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Items: 1 to 20 of 172

1.

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

Boltz VF, Rausch J, Shao W, Hattori J, Luke B, Maldarelli F, Mellors JW, Kearney MF, Coffin JM.

Retrovirology. 2016 Dec 20;13(1):87. doi: 10.1186/s12977-016-0321-6.

2.

Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage.

Peña J, Chen-Harris H, Allen JE, Hwang M, Elsheikh M, Mabery S, Bielefeldt-Ohmann H, Zemla AT, Bowen RA, Borucki MK.

Virus Evol. 2016 Apr 9;2(1):vew008.

3.

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification.

Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, Ransier A, Stockwell TB, Das SR, Gilbert AS, Lambkin-Williams R, Ginsburg GS, Woods CW, Koelle K.

J Virol. 2016 Nov 28;90(24):11247-11258.

4.

DADA2: High-resolution sample inference from Illumina amplicon data.

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP.

Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869.

5.

Rapid and Simultaneous Detection of Major Drug Resistance Mutations in Reverse Transcriptase Gene for HIV-1 CRF01_AE, CRF07_BC and Subtype B in China Using Sequenom MassARRAY® System.

Cheung KW, Peng Q, He L, Cai K, Jiang Q, Zhou B, To SW, Yam WC, Liu L, Chen Z, Wang H.

PLoS One. 2016 Apr 19;11(4):e0153641. doi: 10.1371/journal.pone.0153641.

6.

Reverse genetics in high throughput: rapid generation of complete negative strand RNA virus cDNA clones and recombinant viruses thereof.

Nolden T, Pfaff F, Nemitz S, Freuling CM, Höper D, Müller T, Finke S.

Sci Rep. 2016 Apr 5;6:23887. doi: 10.1038/srep23887.

7.

Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure.

Kyeyune F, Gibson RM, Nankya I, Venner C, Metha S, Akao J, Ndashimye E, Kityo CM, Salata RA, Mugyenyi P, Arts EJ, Quiñones-Mateu ME.

Antimicrob Agents Chemother. 2016 May 23;60(6):3380-97. doi: 10.1128/AAC.00038-16.

8.

Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage.

Zukurov JP, do Nascimento-Brito S, Volpini AC, Oliveira GC, Janini LM, Antoneli F.

Algorithms Mol Biol. 2016 Mar 11;11:2. doi: 10.1186/s13015-016-0064-x.

9.

A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1.

Reisman S, Hatzopoulos T, Läufer K, Thiruvathukal GK, Putonti C.

Evol Bioinform Online. 2016 Jan 18;12:23-7. doi: 10.4137/EBO.S32757.

10.

Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART.

Vazquez-Guillen JM, Palacios-Saucedo GC, Rivera-Morales LG, Garcia-Campos J, Ortiz-Lopez R, Noguera-Julian M, Paredes R, Vielma-Ramirez HJ, Ramirez TJ, Chavez-Garcia M, Lopez-Guillen P, Briones-Lara E, Sanchez-Sanchez LM, Vazquez-Martinez CA, Rodriguez-Padilla C.

PLoS One. 2016 Jan 25;11(1):e0147591. doi: 10.1371/journal.pone.0147591.

11.

Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation.

Panpradist N, Beck IA, Chung MH, Kiarie JN, Frenkel LM, Lutz BR.

PLoS One. 2016 Jan 11;11(1):e0145962. doi: 10.1371/journal.pone.0145962.

12.

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness.

Jayasundara D, Saeed I, Chang BC, Tang SL, Halgamuge SK.

BMC Bioinformatics. 2015;16 Suppl 18:S3. doi: 10.1186/1471-2105-16-S18-S3.

13.

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats.

Sherrill-Mix S, Ocwieja KE, Bushman FD.

Retrovirology. 2015 Sep 17;12:79. doi: 10.1186/s12977-015-0205-1.

14.

Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.

Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI.

PLoS One. 2015 Aug 28;10(8):e0135903. doi: 10.1371/journal.pone.0135903.

15.

Preclinical Characterization and In Vivo Efficacy of GSK8853, a Small-Molecule Inhibitor of the Hepatitis C Virus NS4B Protein.

Pouliot JJ, Thomson M, Xie M, Horton J, Johnson J, Krull D, Mathis A, Morikawa Y, Parks D, Peterson R, Shimada T, Thomas E, Vamathevan J, Van Horn S, Xiong Z, Hamatake R, Peat AJ.

Antimicrob Agents Chemother. 2015 Oct;59(10):6539-50. doi: 10.1128/AAC.00813-15.

16.

Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing.

Sahoo MK, Tan SK, Chen SF, Kapusinszky B, Concepcion KR, Kjelson L, Mallempati K, Farina HM, Fernández-Viña M, Tyan D, Grimm PC, Anderson MW, Concepcion W, Pinsky BA.

J Clin Microbiol. 2015 Oct;53(10):3226-33. doi: 10.1128/JCM.01385-15.

17.

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.

Liu Y, Chiaromonte F, Ross H, Malhotra R, Elleder D, Poss M.

BMC Bioinformatics. 2015 Jun 30;16:202. doi: 10.1186/s12859-015-0607-z.

18.

Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering.

Novitsky V, Zahralban-Steele M, McLane MF, Moyo S, van Widenfelt E, Gaseitsiwe S, Makhema J, Essex M.

J Clin Microbiol. 2015 Aug;53(8):2581-92. doi: 10.1128/JCM.00756-15. Erratum in: J Clin Microbiol. 2016 Apr;54(4):1175.

19.

Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations.

Zhou S, Jones C, Mieczkowski P, Swanstrom R.

J Virol. 2015 Aug;89(16):8540-55. doi: 10.1128/JVI.00522-15.

20.

Single Genome Analysis for the Detection of Linked Multiclass Drug Resistance Mutations in HIV-1-Infected Children After Failure of Protease Inhibitor-Based First-Line Therapy.

Lange CM, Hué S, Violari A, Cotton M, Gibb D, Babiker A, Otwombe K, Panchia R, Dobbels E, Jean-Philippe P, McIntyre JA, Pillay D, Gupta RK.

J Acquir Immune Defic Syndr. 2015 Jun 1;69(2):138-44. doi: 10.1097/QAI.0000000000000568.

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