Pavel Skums

Assistant Professor





Knyazev S, Chhugani K, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Sarwal V, Porozov Y, Wu A, Abedalthagafi M, Nagaraj S, Smith A, Skums P, Ladner J, Lam TT, Wu N, Zelikovsky A, Knight R, Crandall K, Mangul S. (2021). Unlocking capacities of viral genomics for the COVID-19 pandemic response. ArXiv

Kirpich A, Koniukhovskii V, Shvartc V, Skums P, Weppelmann TA, Imyanitov E, Semyonov S, Barsukov K, Gankin Y. (2021). Development of an interactive, agent-based local stochastic model of COVID-19 transmission and evaluation of mitigation strategies illustrated for the state of Massachusetts, USA. PloS one, 16(2)

Skums P, Kirpich A, Icer Baykal P, Zelikovsky A, Chowell G. (2020). Global transmission network of SARS-CoV-2: from outbreak to pandemic. medRxiv : the preprint server for health sciences

Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S. (2020). Benchmarking of computational error-correction methods for next-generation sequencing data. Genome biology, 21(1)

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. (2020). Eleven grand challenges in single-cell data science. Genome biology, 21(1)

Campo DS, Gussler JW, Sue A, Skums P, Khudyakov Y. (2020). Accurate spatiotemporal mapping of drug overdose deaths by machine learning of drug-related web-searches. PloS one, 15(12)

Rogovskyy AS, Caoili SEC, Ionov Y, Piontkivska H, Skums P, Tsyvina V, Zelikovsky A, Waghela SD. (2019). Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits. Infection and immunity, 87(8)

Skums P, Tsyvina V, Zelikovsky A. (2019). Inference of clonal selection in cancer populations using single-cell sequencing data. Bioinformatics (Oxford, England), 35(14)

Cai Z, Skums P, Zelikovsky A. (2019). Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018). Journal of computational biology : a journal of computational molecular cell biology, 26(8)

Tsyvina V, Campo DS, Sims S, Zelikovsky A, Khudyakov Y, Skums P. (2018). Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. BMC bioinformatics, 19(Suppl 11)

Cai Z, Skums P, Zelikovsky A. (2018). Special Issue Preface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017). Journal of computational biology : a journal of computational molecular cell biology, 25(3)

Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y. (2018). QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinformatics (Oxford, England), 34(1)

Glebova O, Knyazev S, Melnyk A, Artyomenko A, Khudyakov Y, Zelikovsky A, Skums P. (2017). Inference of genetic relatedness between viral quasispecies from sequencing data. BMC genomics, 18(Suppl 10)

Longmire AG, Sims S, Rytsareva I, Campo DS, Skums P, Dimitrova Z, Ramachandran S, Medrzycki M, Thai H, Ganova-Raeva L, Lin Y, Punkova LT, Sue A, Mirabito M, Wang S, Tracy R, Bolet V, Sukalac T, Lynberg C, Khudyakov Y. (2017). GHOST: global hepatitis outbreak and surveillance technology. BMC genomics, 18(Suppl 10)

Campo DS, Roh HJ, Pearlman BL, Fierer DS, Ramachandran S, Vaughan G, Hinds A, Dimitrova Z, Skums P, Khudyakov Y. (2016). Increased Mitochondrial Genetic Diversity in Persons Infected With Hepatitis C Virus. Cellular and molecular gastroenterology and hepatology, 2(5)

Palmer BA, Schmidt-Martin D, Dimitrova Z, Skums P, Crosbie O, Kenny-Walsh E, Fanning LJ. (2015). Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses. Journal of virology, 90(7)

Hatia RI, Dimitrova Z, Skums P, Teo EY, Teo CG. (2015). Nosocomial hepatitis C virus transmission from tampering with injectable anesthetic opioids. Hepatology (Baltimore, Md.), 62(1)

Campo DS, Xia GL, Dimitrova Z, Lin Y, Forbi JC, Ganova-Raeva L, Punkova L, Ramachandran S, Thai H, Skums P, Sims S, Rytsareva I, Vaughan G, Roh HJ, Purdy MA, Sue A, Khudyakov Y. (2016). Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings. The Journal of infectious diseases, 213(6)

Forbi JC, Layden JE, Phillips RO, Mora N, Xia GL, Campo DS, Purdy MA, Dimitrova ZE, Owusu DO, Punkova LT, Skums P, Owusu-Ofori S, Sarfo FS, Vaughan G, Roh H, Opare-Sem OK, Cooper RS, Khudyakov YE. (2015). Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana. PloS one, 10(12)

Ganova-Raeva L, Punkova L, Campo DS, Dimitrova Z, Skums P, Vu NH, Dat do T, Dalton HR, Khudyakov Y. (2015). Cryptic Hepatitis B and E in Patients With Acute Hepatitis of Unknown Etiology. The Journal of infectious diseases, 212(12)

Skums P, Bunimovich L, Khudyakov Y. (2015). Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity. Proceedings of the National Academy of Sciences of the United States of America, 112(21)

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM. (2015). Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nature biotechnology, 33(7)

Palmer BA, Dimitrova Z, Skums P, Crosbie O, Kenny-Walsh E, Fanning LJ. (2014). Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing. Journal of virology, 88(23)

Campo DS, Dimitrova Z, Yamasaki L, Skums P, Lau DT, Vaughan G, Forbi JC, Teo CG, Khudyakov Y. (2014). Next-generation sequencing reveals large connected networks of intra-host HCV variants. BMC genomics, (15 Suppl 5)

Forbi JC, Campo DS, Purdy MA, Dimitrova ZE, Skums P, Xia GL, Punkova LT, Ganova-Raeva LM, Vaughan G, Ben-Ayed Y, Switzer WM, Khudyakov YE. (2014). Intra-host diversity and evolution of hepatitis C virus endemic to Côte d'Ivoire. Journal of medical virology, 86(5)

Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y. (2015). Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinformatics (Oxford, England), 31(5)

Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A. (2013). Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC bioinformatics, (14 Suppl 9)

Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, Forbi JC, Yokosawa J, Zelikovsky A, Khudyakov Y. (2012). Efficient error correction for next-generation sequencing of viral amplicons. BMC bioinformatics, (13 Suppl 10)

Mancuso N, Tork B, Skums P, Ganova-Raeva L, Mandoiu I, Zelikovsky A. Reconstructing viral quasispecies from NGS amplicon reads. In silico biology, 11(5-6)

Skums P, Campo DS, Dimitrova Z, Vaughan G, Lau DT, Khudyakov Y. Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response. In silico biology, 11(5-6)

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