publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2021

  1. Multi-omics Analysis Suggests Enhanced Epileptogenesis in the Cornu Ammonis 3 of the Pilocarpine Model of Mesial Temporal Lobe Epilepsy
    Canto, Amanda M., Matos, Alexandre H. B., Godoi, Alexandre B., Vieira, André S., Aoyama, Beatriz B., Rocha, Cristiane S., Henning, Barbara, Carvalho, Benilton S., Pascoal, Vinicius D. B., Veiga, Diogo F. T., Gilioli, Rovilson, Cendes, Fernando, and Lopes-Cendes, Iscia
    Hippocampus Feb 2021
  2. Molecular Diagnosis in a Cohort of 114 Patients with Rare Skeletal Dysplasias
    Silveira, Karina C., Kanazawa, Thatiane Y., Silveira, Cynthia, Lacarrubba-Flores, Maria D. J., Carvalho, Benilton S., and Cavalcanti, Denise P.
    American Journal of Medical Genetics. Part C, Seminars in Medical Genetics Sep 2021
  3. A Field Guide to Cultivating Computational Biology
    Way, Gregory P., Greene, Casey S., Carninci, Piero, Carvalho, Benilton S., Hoon, Michiel, Finley, Stacey D., Gosline, Sara J. C., Lȇ Cao, Kim-Anh, Lee, Jerry S. H., Marchionni, Luigi, Robine, Nicolas, Sindi, Suzanne S., Theis, Fabian J., Yang, Jean Y. H., Carpenter, Anne E., and Fertig, Elana J.
    PLoS biology Oct 2021

2020

  1. Laser microdissection-based Microproteomics of the Hippocampus of a Rat Epilepsy Model Reveals Regional Differences in Protein Abundances
    Canto, Amanda M., Vieira, André S., H B Matos, Alexandre, Carvalho, Benilton S., Henning, Barbara, Norwood, Braxton A., Bauer, Sebastian, Rosenow, Felix, Gilioli, Rovilson, Cendes, Fernando, and Lopes-Cendes, Iscia
    Scientific Reports Mar 2020
  2. Methodological Differences Can Affect Sequencing Depth with a Possible Impact on the Accuracy of Genetic Diagnosis
    Borges, Murilo G., Rocha, Cristiane S., Carvalho, Benilton S., and Lopes-Cendes, Iscia
    Genetics and Molecular Biology Mar 2020
  3. Blood plasma proteomic modulation induced by olanzapine and risperidone in schizophrenia patients
    Garcia-Rosa, Sheila, Carvalho, Benilton S., Guest, Paul C., Steiner, Johann, and Martins-de-Souza, Daniel
    Journal of Proteomics Jul 2020
  4. Inherited Variations in Human pigmentation-related Genes Modulate Cutaneous Melanoma Risk and Clinicopathological Features in Brazilian Population
    Louren√ßo, Gustavo Jacob,¬†Oliveira, Cristiane,¬†Carvalho, Benilton S√°,¬†Torricelli, Caroline,¬†Silva, Janet Keller,¬†Gomez, Gabriela Vilas B√īas,¬†Rinck-Junior, Jos√© Augusto,¬†Oliveira, Wesley Lima,¬†Vazquez, Vinicius Lima,¬†Serrano, Sergio Vicente,¬†Moraes, Aparecida Machado,¬†and Lima, Carmen Silvia Passos
    Scientific Reports Jul 2020
  5. The Brazilian Initiative on Precision Medicine (BIPMed): Fostering Genomic data-sharing of Underrepresented Populations
    Rocha, Cristiane S., Secolin, Rodrigo, Rodrigues, Maíra R., Carvalho, Benilton S., and Lopes-Cendes, Iscia
    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
    Hounkpe, Bidossessi Wilfried, Benatti, Rafaela de Oliveira, Carvalho, Benilton de Sá, and De Paula, Erich Vinicius
    PloS One Oct 2020
  7. Circulating Lymphocytes and Monocytes Transcriptomic Analysis of Patients with Type 2 Diabetes mellitus, Dyslipidemia and Periodontitis
    Corbi, S√Ęmia C. T.,¬†Vasconcellos, Jaira F.,¬†Bastos, Alliny S.,¬†Bussaneli, Diego Girotto,¬†Silva, B√°rbara Roque,¬†Santos, Raquel Alves,¬†Takahashi, Catarina S.,¬†S Rocha, Cristiane,¬†Carvalho, Benilton de S√°,¬†Maurer-Morelli, Cl√°udia V.,¬†Orrico, Silvana R. P.,¬†Barros, Silvana P.,¬†and Scarel-Caminaga, Raquel M.
    Scientific Reports May 2020

2019

  1. Multimodal Analysis of SCN1A Missense Variants Improves Interpretation of Clinically Relevant Variants in Dravet Syndrome
    Gonsales, Marina C., Montenegro, Maria Augusta, Preto, Paula, Guerreiro, Marilisa M., Coan, Ana Carolina, Quast, Monica Paiva, Carvalho, Benilton S., and Lopes-Cendes, Iscia
    Frontiers in Neurology May 2019
  2. Copy Number Alterations Associated with Clinical Features in an Underrepresented Population with Breast Cancer
    Rodrigues-Peres, Raquel M., S Carvalho, Benilton, Anurag, Meenakshi, Lei, Jonathan T., Conz, Livia, Gonçalves, Rodrigo, Cardoso Filho, Cássio, Ramalho, Susana, Paiva, Geisilene R., Derchain, Sophie F. M., Lopes-Cendes, Iscia, Ellis, Matthew J., and Sarian, Luis O.
    Molecular Genetics & Genomic Medicine Jul 2019
  3. Distribution of Local Ancestry and Evidence of Adaptation in Admixed Populations
    Secolin, Rodrigo,¬†Mas-Sandoval, Alex,¬†Arauna, Lara R.,¬†Torres, F√°bio R.,¬†Araujo, T√Ęnia K.,¬†Santos, Marilza L.,¬†Rocha, Cristiane S.,¬†Carvalho, Benilton S.,¬†Cendes, Fernando,¬†Lopes-Cendes, Iscia,¬†and Comas, David
    Scientific Reports Sep 2019
  4. Blood Transcriptome Profile Induced by an Efficacious Vaccine Formulated with Salivary Antigens from Cattle Ticks
    Maruyama, Sandra R., Carvalho, Benilton, González-Porta, Mar, Rung, Johan, Brazma, Alvis, Gustavo Gardinassi, Luiz, Ferreira, Beatriz R., Banin, Tamy M., Veríssimo, Cecília J., Katiki, Luciana M., and Miranda-Santos, Isabel K. F.
    npj Vaccines Sep 2019

2018

  1. Dysregulation of NEUROG2 Plays a Key Role in Focal Cortical Dysplasia
    Avansini, Simoni H.,¬†Torres, F√°bio R.,¬†Vieira, Andr√© S.,¬†Dogini, Danyella B.,¬†Rogerio, Fabio,¬†Coan, Ana C.,¬†Morita, Marcia E.,¬†Guerreiro, Marilisa M.,¬†Yasuda, Clarissa L.,¬†Secolin, Rodrigo,¬†Carvalho, Benilton S.,¬†Borges, Murilo G.,¬†Almeida, Vanessa S.,¬†Ara√ļjo, Patr√≠cia A. O. R.,¬†Queiroz, Luciano,¬†Cendes, Fernando,¬†and Lopes-Cendes, Iscia
    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
    Silva-Alves, Mariana S., Secolin, Rodrigo, Carvalho, Benilton S., Yasuda, Clarissa L., Bilevicius, Elizabeth, Alvim, Marina K. M., Santos, Renato O., Maurer-Morelli, Claudia V., Cendes, Fernando, and Lopes-Cendes, Iscia
    PloS One Mar 2017
  2. MicroRNA hsa-miR-134 Is a Circulating Biomarker for Mesial Temporal Lobe Epilepsy
    Avansini, Simoni H., Sousa Lima, Beatriz Pereira, Secolin, Rodrigo, Santos, Marilza L., Coan, Ana Carolina, Vieira, André S., Torres, Fábio R., Carvalho, Benilton S., Alvim, Marina K. M., Morita, Márcia E., Yasuda, Clarissa L., Pimentel-Silva, Luciana R., Dogini, Danyella B., Rogerio, Fabio, Cendes, Fernando, and Lopes-Cendes, Iscia
    PloS One Mar 2017
  3. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer
    Robertson, A Gordon, Kim, Jaegil, Al-Ahmadie, Hikmat, Bellmunt, Joaquim, Guo, Guangwu, Cherniack, Andrew D, Hinoue, Toshinori, Laird, Peter W, Hoadley, Katherine A, Akbani, Rehan, Castro, Mauro A A, Gibb, Ewan A, Kanchi, Rupa S, Gordenin, Dmitry A, Shukla, Sachet A, Sanchez-Vega, Francisco, Hansel, Donna E, Czerniak, Bogdan A, Reuter, Victor E, Su, Xiaoping, Sa Carvalho, Benilton, Chagas, Vinicius S, Mungall, Karen L, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Lu, Yiling, Klimczak, Leszek J, Zhang, Jiexin, Choo, Caleb, Ojesina, Akinyemi I, Bullman, Susan, Leraas, Kristen M, Lichtenberg, Tara M, Wu, Catherine J, Schultz, Nicholaus, Getz, Gad, Meyerson, Matthew, Mills, Gordon B, McConkey, David J, Network, TCGA Research, Weinstein, John N, Kwiatkowski, David J, and Lerner, Seth P
    Cell Mar 2017

2016

  1. Working with Oligonucleotide Arrays
    Carvalho, Benilton S.
    Methods in Molecular Biology Mar 2016
  2. Cyclooxygenase-1 as a Potential Therapeutic Target for Seizure Suppression: Evidences from Zebrafish Pentylenetetrazole-Seizure Model
    Barbalho, Patrícia Gonçalves, Carvalho, Benilton de Sá, Lopes-Cendes, Iscia, and Maurer-Morelli, Claudia Vianna
    Frontiers in Neurology Mar 2016
  3. MicroRNAs-424 and 206 Are Potential Prognostic Markers in Spinal Onset Amyotrophic Lateral Sclerosis
    Andrade, Helen M. T., Albuquerque, Milena, Avansini, Simoni H., S Rocha, Cristiane, Dogini, Danyella B., Nucci, Anamarli, Carvalho, Benilton, Lopes-Cendes, Iscia, and França, Marcondes C.
    Journal of the Neurological Sciences Sep 2016

2015

  1. Orchestrating high-throughput Genomic Analysis with Bioconductor
    Huber, Wolfgang,¬†Carey, Vincent J,¬†Gentleman, Robert,¬†Anders, Simon,¬†Carlson, Marc,¬†Carvalho, Benilton S,¬†Bravo, Hector Corrada,¬†Davis, Sean,¬†Gatto, Laurent,¬†Girke, Thomas,¬†Gottardo, Raphael,¬†Hahne, Florian,¬†Hansen, Kasper D,¬†Irizarry, Rafael A,¬†Lawrence, Michael,¬†Love, Michael I,¬†MacDonald, James,¬†Obenchain, Valerie,¬†OleŇõ, Andrzej K,¬†Pag√®s, Herv√©,¬†Reyes, Alejandro,¬†Shannon, Paul,¬†Smyth, Gordon K,¬†Tenenbaum, Dan,¬†Waldron, Levi,¬†and Morgan, Martin
    Nature Methods Jan 2015
  2. Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
    Wajnberg, Gabriel, Carvalho, Benilton S., Ferreira, Carlos G., and Passetti, Fabio
    BioMed Research International Jan 2015

2014

  1. Reply: Resting Heart rate: an Independent Predictor of Congestive Heart Failure
    Opdahl, Anders, Ambale Venkatesh, Bharath, Fernandes, Veronica R. S., Wu, Colin O., Nasir, Khurram, Choi, Eui-Young, Almeida, Andre L. C., Rosen, Boaz, Carvalho, Benilton, Edvardsen, Thor, Bluemke, David A., and Lima, João A. C.
    Journal of the American College of Cardiology Jul 2014
  2. Ordering of Mutations in Preinvasive Disease Stages of Esophageal Carcinogenesis
    Weaver, Jamie M J, Ross-Innes, Caryn S, Shannon, Nicholas, Lynch, Andy G, Forshew, Tim, Barbera, Mariagnese, Murtaza, Muhammed, Ong, Chin-Ann J, Lao-Sirieix, Pierre, Dunning, Mark J, Smith, Laura, Smith, Mike L, Anderson, Charlotte L, Carvalho, Benilton, O’Donovan, Maria, Underwood, Timothy J, May, Andrew P, Grehan, Nicola, Hardwick, Richard, Davies, Jim, Oloumi, Arusha, Aparicio, Sam, Caldas, Carlos, Eldridge, Matthew D, Edwards, Paul A W, Rosenfeld, Nitzan, Tavaré, Simon, and Fitzgerald, Rebecca C
    Nature Genetics Jun 2014
  3. Resting Heart Rate as Predictor for Left Ventricular Dysfunction and Heart failure: MESA (Multi-Ethnic Study of Atherosclerosis)
    Opdahl, Anders, Ambale Venkatesh, Bharath, Fernandes, Veronica R. S., Wu, Colin O., Nasir, Khurram, Choi, Eui-Young, Almeida, Andre L. C., Rosen, Boaz, Carvalho, Benilton, Edvardsen, Thor, Bluemke, David A., and Lima, João A. C.
    Journal of the American College of Cardiology Apr 2014

2013

  1. The Challenges of Delivering Bioinformatics Training in the Analysis of high-throughput Data
    Carvalho, Benilton S., and Rustici, Gabriella
    Briefings in Bioinformatics Sep 2013

2011

  1. Comparing Genotyping Algorithms for Illumina’s Infinium whole-genome SNP BeadChips
    Ritchie, Matthew E., Liu, Ruijie, Carvalho, Benilton S., Australia, , (ANZgene), New Zealand Multiple Sclerosis Genetics Consortium, and Irizarry, Rafael A.
    BMC Bioinformatics Mar 2011
  2. Using the R Package crlmm for Genotyping and Copy Number Estimation
    Scharpf, Robert B., Irizarry, Rafael A., Ritchie, Matthew E., Carvalho, Benilton, and Ruczinski, Ingo
    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
    Yegnasubramanian, Srinivasan, Wu, Zhijin, Haffner, Michael C., Esopi, David, Aryee, Martin J., Badrinath, Raghav, He, Tony L., Morgan, James D., Carvalho, Benilton, Zheng, Qizhi, De Marzo, Angelo M., Irizarry, Rafael A., and Nelson, William G.
    BMC Genomics Jun 2011
  4. Performance Assessment of Copy Number Microarray Platforms Using a spike-in Experiment
    Halper-Stromberg, Eitan, Frelin, Laurence, Ruczinski, Ingo, Scharpf, Robert, Jie, Chunfa, Carvalho, Benilton, Hao, Haiping, Hetrick, Kurt, Jedlicka, Anne, Dziedzic, Amanda, Doheny, Kim, Scott, Alan F., Baylin, Steve, Pevsner, Jonathan, Spencer, Forrest, and Irizarry, Rafael A.
    Bioinformatics (Oxford, England) Apr 2011

2010

  1. A framework for oligonucleotide microarray preprocessing
    Carvalho, Benilton S., and Irizarry, Rafael A.
    Bioinformatics Aug 2010
  2. A Multilevel Model to Address Batch Effects in Copy Number Estimation Using SNP Arrays
    Scharpf, R. B., Ruczinski, I., Carvalho, B., Doan, B., Chakravarti, A., and Irizarry, R. A.
    Biostatistics Jul 2010

2009

  1. R/Bioconductor software for Illumina’s Infinium whole-genome genotyping BeadChips
    Ritchie, M. E., Carvalho, B. S., Hetrick, K. N., Tavare, S., and Irizarry, R. A.
    Bioinformatics Aug 2009
  2. Quantifying uncertainty in genotype calls
    Carvalho, Benilton S., Louis, Thomas A., and Irizarry, Rafael A.
    Bioinformatics Nov 2009

2008

  1. Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models
    Wang, Wenyi, Carvalho, Benilton, Miller, Nathaniel D., Pevsner, Jonathan, Chakravarti, Aravinda, and Irizarry, Rafael A.
    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
    Tuefferd, Marianne,¬†De Bondt, An,¬†Van Den Wyngaert, Ilse,¬†Talloen, Willem,¬†Verbeke, Tobias,¬†Carvalho, Benilton,¬†Clevert, Djork-Arne,¬†Alifano, Marco,¬†Raghavan, Nandini,¬†Amaratunga, Dhammika,¬†G√∂hlmann, Hinrich,¬†Bro√ęt, Philippe,¬†and Camilleri-Bro√ęt, Sophie
    Genes, Chromosomes & Cancer Nov 2008
  3. Validation and Extension of an Empirical Bayes Method for SNP Calling on Affymetrix Microarrays
    Lin, Shin, Carvalho, Benilton, Cutler, David J., Arking, Dan E., Chakravarti, Aravinda, and Irizarry, Rafael A.
    Genome Biology Apr 2008
  4. Comprehensive high-throughput Arrays for Relative Methylation (CHARM)
    Irizarry, R. A., Ladd-Acosta, C., Carvalho, B., Wu, H., Brandenburg, S. A., Jeddeloh, J. A., Wen, B., and Feinberg, A. P.
    Genome Research Feb 2008
  5. Arterial Stiffness Is Associated with Regional Ventricular Systolic and Diastolic dysfunction: the Multi-Ethnic Study of Atherosclerosis
    Fernandes, Ver√īnica Rolim S.,¬†Polak, Joseph F.,¬†Cheng, Susan,¬†Rosen, Boaz D.,¬†Carvalho, Benilton,¬†Nasir, Khurram,¬†McClelland, Robyn,¬†Hundley, Gregory,¬†Pearson, Greg,¬†O‚ÄôLeary, Daniel H.,¬†Bluemke, David A.,¬†and Lima, Jo√£o A. C.
    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
    Fernandes, Ver√īnica Rolim,¬†Edvardsen, Thor,¬†Rosen, Boaz,¬†Carvalho, Benilton,¬†Campos, Orlando,¬†Cordeiro, Marco,¬†Kronmal, Richard,¬†Bluemke, David,¬†and Lima, Jo√£o
    Journal of Cardiovascular Magnetic Resonance Nov 2007

2006

  1. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
    Carvalho, B., Bengtsson, H., Speed, T. P., and Irizarry, R. A.
    Biostatistics Dec 2006
  2. Subclinical Atherosclerosis and Incipient Regional Myocardial Dysfunction in Asymptomatic individuals: the Multi-Ethnic Study of Atherosclerosis (MESA)
    Fernandes, Ver√īnica R. S.,¬†Polak, Joseph F.,¬†Edvardsen, Thor,¬†Carvalho, Benilton,¬†Gomes, Antoinette,¬†Bluemke, David A.,¬†Nasir, Khurram,¬†O‚ÄôLeary, Daniel H.,¬†and Lima, Jo√£o A. C.
    Journal of the American College of Cardiology Jun 2006