Research

There is an abundance of publicly available data about various biological systems, but it can be difficult to draw insight from individual datasets. Our lab develops algorithms that integrate these data to help model and understand complex biological systems. Doing this allows us to investigate many different biological conditions, including those with limited data, such as rare diseases. We recognize that our lab won’t have all the answers, or even all of the questions, so we aim to develop tools and processes that any biologist can reuse. Our approach to research prioritizes transparency, rigor, and reproducibility.

2022

Adding an essential oil blend to the diet of juvenile Nile tilapia improves growth and alters the gut microbiota

Micheli Zaminhan-Hassemer, Gustavo Botton Zagolin, Caio Augusto Perazza, David Aciole Barbosa, Fabiano B. Menegidio, Luiz Lehmann Coutinho, Polyana Tizioto, Alexandre Wagner Silva Hilsdorf

Aquaculture  ·  01 Nov 2022

Colorimetric Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) in rapid detection of SARS-CoV-2

Samyra Sthéfane Neves Pereira, Rubens Pasa, Fabiano Bezerra Menegídio, Luanda Medeiros-Santana, Liliane Evangelista Visôtto, Everaldo Antonio Lopes, Karine Frehner Kavalco

Magna Scientia Advanced Research and Reviews  ·  30 Mar 2022

Molecular diagnosis of SARS-CoV-2: A validation of saliva samples

Natalia Verissimo Rodrigues da Silva, Samyra Stéphane Neves Pereira, Karine Frehner Kavalco, Fabiano Bezerra Menegídio, Luanda Medeiros-Santana, Liliane Evangelista Visôtto, Rubens Pasa

GSC Advanced Research and Reviews  ·  28 Feb 2022

2021

Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing

David Aciole Barbosa, Bruno C. Araújo, Giovana Souza Branco, Alexandre S. Simeone, Alexandre W. S. Hilsdorf, Daniela L. Jabes, Luiz R. Nunes, Renata G. Moreira, Fabiano B. Menegidio

Marine Biotechnology  ·  02 Dec 2021

Analysis of mouse faecal dysbiosis, during the development of cachexia, induced by transplantation with Lewis lung carcinoma cells

Yara N. L. F. de Maria, David Aciole Barbosa, Fabiano B. Menegidio, Kaltinaitis B. N. H. Santos, Ana Carolina Humberto, Valquíria C. Alencar, Juliana F. S. Silva, Regina Costa de Oliveira, Miguel L. Batista Jr, Luiz R. Nunes, Daniela L. Jabes

Microbiology  ·  01 Oct 2021

Ten Complete Mitochondrial Genomes of Gymnocharacini (Stethaprioninae, Characiformes). Insights Into Evolutionary Relationships and a Repetitive Element in the Control Region (D-loop)

Rubens Pasa, Fabiano Bezerra Menegídio, Igor Henrique Rodrigues-Oliveira, Iuri Batista da Silva, Matheus Lewi Cruz Bonaccorsi de Campos, Dinaíza Abadia Rocha-Reis, John Seymour Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco

Frontiers in Ecology and Evolution  ·  22 Jul 2021

The Quorum Sensing Auto-Inducer 2 (AI-2) Stimulates Nitrogen Fixation and Favors Ethanol Production over Biomass Accumulation in Zymomonas mobilis

Valquíria Campos Alencar, Juliana de Fátima dos Santos Silva, Renata Ozelami Vilas Boas, Vinícius Manganaro Farnézio, Yara N. L. F. de Maria, David Aciole Barbosa, Alex Tramontin Almeida, Emanuel Maltempi de Souza, Marcelo Müller-Santos, Daniela L. Jabes, Fabiano B. Menegidio, Regina Costa de Oliveira, Tiago Rodrigues, Ivarne Luis dos Santos Tersariol, Adrian R. Walmsley, Luiz R. Nunes

International Journal of Molecular Sciences  ·  26 May 2021

2020

Fungal Dysbiosis Correlates with the Development of Tumor-Induced Cachexia in Mice

Daniela L. Jabes, Yara N. L. F. de Maria, David Aciole Barbosa, Kaltinaitis B. N. H. Santos, Lucas M. Carvalho, Ana Carolina Humberto, Valquíria C. Alencar, Regina Costa de Oliveira, Miguel L. Batista, Fabiano B. Menegidio, Luiz R. Nunes

Journal of Fungi  ·  13 Dec 2020

The Complete Mitochondrial Genome of Two Armored Catfish Populations of the Genus Hypostomus (Siluriformes, Loricariidae, Hypostominae)

Dinaíza Abadia Rocha-Reis, Rubens Pasa, Fabiano Bezerra Menegidio, John Seymour Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco

Frontiers in Ecology and Evolution  ·  04 Dec 2020

Complete mitochondrial genome of the endangered species Brycon nattereri (Characiformes, Characidae)

Snaydia Viegas Resende, Rubens Pasa, Fabiano Bezerra Menegídio, John Seymour (Pat) Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco

F1000Research  ·  18 Nov 2020

Transcriptomic profiling identifies novel transcripts, isomorphs, and noncoding RNAs in Paracoccidioides brasiliensis

Fabiano B Menegidio, David Aciole Barbosa, Valquíria C Alencar, Renata O Vilas Boas, Regina Costa de Oliveira, Daniela L Jabes, Luiz R Nunes

Medical Mycology  ·  21 Jul 2020

2019

ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp.

David Aciole Barbosa, Fabiano Bezerra Menegidio, Valquíria Campos Alencar, Rafael S. Gonçalves, Juliana de Fátima Santos Silva, Renata Ozelami Vilas Boas, Yara Natércia Lima Faustino de Maria, Daniela Leite Jabes, Regina Costa de Oliveira, Luiz R. Nunes

PLOS Neglected Tropical Diseases  ·  15 Jul 2019

Bioportainer Workbench: a versatile and user-friendly system that integrates implementation, management, and use of bioinformatics resources in Docker environments

Fabiano B Menegidio, David Aciole Barbosa, Rafael dos S Gonçalves, Marcio M Nishime, Daniela L Jabes, Regina Costa de Oliveira, Luiz R Nunes

GigaScience  ·  01 Apr 2019

2017

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses

Fabiano B Menegidio, Daniela L Jabes, Regina Costa de Oliveira, Luiz R Nunes

Bioinformatics  ·  04 Sep 2017

Functional and Evolutionary Characterization of a UDP-Xylose Synthase Gene from the Plant Pathogen Xylella fastidiosa, Involved in the Synthesis of Bacterial Lipopolysaccharide

Valquíria Campos Alencar, Daniela Leite Jabes, Fabiano Bezerra Menegidio, Guilherme Lanzi Sassaki, Lucas Rodrigo de Souza, Luciano Puzer, Maria Cecília Zorél Meneghetti, Marcelo Andrade Lima, Ivarne Luis dos Santos Tersariol, Regina Costa de Oliveira, Luiz R. Nunes

Biochemistry  ·  26 Jan 2017

2016

Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa

Bárbara Niza, Marcus V. Merfa, Valquíria C. Alencar, Fabiano B. Menegidio, Luiz R. Nunes, Marcos A. Machado, Marco A. Takita, Alessandra A. de Souza

Genome Announcements  ·  27 Oct 2016

Thioridazine inhibits gene expression control of the cell wall signaling pathway (CWI) in the human pathogenic fungus Paracoccidioides brasiliensis

Daniela Leite Jabes, Ana Claudia de Freitas Oliveira, Valquíria Campos Alencar, Fabiano Bezerra Menegidio, Débora Liliane Souza Reno, Daiene Souza Santos, David Aciole Barbosa, Renata Ozelami Vilas Boas, Rodrigo Luiz de Oliveira Rodrigues Cunha, Tiago Rodrigues, Regina Costa de Oliveira, Luiz R. Nunes

Molecular Genetics and Genomics  ·  08 Mar 2016