Current research and past production

The Phyloinformatics Lab’s research program consists of two interrelated components:

Conceptual aspects of molecular phylogenetics and its computational and epidemiological applications, and
Comparative genomics of animals with a focus on host-pathogen systems.

Our general aims are four:

Facilitate resource-efficient molecular analyses and make data from museum biorepositories more readily available to biomedical research.
Improve genomic resources of non-model organisms with a focus on animals of particular medical or environmental interest.
Develop phylogenetics solutions, especially if they can help improve our understanding of zoonosis.
Integrate “omics” technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) to study complex host-pathogen systems in the context of One Health.

Publications

2024

Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 and JN.1 with In Silico Protein Modeling and Docking

Shirish Yasa, Sayal Guirales-Medrano, Denis Jacob Machado, Colby T. Ford, Daniel A. Janies

Frontiers in Virology · 18 Jul 2024

Changes in HERVs Expression and Interleukins mRNAs Levels in Trophoblastic Cells Infected by ZIKV

Anderson Luís da Costa, Paula Prieto-Oliveira, Márcia Duarte-Barbosa, Robert Andreata-Santos, Cristina M. Peter, Thamires Prolo, Fernando Antoneli, Maria Isabel V. G. de Carvalho, Ricardo Durães-Carvalho, Marcelo Ribeiro da Silva Briones, Juliana T. Maricato, Paolo M. A. Zanotto, Denis Jacob Machado, Luiz Mario Ramos Janini

Preprints · 02 Apr 2024

flaviviruses viruses transcriptomics infection

2023

Replicating Ford et al.’s investigation on the immune consequences and SARS-CoV-2 antibody’s binding affinity using an in silico approach

Cameron Jones, Hannah Zeru, Denis Jacob Machado

ICICPE 2023 · 29 Dec 2023

artificial intelligence genomic epidemiology molecular docking viruses

Echinoderm radial glia in adult cell renewal, indeterminate growth, and regeneration

Vladimir Mashanov, Soji Ademiluyi, Denis Jacob Machado, Robert Reid, Daniel Janies

Frontiers in Neural Circuits · 29 Sep 2023

echinoderms non-model organism invertebrates zoology

Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling

Colby T. Ford, Shirish Yasa, Denis Jacob Machado, Richard Allen White, Daniel A. Janies

Frontiers in Virology · 01 Jan 2023

artificial intelligence genomic epidemiology molecular docking phylogenetics sensitivity analyses viruses zoonoses

2022

EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

Varnika Mittal, Robert W. Reid, Denis Jacob Machado, Vladimir Mashanov, Daniel A. Janies

BMC Genomic Data · 23 Oct 2022

echinoderms non-model organism genomics invertebates zoology database softare

Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research

Vladimir Mashanov, Denis Jacob Machado, Robert Reid, Cory Brouwer, Janice Kofsky, Daniel A. Janies

BMC Genomics · 11 Aug 2022

echinoderms non-model organism genomics invertebates zoology gene annotation gene prediction mitogenome nuclear genome

A subterminal growth zone at arm tip likely underlies life-long indeterminate growth in brittle stars

Vladimir Mashanov, Lauren Whaley, Kenneth Davis, Thomas Heinzeller, Denis Jacob Machado, Robert W. Reid, Janice Kofsky, Daniel Janies

Frontiers in Zoology · 12 Apr 2022

echinoderms gene expression invertebrates non-model organism regeneration zoology

Predictions of the SARS-CoV-2 Omicron Variant (B.1.1.529) Spike Protein Receptor-Binding Domain Structure and Neutralizing Antibody Interactions

Colby T. Ford, Denis Jacob Machado, Daniel A. Janies

Frontiers in Virology · 07 Feb 2022

artificial intelligence genomic epidemiology molecular docking phylogenetics sensitivity analyses viruses zoonoses

2021

Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)

Bruna Trevisan, Denis Jacob Machado, Daniel J. G. Lahr, Fernando P. L. Marques

Frontiers in Genetics · 22 Dec 2021

comparative genomics gene annotation gene prediction genome skimming invertebates mitogenome parasitology zoology

An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis

Denis Jacob Machado, Fernando Portella de Luna Marques, Larry Jiménez-Ferbans, Taran Grant

Cladistics · 21 Dec 2021

phylogenetics clade support clade frequencies sensitivity analyses maximum likelihood software

Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses - SARS-CoV, MERS-CoV and SARS-CoV-2

Denis Jacob Machado, Rachel Scott, Sayal Guirales, Daniel A. Janies

Cladistics · 26 Apr 2021

character categorization coronaviruses gene annotation gene prediction genomic epidemiology outgroup selection phylogenetics sequence alignment sensitivity analyses viruses zoonoses

Evidence of absence treated as absence of evidence: The effects of variation in the number and distribution of gaps treated as missing data on the results of standard maximum likelihood analysis

Denis Jacob Machado, Santiago Castroviejo-Fisher, Taran Grant

Molecular Phylogenetics and Evolution · 01 Jan 2021

phylogenetics clade support clade frequencies sequence alignment sensitivity analyses maximum likelihood

Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions

Denis Jacob Machado, Richard Allen White, Janice Kofsky, Daniel A. Janies

Antimicrobial Stewardship & Healthcare Epidemiology · 01 Jan 2021

coronavirus genomic epidemiology high-throughput sequencing One Health viruses zoonoses

2020

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae)

Victor G.D. Orrico, Taran Grant, Julian Faivovich, Mauricio Rivera‐Correa, Marco A. Rada, Mariana L. Lyra, Carla S. Cassini, Paula H. Valdujo, Walter E. Schargel, Denis J. Machado, Ward C. Wheeler, Cesar Barrio‐Amorós, Daniel Loebmann, Jiří Moravec, Juliana Zina, Mirco Solé, Marcelo J. Sturaro, Pedro L.V. Peloso, Pablo Suarez, Célio F.B. Haddad

Cladistics · 13 Sep 2020

amphibians character categorization outgroup selection phylogenetics vertebrates wildcard taxa zoological taxonomy zoology

FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae

Adriano de Bernadi Schneider, Denis Jacob Machado, Sayal Guirales, Daniel A. Janies

Viruses · 14 Aug 2020

character categorization flaviviruses gene annotation gene prediction genomic epidemiology outgroup selection phylogenetics sequence alignment sensitivity analyses viruses zoonoses software

Active Notch signaling is required for arm regeneration in a brittle star

Vladimir Mashanov, Jennifer Akiona, Maleana Khoury, Jacob Ferrier, Robert Reid, Denis Jacob Machado, Olga Zueva, Daniel Janies

PLOS ONE · 12 May 2020

echinoderms gene expression invertebrates non-model organism regeneration zoology

The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida)

Jih-Pai Lin, Mong-Hsun Tsai, Andreas Kroh, Aaron Trautman, Denis Jacob Machado, Lo-Yu Chang, Robert Reid, Kuan-Ting Lin, Omri Bronstein, Shyh-Jye Lee, Daniel Janies

Genomics · 01 Mar 2020

echinoderms genome skimming invertebrates mitogenome non-model organism zoology

2019

Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies

Bruna Trevisan, Daniel M.C. Alcantara, Denis Jacob Machado, Fernando P.L. Marques, Daniel J.G. Lahr

PeerJ · 13 Sep 2019

genome skimming invertebrates mitogenome non-model organism zoology

2018

A new strategy to infer circularity applied to four new complete frog mitogenomes

Denis Jacob Machado, Daniel Janies, Cory Brouwer, Taran Grant

Ecology and Evolution · 25 Mar 2018

amphibian genome skimming vertebrates mitogenome non-model organism sensitivity analyses zoology software

2017

Phylogenetic Systematics of Dart-Poison Frogs and Their Relatives Revisited (Anura: Dendrobatoidea)

Taran Grant, Marco Rada, Marvin Anganoy-Criollo, Abel Batista, Pedro Henrique Dias, Adriana Moriguchi Jeckel, Denis Jacob Machado, José Vicente Rueda-Almonacid

South American Journal of Herpetology · 01 Sep 2017

amphibians character categorization outgroup selection phylogenetics vertebrates zoological taxonomy zoology