相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Differential nuclear scaffold/matrix attachment marks expressed genes
Amelia K. Linnemann et al.
HUMAN MOLECULAR GENETICS (2009)
Evolution of genome architecture
Eugene V. Koonin
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2009)
Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes
Pavel S. Novichkov et al.
JOURNAL OF BACTERIOLOGY (2009)
Phage-Mediated Intergeneric Transfer of Toxin Genes
John Chen et al.
SCIENCE (2009)
Origin and Early Evolution of Angiosperms
Douglas E. Solds et al.
YEAR IN EVOLUTIONARY BIOLOGY 2008 (2008)
The evolution of domain-content in bacterial genomes
Nacho Molina et al.
BIOLOGY DIRECT (2008)
Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
Maxim Y. Wolf et al.
BIOLOGY DIRECT (2008)
The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner
Nicolas Glansdorff et al.
BIOLOGY DIRECT (2008)
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
Nalini Polavarapu et al.
BMC GENOMICS (2008)
Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif
Thomas R. Burglin
BMC GENOMICS (2008)
Retrotransposons revisited: The restraint and rehabilitation of parasites
John L. Goodier et al.
CELL (2008)
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
D. Allan Drummond et al.
CELL (2008)
The evolution of biology A shift towards the engineering of prediction-generating tools and away from traditional research practice
Lawrence Kelley et al.
EMBO REPORTS (2008)
Wolbachia genome integrated in an insect chromosome:: Evolution and fate of laterally transferred endosymbiont genes
Naruo Nikoh et al.
GENOME RESEARCH (2008)
Positive and negative selection on noncoding DNA in Drosophila simulans
Penelope R. Haddrill et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach
Miklos Csuros et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
The deep archaeal roots of eukaryotes
Natalya Yutin et al.
MOLECULAR BIOLOGY AND EVOLUTION (2008)
Translational control of intron splicing in eukaryotes
Olivier Jaillon et al.
NATURE (2008)
The Trichoplax genome and the nature of placozoans
Mansi Srivastava et al.
NATURE (2008)
Turning a hobby into a job: How duplicated genes find new functions
Gavin C. Conant et al.
NATURE REVIEWS GENETICS (2008)
The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups
Eugene V. Koonin et al.
NATURE REVIEWS MICROBIOLOGY (2008)
Extra-chromosomal elements and the evolution of cellular DNA replication machineries
Adam T. McGeoch et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2008)
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
Eugene V. Koonin et al.
NUCLEIC ACIDS RESEARCH (2008)
Extreme polyploidy in a large bacterium
Jennifer E. Mendell et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
The chemical genomic portrait of yeast: Uncovering a phenotype for all genes
Maureen E. Hillenmeyer et al.
SCIENCE (2008)
The eukaryotic genome as an RNA machine
Paulo P. Amaral et al.
SCIENCE (2008)
Cryptic complexity captured: the Nematostella genome reveals its secrets
David J. Miller et al.
TRENDS IN GENETICS (2008)
Patterns of Positive Selection in Six Mammalian Genomes
Carolin Kosiol et al.
PLOS GENETICS (2008)
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
Konstantinos Liolios et al.
NUCLEIC ACIDS RESEARCH (2008)
A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast
Devin R. Scannell et al.
GENOME RESEARCH (2008)
Evolutionary history of bacteriophages with double-stranded DNA genomes
Galina Glazko et al.
BIOLOGY DIRECT (2007)
Consequences of genome duplication
Marie Semon et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2007)
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
Kira S. Makarova et al.
BIOLOGY DIRECT (2007)
Evaluating the protein coding potential of exonized transposable element sequences
Jittima Piriyapongsa et al.
BIOLOGY DIRECT (2007)
The new biology: beyond the Modern Synthesis
Michael R. Rose et al.
BIOLOGY DIRECT (2007)
Evolution of genes and genomes on the Drosophila phylogeny
Andrew G. Clark et al.
NATURE (2007)
Complete genome sequence of the myxobacterium Sorangium cellulosum
Susanne Schneiker et al.
NATURE BIOTECHNOLOGY (2007)
Yeast genome evolution - the origin of the species
Devin R. Scannell et al.
YEAST (2007)
The Chlamydomonas genome reveals the evolution of key animal and plant functions
Sabeeha S. Merchant et al.
SCIENCE (2007)
Microbial oceanography: paradigms, processes and promise
David M. Karl
NATURE REVIEWS MICROBIOLOGY (2007)
Horizontal gene transfer in chromalveolates
Tetyana Nosenko et al.
BMC EVOLUTIONARY BIOLOGY (2007)
Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes
Julie C. Dunning Hotopp et al.
SCIENCE (2007)
The Biological Big Bang model for the major transitions in evolution
Eugene V. Koonin
BIOLOGY DIRECT (2007)
Human genome ultraconserved elements are ultraselected
Sol Katzman et al.
SCIENCE (2007)
Comparative genomics and evolution of alternative splicing: The pessimists' science
Irena I. Artamonova et al.
CHEMICAL REVIEWS (2007)
Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
Nicholas H. Putnam et al.
SCIENCE (2007)
Coevolution of genomic intron number and splice sites
Manuel Irimia et al.
TRENDS IN GENETICS (2007)
Three distinct modes of intron dynamics in the evolution of eukaryotes
Liran Carmel et al.
GENOME RESEARCH (2007)
A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer
Matthew B. Rogers et al.
BMC EVOLUTIONARY BIOLOGY (2007)
The frailty of adaptive hypotheses for the origins of organismal complexity
Michael Lynch
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Testing hypotheses without considering predictions
Tal Dagan et al.
BIOESSAYS (2007)
The origin of mitochondria in light of a fluid prokaryotic chromosome model
Christian Esser et al.
BIOLOGY LETTERS (2007)
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila
Stanley A. Sawyer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
Jan O. Andersson et al.
BMC GENOMICS (2007)
Pattern pluralism and the Tree of Life hypothesis
W. Ford Doolittle et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
Jane M. Carlton et al.
SCIENCE (2007)
Complexity, connectivity, and duplicability as barriers to lateral gene transfer
Alon Wellner et al.
GENOME BIOLOGY (2007)
The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families
Shibu Yooseph et al.
PLOS BIOLOGY (2007)
Evaluating hypotheses for the origin of eukaryotes
Anthony M. Poole et al.
BIOESSAYS (2007)
Raising the estimate of functional human sequences
Michael Pheasant et al.
GENOME RESEARCH (2007)
Bushes in the tree of life
Antonis Rokas et al.
PLOS BIOLOGY (2006)
The marine viromes of four oceanic regions
Florent E. Angly et al.
PLOS BIOLOGY (2006)
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation
Fyodor A. Kondrashov et al.
BIOLOGY DIRECT (2006)
Comparative genomics of the lactic acid bacteria
K. Makarova et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Evolutionary systems biology: links between gene evolution and function
Eugene V. Koonin et al.
CURRENT OPINION IN BIOTECHNOLOGY (2006)
The ancient Virus World and evolution of cells
Eugene V. Koonin et al.
BIOLOGY DIRECT (2006)
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
G. A. Tuskan et al.
SCIENCE (2006)
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
Daniel L. Halligan et al.
GENOME RESEARCH (2006)
Multiple secondary origins of the anaerobic lifestyle in eukaryotes
T. Martin Embley
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)
Unifying measures of gene function and evolution
Yuri I. Wolf et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)
The obligate human pathogen, Neisseria gonorrhoeae, is polyploid
Deborah M. Tobiason et al.
PLOS BIOLOGY (2006)
Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution
Ben-Yang Liao et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
Genomics and the irreducible nature of eukaryote cells
CG Kurland et al.
SCIENCE (2006)
An integrated view of protein evolution
C Pál et al.
NATURE REVIEWS GENETICS (2006)
Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life
D Prangishvill et al.
VIRUS RESEARCH (2006)
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
LA Iyer et al.
VIRUS RESEARCH (2006)
The origin of viruses and their possible roles in major evolutionary transitions
P Forterre
VIRUS RESEARCH (2006)
Eukaryotic evolution, changes and challenges
TM Embley et al.
NATURE (2006)
Introns and the origin of nucleus-cytosol compartmentalization
W Martin et al.
NATURE (2006)
The evolution of spliceosomal introns: patterns, puzzles and progress
SW Roy et al.
NATURE REVIEWS GENETICS (2006)
Evolutionary conservation of expression profiles between human and mouse orthologous genes
BY Liao et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
A single determinant dominates the rate of yeast protein evolution
DA Drummond et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
Genome-wide identification of human functional DNA using a neutral indel model
Gerton Lunter et al.
PLOS COMPUTATIONAL BIOLOGY (2006)
Evolution of primate gene expression
Philipp Khaitovich et al.
NATURE REVIEWS GENETICS (2006)
Distribution of the strength of selection against amino acid replacements in human proteins
LY Yampolsky et al.
HUMAN MOLECULAR GENETICS (2005)
Adaptive evolution of non-coding DNA in Drosophila
P Andolfatto
NATURE (2005)
Why highly expressed proteins evolve slowly
DA Drummond et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Two rounds of whole genome duplication in the ancestral vertebrate
P Dehal et al.
PLOS BIOLOGY (2005)
Genomic perspectives in microbial oceanography
EF DeLong et al.
NATURE (2005)
Hox clusters as models for vertebrate genome evolution
S Hoegg et al.
TRENDS IN GENETICS (2005)
Lateral gene transfer in eukaryotes
JO Andersson
CELLULAR AND MOLECULAR LIFE SCIENCES (2005)
Do orthologous gene phylogenies really support tree-thinking?
E Bapteste et al.
BMC EVOLUTIONARY BIOLOGY (2005)
Genomes, phylogeny, and evolutionary systems biology
M Medina
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Comparative metagenomics of microbial communities
SG Tringe et al.
SCIENCE (2005)
Robustness, evolvability, and neutrality
A Wagner
FEBS LETTERS (2005)
Paradigm change in evolutionary microbiology
Maureen A. O'Malley et al.
STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE PART C-STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES (2005)
One-component systems dominate signal transduction in prokaryotes
LE Ulrich et al.
TRENDS IN MICROBIOLOGY (2005)
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
XL He et al.
GENETICS (2005)
Microeconomic principles explain an optimal genome size in bacteria
JAG Ranea et al.
TRENDS IN GENETICS (2005)
Mobile genetic elements: The agents of open source evolution
LS Frost et al.
NATURE REVIEWS MICROBIOLOGY (2005)
Horizontal gene transfer, genome innovation and evolution
JP Gogarten et al.
NATURE REVIEWS MICROBIOLOGY (2005)
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
KS Makarova et al.
NUCLEIC ACIDS RESEARCH (2005)
The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
CI Castillo-Davis et al.
GENOME RESEARCH (2004)
The evolutionary dynamics of eukaryotic gene order
LD Hurst et al.
NATURE REVIEWS GENETICS (2004)
How prevalent is functional alternative splicing in the human genome?
R Sorek et al.
TRENDS IN GENETICS (2004)
The ring of life provides evidence for a genome fusion origin of eukaryotes
MC Rivera et al.
NATURE (2004)
A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
C Esser et al.
MOLECULAR BIOLOGY AND EVOLUTION (2004)
Frequent false detection of positive selection by the likelihood method with branch-site models
JZ Zhang
MOLECULAR BIOLOGY AND EVOLUTION (2004)
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
RL Charlebois et al.
GENOME RESEARCH (2004)
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging
LM Iyer et al.
NUCLEIC ACIDS RESEARCH (2004)
Conservation and coevolution in the scale-free human gene coexpression network
IK Jordan et al.
MOLECULAR BIOLOGY AND EVOLUTION (2004)
Ultraconserved elements in the human genome
G Bejerano et al.
SCIENCE (2004)
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
EV Koonin et al.
GENOME BIOLOGY (2004)
Hox cluster duplications and the opportunity for evolutionary novelties
GP Wagner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
DM Krylov et al.
GENOME RESEARCH (2003)
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution
IB Rogozin et al.
CURRENT BIOLOGY (2003)
Scaling laws in the functional content of genomes
E van Nimwegen
TRENDS IN GENETICS (2003)
Horizontal gene transfer: A critical view
CG Kurland et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
The balance of driving forces during genome evolution in prokaryotes
V Kunin et al.
GENOME RESEARCH (2003)
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes
G Panopoulou et al.
GENOME RESEARCH (2003)
Messenger RNA surveillance and the evolutionary proliferation of introns
M Lynch et al.
MOLECULAR BIOLOGY AND EVOLUTION (2003)
Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences
FA Kondrashov et al.
TRENDS IN GENETICS (2003)
The genetic core of the universal ancestor
JK Harris et al.
GENOME RESEARCH (2003)
A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions
GV Glazko et al.
TRENDS IN GENETICS (2003)
Origin of a substantial fraction of human regulatory sequences from transposable elements
IK Jordan et al.
TRENDS IN GENETICS (2003)
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells
W Martin et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2003)
Lateral gene transfer: when will adolescence end?
JG Lawrence et al.
MOLECULAR MICROBIOLOGY (2003)
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
BG Mirkin et al.
BMC EVOLUTIONARY BIOLOGY (2003)
Gene organization: Selection, selfishness, and serendipity
JG Lawrence
ANNUAL REVIEW OF MICROBIOLOGY (2003)
Vertebrate evolution: doubling and shuffling with a full deck
D Durand
TRENDS IN GENETICS (2003)
Large-scale comparison of intron positions among animal, plant, and fungal genes
A Fedorov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Prokaryotic evolution in light of gene transfer
JP Gogarten et al.
MOLECULAR BIOLOGY AND EVOLUTION (2002)
The structure of the protein universe and genome evolution
EV Koonin et al.
NATURE (2002)
Birth and death of protein domains: A simple model of evolution explains power law behavior
Georgy P. Karev et al.
BMC EVOLUTIONARY BIOLOGY (2002)
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
W Martin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Genome trees and the Tree of Life
YI Wolf et al.
TRENDS IN GENETICS (2002)
Extensive genomic duplication during early chordate evolution
A McLysaght et al.
NATURE GENETICS (2002)
Microevolutionary genomics of bacteria
IK Jordan et al.
THEORETICAL POPULATION BIOLOGY (2002)
Genomes in flux: The evolution of archaeal and proteobacterial gene content
B Snel et al.
GENOME RESEARCH (2002)
An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle
W Martin et al.
BIOLOGICAL CHEMISTRY (2001)
Genomic and phylogenetic perspectives on the evolution of prokaryotes
JR Brown
SYSTEMATIC BIOLOGY (2001)
The complete genome of the crenarchaeon Sulfolobus solfataricus P2
Q She et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Protein dispensability and rate of evolution
AE Hirsh et al.
NATURE (2001)
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
NT Perna et al.
NATURE (2001)
The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome
C Brochier et al.
TRENDS IN GENETICS (2000)
The evolutionary fate and consequences of duplicate genes
M Lynch et al.
SCIENCE (2000)
Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis
AP de Koning et al.
MOLECULAR BIOLOGY AND EVOLUTION (2000)
Genome rearrangement by replication-directed translocation
ERM Tillier et al.
NATURE GENETICS (2000)
From complete genomes to measures of substitution rate variability within and between proteins
NV Grishin et al.
GENOME RESEARCH (2000)
Genome data: what do we learn?
WC Nierman et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2000)