The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and “Deep” Sequencing to Plasma RNA and Proviral DNA

(2010) Luke C Swenson et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Maraviroc versus Efavirenz, Both in Combination with Zidovudine‐Lamivudine, for the Treatment of Antiretroviral‐Naive Subjects with CCR5‐Tropic HIV‐1 Infection

(2010) David A. Cooper et al.   JOURNAL OF INFECTIOUS DISEASES

Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing

(2009) John Archer et al.   AIDS

When and how to use maraviroc in HIV-infected patients

(2009) Vincent Soriano et al.   AIDS

Use of Massive Parallel Pyrosequencing for Near Full-Length Characterization of a Unique HIV Type 1 BF Recombinant Associated with a Fatal Primary Infection

(2009) Alessandro Bruselles et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use

(2009) Thuy Le et al.   PLoS One

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

(2009) Athe M. N. Tsibris et al.   PLoS One

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

(2009) Gabriella Rozera et al.   Retrovirology

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS