Rohit Singh Lab: {Publications}
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Foundation Models
Representation Learning
Causal Inference
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Protein Design
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2026
2025
2024
2023 & earlier
- Karpurapu A, Gersbach C, Singh R. DeltaNMF: A Two-Stage Neural NMF for Differential Gene Program Discovery. To appear, RECOMB 2026 (paper, via bioRxiv. GitHub).
- Pratapa A, Tata PR, Singh R. USHER: Guiding Foundation Model Representations through Distribution Shifts. To appear, RECOMB 2026 (paper, via bioRxiv. GitHub).
- Liang H, Berger B, Singh R. Foundation model reveals the shared organization of transcription and topologically associating domains. Under review, 2025 (paper, via bioRxiv).
- Pratapa A, Mansouri S, Nikulina N, Matuck B, Schneider MA, Byrd KM, Savai R, Tata PR, Singh R. SAME: Topology-flexible transforms enable robust integration of multimodal spatial omics. Under review, 2025 (paper, via bioRxiv. GitHub).
- Shankar P, Liang H, Chitra U, Singh R. Decoding the causal drivers of spatial cellular topology. Presented at RECOMB-Seq 2025. To appear, iScience (paper, via bioRxiv. GitHub).
- Keenen MM, Yang L, Liang H, Farmer VJ, Worota RE, Singh R, Gladfelter AS, Coyne CB. Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing. eLife, 2025 (paper; bioRxiv preprint).
- Singh R, Wu A, Mudide A, Berger B. Unraveling causal gene regulation from the RNA velocity graph using Velorama. Cell Systems, 2024 (paper; bioRxiv preprint; http://cb.csail.mit.edu/cb/velorama/. GitHub). Presented at RECOMB 2023. Invited for consideration by both Cell Systems and Genome Research.
- Ozbay S, Parekh A, Singh R. Local transcriptional covariation produces accurate estimates of cell phenotype. To appear, Bioinformatics (paper, via bioRxiv. GitHub).
- Wu A, Singh R, Walsh CA, Berger B. An econometric lens resolves cell-state parallax. Under review, 2023 (paper, via bioRxiv. http://cb.csail.mit.edu/cb/gridnet/).
- Wu A, Markovich T, Berger B, Hammerla N, Singh R. Causally-guided Regularization of Graph Attention Improves Generalizability. TMLR, 2023 (paper, via arXiv). In collaboration with Twitter Research.
- Singh R, Li J, Tattikota S, Liu Y, et al. Optimal transport analysis of single-cell transcriptomics directs hypotheses prioritization and validation. Under review, 2022 (paper, via bioRxiv. http://cb.csail.mit.edu/cb/haystack/).
- Singh R, Wu A, Berger B. Granger causal inference on DAGs identifies genomic loci regulating transcription. Int'l Conf. on Learning Representations (ICLR) 2022 (scored in the top ~1% of submissions) (paper, via arXiv. https://github.com/alexw16/gridnet).
- Singh R, Berger B. Deciphering the species-level structure of topologically associating domains. Under review, 2021 (paper, via bioRxiv. http://cb.csail.mit.edu/cb/tadmap/. GitHub).
- Singh R, Hie B, Narayan A, Berger B. Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities. Genome Biology, 2021 (paper, via the journal. http://cb.csail.mit.edu/cb/schema/).
- Singh R, Palmer N, Gifford D, Berger B, Bar-Joseph Z. Active Learning for Sampling in Time-Series Experiments With Application to Gene Expression Analysis. Proc. of the 22nd International Conference on Machine Learning (ICML), 2005. (paper)
- Erden M, Zhang X, Devkota K, Singh R, Cowen L. Learning a PRECISE language for small-molecule binding. Under review, 2026 (paper, via bioRxiv. GitHub).
- NaderiAlizadeh N, Singh R. EvoPool: Evolution-Guided Pooling of Protein Language Model Embeddings. Under review, 2026 (paper, via bioRxiv).
- Catrina D, Bepler C, Sledzieski S, Singh R. Reverse Distillation: Consistently Scaling Protein Language Model Representations. ICLR, 2026 (paper, via arXiv. GitHub).
- Erden M, Devkota K, Varghese L, Cowen L, Singh R. Learning a CoNCISE language for small-molecule binding. Int'l Conf on Research in Comp Mol Bio (RECOMB), 2025 (paper, via bioRxiv. GitHub).
- Singh R, Im C, et al. Learning the Language of Antibody Hypervariability. PNAS, 2025 (paper; bioRxiv preprint. GitHub).
- NaderiAlizadeh N, Singh R. Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport. Bioinformatics Advances, 2025 (paper; bioRxiv preprint. GitHub).
- Forrester MT, Egol JR, Ozbay S, Waddell FD, Singh R, Tata PR. Topology-Driven Discovery of Transmembrane Protein S-Palmitoylation. Journal of Biological Chemistry, 2025 (paper, via bioRxiv).
- Jha K, Shonai D, Parekh A, Uezu A, Fujiyama T, Yamamoto H, Parameswaran P, Yanagisawa M, Singh R, Soderling SH. Deep Learning-coupled Proximity Proteomics to Deconvolve Kinase Signaling In Vivo. Under review, 2025 (paper, via bioRxiv).
- Sledzieski S, Versavel C, Singh R, Ocitti F, Devkota K, Kumar L, Shpilker P, Roger L, Yang J, Lewinski N, Putnam H, Klein-Seetharaman J, Berger B, Cowen L. Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC. Under review, 2024 (paper, via bioRxiv).
- Devkota K, Cowen L, Singh R. Interactome-scale comparison of co-immunoprecipitation and yeast two-hybrid assays for protein interaction prediction. Presented at the ICML AccML.bio Workshop, 2024 (paper).
- Dong C, Kan C, Devkota K, Singh R. Allo-Allo: Data-efficient prediction of allosteric sites. Under review, 2024 (paper, via bioRxiv).
- Devkota K, Shonai D, Mao J, Soderling S, Singh R. Miniaturizing, Modifying, and Augmenting Nature's Proteins with Raygun. Under review, 2024 (paper, via bioRxiv; Github).
- Singh R, Sledzieski S, Bryson B, Cowen L, Berger B. Contrastive learning in protein language space predicts interactions between drugs and protein targets. PNAS, 2023 (paper; bioRxiv preprint. GitHub).
- Sledzieski S, Devkota K, Singh R, Cowen L, Berger B. TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. Bioinformatics, 2023 (paper. GitHub).
- Sledzieski S, Singh R, Cowen L, Berger B. Contrasting drugs from decoys. NeurIPS MLSB: Workshop on Machine Learning in Structural Biology, 2022 (bioRxiv).
- Singh R, Devkota K, Sledzieski S, Berger B, Cowen L. Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinformatics, 2022. Presented at ISMB 2022 (paper).
- Sledzieski S, Singh R, Cowen L, Berger B. Adapting Protein Language Models to DTI Prediction. NeurIPS MLSB: Workshop on Machine Learning in Structural Biology, 2021 (paper).
- Sledzieski S, Singh R, Cowen L, Berger B. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Systems, 2021 (paper).
- Sledzieski S, Singh R, Cowen L, Berger B. Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model. Proc of Int'l Conf on Research in Comp Mol Bio (RECOMB) 2021 (preprint, via bioRxiv).
- Park D, Singh R, Baym M, Liao CS, Berger B. IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res. 2011 Jan;39(Database issue):D295-300 (paper, via Pubmed Central. http://isobase.csail.mit.edu).
- Hosur R, Singh R, Berger B. Sparse estimation for structural variability. Algorithms Mol Biol. 2011; 6: 12 (paper, via Pubmed Central).
A preliminary version of this paper was presented at WABI 2010. - Singh R, Park D, Xu J, Hosur R, Berger B. Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W508-15 (paper, via Pubmed Central. http://struct2net.csail.mit.edu)
- Liao CS, Lu K, Baym M, Singh R, Berger B. IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics. 2009 June 15; 25(12): i253-i258 (paper, via Pubmed Central. http://isorank.csail.mit.edu).
A preliminary version of this work was presented at Int'l Conf on Intelligent Systems for Mol Bio (ISMB) 2009. - Kaplow IM, Singh R, Friedman A, Bakal C, Perrimon N, Berger B. RNAiCut: automated detection of significant genes from functional genomic screens. Nature Methods. 2009 Jul;6(7):476-7 (paper, via Nature Methods. http://rnaicut.csail.mit.edu)
- Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci (PNAS) U S A. 2008 Sep 2;105(35):12763-8 (paper, via PNAS. Citations. http://isorank.csail.mit.edu)
- Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks. Pac Symp Biocomput. (PSB) 2008:303-14 (paper, via PSB. http://isorank.csail.mit.edu)
- Singh R, Berger B. Influence Flow: Integrating Pathway-specific RNAi data and Protein Interaction Data. Int'l Symp of Intelligent Sys in Mol Bio (ISMB) 2007, PLoS Track (Extended Abstract).
More detail is available in my PhD thesis. As per the ISMB PLoS Track rules, the extended abstract should be cited as "Personal Communications" - Sterner B, Singh R, Berger B. Predicting and annotating catalytic residues: an information theoretic approach. J Comput Biol. 2007 Oct;14(8):1058-7 (paper, via JCB)
- Singh R, Xu J, Berger B. Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. Proc of Int'l Conf on Research in Comp Mol Bio (RECOMB) 2007 (paper. Citations. http://isorank.csail.mit.edu)
- Sontag D, Singh R, Berger B. Probabilistic modeling of systematic errors in two-hybrid experiments. Pac Symp Biocomput (PSB) 2007 (paper, via PSB. http://groups.csail.mit.edu/cb/probmod2H)
- Singh R, Xu J, Berger B. Struct2net: integrating structure into protein-protein interaction prediction. Pac Symp Biocomput (PSB) 2006 (paper, via PSB. http://struct2net.csail.mit.edu)
- Singh R, Berger B. Chaintweak: sampling from the neighbourhood of a protein conformation. Pac Symp Biocomput (PSB) 2005:52-63 (paper, via PSB. http://theory.csail.mit.edu/chaintweak/)
- Singh R, Saha M. Identifying structural motifs in proteins. Pac Symp Biocomput (PSB) 2003:228-39 (paper, via PSB.)
- Marston DJ, Watanabe A, Kapingidza AB, Harris C, Van Itallie E, Devkota K, Christopher J, Liu P, Pun B, Rhodes B, Frazier M, Winters K, Burre H, Kannan P, Liang X, Kelsoe G, Wiehe K, Singh R, Wrapp D, Kuraoka M, Azoitei ML. Iterative immunogen optimization to focus immune responses on a conserved, subdominant viral epitope. Under review, 2025 (paper, via bioRxiv).
- Matuck BF, Huynh KLA, ..., Pratapa A, ..., Singh R, Tata PR, ..., Byrd KM. The Immunoregulatory Architecture of the Adult Oral Cavity. Under review, 2024 (paper, via bioRxiv).
- Ewen-Campen B, Luan H, Xu J, Singh R, Joshi N, Thakkar T, Berger B, et al. split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80. PNAS, 2023 (paper).
- Kumar L, Brenner N, Sledzieski S, Olaosebikan M, Roger LM, et al. Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome. PLoS One, 2023 (paper).
- Deshpande H, Nam U, Singh R.Classification of Music Signals In The Visual Domain. Proc of Digital Audio Effects Conf, 2001
- Lahoti A, Singh R, Mukerjee A.A Multidimensional Interval Algebra Approach for Identifying Block-Structured Media.Proc of IAPR Int'l Workshop on Graphics Recognition (GREC) 1999. (paper, via LNCS)
- Singh R, Lahoti A, Mukerjee A.Document Block Layout Analysis and Document Template Generation. Proc of Document Layout Interpretation and Analysis Workshop (DLIA) 1999 (paper)
PhD Thesis: Algorithms for the Analysis of Protein Interaction Networks ( PDF | Defense Talk )
- Winner of the George M. Sprowls Award for the Best PhD Theses in Computer Science at MIT
MS Thesis: Identifying Structural Motifs in Proteins ( PDF )
- Winner of the Christopher Stephenson Award for the Best M.S. Thesis in Computer Science at Stanford University
- Allen Chefitz and Rohit Singh. Self-administered, Non-invasive, Transcutaneous Viral Detector. USPTO 17/079649. Filed on Oct 26, 2022. Issued on Jan 20, 2022.
- Bonnie Berger Leighton and Rohit Singh. Method for identifying network similarity by matching neighborhood topology. USPTO #8000262. Filed on Apr 18, 2008; issued on Aug 16, 2011. The patent covers much of the core technology around the IsoRank algorithm.