Juyal A, Hosseini R, Novikov D, Grinshpon M, Zelikovsky A
J Comput Biol. 2023; 30(9):1009-1018.
PMID: 37695837
PMC: 10518690.
DOI: 10.1089/cmb.2023.0154.
Luo X, Kang X, Schonhuth A
Genome Biol. 2022; 23(1):29.
PMID: 35057847
PMC: 8771625.
DOI: 10.1186/s13059-021-02587-6.
Christley S, Cockrell C, An G
Computation (Basel). 2021; 3(1):2-28.
PMID: 34765258
PMC: 8580329.
DOI: 10.3390/computation3010002.
Pham L, Parlavantzas N, Le H, Bui Q
Animals (Basel). 2021; 11(9).
PMID: 34573709
PMC: 8469528.
DOI: 10.3390/ani11092743.
Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal P
Genome Biol. 2021; 22(1):249.
PMID: 34446078
PMC: 8390189.
DOI: 10.1186/s13059-021-02443-7.
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread.
Dhar S, Zhang C, Mandoiu I, Bansal M
IEEE/ACM Trans Comput Biol Bioinform. 2021; 19(1):230-242.
PMID: 34255632
PMC: 8956368.
DOI: 10.1109/TCBB.2021.3096455.
Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.
Knyazev S, Tsyvina V, Shankar A, Melnyk A, Artyomenko A, Malygina T
Nucleic Acids Res. 2021; 49(17):e102.
PMID: 34214168
PMC: 8464054.
DOI: 10.1093/nar/gkab576.
Analysis of heterogeneous genomic samples using image normalization and machine learning.
Basodi S, Baykal P, Zelikovsky A, Skums P, Pan Y
BMC Genomics. 2020; 21(Suppl 6):405.
PMID: 33349236
PMC: 7751093.
DOI: 10.1186/s12864-020-6661-6.
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.
Knyazev S, Hughes L, Skums P, Zelikovsky A
Brief Bioinform. 2020; 22(1):96-108.
PMID: 32568371
PMC: 8485218.
DOI: 10.1093/bib/bbaa101.
The dawn of precision medicine in HIV: state of the art of pharmacotherapy.
Mu Y, Kodidela S, Wang Y, Kumar S, Cory T
Expert Opin Pharmacother. 2018; 19(14):1581-1595.
PMID: 30234392
PMC: 6291855.
DOI: 10.1080/14656566.2018.1515916.
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.
Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S
Bioinformatics. 2018; 34(1):163-170.
PMID: 29304222
PMC: 6355096.
DOI: 10.1093/bioinformatics/btx402.
Antiviral drug resistance as an adaptive process.
Irwin K, Renzette N, Kowalik T, Jensen J
Virus Evol. 2017; 2(1):vew014.
PMID: 28694997
PMC: 5499642.
DOI: 10.1093/ve/vew014.
Fitness Inference from Short-Read Data: Within-Host Evolution of a Reassortant H5N1 Influenza Virus.
Illingworth C
Mol Biol Evol. 2015; 32(11):3012-26.
PMID: 26243288
PMC: 4651230.
DOI: 10.1093/molbev/msv171.
Bioinformatic analysis of HIV-1 entry and pathogenesis.
Aiamkitsumrit B, Dampier W, Antell G, Rivera N, Martin-Garcia J, Pirrone V
Curr HIV Res. 2014; 12(2):132-61.
PMID: 24862329
PMC: 4382797.
DOI: 10.2174/1570162x12666140526121746.
The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients.
Beerenwinkel N, Montazeri H, Schuhmacher H, Knupfer P, von Wyl V, Furrer H
PLoS Comput Biol. 2013; 9(8):e1003203.
PMID: 24009493
PMC: 3757085.
DOI: 10.1371/journal.pcbi.1003203.
Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging.
Deng L, Gregory A, Yilmaz S, Poulos B, Hugenholtz P, Sullivan M
mBio. 2012; 3(6).
PMID: 23111870
PMC: 3487772.
DOI: 10.1128/mBio.00373-12.
Managing drug resistance in cancer: lessons from HIV therapy.
Bock C, Lengauer T
Nat Rev Cancer. 2012; 12(7):494-501.
PMID: 22673150
DOI: 10.1038/nrc3297.
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes.
Doherty K, Nakka P, King B, Rhee S, Holmes S, Shafer R
BMC Bioinformatics. 2011; 12:477.
PMID: 22172090
PMC: 3305535.
DOI: 10.1186/1471-2105-12-477.
Inferring viral quasispecies spectra from 454 pyrosequencing reads.
Astrovskaya I, Tork B, Mangul S, Westbrooks K, Mandoiu I, Balfe P
BMC Bioinformatics. 2011; 12 Suppl 6:S1.
PMID: 21989211
PMC: 3194189.
DOI: 10.1186/1471-2105-12-S6-S1.
Clinical evaluation of the potential utility of computational modeling as an HIV treatment selection tool by physicians with considerable HIV experience.
Larder B, Revell A, Mican J, Agan B, Harris M, Torti C
AIDS Patient Care STDS. 2011; 25(1):29-36.
PMID: 21214377
PMC: 3030912.
DOI: 10.1089/apc.2010.0254.