Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning

An Automated Data-Driven Pipeline for Improving Heterologous Enzyme Expression

(2019) Emily E. Wrenbeck et al.   ACS Synthetic Biology

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Massively parallel screening of synthetic microbial communities

(2019) Jared Kehe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Interaction Network Inference in Microfluidic Droplets

(2019) Ryan H. Hsu et al.   Cell Systems

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics

(2019) Claire N. Bedbrook et al.   NATURE METHODS

Machine Learning in Enzyme Engineering

(2019) Stanislav Mazurenko et al.   ACS Catalysis

Multiplexed assays of variant effects contribute to a growing genotype–phenotype atlas

(2018) Jochen Weile et al.   HUMAN GENETICS

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

Deep generative models of genetic variation capture the effects of mutations

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

Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit

(2018) Justin R Klesmith et al.   BIOINFORMATICS

PUlasso: High-dimensional variable selection with presence-only data

(2018) Hyebin Song et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

A framework for exhaustively mapping functional missense variants

(2017) Jochen Weile et al.   Molecular Systems Biology

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

(2016) Luciano A. Abriata et al.   BMC BIOINFORMATICS

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

(2016) Michael Doud et al.   Viruses-Basel

OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis

(2016) Indro Neil Ghosh et al.   ACS Synthetic Biology

Software for the analysis and visualization of deep mutational scanning data

(2015) Jesse D Bloom   BMC BIOINFORMATICS

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

(2014) J. I. Boucher et al.   GENETICS

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Directed evolution of an ultrastable carbonic anhydrase for highly efficient carbon capture from flue gas

(2014) Oscar Alvizo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network

(2014) R. K. Jha et al.   PROTEIN ENGINEERING DESIGN & SELECTION

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Massive functional mapping of a 5′-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing

(2013) Erik Holmqvist et al.   NUCLEIC ACIDS RESEARCH

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene

(2013) William P. Robins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

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

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Presence-Only Data and the EM Algorithm

(2008) Gill Ward et al.   BIOMETRICS