Search | Genome Research

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

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Kevin Judd McKernan
Heather E. Peckham
Gina L. Costa
Stephen F. McLaughlin
Yutao Fu
Eric F. Tsung Christopher R. Clouser Cisyla Duncan Jeffrey K. Ichikawa Clarence C. Lee Zheng Zhang Swati S. Ranade Eileen T. Dimalanta Fiona C. Hyland Tanya D. Sokolsky Lei Zhang Andrew Sheridan Haoning Fu Cynthia L. Hendrickson Bin Li Lev Kotler Jeremy R. Stuart Joel A. Malek Jonathan M. Manning Alena A. Antipova Damon S. Perez Michael P. Moore Kathleen C. Hayashibara Michael R. Lyons Robert E. Beaudoin Brittany E. Coleman Michael W. Laptewicz Adam E. Sannicandro Michael D. Rhodes Rajesh K. Gottimukkala Shan Yang Vineet Bafna Ali Bashir Andrew MacBride Can Alkan Jeffrey M. Kidd
... [+36 authors] ...,
Evan E. Eichler
Martin G. Reese
Francisco M. De La Vega
Alan P. Blanchard

First Published June 22, 2009

Evolution of protein domain promiscuity in eukaryotes

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

First Published January 29, 2008

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Laurie Gordon
Shan Yang
Mary Tran-Gyamfi
Dan Baggott
Mari Christensen
Aaron Hamilton Richard Crooijmans
... [+2 authors] ...,
Martien Groenen
Susan Lucas
Ivan Ovcharenko
Lisa Stubbs

First Published October 5, 2007

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

A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors

Stuart Huntley
Daniel M. Baggott
Aaron T. Hamilton
Mary Tran-Gyamfi
Shan Yang
Joomyeong Kim
Laurie Gordon
Elbert Branscomb
Lisa Stubbs

First Published April 10, 2006

Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents

Kateryna D. Makova
Shan Yang
Francesca Chiaromonte

First Published April 1, 2004

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

Shan Yang
Arian F. Smit
Scott Schwartz
Francesca Chiaromonte
Krishna M. Roskin
David Haussler
Webb Miller
Ross C. Hardison

First Published April 1, 2004

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

First Published January 1, 2003

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

Ross C. Hardison
Krishna M. Roskin
Shan Yang
Mark Diekhans
W. James Kent
Ryan Weber Laura Elnitski Jia Li Michael O'Connor Diana Kolbe Scott Schwartz Terrence S. Furey Simon Whelan Nick Goldman
... [+9 authors] ...,
Arian Smit
Webb Miller
Francesca Chiaromonte
David Haussler

First Published January 1, 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

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

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Evolution of protein domain promiscuity in eukaryotes

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

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

A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors

Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

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

Distinguishing Regulatory DNA From Neutral Sites

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian 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