De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids

(2019) Xuan Zhuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of protein diversity by de novo origination in Oryza

(2019) Li Zhang et al.   Nature Ecology & Evolution

Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes

(2019) Anouk Willemsen et al.   Genome Biology and Evolution

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

(2019) Éléonore Durand et al.   GENOME RESEARCH

De Novo Emergence of Peptides That Confer Antibiotic Resistance

(2019) Michael Knopp et al.   mBio

The degradation pathway of a model misfolded protein is determined by aggregation propensity

(2018) Zhihao Sun et al.   MOLECULAR BIOLOGY OF THE CELL

A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli

(2018) Ann E Donnelly et al.   Nature Chemical Biology

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover

(2018) Jonathan F. Schmitz et al.   Nature Ecology & Evolution

The role of phospholipid molecular species in determining the physical properties of yeast membranes

(2017) Mike F. Renne et al.   FEBS LETTERS

Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy

(2017) Bryan A. Moyers et al.   Genome Biology and Evolution

A Molecular Portrait of De Novo Genes in Yeasts

(2017) Nikolaos Vakirlis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

Random protein sequences can form defined secondary structures and are well-tolerated in vivo

(2017) Vyacheslav Tretyachenko et al.   Scientific Reports

High GC content causes orphan proteins to be intrinsically disordered

(2017) Walter Basile et al.   PLoS Computational Biology

Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth

(2017) Benjamin A. Wilson et al.   Nature Ecology & Evolution

Random sequences are an abundant source of bioactive RNAs or peptides

(2017) Rafik Neme et al.   Nature Ecology & Evolution

Interactions between intersubunit transmembrane domains regulate the chaperone-dependent degradation of an oligomeric membrane protein

(2016) Teresa M. Buck et al.   BIOCHEMICAL JOURNAL

Effects of protein crowding on membrane systems

(2016) Gernot Guigas et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

On the Origin of De Novo Genes inArabidopsis thalianaPopulations

(2016) Zi-Wen Li et al.   Genome Biology and Evolution

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle

(2016) B. R. Nelson et al.   SCIENCE

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

(2016) M. Costanzo et al.   SCIENCE

High-Throughput Identification of Adaptive Mutations in Experimentally Evolved Yeast Populations

(2016) Celia Payen et al.   PLoS Genetics

Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

(2016) Rafik Neme et al.   eLife

Detection of orphan domains in Drosophila using “hydrophobic cluster analysis”

(2015) Tristan Bitard-Feildel et al.   BIOCHIMIE

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

Elucidating evolutionary features and functional implications of orphan genes in Leishmania major

(2015) Sumit Mukherjee et al.   INFECTION GENETICS AND EVOLUTION

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

(2015) Konstantinos D. Tsirigos et al.   NUCLEIC ACIDS RESEARCH

The relativity of biological function

(2015) Manfred D. Laubichler et al.   THEORY IN BIOSCIENCES

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

Endoplasmic reticulum stress response in yeast and humans

(2014) Haoxi Wu et al.   BIOSCIENCE REPORTS

Comparative genomics reveals molecular features unique to the songbird lineage

(2014) Morgan Wirthlin et al.   BMC GENOMICS

Development of Ultra-High-Density Screening Tools for Microbial “Omics”

(2014) Gordon J. Bean et al.   PLoS One

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

Pleiotropy of the de novo-originated gene MDF1

(2014) Dan Li et al.   Scientific Reports

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

(2014) Julie L Aspden et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Integration of New Genes into Cellular Networks, and Their Structural Maturation

(2013) G. Abrusan   GENETICS

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

(2013) Lothar Wissler et al.   Genome Biology and Evolution

Hsp70 Targets a Cytoplasmic Quality Control Substrate to the San1p Ubiquitin Ligase

(2013) Christopher J. Guerriero et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Scalable web services for the PSIPRED Protein Analysis Workbench

(2013) Daniel W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

De novo selection of oncogenes

(2013) K. M. Chacon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast

(2012) Wenfeng Qian et al.   Cell Reports

Functional Analysis With a Barcoder Yeast Gene Overexpression System

(2012) Alison C. Douglas et al.   G3-Genes Genomes Genetics

Mechanisms for quality control of misfolded transmembrane proteins

(2011) Scott A. Houck et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

A 3D analysis of yeast ER structure reveals how ER domains are organized by membrane curvature

(2011) Matt West et al.   JOURNAL OF CELL BIOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

The unfolded protein response supports cellular robustness as a broad-spectrum compensatory pathway

(2011) G. Thibault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

(2011) Devin R. Scannell et al.   G3-Genes Genomes Genetics

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

(2011) Jared W. Wenger et al.   PLoS Genetics

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

(2010) Dan Li et al.   CELL RESEARCH

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

(2010) Anastasia Baryshnikova et al.   NATURE METHODS

Steric confinement of proteins on lipid membranes can drive curvature and tubulation

(2010) Jeanne C. Stachowiak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination

(2010) S. G. Peisajovich et al.   SCIENCE

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Intrinsic Protein Disorder and Interaction Promiscuity Are Widely Associated with Dosage Sensitivity

(2009) Tanya Vavouri et al.   CELL

Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies

(2009) M. R. Hemm et al.   JOURNAL OF BACTERIOLOGY

Membrane expansion alleviates endoplasmic reticulum stress independently of the unfolded protein response

(2009) Sebastian Schuck et al.   JOURNAL OF CELL BIOLOGY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Identifying and Quantifying Orphan Protein Sequences in Fungi

(2009) Diana Ekman et al.   JOURNAL OF MOLECULAR BIOLOGY

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Toward a quantitative theory of intrinsically disordered proteins and their function

(2009) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs

(2009) J. Prilusky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

Transmembrane helix predictions revisited

(2002) Chien Peter Chen et al.   PROTEIN SCIENCE