Ankit Sinha

FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

In the same cell, the proteome defines cellular state and the transcriptome marks transitions

The paper quantifies proteins and transcripts in the same cell, finding that the proteome defines stable cell states while the transcriptome reflects transitions.

Deep Visual Proteomics links vascular smooth muscle cell phenotypes to atherosclerotic plaque stability

This study uses Deep Visual Proteomics to analyze VSMC phenotypes in atherosclerotic plaques, finding spatially distinct phenotype distributions and a shift toward dedifferentiated states in unstable plaques.

Capture of Post-Pluripotency Human Neuromesodermal and Neural Tube Axial Stem Cell States

The paper captures two human axial stem cell states and identifies regulatory networks and mechanisms underlying their maintenance and differentiation.

Identification of Covalent Modifications Regulating Immune Signaling Complex Composition and Phenotype

The paper introduces a method to identify covalent modifications and protein interactions regulating immune signaling complex composition and function in monocytes.