Pavel Skums
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Eleven grand challenges in single-cell data science
D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ...
Genome biology 21 (1), 1-35, 2020
Good laboratory practice for clinical next-generation sequencing informatics pipelines
AS Gargis, L Kalman, DP Bick, C Da Silva, DP Dimmock, BH Funke, ...
Nature biotechnology 33 (7), 689-693, 2015
Efficient error correction for next-generation sequencing of viral amplicons
P Skums, Z Dimitrova, DS Campo, G Vaughan, L Rossi, JC Forbi, ...
BMC Bioinformatics 13 (Suppl 10), S6, 2012
Accurate genetic detection of hepatitis C virus transmissions in outbreak settings
DS Campo, GL Xia, Z Dimitrova, Y Lin, JC Forbi, L Ganova-Raeva, ...
The Journal of infectious diseases 213 (6), 957-965, 2016
Next-generation sequencing reveals large connected networks of intra-host HCV variants
DS Campo, Z Dimitrova, L Yamasaki, P Skums, DTY Lau, G Vaughan, ...
BMC genomics 15 (5), 1-9, 2014
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
P Skums, A Zelikovsky, R Singh, W Gussler, Z Dimitrova, S Knyazev, ...
Bioinformatics 34 (1), 163-170, 2018
Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity
P Skums, L Bunimovich, Y Khudyakov
Proceedings of the National Academy of Sciences 112 (21), 6653-6658, 2015
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, ...
BMC bioinformatics 14 (9), 1-13, 2013
A large HCV transmission network enabled a fast-growing HIV outbreak in rural Indiana, 2015
S Ramachandran, H Thai, JC Forbi, RR Galang, Z Dimitrova, G Xia, Y Lin, ...
EBioMedicine 37, 374-381, 2018
GHOST: global hepatitis outbreak and surveillance technology
AG Longmire, S Sims, I Rytsareva, DS Campo, P Skums, Z Dimitrova, ...
BMC genomics 18 (10), 21-32, 2017
Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing
BA Palmer, Z Dimitrova, P Skums, O Crosbie, E Kenny-Walsh, LJ Fanning
Journal of virology 88 (23), 13709-13721, 2014
Reconstructing viral quasispecies from NGS amplicon reads
N Mancuso, B Tork, P Skums, L Ganova-Raeva, I Măndoiu, A Zelikovsky
In silico biology 11 (5, 6), 237-249, 2011
Cliquesnv: Scalable reconstruction of intra-host viral populations from ngs reads
S Knyazev, V Tsyvina, A Melnyk, A Artyomenko, T Malygina, YB Porozov, ...
BioRxiv, 264242, 2018
Bioinformatics research and applications
H Wang, J Fazekas, M Booth, Q Liu, D Che
Drug resistance of a viral population and its individual intrahost variants during the first 48 hours of therapy
DS Campo, P Skums, Z Dimitrova, G Vaughan, JC Forbi, CG Teo, ...
Clinical Pharmacology & Therapeutics 95 (6), 627-635, 2014
Edge intersection graphs of linear 3-uniform hypergraphs
PV Skums, SV Suzdal, RI Tyshkevich
Discrete Mathematics 309 (11), 3500-3517, 2009
Inference of genetic relatedness between viral quasispecies from sequencing data
O Glebova, S Knyazev, A Melnyk, A Artyomenko, Y Khudyakov, ...
BMC genomics 18 (10), 81-88, 2017
Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry
Z Dimitrova, DS Campo, S Ramachandran, G Vaughan, L Ganova-Raeva, ...
In silico biology 11 (5-6), 183-192, 2012
Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads
N Mancuso, B Tork, P Skums, I Măndoiu, A Zelikovsky
2011 IEEE International Conference on Bioinformatics and Biomedicine …, 2011
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), 96-108, 2021
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