Lista de obras - Marc Robinson-Rechavi - Dominio Público Uruguay

A benchmark of gene expression tissue-specificity metrics

artículo científico publicado en 2016

A conserved retinoid X receptor (RXR) from the mollusk Biomphalaria glabrata transactivates transcription in the presence of retinoids.

artículo científico publicado en 2005

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network

artículo científico publicado en 2007

Abstract 2463: Prototype open-access biomarker knowledgebase for genetic tests for breast cancer

scholarly article

Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo

scientific article published on 01 December 2018

Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo

article

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

artículo científico publicado en 2010

An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes.

artículo científico publicado en 2001

An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

artículo científico publicado en 2022

An ontology to clarify homology-related concepts

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

artículo científico publicado en 2017

Bgee

gene expression database

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

artículo científico publicado en 2016

Big data and other challenges in the quest for orthologs

artículo científico publicado en 2014

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation

Bioinformatics of Nuclear Receptors

article published in 2003

Bioinformatics of nuclear receptors

artículo científico publicado en 2003

Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains

article

Community-wide plasmid gene mobilization and selection

artículo científico publicado en 2013

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs

artículo científico publicado en 2012

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds ⬇️

artículo científico publicado en 2014

Comparative modular analysis of gene expression in vertebrate organs

artículo científico publicado en 2012

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

artículo científico publicado en 2011

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

artículo científico publicado en 2005

Convergent consequences of parthenogenesis on stick insect genomes

artículo científico publicado en 2022

Convergent evolution of venom gland transcriptomes across Metazoa

artículo científico publicado en 2022

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human

artículo científico publicado en 2012

Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

scientific article published on 20 May 2020

Cross-species functional modules link proteostasis to human normal aging

scientific article published on 03 July 2019

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

artículo científico publicado en 2013

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions ⬇️

artículo científico publicado en 2015

Determinants of protein evolutionary rates in light of ENCODE functional genomics

Developmental Constraints on Genome Evolution in Four Bilaterian Model Species

scientific article published in 2018

Developmental constraints on genome evolution in four bilaterian model species

Developmental constraints on vertebrate genome evolution

artículo científico publicado en 2008

Enabling semantic queries across federated bioinformatics databases

scientific article published on 01 January 2019

Euteleost fish genomes are characterized by expansion of gene families

artículo científico publicado en 2001

Evidence for an episodic model of protein sequence evolution

artículo científico publicado en 2009

Evidence for polygenic adaptation to pathogens in the human genome

artículo científico publicado en 2013

Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport

artículo científico publicado en 2011

Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems

artículo científico publicado en 2004

Evolutionary rates of duplicate genes in fish and mammals

artículo científico publicado en 2001

Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes

artículo científico publicado en 2005

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

artículo científico publicado en 2006

Generating Homology Relationships by Alignment of Anatomical Ontologies

artículo científico publicado en 2009

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

artículo científico publicado en 2004

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

artículo científico publicado en 2008

Genomic Features of Parthenogenetic Animals

scientific article published on 28 September 2020

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

artículo científico publicado en 2019

Genomic features of asexual animals

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

artículo científico publicado en 2019

Genomics is changing Evo-Devo

artículo científico publicado en 2015

Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy

artículo científico publicado en 2010

How confident can we be that orthologs are similar, but paralogs differ?

artículo científico publicado en 2009

How many nuclear hormone receptors are there in the human genome?

artículo científico publicado en 2001

How much does the amphioxus genome represent the ancestor of chordates? ⬇️

artículo científico publicado el 28 de febrero de 2012

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics

artículo científico publicado en 2014

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics

scientific article published on 03 July 2016

Identifying gene function and module connections by the integration of multispecies expression compendia

artículo científico publicado en 2019

Impact of changes in GC content on the silent molecular clock in murids

artículo científico publicado en 1997

Inference of Evolutionary Forces Acting on Human Biological Pathways

artículo científico publicado en 2015

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

artículo científico publicado en 2020

Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor

artículo científico publicado en 2010

Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY.

artículo científico publicado en 2003

Large-Scale Analyses of Positive Selection Using Codon Models

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection

scientific article published in 2019

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution

artículo científico publicado en 2010

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

artículo científico publicado en 2022

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

Low number of fixed somatic mutations in a long-lived oak tree.

artículo científico publicado en 2017

Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair

artículo científico publicado en 2011

Methods detecting rhythmic gene expression are biologically relevant only for strong signal

scientific article published on 17 March 2020

Modeling Codon Rate Variation: Robust Inference of Protein and Nucleotide Selection

Molecular evidence for a functional ecdysone signaling system in Brugia malayi

artículo científico publicado en 2010

Molecular evolution of angrogen receptors in fish

scientific article published in 2003

Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT.

artículo científico publicado en 1997

Molecular signaling in zebrafish development and the vertebrate phylotypic period

artículo científico publicado en 2010

NUREBASE: database of nuclear hormone receptors ⬇️

artículo científico publicado el 1 de enero de 2002

Neofunctionalization in vertebrates: the example of retinoic acid receptors

artículo científico publicado en 2006

No evidence for the radiation time lag model after whole genome duplications in Teleostei

artículo científico publicado en 2017

No evidence for the radiation time lag model after whole genome duplications in Teleostei

Nuclear gene LCAT supports rodent monophyly

artículo científico publicado en 2000

Nuclear receptors are markers of animal genome evolution

artículo científico publicado en 2003

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

scientific article published in 2021

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data

artículo científico publicado en 2020

One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity

artículo científico publicado en 2006

Optimization strategies for fast detection of positive selection on phylogenetic trees

artículo científico publicado en 2014

Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis

artículo científico publicado en 2007

Patterns of positive selection in seven ant genomes

artículo científico publicado en 2014

Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

artículo científico publicado en 2021

Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals

artículo científico publicado en 2008

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

artículo científico publicado en 2008

Phylogenetic code in the cloud - can it meet the expectations?

artículo científico publicado en 2010

Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

artículo científico publicado en 2003

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

artículo científico publicado en 2020

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

scholarly article published 5 October 2019

RRTree: relative-rate tests between groups of sequences on a phylogenetic tree

artículo científico publicado en 2000

Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXR.

artículo científico publicado en 2003

Re: Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

artículo científico publicado en 2012

Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes

scientific article published on 01 February 2019

Repeated evolution of asexuality involves convergent gene expression changes

artículo científico publicado en 2018

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs ⬇️

artículo científico publicado el 17 de mayo de 2012

Robust inference of positive selection on regulatory sequences in the human brain

artículo científico publicado en 2020

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates

artículo científico publicado en 2017

Selectome update: quality control and computational improvements to a database of positive selection

artículo científico publicado en 2013

Selectome: a database of positive selection

artículo científico publicado en 2008

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

artículo científico publicado en 2015

Sex Differentiation In Grayling (Salmonidae) Goes Through An All-Male Stage And Is Delayed In Genetic Males Who Instead Grow Faster

article published in 2017

Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster

artículo científico publicado en 2017

Sex-Specific Changes In Gene Expression And Delayed Sex Differentiation In Response To Estrogen Pollution In Grayling (Salmonidae)

article

Sex-biased gene expression is repeatedly masculinized in asexual females

artículo científico publicado en 2019

Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

scientific article published on 15 July 2019

Single-cell transcriptomics allows novel insights into aging and circadian processes

artículo científico publicado en 2020

SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

artículo científico publicado en 2012

Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes

artículo científico publicado en 2020

State aggregation for fast likelihood computations in molecular evolution

artículo científico publicado en 2017

Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects.

artículo científico publicado en 2009

Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability

artículo científico publicado en 2005

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

artículo científico publicado en 2020

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC ⬇️

artículo científico publicado el 4 de abril de 2013

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

artículo científico publicado en 2015

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

artículo científico publicado en 2016

The SIB Swiss Institute of Bioinformatics Semantic Web of data

artículo científico publicado en 2023

The amphioxus genome and the evolution of the chordate karyotype

artículo científico publicado en 2008

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

artículo científico publicado en 2008

The challenge of modeling nuclear receptor regulatory networks in mammalian cells

artículo científico publicado en 2010

The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes

artículo científico publicado en 2009

The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates

artículo científico publicado en 2013

The nuclear receptor superfamily

artículo científico publicado en 2003

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

artículo científico publicado en 2015

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.

artículo científico publicado en 2016

Tissue-specificity of gene expression diverges slowly between orthologs, and rapidly between paralogs

article

USAGE OPTIMIZATION OF UNEVENLY SAMPLED DATA THROUGH THE COMBINATION OF QUARTET TREES: A EUTHERIAN DRAFT PHYLOGENY BASED ON 640 NUCLEAR AND MITOCHONDRIAL PROTEINS ⬇️

scholarly article by Marc Robinson-Rechavi & DAN GRAUR published 1 January 2001 in Israel Journal of Zoology

Uncovering hidden duplicated content in public transcriptomics data

artículo científico publicado en 2013

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

artículo científico publicado en 2014

Update of NUREBASE: nuclear hormone receptor functional genomics

artículo científico publicado en 2004

What to compare and how: Comparative transcriptomics for Evo-Devo

artículo científico publicado en 2015

When orthologs diverge between human and mouse ⬇️

artículo científico publicado el 15 de junio de 2011

gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution.

artículo científico publicado en 2012

vHOG, a multispecies vertebrate ontology of homologous organs groups

artículo científico publicado en 2012

Lista de obras de Marc Robinson-Rechavi

A benchmark of gene expression tissue-specificity metrics

A conserved retinoid X receptor (RXR) from the mollusk Biomphalaria glabrata transactivates transcription in the presence of retinoids.

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network

Abstract 2463: Prototype open-access biomarker knowledgebase for genetic tests for breast cancer

Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo

Adaptive evolution of animal proteins over development: support for the Darwin selection opportunity hypothesis of Evo-Devo

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes.

An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

An ontology to clarify homology-related concepts

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

Bgee

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

Big data and other challenges in the quest for orthologs

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation

Bioinformatics of Nuclear Receptors

Bioinformatics of nuclear receptors

Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brains

Community-wide plasmid gene mobilization and selection

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds ⬇️

Comparative modular analysis of gene expression in vertebrate organs

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Convergent consequences of parthenogenesis on stick insect genomes

Convergent evolution of venom gland transcriptomes across Metazoa

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human

Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)

Cross-species functional modules link proteostasis to human normal aging

Cross-species functional modules link proteostasis to human normal aging

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions ⬇️

Determinants of protein evolutionary rates in light of ENCODE functional genomics

Developmental Constraints on Genome Evolution in Four Bilaterian Model Species

Developmental constraints on genome evolution in four bilaterian model species

Developmental constraints on vertebrate genome evolution

Enabling semantic queries across federated bioinformatics databases

Euteleost fish genomes are characterized by expansion of gene families

Evidence for an episodic model of protein sequence evolution

Evidence for polygenic adaptation to pathogens in the human genome

Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport

Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems

Evolutionary rates of duplicate genes in fish and mammals

Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

Generating Homology Relationships by Alignment of Anatomical Ontologies

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Genomic Features of Parthenogenetic Animals

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Genomic features of asexual animals

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

Genomics is changing Evo-Devo

Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy

How confident can we be that orthologs are similar, but paralogs differ?

How many nuclear hormone receptors are there in the human genome?

How much does the amphioxus genome represent the ancestor of chordates? ⬇️

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics

Identifying gene function and module connections by the integration of multispecies expression compendia

Impact of changes in GC content on the silent molecular clock in murids

Inference of Evolutionary Forces Acting on Human Biological Pathways

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor

Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY.

Large-Scale Analyses of Positive Selection Using Codon Models

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection

Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

Low Rate of Somatic Mutations in a Long-Lived Oak Tree

Low number of fixed somatic mutations in a long-lived oak tree.

Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair

Methods detecting rhythmic gene expression are biologically relevant only for strong signal

Modeling Codon Rate Variation: Robust Inference of Protein and Nucleotide Selection

Molecular evidence for a functional ecdysone signaling system in Brugia malayi

Molecular evolution of angrogen receptors in fish

Molecular phylogeny of rodents, with special emphasis on murids: evidence from nuclear gene LCAT.

Molecular signaling in zebrafish development and the vertebrate phylotypic period

NUREBASE: database of nuclear hormone receptors ⬇️