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

Journal of Biomolecular Structure and Dynamics

Development of CHARMM36-compatible parameters for siroheme group and molecular dynamics simulations of dissimilatory sulfite reductase with GROMACS

Lima, Camilo Henrique da Silva; et al.

DOI: View at Journal
Science Direct

Reduced chlorhexidine susceptibility in multidrug-resistant Klebsiella pneumoniae; genomic and functional analysis of invasive isolates

Gales, Ana Cristina; et al.

DOI: View at Journal
Springer Nature

Application of Clinical Genomics to the Diagnosis of Mendelian Diseases

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

Population Genomics and Genetic Diversity

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

From Variant Analysis to the Report of Results

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

Annotation and Classification of Variants According to the Criteria of the American College of Medical Genetics (ACMG)

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

DNA Sequencing

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

Introduction to Clinical Genomics

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

Ethical, Legal and Social Issues (ELSI)

Marti, Marcelo; et al.

DOI: View at Springer
Springer Nature

From Genome to Variants and Their Meaning

Marti, Marcelo; et al.

DOI: View at Springer
View Journal

Co-occurrence of muddy off flavor and cyanotoxin genes in the polluted Guandu river waters (Rio de Janeiro, Brazil)

Tschoeke, Diogo A.; et al.

DOI: View at Journal
Springer Nature

Early detection of dengue outbreaks from routine primary health care records: evaluation by an extended version of the Mixed Model of Artificial Intelligence and Next-Generation (MMAING)

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Springer
Springer Nature

(The) Human Genome(s)

Marti, Marcelo; et al.

DOI: View at Springer
View Journal

Retraction notice to “Collapse of scallop Nodipecten nodosus production in the tropical Southeast Brazil as a possible consequence of global warming and water pollution” [Sci. Total Environ. 904 (2023) 166873]

Tschoeke, Diogo A.; et al.

DOI: View at Journal
View PDF

LASSBio-classFLOW: A Semi-Automated KNIME Workflow for Classification Model Benchmarking and Virtual Screening

Lima, Lídia Moreira; et al.

DOI: View at PDF
Springer Nature

GenPhenia: using deep neural networks to accelerate rare-disease diagnosis

Turjanski, Adrian; Marti, Marcelo; et al.

DOI: View at Springer
Research Square

CRISPRi loss-of-function mutations revealed through experimental evolution in Burkholderia cenocepacia

Cardona, Silvia T.; et al.

DOI: View at Research
ACS Omega

Leishmanicidal Activity of a Hydrazone Derivative Loaded into Nanocarrier Systems

Lima, Lídia Moreira; et al.

DOI: View at ACS Omega
Springer Nature

Lytic activity of F8-like phage φSPM-1 against One Health lineages of carbapenem-resistant Pseudomonas aeruginosa

Gales, Ana Cristina; et al.

DOI: View at Springer
Frontiers

Porphyromonas gingivalis outer membrane vesicles induce an activated but permissive neutrophil phenotype

Tribelli, Paula Maria; et al.

DOI: View at Frontiers
Research Square

Automated dataset integrating structural and bioactivity data for structure-based drug discovery

Dardenne, Laurent E.; Silva, Matheus Müller Pereira; Guedes, Isabella Alvim; et al.

DOI: View at Research Square
Research Square

Mapping the resistance landscape: A large-scale study of polymyxin-resistant pathogens circulating in low-and middle-income countries

Gales, Ana Cristina; et al.

DOI: View at Research Square
View Journal

Critical role of Asp283 in modulating calcium-dependent autoprocessing of yeast Metacaspase ScMCA-Ia

Marcondes, Marcelo Ferreira Machado; et al.

DOI: View at Journal
Karger

Double heterozygous PROK2 p.(Ile55Ter)-PROKR2 p.(Arg85Leu) variants: case report of an oligogenic case of congenital hypogonadotropic hypogonadism with anosmia

Marti, Marcelo; et al.

DOI: View at Karger
Springer Nature

Deeply conserved and expressed small ORFs in the model beetle Tribolium castaneum

Tschoeke, Diogo Antonio; et al.

DOI: View at Springer
Springer Nature

Genotypic features of antimicrobial resistance, virulence determinants, and clonal lineages of Enterococcus spp. reported in Brazil: a scoping review with marked regional asymmetry

Gales, Ana Cristina; et al.

DOI: View at Springer
ACS Omega

Molecular Modeling and In Vitro Evaluation of Thioureas and Arylthioureas as Urease Inhibitors

Lima, Camilo Henrique da Silva; et al.

DOI: View at ACS Omega
Nature Medicine

Genomas Brasil program: building precision public health within Brazil’s Unified Health System

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Nature Medicine
Science Direct

Integrated in silico and in vitro approaches reveal novel coumarin hybrids targeting influenza A virus RNA-dependent RNA polymerase

Lima, Camilo Henrique da Silva; et al.

DOI: View at Journal
ASM Microbiology Spectrum

Genomic epidemiology of carbapenemase-producing Enterobacter cloacae complex in Argentina: a retrospective analysis (2016–2022)

Gomez, Sonia Alejandra; et al.

DOI: View at IJPDS
The Lancet

Hypervirulent Klebsiella pneumoniae K1-ST23 in Latin America: a neglected One Health threat

Gales, Ana Cristina; et al.

DOI: View at The Lancet
PLOS Biology

Towards globally equitable bioinformatics adoption

Turjanski, Adrian G.; et al.

DOI: View at PLOS Biology
SciELO Brasil

Using Machine Learning to Predict Chemical Reaction Outcomes in Environmental Applications

Guedes, Isabella Alvim; Dardenne, Laurent E.; et al.

DOI: View at SciELO Brasil
bioRXiv

Exploring the potential role of the TETRATRICOPEPTIDE THIOREDOXIN-LIKE gene family in nitrogen-fixing and water-restricted soybean plants

Sotelo-Silveira, Jose Roberto; et al.

DOI: View at bioRXiv
European Journal of Preventive Cardiology

Attempted before, achieved now: Cytisinicline in a structured smoking cessation program

Figueiredo, Agnes Marie Sá; et al.

DOI: View at Journal
bioRXiv

In silico structural analysis of EthA substitutions for ranking priority mutations leading to ethionamide resistance in Mycobacterium tuberculosis

Galvão, Teca Calcagno; et al.

DOI: View at bioRXiv
International Journal of Population Data Science

From CIDACS Experience to a National Data Strategy for Population Health Sciences and Public Health Purposes: A Brazilian Case

Ramos, Pablo Ivan Pereira; et al.

DOI: View at IJPDS
Frontiers

Minireview Kefir as a source of antimicrobial compounds against bacterial pathogens

Perez-Rueda, Ernesto; et al.

DOI: View at Frontiers
ABRAPCORP

Desafios da comunicação estratégica em saúde: o caso da resistência aos antimicrobianos

Gales, Ana Cristina; et al.

DOI: View at Congress
Science Direct

Integrative in silico and in vitro discovery of a novel thiazolidinone derivative as arginase inhibitor with potent antileishmanial activity

Lima, Camilo Henrique da Silva; et al.

DOI: View at Journal
International Journal of Population Data Science

Enhancing geocoding in Brazil through language model-based preprocessing

Ramos, Pablo Ivan Pereira; et al.

DOI: View at IJPDS
Revista Virtual de Química

Integrando Inscrições Químicas por Meio de Recursos Digitais: Relato Docente de uma Sequência Didática sobre a Tuberculose e seu Tratamento

Lima, Camilo Henrique da Silva; et al.

DOI: View at Revista Virtual
PubMed Central

Compound Heterozygous Variants in the Phospholipase Gene PNPLA6 Cause Hypopituitarism and Vision Loss

Marti, Marcelo; et al.

DOI: View at PubMed
Critical Care Clinic

Antimicrobial Resistance in Patients with Sepsis

Gales, Ana Cristina; et al.

DOI: View at Clinic
Science Direct

From parasite biology to predictive metabolic models

Ramos, Pablo Ivan Pereira; Azevedo, Lucas Gentil; et al.

DOI: View at Journal
Springer Nature

Genomics of Hospital-Associated Brazilian Multidrug-Resistant Klebsiella pneumoniae: Abundance of Resistance and Virulence Genes and Mosaicism of the blaKPC−2 Genetic Context Among Enterobacterales

Nicolás, Marisa Fabiana; et al.

DOI: View at Springer
ChemMedChem

How and Why Does Knowledge-Based Biased Docking Improve Molecular Docking Performance?

Turjanski, Adrian G.; et al.

DOI: View at ChemMedChem
Springer Nature

Evaluation of phenyl hydrazide-based compounds as myeloperoxidase inhibitors

Farias, André Borges; et al.

DOI: View at Springer
Scientific Reports

Cafestol-derivatives as potential FXR agonists and CYP7A1 inhibitors and their impact on hypercholesterolemia: an in silico study

Lima, Camilo Henrique da Silva; et al.

DOI: View at Reports
Journal of Molecular Structure

Crystal structure and computational study of cyclohexylammonium 5-bromo-6-chloro uracil anion: evidence for covalent and stacked dimers providing new structural insights into aggregation in uracil anion salts and related compounds

Lima, Camilo Henrique da Silva; et al.

DOI: View at Journal
Applied and Environmental Microbiology

Burkholderia vietnamiensis genes involved in extracellular medium-chain-length polyhydroxyalkanoate degradation

Porto, Dario Fernandez; Cardona, Silvia T.; et al.

DOI: View at Applied
Bacteria

Linking Genomic Virulence and Antimicrobial Resistance Determinants to Host-Interaction Phenotypes in the Emerging Bovine Mastitis Pathogen Enterococcus lactis

Porto, Dario Fernandez; et al.

DOI: View at Bacteria
The Lancet Regional Health

Implementation of AESOP early-warning system for respiratory disease: a pilot and validation study using routinely collected data in Amazonas, Brazil

Tschoeke, Diogo Antonio; Ramos, Pablo Ivan Pereira; et al.

DOI: View at Lancet
View Journal

Rhodolith metagenome diversity shifts across the Great Amazon System

Tschoeke, Diogo Antonio; et al.

DOI: View at Journal
International Journal of Digital Humanities

A methodological framework for the use of AI tools in automated workflows for generating validated and structured historical datasets

Galán-Vásquez, Edgardo; et al.

DOI: View at Journal
arXiv preprint

A Gate-Based Quantum Genetic Algorithm for Real-Valued Global Optimization

Dardenne, Laurent Emmanuel; et al.

DOI: View at arXiv
ChemMedChem

How and Why Does Knowledge-Based Biased Docking Improve Molecular Docking Performance?

Martí, Marcelo; et al.

DOI: View at ChemMedChem
ACS Bio & Med Chem Au

Targeting FLT3 in Acute Myeloid Leukemia: Structural Insights and Key Challenges

Lima, Lídia Moreira; et al.

DOI: View at ACS Bio
Human Molecular Genetics

Updated compendium of genes and variants associated with congenital hypogonadotropic hypogonadism: systematic review, classification pipeline, and network analysis

Martí, Marcelo; et al.

DOI: View at Human
International Dairy Journal

Effects of omega-3 enriched oil on probiotic Lacticaseibacillus casei BL23 in a miniature yogurt system

Palomino, Maria Mercedes; et al.

DOI: View at Journal
npj Digital Public Health

Anticipating influenza-like illness outbreaks via syndromic surveillance using over-the-counter drug sales and primary health care data

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Digital
Applied and Environmental Microbiology

From genome to lifestyle: adaptive strategies of Pseudomonas sp. AU10 and its Antarctic lineage

Smircich, Pablo; et al.

DOI: View at Applied and Environmental
Rhizosphere

Functional auxin signaling and phosphorus acquisition induced in planta by the extremophile bacterium Pseudomonas extremaustralis

Tribelli, Paula Maria; et al.

DOI: View at Rhizosphere
Applied and Environmental Microbiology

Burkholderia vietnamiensis genes involved in extracellular medium-chain-length polyhydroxyalkanoate degradation

Cardona, Silvia T.; et al.

DOI: View at Applied and Environmental
medRxiv

Early transcriptional signature in chikungunya predicts chronic arthralgia and reveals deficient antiviral response

Ramos, Pablo Ivan Pereira; et al.

DOI: View at medRxiv
RNA

Neuronal Subtype–Specific Ribosomal Protein mRNA Expression

Smircich, Pablo; et al.

DOI: View at RNA
bioRxiv

Solving the Diagnostic Odyssey with Synthetic Phenotype Data

Martí, Marcelo; et al.

DOI: View at bioRxiv
View Journal

Implementation of AESOP early-warning system for respiratory disease: a pilot and validation study using routinely collected data in Amazonas, Brazil

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Journal
Journal of Chemical Information and Modeling

Best Practices in Mixed-Solvent Molecular Dynamics and Solvent-Site-Biased Docking

Martí, Marcelo; et al.

DOI: View at Journal
Glycobiology

Water-guided docking improves prediction of protein–glycan complexes

Martí, Marcelo; et al.

DOI: View at Glycobiology
mSystems

Empowering global disease surveillance with CURED: a tool for rapid identification of unique genomic biomarkers

Figueiredo, Agnes Marie Sá; et al.

DOI: View at mSystems
Ambio

Wildfire smoke and antimicrobial resistance: A hidden link demanding global attention

Gales, Ana Cristina; et al.

DOI: View Journal
International Journal of Antimicrobial Agents

Corrigendum to "Phage therapy for KPC-producing Klebsiella pneumoniae decolonization in high-risk patients: The KIDNAP Study Protocol"

Gales, Ana Cristina; et al.

DOI: View Journal
The Lancet Regional Health – Americas

Daily Chlorhexidine Bathing for the Prevention of Nosocomial Infections in Critically Ill Patients (CLEAN-IT)

Gales, Ana Cristina; et al.

DOI: View at The Lancet
npj Antimicrobials and Resistance

Artificial intelligence for early detection and risk prediction of antimicrobial resistance in aquatic ecosystems

Gales, Ana Cristina; et al.

The Brazilian Journal of Infectious Diseases

Implementation of a Bundle of Measures to Prevent the Dissemination of Resistant Microorganisms in Two Brazilian Public Hospitals

Gales, Ana Cristina; et al.

DOI: View at BJID
The Brazilian Journal of Infectious Diseases

Antimicrobial Resistance Genes in Enterococcus spp. in Brazil: Clinical, Food, Environmental, and Animal Evidence

Gales, Ana Cristina; et al.

DOI: View at BJID
The Brazilian Journal of Infectious Diseases

Phenotypic and Genotypic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Isolated in a State of the Brazilian Amazon

Gales, Ana Cristina; et al.

DOI: View at BJID
The Brazilian Journal of Infectious Diseases

Genomic Analysis of Pseudomonas aeruginosa Carrying blaGES-1 and blaKPC-2 Isolated from Bloodstream Infection in Rondônia

Gales, Ana Cristina; et al.

DOI: View at BJID
Microbiology Spectrum

Synergistic effects of ceftriaxone combined with BLI-489 against NDM-producing Klebsiella pneumoniae

Gales, Ana Cristina; et al.

DOI: View at Spectrum
JAC-Antimicrobial Resistance

Management of metallo-β-lactamase-producing Enterobacterales infections: a modified Delphi study

Gales, Ana Cristina; et al.

DOI: View at JAC
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

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

DOI: View at ChemRxiv
ACS Omega

Machine Learning and Molecular Modeling for Drug Repurposing Targeting Potential PI3Kα Inhibitors in Post-CoViD-19 Pulmonary Fibrosis

Lima, Camilo Henrique da Silva; et al.

DOI: View at ACS Omega
eLife

Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity in Trypanosoma cruzi populations

Smircich, Pablo; Sotelo-Silveira, Jose Roberto; et al.

DOI: View at eLife
Pharmaceuticals

Phosphatidylinositol-3-Kinase (PI3K) and Histone Deacetylase (HDAC) Multitarget Inhibitors: An Update on Clinical and Preclinical Candidates

Lima, Lidia Moreira; et al.

DOI: View at MDPI
Frontiers in Microbiology

Description and complete genome sequence of Mycobacterium venezuelense sp. nov., a rapidly growing species recovered from a soft tissue infection

Sisco Zerpa, Maria Carolina Del Valle; et al.

DOI: View at Frontiers
Molecular Ecology

Genetic Diversity of Polymyxin Resistance Genes in Klebsiella pneumoniae Clinical Isolates

Galvão, Teca Calcagno; et al.

DOI: View at Wiley
International Journal of Antimicrobial Agents

In Reply to the Letter to Editor Regarding "Phage Therapy for KPC-Producing Klebsiella pneumoniae Decolonization in High-Risk Patients: The KIDNAP Study Protocol - A Prospective Feasibility and Proof of Concept Study in the Brazilian Context"

Gales, Ana Cristina; et al.

DOI: View at Wiley
The Brazilian Journal of Infectious Diseases

Impact of Antimicrobial Use on Resistance in Gram-Negative Bacilli: A Secondary Analysis of ANVISA Data (2019–2023)

Gales, Ana Cristina; et al.

DOI: View at Wiley
The Brazilian Journal of Infectious Diseases

Laboratory-Confirmed Central Venous Catheter–Associated Bloodstream Infections in Intensive Care Units in Brazil: Ecological Study with ANVISA Data 2019–2023

Gales, Ana Cristina; et al.

DOI: View at Wiley
Open Forum Infectious Diseases

Optimizing Management of Infections Caused by Metallo-β-Lactamase (MBL)–Producing Enterobacterales: An International Modified Delphi Study

Gales, Ana Cristina; et al.

DOI: View at Wiley
International Journal of Molecular Sciences

LASSBio-1986 as a Multifunctional Antidiabetic Lead: SGLT1/2 Docking, Redox-Inflammatory Modulation and Metabolic Benefits in C57BL/6 Mice

Lima, Lidia Moreira; et al.

Journal of Chromatography B

Bioanalytical HPLC–DAD method for determining (E)-1-4(trifluoromethyl) benzylidene)-5-(2-4-dichlorozoyl) carbonylhydrazine (LASSBio-1736), a promising antileishmanial compound in canine plasma applied to pharmacokinetic studies

lima, Lidia Moreira; et al.

DOI: View at Wiley
ACS Omega

Big Data for Drug Discovery: Some Historical Landscape, Considerations, and Applications for a Medicinal Chemist

Lima, Lidia Moreira; et al.

ACS Omega

New Dual Pan-PI3K/mTOR Inhibitor: Design, Synthesis, Cytotoxic Action, Permeation, Metabolic Stability, and In Silico Protein-Ligand Interaction

Lima, Lidia Moreira; et al.

Memórias do Instituto Oswaldo Cruz

Transcriptomic dynamics reveals sequential acquisition of complement resistance during prolonged starvation of Trypanosoma cruzi epimastigote

Smircich, Pablo; et al.

DOI: View at Wiley
PLoS One

Beyond the transcript: Chromatin implications in trans-splicing in Trypanosomatids

Smircich, Pablo; et al.

DOI: View at Wiley
Antibiotics

Oxidative Stress Reshapes Porphyromonas gingivalis Outer Membrane Vesicles and Impairs OMV-Mediated Invasion and Persistence in Trophoblast Cells

Tribelli, Paula Maria; et al.

DOI: View at Wiley
Revista Argentina de Microbiología

Predictors of rectal carriage of carbapenemase-producing Gram-negative bacteria in general wards: A case–control study

Gomez, Sonia Alejandra; et al.

DOI: View at Wiley
npj Antimicrobials and Resistance

Global perspectives on Klebsiella epidemiology and biology: conference report on the KLEBS 2024 symposium

Galvão, Teca Calcagno; et al.

2025

Europe PMC

Burkholderia vietnamiensis Genes Involved in Extracellular Medium-Chain-Length Polyhydroxyalkanoate Degradation

Cardona, Silvia T.; et al.

DOI: View at Europe
Microbial Ecology

Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Microbial
BMC Infectious Diseases

Genomic characterization of XDR Mycobacterium tuberculosis isolates in Argentina (2006–2015)

Turjanski, Adrian G.; Porto, Dario Fernandez do; Martí, Marcelo; Palomino, Maria Mercedes; et al.

DOI: View at BMC
bioRxiv (Preprint)

Transcriptional Profiling and Co-expression Integration for the Filtering of Relevant Bacterial sRNA–mRNA Interactions: Application to Staphylococcus aureus Biofilm

Figueiredo, Agnes Marie Sá; Galán-Vásquez, Edgardo; Nicolás, Marisa Fabiana; et al.

DOI: View at bioRxiv
Royal Society Open Science

An integrated framework for modelling respiratory disease transmission and designing surveillance networks using a sentinel index

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Royal
Journal of Medical Microbiology

Matrix-assisted laser desorption/ionization-time of flight MS as a tool for clonal discrimination in Streptococcus dysgalactiae subsp. equisimilis

Figueiredo, Agnes Marie Sá; et al.

DOI: View Journal
Ciência & Saúde Coletiva

Leveraging the power of digital health to fight pandemics: The example of ÆSOP

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Ciência & Saúde
Frontiers in Microbiology

Decoding the evolutionary history of ST30 Staphylococcus aureus: insights into a potentially silent MSSA bloodstream pathogen

Figueiredo, Agnes Marie Sá; et al.

DOI: View at Frontiers
Clinical Microbiology Reviews

Current and future options for the treatment of serious infections due to carbapenem-resistant Pseudomonas aeruginosa

Gales, Ana Cristina; et al.

DOI: View Journal
Antimicrobial Agents and Chemotherapy

ISAba1-mediated blaADC disruption restores third-generation cephalosporin susceptibility in a clinical Acinetobacter baumannii isolate

Gales, Ana Cristina; et al.

DOI: View Journal
CMI Communications

Phage research in South America: A descriptive overview of trends and gaps

Gales, Ana Cristina; et al.

DOI: View at Elsevier
International Journal of Antimicrobial Agents

Phage therapy for KPC-producing Klebsiella pneumoniae decolonization in high-risk patients: The KIDNAP Study Protocol

Gales, Ana Cristina; et al.

DOI: View Journal
The Brazilian Journal of Infectious Diseases

Guideline for antimicrobial treatment of multidrug-resistant Gram-negative infections: practice recommendations of the Brazilian Society of Infectious Diseases

Gales, Ana Cristina; et al.

DOI: View at BJID
Anthropocene Science

Impact of Climate Change-Mediated Tragedies: An Account of Extreme Rainfall Event in Rio Grande do Sul, Brazil

Gales, Ana Cristina; et al.

DOI: View at Springer
Expert Opinion on Therapeutic Patents

The potential of bacteriophages in treating multidrug-resistant ESKAPE pathogen infections

Gales, Ana Cristina; et al.

DOI: View Journal
Clinical Microbiology and Infection

How do I manage difficult-to-treat Pseudomonas aeruginosa infections?: Key questions for today's clinicians

Gales, Ana Cristina; et al.

DOI: View Journal
One Health

Phylogenomic analysis of aquatic and clinical OXA-23-positive Acinetobacter baumannii belonging to the international clone 5 (ST79) from Southeast Brazil

Gales, Ana Cristina; et al.

DOI: View Journal
Journal of Global Antimicrobial Resistance

Salmonella Minnesota sequence type 548 harboring a type 2 IncC megaplasmid of antimicrobial resistance and virulence infecting a companion animal

Gales, Ana Cristina; et al.

DOI: View Journal
JAC-Antimicrobial Resistance

The impact of the COVID-19 pandemic on antimicrobial usage: an international patient-level cohort study

Gales, Ana Cristina; et al.

DOI: View Journal
The Brazilian Journal of Infectious Diseases

Experience in Ceftazidime-Avibactam for treatment of MDR BGN infection in Oncologic Children

Gales, Ana Cristina; et al.

DOI: View Journal
Database

ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0

Borges Farias, André; et al.

DOI: View at Database
Scientific Reports

In vitro assays identified thiohydantoins with anti-trypanosomatid activity and molecular modelling studies indicated possible selective CYP51 inhibition

Lima, Camilo Henrique da Silva; et al.

DOI: View at Nature
Scientific Reports

In silico evaluation of N-aryl-1,10-phenanthroline-2-amines as potential inhibitors of T. cruzi GP63 zinc-metalloprotease

Lima, Camilo Henrique da Silva; et al.

DOI: View at Nature
Current Medicinal Chemistry

Natural and Synthetic Coumarins as Potential Drug Candidates against SARS-CoV-2/COVID-19

Lima, Camilo Henrique da Silva; et al.

ACS Omega

Molecular Dynamics Studies on Trypanosoma cruzi Dihydroorotate Dehydrogenase Complexes: An Analysis of the Inhibitor Influence

Lima, Camilo Henrique da Silva; et al.

Journal of Natural Pesticide Research

Larvicidal effects of Myrciaria floribunda nanoemulsion against Aedes aegypti

Lima, Camilo Henrique da Silva; et al.

Frontiers in Microbiology

Phylogenomic insights into LA-MRSA from Argentine pig farm environments: novel OptrA variant and regional emergence of an ST9 lineage

Porto, Dario Fernandez do; et al.

DOI: View at Frontiers
Environmental Microbiology Reports

Genomic Analysis and Virulence Features of Vibrio cholerae Non-O1/Non-O139 Harbouring CARB-Type β-Lactamases

Porto, Dario Fernandez do; et al.

Microbial Pathogenesis

Genome characterization of Enterococcus lactis strain isolated from bovine subclinical mastitis

Porto, Dario Fernandez do; et al.

DOI: View Journal
PLoS Pathogens

Expanding kinetoplastid genome annotation through protein structure comparison

Porto, Dario Fernandez do; Smircich, Pablo; et al.

DOI: View at PLoS
Bacterial Enzymes as Targets for Drug Discovery

Computational tools to identify potential drug targets in bacteria

Porto, Dario Fernandez do; et al.

Science of the Total Environment

Co-occurrence of SARS-CoV-2 variants in rivers and sewage in India and Brazil

Tschoeke, Diogo Antonio; Ramos, Pablo Ivan Pereira; et al.

DOI: View at ScienceDirect
Microbial Ecology

Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments

Tschoeke, Diogo Antonio; et al.

Pharmaceuticals

Novel Multifunctional Cannabidiol-Based Analogues with In Silico, In Vitro, and In Vivo Anti-SARS-CoV-2 Effect

Guedes, Isabella Alvim; Dardenne, Laurent Emmanuel; et al.

ChemRxiv (Preprint)

Data-centric training enables meaningful interaction learning in protein–ligand binding affinity prediction

Dardenne, Laurent Emmanuel; et al.

Bioorganic Chemistry

The discovery of a new uncompetitive inhibitor of nucleoside hydrolase from Leishmania donovani

Lima, Lidia Moreira; et al.

DOI: View Journal
Pharmaceuticals

Drug Discovery for Histone Deacetylase Inhibition: Past, Present and Future of Zinc-Binding Groups

Lima, Lidia Moreira; et al.

European Journal of Medicinal Chemistry

Design, synthesis and pharmacological evaluation of multitarget GPR40 agonists/HDAC6 inhibitors for Alzheimer's disease

Lima, Lidia Moreira; et al.

DOI: View Journal
ACS Infectious Diseases

Collaborative Synthesis for Neglected Diseases through the Open Synthesis Network: Arylaminopyrazoles as Chagas Disease Treatments

Lima, Lidia Moreira; et al.

DOI: View at ACS
ACS Pharmacology & Translational Science

Hit-to-Lead Studies of Pyrazinylpiperazines against Visceral Leishmaniasis: Pharmacokinetic Profile and In Vivo Efficacy

Lima, Lidia Moreira; et al.

Biotech

Towards a Survival-Based Cellular Assay for the Selection of Protease Inhibitors in Escherichia coli

Machado, Marcelo Ferreira Marcondes; et al.

DOI: View Journal
Biochimica et Biophysica Acta – Proteins and Proteomics

Role of N-terminal of metacaspase of Candida albicans in calcium binding

Machado, Marcelo Ferreira Marcondes; et al.

DOI: View at Elsevier
Frontiers in Bioinformatics

Beyond Tanimoto: a learned bioactivity similarity index enhances ligand discovery

Martí, Marcelo; et al.

DOI: View at Frontiers
Revista Argentina de Microbiología

Optimized DNA extraction protocol for Staphylococcus aureus strains utilizing liquid nitrogen

Palomino, Maria Mercedes; et al.

International Journal of Molecular Sciences

Pulmonary Myeloid Cells in Mild Cases of COVID-19 Upregulate the Intracellular Fc Receptor TRIM21

Henriques-Pons, A.; Castro, M. C. S.; Silva, V. S.; Costa, M. O. C.; Nicolás, M. F.

DOI: View Journal
ACS Omega

PAPreC: A Pipeline for Antigenicity Prediction Comparison Methods across Bacteria

Martins, Y. C.; Cerqueira e Costa, M. O.; Nicolás, M. F.; et al.

DOI: View at ACS
The Lancet Regional Health – Americas

Primary health care data-based early warning system for dengue outbreaks: a nationwide case study in Brazil

Ramos, Pablo Ivan Pereira; et al.

The Journal of Immunology

Immunoregulatory macrophages induced by mycobacterial nonpolar lipids

Ramos, Pablo Ivan Pereira; et al.

DOI: View Journal
Frontiers in Immunology

rBCG-LTAK63 Enhances Protection Against Tuberculosis by Inducing Autophagy and Circadian Gene Regulation

Ramos, Pablo Ivan Pereira; et al.

DOI: View at Frontiers
BMC Genomics

Exploring a gene co-expression network throughout the Trypanosoma cruzi life cycle

Smircich, Pablo; Sotelo-Silveira, Jose Roberto; et al.

DOI: View Journal
bioRxiv (Preprint)

Metabolic reshaping drives novel melanin production from tryptophan in a cystic fibrosis Pseudomonas aeruginosa clinical isolate

Tribelli, Paula Maria; et al.

medRxiv (Preprint)

Microenvironment-driven phenotypic shifts in Staphylococcus aureus from children with cystic fibrosis: a longitudinal cohort study

Tribelli, Paula Maria; et al.

DOI: View at medRxiv
Microbial Biotechnology

Genetic Dissection of Cyclic di-GMP Signalling in Pseudomonas aeruginosa via Systematic Diguanylate Cyclase Disruption

Tribelli, Paula Maria; et al.

DOI: View Journal
Biophysical Reviews

RND/HAE-1 members in the Pseudomonadota phylum: exploring multidrug resistance

Torres, Pedro H. M.; et al.

Journal of Biological Chemistry

Abstract 1200 Expanding antimicrobial targets and new classes of growth inhibitors with CIMPLE-seq

Cardona, Silvia T.; et al.

npj Antimicrobials and Resistance

Innovative perspectives on the discovery of small molecule antibiotics

Cardona, Silvia T.; et al.

US Patent Application

Aqueous Hop Extracts and Their Use as Antimicrobial Agents

Cardona, Silvia T.; et al.

Frontiers in Pharmacology

Multidrug resistant bacteria: new therapeutic approaches for a challenging problem

Gomez, Sonia Alejandra; et al.

DOI: View at Frontiers
Frontiers in Immunology

Clinical isolates of Providencia rettgeri and Providencia Stuartii evades neutrophil-mediated killing

Gomez, Sonia Alejandra; et al.

DOI: View at Frontiers
Frontiers in Pharmacology

Effectiveness of infection control measures informed by a modified Blue-Carba test in general wards

Gomez, Sonia Alejandra; et al.

DOI: View at Frontiers
Infection, Genetics and Evolution

Plasmid diversity in Klebsiella pneumoniae ST307 co-producing KPC plus NDM recovered during the COVID-19 pandemic

Gomez, Sonia Alejandra; et al.

DOI: View Journal
Journal of Global Antimicrobial Resistance

Emerging resistance to novel β-lactam β-lactamase inhibitor combinations in Klebsiella pneumoniae bearing KPC variants

Gomez, Sonia Alejandra; et al.

Journal of Global Antimicrobial Resistance

Novel allelic variants of blaOXA-48-like carried on IncN2 and IncC2 plasmids isolated from clinical cases in Argentina

Gomez, Sonia Alejandra; et al.

Microbiological Research

Klebsiella pneumoniae ST258 impairs intracellular elastase mobilization and persists within human neutrophils

Gomez, Sonia Alejandra; et al.

Parasitology Research

Immunolocalization and 3D modeling of three unique proteins belonging to the costa of Tritrichomonas foetus

Chaves, Camila Rodrigues; et al.

Scientific Reports

Statine-based peptidomimetics as SARS-CoV-2 Papain-like protease inhibitors: in Silico and in vitro studies

Lima, Camilo Henrique da Silva; et al.

Scientific Reports

Genomic, socio-environmental, and sequencing capability patterns in the surveillance of SARS-CoV-2 in Latin America and the Caribbean up to 2023

Porto, Dario Fernadez; et al.

Science of the Total Environment

Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil

Tschoeke, Diogo Antonio; et al.

DOI: View Journal
BMC Microbiology

Bacillus velezensis Bac-9, isolated from kefir, possesses antifungal activity and improves resistance of tomato plant against whitefly Bemisia tabaci

Perez-Rueda, Ernesto; et al.

Scientific Reports

Comparative genomic analysis of resistance and virulence genes in Staphylococcus epidermidis and their impact on clinical outcome of musculoskeletal infections

Santos, Fernanda Fernades; et al.

Future Virology

New antiviral peptides inhibit in vitro infection of SARS-CoV-2

Guedes, Isabella Alvim; et al.

bioRxiv (Preprint)

Conserved Axonal Transcriptome Dynamics Underlie PGE 2 -Induced Sensitisation and Identify Tnfrsf12a/ Fn14 as a Regulator of Neuronal Excitability in DRG Neurons

Sotelo-Silveira, Jose Roberto; et al.

DOI: View Journal
ACS Omega

Exploring the Conformational Effects of N- and C-Methylation of N-Acylhydrazones

Lima, Lidia Moreira; et al.

ACS Omega

Synthesis, Characterization, and Toxicity Assessment of Superparamagnetic Iron Oxide Nanoparticles Coated with Antitumor Molecules

Lima, Lidia Moreira; et al.

International Journal of Molecular Sciences

A Pharmacologic Approach Against Glioblastoma — A Synergistic Combination of a Quinoxaline-Based and a PI3K/mTOR Dual Inhibitor

Lima, Lidia Moreira; et al.

DOI: View Journal
Expert Opinion on Therapeutic Patents

Rho kinase inhibitors: a patent review (2017-2023)

Lima, Lidia Moreira; et al.

ACS Infectious Diseases

Collaborative Synthesis for Neglected Diseases through the Open Synthesis Network: Structure-Activity Relationships of Arylaminopyrazoles as Chagas Disease Treatments

Lima, Lidia Moreira; et al.

Anti-Cancer Agents in Medicinal Chemistry

State of the Art of IDH Inhibitors: Emerging Questions and Perspectives

Lima, Lidia Moreira; et al.

Pharmaceuticals

Mechanistic Advances in the Therapeutic Application of Bixin for Lung Inflammation In Vitro and In Vivo

Lima, Lidia Moreira; et al.

Archiv der Pharmazie

Investigation on LASSBio-1971 and LASSBio-1974 Cellular Cytotoxic Mechanism and Their Comparative DMPK Profile

Lima, Lidia Moreira; et al.

Pharmaceuticals

Unraveling the Antihyperglycemic Effects of Dipeptyl Peptidase-4 Inhibitors in Rodents: A Multi-Faceted Approach Combining Effects on Glucose Homeostasis, Molecular Docking, and ADMET Profiling

Lima, Lidia Moreira; et al.

Frontiers in Immunology

The immunomodulatory and antitumor properties of the bacterial metalloprotease Oligopeptidase A are mediated by TLR4/MyD88/TRIF and MAPK signaling pathways

Machado, Marcelo Ferreira Marcondes; et al.

Repeat Amino Acid Sequences in Proteins

Aromatic Clusters in Proteins: Folding, Drug Interactions and Protein-Protein Complexes

Marti, Marcelo; et al.

4th Molecular Biosystems Conference

Differential composition of the translational machinery of Trypanosoma cruzi during metacyclogenesis and cell cycle

Smircich, Pablo; et al.

DOI: View Journal
Parasitology Research

Immunolocalization and 3D modeling of three unique proteins belonging to the costa of Tritrichomonas foetus

Tores, Pedro H. M.; et al.

Frontiers in Pharmacology

Effectiveness of infection control measures informed by a modified Blue-Carba test in reducing rectal carriage of carbapenemase-producing bacteria in general wards

Gomez, Sonia Alejandra; et al.

DOI: View Journal
Frontiers in Pharmacology

From genomics to treatment: overcoming pan-drug-resistant Klebsiella pneumoniae in clinical settings

Gomez, Sonia Alejandra; et al.

DOI: View Journal

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

Farias, André Borges; Martinez, Gustavo Sganzerla; 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