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Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance.
Connor R, Yarmosh DA, Maier W, Shakya M, Martin R, Bradford R, Brister JR, Chain PS, Copeland CA, di Iulio J, Hu B, Ebert P, Gunti J, Jin Y, Katz KS, Kochergin A, LaRosa T, Li J, Li PE, Lo CC, Rashid S, Maiorova ES, Xiao C, Zalunin V, Pruitt KD. Connor R, et al. Among authors: kochergin a. bioRxiv [Preprint]. 2022 Nov 3:2022.11.03.515010. doi: 10.1101/2022.11.03.515010. bioRxiv. 2022. PMID: 36380755 Free PMC article. Updated. Preprint.
Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.
Connor R, Shakya M, Yarmosh DA, Maier W, Martin R, Bradford R, Brister JR, Chain PSG, Copeland CA, di Iulio J, Hu B, Ebert P, Gunti J, Jin Y, Katz KS, Kochergin A, LaRosa T, Li J, Li PE, Lo CC, Rashid S, Maiorova ES, Xiao C, Zalunin V, Purcell L, Pruitt KD. Connor R, et al. Among authors: kochergin a. Viruses. 2024 Mar 11;16(3):430. doi: 10.3390/v16030430. Viruses. 2024. PMID: 38543795 Free PMC article.
A web-based genotyping resource for viral sequences.
Rozanov M, Plikat U, Chappey C, Kochergin A, Tatusova T. Rozanov M, et al. Among authors: kochergin a. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W654-9. doi: 10.1093/nar/gkh419. Nucleic Acids Res. 2004. PMID: 15215470 Free PMC article.
NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update.
Clough E, Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Lee H, Zhang N, Serova N, Wagner L, Zalunin V, Kochergin A, Soboleva A. Clough E, et al. Among authors: kochergin a. Nucleic Acids Res. 2024 Jan 5;52(D1):D138-D144. doi: 10.1093/nar/gkad965. Nucleic Acids Res. 2024. PMID: 37933855 Free PMC article.