Scholars@Duke
Rohit Singh

Rohit Singh

Assistant Professor of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Biostatistics

Selected Publications

Topology-Driven Discovery of Transmembrane Protein S-Palmitoylation.

Journal Article bioRxiv · September 8, 2024 Protein S-palmitoylation is a reversible lipophilic posttranslational modification regulating a diverse number of signaling pathways. Within transmembrane proteins (TMPs), S-palmitoylation is implicated in conditions from inflammatory disorders to respirat ... Full text Link to item Cite

TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions.

Journal Article Bioinformatics · November 1, 2023 MOTIVATION: High-quality computational structural models are now precomputed and available for nearly every protein in UniProt. However, the best way to leverage these models to predict which pairs of proteins interact in a high-throughput manner is not im ... Full text Link to item Cite

Contrastive learning in protein language space predicts interactions between drugs and protein targets.

Journal Article Proc Natl Acad Sci U S A · June 13, 2023 Sequence-based prediction of drug-target interactions has the potential to accelerate drug discovery by complementing experimental screens. Such computational prediction needs to be generalizable and scalable while remaining sensitive to subtle variations ... Full text Link to item Cite

split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80.

Journal Article Proc Natl Acad Sci U S A · June 13, 2023 The split-Gal4 system allows for intersectional genetic labeling of highly specific cell types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be contro ... Full text Link to item Cite

Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome.

Journal Article PLoS One · 2023 With the ease of gene sequencing and the technology available to study and manipulate non-model organisms, the extension of the methodological toolbox required to translate our understanding of model organisms to non-model organisms has become an urgent pr ... Full text Link to item Cite

Topsy-Turvy: integrating a global view into sequence-based PPI prediction.

Journal Article Bioinformatics · June 24, 2022 SUMMARY: Computational methods to predict protein-protein interaction (PPI) typically segregate into sequence-based 'bottom-up' methods that infer properties from the characteristics of the individual protein sequences, or global 'top-down' methods that in ... Full text Link to item Cite

GRANGER CAUSAL INFERENCE ON DAGS IDENTIFIES GENOMIC LOCI REGULATING TRANSCRIPTION

Conference ICLR 2022 - 10th International Conference on Learning Representations · January 1, 2022 When a dynamical system can be modeled as a sequence of observations, Granger causality is a powerful approach for detecting predictive interactions between its variables. However, traditional Granger causal inference has limited utility in domains where t ... Cite

D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions.

Journal Article Cell Syst · October 20, 2021 We combine advances in neural language modeling and structurally motivated design to develop D-SCRIPT, an interpretable and generalizable deep-learning model, which predicts interaction between two proteins using only their sequence and maintains high accu ... Full text Link to item Cite

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities.

Journal Article Genome Biol · May 3, 2021 A complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene expression. Technological advances in single-cell profiling have enabled researchers to assay multiple ... Full text Link to item Cite

Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling.

Journal Article Sci Signal · October 25, 2011 Characterizing the extent and logic of signaling networks is essential to understanding specificity in such physiological and pathophysiological contexts as cell fate decisions and mechanisms of oncogenesis and resistance to chemotherapy. Cell-based RNA in ... Full text Link to item Cite

Sparse estimation for structural variability.

Journal Article Algorithms Mol Biol · April 19, 2011 BACKGROUND: Proteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true variability, efficiently is challengin ... Full text Link to item Cite

IsoBase: a database of functionally related proteins across PPI networks.

Journal Article Nucleic Acids Res · January 2011 We describe IsoBase, a database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo Sapiens. Nearly all existing algorithm ... Full text Link to item Cite

Sparse estimation for structural variability

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · November 10, 2010 Proteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true variability, efficiently is challenging due to the ... Full text Cite

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.

Journal Article Nucleic Acids Res · July 2010 Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for exper ... Full text Link to item Cite

IsoRankN: spectral methods for global alignment of multiple protein networks.

Conference Bioinformatics · June 15, 2009 MOTIVATION: With the increasing availability of large protein-protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to ... Full text Link to item Cite

Graph algorithms for biological systems analysis

Conference Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms · December 1, 2008 The post-genomic era has witnessed an explosion in the quality, quantity and variety of biological data-sequence, structure, and networks. However, when building computational models on these data, some abstractions recur often. In particular, graph-based ... Cite

Global alignment of multiple protein interaction networks with application to functional orthology detection.

Journal Article Proc Natl Acad Sci U S A · September 2, 2008 Protein-protein interactions (PPIs) and their networks play a central role in all biological processes. Akin to the complete sequencing of genomes and their comparative analysis, complete descriptions of interactomes and their comparative analysis is funda ... Full text Link to item Cite

Global alignment of multiple protein interaction networks.

Conference Pac Symp Biocomput · 2008 UNLABELLED: We describe an algorithm for global alignment of multiple protein-protein interaction (PPI) networks, the goal being to maximize the overall match across the input networks. The intuition behind our algorithm is that a protein in one PPI networ ... Link to item Cite

Predicting and annotating catalytic residues: an information theoretic approach.

Journal Article J Comput Biol · October 2007 We introduce a computational method to predict and annotate the catalytic residues of a protein using only its sequence information, so that we describe both the residues' sequence locations (prediction) and their specific biochemical roles in the catalyze ... Full text Link to item Cite

Pairwise global alignment of protein interaction networks by matching neighborhood topology

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2007 We describe an algorithm, ISORANK, for global alignment of two protein-protein interaction (PPI) networks. ISORANK aims to maximize the overall match between the two networks; in contrast, much of previous work has focused on the local alignment problem- i ... Full text Cite

Probabilistic modeling of systematic errors in two-hybrid experiments.

Conference Pac Symp Biocomput · 2007 UNLABELLED: We describe a novel probabilistic approach to estimating errors in two-hybrid (2H) experiments. Such experiments are frequently used to elucidate protein-protein interaction networks in a high-throughput fashion; however, a significant challeng ... Link to item Cite

Struct2net: integrating structure into protein-protein interaction prediction.

Conference Pac Symp Biocomput · 2006 UNLABELLED: This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and co-localization, etc., Given two protein sequences, the ... Link to item Cite

Active learning for sampling in time-series experiments with application to gene expression analysis

Conference ICML 2005 - Proceedings of the 22nd International Conference on Machine Learning · December 1, 2005 Many time-series experiments seek to estimate some signal as a continuous function of time. In this paper, we address the sampling problem for such experiments: determining which time-points ought to be sampled in order to minimize the cost of data collect ... Cite

Chaintweak: sampling from the neighbourhood of a protein conformation.

Conference Pac Symp Biocomput · 2005 When searching for an optimal protein structure, it is often necessary to generate a set of structures similar, e.g., within 4A Root Mean Square Deviation (RMSD), to some base structure. Current methods to do this are designed to produce only small deviati ... Link to item Cite

Identifying structural motifs in proteins.

Journal Article Pac Symp Biocomput · 2003 In biological macromolecules, structural patterns (motifs) are often repeated across different molecules. Detection of these common motifs in a new molecule can provide useful clues to the functional properties of such a molecule. We formulate the problem ... Link to item Cite