Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. - Nilanjana Banerjee; Andrea Califano (Comparative Genomics, 2006)

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. - Kai Wang 045; Ilya Nemenman; Nilanjana Banerjee; Adam A. Margolin; Andrea Califano (RECOMB, 2006)

Towards identification of thematic overlaps in gene sets. - Nilanjana Banerjee; Vinay Varadan; Sitharthan Kamalakaran; Angel Janevski (GENSiPS, 2009)

Tools for High Throughput Differential Methylation Study in Cancer. - Nevenka Dimitrova; Sitharthan Kamalakaran; Angel Janevski; Nilanjana Banerjee; Vinay Varadan; Robert Lucito; James Hicks (ICT Innovations, 2009)

PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment. - Angel Janevski; Sitharthan Kamalakaran; Nilanjana Banerjee; Vinay Varadan; Nevenka Dimitrova (BMC Bioinform., 2009)

Pathway and network analysis probing epigenetic influences on chemosensitivity in ovarian cancer. - Nilanjana Banerjee; Angel Janevski; Sitharthan Kamalakaran; Vinay Varadan; Robert Lucito; Nevenka Dimitrova (GENSiPS, 2010)

Comparative copy number variation from whole genome sequencing. - Angel Janevski; Vinay Varadan; Sitharthan Kamalakaran; Nilanjana Banerjee; Nevenka Dimitrova (GENSiPS, 2011)

Statistical assessment of gene fusion detection algorithms using RNA Sequencing Data. - Vinay Varadan; Angel Janevski; Sitharthan Kamalakaran; Nilanjana Banerjee; Nevenka Dimitrova; Lyndsay N. Harris (SSP, 2012)

Identifying RNAseq-based coding-noncoding co-expression interactions in breast cancer. - Nilanjana Banerjee; Sonia Chothani; Lyndsay N. Harris; Nevenka Dimitrova (GENSiPS, 2013)

Non-linear Bayesian framework to determine the transcriptional effects of cancer-associated genomic aberrations. - Abolfazl Razi; Nilanjana Banerjee; Nevenka Dimitrova; Vinay Varadan (EMBC, 2015)

A Machine Learning Approach to Identify EHR-based Cohorts of Pain Sensitivity for Genetic Analysis. - Amelia J. Averitt; Nilanjana Banerjee; Michael Cantor (AMIA, 2021)

Deep Representational Clustering for Endotype Discovery. - Amelia J. Averitt; Justin Mower; Nilanjana Banerjee (AMIA, 2022)