Filling gaps in a metabolic network using expression information. - Peter V. Kharchenko; Dennis Vitkup; George M. Church (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Identifying metabolic enzymes with multiple types of association evidence. - Peter V. Kharchenko; Lifeng Chen; Yoav Freund; Dennis Vitkup; George M. Church (BMC Bioinform., 2006)

Comparative analysis of metazoan chromatin organization Open. - Joshua Wing Kei Ho; Youngsook L. Jung; Tao Liu 022; Burak Han Alver; Soohyun Lee; Kohta Ikegami; Kyung-Ah Sohn; Aki Minoda; Michael Y. Tolstorukov; Alex Appert; Stephen C. J. Parker; Tingting Gu; et al. (Nat., 2014)

RNA velocity of single cells. - Gioele La Manno; Ruslan A. Soldatov; Amit Zeisel; Emelie Braun; Hannah Hochgerner; Viktor Petukhov; Katja Lidschreiber; Maria E. Kastriti; Peter Lönnerberg; Alessandro Furlan; Jean Fan; Lars E. Borm; et al. (Nat., 2018)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data. - Louis Faure; Ruslan A. Soldatov; Peter V. Kharchenko; Igor Adameyko (Bioinform., 2023)

Analysis CNVs in Cancer and Normal Tissues with Transcriptomics Data. - Peter V. Kharchenko (BIOSTEC, 2025)