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Genomics, Proteomics & Bioinformatics|February 26, 2026
Unraveling the Phylogenetic Signal of Gene Expression from Single-cell RNA-seq DataJoao M Alves, Laura Tomás, David PosadaGenome Biology|January 27, 2022
CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq dataAlexey Kozlov, Joao M Alves, Alexandros Stamatakis, et al.Genome Biology and Evolution|April 1, 2014
The 8p23 inversion polymorphism determines local recombination heterogeneity across human populationsJoao M Alves, Lounès Chikhi, António Amorim, et al.Current Genomics|June 5, 2013
On the structural plasticity of the human genome: chromosomal inversions revisitedJoao M Alves, Alexandra M Lopes, Lounès Chikhi, et al.Nature Communications|November 15, 2019
Rapid evolution and biogeographic spread in a colorectal cancerJoao M Alves, Sonia Prado-López, José Manuel Cameselle-Teijeiro, et al.Genome Biology|December 1, 2022
SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing dataSenbai Kang, Nico Borgsmüller, Monica Valecha, et al.BMC Genomics|June 15, 2010
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studiesMichael D Harwich, Joao M Alves, Gregory A Buck, et al.Computational and Structural Biotechnology Journal|July 21, 2025
Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell lineNair Varela-Rouco, Nuria Estévez-Gómez, Cristóbal Fernández-Santiago, et al.Genome Biology and Evolution|November 13, 2015
Reassessing the Evolutionary History of the 17q21 Inversion PolymorphismJoao M Alves, Ana C Lima, Isa A Pais, et al.Cellular Oncology (Dordrecht, Netherlands)|October 6, 2025
Genomic diversity and BCL9L mutational status in circulating tumor cells predict overall survival in metastatic colorectal cancerJoao M Alves, Nuria Estévez-Gómez, Roberto Piñeiro, et al.Pageof 2