Studying genomes through the aeons: protein families, pseudogenes and proteome evolution (Q33959836)

30 July 2017

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title

Studying genomes through the aeons: protein families, pseudogenes and proteome evolution (English)

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30 July 2017

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2

Mark Gerstein

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30 July 2017

Paul M Harrison

1

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PubMed ID

12083509

30 July 2017

language of work or name

English

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publication date

1 May 2002

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Journal of Molecular Biology

30 July 2017

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30 July 2017

318

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30 July 2017

1155-1174

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30 July 2017

5

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Gene duplication and the structure of eukaryotic genomes

30 July 2017

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The frequency distribution of gene family sizes in complete genomes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Highly specific protein sequence motifs for genome analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

InterPro--an integrated documentation resource for protein families, domains and functional sites

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

ProtoMap: automatic classification of protein sequences and hierarchy of protein families

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The SYSTERS protein sequence cluster set.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

SCOP: a structural classification of proteins database for the investigation of sequences and structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Using the CATH domain database to assign structures and functions to the genome sequences.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Gene ontology: tool for the unification of biology

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

MIPS: a database for genomes and protein sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Genes and proteins of Escherichia coli (GenProtEc)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

How representative are the known structures of the proteins in a complete genome? A comprehensive structural census

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

A structural census of the current population of protein sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Analysis of Protein Domain Families inCaenorhabditis elegans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Genome analysis: Assigning protein coding regions to three-dimensional structures

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Estimating the number of protein folds and families from complete genome data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Initial sequencing and analysis of the human genome

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The genome sequence of Drosophila melanogaster

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The origins of genomic duplications in Arabidopsis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The evolutionary fate and consequences of duplicate genes

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Yeast genome evolution in the post-genome era.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Updated map of duplicated regions in the yeast genome

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Molecular evidence for an ancient duplication of the entire yeast genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Towards a truly integrative biology through the functional genomics of yeast

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The minimal genome concept

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Robustness against mutations in genetic networks of yeast.

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

A genetic uncertainty problem

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Marginal fitness contributions of nonessential genes in yeast

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Characterization of the yeast transcriptome

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Protein dispensability and rate of evolution

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Processed pseudogenes: characteristics and evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Human LINE retrotransposons generate processed pseudogenes

7 January 2021

1 reference

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7 January 2021

Vertebrate pseudogenes

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Horizontal gene transfer among microbial genomes: new insights from complete genome analysis

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The complete genome sequence of Escherichia coli K-12

7 January 2021

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https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

7 January 2021

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Intraspecies variation in bacterial genomes: the need for a species genome concept

7 January 2021

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Microbial genomes: dealing with diversity

7 January 2021

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Massive gene decay in the leprosy bacillus

7 January 2021

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The genome sequence of Rickettsia prowazekii and the origin of mitochondria

7 January 2021

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Mechanisms of evolution in Rickettsia conorii and R. prowazekii

7 January 2021

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Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes

7 January 2021

1 reference

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Genome sequence of Yersinia pestis, the causative agent of plague

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

SGD: Saccharomyces Genome Database

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Protein-only inheritance in yeast: something to get [PSI+]-ched about

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Translation termination efficiency can be regulated in Saccharomyces cerevisiae by environmental stress through a prion-mediated mechanism

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Yeast prions and their prion-forming domain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

A yeast prion provides a mechanism for genetic variation and phenotypic diversity

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Comparison of the complete protein sets of worm and yeast: orthology and divergence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Genome sequence of the nematode C. elegans: a platform for investigating biology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Comparative genomics of the eukaryotes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Neurobiology of the Caenorhabditis elegans genome.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs

7 January 2021

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The complete human olfactory subgenome

7 January 2021

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The human olfactory receptor repertoire

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The evolution of an alpha-esterase pseudogene inactivated in the Drosophila melanogaster lineage.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

High intrinsic rate of DNA loss in Drosophila.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Pseudogene evolution and natural selection for a compact genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Evolution of genome size: new approaches to an old problem.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Updating the str and srj (stl) families of chemoreceptors in Caenorhabditis nematodes reveals frequent gene movement within and between chromosomes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

A question of size: the eukaryotic proteome and the problems in defining it.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The Sequence of the Human Genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Gene index analysis of the human genome estimates approximately 120,000 genes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The DNA sequence of human chromosome 22

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The DNA sequence of human chromosome 21

7 January 2021

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Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence

7 January 2021

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Analysis of expressed sequence tags indicates 35,000 human genes

7 January 2021

1 reference

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Frequent alternative splicing of human genes

7 January 2021

1 reference

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EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.

7 January 2021

1 reference

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Computational inference of homologous gene structures in the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Nature and structure of human genes that generate retropseudogenes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

The gene family encoding the mouse ribosomal protein L32 contains a uniquely expressed intron-containing gene and an unmutated processed gene

7 January 2021

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Do all SINEs lead to LINEs?

7 January 2021

1 reference

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SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes

7 January 2021

1 reference

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Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes

7 January 2021

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Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2802%2900109-2

Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes.

7 January 2021

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Evolution of immunoglobulin VH pseudogenes in chickens

7 January 2021

1 reference

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Lineage-specific loss and divergence of functionally linked genes in eukaryotes

7 January 2021

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mRNA quality control: Marking the message for life or death.

7 January 2021

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10.1016/S0022-2836(02)00109-2

7 January 2021

Identifiers

DOI

1 reference

30 July 2017

1 reference

PubMed ID

12083509