List of works by Francisco Prosdocimi

A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni

scientific article

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei ⬇️

scientific article published on 15 December 2017

A neutral evolution test derived from a theoretical amino acid substitution model

scientific article published on 31 January 2019

A procedure to recruit members to enlarge protein family databases--the building of UECOG (UniRef-Enriched COG Database) as a model

article

A set of amino acids found to occur more frequently in human and fly than in plant and yeast proteomes consists of non-essential amino acids.

scientific article published on 2 May 2006

Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

scientific article published in 2019

Accessing optimal primer distance from insert.

scientific article

Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

scientific article

Angiogenesis and evading immune destruction are the main related transcriptomic characteristics to the invasive process of oral tongue cancer

scientific article published on 31 January 2018

Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails

scientific article published on 07 February 2019

Be Introduced to the First Universal Common Ancestor (FUCA): The Great-Grandmother of LUCA (Last Universal Common Ancestor)

Brazilian Bothrops diporus, in fact a lineage of Bothrops pubescens: Mitogenomic, venomic and ontogenetic studies

scientific article published on 01 April 2020

Buds of the tree: the highway to the last universal common ancestor

Clustering of Schistosoma mansoni mRNA sequences and analysis of the most transcribed genes: implications in metabolism and biology of different developmental stages

scientific article

Clustering of Schistosoma mansoni mRNA sequences and analysis of the most transcribed genes: implications in metabolism and biology of different developmental stages

article

Comparative genomics and phylogenomics of Trichostrongyloidea mitochondria reveal insights for molecular diagnosis and evolutionary biology of nematode worms

scholarly article by Livia Loiola dos Santos et al published December 2017 in Gene reports

Comparative mitogenomic analyses of Amazona parrots and Psittaciformes

scientific article published on 01 July 2018

Complete chloroplast genome of the orchid Cattleya crispata (Orchidaceae:Laeliinae), a Neotropical rupiculous species

scientific article published on 20 January 2015

Complete mitochondrial genome of the brown mussel Perna perna (Bivalve, Mytilidae).

scientific article published on 28 January 2015

Complete mitochondrial genome of the versicoloured emerald hummingbird Amazilia versicolor, a polymorphic species

scientific article published on 11 March 2015

Conceptual challenges for the emergence of the biological system: Cell theory and self-replication

scientific article published on 30 July 2018

Controversies in modern evolutionary biology: the imperative for error detection and quality control

scientific article

Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes

Copaifera langsdorffii Novel Putative lncRNA: Interspecies Conservation Analysis in Adaptive Response to Different Biomes

Correction for Mesquita et al., Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

article published in the Proceedings of the National Academy of Sciences of the United States of America

DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)

scientific article published on 17 June 2019

Deep Ancestry of Orthologs and a Theoretical, Gradualist Perspective for the Formation of the LUCA’s (Last Universal Common Ancestor) Genome

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Diet as a Pressure on the Amino Acid Content of Proteomes

Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences.

scientific article published on 5 October 2007

Efficient secondary database driven annotation using model organism sequences.

scientific article published in January 2006

Entering the labyrinth: A hypothesis about the emergence of metabolism from protobiotic routes

scientific article published in 2022

Essential amino acid usage and evolutionary nutrigenomics of eukaryotes--insights into the differential usage of amino acids in protein domains and extra-domains

scientific article published on 16 September 2008

Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values.

scientific article

Evidences for Viral Strain Selection in Late Stages of HIV Infection: An Analysis of Vpu Alleles

article

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data

scientific article

Gene discovery through transcriptome sequencing for the invasive mussel Limnoperna fortunei ⬇️

scientific article

Genetic algorithm for analysis of mutations in Parkinson's disease

scientific article

Genetic diversity and aquaculture conservation for a threatened Neotropical catfish

scientific article published in 2020

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

scientific article

In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

scientific article published on 19 July 2016

Initial implementation of a comparative data analysis ontology

scientific article (publication date: 3 July 2009)

Is it possible that cells have had more than one origin?

article published in 2021

Knowledge Standardization in Evolutionary Biology: The Comparative Data Analysis Ontology

scholarly article published 2009

LEARNING COMPREHENSIBLE CLASSIFICATION RULES FROM GENE EXPRESSION DATA USING GENETIC PROGRAMMING AND BIOLOGICAL ONTOLOGIES

article

Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses

scientific article published on 24 December 2014

MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

scientific article published on 03 April 2020

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

scientific article

No budget mitogenomics: Assembling 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

No budget mitogenomics: Assembling 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data

Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes

article published in 2018

Nucleic acid binding properties of SmZF1, a zinc finger protein of Schistosoma mansoni.

scientific article

Organic Codes: A Unifying Concept for Life

Oxidation of monoterpenes in Protium heptaphyllum oleoresins

scientific article

Parrot Genomes and the Evolution of Heightened Longevity and Cognition

scientific article published on 06 December 2018

Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii

scientific article published in 2022

Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth

scientific article published in 2022

Proceedings of the 4th World Conference on Research Integrity

Protein families, natural history and biotechnological aspects of spider silk

scientific article

Sequence variations of Env signal peptide alleles in different clinical stages of HIV infection.

scientific article published on 26 July 2011

Sex-biased gene flow in African Americans but not in American Caucasians

scientific article

Spinning gland transcriptomics from two main clades of spiders (order: Araneae)--insights on their molecular, anatomical and behavioral evolution

scientific article

Survey of genome organization and gene content of Corynebacterium pseudotuberculosis

scientific article

Symbiont modulates expression of specific gene categories in Angomonas deanei

scientific article (publication date: November 2016)

The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses

scientific article published on 05 August 2020

The Genetics of the Golden Mussel (Limnoperna fortunei): Are Genes Related to Invasiveness?

article

The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems (Origin of Life)

scientific article published on 11 August 2020

The assembly and annotation of the complete Rufous-bellied thrush mitochondrial genome

scientific article published on 18 December 2015

The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae

scientific article published on 27 November 2015

The complete mitochondrial genome of the ruby-topaz hummingbird Chrysolampis mosquitus through Illumina sequencing

scientific article

The complete mitochondrial genome of the southern purple-spotted gudgeon Mogurnda adspersa (Perciformes: Eleotridae) through pyrosequencing

scientific article published on 24 March 2014

The complete mitochondrial genome of the subsocial cockroach <i>Nauphoeta cinerea</i> and phylogenomic analyses of Blattodea mitogenomes suggest reclassification of superfamilies

scientific article published on 06 February 2017

The complete mitochondrial genome of the threatened Neotropical catfish Lophiosilurus alexandri (Silurifomes: Pseudopimelodidae) and phylogenomic analysis indicate monophyly of Pimelodoidea

scientific article published on 19 September 2016

The complete mitochondrial genome of two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae).

scientific article

The genome of Anopheles darlingi, the main neotropical malaria vector

scientific article published on 12 June 2013

The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?

scientific article published on 27 January 2017

Transcriptomic and proteomic analysis from black widow spider venom (Latrodectus curacaviensis)

scientific article published on 01 April 2020

Two Dogmas for the Emergence of Biological Systems: Cell Theory and Self-Replication

Viruses as a survival strategy in the armory of life

scientific article published on 14 October 2019

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

mitoMaker: A Pipeline for Automatic Assembly and Annotation of Animal Mitochondria Using Raw NGS Data

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