List of works - Edward M. Rubin

A high-resolution enhancer atlas of the developing telencephalon

scientific article published on 31 January 2013

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

scientific article

A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter

scientific article (publication date: 26 May 2006)

A vast collection of microbial genes that are toxic to bacteria

scientific article

Accelerated evolution of conserved noncoding sequences in humans

scientific article

Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns

Analysis of apolipoprotein A5, c3, and plasma triglyceride concentrations in genetically engineered mice

scientific article

Apolipoprotein A-I and the molecular variant apoA-I(Milano): evaluation of the antiatherogenic effects in knock-in mouse model.

scientific article

Apolipoprotein A-V deficiency results in marked hypertriglyceridemia attributable to decreased lipolysis of triglyceride-rich lipoproteins and removal of their remnants

scientific journal article

Apolipoprotein A5, a crucial determinant of plasma triglyceride levels, is highly responsive to peroxisome proliferator-activated receptor alpha activators

scientific article (publication date: 16 May 2003)

Apolipoprotein A5, a newly identified gene that affects plasma triglyceride levels in humans and mice

scientific article (publication date: April 2003)

Application of sequence-based methods in human microbial ecology

scientific article published on 6 February 2006

Automated whole-genome multiple alignment of rat, mouse, and human

scientific article published on April 2004

ChIP-Seq identification of weakly conserved heart enhancers

scientific article

ChIP-seq accurately predicts tissue-specific activity of enhancers

scientific article (publication date: 12 February 2009)

Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs

scientific article

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

scientific article

Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene

scientific article published in February 2005

Comparative genomic tools and databases: providing insights into the human genome

scientific article

Comparative genomics at the vertebrate extremes

scientific article published on June 2004

Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene

scientific article

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

scientific article published on 31 October 2015

Convergent evolution in primates and an insectivore.

scientific article published in January 2004

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

scientific article published on 19 March 2018

Deletion of ultraconserved elements yields viable mice

scientific article published in September 2007

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

scientific article published on January 2007

Erratum: Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

scholarly article published in Nature Biotechnology

Evolution. Searching for new branches on the tree of life

scientific article published in November 2014

Exploiting human--fish genome comparisons for deciphering gene regulation

scientific article published in October 2004

Facile Recoding of Selenocysteine in Nature

scientific article published on 16 March 2016

Fine tuning of craniofacial morphology by distant-acting enhancers

scientific article

Functional annotation of mouse mutations in embryonic stem cells by use of expression profiling

scientific article published on January 2004

Functional autonomy of distant-acting human enhancers

scientific article published on 05 March 2009

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

scientific article

Genome-wide compendium and functional assessment of in vivo heart enhancers

scientific article published on 05 October 2016

Genome-wide experimental determination of barriers to horizontal gene transfer

scientific article published on 18 October 2007

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

scientific article (publication date: March 2014)

Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease

scientific article

Genomic sequencing of Pleistocene cave bears

scientific article

Genomic views of distant-acting enhancers

scientific article

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

scientific article published on 27 January 2016

Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11.

scientific article published on May 2004

Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons

scientific article published on 25 March 2004

High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery

scientific article published on September 16, 2011

Human-specific gain of function in a developmental enhancer

scientific article published on September 2008

Identification of ancient remains through genomic sequencing

scientific article (publication date: August 2008)

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

scientific article

In vivo characterization of a vertebrate ultraconserved enhancer

scientific article

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insights into the phylogeny and coding potential of microbial dark matter

scientific article

Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: role of upstream stimulatory factor

scientific article

Intraspecies sequence comparisons for annotating genomes

scientific article

Knockdown expression and hepatic deficiency reveal an atheroprotective role for SR-BI in liver and peripheral tissues

scientific article

Large-scale discovery of enhancers from human heart tissue

scientific article published on 4 December 2011

Linkage and association between distinct variants of the APOA1/C3/A4/A5 gene cluster and familial combined hyperlipidemia

scientific article published on 09 October 2003

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny

scientific article published on 9 September 2005

Megabase deletions of gene deserts result in viable mice

scientific article published in October 2004

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

scientific article

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

scientific article

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

scientific article

Paleontology. New tricks with old bones

scientific article

Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments

scholarly article published 1 April 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

scientific article published on 22 January 2004

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

scientific article

Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry

scientific article

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

scientific article

Primate-specific evolution of an LDLR enhancer

scientific article published on 2 August 2006

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

scientific article published on October 2016

Rapid and pervasive changes in genome-wide enhancer usage during mammalian development

scientific article published on December 2013

Relative contribution of variation within the APOC3/A4/A5 gene cluster in determining plasma triglycerides

scientific article

SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data

scientific article

Scanning Human Gene Deserts for Long-Range Enhancers ⬇️

scientific article published on October 17, 2003

Sequencing and analysis of Neanderthal genomic DNA

scientific article

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production

scientific article

Stop codon reassignments in the wild

scientific article

Strategies and tools for whole-genome alignments

scientific article

Symbiosis insights through metagenomic analysis of a microbial consortium

scientific article

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

scientific article

Targeted replacement of mouse apolipoprotein A-I with human ApoA-I or the mutant ApoA-IMilano. Evidence of APOA-IM impaired hepatic secretion.

scientific article published on 5 December 2002

Tenascin-X deficiency mimics Ehlers-Danlos syndrome in mice through alteration of collagen deposition

scientific journal article

The DNA sequence and biology of human chromosome 19

scientific article

The DNA sequence and comparative analysis of human chromosome 5

scientific article

The Epigenomic Landscape of Prokaryotes

scientific article

The airborne metagenome in an indoor urban environment

scientific article

The future of DNA sequencing

scientific article published in Nature

The sequence and analysis of duplication-rich human chromosome 16

scientific article

Tissue-specific RNA expression marks distant-acting developmental enhancers

scientific article

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis

scientific article

Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing

scholarly article

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

scientific article

Transfer RNAs with novel cloverleaf structures

scientific article

Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels

scientific article (publication date: 15 November 2002)

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

scientific article

Uncovering Earth’s virome

scientific article (publication date: 17 August 2016)

[Facile Recoding of Selenocysteine in Nature].

scientific article published on 15 March 2016

rVista for comparative sequence-based discovery of functional transcription factor binding sites

scientific article published on May 2002

List of works by Edward M. Rubin

A high-resolution enhancer atlas of the developing telencephalon

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter

A vast collection of microbial genes that are toxic to bacteria

Accelerated evolution of conserved noncoding sequences in humans

Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns

Analysis of apolipoprotein A5, c3, and plasma triglyceride concentrations in genetically engineered mice

Apolipoprotein A-I and the molecular variant apoA-I(Milano): evaluation of the antiatherogenic effects in knock-in mouse model.

Apolipoprotein A-V deficiency results in marked hypertriglyceridemia attributable to decreased lipolysis of triglyceride-rich lipoproteins and removal of their remnants

Apolipoprotein A5, a crucial determinant of plasma triglyceride levels, is highly responsive to peroxisome proliferator-activated receptor alpha activators

Apolipoprotein A5, a newly identified gene that affects plasma triglyceride levels in humans and mice

Application of sequence-based methods in human microbial ecology

Automated whole-genome multiple alignment of rat, mouse, and human

ChIP-Seq identification of weakly conserved heart enhancers

ChIP-seq accurately predicts tissue-specific activity of enhancers

Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene

Comparative genomic tools and databases: providing insights into the human genome

Comparative genomics at the vertebrate extremes

Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

Convergent evolution in primates and an insectivore.

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

Deletion of ultraconserved elements yields viable mice

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

Erratum: Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Evolution. Searching for new branches on the tree of life

Exploiting human--fish genome comparisons for deciphering gene regulation

Facile Recoding of Selenocysteine in Nature

Fine tuning of craniofacial morphology by distant-acting enhancers

Functional annotation of mouse mutations in embryonic stem cells by use of expression profiling

Functional autonomy of distant-acting human enhancers

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Genome-wide compendium and functional assessment of in vivo heart enhancers

Genome-wide experimental determination of barriers to horizontal gene transfer

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease

Genomic sequencing of Pleistocene cave bears

Genomic views of distant-acting enhancers

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11.

Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons

High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery

Human-specific gain of function in a developmental enhancer

Identification of ancient remains through genomic sequencing

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

In vivo characterization of a vertebrate ultraconserved enhancer

Initial sequencing and comparative analysis of the mouse genome

Insights into the phylogeny and coding potential of microbial dark matter

Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: role of upstream stimulatory factor

Intraspecies sequence comparisons for annotating genomes

Knockdown expression and hepatic deficiency reveal an atheroprotective role for SR-BI in liver and peripheral tissues

Large-scale discovery of enhancers from human heart tissue

Linkage and association between distinct variants of the APOA1/C3/A4/A5 gene cluster and familial combined hyperlipidemia

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny

Megabase deletions of gene deserts result in viable mice

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community

Paleontology. New tricks with old bones

Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Primate-specific evolution of an LDLR enhancer

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

Rapid and pervasive changes in genome-wide enhancer usage during mammalian development

Relative contribution of variation within the APOC3/A4/A5 gene cluster in determining plasma triglycerides

SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data

Scanning Human Gene Deserts for Long-Range Enhancers ⬇️

Sequencing and analysis of Neanderthal genomic DNA

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production

Stop codon reassignments in the wild

Strategies and tools for whole-genome alignments