Multi-Dimensional Interval Algebra with Symmetry for Describing Block Layouts. - Ankur Lahoti; Rohit Singh 001; Amitabha Mukerjee (GREC, 1999)

Identifying Structural Motifs in Proteins. - Rohit Singh 001; Mitul Saha (Pacific Symposium on Biocomputing, 2003)

Active learning for sampling in time-series experiments with application to gene expression analysis. - Rohit Singh 001; Nathan P. Palmer; David K. Gifford; Bonnie Berger; Ziv Bar-Joseph (ICML, 2005)

ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. - Rohit Singh 001; Bonnie Berger (Pacific Symposium on Biocomputing, 2005)

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (Pacific Symposium on Biocomputing, 2006)

Probabilistic Modeling of Systematic Errors in Two-Hybrid Experiments. - David A. Sontag; Rohit Singh 001; Bonnie Berger (Pacific Symposium on Biocomputing, 2007)

Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (RECOMB, 2007)

Predicting and Annotating Catalytic Residues: An Information Theoretic Approach. - Beckett W. Sterner; Rohit Singh 001; Bonnie Berger (J. Comput. Biol., 2007)

Global Alignment of Multiple Protein Interaction Networks. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (Pacific Symposium on Biocomputing, 2008)

Graph algorithms for biological systems analysis. - Bonnie Berger; Rohit Singh 001; Jinbo Xu (SODA, 2008)

Global alignment of multiple protein interaction networks with application to functional orthology detection. - Rohit Singh 001; Jinbo Xu; Bonnie Berger (Proc. Natl. Acad. Sci. USA, 2008)

IsoRankN: spectral methods for global alignment of multiple protein networks. - Chung-Shou Liao; Kanghao Lu; Michael Baym; Rohit Singh 001; Bonnie Berger (Bioinform., 2009)

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. - Rohit Singh 001; Daniel Park; Jinbo Xu; Raghavendra Hosur; Bonnie Berger (Nucleic Acids Res., 2010)

Sparse estimation for structural variability. - Raghavendra Hosur; Rohit Singh 001; Bonnie Berger (Algorithms Mol. Biol., 2011)

IsoBase: a database of functionally related proteins across PPI networks. - Daniel Park; Rohit Singh 001; Michael Baym; Chung-Shou Liao; Bonnie Berger (Nucleic Acids Res., 2011)

Algorithms for the analysis of protein interaction networks. - Rohit Singh 001 (2012)

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities. - Rohit Singh 001; Brian Hie; Ashwin Narayan; Bonnie Berger (Zenodo, 2021)

Granger causal inference on DAGs identifies genomic loci regulating transcription. - Alexander P. Wu; Rohit Singh 001; Bonnie Berger (ICLR, 2022)

Topsy-Turvy: integrating a global view into sequence-based PPI prediction. - Rohit Singh 001; Kapil Devkota; Samuel Sledzieski; Bonnie Berger; Lenore Cowen (Bioinform., 2022)

Causally-guided Regularization of Graph Attention Improves Generalizability. - Alexander P. Wu; Thomas Markovich; Bonnie Berger; Nils Yannick Hammerla; Rohit Singh 001 (Trans. Mach. Learn. Res., 2023)

TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. - Samuel Sledzieski; Kapil Devkota; Rohit Singh 001; Lenore Cowen; Bonnie Berger (Bioinform., 2023)

Learning a CoNCISE Language for Small-Molecule Binding. - Mert Erden; Kapil Devkota; Lia Varghese; Lenore Cowen; Rohit Singh 001 (RECOMB, 2025)

Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. - Samuel Sledzieski; Charlotte Versavel; Rohit Singh 001; Faith Ocitti; Kapil Devkota; Lokender Kumar; Polina Shpilker; Liza Roger; Jinkyu Yang; Nastassja Lewinski; Hollie Putnam; Bonnie Berger; et al. (RECOMB, 2025)