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
Technology dictates algorithms: recent developments in read alignment
M Alser, J Rotman, D Deshpande, K Taraszka, H Shi, PI Baykal, HT Yang, ...
Genome biology 22 (1), 249, 2021
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
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
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
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, 1-13, 2013
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
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
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
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, ...
Nucleic acids research 49 (17), e102-e102, 2021
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
Benchmarking of computational error-correction methods for next-generation sequencing data
K Mitchell, JJ Brito, I Mandric, Q Wu, S Knyazev, S Chang, LS Martin, ...
Genome biology 21 (1), 1-13, 2020
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
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
Unlocking capacities of genomics for the COVID-19 response and future pandemics
S Knyazev, K Chhugani, V Sarwal, R Ayyala, H Singh, S Karthikeyan, ...
Nature Methods 19 (4), 374-380, 2022
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, ...
Journal of Computational Biology 28 (11), 1113-1129, 2021
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