Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues. - Shamil R. Sunyaev; Igor V. Rodchenkov; Frank Eisenhaber; Eugene N. Kuznetsov (RECOMB, 1998)

Session Introduction: Inferring SNP Function Using Evolutionary, Structural and Computational Methods. - Matthew W. Dimmic; Shamil R. Sunyaev; Carlos D. Bustamante (Pacific Symposium on Biocomputing, 2005)

Analysis of Sequence Conservation at Nucleotide Resolution. - Saurabh Asthana; Mikhail A. Roytberg; John A. Stamatoyannopoulos; Shamil R. Sunyaev (PLoS Comput. Biol., 2007)

Interpreting Population Sequencing Data. - Shamil R. Sunyaev (ISBRA, 2009)

Assigning spectrum-specific P-values to protein identifications by mass spectrometry. - Victor Spirin; Alexander Shpunt; Jan Seebacher; Marc Gentzel; Andrej Shevchenko; Steven Gygi; Shamil R. Sunyaev (Bioinform., 2011)

Network-based inference from complex proteomic mixtures using SNIPE. - David P. Nusinow; Adam Kiezun; Daniel J. O'Connell; Joel M. Chick; Yingzi Yue; Richard L. Maas; Steven Gygi; Shamil R. Sunyaev (Bioinform., 2012)

Integrative analysis of 111 reference human epigenomes Open. - Roadmap Epigenomics Consortium; Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi Moussavi; Pouya Kheradpour; ZhiZhuo Zhang; Jianrong Wang; Michael J. Ziller; Viren Amin; et al. (Nat., 2015)

novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data. - Anwoy Kumar Mohanty; Dana Vuzman; Laurent C. Francioli; Christopher Cassa; Ágnes Tóth-Petróczy; Shamil R. Sunyaev (Bioinform., 2019)

FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. - Hufeng Zhou; Theodore Arapoglou; Xihao Li; Zilin Li; Xiuwen Zheng 001; Jill Moore; Abhijith Asok; Sushant Kumar; Elizabeth E. Blue; Steven Buyske; Nancy J. Cox; Adam Felsenfeld; et al. (Nucleic Acids Res., 2023)

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Lane Fitzsimmons; Maria T. Acosta; David R. Adams; Ben Afzali; Ali Al-Beshri; Eric Allenspach; Aimee Allworth; Raquel L. Alvarez; Justin Alvey; Ashley Andrews; Euan A. Ashley; Carlos A. Bacino; et al. (BioData Min., 2025)