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An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

Ulrich Omasits
Adithi R. Varadarajan
Michael Schmid
Sandra Goetze
Damianos Melidis
Marc Bourqui Olga Nikolayeva Maxime Québatte Andrea Patrignani Christoph Dehio
... [+5 authors] ...,
Juerg E. Frey
Mark D. Robinson
Bernd Wollscheid
Christian H. Ahrens

First Published November 15, 2017

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

Tugce Bilgin Sonay
Tiago Carvalho
Mark D. Robinson
Maja P. Greminger
Michael Krützen
David Comas Gareth Highnam
... [+2 authors] ...,
David Mittelman
Andrew Sharp
Tomàs Marques-Bonet
Andreas Wagner

First Published August 19, 2015

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

Ulrich Omasits
Maxime Quebatte
Daniel J. Stekhoven
Claudia Fortes
Bernd Roschitzki
Mark D. Robinson
Christoph Dehio
Christian H. Ahrens

First Published July 22, 2013

Copy-number-aware differential analysis of quantitative DNA sequencing data

Mark D. Robinson
Dario Strbenac
Clare Stirzaker
Aaron L. Statham
Jenny Song
Terence P. Speed
Susan J. Clark

First Published August 9, 2012

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

Aaron L. Statham
Mark D. Robinson
Jenny Z. Song
Marcel W. Coolen
Clare Stirzaker
Susan J. Clark

First Published March 30, 2012

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer

Fátima Valdés-Mora
Jenny Z. Song
Aaron L. Statham
Dario Strbenac
Mark D. Robinson
Shalima S. Nair
... [+1 authors] ...,
Kate I. Patterson
David J. Tremethick
Clare Stirzaker
Susan J. Clark

First Published July 25, 2011

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

Mark D. Robinson
Clare Stirzaker
Aaron L. Statham
Marcel W. Coolen
Jenny Z. Song
Shalima S. Nair
Dario Strbenac
Terence P. Speed
Susan J. Clark

First Published November 2, 2010

Complex selection on 5′ splice sites in intron-rich organisms

Manuel Irimia
Scott William Roy
Daniel E. Neafsey
Josep F. Abril
Jordi Garcia-Fernandez
Eugene V. Koonin

First Published September 10, 2009

Evolution of protein domain promiscuity in eukaryotes

Malay Kumar Basu
Liran Carmel
Igor B. Rogozin
Eugene V. Koonin

First Published January 29, 2008

Three distinct modes of intron dynamics in the evolution of eukaryotes

Liran Carmel
Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published May 10, 2007

Evolutionarily conserved genes preferentially accumulate introns

Liran Carmel
Igor B. Rogozin
Yuri I. Wolf
Eugene V. Koonin

First Published May 10, 2007

Origins and impact of constraints in evolution of gene families

Boris E. Shakhnovich
Eugene V. Koonin

First Published October 19, 2006

Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published January 5, 2004

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

Dmitri M. Krylov
Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published October 2, 2003

The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes

Olivier Lespinet
Yuri I. Wolf
Eugene V. Koonin
L. Aravind

First Published July 1, 2002

Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria

I. King Jordan
Igor B. Rogozin
Yuri I. Wolf
Eugene V. Koonin

First Published May 16, 2002

Prokaryotic Homologs of the Eukaryotic DNA-End-Binding Protein Ku, Novel Domains in the Ku Protein and Prediction of a Prokaryotic Double-Strand Break Repair System

L. Aravind
Eugene V. Koonin

First Published August 1, 2001

Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes

I. King Jordan
Kira S. Makarova
John L. Spouge
Yuri I. Wolf
Eugene V. Koonin

First Published March 13, 2001

Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic Context

Yuri I. Wolf
Igor B. Rogozin
Alexey S. Kondrashov
Eugene V. Koonin

First Published February 8, 2001

Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach

Eugene V. Koonin
Yuri I. Wolf
L. Aravind

First Published February 1, 2001

Eukaryote-specific Domains in Translation Initiation Factors: Implications for Translation Regulation and Evolution of the Translation System

L. Aravind
Eugene V. Koonin

First Published August 1, 2000

From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins

Nick V. Grishin
Yuri I. Wolf
Eugene V. Koonin

First Published July 1, 2000

The Bacterial Replicative Helicase DnaB Evolved from a RecA Duplication

Detlef D. Leipe
L. Aravind
Nick V. Grishin
Eugene V. Koonin

First Published January 1, 2000

Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events

Yuri I. Wolf
L. Aravind
Nick V. Grishin
Eugene V. Koonin

First Published August 1, 1999

Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell

Kira S. Makarova
L. Aravind
Michael Y. Galperin
Nick V. Grishin
Roman L. Tatusov
Yuri I. Wolf
Eugene V. Koonin

First Published July 1, 1999

Distribution of Protein Folds in the Three Superkingdoms of Life

Yuri I. Wolf
Steven E. Brenner
Paul A. Bash
Eugene V. Koonin

First Published January 1, 1999

+: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes" > AAA⁺: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes

Andrew F. Neuwald
L. Aravind
John L. Spouge
Eugene V. Koonin

First Published January 1, 1999

Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily

Christopher J. Leonard
L. Aravind
Eugene V. Koonin

First Published October 1, 1998

Analogous Enzymes: Independent Inventions in Enzyme Evolution

Michael Y. Galperin
D. Roland Walker
Eugene V. Koonin

First Published August 1, 1998

Big Time for Small Genomes

Eugene V. Koonin

First Published May 1, 1997

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Your search for returned 30 results

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

Copy-number-aware differential analysis of quantitative DNA sequencing data

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

Complex selection on 5′ splice sites in intron-rich organisms

Evolution of protein domain promiscuity in eukaryotes

Three distinct modes of intron dynamics in the evolution of eukaryotes

Evolutionarily conserved genes preferentially accumulate introns

Origins and impact of constraints in evolution of gene families

Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes

Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria

Prokaryotic Homologs of the Eukaryotic DNA-End-Binding Protein Ku, Novel Domains in the Ku Protein and Prediction of a Prokaryotic Double-Strand Break Repair System

Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes

Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic Context

Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach

Eukaryote-specific Domains in Translation Initiation Factors: Implications for Translation Regulation and Evolution of the Translation System

From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins

The Bacterial Replicative Helicase DnaB Evolved from a RecA Duplication

Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events

Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell

Distribution of Protein Folds in the Three Superkingdoms of Life

+: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes" > AAA⁺: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes

Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily

Analogous Enzymes: Independent Inventions in Enzyme Evolution

Big Time for Small Genomes

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Your search for returned 30 results