publications

2024

1. A mesomelic skeletal dysplasia, Kantaputra-like, not related to HOXD cluster region, and with phenotypic gender differences

   Maria Dora Jazmin Lacarrubba-Flores, Karina Costa Silveira, Cynthia Silveira, and 2 more authors

   Am. J. Med. Genet. A, Feb 2024

   Abs

   Mesomelic skeletal dysplasia is a heterogeneous group of skeletal disorders that has grown since the molecular basis of these conditions is in the process of research and discovery. Here, we report a Brazilian family with eight affected members over three generations with a phenotype similar to mesomelic Kantaputra dysplasia. This family presents marked shortening of the upper limbs with hypotrophy of the lower limbs and clubfeet without synostosis. Array-based CNV analysis and exome sequencing of four family members failed to show any region or gene candidate. Interestingly, males were more severely affected than females in this family, suggesting that gender differences could play a role in the phenotypic expressivity of this condition.

2022

1. Benchmarking the proteomic profile of animal models of mesial temporal epilepsy

   Amanda M Canto, Alexandre B Godoi, Alexandre H B Matos, and 18 more authors

   Ann. Clin. Transl. Neurol., Apr 2022

   Abs

   OBJECTIVES: We compared the proteomic signatures of the hippocampal lesion induced in three different animal models of mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE+HS): the systemic pilocarpine model (PILO), the intracerebroventricular kainic acid model (KA), and the perforant pathway stimulation model (PPS). METHODS: We used shotgun proteomics to analyze the proteomes and find enriched biological pathways of the dorsal and ventral dentate gyrus (DG) isolated from the hippocampi of the three animal models. We also compared the proteomes obtained in the animal models to that from the DG of patients with pharmacoresistant MTLE+HS. RESULTS: We found that each animal model presents specific profiles of proteomic changes. The PILO model showed responses predominantly related to neuronal excitatory imbalance. The KA model revealed alterations mainly in synaptic activity. The PPS model displayed abnormalities in metabolism and oxidative stress. We also identified common biological pathways enriched in all three models, such as inflammation and immune response, which were also observed in tissue from patients. However, none of the models could recapitulate the profile of molecular changes observed in tissue from patients. SIGNIFICANCE: Our results indicate that each model has its own set of biological responses leading to epilepsy. Thus, it seems that only using a combination of the three models may one replicate more closely the mechanisms underlying MTLE+HS as seen in patients.

2. Plasma proteomic signature of major depressive episode in the elderly

   Licia C Silva-Costa, Bradley J Smith, Victor Corasolla Carregari, and 7 more authors

   J. Proteomics, Oct 2022

   Abs

   Depression is a complex and multifactorial disease, affecting about 6.5% of the elderly population in what is referred to as late-life depression (LLD). Despite its public health relevance, there is still limited information about the molecular mechanisms of LLD. We analyzed the blood plasma of 50 older adults, 19 with LLD and 31 controls, through untargeted mass spectrometry, and used systems biology tools to identify biochemical pathways and biological processes dysregulated in the disease. We found 96 differentially expressed proteins between LLD patients and control individuals. Using elastic-net regression, we generated a panel of 75 proteins that comprises a potential model for determining the molecular signature of LLD. We also showed that biological pathways related to vesicle-mediated transport and voltage-dependent calcium channels may be dysregulated in LLD. These data can help to build an understanding of the molecular basis of LLD, offering an integrated view of the biomolecular alterations that occur in this disorder. SIGNIFICANCE: Major depressive disorder in the elderly, called late-life depression (LLD), is a common and disabling disorder, with recent prevalence estimates of 6.5% in the general population. Despite the public health relevance, there is still limited information about the molecular mechanisms of LLD. The findings in this paper shed light on LLD heterogeneous biological mechanisms. We uncovered a potential novel biomolecular signature for LLD and biological pathways related to this condition which can be targets for the development of novel interventions for prevention, early diagnosis, and treatment of LLD.

2021

1. Multi-omics Analysis Suggests Enhanced Epileptogenesis in the Cornu Ammonis 3 of the Pilocarpine Model of Mesial Temporal Lobe Epilepsy

   Amanda M. Canto, Alexandre H. B. Matos, Alexandre B. Godoi, and 10 more authors

   Hippocampus, Feb 2021
2. Molecular Diagnosis in a Cohort of 114 Patients with Rare Skeletal Dysplasias

   Karina C. Silveira, Thatiane Y. Kanazawa, Cynthia Silveira, and 3 more authors

   American Journal of Medical Genetics. Part C, Seminars in Medical Genetics, Sep 2021
3. A Field Guide to Cultivating Computational Biology

   Gregory P. Way, Casey S. Greene, Piero Carninci, and 13 more authors

   PLoS biology, Oct 2021

2020

1. Laser microdissection-based Microproteomics of the Hippocampus of a Rat Epilepsy Model Reveals Regional Differences in Protein Abundances

   Amanda M. Canto, André S. Vieira, Alexandre H B Matos, and 8 more authors

   Scientific Reports, Mar 2020
2. Methodological Differences Can Affect Sequencing Depth with a Possible Impact on the Accuracy of Genetic Diagnosis

   Murilo G. Borges, Cristiane S. Rocha, Benilton S. Carvalho, and 1 more author

   Genetics and Molecular Biology, Mar 2020
3. Blood plasma proteomic modulation induced by olanzapine and risperidone in schizophrenia patients

   Sheila Garcia-Rosa, Benilton S. Carvalho, Paul C. Guest, and 2 more authors

   Journal of Proteomics, Jul 2020
4. Inherited Variations in Human pigmentation-related Genes Modulate Cutaneous Melanoma Risk and Clinicopathological Features in Brazilian Population

   Gustavo Jacob Lourenço, Cristiane Oliveira, Benilton Sá Carvalho, and 9 more authors

   Scientific Reports, Jul 2020
5. The Brazilian Initiative on Precision Medicine (BIPMed): Fostering Genomic data-sharing of Underrepresented Populations

   Cristiane S. Rocha, Rodrigo Secolin, Maíra R. Rodrigues, and 2 more authors

   npj Genomic Medicine, Oct 2020
6. Identification of Common and Divergent Gene Expression Signatures in Patients with Venous and Arterial Thrombosis Using Data from Public Repositories

   Bidossessi Wilfried Hounkpe, Rafaela de Oliveira Benatti, Benilton de Sá Carvalho, and 1 more author

   PloS One, Oct 2020
7. Circulating Lymphocytes and Monocytes Transcriptomic Analysis of Patients with Type 2 Diabetes mellitus, Dyslipidemia and Periodontitis

   Sâmia C. T. Corbi, Jaira F. Vasconcellos, Alliny S. Bastos, and 10 more authors

   Scientific Reports, May 2020

2019

1. Multimodal Analysis of SCN1A Missense Variants Improves Interpretation of Clinically Relevant Variants in Dravet Syndrome

   Marina C. Gonsales, Maria Augusta Montenegro, Paula Preto, and 5 more authors

   Frontiers in Neurology, May 2019
2. Copy Number Alterations Associated with Clinical Features in an Underrepresented Population with Breast Cancer

   Raquel M. Rodrigues-Peres, Benilton S Carvalho, Meenakshi Anurag, and 10 more authors

   Molecular Genetics & Genomic Medicine, Jul 2019
3. Distribution of Local Ancestry and Evidence of Adaptation in Admixed Populations

   Rodrigo Secolin, Alex Mas-Sandoval, Lara R. Arauna, and 8 more authors

   Scientific Reports, Sep 2019
4. Blood Transcriptome Profile Induced by an Efficacious Vaccine Formulated with Salivary Antigens from Cattle Ticks

   Sandra R. Maruyama, Benilton Carvalho, Mar González-Porta, and 8 more authors

   npj Vaccines, Sep 2019

2018

1. Dysregulation of NEUROG2 Plays a Key Role in Focal Cortical Dysplasia

   Simoni H. Avansini, Fábio R. Torres, André S. Vieira, and 14 more authors

   Annals of Neurology, Mar 2018

2017

1. A Prediction Algorithm for Drug Response in Patients with Mesial Temporal Lobe Epilepsy Based on Clinical and Genetic Information

   Mariana S. Silva-Alves, Rodrigo Secolin, Benilton S. Carvalho, and 7 more authors

   PloS One, Mar 2017
2. MicroRNA hsa-miR-134 Is a Circulating Biomarker for Mesial Temporal Lobe Epilepsy

   Simoni H. Avansini, Beatriz Pereira Sousa Lima, Rodrigo Secolin, and 13 more authors

   PloS One, Mar 2017
3. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

   A Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, and 40 more authors

   Cell, Mar 2017

2016

1. Working with Oligonucleotide Arrays

   Benilton S. Carvalho

   Methods in Molecular Biology, Mar 2016
2. Cyclooxygenase-1 as a Potential Therapeutic Target for Seizure Suppression: Evidences from Zebrafish Pentylenetetrazole-Seizure Model

   Patrícia Gonçalves Barbalho, Benilton de Sá Carvalho, Iscia Lopes-Cendes, and 1 more author

   Frontiers in Neurology, Mar 2016
3. MicroRNAs-424 and 206 Are Potential Prognostic Markers in Spinal Onset Amyotrophic Lateral Sclerosis

   Helen M. T. Andrade, Milena Albuquerque, Simoni H. Avansini, and 6 more authors

   Journal of the Neurological Sciences, Sep 2016

2015

1. Orchestrating high-throughput Genomic Analysis with Bioconductor

   Wolfgang Huber, Vincent J Carey, Robert Gentleman, and 23 more authors

   Nature Methods, Jan 2015
2. Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma

   Gabriel Wajnberg, Benilton S. Carvalho, Carlos G. Ferreira, and 1 more author

   BioMed Research International, Jan 2015

2014

1. Reply: Resting Heart rate: an Independent Predictor of Congestive Heart Failure

   Anders Opdahl, Bharath Ambale Venkatesh, Veronica R. S. Fernandes, and 9 more authors

   Journal of the American College of Cardiology, Jul 2014
2. Ordering of Mutations in Preinvasive Disease Stages of Esophageal Carcinogenesis

   Jamie M J Weaver, Caryn S Ross-Innes, Nicholas Shannon, and 25 more authors

   Nature Genetics, Jun 2014
3. Resting Heart Rate as Predictor for Left Ventricular Dysfunction and Heart failure: MESA (Multi-Ethnic Study of Atherosclerosis)

   Anders Opdahl, Bharath Ambale Venkatesh, Veronica R. S. Fernandes, and 9 more authors

   Journal of the American College of Cardiology, Apr 2014

2013

1. The Challenges of Delivering Bioinformatics Training in the Analysis of high-throughput Data

   Benilton S. Carvalho, and Gabriella Rustici

   Briefings in Bioinformatics, Sep 2013

2011

1. Comparing Genotyping Algorithms for Illumina’s Infinium whole-genome SNP BeadChips

   Matthew E. Ritchie, Ruijie Liu, Benilton S. Carvalho, and 3 more authors

   BMC Bioinformatics, Mar 2011
2. Using the R Package crlmm for Genotyping and Copy Number Estimation

   Robert B. Scharpf, Rafael A. Irizarry, Matthew E. Ritchie, and 2 more authors

   Journal of Statistical Software, May 2011
3. Chromosome-wide Mapping of DNA Methylation Patterns in Normal and Malignant Prostate Cells Reveals Pervasive Methylation of gene-associated and Conserved Intergenic Sequences

   Srinivasan Yegnasubramanian, Zhijin Wu, Michael C. Haffner, and 10 more authors

   BMC Genomics, Jun 2011
4. Performance Assessment of Copy Number Microarray Platforms Using a spike-in Experiment

   Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, and 13 more authors

   Bioinformatics (Oxford, England), Apr 2011

2010

1. A framework for oligonucleotide microarray preprocessing

   Benilton S. Carvalho, and Rafael A. Irizarry

   Bioinformatics, Aug 2010
2. A Multilevel Model to Address Batch Effects in Copy Number Estimation Using SNP Arrays

   R. B. Scharpf, I. Ruczinski, B. Carvalho, and 3 more authors

   Biostatistics, Jul 2010

2009

1. R/Bioconductor software for Illumina’s Infinium whole-genome genotyping BeadChips

   M. E. Ritchie, B. S. Carvalho, K. N. Hetrick, and 2 more authors

   Bioinformatics, Aug 2009
2. Quantifying uncertainty in genotype calls

   Benilton S. Carvalho, Thomas A. Louis, and Rafael A. Irizarry

   Bioinformatics, Nov 2009

2008

1. Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models

   Wenyi Wang, Benilton Carvalho, Nathaniel D. Miller, and 3 more authors

   Journal of Computational Biology, Sep 2008
2. Genome-wide Copy Number Alterations Detection in Fresh Frozen and Matched FFPE Samples Using SNP 6.0 Arrays

   Marianne Tuefferd, An De Bondt, Ilse Van Den Wyngaert, and 10 more authors

   Genes, Chromosomes & Cancer, Nov 2008
3. Validation and Extension of an Empirical Bayes Method for SNP Calling on Affymetrix Microarrays

   Shin Lin, Benilton Carvalho, David J. Cutler, and 3 more authors

   Genome Biology, Apr 2008
4. Comprehensive high-throughput Arrays for Relative Methylation (CHARM)

   R. A. Irizarry, C. Ladd-Acosta, B. Carvalho, and 5 more authors

   Genome Research, Feb 2008
5. Arterial Stiffness Is Associated with Regional Ventricular Systolic and Diastolic dysfunction: the Multi-Ethnic Study of Atherosclerosis

   Verônica Rolim S. Fernandes, Joseph F. Polak, Susan Cheng, and 9 more authors

   Arteriosclerosis, Thrombosis, and Vascular Biology, Jan 2008

2007

1. The Influence of Left Ventricular Size and Global Function on Regional Myocardial Contraction and Relaxation in an Adult Population Free of Cardiovascular Disease: A Tagged CMR Study of the MESA Cohort

   Verônica Rolim Fernandes, Thor Edvardsen , Boaz Rosen, and 6 more authors

   Journal of Cardiovascular Magnetic Resonance, Nov 2007

2006

1. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data

   B. Carvalho, H. Bengtsson, T. P. Speed, and 1 more author

   Biostatistics, Dec 2006
2. Subclinical Atherosclerosis and Incipient Regional Myocardial Dysfunction in Asymptomatic individuals: the Multi-Ethnic Study of Atherosclerosis (MESA)

   Verônica R. S. Fernandes, Joseph F. Polak, Thor Edvardsen, and 6 more authors

   Journal of the American College of Cardiology, Jun 2006