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Items: 26


Inference of clonal selection in cancer populations using single-cell sequencing data.

Skums P, Tsyvina V, Zelikovsky A.

Bioinformatics. 2019 Jul 15;35(14):i398-i407. doi: 10.1093/bioinformatics/btz392.


Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018).

Cai Z, Skums P, Zelikovsky A.

J Comput Biol. 2019 Aug;26(8):767-768. doi: 10.1089/cmb.2019.29022.zc. No abstract available.


Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits.

Rogovskyy AS, Caoili SEC, Ionov Y, Piontkivska H, Skums P, Tsyvina V, Zelikovsky A, Waghela SD.

Infect Immun. 2019 Jul 23;87(8). pii: e00246-19. doi: 10.1128/IAI.00246-19. Print 2019 Aug.


Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants.

Tsyvina V, Campo DS, Sims S, Zelikovsky A, Khudyakov Y, Skums P.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):360. doi: 10.1186/s12859-018-2333-9.


Special Issue Preface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017).

Cai Z, Skums P, Zelikovsky A.

J Comput Biol. 2018 Mar;25(3):251-252. doi: 10.1089/cmb.2018.29012.zc. No abstract available.


QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.

Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y.

Bioinformatics. 2018 Jan 1;34(1):163-170. doi: 10.1093/bioinformatics/btx402.


Inference of genetic relatedness between viral quasispecies from sequencing data.

Glebova O, Knyazev S, Melnyk A, Artyomenko A, Khudyakov Y, Zelikovsky A, Skums P.

BMC Genomics. 2017 Dec 6;18(Suppl 10):918. doi: 10.1186/s12864-017-4274-5.


GHOST: global hepatitis outbreak and surveillance technology.

Longmire AG, Sims S, Rytsareva I, Campo DS, Skums P, Dimitrova Z, Ramachandran S, Medrzycki M, Thai H, Ganova-Raeva L, Lin Y, Punkova LT, Sue A, Mirabito M, Wang S, Tracy R, Bolet V, Sukalac T, Lynberg C, Khudyakov Y.

BMC Genomics. 2017 Dec 6;18(Suppl 10):916. doi: 10.1186/s12864-017-4268-3.


Increased Mitochondrial Genetic Diversity in Persons Infected With Hepatitis C Virus.

Campo DS, Roh HJ, Pearlman BL, Fierer DS, Ramachandran S, Vaughan G, Hinds A, Dimitrova Z, Skums P, Khudyakov Y.

Cell Mol Gastroenterol Hepatol. 2016 May 26;2(5):676-684. doi: 10.1016/j.jcmgh.2016.05.012. eCollection 2016 Sep.


Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses.

Palmer BA, Schmidt-Martin D, Dimitrova Z, Skums P, Crosbie O, Kenny-Walsh E, Fanning LJ.

J Virol. 2015 Dec 30;90(7):3318-29. doi: 10.1128/JVI.02995-15.


Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana.

Forbi JC, Layden JE, Phillips RO, Mora N, Xia GL, Campo DS, Purdy MA, Dimitrova ZE, Owusu DO, Punkova LT, Skums P, Owusu-Ofori S, Sarfo FS, Vaughan G, Roh H, Opare-Sem OK, Cooper RS, Khudyakov YE.

PLoS One. 2015 Dec 18;10(12):e0145530. doi: 10.1371/journal.pone.0145530. eCollection 2015.


Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings.

Campo DS, Xia GL, Dimitrova Z, Lin Y, Forbi JC, Ganova-Raeva L, Punkova L, Ramachandran S, Thai H, Skums P, Sims S, Rytsareva I, Vaughan G, Roh HJ, Purdy MA, Sue A, Khudyakov Y.

J Infect Dis. 2016 Mar 15;213(6):957-65. doi: 10.1093/infdis/jiv542. Epub 2015 Nov 17.


Cryptic Hepatitis B and E in Patients With Acute Hepatitis of Unknown Etiology.

Ganova-Raeva L, Punkova L, Campo DS, Dimitrova Z, Skums P, Vu NH, Dat do T, Dalton HR, Khudyakov Y.

J Infect Dis. 2015 Dec 15;212(12):1962-9. doi: 10.1093/infdis/jiv315. Epub 2015 Jun 8.


Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM.

Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237. No abstract available.


Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity.

Skums P, Bunimovich L, Khudyakov Y.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6653-8. doi: 10.1073/pnas.1422942112. Epub 2015 May 4.


Nosocomial hepatitis C virus transmission from tampering with injectable anesthetic opioids.

Hatia RI, Dimitrova Z, Skums P, Teo EY, Teo CG.

Hepatology. 2015 Jul;62(1):101-10. doi: 10.1002/hep.27800. Epub 2015 Apr 22.


Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.

Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y.

Bioinformatics. 2015 Mar 1;31(5):682-90. doi: 10.1093/bioinformatics/btu726. Epub 2014 Oct 29.


Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing.

Palmer BA, Dimitrova Z, Skums P, Crosbie O, Kenny-Walsh E, Fanning LJ.

J Virol. 2014 Dec;88(23):13709-21. doi: 10.1128/JVI.01732-14. Epub 2014 Sep 17.


Next-generation sequencing reveals large connected networks of intra-host HCV variants.

Campo DS, Dimitrova Z, Yamasaki L, Skums P, Lau DT, Vaughan G, Forbi JC, Teo CG, Khudyakov Y.

BMC Genomics. 2014;15 Suppl 5:S4. doi: 10.1186/1471-2164-15-S5-S4. Epub 2014 Jul 14.


Intra-host diversity and evolution of hepatitis C virus endemic to Côte d'Ivoire.

Forbi JC, Campo DS, Purdy MA, Dimitrova ZE, Skums P, Xia GL, Punkova LT, Ganova-Raeva LM, Vaughan G, Ben-Ayed Y, Switzer WM, Khudyakov YE.

J Med Virol. 2014 May;86(5):765-71. doi: 10.1002/jmv.23897. Epub 2014 Feb 12.


Drug resistance of a viral population and its individual intrahost variants during the first 48 hours of therapy.

Campo DS, Skums P, Dimitrova Z, Vaughan G, Forbi JC, Teo CG, Khudyakov Y, Lau DT.

Clin Pharmacol Ther. 2014 Jun;95(6):627-35. doi: 10.1038/clpt.2014.20. Epub 2014 Jan 31.


Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.

Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A.

BMC Bioinformatics. 2013;14 Suppl 9:S2. doi: 10.1186/1471-2105-14-S9-S2. Epub 2013 Jun 28.


Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response.

Skums P, Campo DS, Dimitrova Z, Vaughan G, Lau DT, Khudyakov Y.

In Silico Biol. 2011-2012;11(5-6):263-9. doi: 10.3233/ISB-2012-0460.


Reconstructing viral quasispecies from NGS amplicon reads.

Mancuso N, Tork B, Skums P, Ganova-Raeva L, Măndoiu I, Zelikovsky A.

In Silico Biol. 2011-2012;11(5-6):237-49. doi: 10.3233/ISB-2012-0458.


Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry.

Dimitrova Z, Campo DS, Ramachandran S, Vaughan G, Ganova-Raeva L, Lin Y, Forbi JC, Xia G, Skums P, Pearlman B, Khudyakov Y.

In Silico Biol. 2011-2012;11(5-6):183-92. doi: 10.3233/ISB-2012-0453.


Efficient error correction for next-generation sequencing of viral amplicons.

Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, Forbi JC, Yokosawa J, Zelikovsky A, Khudyakov Y.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S6. doi: 10.1186/1471-2105-13-S10-S6.

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