BloodExpress: a database of gene expression in mouse haematopoiesis. - Diego Miranda-Saavedra; Subhajyoti De; Matthew W. B. Trotter; Sarah A. Teichmann; Berthold Göttgens (Nucleic Acids Res., 2009)

CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. - Brent S. Pedersen; Ivana V. Yang; Subhajyoti De (Bioinform., 2013)

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. - Subhajyoti De; Brent S. Pedersen; Katerina J. Kechris (Briefings Bioinform., 2014)

Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells. - Ondrej Podlaha; Subhajyoti De; Mithat Gonen; Franziska Michor (PLoS Comput. Biol., 2014)

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. - Vinod Kumar Yadav; Subhajyoti De (Briefings Bioinform., 2015)

SomVarIUS: somatic variant identification from unpaired tissue samples. - Kyle S. Smith; Vinod Kumar Yadav; Shanshan Pei; Daniel A. Pollyea; Craig T. Jordan; Subhajyoti De (Bioinform., 2016)

IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. - Jennifer Hintzsche; Jihye Kim 004; Vinod Kumar Yadav; Carol Amato; Steven E. Robinson; Eric Seelenfreund; Yiqun Shellman; Joshua Wisell; Allison Applegate; Martin McCarter; Neil Box; John Tentler; et al. (J. Am. Medical Informatics Assoc., 2016)

Mutational signatures and mutable motifs in cancer genomes. - Igor B. Rogozin; Youri I. Pavlov; Alexander Goncearenco; Subhajyoti De; Artem G. Lada; Eugenia Poliakov; Anna R. Panchenko; David N. Cooper (Briefings Bioinform., 2018)

Joint Segmentation and Fine-Grained Classification of Nuclei in Histopathology Images. - Hui Qu; Gregory M. Riedlinger; Pengxiang Wu; Qiaoying Huang; Jingru Yi; Subhajyoti De; Dimitris N. Metaxas (ISBI, 2019)

Improving Nuclei/Gland Instance Segmentation in Histopathology Images by Full Resolution Neural Network and Spatial Constrained Loss. - Hui Qu; Zhennan Yan; Gregory M. Riedlinger; Subhajyoti De; Dimitris N. Metaxas (MICCAI (1), 2019)

Weakly Supervised Deep Nuclei Segmentation using Points Annotation in Histopathology Images. - Hui Qu; Pengxiang Wu; Qiaoying Huang; Jingru Yi; Gregory M. Riedlinger; Subhajyoti De; Dimitris N. Metaxas (MIDL, 2019)

Weakly Supervised Deep Nuclei Segmentation Using Partial Points Annotation in Histopathology Images. - Hui Qu; Pengxiang Wu; Qiaoying Huang; Jingru Yi; Zhennan Yan; Kang Li 004; Gregory M. Riedlinger; Subhajyoti De; Shaoting Zhang 001; Dimitris N. Metaxas (IEEE Trans. Medical Imaging, 2020)

Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues. - Bassel Ghaddar; Martin J. Blaser; Subhajyoti De (Nat. Comput. Sci., 2023)

Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census. - Bassel Ghaddar; Subhajyoti De (Bioinform., 2023)

Oncointerpreter.ai enables interactive, personalized summarization of cancer diagnostics data. - Arihant Tripathi; Brett Ecker; Patrick Boland; Saum Ghodoussipour; Gregory R. Riedlinger; Subhajyoti De (J. Am. Medical Informatics Assoc., 2025)