of the Int. Workshop on Algorithms for Bioinformatics (WABI'07). Lecture Notes in Bioinformatics 4645. Springer. September, 2007. (pp. 61-72)

• A. Höglund, T. Blum, S. Brady, P. Dönnes, J. San Miguel, M. Rocherford, O. Kohlbacher and H. Shatkay.
  Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data. Proceedings of the Pacific Symposium on Biocomputing, (PSB'06). January, 2006 (pp. 16-27) . (Also selected for oral presentation during PSB.).

• N. Chen, H. Shatkay, and D. Blostein.
  Exploring a new space of features for document classification: figure clustering.
  Proceedings of The 2006 Conference of the IBM Center for Advanced Studies on Collaborative research. (CASCON'06). September, 2006.

• N. Chen, H. Shatkay, and D. Blostein.
  Use of Figures in Literature Mining for Biomedical Digital Libraries.
  Proceedings of The IEEE International Conference on Document Image Analysis for Libraries. (DIAL'06). April,2006. (pp. 180-197).

• T.H. Falk, H. Shatkay, and W.-Y. Chan.
  Breast Cancer Prognosis via Gaussian Mixture Modeling.
  Proceedings of the Canadian Conference on Electrical and Computer Engineering. (CCECE'06) May, 2006.

• Z. Zheng, S. Brady, A. Garg and H. Shatkay.
  Applying Probabilistic Thematic Clustering for Classification in the TREC 2005 Genomics Track. Proc. of the Text Retrieval Conference (TREC), 2005. November, 2005.

• H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski,
  Genes, Themes and Microarrays: Using Information Retrieval for Large Scale Gene Analysis.
  Proc. of the Int. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2000. (pp. 317-328).

• H. Shatkay and W.J. Wilbur.
  Finding Themes in Medline Documents: Statistical Similarity Search.
  Proc. of the IEEE Conference on Advances in Digital Libraries (ADL), 2000. (pp. 183-192).

• H. Shatkay.
  Learning Hidden Markov Models with Geometrical Constraints.
  Proc. of the Int. Conf. on Uncertainty in Artificial Intelligence (UAI),1999. (pp. 602-611).

• H. Shatkay and L.P. Kaelbling.
  Heading in the Right Direction.
  Proc. of the Int. Conf. on Machine Learning (ICML), 1998. (pp. 531-539).

• H. Shatkay and L.P. Kaelbling,
  Learning Topological Maps with Weak Local Odometric Information. Proc. of the Int. Joint Conf. on Artificial Intelligence (IJCAI), 1997. (pp. 920-929).

• H. Shatkay and S.B. Zdonik.
  Approximate Queries and Representations for Large Data Sequences. Proc. of the Int. Conf. on Data Engineering (ICDE), 1996. (pp. 536-545)

Other Publications, Workshop Papers, Posters and Abstracts (Journals; Conferences)

(not completely up-to-date)

• Q.A. Rahman, S. Kanagalingam, A. Pinheiro, T. Abraham and H. Shatkay
  What We Found on Our Way to Building a Classifier: A Critical Analysis of the AHA Screening Questionnaire.
  Notes of the ICML Workshop on Machine Learning for Clinical Data Analysis at the International Conference on Machine Learning, 2012.

• A. Wong and H. Shatkay. Predicting Protein Function using Text Data from the Biomedical Literature. Extended abstract and oral presentation.
  The Workshop of the Automated Protein Function (AFP) SIG on Critical Assessment of Function Annotations (CAFA). ISMB, 2011.

• T. Blum, S. Briesemeister, S. Brady, Y. Lam, O. Kohlbacher and H. Shatkay
  MultiLoc2 and SherLoc2: Improved Prediction of Subcellular Protein Localization Poster and Abstract.
  The International Conference on Research in Computational Molecular Biology, RECOMB, April, 2009.

• H. Shatkay, A. Rzhetsky and W.J. Wilbur.
  Searching for High-Utility Text in the Biomedical Literature: A Preliminary Report. Selected for oral presentation at the BioLINK Workshop. Notes of The Joint ISMB BioLINK SIG and the ACL Workshop on Linking Biological Literature, Ontologies and Databases. Held jointly with ISMB, 2005.

• H. Shatkay and L. Zheng.
  BLIMP: Biomedical Literature (and text) Mining Publications Forum: A Web-Based Resource. Poster and Abstract.
  The International Conference on Intelligent Systems for Molecular, ISMB, June, 2005.

• H. Shatkay and L. Zheng.
  BLIMP: Biomedical Literature (and text) Mining Publications Forum: A Web-Based Resource, Poster and Abstract.
  BioLINK SIG Workshop on Linking Literature, Information and Knowledge for Biology, ISMB, June, 2005.

• H. Shatkay, J. Miller, C. Mobarry, M. Flanigan, S. Yooseph and G. Sutton, {\it ThurGood: Evaluating Assembly-to-Assembly Mapping}, Poster and Abstract, The International Conference on Intelligent Systems for Molecular Biology (ISMB), August, 2004.

• H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski, Using Information Retrieval for Large Scale Gene Analysis.
  Abstract and invited talk at the Dagstuhl Seminar on Bioinformatics, Schloss Dagstuhl, Wadern Germany, December 2000.

• H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski, Information Retrieval Meets Gene Analysis. Abstract and poster.
  The Fourth TIGR Annual Symposium on Computational Genomics, Baltimore MD, November, 2000.

• H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski, {\it Genes, Themes and Microarrays: Automated Genome-Wide Extraction of Gene Function from PubMed}, Abstract and poster at the NIH Research Festival, Bethesda MD, October, 2000.

• H. Shatkay, S. Edwards, W.J. Wilbur and M. Boguski.
  Genes, Themes and Microarrays: Automated Genome-Wide Extraction of Gene Function from PubMed. Selected for Oral presentation (selection ratio: 1 out of 5 abstracts) at the Genome Sequencing and Biology meeting at Cold Spring Harbor, May, 2000.

• H. Shatkay.
  Learning Models for Robot Navigation, Ph.D. dissertation and Technical Report cs-98-11, Brown University, Department of Computer Science, Providence, RI, December, 1998. Abstract. Complete pdf.

• H. Shatkay and L.P. Kaelbling.
  Learning Hidden Markov Models with Geometric Information, Technical Report cs-97-04, Department of Computer Science, Brown University, 1997.

• H. Shatkay.
  The Fourier Transform - a Primer, Technical Report CS-95-37, Department of Computer Science, Brown University, 1995. (PDF).

• H. Shatkay.
  Approximate Queries and Representations for Large Data Sequences, Technical Report cs-95-03, Department of Computer Science, Brown University, 1995.

• H. Shatkay.
  A Type System for Eshkol - an Object Oriented DBMS, MSc Thesis, The Hebrew University, Jerusalem, Israel, 1991. Abstract (PDF).