2021

  • ”SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework"
    P. Skums, F. Mohebbi, V. Tsyvina, P. Icer, Y. Khudyakov.
    RECOMB 2022 (accepted)

  • ”From Alpha to Zeta: Identifying variants and subtypes of SARS-CoV-2 via clustering"
    A. Melnyk, F. Mohebbi, S. Knyazev, B. Sahoo, R. Hosseini, P. Skums, A. Zelikovsky, M. Patterson
    Journal of Computational Biology 11 (2021): 1113-1129.
    Journal

  • ”Scalable reconstruction of SARS-CoV-2 phylogeny with recurrent mutations"
    D. Novikov, S. Knyazev, M. Grinshpon, P. Icer, P. Skums, A Zelikovsky
    Journal of Computational Biology 28(11), 1130-1141
    Journal

  • ”Investigating the first wave of the COVID-19 pandemic in Ukraine using epidemiological and genomic sequencing data"
    Y. Gankin, V. Koniukhovskii, A. Nemira, G. Chowell, T. A. Weppelmann, P. Skums, A. Kirpich
    Infection, Genetics and Evolution, 95:105087
    Journal

  • ”SARS-CoV-2 transmission dynamics in Belarus in 2020 revealed by genomic and incidence data analysis"
    A. Nemira, A. E. Adeniyi, E. L. Gasich, K. Y.Bulda, L. N. Valentovich, A. G. Krasko, O. Glebova, A. Kirpich, P. Skums
    Communications Medicine 1, 31. Journal Software

  • ”Scale-free Spanning Trees and their Application in Genomic Epidemiology"
    Y. Orlovich, V. Kaibel, K. Kukharenko, P. Skums
    Journal of Computational Biology 28(10), 945-960.
    Journal

  • ”Technology dictates algorithms: Recent developments in read alignment"
    M. Alser, J. Rotman, K. Taraszka, H. Shi, P. Icer Baykal, H. Taegyun Yang, V. Xue, S. Knyazev, B. D. Singer, B. Balliu, D. Koslicki, P. Skums, A. Zelikovsky, C. Alkan, O. Mutlu, S. Mangul
    Genome Biology 22 (1), 1-34
    Journal

  • ”Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction"
    S. Knyazev, V. Tsyvina, A. Shankar, A. Melnyk, A. Artyomenko, T. Malygina, Y.Porozov, E. Campbell, S. Mangul, W. Switzer, P. Skums, A. Zelikovsky
    Nucleic Acids Research: gkab576
    Journal Software

  • ”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"
    A. Kirpich, V. Koniukhovskii, V. Shvartc, P. Skums, T.A. Weppelmann, E. Imyanitov, S. Semyonov, K. Barsukov and Y. Gankin
    PLoS One 16(2): : e0247182
    Journal

  • ”Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections"
    P. Icer Baykal, J. Lara, Y. Khudyakov, A. Zelikovsky, P. Skums
    Virus Evolution 7(1): veaa103
    Journal Software

  • ”Epidemiological Data Analysis of Viral Quasispecies in the Next-Generation Sequencing Era"
    S. Knyazev, L. Hughes, P. Skums, A. Zelikovsky
    Briefings in Bioinformatics, 22(1)
    Journal

2020

  • ”Analysis of heterogeneous genomic samples using image normalization and machine learning"
    S. Basodi, P. Icer Baykal, A. Zelikovsky, P. Skums, Y. Pan
    BMC Genomics 21:405
    Journal Software

  • ”Using earth mover’s distance for viral outbreak investigations"
    A. Melnyk, S. Knyazev, F. Vannberg, L. Bunimovich, P. Skums, A. Zelikovsky
    BMC Genomics 21(Suppl 5):582
    Journal Software

  • ”Accurate spatiotemporal mapping of drug overdose deaths by machine learning of drug-related web-searches"
    D. Campo, J. Gussler, A. Sue, P. Skums, Y. Khudyakov
    PLOS One 15(12): e0243622
    Journal

  • ”Inference of mutability landscapes of tumors from single cell sequencing data"
    V. Tsyvina, A. Zelikovsky, S. Snir, P. Skums
    PLOS Computational Biology 16(11): e1008454
    Journal Software

  • ”Graph fractal dimension and the structure of fractal networks"
    P. Skums and L. Bunimovich
    Journal of Complex Networks 8 (4)
    Journal

  • ”Benchmarking of computational error-correction methods for next-generation sequencing via unique molecular identifier"
    K. Mitchell, I. Mandric, L. Martin, E. Gerasimov, R. Littman, B. Hill, N. C. Wu, H. Yang, K. Hsieh, L. Chen, T. Shabani, G. Shabanets, D. Yao, R. Sun, J. Schroeder, E. Eskin, A. Zelikovsky, P. Skums, M. Pop, S. Mangul
    Genome Biology 21 (71).
    Journal

  • ”Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms"
    F. Zhao, P. Skums, A. Zelikovsky, E. L Sevigny, M. H. Swahn, S. M. Strasser, Y. Wu
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2020.2978476
    Journal

  • ”Eleven Grand Challenges in Single-Cell Data Science"
    D. Lähnemann, J. Koester, E. Szczurek, D. McCarthy, S. Hicks, M. D. Robinson, C. Vallejos, N. Beerenwinkel, K. Campbell, A. Mahfouz, L. Pinello, P. Skums, A. Stamatakis, C. Attolini, S. Aparicio, J. Baaijens, M. Balvert, B. de Barbanson, A. Cappuccio, G. Corleone, B. Dutilh, M. Florescu, V. Guryev, R. Holmer, K. Jahn, T. Jessurun Lobo, E. Keizer, I. Khatri, S. Kiełbasa, J. Korbel, A. Kozlov, T.-H. Kuo, B. Lelieveldt, I. Mandoiu, J. Marioni, T. Marschall, F. Mölder, A. Niknejad, L. Rączkowski, M. Reinders, J. de Ridder, A.-E. Saliba, A. Somarakis, O. Stegle, F. Theis, H. Yang, A. Zelikovsky, A. McHardy, B. Raphael, S. Shah, A. Schonhuth
    Genome Biology, 21 (31)
    Journal

2019

  • ”Delineating surface epitopes of Lyme disease pathogen targeted by highly protective antibodies of New Zealand White rabbits"
    A. Rogovskyy, S. Caoili, Y. Ionov, H. Piontkivska, P. Skums, V. Tsyvina, A. Zelikovsky, S. Waghela
    Infection and Immunity, 13:IAI-00246
    Journal

  • ”Inference of clonal selection in cancer populations using single-cell sequencing data"
    P Skums, V Tsyvina, A Zelikovsky
    Bioinformatics, 35 (14): i398-i407
    Journal Software

  • ”Detecting Illicit Drug Ads in Google+ Using Machine Learning”.
    F. Zhao, P. Skums, A. Zelikovsky, E. L. Sevigny, M. H. Swahn, S. M. Strasser, Y. Wu
    Lecture Notes in Bioinformatics, V. 11490, pp. 171-179
    Proceedings

2018

  • QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
    P. Skums, A. Zelikovsky, R. Singh, W. Gussler, Z. Dimitrova, S. Knyazev, I. Mandric, S. Ramachandran, D. Campo, D. Jha, L. Bunimovich, E. Costenbader, C. Sexton, S. O'Connor,G.-l. Xia and Y. Khudyakov
    Bioinformatics, 34 (1), 163–170
    Journal Software

  • A large HCV transmission network enabled a fast-growing HIV outbreak in rural Indiana, 2015,
    S. Ramachandran, H. Thai, J. C. Forbi, R. R. Galang, Z. Dimitrova, G.-l. Xia, Y. Lin et al.
    EBioMedicine
    Journal

  • Fast estimation ofgenetic relatedness between members of heterogeneous populations of closely related genomic variants,
    V Tsyvina, DS Campo, S Sims, A Zelikovsky, Y Khudyakov, and P Skums
    BMC Bioinformatics 19(Suppl 11): 360
    Journal Software

  • Predicting Opioid Epidemic by Using Twitter Data,
    Y. Wu, P. Skums, A. Zelikovsky, D. Campo Rendon, X. Liao
    Lecture Notes in Bioinformatics, V. 10847, pp. 314-318
    Proceedings

2017

  • Inference of genetic relatedness between viral quasispecies from sequencing data,
    O. Glebova, S. Knyazev, A. Melnick, A. Artyomenko, Y. Khudyakov, A. Zelikovsky and P. Skums,
    BMC Bioinformatics, 18 (10), 918
    Journal Software

  • GHOST: Global Health Outbreak and Surveillance Technology,
    A. G. Longmire, S. Sims, I. Rytsareva, D. S. Campo Rendon, Z. Dimitrova, S. Ramachandran, M. Medrzycki, H. Thai, L. Ganova-Raeva, Y. Lin, L. T. Punkova, A. Sue, P. Skums, M. Mirabito, S. Wang, R. Tracy, V. Bolet, T. Sukalac, C. Lynberg and Y. Khudyakov
    BMC Bioinformatics, 18 (10), 916
    Journal

  • Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media
    D. Jha, P. Skums, A. Zelikovsky, Y. Khudyakov, and R. Singh
    Lecture Notes in Bioinformatics, V. 10330, pp. 425-430
    Proceedings

  • Agent-Based in Silico Evolution of HCV Quasispecies
    A. Artyomenko, P. B. Icer, P. Skums, S. Ramachandran, Y. Khudyakov, and A. Zelikovsky
    Lecture Notes in Bioinformatics, V. 10330, pp. 420-424
    Proceedings


2016

  • Increased mitochondrial genetic diversity in persons infected with hepatitis C virus
    D. S. Campo, H.-J. Roh, B.Pearlman, D.S. Fierer, S. Ramachandran, G. Vaughan, Z. Dimitrova, P. Skums, Y Khudyakov
    Cellular and Molecular Gastroenterology and Hepatology, 2(5), 676-684
    Journal

  • Accurate genetic detection of hepatitis C virus transmissions in outbreak settings
    D.S. Campo, G.-.L Xia, Z. Dimitrova, Y. Lin, J.C. Forbi, L. Ganova-Raeva, L. Punkova, S. Ramachandran, H. Thai, P. Skums, S. Sims, I. Rytsareva, G. Vaughan, H.J. Roh, M.A. Purdy, A. Sue, Y. Khudyakov
    The Journal of Infectious Diseases, 213 (6), 957-965
    Journal

  • Graph Hausdorff dimension, Kolmogorov complexity and construction of fractal graphs
    L. Bunimovich and P. Skums
    arXiv:1607.04703
    Preprint

  • 2015

    • Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity
      P. Skums, L. Bunimovich, Y. Khudyakov
      Proc Natl Acad Sci USA, 112 (21), 6653-6658
      Journal

    • Nosocomial hepatitis C virus transmission from tampering with injectable anesthetic opioids
      R. Hatia, Z. Dimitrova, P. Skums, E. Teo and C.-G. Teo
      Hepatology, 62(1):101-110
      Journal

    • Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling
      P. Skums, A. Artyomenko, O. Glebova, S. Ramachandran, I.I. Mandoiu, D. S. Campo, Z. Dimitrova, A. Zelikovsky, and Y. Khudyakov
      Bioinformatics, 31(5): 682-690
      Journal Software

    • Network analysis of the chronic Hepatitis C virome defines HVR1 evolutionary phenotypes in the context of humoral immune responses
      B. Palmer, D. Schmidt-Martin, Z. Dimitrova, P. Skums, O. Crosbie, E. Kenny-Walsh, L. Fanning
      Journal of Virology, 90(7):3318-29
      Journal

    • Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana
      J.C. Forbi, J.E. Layden, R.O. Phillips, N. Mora, G.L. Xia, D.S. Campo, M. Purdy, Z. Dimitrova, D.O. Owusu, L. Punkova, P. Skums, S. Owusu-Ofori, F.S. Sarfo, G. Vaughan, H. Roh, O.K. Opare-Sem, R.S. Cooper, Y.E.Khudyakov
      PLoS One, 18;10(12):e0145530
      Journal

    • Good laboratory practice for clinical next-generation sequencing informatics pipelines
      A.S. Gargis, L. Kalman, D.P Bick, C. da Silva, D. P. Dimmock, B. H Funke, S. Gowrisankar, M. R Hegde, S. Kulkarni, C. E Mason, R. Nagarajan, K. V Voelkerding, E. A Worthey, N. Aziz, J. Barnes, S. F Bennett, H. Bisht, D. M Church, Z. Dimitrova, S. R Gargis, N. Hafez, T. Hambuch, F. C L Hyland, R. A. Luna, D. MacCannell,T. Mann, M. R McCluskey, T. K McDaniel, L. M Ganova-Raeva, H. L Rehm, J. Reid, D. S Campo, R. B Resnick, P. G Ridge, M. L Salit, P. Skums, L.-J. C Wong, B. A Zehnbauer, J. M Zook and I. M Lubin
      Nature Biotechnology, 33: 689–693
      Journal

    • Cryptic hepatitis B and E in acute hepatitis of unknown etiology
      L. Ganova-Raeva, L. Punkova, D. S. Campo, Z. Dimitrova, P. Skums, N. H. Vu, D.T. Dat, H. R. Dalton and Y. Khudyakov
      The Journal of Infectious Diseases, 212 (12): 1962-1969
      Journal

    • Algorithms for prediction of viral transmission using analysis of intra-host viral populations
      P. Skums, O. Glebova, D.S. Campo, N. Li, Z. Dimitrova, S. Sims, L. Bunimovich, A. Zelikovsky, Yu. Khudyakov
      In Computational Advances in Bio and Medical Sciences (ICCABS), 2015 IEEE 5th International Conference, doi: 10.1109/ICCABS.2015.7344725
      Proceedings

    2014

    • Analysis of the evolution and structure of a complex intra-host viral population in chronic Hepatitis C mapped by ultra-deep pyrosequencing
      B. Palmer, Z. Dimitrova, {\bf P. Skums}, O. Crosbie,E. Kenny-Walsh and L. Fanning
      Journal of Virology, 88(23), 13709-13721
      Journal

    • Drug-resistance of a viral population and its individual intra-host variants during the first 48 hours of therapy
      D.S. Campo, P. Skums, Z. Dimitrova, G. Vaughan, J. Forbi, C.-G. Teo, Y. Khudyakov and D. T.-Y. Lau
      Clinical Pharmacology and Therapeutics, 95(6):627-635
      Journal

    • Next-generation sequencing reveals large connected networks of intra-host HCV variants
      D. S. Campo, Z. Dimitrova, L. Yamasaki, P. Skums, D. T.-Y. Lau, G. Vaughan, J. C. Forbi, C.-G. Teo and Y. Khudyakov
      BMC Genomics, 15(Suppl 5):S4
      Journal

    • Intra-host diversity and evolution of hepatitis C virus endemic to Cote d'Ivoire
      J. C. Forbi, D. S. Campo, M. A. Purdy, Z. E. Dimitrova, P. Skums, G.-l. Xia, L. T. Punkova, L. M. Ganova-Raeva, G. Vaughan, Y. Ben-Ayed, W. M. Switzer, Y. E.Khudyakov
      Journal of Medical Virology, V. 86, I. 5, P. 765-771
      Journal

    • 2013

      • Reconstruction of Viral Population Structure from Next-Generation Sequencing Data Using Multicommodity Flows
        P. Skums, N. Mancuso, A. Artyomenko, B. Tork, I. Mandoiu, Y. Khudyakov and A. Zelikovsky
        BMC Bioinformatics, 14(Suppl 9):S2
        Journal Software

      • H-product of graphs, H-threshold graphs and threshold-width of graphs
        P. Skums
        Discrete Mathematics, Vol. 313, I. 21, P. 2390-2400
        Journal

      • Krausz dimension and its generalizations in special graph classes
        O. Glebova, Y. Metelsky, P. Skums
        Discrete Mathematics and Theoretical Computer Science, Vol. 15:1, 107-120
        Journal

      • Alignment of DNA mass-spectral profiles using network flows
        P. Skums, O. Glebova, A. Zelikovsky, Z. Dimitrova, D. S. Campo, L. Ganova-Raeva and Y. Khudyakov
        Lecture Notes in Bioinformatics, Vol. 7875, P. 149-161
        Proceedings Software

      • 2012

        • Efficient error correction for next-generation sequencing of viral amplicons
          P. Skums, Z. Dimitrova, D. S. Campo, G. Vaughan, L. Rossi, J. C. Forbi, J. Yokosawa, A. Zelikovsky and Y. Khudyakov
          BMC Bioinformatics, 13 (Suppl 10):S6
          Journal Software

        • Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response
          P. Skums, D. S. Campo, Z. Dimitrova, G. Vaughan, D. T. Lau and Y. Khudyakov
          In Silico Biol, 11(5):263-9
          Journal

        • Reconstructing Viral Quasispecies from NGS Amplicon Reads
          N. Mancuso, B. Tork, P. Skums, L. Ganova-Raeva, I. Mandoiu and A. Zelikovsky
          In Silico Biol, 11(5):237-49
          Journal

        • Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry
          Z. Dimitrova, D. S. Campo, S. Ramachandran, G. Vaughan, L. Ganova-Raeva, Y. Lin, J. C. Forbi, G. Xia, P. Skums, B. Pearlman, Y. Khudyakov
          In Silico Biol, 11(5):183-92
          Journal

        • 2010

          • Operator decomposition of graphs and the reconstruction conjecture
            P.V. Skums, S.V. Suzdal, R.I. Tyshkevich
            Discrete Mathematics, 310, P. 423-429
            Journal

          • Algebraic decomposition of graphs
            R.I. Tyshkevich, P.V. Skums, S.V. Suzdal
            Proc. of the Institute of Mathematics of NASB, V. 18. P. 99 - 115

          2009

          • Edge intersection graphs of linear 3-uniform hypergraphs
            P.V. Skums, S.V. Suzdal, R.I. Tyshkevich
            Discrete Mathematics, 309, P. 3500-3517
            Journal

          • Reconstruction conjecture for graphs with restrictions on 4-paths
            P.V. Skums, R.I. Tyshkevich
            Discrete Analysis and Operations research, Vol. 16. N. 4. P. 87 - 96.

          • Network Design, Survivable Routing and Channel Assignment in WDM and TDM Optical Networks
            Yu. Metelsky, Yu. Orlovich, P. Skums, Y. Wang, Daoliang Yang, U. Irkhin, D. Dmitriev
            In International Network Optimization Conference (INOC 2009), G.Bigi, A. Frangioni and M.G. Scutella editors, paper MC3-2, 6 p.
            Journal

          • Reconstruction conjecture for P_4-disconnected and P_4-tidy graphs
            P. Skums, R. Tyshkevich
            In Odessa Workshop on Discrete Mathematics, I. 8, P. 46-50


          2007

          • Bipartite operator decomposition of graphs and the reconstruction conjecture
            P.V. Skums, R.I. Tyshkevich
            Electronic Notes in Discrete Mathematics, Vol. 29. P. 201-205

          • Reconstruction conjecture in the classes of (P,Q)-decomposable and P_4-disconnected graphs
            P.V. Skums, R.I. Tyshkevich
            In 3rd international scientific conference "Scheduling theory and decomposition methods", P. 146-149

          • Operator decomposition of graphs and the reconstruction conjecture
            P.V. Skums, S.V. Suzdal, R.I. Tyshkevich
            Electronic Notes in Discrete Mathematics, Vol. 28, p. 11-16
            Journal

          2006

          • Reconstruction of graphs with special homogeneous sets
            P.V. Skums, R.I. Tyshkevich
            Electronic Notes in Discrete Mathematics, Vol. 27, p. 97 - 98

          • Squares of intersection graphs and induced matchings
            Yu.L. Orlovich, P.V. Skums
            Electronic Notes in Discrete Mathematics, Vol. 24, p. 223 - 230
            Journal

          2005

          • Krausz decomposition in the class of split graphs
            P.V. Skums
            Vestnik BGU, N. 3, P. 96 - 100.

          • On one extension of the class of split graphs
            P.V. Skums, S.V. Suzdal, R.I. Tyshkevich
            Vestsi NAN Belarusi, N. 4, P. 65 - 71.

          • Recognizing edge intersection graphs of linear 3-uniform hypergraphs in the class of {Butterfly, Gem}-free graphs
            P.V. Skums, R.I. Tyshkevich
            Proc. of the Institute of Mathematics of NASB, V. 13. P. 74 - 81.

          • Edge intersection graphs of linear 3-uniform hypergraphs
            P.V. Skums, S.V. Suzdal, R.I. Tyshkevich
            Electronic Notes in Discrete Mathematics, Vol. 22, p. 33 - 40.
            Journal

          2004

          • On the polynomial solvability threshold for the problem of recognizing edge intersection graphs of linear 3-uniform hypergraphs
            P.V. Skums, S.V. Suzdal, R.I. Tyshkevich
            Dokladi NASB, V. 48, N.4, P. 29-34