Pavel Skums

79 papers B 2Journal 34Unranked 30
YearRankTypeTitle / Venue / Authors
2026 — ed.
Computational Advances in Bio and Medical Sciences - 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers
ICCABS
Mohammed Alser, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, Alexander Zelikovsky
2025 — ed.
Computational Advances in Bio and Medical Sciences - 12th International Conference, ICCABS 2023, Norman, OK, USA, December 11-13, 2023, Revised Selected Papers
ICCABS
Mukul S. Bansal, Wei Chen, Yury Khudyakov, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Sharma V. Thankachan, Alexander Zelikovsky
2025 J jnl
Editorial: Special Section on Computational Advances in Bio and Medical Sciences.
IEEE Trans. Comput. Biol. Bioinform.
Ion I. Mandoiu, Marmar R. Moussa, Sanguthevar Rajasekaran, Pavel Skums, Sharma V. Thankachan, Alex Zelikovsky
2025 — conf
Epistatic Density of Viral Variants in Acute and Chronic HCV Patients.
ICCABS
Alina Nemira, Akshay Juyal, Pavel Skums, Alexander Zelikovsky
2024 — ed.
Bioinformatics Research and Applications - 20th International Symposium, ISBRA 2024, Kunming, China, July 19-21, 2024, Proceedings, Part I
ISBRA (1)
Wei Peng, Zhipeng Cai, Pavel Skums
2024 — ed.
Bioinformatics Research and Applications - 20th International Symposium, ISBRA 2024, Kunming, China, July 19-21, 2024, Proceedings, Part II
ISBRA (2)
Wei Peng, Zhipeng Cai, Pavel Skums
2024 — ed.
Bioinformatics Research and Applications - 20th International Symposium, ISBRA 2024, Kunming, China, July 19-21, 2024, Proceedings, Part III
ISBRA (3)
Wei Peng, Zhipeng Cai, Pavel Skums
2024 B conf
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes.
RECOMB
Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
2023 — conf
Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire.
ISBRA
Hossein Saghaian, Pavel Skums, Yurij Ionov, Alex Zelikovsky
2023 J jnl
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhipeng Cai, Min Li, Pavel Skums, Yanjie Wei
2023 J jnl
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021).
J. Comput. Biol.
Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2022 J jnl
17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021).
J. Comput. Biol.
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
2022 — ed.
Computational Advances in Bio and Medical Sciences: 11th International Conference, ICCABS 2021, Virtual Event, December 16-18, 2021, Revised Selected Papers
ICCABS
Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2022 J jnl
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms.
IEEE ACM Trans. Comput. Biol. Bioinform.
Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yan Huang, Yubao Wu
2022 J jnl
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhipeng Cai, Min Li, Pavel Skums
2022 J jnl
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhipeng Cai, Giri Narasimhan, Pavel Skums
2022 J jnl
Primary case inference in viral outbreaks through analysis of intra-host variant population.
BMC Bioinform.
Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury Khudyakov
2022 B conf
SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory Framework.
RECOMB
Pavel Skums, Fatemeh Mohebbi, Vyacheslav Tsyvina, Pelin Icer, Sumathi Ramachandran, Yury Khudyakov
2021 — conf
A Novel Network Representation of SARS-CoV-2 Sequencing Data.
ISBRA
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
2021 — ed.
Bioinformatics Research and Applications - 17th International Symposium, ISBRA 2021, Shenzhen, China, November 26-28, 2021, Proceedings
ISBRA
Yanjie Wei, Min Li, Pavel Skums, Zhipeng Cai
2021 — ed.
Computational Advances in Bio and Medical Sciences - 10th International Conference, ICCABS 2020, Virtual Event, December 10-12, 2020, Revised Selected Papers
ICCABS
Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alex Zelikovsky
2021 J jnl
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.
Briefings Bioinform.
Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky
2021 J jnl
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering.
J. Comput. Biol.
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
2021 J jnl
Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations.
J. Comput. Biol.
Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin B. Icer, Pavel Skums, Alex Zelikovsky
2021 J jnl
Scale-Free Spanning Trees and Their Application in Genomic Epidemiology.
J. Comput. Biol.
Yury L. Orlovich, Kirill Kukharenko, Volker Kaibel, Pavel Skums
2021 J jnl
Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020).
J. Comput. Biol.
Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2021 J jnl
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020).
J. Comput. Biol.
Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky
2021 J jnl
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020).
J. Comput. Biol.
Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky
2021 J jnl
Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019).
J. Comput. Biol.
Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2020 — conf
Benchmarking of computational error-correction methods for next-generation sequencing data.
BCB
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
2020 — ed.
Bioinformatics Research and Applications - 16th International Symposium, ISBRA 2020, Moscow, Russia, December 1-4, 2020, Proceedings
ISBRA
Zhipeng Cai, Ion I. Mandoiu, Giri Narasimhan, Pavel Skums, Xuan Guo
2020 — conf
Clustering Based Identification of SARS-CoV-2 Subtypes.
ICCABS
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
2020 — ed.
Computational Advances in Bio and Medical Sciences - 9th International Conference, ICCABS 2019, Miami, FL, USA, November 15-17, 2019, Revised Selected Papers
ICCABS
Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
2020 J jnl
Graph fractal dimension and the structure of fractal networks.
J. Complex Networks
Pavel Skums, Leonid Bunimovich
2020 J jnl
Inference of mutability landscapes of tumors from single cell sequencing data.
PLoS Comput. Biol.
Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums
2020 J jnl
Preface Special Issue: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019).
J. Comput. Biol.
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
2019 J jnl
12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr.
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
2019 — ed.
Bioinformatics Research and Applications - 15th International Symposium, ISBRA 2019, Barcelona, Spain, June 3-6, 2019, Proceedings
ISBRA
Zhipeng Cai, Pavel Skums, Min Li
2019 — conf
Characteristics of Bitcoin Transactions on Cryptomarkets.
SpaCCS
Xucan Chen, Mohammad Al Hasan, Xintao Wu, Pavel Skums, Mohammad Javad Feizollahi, Marie Ouellet, Eric L. Sevigny, David Maimon, Yubao Wu
2019 — conf
Detecting Illicit Drug Ads in Google+ Using Machine Learning.
ISBRA
Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yubao Wu
2019 J jnl
Graph fractal dimension and structure of fractal networks: a combinatorial perspective.
CoRR
Pavel Skums, Leonid Bunimovich
2019 J jnl
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
2019 J jnl
Inference of clonal selection in cancer populations using single-cell sequencing data.
Bioinform.
Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky
2019 J jnl
Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018).
J. Comput. Biol.
Zhipeng Cai, Pavel Skums, Alexander Zelikovsky
2019 — conf
Python Scrapers for Scraping Cryptomarkets on Tor.
SpaCCS
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
2019 — conf
Workshop on Computational Advances in Molecular Epidemiology.
BCB
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
2018 — conf
ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome.
BCB
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
2018 — ed.
Bioinformatics Research and Applications - 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings
ISBRA
Fa Zhang, Zhipeng Cai, Pavel Skums, Shihua Zhang
2018 J jnl
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants.
BMC Bioinform.
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
2018 — conf
Predicting Opioid Epidemic by Using Twitter Data.
ISBRA
Yubao Wu, Pavel Skums, Alex Zelikovsky, David Stiven Campo Rendon, Xueting Liao
2018 J jnl
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.
Bioinform.
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
2017 — conf
Agent-Based in Silico Evolution of HCV Quasispecies.
ISBRA
Alexander Artyomenko, Pelin B. Icer, Pavel Skums, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky
2017 — conf
Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning.
ICCABS
Pelin Icer Baykal, Alexander Artyomenko, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
2017 — conf
CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology.
BCB
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
2017 — conf
Classification of HCV infections through sequence image normalization.
ICCABS
Sunitha Basodi, Pelin Burcak Icer, Pavel Skums, Yury Khudyakov, Alexander Zelikovsky, Yi Pan
2017 — conf
Efficient filtering algorithm for detection of genetic similarity between large genomic datasets.
ICCABS
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
2017 — conf
Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media.
ISBRA
Deeptanshu Jha, Pavel Skums, Alex Zelikovsky, Yury Khudyakov, Rahul Singh
2016 — ed.
Bioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings
ISBRA
Anu G. Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky
2015 — conf
Algorithms for prediction of viral transmission using analysis of intra-host viral populations.
ICCABS
Pavel Skums, Olga Glebova, David S. Campo, Nana Li, Zoya Dimitrova, Seth Sims, Leonid Bunimovich, Alex Zelikovsky, Yury Khudyakov
2015 J jnl
Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.
Bioinform.
Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, Ion I. Mandoiu, David S. Campo, Zoya Dimitrova, Alex Zelikovsky, Yuri Khudyakov
2014 — conf
Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data.
ICCABS
Pavel Skums, Alexander Artyomenko, Olga Glebova, Alex Zelikovsky, David S. Campo, Zoya Dimitrova, Yuri Khudyakov
2014 — conf
New computational methods for assessing the genetic relatedness of close viral variants.
ICCABS
David S. Campo, Zoya Dimitrova, Guo-liang Xia, Pavel Skums, Lilia Ganova-Raeva, Yuri Khudyakov
2013 — conf
Alignment of DNA Mass-Spectral Profiles Using Network Flows.
ISBRA
Pavel Skums, Olga Glebova, Alex Zelikovsky, Zoya Dimitrova, David Stiven Campo Rendon, Lilia Ganova-Raeva, Yuri Khudyakov
2013 — conf
Computational analysis and modelling of intra-host adaptation of hepatitis C virus: The role of immune cross-reactivity of HCV quasispecies.
ICCABS
Pavel Skums, David S. Campo, Zoya Dimitrova, Leonid Bunimovich, Yuri Khudyakov
2013 — conf
Estimation of viral population structure from amplicon-based reads.
ICCABS
Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
2013 J jnl
Krausz dimension and its generalizations in special graph classes.
Discret. Math. Theor. Comput. Sci.
Pavel Skums, Yury Metelsky, Olga Glebova
2013 — conf
Mutational robustness of hepatitis C virus intra-host variants.
ICCABS
David S. Campo, Zoya Dimitrova, Pavel Skums, Yuri Khudyakov
2013 — conf
Optimizing pooling strategies for the massive next-generation sequencing of viral samples.
ICCABS
Pavel Skums, Olga Glebova, Alex Zelikovsky, Ion I. Mandoiu, Yuri Khudyakov
2013 J jnl
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.
BMC Bioinform.
Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu, Yuri Khudyakov, Alex Zelikovsky
2013 — conf
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies.
ICCABS
Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
2012 J jnl
Efficient error correction for next-generation sequencing of viral amplicons.
BMC Bioinform.
Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov
2012 J jnl
Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry.
Silico Biol.
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
2012 J jnl
Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response.
Silico Biol.
Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov
2012 J jnl
Reconstructing viral quasispecies from NGS amplicon reads.
Silico Biol.
Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alex Zelikovsky
2012 — conf
Workshop: A maximum likelihood method for quasispecies spectrum assembly.
ICCABS
Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alexander Zelikovsky
2011 — conf
Assessments of intra- and inter-host diversity of hepatitis C virus using Next Generation Sequencing and Mass spectrometry.
BIBM Workshops
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
2011 — conf
Modelling differential interferon resistance of HCV quasispecies.
BIBM Workshops
Pavel Skums, David S. Campo, Zoya Dimitrova, Gilberto Vaughan, Daryl T. Lau, Yuri Khudyakov
2011 — conf
Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads.
BIBM Workshops
Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion I. Mandoiu, Alexander Zelikovsky
2006 J jnl
Reconstruction of graphs with special homogeneous sets.
Electron. Notes Discret. Math.
Pavel Skums, Regina Tyshkevich