The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs

Hybridization is a recurrent evolutionary stimulus in wild yeast speciation

(2019) Chris Eberlein et al.   Nature Communications

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

(2018) Eviatar Natan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions

(2018) Georg K. A. Hochberg et al.   SCIENCE

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

(2018) Eviatar Natan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The genetic landscape of a physical interaction

(2018) Guillaume Diss et al.   eLife

QuantSeq 3′ mRNA sequencing for RNA quantification

(2018) Pamela Moll et al.   NATURE METHODS

Changes of Cell Biochemical States Are Revealed in Protein Homomeric Complex Dynamics

(2018) Bram Stynen et al.   CELL

Global analysis of protein homomerization in Saccharomyces cerevisiae

(2018) Yeonsoo Kim et al.   GENOME RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Extended Linkers Improve the Detection of Protein-protein Interactions (PPIs) by Dihydrofolate Reductase Protein-fragment Complementation Assay (DHFR PCA) in Living Cells

(2017) Andrée-Ève Chrétien et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative analysis of protein interaction network dynamics in yeast

(2017) Albi Celaj et al.   Molecular Systems Biology

PDB-wide identification of biological assemblies from conserved quaternary structure geometry

(2017) Sucharita Dey et al.   NATURE METHODS

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

(2017) Miguel C Teixeira et al.   NUCLEIC ACIDS RESEARCH

Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis

(2017) Guido Uguzzoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene duplication can impart fragility, not robustness, in the yeast protein interaction network

(2017) Guillaume Diss et al.   SCIENCE

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network

(2017) Matej Usaj et al.   G3-Genes Genomes Genetics

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

(2017) Audrey P. Gasch et al.   PLOS BIOLOGY

Editorial: Role of Protein-Protein Interactions in Metabolism: Genetics, Structure, Function

(2017) Amit V. Pandey et al.   Frontiers in Pharmacology

Functional determinants of protein assembly into homomeric complexes

(2017) L. Therese Bergendahl et al.   Scientific Reports

A Mutation Model from First Principles of the Genetic Code

(2016) Steinar Thorvaldsen   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Pooled-matrix protein interaction screens using Barcode Fusion Genetics

(2016) N. Yachie et al.   Molecular Systems Biology

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

(2016) X. Lan et al.   SCIENCE

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Structure, Dynamics, Assembly, and Evolution of Protein Complexes

(2015) Joseph A. Marsh et al.   Annual Review of Biochemistry

Compensatory Drift and the Evolutionary Dynamics of Dosage-Sensitive Duplicate Genes

(2015) A. Thompson et al.   GENETICS

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan et al.   NATURE

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

(2015) A. H. Kachroo et al.   SCIENCE

Paralogue Interference Affects the Dynamics after Gene Duplication

(2015) Elisabeth Kaltenegger et al.   TRENDS IN PLANT SCIENCE

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

Origin of the Yeast Whole-Genome Duplication

(2015) Kenneth H. Wolfe   PLOS BIOLOGY

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

(2015) Param Priya Singh et al.   PLoS Computational Biology

Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles

(2015) Jeffrey R. Brender et al.   PLoS Computational Biology

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

(2015) Samuel Rochette et al.   Jove-Journal of Visualized Experiments

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

The complex portal - an encyclopaedia of macromolecular complexes

(2014) Birgit H.M. Meldal et al.   NUCLEIC ACIDS RESEARCH

Evolutionary cell biology: Two origins, one objective: Fig. 1.

(2014) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images

(2014) Omar Wagih et al.   G3-Genes Genomes Genetics

Extracting Insight from Noisy Cellular Networks

(2013) Christian R. Landry et al.   CELL

Modulation of the yeast protein interactome in response to DNA damage

(2013) Samuel Rochette et al.   Journal of Proteomics

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

(2013) Christopher R. Baker et al.   SCIENCE

The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes

(2013) Mario A. Fares et al.   PLoS Genetics

Evolutionary principles of modular gene regulation in yeasts

(2013) Dawn A Thompson et al.   eLife

PatA and PatB Form a Functional Heterodimeric ABC Multidrug Efflux Transporter Responsible for the Resistance of Streptococcus pneumoniae to Fluoroquinolones

(2012) Emilie Boncoeur et al.   BIOCHEMISTRY

Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication

(2012) Isabelle Gagnon-Arsenault et al.   Journal of Proteomics

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

qPCA: a scalable assay to measure the perturbation of protein–protein interactions in living cells

(2012) Luca Freschi et al.   Molecular BioSystems

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

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

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

(2012) E. D. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Determinants of Homodimerization Specificity in Histidine Kinases

(2011) Orr Ashenberg et al.   JOURNAL OF MOLECULAR BIOLOGY

The Evolution of Multimeric Protein Assemblages

(2011) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Duplicability of self-interacting human genes

(2010) Asa Perez-Bercoff et al.   BMC EVOLUTIONARY BIOLOGY

A Consensus of Core Protein Complex Compositions for Saccharomyces cerevisiae

(2010) Joris J. Benschop et al.   MOLECULAR CELL

Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans- regulation effects

(2010) Dong Dong et al.   NUCLEIC ACIDS RESEARCH

Need-Based Up-Regulation of Protein Levels in Response to Deletion of Their Duplicate Genes

(2010) Alexander DeLuna et al.   PLOS BIOLOGY

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

(2009) Patrick P. Edger et al.   CHROMOSOME RESEARCH

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Cell Signaling in Space and Time: Where Proteins Come Together and When They're Apart

(2009) J. D. Scott et al.   SCIENCE

Questioning the Ubiquity of Neofunctionalization

(2009) Todd A. Gibson et al.   PLoS Computational Biology

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

Up-to-date catalogues of yeast protein complexes

(2008) Shuye Pu et al.   NUCLEIC ACIDS RESEARCH

The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication

(2008) A. Presser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence of symmetry in homooligomeric biological assemblies

(2008) I. Andre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

An in Vivo Map of the Yeast Protein Interactome

(2008) K. Tarassov et al.   SCIENCE

Choose your partners: dimerization in eukaryotic transcription factors

(2008) Grigoris D. Amoutzias et al.   TRENDS IN BIOCHEMICAL SCIENCES

Evolution of a New Function by Degenerative Mutation in Cephalochordate Steroid Receptors

(2008) Jamie T. Bridgham et al.   PLoS Genetics