CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. - Anil G. Jegga; Ashima Gupta; Sivakumar Gowrisankar; Mrunal A. Deshmukh; Steven Connolly; Kevin Finley; Bruce J. Aronow (Nucleic Acids Res., 2005)

Identifying Functional Binding Motifs of Tumor Protein p53 Using Support Vector Machines. - Amit U. Sinha; Mukta Phatak; Raj Bhatnagar; Anil G. Jegga (ICMLA, 2007)

Improved human disease candidate gene prioritization using mouse phenotype. - Jing Chen 021; Huan Xu; Bruce J. Aronow; Anil G. Jegga (BMC Bioinform., 2007)

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. - Anil G. Jegga; Jing Chen 021; Sivakumar Gowrisankar; Mrunal A. Deshmukh; Ranga Chandra Gudivada; Sue Kong; Vivek Kaimal; Bruce J. Aronow (Nucleic Acids Res., 2007)

PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. - Anil G. Jegga; Sivakumar Gowrisankar; Jing Chen 021; Bruce J. Aronow (Nucleic Acids Res., 2007)

Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge. - Ranga Chandra Gudivada; Xiaoyan A. Qu; Jing Chen 021; Anil G. Jegga; Eric K. Neumann; Bruce J. Aronow (J. Biomed. Informatics, 2008)

Disease candidate gene identification and prioritization using protein interaction networks. - Jing Chen 021; Bruce J. Aronow; Anil G. Jegga (BMC Bioinform., 2009)

Correction: Disease candidate gene identification and prioritization using protein interaction networks. - Jing Chen 021; Bruce J. Aronow; Anil G. Jegga (BMC Bioinform., 2009)

Regression based predictor for p53 transactivation. - Sivakumar Gowrisankar; Anil G. Jegga (BMC Bioinform., 2009)

Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. - Xiaoyan A. Qu; Ranga Chandra Gudivada; Anil G. Jegga; Eric K. Neumann; Bruce J. Aronow (BMC Bioinform., 2009)

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. - Jing Chen 021; Eric E. Bardes; Bruce J. Aronow; Anil G. Jegga (Nucleic Acids Res., 2009)

Mining Maximally Banded Matrices in Binary Data. - Faris Alqadah; Raj Bhatnagar; Anil G. Jegga (SDM, 2010)

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. - Vivek Kaimal; Eric E. Bardes; Scott C. Tabar; Anil G. Jegga; Bruce J. Aronow (Nucleic Acids Res., 2010)

PhenoHM: human-mouse comparative phenome-genome server. - Divya Sardana; Suresh Vasa; Nishanth Vepachedu; Jing Chen 021; Ranga Chandra Gudivada; Bruce J. Aronow; Anil G. Jegga (Nucleic Acids Res., 2010)

A novel framework for detecting maximally banded matrices in binary data. - Faris Alqadah; Raj Bhatnagar; Anil G. Jegga (Stat. Anal. Data Min., 2010)

Drug repositioning for orphan diseases. - Divya Sardana; Cheng Zhu; Minlu Zhang; Ranga Chandra Gudivada; Lun Yang; Anil G. Jegga (Briefings Bioinform., 2011)

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome - Clozapine-Induced Agranulocytosis as a Case Study. - Lun Yang; Kejian Wang; Jian Chen; Anil G. Jegga; Heng Luo 002; Leming Shi; Chunling Wan; Xizhi Guo; Shengying Qin; Guang He; Guoyin Feng; Lin He 007 (PLoS Comput. Biol., 2011)

A vertex similarity-based framework to discover and rank orphan disease-related genes. - Cheng Zhu; Akash Kushwaha; Kenneth Berman; Anil G. Jegga (BMC Syst. Biol., 2012)

A Biclustering Algorithm to Discover Functional Modules from ENCODE ChIP-Seq Data. - Chao Wu; Arjun Bakshi; Bruce J. Aronow; Anil G. Jegga; Raj Bhatnagar (ICDM Workshops, 2013)

Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia. - Kazuhiko Bessho; Kumar Shanmukhappa; Rachel Sheridan; Pranavkumar Shivakumar; Reena Mourya; Stephanie Walters; Vivek Kaimal; Eric Dilbone; Anil G. Jegga; Jorge A. Bezerra (BMC Syst. Biol., 2013)

Computational drug repositioning through heterogeneous network clustering. - Chao Wu; Ranga Chandra Gudivada; Bruce J. Aronow; Anil G. Jegga (BMC Syst. Biol., 2013)

Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. - Louise Deléger; Katalin Molnár; Guergana Savova; Fei Xia 004; Todd Lingren; Qi Li 004; Keith Marsolo; Anil G. Jegga; Megan Kaiser; Laura Stoutenborough; Imre Solti (J. Am. Medical Informatics Assoc., 2013)

Mining FDA drug labels for medical conditions. - Qi Li 004; Louise Deléger; Todd Lingren; Haijun Zhai; Megan Kaiser; Laura Stoutenborough; Anil G. Jegga; Kevin Bretonnel Cohen; Imre Solti (BMC Medical Informatics Decis. Mak., 2013)

ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. - Chao Wu; Eric E. Bardes; Anil G. Jegga; Bruce J. Aronow (Nucleic Acids Res., 2014)

A multi-context feature learning approach to identify disease-specific gene neighborhoods. - Sudhir Ghandikota; Anil G. Jegga (BCB, 2020)

Triangle-Based Tripartite Graph Clustering. - Yizong Cheng; Jaswanth K. Yella; Anil G. Jegga (BIBM, 2020)

Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19. - Sudhir Ghandikota; Mihika Sharma; Anil G. Jegga (Patterns, 2021)

Multimodal feature learning framework for disease biomarker discovery. - Sudhir Ghandikota; Jaswanth K. Yella; Anil G. Jegga (BIBM, 2022)

GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. - Jaswanth K. Yella; Sudhir Ghandikota; Anil G. Jegga (BIBM, 2022)

MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention. - Jaswanth K. Yella; Anil G. Jegga (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)