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Sergey Knyazev
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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
572018
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
54*2021
Dietary supplements and nutraceuticals under investigation for COVID-19 prevention and treatment
R Lordan, HM Rando, CS Greene
Msystems 6 (3), e00122-21, 2021
412021
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), 1-34, 2021
402021
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
272021
Identification and Development of Therapeutics for COVID-19
HM Rando, N Wellhausen, S Ghosh, AJ Lee, AA Dattoli, F Hu, JB Byrd, ...
Msystems 6 (6), e00233-21, 2021
24*2021
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
242017
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
222020
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
20*2021
MicrobeTrace: retooling molecular epidemiology for rapid public health response
EM Campbell, A Boyles, A Shankar, J Kim, S Knyazev, R Cintron, ...
PLoS computational biology 17 (9), e1009300, 2021
182021
Pathogenesis, symptomatology, and transmission of SARS-CoV-2 through analysis of viral genomics and structure
HM Rando, AL MacLean, AJ Lee, R Lordan, S Ray, V Bansal, AN Skelly, ...
Msystems 6 (5), e00095-21, 2021
172021
Modeling conformational redox‐switch modulation of human succinic semialdehyde dehydrogenase
G Tamazian, J Ho Chang, S Knyazev, E Stepanov, KJ Kim, Y Porozov
Proteins: Structure, Function, and Bioinformatics 83 (12), 2217-2229, 2015
122015
Repeat-aware evaluation of scaffolding tools
I Mandric, S Knyazev, A Zelikovsky
Bioinformatics 34 (15), 2530-2537, 2018
112018
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
8*2022
Using earth mover’s distance for viral outbreak investigations
A Melnyk, S Knyazev, F Vannberg, L Bunimovich, P Skums, A Zelikovsky
BMC genomics 21 (5), 1-9, 2020
72020
Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative
R Johnson, Y Ding, V Venkateswaran, A Bhattacharya, K Boulier, A Chiu, ...
Genome medicine 14 (1), 1-23, 2022
5*2022
Molecular epidemiological analysis of the origin and transmission dynamics of the HIV-1 CRF01_AE sub-epidemic in Bulgaria
I Alexiev, EM Campbell, S Knyazev, Y Pan, L Grigorova, R Dimitrova, ...
Viruses 13 (1), 116, 2021
52021
Molecular epidemiology of the HIV-1 subtype b sub-epidemic in Bulgaria
I Alexiev, E M. Campbell, S Knyazev, Y Pan, L Grigorova, R Dimitrova, ...
Viruses 12 (4), 441, 2020
32020
A Novel Network Representation of SARS-CoV-2 Sequencing Data
S Knyazev, D Novikov, M Grinshpon, H Singh, R Ayyala, V Sarwal, ...
International Symposium on Bioinformatics Research and Applications, 165-175, 2021
2*2021
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, 2021
22021
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Articles 1–20