2022
- ”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.
Cell Systems, V. 13, I. 10, p. 844-856.e4, (2022}
Journal
Software
- ”Sensory nerves impede the formation of tertiary lymphoid structures and development of protective anti-melanoma immune responses"
K. Vats, O. Kruglov, B. Sahoo, V. Soman, G. V. Shurin, U. R. Chandran, P. Skums, A. Zelikovsky, M. R. Shurin, W. J. Storkus, Y. L. Bunimovich.
Cancer Immunology Research, cir.22.0110, (2022)
Journal
- ”Unlocking capacities of viral genomics for the COVID-19 pandemic response"
S. Knyazev, K. Chhugani, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, Z. Comarova, A. Lu, V. Sarwal, Y. Porozov, A. Wu, M. Abedalthagafi, S. Nagaraj, A. Smith, P. Skums, J. Ladner, T. T.-Y. Lam, N. Wu, A. Zelikovsky, R. Knight, K. Crandall, S. Mangul,
Nature Methods, https://doi.org/10.1038/s41592-022-01444-z, (2022)
Journal
- ”Excess mortality in Belarus during the COVID-19 pandemic: the case of a country with limited non-pharmaceutical interventions and limited reporting"
A. Kirpich, A. Shishkin, T. A. Weppelmann, A. Perez Tchernov, P. Skums, Y. Gankin.
Scientific Reports, 12-5475, (2022)
Journal
- ”Primary case inference in viral outbreaks through analysis of intra-host variant population"
J. Gussler, D. S. Campo, Z. Dimitrova, P. Skums, Y Khudyakov
BMC Bioinformatics 23 (1), 1-14, (2022)
Journal
- ”An investigation of spatial-temporal patterns and predictions of the COVID-19 pandemic in Colombia, 2020-2021"
A. Tariq, T. Chakhaia, S. Dahal, A. Ewing, X. Hua, S. K.Ofori, O. Prince, A. Salindri, A. E. Adeniyi, J. M. Banda, P. Skums, R. Luo, L. Y. Lara-Diaz, R. Burger, I. C.-H. Fung, E. Shim, A. Kirpich, A. Srivastava, G. Chowell
PLoS Neglected Tropical Diseases, 16 (3), e0010228, (2022)
Journal
2021
- ”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