Vibhor Kumar

The paper introduces NIRD, a method for inferring gene networks from sparse single-cell data, showing improved performance and consistency across datasets.

The paper evaluates deconvolution methods for inferring immune infiltration from bulk gene expression using a DREAM Challenge, finding that some community-contributed methods, especially deep learning-based ones, perform well.

The paper uses epigenetic features to predict disease-associated genes and their regulators, emphasizing cell-type context and validating findings with genomic data.

scEpiSearch enables accurate matching of single-cell open-chromatin profiles to large reference datasets, improving co-embedding and classification of epigenomic states across species and platforms.

The paper introduces a graph-wavelet model to predict protein biophysical properties and assess mutational effects by analyzing amino-acid features in protein structures.

The paper predicts gene functions using epigenomic patterns and TF binding, achieving high accuracy and validating results with CRISPR screens and PubMed data.

The paper develops a method to predict both local and long-range chromatin interactions using single-cell open-chromatin profiles, revealing insights into cis-regulatory elements in the human brain.

FITs recovers true signals from sparse and noisy single-cell open-chromatin profiles by using a forest of imputation trees to avoid bias and preserve cell-type-specific activity.

UniPath uses pathway and gene-set enrichment scores to analyze single-cell epigenome and transcriptome data, revealing biologically meaningful co-clustering and aiding in cancer cell regulation inference.

This paper introduces GWNet, a graph-wavelet method for gene-network inference that improves consistency in single-cell transcriptome analysis, revealing age-related regulatory changes in lung cells.

This paper introduces TPDS, a dimension reduction method that preserves both distance and local topology, improving classification and handling outliers in biomedical datasets.