Publications (71) JOAO MIGUEL FERNANDES ALVES publications

2023

  1. Complete genome sequence of the archetype bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI12708, isolated from human feces, circa 1980

    Microbiology Resource Announcements, Vol. 12, Núm. 9

  2. Genomes of Endotrypanum monterogeii from Panama and Zelonia costaricensis from Brazil: Expansion of Multigene Families in Leishmaniinae Parasites That Are Close Relatives of Leishmania spp.

    Pathogens, Vol. 12, Núm. 12

2022

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

    Genome Biology, Vol. 23, Núm. 1

  2. Clonality and timing of relapsing colorectal cancer metastasis revealed through whole-genome single-cell sequencing

    Cancer Letters, Vol. 543

  3. Comparative analysis of capture methods for genomic profiling of circulating tumor cells in colorectal cancer

    Genomics, Vol. 114, Núm. 6

  4. Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes

    Gut Microbes, Vol. 14, Núm. 1

  5. Genetic and morphological polymorphisms of Aedes scapularis (Diptera: Culicidae), vector of filariae and arboviruses

    Infection, Genetics and Evolution, Vol. 97

  6. SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data

    Genome Biology, Vol. 23, Núm. 1

  7. Single-cell mtDNA heteroplasmy in colorectal cancer

    Genomics, Vol. 114, Núm. 2

  8. The Importance of Glycerophospholipid Production to the Mutualist Symbiosis of Trypanosomatids

    Pathogens, Vol. 11, Núm. 1

2021

  1. Completion of the gut microbial epi-bile acid pathway

    Gut Microbes, Vol. 13, Núm. 1, pp. 1-20

  2. Editorial: Symbioses Between Protists and Bacteria/Archaea

    Frontiers in Microbiology

  3. Endosymbiont capture, a repeated process of endosymbiont transfer with replacement in Trypanosomatids angomonas Spp.

    Pathogens, Vol. 10, Núm. 6

  4. Phylogeny and temporal diversification of mosquitoes (Diptera: Culicidae) with an emphasis on the Neotropical fauna

    Systematic Entomology, Vol. 46, Núm. 4, pp. 798-811

2020

  1. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

    Nature Communications, Vol. 11, Núm. 1

  2. Bacterial steroid-17,20-desmolase is a taxonomically rare enzymatic pathway that converts prednisone to 1,4-androstanediene-3,11,17-trione, a metabolite that causes proliferation of prostate cancer cells

    Journal of Steroid Biochemistry and Molecular Biology, Vol. 199

  3. Population genomics reveals the expansion of highly inbred plasmodium vivax lineages in the main malaria hotspot of Brazil

    PLoS Neglected Tropical Diseases, Vol. 14, Núm. 10, pp. 1-16

  4. The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice

    Gut Microbes, Vol. 11, Núm. 3, pp. 381-404

2019

  1. Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids

    Applied and Environmental Microbiology, Vol. 85, Núm. 7

  2. First record of translocation in Culicidae (Diptera) mitogenomes: Evidence from the tribe Sabethini

    BMC Genomics, Vol. 20, Núm. 1