Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity

Antibody informatics for drug discovery

(2014) Hiroki Shirai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

(2014) Katherine J.L. Jackson et al.   Cell Host & Microbe

Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis

(2014) Johannes Trück et al.   JOURNAL OF IMMUNOLOGY

Antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server

(2014) Paolo Marcatili et al.   Nature Protocols

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

Quantifying selection in immune receptor repertoires

(2014) Yuval Elhanati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines

(2014) S. Becattini et al.   SCIENCE

Improving Contact Prediction along Three Dimensions

(2014) Christoph Feinauer et al.   PLoS Computational Biology

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

Convergent Antibody Signatures in Human Dengue

(2013) Poornima Parameswaran et al.   Cell Host & Microbe

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing

(2012) K. Larimore et al.   JOURNAL OF IMMUNOLOGY

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

(2012) A. Murugan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Rep-Seq: uncovering the immunological repertoire through next-generation sequencing

(2011) Jennifer Benichou et al.   IMMUNOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

(2011) X. Wu et al.   SCIENCE

Maximum entropy models for antibody diversity

(2010) T. Mora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Clustering with shallow trees

(2009) M Bailly-Bechet et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Competition between recombination and epistasis can cause a transition from allele to genotype selection

(2009) R. A. Neher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

High-Throughput Sequencing of the Zebrafish Antibody Repertoire

(2009) J. A. Weinstein et al.   SCIENCE

IMGT(R), the international ImMunoGeneTics information system(R)

(2008) M.-P. Lefranc et al.   NUCLEIC ACIDS RESEARCH

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