Lista de obras - David Posada - Dominio Público Uruguay

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

artículo científico publicado en 2016

A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

artículo científico publicado en 2016

A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints

scholarly article by D.P. Martin published in January 2005

A coalescent model of recombination hotspots

artículo científico publicado en 2003

A comparison of phylogenetic network methods using computer simulation

artículo científico publicado en 2008

A comparison of tools for the simulation of genomic next-generation sequencing data

artículo científico publicado en 2016

ALTER: program-oriented conversion of DNA and protein alignments

artículo científico publicado en 2010

Accurate Selection of Models of Protein Evolution

Advances in understanding the evolution of HIV.

artículo científico publicado en 1999

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1

artículo científico publicado en 2009

An exact nonparametric method for inferring mosaic structure in sequence triplets

artículo científico publicado en 2007

Analysing recombination in nucleotide sequences

artículo científico publicado en 2011

Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?

Author Correction: A comparison of tools for the simulation of genomic next-generation sequencing data

artículo científico publicado en 2018

Automated phylogenetic detection of recombination using a genetic algorithm

artículo científico publicado en 2006

Automatic Prediction of the Genetic Code

Base-Pairing Versatility Determines Wobble Sites in tRNA Anticodons of Vertebrate Mitogenomes ⬇️

artículo científico publicado el 9 de mayo de 2012

Bioinformatics for DNA Sequence Analysis

article

Cancer Molecular Evolution

artículo científico publicado en 2015

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

artículo científico publicado en 2022

Characterization of Reticulate Networks Based on the Coalescent with Recombination

scientific article published in 2009

Characterization of phylogenetic networks with NetTest

artículo científico publicado en 2010

Characterization of reticulate networks based on the coalescent with recombination

artículo científico publicado en 2008

Coalescent simulation of intracodon recombination

artículo científico publicado en 2009

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

artículo científico publicado en 2015

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

artículo científico publicado en 2013

Computational Design of Centralized HIV-1 Genes ⬇️

artículo científico publicado el 1 de diciembre de 2010

Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

artículo científico publicado en 2016

Cryptic diversity within the endemic prehensile-tailed geckoUrocotyledon inexpectataacross the Seychelles Islands: patterns of phylogeographical structure and isolation at the multilocus level

Disease progression and evolution of the HIV-1 env gene in 24 infected infants

artículo científico publicado en 2007

Effective population sizes: missing measures and missing concepts

article published in 1999

Effective population sizes: missing measures and missing concepts

Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial

artículo científico publicado en 2009

Evaluation of methods for detecting recombination from DNA sequences: computer simulations

artículo científico publicado en 2001

Evaluation of methods for detecting recombination from DNA sequences: empirical data

artículo científico publicado en 2002

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora)

artículo científico publicado en 2003

Evolutionary history ofTrachylepisskinks in the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure

GARD: a genetic algorithm for recombination detection

artículo científico publicado en 2006

GenDecoder: genetic code prediction for metazoan mitochondria

artículo científico publicado en 2006

Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity

artículo científico publicado en 2011

Genetic Identification of the Northeastern Atlantic Spiny Spider Crab as Maja Brachydactyla Balss, 1922

scientific article published in 2008

Genetic code prediction for metazoan mitochondria with GenDecoder

artículo científico publicado en 2009

Genetic variation at MHC, mitochondrial and microsatellite loci in isolated populations of Brown trout (Salmo trutta)

Genetic variation of the spiny spider crab Maja brachydactyla in the northeastern Atlantic

article published in 2008

Genome-wide heterogeneity of nucleotide substitution model fit.

artículo científico

GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes

article

Grid selection of models of nucleotide substitution.

artículo científico publicado en 2010

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

artículo científico publicado en 2014

HIV-1 infected monozygotic twins: a tale of two outcomes

artículo científico publicado en 2011

HPC selection of models of DNA substitution

article

High-performance computing selection of models of DNA substitution for multicore clusters

How does recombination affect phylogeny estimation?

artículo científico publicado en 2000

Identification and characterization of microsatellite loci in the spiny spider crab Maja brachydactyla

Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba

artículo científico publicado en 2007

Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba

artículo científico publicado en 2005

Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates

artículo científico publicado en 2010

Infinitely Long Branches and an Informal Test of Common Ancestry

Infinitely long branches and an informal test of common ancestry

artículo científico publicado en 2016

Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada

artículo científico publicado en 2012

Intraspecific gene genealogies: trees grafting into networks

artículo científico publicado en 2001

Introgression and genetic structure in northern Spanish Atlantic salmon (Salmo salar L.) populations according to mtDNA data

article

Inverted replication of vertebrate mitochondria.

artículo científico publicado en 2008

Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients

artículo científico publicado en 2007

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters

artículo científico publicado en 2022

Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial

artículo científico publicado en 2006

Low-mitochondrial diversity and lack of structure in the velvet swimming crab Necora puber along the Galician coast

artículo científico publicado en 2009

MODELTEST: testing the model of DNA substitution

artículo científico publicado en 1998

Mitochondrial DNA phylogeography and population history of the grey wolf canis lupus

artículo científico publicado en 1999

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

artículo científico publicado en 2004

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online

artículo científico publicado en 2006

Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae)

scholarly article by Graciela Sotelo et al published October 2009 in Molecular Phylogenetics and Evolution

Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species

article

MtArt: A New Model of Amino Acid Replacement for Arthropoda

article

Multigene phylogeny of Malagasy day geckos of the genus Phelsuma

artículo científico publicado en 2009

Multilocus inference of species trees and DNA barcoding

artículo científico publicado en 2016

Multiregional Tumor Trees Are Not Phylogenies

artículo científico publicado en 2017

Mytilus galloprovincialis Lmk. in northern Africa

article

NGSphy: phylogenomic simulation of next-generation sequencing data

artículo científico publicado en 2018

NGSphy: phylogenomic simulation of next-generation sequencing data

Nested clade analysis statistics

article

Nested clade phylogeographic analysis for conservation genetics

article

New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex

artículo científico publicado en 2003

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy

artículo científico publicado en 2006

Origin and length distribution of unidirectional prokaryotic overlapping genes

artículo científico publicado en 2014

PHYLOGEOGRAPHIC HISTORY OF THE LAND SNAIL CANDIDULA UNIFASCIATA (HELICELLINAE, STYLOMMATOPHORA): FRAGMENTATION, CORRIDOR MIGRATION, AND SECONDARY CONTACT

Parallel evolution of the genetic code in arthropod mitochondrial genomes.

artículo científico publicado en 2006

Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries?

artículo científico publicado en 2006

Pharmacogenetic study of statin therapy and cholesterol reduction

artículo científico publicado en 2004

Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand

artículo científico publicado en 2011

Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America

artículo científico publicado en 2009

Phylogenetic Approaches to Molecular Epidemiology

scholarly article published 2002

Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations

artículo científico publicado en 2006

Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail

artículo científico publicado en 2007

Phylogenetic models of molecular evolution: next-generation data, fit, and performance

artículo científico publicado en 2013

Phylogenetics of HIV

article

Phylogenomics for Systematic Biology

artículo científico publicado en 2016

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

scientific article published on 25 April 2019

Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact

artículo científico publicado en 2002

Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands

artículo científico publicado en 2013

Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigaster

artículo científico publicado en 2004

Polymorphisms in the sequences of Marteilia internal transcribed spacer region of the ribosomal RNA genes (ITS-1) in Spain: genetic types are not related with bivalve hosts

artículo científico publicado en 2005

Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groups

artículo científico publicado en 2000

ProtTest 3: fast selection of best-fit models of protein evolution

artículo científico publicado en 2011

ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution

article published in 2011

ProtTest: selection of best-fit models of protein evolution

artículo científico publicado en 2005

Protein evolution along phylogenetic histories under structurally constrained substitution models.

artículo científico publicado en 2013

Proving universal common ancestry with similar sequences

artículo científico

RDP2: recombination detection and analysis from sequence alignments

artículo científico publicado en 2004

RDP3: a flexible and fast computer program for analyzing recombination

artículo científico publicado en 2010

RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.

artículo científico publicado en 2015

Rapid evolution and biogeographic spread in a colorectal cancer

scientific article published on 13 November 2019

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography

artículo científico publicado en 2007

Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method

artículo científico publicado en 2006

Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy

artículo científico publicado en 2007

Recombination in evolutionary genomics

artículo científico publicado en 2002

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

artículo científico publicado en 2021

Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1).

artículo científico publicado en 2001

Selecting the Best-Fit Model of Nucleotide Substitution

article

Selecting the best-fit model of nucleotide substitution

artículo científico publicado en 2001

Selection of models of DNA evolution with jModelTest

artículo científico publicado en 2009

Selective Pressures on Human Cancer Genes along the Evolution of Mammals

article

Sensitivity to sequencing depth in single-cell cancer genomics.

artículo científico publicado en 2018

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

artículo científico publicado en 2015

Simple (Wrong) Models for Complex Trees: A Case from Retroviridae

scientific article published in 2001

Simulating haplotype blocks in the human genome

artículo científico publicado en 2003

Simulation of coding sequence evolution

Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories

artículo científico publicado en 2014

Spatio-temporal genetic variability in sea trout (Salmo trutta) populations from north-western Spain

article

Spatio-temporal genetic variability of sea trout populations in Northwestern Spain

article

Species Tree Estimation from Genome-Wide Data with guenomu

artículo científico publicado en 2017

Species Tree Estimation from Genome-wide Data with Guenomu

TCS: a computer program to estimate gene genealogies

artículo científico publicado en 2000

Testing for universal common ancestry

artículo científico publicado en 2014

The causes and consequences of HIV evolution

artículo científico publicado en 2004

The effect of branch length variation on the selection of models of molecular evolution

artículo científico publicado en 2001

The effect of recombination on the accuracy of phylogeny estimation

artículo científico publicado en 2002

The effect of recombination on the reconstruction of ancestral sequences

artículo científico publicado en 2010

The evolution and appearance of C3 duplications in fish originate an exclusive teleost c3 gene form with anti-inflammatory activity

artículo científico publicado en 2014

The evolution of the mitochondrial genetic code in arthropods revisited

artículo científico publicado en 2012

The evolutionary value of recombination is constrained by genome modularity

artículo científico publicado en 2005

The evolutionary value of recombination is constrained by genome modularity

scholarly article by Darren Patrick Martin published in January 2005

The inversion of the Control Region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication

artículo científico publicado en 2014

The mussel Xenostrobus securis: a well-established alien invader in the Ria de Vigo (Spain, NE Atlantic)

article

Tree scanning: a method for using haplotype trees in phenotype/genotype association studies

artículo científico publicado en 2004

TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees

artículo científico publicado en 2005

Unsorted homology within locus and species trees

artículo científico publicado en 2014

Unveiling the Molecular Clock in the Presence of Recombination

scientific article published in 2001

Using MODELTEST and PAUP* to select a model of nucleotide substitution

artículo científico publicado en 2003

Using models of nucleotide evolution to build phylogenetic trees

artículo científico publicado en 2005

Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals

artículo científico publicado en 2009

Widespread recombination in published animal mtDNA sequences.

artículo científico publicado en 2005

jModelTest 2: more models, new heuristics and parallel computing

artículo científico publicado en 2012

jModelTest: phylogenetic model averaging

artículo científico publicado en 2008

jmodeltest.org: selection of nucleotide substitution models on the cloud

artículo científico publicado en 2014

Lista de obras de David Posada

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints

A coalescent model of recombination hotspots

A comparison of phylogenetic network methods using computer simulation

A comparison of tools for the simulation of genomic next-generation sequencing data

ALTER: program-oriented conversion of DNA and protein alignments

Accurate Selection of Models of Protein Evolution

Advances in understanding the evolution of HIV.

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1

An exact nonparametric method for inferring mosaic structure in sequence triplets

Analysing recombination in nucleotide sequences

Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?

Author Correction: A comparison of tools for the simulation of genomic next-generation sequencing data

Automated phylogenetic detection of recombination using a genetic algorithm

Automatic Prediction of the Genetic Code

Base-Pairing Versatility Determines Wobble Sites in tRNA Anticodons of Vertebrate Mitogenomes ⬇️

Bioinformatics for DNA Sequence Analysis

Cancer Molecular Evolution

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

Characterization of Reticulate Networks Based on the Coalescent with Recombination

Characterization of phylogenetic networks with NetTest

Characterization of reticulate networks based on the coalescent with recombination

Coalescent simulation of intracodon recombination

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

Computational Design of Centralized HIV-1 Genes ⬇️

Correction: A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

Cryptic diversity within the endemic prehensile-tailed geckoUrocotyledon inexpectataacross the Seychelles Islands: patterns of phylogeographical structure and isolation at the multilocus level

Disease progression and evolution of the HIV-1 env gene in 24 infected infants

Effective population sizes: missing measures and missing concepts

Effective population sizes: missing measures and missing concepts

Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial

Evaluation of methods for detecting recombination from DNA sequences: computer simulations

Evaluation of methods for detecting recombination from DNA sequences: empirical data

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora)

Evolutionary history ofTrachylepisskinks in the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure

GARD: a genetic algorithm for recombination detection

GenDecoder: genetic code prediction for metazoan mitochondria

Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity

Genetic Identification of the Northeastern Atlantic Spiny Spider Crab as Maja Brachydactyla Balss, 1922

Genetic code prediction for metazoan mitochondria with GenDecoder

Genetic variation at MHC, mitochondrial and microsatellite loci in isolated populations of Brown trout (Salmo trutta)

Genetic variation of the spiny spider crab Maja brachydactyla in the northeastern Atlantic

Genome-wide heterogeneity of nucleotide substitution model fit.

GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes

Grid selection of models of nucleotide substitution.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

HIV-1 infected monozygotic twins: a tale of two outcomes

HPC selection of models of DNA substitution

High-performance computing selection of models of DNA substitution for multicore clusters

How does recombination affect phylogeny estimation?

Identification and characterization of microsatellite loci in the spiny spider crab Maja brachydactyla

Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba

Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba

Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates

Infinitely Long Branches and an Informal Test of Common Ancestry

Infinitely long branches and an informal test of common ancestry

Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada

Intraspecific gene genealogies: trees grafting into networks

Introgression and genetic structure in northern Spanish Atlantic salmon (Salmo salar L.) populations according to mtDNA data

Inverted replication of vertebrate mitochondria.

Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients

Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters

Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial

Low-mitochondrial diversity and lack of structure in the velvet swimming crab Necora puber along the Galician coast

MODELTEST: testing the model of DNA substitution

Mitochondrial DNA phylogeography and population history of the grey wolf canis lupus

Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online

Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae)

Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species

MtArt: A New Model of Amino Acid Replacement for Arthropoda

Multigene phylogeny of Malagasy day geckos of the genus Phelsuma

Multilocus inference of species trees and DNA barcoding

Multiregional Tumor Trees Are Not Phylogenies

Mytilus galloprovincialis Lmk. in northern Africa

NGSphy: phylogenomic simulation of next-generation sequencing data

NGSphy: phylogenomic simulation of next-generation sequencing data