Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

Rapid deep sequencing of patient-derived HIV with ion semiconductor technology

(2013) Max W. Chang et al.   JOURNAL OF VIROLOGICAL METHODS

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional conservation of HIV-1 Gag: implications for rational drug design

(2013) Guangdi Li et al.   Retrovirology

Extreme Genetic Fragility of the HIV-1 Capsid

(2013) Suzannah J. Rihn et al.   PLoS Pathogens

Mutations in HIV-1gagandpolCompensate for the Loss of Viral Fitness Caused by a Highly Mutated Protease

(2012) Milan Kožíšek et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Context Surrounding Processing Sites Is Crucial in Determining Cleavage Rate of a Subset of Processing Sites in HIV-1 Gag and Gag-Pro-Pol Polyprotein Precursors by Viral Protease

(2012) Sook-Kyung Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

(2012) Christine M. Malboeuf et al.   NUCLEIC ACIDS RESEARCH

Computational Identification of Novel Amino-Acid Interactions in HIV Gag via Correlated Evolution

(2012) Olga V. Kalinina et al.   PLoS One

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Immunodeficiency Virus gag and protease: partners in resistance

(2012) Axel Fun et al.   Retrovirology

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease

(2012) Omar Haq et al.   PLoS Computational Biology

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

A Cleavage Enzyme-Cytometric Bead Array Provides Biochemical Profiling of Resistance Mutations in HIV-1 Gag and Protease

(2011) Sebastian Breuer et al.   BIOCHEMISTRY

Detecting coevolving positions in a molecule: why and how to account for phylogeny

(2011) J. Y. Dutheil   BRIEFINGS IN BIOINFORMATICS

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

(2011) S. Gianella et al.   JOURNAL OF VIROLOGY

Mutational patterns in the frameshift-regulating site of HIV-1 selected by protease inhibitors

(2011) Elena Knops et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1

(2011) Binhua Liang et al.   PLoS One

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

(2011) V. Dahirel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three Residues in HIV-1 Matrix Contribute to Protease Inhibitor Susceptibility and Replication Capacity

(2010) Chris M. Parry et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics

(2010) Morgane Rolland et al.   PLoS One

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog et al.   PLoS One

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

Failure of Treatment with First‐Line Lopinavir Boosted with Ritonavir Can Be Explained by Novel Resistance Pathways with Protease Mutation 76V

(2009) Monique Nijhuis et al.   JOURNAL OF INFECTIOUS DISEASES

Human Immunodeficiency Virus Type 1 Protease-Correlated Cleavage Site Mutations Enhance Inhibitor Resistance

(2009) M. Kolli et al.   JOURNAL OF VIROLOGY

Positive Selection Pressure Introduces Secondary Mutations at Gag Cleavage Sites in Human Immunodeficiency Virus Type 1 Harboring Major Protease Resistance Mutations

(2009) S. Banke et al.   JOURNAL OF VIROLOGY

Non-Cleavage Site Gag Mutations in Amprenavir-Resistant Human Immunodeficiency Virus Type 1 (HIV-1) Predispose HIV-1 to Rapid Acquisition of Amprenavir Resistance but Delay Development of Resistance to Other Protease Inhibitors

(2009) M. Aoki et al.   JOURNAL OF VIROLOGY

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

(2009) A. F.Y. Poon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update

(2009) Diane E. Bennett et al.   PLoS One

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

(2008) J Gregory Caporaso et al.   BMC EVOLUTIONARY BIOLOGY

The structural biology of HIV assembly

(2008) Barbie K Ganser-Pornillos et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

(2008) Jonathan M. Carlson et al.   PLoS Computational Biology