Publications in Google Scholar Google Scholar

Publications in PubMed PubMed

Publications in Peer Reviewed Journals (Conferences; Other Venues)

• X. Jiang, P. Li, J. Kadin, J.A. Blake, M. Ringwald and H. Shatkay
  Integrating Image Caption Information into Biomedical Document Classification in Support of Biocuration
  Database , 2020. (Early access April, 2020).

• P. Li, X. Jiang and H. Shatkay
  Figure and Caption Extraction from Biomedical Documents.
  Bioinformatics , 35(21), 2019.

• X. Jiang, M. Ringwald, J. Black, C. Arighi, G. Zhang and H. Shatkay. An Effective Biomedical Document Classification Scheme in Support of Biocuration: Addressing Class Imbalance. .
  Database . 2019 .

• M. Bhattacharya, D.Y. Lu, S.M. Kudchadkar, G. Villareal Greenland, S. Sivalokanathan, P. Lingamaneni, C.P. Corona-Villalobos, Y. Guan, J.E. Marine, J.E. Olgin, S. Zimmerman, T.P. Abrahram, H. Shatkay and M.R. Abraham.
  Identifying Ventricular Arrhythmias and their Predictors by Applying Machine Learning Methods to Electronic Health Records in Patients with Hypertrophic Cardiomyopathy (HCM-Var-Risk Model).
  The American Journal of Cardiology, 123 (10), 2019..

• M. Bhattacharya, C. Jurkovitz and H. Shatkay .
  Co-occurrence of Medical Conditions: Exposing Patterns through Probabilistic Topic Modeling of SNOMED Codes.
  Journal of Biomedical Informatics, 82, 2018.

• P. Li, X. Jiang, C. Kambhamettu and H. Shatkay
  Compound Image Segmentation of Published Biomedical Figures.
  Bioinformatics , 34(7), 2018. (Early access October, 2017).

• L. Nahlawi, C. Goncalves, F. Imani, M. Gaed, J.A. Gomez, M. Mousa, E. Gibson, A. Fenster, A.D. Ward, P. Abolmaesumi, H. Shatkay and P. Mousavi.
  Stochastic Modeling of Temporal Enhanced Ultrasound: Impact of Temporal Properties on Prostate Cancer Characterization.
  IEEE Transactions on Biomedical Engineering, Early access, TBME-00635-2017.R1, 2017.

• X. Jiang, M. Ringwald, J. Black and H. Shatkay. Effective Biomedical Document Classification for Identifying Publications Relevant to the Mouse Gene Expression Database (GXD).
  Database . 2017 (1).

• R. Simha, S. Briesemeister, O. Kohlbacher and H. Shatkay. Protein (Multi-)Location Prediction: Utilizing Interdependencies via a Generative Model a Probabilistic Framework.
  Bioinformatics 31(8). 2015. (Also presented as a conference paper at ISMB'15)
  

• H. Shatkay, S. Brady and A. Wong. Text as Data: Using Text-Based Features for Proteins Representation and for Computational Prediction of their Characterisitics.
  Methods, Elsevier. 2015.

• Q.A. Rahman, L. Tereshchenko, M. Kongkatong, T. Abraham, M.R. Abraham and H. Shatkay. Utilizing ECG-based Heartbeat Classification for Hypertrophic Cardiomyopathy Identification.
  IEEE Transactions on NanoBioscience 14(5). 2015.

• R. Simha and H. Shatkay. Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework.
  Algorithms for Molecular Biology 9:8. 2014.
  

• K. Verspoor, H. Shatkay, L. Hirschman and C. Blaschke. Summary of the BioLINK SIG 2013 at ISMB/ECCB 2013.
  Bioinformatics btu412. 2014.
• 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.
  

• 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 and 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 and 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 and 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

• 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.

Publications in Peer Reviewed Conferences (Journals; Other Venues)

• P. Li, X. Jiang and H. Shatkay. Extracting Figures and Captions from Scientific Publications
  Proc. of the ACM Int. Conference on Information and Knowledge Management (CIKM), 2018.

• M. Bhattacharya, C. Jurkovitz and H. Shatkay. Assessing Chronic Kidney Disease from Office Visit Records Using Hierarchical Meta-Classification of an Imbalanced Dataset.
  Proc. of the IEEE Int. Conference on Bioinformatics and Biomedicine (BIBM), November, 2017.

• G. Zhang, M. Bhattacharya, HY Wu, P. Li, L. Li and H. Shatkay. Identifying Articles Relevant to Drug-Drug Interaction: Addressing Class Imbalance.
  Proc. of the IEEE Int. Conference on Bioinformatics and Biomedicine (BIBM), November, 2017.

• P. Li, X. Jiang, C. Kambhamettu and H. Shatkay
  Segmenting Compound Biomedical Figures into Their Constituent Panels
  Proc. of CLEF 2017,Conference and Labs of the Evaluation Forum. 2017.

• L. Nahlawi, C. Goncalves, F. Imani, M. Gaed, J.A. Gomez, M. Mousa, E. Gibson, A. Fenster, A.D. Ward, P. Abolmaesumi, P. Mousavi and H. Shatkay.
  Models of Temporal Enhanced Ultrasound Data for Prostate Cancer Diagnosis: The Impact of Time-Series Order.
  Proc. of the Conference of the Int. Society for Optics and Photonics (SPIE), V. 10135, Medical Imaging 2017: Image-Guided Procedures, Robotic Interventions, and Modeling .

• M. Bhattacharya, C. Jurkovitz and H. Shatkay. Identifying Patterns of Associated-Conditions through Topic Models of Electronic Medical Records.
  Proc. of the IEEE Int. Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China, December, 2016.

• L. Nahlawi, F. Imani, M. Gaed, J.A. Gomez, M. Mousa, E. Gibson, A. Fenster, A.D. Ward, P. Abolmaesumi, H. Shatkay and P. Mousavi.
  Prostate Cancer: Improved Detection by Temporal Analysis of Radio-Frequency Ultrasound Echo Data.
  Proc. of the Int. Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2016.

• R. Simha and H. Shatkay.
  Improved Multi-Label Classification using Inter-dependence Structure via a Generative Mixture Model .
  Proc. of the European Conference on Artificial Intelligence (ECAI), 2016.

• P. Li, S. Sorenson, A. Kolagunda, X. Jiang, X. Wang C. Kambhamettu and H. Shatkay
  UDEL CIS at Image-CLEF Medical Task 2016.
  Working Notes of CLEF. 2016.

• L. Nahlawi, F. Imani, M. Gaed, J.A. Gomez, M. Mousa, E. Gibson, A. Fenster, A.D. Ward, P. Abolmaesumi, P. Mousavi and H. Shatkay.
  Using Hidden Markov Models to capture Temporal Aspects of Ultrasound Data in Prostate Cancer.
  Proc. of the IEEE Int. Conference on Bioinformatics and Bioedicine (BIBM), Bethesda, Maryland, November, 2015.

• K. Ma, H. Jeong, R. MV, G. Somanath, R. Tarpine, K, Schutter, D. Blostein, S. Istrail, C. Kambhamettu and H. Shatkay.
  Utilizing Image-based Features in Biomedical Document Classification.
  Proc. of the IEEE Int. Conference on Image Processing (ICIP'15). 2015.

• X. Wang, X. Jiang, A. Kolagunda, H. Shatkay and C. Kambhamettu.
  CIS UDEL Working Notes on Image-CLEF 2015: Compound Figure Detection Task.
  Working Notes of CLEF. 2015.

• Q.A. Rahman, L. Tereshchenko, M. Kongkatong, T. Abraham, M.R. Abraham, and H. Shatkay.
  Identifying Hypertrophic Cardiomyopathy Patients by Classifying Individual Heartbeats from 12-lead ECG Signals.
  Proc. of the IEEE Int. Conference on Bioinformatics and Bioedicine (BIBM), Belfast, Ireland, November, 2014.

• K. Ma, M. Canepa, J. Strait and H. Shatkay.
  Using Unsupervised Learning to Determine Risk Level for Left Ventricular Diastolic Dysfunction.
  Proc. of the IEEE Int. Conference on Bioinformatics and Bioedicine (BIBM), Belfast, Ireland, November, 2014.

• M. Bhattacharya, D. Ehrenthal and H. Shatkay.
  Identifying Growth-Patterns in Children by Applying Cluster analysis to Electronic Medical Records.
  Proc. of the IEEE Int. Conference on Bioinformatics and Bioedicine (BIBM), Belfast, Ireland, November, 2014.

• 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.
  Proc. of the Int. Conference on Brain and Health Informatics, Gunma, Japan, October, 2013.

• R. Simha and H. Shatkay.
  Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework .
  Proc. of the International Workshop on Algorithms for Bioinformatics (WABI'13). September, 2013.

• 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, J.Y. Jung and H. Shatkay.
  Functionally Informative Tag SNP Selection Using a Pareto-Optimal Approach: Playing the Game of Life.
  In Highlights from the Fifth ISCB Student Council Symposium, BMC Bioinformatics, V. 10, , 2009.

• 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)

• M. Bhattacharya, D.Y. Lu, P. Lingamaneni, S. KKudchadkar, G. Villareal, S. Sivalokanathan, P.C. Villalobos, S. Zimmerman, T.P. Abrahram, M.R. Abraham and H. Shatkay.
  Identifying Ventricular Arrhythmia Cases and Their Predictors by Applying Machine Learning Methods to Electronic Health Records (EHR) of Hypertrophic Cardiomyopathy (HCM) Patients.
  Abstract presentation at the 2017 Symposium of the American Heart Association (AHA). Circulation, 2017.

• P. Patel, S. Mathioni, A. Kakrana, H. Shatkay and B. Myers.
  Machine Learning Identifies Unique Features of Reproductive Phased, Secondary, Small Interfering RNAs in Rice and Maize.
  Abstract at the 2018 Plant and Animal Genome Conference. San Diego, 2017.

• 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.

• S. Kanagalingam, A. Pinheiro, H. Shatkay, Q.A. Rahman, V.L. Dimaano, M. Santaularia-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.
  Abstract and oral presentation at the 2010 Symposium of the American Heart Association (AHA). Circulation, 2010.

• 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.

• 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).