Publications

A collection of our scientific contributions to the fields of bioinformatics, molecular modeling, and antimicrobial resistance, reflecting our commitment to advancing global health through computational research.

2026

ChemRxiv (Preprint)

Structure-based strategy reveals a novel ligand binding site in Staphylococcus aureus catabolite control protein A: implications for transcriptional regulation and drug design

Farias, André Borges; Sisco, Maria Carolina; Costa, Maiana de Oliveira Cerqueira; Perez-Rueda, Ernesto; Nicolás, Marisa Fabiana

DOI: View at ChemRxiv

2025

ACS Omega (Vol. 10, No. 6)

PAPreC: a pipeline for antigenicity prediction comparison methods across Bacteria

Martins, Yasmmin C; Cerqueira e Costa, Maiana O; Palumbo, Miranda C; Do Porto, Dario F; Custodio, Fabio L; Trevizani, Raphael; Nicolás, Marisa Fabiana

International Journal of Molecular Sciences (Vol. 26, No. 6)

Pulmonary Myeloid Cells in Mild Cases of COVID-19 Upregulate the Intracellular Fc Receptor TRIM21 and Transcribe Proteasome-Associated Molecules

Henriques-Pons, A.; Castro, M. C. S.; Silva, V. S.; Costa, M. O. C.; et al.

2024

Briefings in Bioinformatics (Vol. 25, No. 6)

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability

Borges Farias, André; Sganzerla Martinez, Gustavo; Galán-Vásquez, Edgardo; Nicolás, Marisa Fabiana; Pérez-Rueda, Ernesto

2020 - 2023

Frontiers in Microbiology (2023)

The gene regulatory network of Staphylococcus aureus ST239-SCC mec III strain Bmb9393

Costa, M. O. C.; Nascimento, A. P. B.; Martins, Y. C.; Santos, M. T.; Figueiredo, A. M. S.; Perez-Rueda, E.; Nicolás, M. F.

Bioinformatics Advances (2023)

PPIntegrator: semantic integrative system for protein–protein interaction

Martins, Y. C.; Ziviani, A.; Costa, M. O. C.; Cavalcanti, M. C. R.; Nicolás, M. F.; Vasconcelos, A. T. R.

Frontiers in Cellular and Infection Microbiology (2022)

Pathway driven target selection in Klebsiella pneumoniae: Insights into carbapenem exposure

Serral, F.; Pardo, A. M.; Sosa, E.; Palomino, M. M.; Nicolás, M. F.; Turjanski, A. G.; Ramos, P. I. P.; Porto, D. F.

Scientific Reports (2021)

Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2

Guedes, I. A.; Costa, L. S. C.; Santos, K. B.; et al.

Frontiers in Bioinformatics (2021)

Large-scale protein interactions prediction by multiple evidence analysis associated with an in-silico curation strategy

Martins, Yasmmin Côrtes; Ziviani, Artur; Nicolás, Marisa Fabiana; de Vasconcelos, Ana Tereza Ribeiro

Clinical Infectious Diseases (2020)

An emerging clone, KPC-2-producing Klebsiella pneumoniae ST16, associated with high mortality rates

Andrey, Diego O.; Dantas, Priscila; Martins, Willames; Nicolás, Marisa F.; et al.

2010 - 2019

Frontiers in Microbiology (2019)

Local diversification of methicillin-resistant Staphylococcus aureus ST239 in South America

Botelho, A. M. N.; Costa, M. O. C.; et al.

Scientific Reports (2018)

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets

Ramos, P. I. P.; Porto, D. F.; Lanzarotti, E.; et al.

Aquatic Toxicology (2018)

Characterization of Laguncularia racemosa transcriptome and molecular response to oil pollution

de Freitas Guedes, F. A.; de Barros Rossetto, P.; Nicolás, Marisa Fabiana; et al.

Memórias do Instituto Oswaldo Cruz (2017)

Complete genome sequence of community-associated MRSA (strain USA400-0051)

Côrtes, Marina Farrel; Costa, Maiana O. C.; Nicolás, Marisa F.; Figueiredo, Agnes

Genome Biology and Evolution (2016)

Complete genome sequence of the MRSA isolate HC1335 from ST239 lineage

Botelho, Ana M. N.; Costa, Maiana O. C.; Nicolás, Marisa F.; et al.

BMC Microbiology (2012)

AtlasT4SS: a curated database for type IV secretion systems

Souza, Rangel C.; Saji, G. D. R. Q.; Costa, M. O. C.; Nicolás, Marisa F.; et al.

BMC Genomics (2012)

Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899

Ormeño-Orrillo, E.; Menna, P.; Almeida, L. G. P.; et al.

Frontiers in Microbiology (2016)

Exploratory investigation of Bacteroides fragilis transcriptional response during in vitro exposure to metronidazole

Freitas, M. C. R.; Resende, J. A.; Saji, G. D. R. Q.; Vasconcelos, A. T. R.; Nicolás, M. F.; Diniz, C. G.

International Journal of Medical Microbiology (2016)

A unique SaeS allele overrides cell-density dependent expression of saeR and lukSF-PV in CA-MRSA

Ramundo, M. S.; Beltrame, C. O.; Botelho, A. M. N.; Nicolás, M. F.; Guedes, I. A.; Dardenne, L. E.; et al.

Tuberculosis (2016)

A whole genome bioinformatic approach to determine potential latent phase specific targets in Mycobacterium tuberculosis

Defelipe, L. A.; Porto, D. F.; Ramos, P. I. P.; Nicolás, M. F.; Sosa, E.; Marti, M. A.

Antimicrobial Agents and Chemotherapy (2015)

Characterization of BKC-1 class A carbapenemase from Klebsiella pneumoniae clinical isolates in Brazil

Nicoletti, A. G.; Marcondes, M. F. M.; Martins, W. M. B. S.; Nicolás, M. F.; Vasconcelos, A. T. R.; Gales, A. C.

BMC Genomics (2014)

Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13

Ramos, P. I. P.; Almeida, L. G. P.; Lima, N. C. B.; Girardello, R.; Nicolás, M. F.; et al.

Genome Announcements (2013)

Complete genome sequence of a variant of the MRSA ST239 lineage, strain BMB9393

Costa, M. O. C.; Beltrame, C. O.; Ferreira, F. A.; Souza, R. C.; Nicolás, M. F.; Figueiredo, A. M. S.

2000 - 2009

Functional & Integrative Genomics (2009)

Novel genes related to nodulation, secretion systems, and surface structures revealed by a genome draft of Rhizobium tropici

Pinto, F. G. S.; Chueire, L. M. O.; Vasconcelos, A. T. R.; Nicolás, M. F.; Hungria, M.

Nucleic Acids Research (2008)

The Universal Protein Resource (UniProt)

Bairoch, A.; Bougueleret, L.; Altairac, S.; et al.

Soil Biology and Biochemistry (2008)

Genomic panorama of Bradyrhizobium japonicum CPAC 15

Godoy, L. P.; Vasconcelos, A. T. R.; Chueire, L. M. O.; Souza, R. C.; Nicolás, M. F.; Hungria, M.

Journal of Bacteriology (2005)

Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma

Vasconcelos, A. T. R.; Ferreira, H. B.; Bizarro, C. V.; Nicolás, M. F.; et al.

PNAS (2003)

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Vasconcelos, A. T. R.; De Almeida, D. F.; Hungria, M.; Nicolás, M. F.; et al.

1996 - 1999

Applied Soil Ecology (1998)

Persistence of Bradyrhizobium japonicum in arable soils of Argentina

Brutti, L.; Rivero, E.; Basurco, J. C. P.; Nicolás, M. F.; et al.

Relatório de Pesquisa (1996)

Comparação de composição de polissacarídeos extracelulares em extirpes de Bradyrhizobium por HPLC

Nicolás, Marisa Fabiana