Lista de obras -

A hapless mathematical contribution to biology

artículo científico publicado en 2022

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes

artículo científico publicado en 2008

ANGES: reconstructing ANcestral GEnomeS maps

artículo científico publicado en 2012

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

artículo científico publicado en 2017

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

artículo científico publicado en 2009

Ancestral gene synteny reconstruction improves extant species scaffolding

artículo científico publicado en 2015

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.

artículo científico publicado en 2010

Bayesian sampling of genomic rearrangement scenarios via double cut and join ⬇️

artículo científico publicado el 29 de octubre de 2010

Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

artículo científico publicado en 2016

Cassis: detection of genomic rearrangement breakpoints

artículo científico publicado en 2010

Combinatorics of Genome Rearrangements

Comparative Methods for Reconstructing Ancient Genome Organization.

artículo científico publicado en 2018

Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes

artículo científico publicado en 2009

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

artículo científico publicado en 2017

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

artículo científico publicado en 2010

Efficient Gene Tree Correction Guided by Genome Evolution

artículo científico publicado en 2016

Efficient exploration of the space of reconciled gene trees

artículo científico publicado en 2013

Evolution of gene neighborhoods within reconciled phylogenies

artículo científico publicado en 2012

Evolution under reversals: parsimony and conservation of common intervals

artículo científico publicado en 2007

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

artículo científico publicado en 2020

Exploring the solution space of sorting by reversals, with experiments and an application to evolution

artículo científico publicado en 2008

FPSAC: fast phylogenetic scaffolding of ancient contigs.

artículo científico publicado en 2013

Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes

artículo científico publicado en 2009

Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?

artículo científico publicado en 2016

Gene transfers can date the tree of life

article

Gene transfers, like fossils, can date the Tree of Life

article

Gene tree correction guided by orthology

artículo científico publicado en 2013

Gene tree species tree reconciliation with gene conversion

artículo científico publicado en 2019

Genome rearrangements with indels in intergenes restrict the scenario space

artículo científico publicado en 2016

Genome-scale coestimation of species and gene trees.

artículo científico publicado en 2012

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

artículo científico publicado en 2015

Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae.

artículo científico publicado en 2010

Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops

artículo científico publicado en 2015

Lateral gene transfer as a support for the tree of life

artículo científico publicado en 2012

Lateral gene transfer from the dead

artículo científico publicado en 2013

Lateral gene transfer, rearrangement, reconciliation

artículo científico publicado en 2013

Leveraging evolutionary relationships to improve Anopheles genome assemblies

Linearization of ancestral multichromosomal genomes

artículo científico publicado en 2012

Mapping ancestral genomes with massive gene loss: a matrix sandwich problem ⬇️

artículo científico publicado en 2011

Moments of genome evolution by Double Cut-and-Join

artículo científico publicado en 2015

Multichromosomal median and halving problems under different genomic distances

artículo científico publicado en 2009

Palaeogenomics of plants: synteny-based modelling of extinct ancestors

artículo científico publicado en 2010

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

artículo científico publicado en 2012

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

artículo científico publicado en 2018

Precise detection of rearrangement breakpoints in mammalian chromosomes

artículo científico publicado en 2008

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

artículo científico publicado en 2015

Reconstructing the architecture of the ancestral amniote genome

artículo científico publicado en 2011

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

artículo científico publicado en 2015

Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses

artículo científico publicado en 2017

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

artículo científico publicado en 2021

The inference of gene trees with species trees

artículo científico publicado en 2014

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

scientific article published on 16 July 2020

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

artículo científico publicado en 2010

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

scientific article published on 01 February 2020

Lista de obras de

A hapless mathematical contribution to biology

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes

ANGES: reconstructing ANcestral GEnomeS maps

Algorithms for computing the double cut and join distance on both gene order and intergenic sizes

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Ancestral gene synteny reconstruction improves extant species scaffolding

Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.

Bayesian sampling of genomic rearrangement scenarios via double cut and join ⬇️

Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

Cassis: detection of genomic rearrangement breakpoints

Combinatorics of Genome Rearrangements

Comparative Methods for Reconstructing Ancient Genome Organization.

Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

Efficient Gene Tree Correction Guided by Genome Evolution

Efficient exploration of the space of reconciled gene trees

Evolution of gene neighborhoods within reconciled phylogenies

Evolution under reversals: parsimony and conservation of common intervals

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Exploring the solution space of sorting by reversals, with experiments and an application to evolution

FPSAC: fast phylogenetic scaffolding of ancient contigs.

Footprints of inversions at present and past pseudoautosomal boundaries in human sex chromosomes

Francisella IglG protein and the DUF4280 proteins: PAAR-like proteins in non-canonical Type VI secretion systems?

Gene transfers can date the tree of life

Gene transfers, like fossils, can date the Tree of Life

Gene tree correction guided by orthology

Gene tree species tree reconciliation with gene conversion

Genome rearrangements with indels in intergenes restrict the scenario space

Genome-scale coestimation of species and gene trees.

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Guided genome halving: provably optimal solutions provide good insights into the preduplication ancestral genome of Saccharomyces cerevisiae.

Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops

Lateral gene transfer as a support for the tree of life

Lateral gene transfer from the dead

Lateral gene transfer, rearrangement, reconciliation

Leveraging evolutionary relationships to improve Anopheles genome assemblies

Linearization of ancestral multichromosomal genomes

Mapping ancestral genomes with massive gene loss: a matrix sandwich problem ⬇️

Moments of genome evolution by Double Cut-and-Join

Multichromosomal median and halving problems under different genomic distances

Palaeogenomics of plants: synteny-based modelling of extinct ancestors

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Precise detection of rearrangement breakpoints in mammalian chromosomes

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Reconstructing the architecture of the ancestral amniote genome

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses

Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation

The inference of gene trees with species trees

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages