Protein design and variant prediction using autoregressive generative models

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

(2021) Anna G. Green et al.   Nature Communications

UDSMProt: universal deep sequence models for protein classification

(2020) Nils Strodthoff et al.   BIOINFORMATICS

Pan-cancer analysis of whole genomes

(2020)   NATURE

How repertoire data is changing antibody science

(2020) Claire Marks et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Generation and design of nanobodies

(2020) Serge Muyldermans   FEBS Journal

Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations

(2020) Benjamin J Livesey et al.   Molecular Systems Biology

A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences

(2020) Johannes Linder et al.   Cell Systems

Large-scale network analysis reveals the sequence space architecture of antibody repertoires

(2019) Enkelejda Miho et al.   Nature Communications

Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation

(2019) Chia Chiu Lim et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape

(2019) Victoria O. Pokusaeva et al.   PLoS Genetics

Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell

(2019) Antonio Deiana et al.   PLoS One

Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

(2019) Ge Liu et al.   BIOINFORMATICS

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships

(2018) Taylor L. Mighell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Yeast surface display platform for rapid discovery of conformationally selective nanobodies

(2018) Conor McMahon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

High-throughput immune repertoire analysis with IGoR

(2018) Quentin Marcou et al.   Nature Communications

Yeast surface display platform for rapid discovery of conformationally selective nanobodies

(2018) Conor McMahon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Synthetic single domain antibodies for the conformational trapping of membrane proteins

(2018) Iwan Zimmermann et al.   eLife

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

(2018) Vanessa E. Gray et al.   Cell Systems

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Design of metalloproteins and novel protein folds using variational autoencoders

(2018) Joe G. Greener et al.   Scientific Reports

Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds

(2018) Arjun Ravikumar et al.   CELL

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

Nonspecificity in a nonimmune human scFv repertoire

(2017) Ryan L. Kelly et al.   mAbs

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Biophysical properties of the clinical-stage antibody landscape

(2017) Tushar Jain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of anti-botulinum neurotoxin single domain antibodies with additional optimization for improved production and stability

(2017) Lisa C. Shriver-Lake et al.   TOXICON

Effects of short indels on protein structure and function in human genomes

(2017) Maoxuan Lin et al.   Scientific Reports

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

(2016) Brandon J. DeKosky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation and analyses of human synthetic antibody libraries and their application for protein microarrays

(2016) Anna Säll et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Antibody repertoire profiling with mimotope arrays

(2016) Shina Pashova et al.   Human Vaccines & Immunotherapeutics

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

(2016) Lorenzo Asti et al.   PLoS Computational Biology

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Mining human antibody repertoires

(2014) Roger R. Beerli et al.   mAbs

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

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

Molecular Evolution of Broadly Neutralizing Llama Antibodies to the CD4-Binding Site of HIV-1

(2014) Laura E. McCoy et al.   PLoS Pathogens

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Nanobodies: Natural Single-Domain Antibodies

(2013) Serge Muyldermans   Annual Review of Biochemistry

Antibody Polyreactivity in Health and Disease: Statu Variabilis

(2013) J. D. Dimitrov et al.   JOURNAL OF IMMUNOLOGY

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

(2013) Brandon J DeKosky et al.   NATURE BIOTECHNOLOGY

Contributions of the Complementarity Determining Regions to the Thermal Stability of a Single-Domain Antibody

(2013) Dan Zabetakis et al.   PLoS One

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

Beyond natural antibodies: the power of in vitro display technologies

(2011) Andrew R M Bradbury et al.   NATURE BIOTECHNOLOGY

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Protein 3D Structure Computed from Evolutionary Sequence Variation

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

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

Maximum entropy models for antibody diversity

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

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Unfoldomics of human diseases: linking protein intrinsic disorder with diseases

(2009) Vladimir N Uversky et al.   BMC GENOMICS

Directed evolution: new parts and optimized function

(2009) Michael J Dougherty et al.   CURRENT OPINION IN BIOTECHNOLOGY

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Modularity of intrinsic disorder in the human proteome

(2009) Melissa M. Pentony et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS