Pavel Skums

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 46

Top Topics

Computational Approaches

Grand Challenges

International Symposium

Top Venues

J. Comput. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes. RECOMB (2024)
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). J. Comput. Biol. 30 (8) (2023)
Hossein Saghaian, Pavel Skums, Yurij Ionov, Alex Zelikovsky
Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire. ISBRA (2023)
Zhipeng Cai, Min Li, Pavel Skums, Yanjie Wei
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). J. Comput. Biol. 30 (4) (2023)
Zhipeng Cai, Pavel Skums, Alexander Zeilkovsky
18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). J. Comput. Biol. 30 (9) (2023)
Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury Khudyakov
Primary case inference in viral outbreaks through analysis of intra-host variant population. BMC Bioinform. 23 (1) (2022)
Zhipeng Cai, Min Li, Pavel Skums
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Pavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer, Sumathi Ramachandran, Yury Khudyakov
SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory Framework. RECOMB (2022)
Zhipeng Cai, Giri Narasimhan, Pavel Skums
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021). J. Comput. Biol. 29 (10) (2022)
Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yan Huang, Yubao Wu
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019). J. Comput. Biol. 28 (2) (2021)
Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). J. Comput. Biol. 28 (7) (2021)
Yury L. Orlovich, Kirill Kukharenko, Volker Kaibel, Pavel Skums
Scale-Free Spanning Trees and Their Application in Genomic Epidemiology. J. Comput. Biol. 28 (10) (2021)
Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin B. Icer, Pavel Skums, Alex Zelikovsky
Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations. J. Comput. Biol. 28 (11) (2021)
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. J. Comput. Biol. 28 (11) (2021)
Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). J. Comput. Biol. 28 (8) (2021)
Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020). J. Comput. Biol. 28 (11) (2021)
Sergey Knyazev, Daniel Novikov, Mark Grinshpon, Harman Singh, Ram Ayyala, Varuni Sarwal, Roya Hosseini, Pelin Icer Baykal, Pavel Skums, Ellsworth Campbell, Serghei Mangul, Alex Zelikovsky
A Novel Network Representation of SARS-CoV-2 Sequencing Data. ISBRA (2021)
Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. Briefings Bioinform. 22 (1) (2021)
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
Preface Special Issue: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019). J. Comput. Biol. 27 (2) (2020)
Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums
Inference of mutability landscapes of tumors from single cell sequencing data. PLoS Comput. Biol. 16 (11) (2020)
Pavel Skums, Leonid Bunimovich
Graph fractal dimension and the structure of fractal networks. J. Complex Networks 8 (4) (2020)
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
Clustering Based Identification of SARS-CoV-2 Subtypes. ICCABS (2020)
Keith Mitchell, Jaqueline J. Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S. Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Littman, Brian L. Hill, Nicholas C. Wu, Harry (Taegyun) Yang, Kevin Hsieh, Linus Chen, Eli Littman, Taylor Shabani, German Enik, Douglas Yao, Ren Sun, Jan Schroeder, Eleazar Eskin, Alex Zelikovsky, Pavel Skums, Mihai Pop, Serghei Mangul
Benchmarking of computational error-correction methods for next-generation sequencing data. BCB (2020)
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018). J. Comput. Biol. 26 (8) (2019)
Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (4) (2019)
Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yubao Wu
Detecting Illicit Drug Ads in Google+ Using Machine Learning. ISBRA (2019)
Yubao Wu, Fengpan Zhao, Xucan Chen, Pavel Skums, Eric L. Sevigny, David Maimon, Marie Ouellet, Monica Haavisto Swahn, Sheryl M. Strasser, Mohammad Javad Feizollahi, Youfang Zhang, Gunjan Sekhon
Python Scrapers for Scraping Cryptomarkets on Tor. SpaCCS (2019)
Xucan Chen, Mohammad Al Hasan, Xintao Wu, Pavel Skums, Mohammad Javad Feizollahi, Marie Ouellet, Eric L. Sevigny, David Maimon, Yubao Wu
Characteristics of Bitcoin Transactions on Cryptomarkets. SpaCCS (2019)
Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky
Inference of clonal selection in cancer populations using single-cell sequencing data. Bioinform. 35 (14) (2019)
Pavel Skums, Leonid Bunimovich
Graph fractal dimension and structure of fractal networks: a combinatorial perspective. CoRR (2019)
David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7 (2019)
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
Workshop on Computational Advances in Molecular Epidemiology. BCB (2019)
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome. BCB (2018)
Yubao Wu, Pavel Skums, Alex Zelikovsky, David Stiven Campo Rendon, Xueting Liao
Predicting Opioid Epidemic by Using Twitter Data. ISBRA (2018)
Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David S. Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhán O'Connor, Guo-liang Xia, Yury Khudyakov
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinform. 34 (1) (2018)
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
Preface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017). J. Comput. Biol. 25 (3) (2018)
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. BMC Bioinform. (11) (2018)
Pelin Icer Baykal, Alexander Artyomenko, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning. ICCABS (2017)
Sunitha Basodi, Pelin Burcak Icer, Pavel Skums, Yury Khudyakov, Alexander Zelikovsky, Yi Pan
Classification of HCV infections through sequence image normalization. ICCABS (2017)
Deeptanshu Jha, Pavel Skums, Alex Zelikovsky, Yury Khudyakov, Rahul Singh
Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media. ISBRA (2017)
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
Efficient filtering algorithm for detection of genetic similarity between large genomic datasets. ICCABS (2017)
Alexander Artyomenko, Pelin B. Icer, Pavel Skums, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky
Agent-Based in Silico Evolution of HCV Quasispecies. ISBRA (2017)
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology. BCB (2017)
Pavel Skums, Olga Glebova, David S. Campo, Nana Li, Zoya Dimitrova, Seth Sims, Leonid Bunimovich, Alex Zelikovsky, Yury Khudyakov
Algorithms for prediction of viral transmission using analysis of intra-host viral populations. ICCABS (2015)
Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, Ion I. Mandoiu, David S. Campo, Zoya Dimitrova, Alex Zelikovsky, Yuri Khudyakov
Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinform. 31 (5) (2015)
David S. Campo, Zoya Dimitrova, Guo-liang Xia, Pavel Skums, Lilia Ganova-Raeva, Yuri Khudyakov
New computational methods for assessing the genetic relatedness of close viral variants. ICCABS (2014)
Pavel Skums, Alexander Artyomenko, Olga Glebova, Alex Zelikovsky, David S. Campo, Zoya Dimitrova, Yuri Khudyakov
Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data. ICCABS (2014)
Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. ICCABS (2013)
Pavel Skums, David S. Campo, Zoya Dimitrova, Leonid Bunimovich, Yuri Khudyakov
Computational analysis and modelling of intra-host adaptation of hepatitis C virus: The role of immune cross-reactivity of HCV quasispecies. ICCABS (2013)
Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu, Yuri Khudyakov, Alex Zelikovsky
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC Bioinform. 14 (S-9) (2013)
Pavel Skums, Yury Metelsky, Olga Glebova
Krausz dimension and its generalizations in special graph classes. Discret. Math. Theor. Comput. Sci. 15 (1) (2013)
Pavel Skums
H-threshold graphs and threshold-width of graphs. Discret. Math. 313 (21) (2013)
Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
Estimation of viral population structure from amplicon-based reads. ICCABS (2013)
Pavel Skums, Olga Glebova, Alex Zelikovsky, Zoya Dimitrova, David Stiven Campo Rendon, Lilia Ganova-Raeva, Yuri Khudyakov
Alignment of DNA Mass-Spectral Profiles Using Network Flows. ISBRA (2013)
Pavel Skums, Olga Glebova, Alex Zelikovsky, Ion I. Mandoiu, Yuri Khudyakov
Optimizing pooling strategies for the massive next-generation sequencing of viral samples. ICCABS (2013)
David S. Campo, Zoya Dimitrova, Pavel Skums, Yuri Khudyakov
Mutational robustness of hepatitis C virus intra-host variants. ICCABS (2013)
Zoya Dimitrova, David S. Campo, Sumathi Ramachandran, Gilberto Vaughan, Lilia Ganova-Raeva, Yulin Lin, Joseph C. Forbi, Guo-liang Xia, Pavel Skums, Brian L. Pearlman, Yuri Khudyakov
Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry. Silico Biol. 11 (5-6) (2012)
Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alexander Zelikovsky
Workshop: A maximum likelihood method for quasispecies spectrum assembly. ICCABS (2012)
Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alex Zelikovsky
Reconstructing viral quasispecies from NGS amplicon reads. Silico Biol. 11 (5-6) (2012)
Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov
Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response. Silico Biol. 11 (5-6) (2012)
Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov
Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinform. 13 (S-10) (2012)
Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov
Modelling differential interferon resistance of HCV quasispecies. BIBM Workshops (2011)
Zoya Dimitrova, David S. Campo, Sumathi Ramachandran, Gilberto Vaughan, Lilia Ganova-Raeva, Yulin Lin, Joseph C. Forbi, Guo-liang Xia, Pavel Skums, Brian L. Pearlman, Yuri Khudyakov
Assessments of intra- and inter-host diversity of hepatitis C virus using Next Generation Sequencing and Mass spectrometry. BIBM Workshops (2011)
Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion I. Mandoiu, Alexander Zelikovsky
Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads. BIBM Workshops (2011)
Pavel Skums, Regina Tyshkevich
Reconstruction of graphs with special homogeneous sets. Electron. Notes Discret. Math. 27 (2006)