Articles


A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction
Leonardo de Oliveira Martins, Diego Mallo, David Posada. Systematic Biology 65 (3): 397-416, 2016
doi: 10.1093/sysbio/syu082

SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees
        Diego Mallo, Leonardo de Oliveira Martins, David Posada. Systematic Biology 65 (2): 334-344, 2016
       
doi: 10.1093/sysbio/syv082

Species Tree Estimation from Genome-wide Data with Guenomu
        Leonardo de Oliveira Martins, David Posada. biorxiv, 023861, 2015
        doi: 10.1101/023861

Infinitely Long Branches and an Informal Test of Common Ancestry
        Leonardo de Oliveira Martins, David Posada. biorxiv, 023903, 2015
       doi: 10.1101/023903 (accepted in Biology Direct, DOI: 10.1186/s13062-016-0120-y)

Estimation of Species Trees
Diego Mallo, Leonardo de Oliveira Martins, David Posada. eLS. a0025781, 2014

Unsorted Homology within Locus and Species Trees
Diego Mallo, Leonardo de Oliveira Martins, David Posada. Systematic Biology 63(6), 988-992, 2014
doi: 10.1093/sysbio/syu050

Testing for Universal Common Ancestry
Leonardo de Oliveira Martins, David Posada. Systematic Biology 63 (5), 838-842, 2014
doi: 10.1093/sysbio/syu041

Phylogenetic Likelihood
Leonardo de Oliveira Martins, Diego Mallo, David Posada. eLS. a0005141, 2013
doi:10.1002/9780470015902.a0005141

Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count
Maria Clara Bizinoto, Shiori Yabe, Élcio Leal, Hirohisa Kishino, Leonardo de Oliveira Martins, Mariana Leão de Lima, Edsel Renata Morais, Ricardo Sobhie Diaz and Luiz Mário Janini. BMC Infectious Diseases 13, 173, 2013
doi:10.1186/1471-2334-13-173

Proving universal common ancestry with similar sequences
Leonardo de Oliveira Martins and David Posada. Trends in Evolutionary Biology 4(1), e5, 2012
doi:10.4081/eb.2012.e5

Evolutionary Process of Deep-Sea Bathymodiolus Mussels
Jun-Ichi Miyazaki, Leonardo de Oliveira Martins, Yuko Fujita, Hiroto Matsumoto and Yoshihiro Fujiwara. PLoS ONE 5(4), e10363, 2010
doi:10.1371/journal.pone.0010363


Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites
Hiromi Sawai, Hiroto Otani, Nobuko Arisue, Nirianne Palacpac, Leonardo de Oliveira Martins, Sisira Pathirana, Shiroma Handunnetti, Satoru Kawai, Hirohisa Kishino, Toshihiro Horiiand Kazuyuki Tanabe. BMC Evolutionary Biology 10, 52, 2010
doi:10.1186/1471-2148-10-52


Distribution of distances between topologies and its effect on detection of phylogenetic recombination
Leonardo de Oliveira Martins and Hirohisa Kishino. Annals of the Institute of Statistical Mathematics 62 (1), 145-159, 2010
doi:10.1007/s10463-009-0259-8


Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America
Élcio Leal, Leonardo O. Martins, L. Mario Janini and Ricardo S. Diaz. Retrovirology: Research and Treatment 1, 1-14, 2008
[online access]

Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees
Leonardo de Oliveira Martins, Elcio Leal and Hirohisa Kishino. PLoS ONE 3(7): e2651, 2008
doi:10.1371/journal.pone.0002651


A likelihood-based index of protein-protein binding affinities with application to influenza HA escape from antibodies
Teruaki Watabe, Hirohisa Kishino, Leonardo de Oliveira Martins, and Yasuhiro Kitazoe. Molecular Biology and Evolution 24(8), 1627-1638, 2007
doi:10.1093/molbev/msm079


Evolutionary relationships of deep-sea mussels inferred by mitochondrial DNA sequences
H Iwasaki, A Kyuno, M Shintaku, Y Fujita, Y Fujiwara, K Fujikura, J Hashimoto, L de O Martins, A Gebruk, and J-I Miyazaki. Marine Biology 149(5), Springer, 1111-1122, 2006
doi:10.1007/s00227-006-0268-6


Phylogeography of loaches of the genus lefua (balitoridae, cypriniformes) inferred from mitochondrial DNA sequences
Motohiro Mihara, Takehiko Sakai, Koushin Nakao, Leonardo de Oliveira Martins, Kazumi Hosoya, and Jun-Ichi Miyazaki. Zoological Science 22(2), 157-68, 2005
doi:10.2108/zsj.22.157


Book chapters

How is it possible not to accept Evolution? (in portuguese, "Como é possível não aceitar a evolução?")
Mariana Costa and Leonardo de Oliveira Martins. In A book about Evolution, Rita Campos et al. (eds.), 22-26, 2014 [download PDF]

Viral genomic recombination: HIV subtyping and detecting new variants (in japanese, "ウイルスゲノムの組換えーHIVのサブタイピング新種の検出")
Leonardo de Oliveira Martins. In Biostatistics in practice: from molecule to ecology, Biometrics Laboratory at the University of Tokyo (eds.), 148-164, 2003 [find at amazon.co.jp]

Others

Amino acid substitution matrices estimated by maximum likelihood
Leonardo de Oliveira Martins, and PMA Zanotto. Genome Informatics Series, Universal Academy Press Inc., 380-381, 2001
fprotml: Protein analysis using maximum likelihood
Leonardo de Oliveira Martins. Currents in Computational Molecular Biology 2001, ACM Press, 197-198, 2001

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