Saptarshi Pyne

This study uses single-cell RNA sequencing to identify gene regulatory networks in mucilage-producing roots across maize, sorghum, and Medicago truncatula, revealing shared and species-specific regulators.

The paper investigates how loss of PTPRB function affects VEGFR1 activation in tumors, finding that PTPRB deficiency leads to ligand-independent dimerization and sustained phosphorylation of VEGFR1, promoting tumor vascularization.

This paper constructs a gene regulatory network for Aspergillus fumigatus using RNA-seq data, validates it with experimental cases, and provides an online resource called GRAsp.

The paper introduces MERLIN+P+TFA to robustly estimate transcription factor activity and infer gene regulatory networks from bulk and single-cell data, showing improved accuracy in yeast and mammalian systems.

The paper benchmarks eleven network inference methods on scRNA-seq datasets to evaluate their performance in recovering gene regulatory networks.

This paper introduces scMTNI, a framework to infer cell type-specific gene regulatory networks on cell lineages using scRNA-seq and scATAC-seq data, showing its effectiveness on simulated and real datasets.

This paper introduces two memory-efficient algorithms for reconstructing time-varying gene regulatory networks without assuming smooth time variation, achieving state-of-the-art accuracy on benchmark datasets.

This paper introduces TGS and TGS+ algorithms for reconstructing time-varying gene regulatory networks, showing superior true positive detection but challenges in false positive rejection and memory usage.