Rohit Singh

Conference Lecture Notes in Computer Science · January 1, 2025 We introduce PHILHARMONIC, a computational framework that couples deep learning de novo network inference with robust unsupervised spectral clustering algorithms to uncover functional relationships and high-level organization in non-model organisms. Our no ... Full text 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

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

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.

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

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