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2020 – today
- 2023
- [c47]Juan Trelles Trabucco, Carla Floricel, Cecilia N. Arighi, Hagit Shatkay, Daniela Raciti, Martin Ringwald, G. Elisabeta Marai:
MouseScholar: Evaluating an Image+Text Search System for Biocuration. BIBM 2023: 1473-1480 - 2022
- [j36]Shijun Zhang
, Heng-Yi Wu, Lei Wang, Gongbo Zhang, Luis M. Rocha
Translational drug-interaction corpus. Database J. Biol. Databases Curation 2022(2022) (2022) - [j35]Shixiao Liang, Aaron Higuera, Christina Peters, Venkat Roy, Waheed U. Bajwa, Hagit Shatkay, Christopher D. Tunnell:
Domain-Informed Neural Networks for Interaction Localization Within Astroparticle Experiments. Frontiers Artif. Intell. 5: 832909 (2022) - [j34]Kasra Nezamabadi
Toward ECG-based analysis of hypertrophic cardiomyopathy: a novel ECG segmentation method for handling abnormalities. J. Am. Medical Informatics Assoc. 29(11): 1879-1889 (2022) - 2021
- [j33]Pengyuan Li
Corrigendum to: Utilizing image and caption information for biomedical document classification. Bioinform. 37(19): 3389 (2021) - [j32]Pengyuan Li
Utilizing image and caption information for biomedical document classification. Bioinform. 37(Supplement): 468-476 (2021) - [c46]Juan Trelles Trabucco, Pengyuan Li
ANIMO: Annotation of Biomed Image Modalities. BIBM 2021: 1069-1076 - [i11]Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay:
Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of SNOMED codes. CoRR abs/2109.09199 (2021) - [i10]Moumita Bhattacharya, Dai-Yin Lu, Ioannis Ventoulis, Gabriela V. Greenland, Hulya Yalcin, Yufan Guan, Joseph E. Marine, Jeffrey E. Olgin, Stefan L. Zimmerman, Theodore P. Abraham, M. Roselle Abraham, Hagit Shatkay:
Machine Learning Methods for Identifying Atrial Fibrillation Cases and Their Predictors in Patients With Hypertrophic Cardiomyopathy: The HCM-AF-Risk Model. CoRR abs/2109.09207 (2021) - [i9]Moumita Bhattacharya, Dai-Yin Lu, Shibani M. Kudchadkar, Gabriela Villarreal Greenland, Prasanth Lingamaneni, Celia P. Corona-Villalobos, Yufan Guan, Joseph E. Marine, Jeffrey E. Olgin, Stefan L. Zimmerman, Theodore P. Abraham, Hagit Shatkay, Maria Roselle 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). CoRR abs/2109.09210 (2021) - [i8]Shixiao Liang, Aaron Higuera
Domain-informed neural networks for interaction localization within astroparticle experiments. CoRR abs/2112.07995 (2021) - 2020
- [j31]Xiangying Jiang, Pengyuan Li
Integrating image caption information into biomedical document classification in support of biocuration. Database J. Biol. Databases Curation 2020 (2020) - [j30]Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay:
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database J. Biol. Databases Curation 2020 (2020) - [c45]Juan Trelles Trabucco, Pengyuan Li, Cecilia N. Arighi, Hagit Shatkay, G. Elisabeta Marai:
Modality-Classification of Microscopy Images Using Shallow Variants of Deep Networks. BIBM 2020: 2379-2385
2010 – 2019
- 2019
- [j29]Xiangying Jiang, Martin Ringwald, Judith A. Blake, Cecilia N. Arighi
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance. Database J. Biol. Databases Curation 2019: baz045 (2019) - [j28]Pengyuan Li
Figure and caption extraction from biomedical documents. Bioinform. 35(21): 4381-4388 (2019) - [r1]Hagit Shatkay:
Biomedical Text Mining. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 1099-1109 - [i7]Hagit Shatkay, Stanley B. Zdonik:
Approximate Queries and Representations for Large Data Sequences. CoRR abs/1904.09262 (2019) - 2018
- [j27]Pengyuan Li
Compound image segmentation of published biomedical figures. Bioinform. 34(7): 1192-1199 (2018) - [j26]Moumita Bhattacharya
Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of snomed codes. J. Biomed. Informatics 82: 31-40 (2018) - [j25]Moumita Bhattacharya, Claudine Jurkovitz
Chronic Kidney Disease stratification using office visit records: Handling data imbalance via hierarchical meta-classification. BMC Medical Informatics Decis. Mak. 18(S-4): 35-44 (2018) - [j24]Layan Nahlawi
Stochastic Modeling of Temporal Enhanced Ultrasound: Impact of Temporal Properties on Prostate Cancer Characterization. IEEE Trans. Biomed. Eng. 65(8): 1798-1809 (2018) - [c44]Gongbo Zhang, Debarati Roychowdhury, Pengyuan Li
Identifying Experimental Evidence in Biomedical Abstracts Relevant to Drug-Drug Interactions. BCB 2018: 414-418 - [c43]Moumita Bhattacharya, Claudine Jurkovitz
Co-occurrence of Medical Conditions: Exposing Patterns Through Probabilistic Topic Modeling. BCB 2018: 570 - [c42]Pengyuan Li
Extracting Figures and Captions from Scientific Publications. CIKM 2018: 1595-1598 - 2017
- [j23]Xiangying Jiang, Martin Ringwald, Judith A. Blake
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database J. Biol. Databases Curation 2017: bax017 (2017) - [c41]Moumita Bhattacharya, Claudine Jurkovitz
Assessing chronic kidney disease from office visit records using hierarchical meta-classification of an imbalanced dataset. BIBM 2017: 663-670 - [c40]Gongbo Zhang, Moumita Bhattacharya, Heng-Yi Wu, Pengyuan Li
Identifying articles relevant to drug-drug interaction: Addressing class imbalance. BIBM 2017: 1141-1147 - [c39]Pengyuan Li
Segmenting Compound Biomedical Figures into Their Constituent Panels. CLEF 2017: 199-210 - [c38]Layan Nahlawi, Caroline Goncalves, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson
Models of temporal enhanced ultrasound data for prostate cancer diagnosis: the impact of time-series order. Medical Imaging: Image-Guided Procedures 2017: 101351D - [i6]Moumita Bhattacharya, Deborah Ehrenthal, Hagit Shatkay:
Identifying Growth-Patterns in Children by Applying Cluster analysis to Electronic Medical Records. CoRR abs/1708.07058 (2017) - [i5]Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay:
Identifying Patterns of Associated-Conditions through Topic Models of Electronic Medical Records. CoRR abs/1711.10960 (2017) - 2016
- [c37]Moumita Bhattacharya, Claudine Jurkovitz
Identifying patterns of associated-conditions through topic models of Electronic Medical Records. BIBM 2016: 466-469 - [c36]Pengyuan Li, Scott Sorensen, Abhishek Kolagunda, Xiangying Jiang, Xiaolong Wang, Chandra Kambhamettu, Hagit Shatkay:
UDEL CIS Working Notes in ImageCLEF 2016. CLEF (Working Notes) 2016: 334-346 - [c35]Ramanuja Simha
Improved Multi-Label Classification Using Inter-Dependence Structure via a Generative Mixture Model. ECAI 2016: 1336-1343 - [c34]Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward
Prostate Cancer: Improved Tissue Characterization by Temporal Modeling of Radio-Frequency Ultrasound Echo Data. MICCAI (1) 2016: 644-652 - 2015
- [j22]Karin Verspoor
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. Bioinform. 31(2): 297-298 (2015) - [j21]Ramanuja Simha
Protein (multi-)location prediction: utilizing interdependencies via a generative model. Bioinform. 31(12): 365-374 (2015) - [c33]Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward
Using Hidden Markov Models to capture temporal aspects of ultrasound data in prostate cancer. BIBM 2015: 446-449 - [c32]Xiaolong Wang, Xiangying Jiang, Abhishek Kolagunda, Hagit Shatkay, Chandra Kambhamettu:
CIS UDEL Working Notes on ImageCLEF 2015: Compound Figure Detection Task. CLEF (Working Notes) 2015 - [c31]Kaidi Ma, Hogyeong Jeong, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu, Hagit Shatkay:
Utilizing image-based features in biomedical document classification. ICIP 2015: 4451-4455 - 2014
- [j20]Ramanuja Simha
Protein (multi-)location prediction: using location inter-dependencies in a probabilistic framework. Algorithms Mol. Biol. 9: 8 (2014) - [c30]Quazi Abidur Rahman, Larisa G. Tereshchenko
Identifying hypertrophic cardiomyopathy patients by classifying individual heartbeats from 12-lead ECG signals. BIBM 2014: 224-229 - [c29]Kaidi Ma, Marco Canepa
Using unsupervised learning to determine risk level for left ventricular diastolic dysfunction. BIBM 2014: 344-347 - [c28]Moumita Bhattacharya, Deborah Ehrenthal, Hagit Shatkay:
Identifying growth-patterns in children by applying cluster analysis to electronic medical records. BIBM 2014: 348-351 - 2013
- [j19]Andrew Wong, Hagit Shatkay:
Protein Function Prediction using Text-based Features extracted from the Biomedical Literature: The CAFA Challenge. BMC Bioinform. 14(S-3): S14 (2013) - [c27]Quazi Abidur Rahman, Sivajothi Kanagalingam, Aurelio Pinheiro, Theodore Abraham, Hagit Shatkay:
What We Found on Our Way to Building a Classifier: A Critical Analysis of the AHA Screening Questionnaire. Brain and Health Informatics 2013: 225-236 - [c26]Ramanuja Simha
Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework. WABI 2013: 3-17 - [i4]Hagit Shatkay:
Learning Hidden Markov Models with Geometrical Constraints. CoRR abs/1301.6740 (2013) - [i3]Ramanuja Simha, Hagit Shatkay:
Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework. CoRR abs/1307.7795 (2013) - 2012
- [j18]Anália Lourenço
Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. BMC Bioinform. 13: 180 (2012) - [c25]Hagit Shatkay, Ramya Narayanaswamy, Santosh S. Nagaral, Na Harrington, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu:
OCR-Based Image Features for Biomedical Image and Article Classification: Identifying Documents Relevant to Genomic Cis-Regulatory Elements. AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text 2012 - [c24]Hagit Shatkay, Ramya Narayanaswamy, Santosh S. Nagaral, Na Harrington, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu:
OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements. BCB 2012: 98-104 - [c23]Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii
Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. BIBM 2012: 1-4 - [c22]Anita de Waard
Detecting and using document structure in scientific text. IHI 2012: 883-884 - 2011
- [j17]Anália Lourenço
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. BMC Bioinform. 12(S-8): S12 (2011) - [j16]Martin Krallinger
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12(S-8): S3 (2011) - [c21]Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Hongzhan Huang, Hagit Shatkay, Cathy H. Wu
An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents. BIBM 2011: 578-581 - [i2]Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha:
A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature. CoRR abs/1103.4090 (2011) - [i1]Leslie Pack Kaelbling, Hagit Shatkay:
Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Topological-Geometrical Gap. CoRR abs/1106.0680 (2011) - 2010
- [c20]Hagit Shatkay, Doheon Lee, Min Song, Shamkant B. Navathe:
DTMBIO workshop summary. CIKM 2010: 1971-1972 - [e3]Miguel P. Rocha, Florentino Fernández Riverola, Hagit Shatkay, Juan M. Corchado:
Advances in Bioinformatics - 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010), Guimarães, Portugal, 16-18 June 2010. Advances in Intelligent and Soft Computing 74, Springer 2010, ISBN 978-3-642-13213-1 [contents] - [e2]Christian Blaschke, Hagit Shatkay:
Linking Literature, Information, and Knowledge for Biology - Workshop of the BioLink Special Interest Group, ISMB/ECCB 2009, Stockholm, Sweden, June 28-29, 2009, Revised Selected Papers. Lecture Notes in Computer Science 6004, Springer 2010, ISBN 978-3-642-13130-1 [contents]
2000 – 2009
- 2009
- [j15]Phil Hyoun Lee, Hagit Shatkay:
An integrative scoring system for ranking SNPs by their potential deleterious effects. Bioinform. 25(8): 1048-1055 (2009) - [j14]Phil Hyoun Lee, Jae-Yoon Jung, Hagit Shatkay:
Functionally informative tag SNP selection using a pareto-optimal approach: playing the game of life. BMC Bioinform. 10(S-13): 0 (2009) - [j13]Andrey Rzhetsky
How to Get the Most out of Your Curation Effort. PLoS Comput. Biol. 5(5) (2009) - 2008
- [j12]Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. Bioinform. 24(18): 2086-2093 (2008) - [j11]Phil Hyoun Lee, Hagit Shatkay:
Ranking single nucleotide polymorphisms by potential deleterious effects. BMC Bioinform. 9(S-10) (2008) - [j10]Phil Hyoun Lee, Hagit Shatkay:
F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res. 36(Database-Issue): 820-824 (2008) - [c19]Phil Hyoun Lee, Hagit Shatkay:
Ranking single nucleotide polymorphisms by potential deleterious effects. AMIA 2008 - [c18]Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia:
Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. BioLINK@ISMB/ECCB 2008: 1-7 - [c17]Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay:
Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...). BioLINK@ISMB/ECCB 2008: 33-42 - [c16]Scott Brady, Hagit Shatkay:
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location. Pacific Symposium on Biocomputing 2008: 604-615 - 2007
- [j9]Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinform. 23(11): 1410-1417 (2007) - [c15]Jess J. Shen, Phil Hyoun Lee, Jeanette J. A. Holden, Hagit Shatkay:
Using Cluster Ensemble and Validation to Identify Subtypes of Pervasive Developmental Disorders. AMIA 2007 - [c14]Phil Hyoun Lee, Hagit Shatkay:
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies. WABI 2007: 61-72 - 2006
- [j8]Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, Michael K. Showe:
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier. Bioinform. 22(11): 1325-1334 (2006) - [j7]Monica Chagoyen
Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinform. 7: 41 (2006) - [j6]W. John Wilbur, Andrey Rzhetsky
New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinform. 7: 356 (2006) - [c13]Nawei Chen, Hagit Shatkay, Dorothea Blostein:
Exploring a new space of features for document classification: figure clustering. CASCON 2006: 369-372 - [c12]Tiago H. Falk
Breast Cancer Prognosis via Gaussian Mixture Regression. CCECE 2006: 987-990 - [c11]Nawei Chen, Hagit Shatkay, Dorothea Blostein:
Use of Figures in Literature Mining for Biomedical Digital Libraries. DIAL 2006: 180-197 - [c10]Phil Hyoun Lee, Hagit Shatkay:
BNTagger: improved tagging SNP selection using Bayesian networks. ISMB (Supplement of Bioinformatics) 2006: 211-219 - [c9]Hagit Shatkay, Nawei Chen, Dorothea Blostein:
Integrating image data into biomedical text categorization. ISMB (Supplement of Bioinformatics) 2006: 446-453 - [c8]Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay:
Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data . Pacific Symposium on Biocomputing 2006: 16-27 - 2005
- [j5]Hagit Shatkay:
Hairpins in bookstacks: Information retrieval from biomedical text. Briefings Bioinform. 6(3): 222-238 (2005) - [c7]Z. H. Zheng, Scott Brady, Akash Garg, Hagit Shatkay:
Applying Probabilistic Thematic Clustering for Classification in the TREC 2005 Genomics Track. TREC 2005 - [e1]K. Bretonnel Cohen, Lynette Hirschman, Hagit Shatkay, Christian Blaschke:
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics@ISMB 2005, Detroit, MI, USA June 24, 2005. Association for Computational Linguistics 2005 [contents] - 2004
- [j4]Hagit Shatkay, Jason R. Miller
ThurGood: Evaluating Assembly-to-Assembly Mapping. J. Comput. Biol. 11(5): 800-811 (2004) - 2003
- [j3]Hagit Shatkay, Ronen Feldman:
Mining the Biomedical Literature in the Genomic Era: An Overview. J. Comput. Biol. 10(6): 821-855 (2003) - 2002
- [j2]Hagit Shatkay, Stephen Edwards, Mark Boguski:
Information Retrieval Meets Gene Analysis. IEEE Intell. Syst. 17(2): 45-53 (2002) - [j1]Hagit Shatkay, Leslie Pack Kaelbling:
Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Topological-Geometrical Gap. J. Artif. Intell. Res. 16: 167-207 (2002) - 2000
- [c6]Hagit Shatkay, W. John Wilbur:
Finding Themes in Medline Documents: Probabilistic Similarity Search. ADL 2000: 183-192 - [c5]Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski:
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis. ISMB 2000: 317-328
1990 – 1999
- 1999
- [c4]Hagit Shatkay:
Learning Hidden Markov Models with Geometrical Constraints. UAI 1999: 602-611 - 1998
- [c3]Hagit Shatkay, Leslie Pack Kaelbling:
Heading in the Right Direction. ICML 1998: 531-539 - 1997
- [c2]Hagit Shatkay, Leslie Pack Kaelbling:
Learning Topological Maps with Weak Local Odometric Information. IJCAI (2) 1997: 920-929 - 1996
- [c1]Hagit Shatkay, Stanley B. Zdonik:
Approximate Queries and Representations for Large Data Sequences. ICDE 1996: 536-545
Coauthor Index
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