papers.bib

---
---

@ARTICLE{Canto2022-qr,
  title     = "Benchmarking the proteomic profile of animal models of mesial
               temporal epilepsy",
  author    = "Canto, Amanda M and Godoi, Alexandre B and Matos, Alexandre H B
               and Geraldis, Jaqueline C and Rogerio, Fabio and Alvim, Marina K
               M and Yasuda, Clarissa L and Ghizoni, Enrico and Tedeschi,
               Helder and Veiga, Diogo F T and Henning, Barbara and Souza,
               Welliton and Rocha, Cristiane S and Vieira, Andr{\'e} S and
               Dias, Elayne V and Carvalho, Benilton S and Gilioli, Rovilson
               and Arul, Albert B and Robinson, Ren{\~a} A S and Cendes,
               Fernando and Lopes-Cendes, Iscia",
  abstract  = "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.",
  journal   = "Ann. Clin. Transl. Neurol.",
  publisher = "Wiley",
  volume    =  9,
  number    =  4,
  pages     = "454--467",
  month     =  apr,
  year      =  2022,
  copyright = "http://creativecommons.org/licenses/by-nc-nd/4.0/",
  language  = "en"
}

@ARTICLE{Lacarrubba-Flores2024-rk,
  title    = "A mesomelic skeletal dysplasia, Kantaputra-like, not related to
              {HOXD} cluster region, and with phenotypic gender differences",
  author   = "Lacarrubba-Flores, Maria Dora Jazmin and da Costa Silveira,
              Karina and Silveira, Cynthia and Carvalho, Benilton S and
              Cavalcanti, Denise Pontes",
  abstract = "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.",
  journal  = "Am. J. Med. Genet. A",
  volume   =  194,
  number   =  2,
  pages    = "328--336",
  month    =  feb,
  year     =  2024,
  keywords = "Kantaputra dysplasia; mesomelic shortening; skeletal dysplasia",
  language = "en"
}

@ARTICLE{Silva-Costa2022-vo,
  title     = "Plasma proteomic signature of major depressive episode in the
               elderly",
  author    = "Silva-Costa, Licia C and Smith, Bradley J and Carregari, Victor
               Corasolla and Souza, Gustavo H M F and Vieira, Erica M and
               Mendes-Silva, Ana Paula and de Almeida, Val{\'e}ria and
               Carvalho, Benilton S and Diniz, Breno S and Martins-de-Souza,
               Daniel",
  abstract  = "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.",
  journal   = "J. Proteomics",
  publisher = "Elsevier BV",
  volume    =  269,
  number    =  104713,
  pages     = "104713",
  month     =  oct,
  year      =  2022,
  keywords  = "Aging; Late-life depression; Proteomics; Senescence",
  language  = "en"
}

@article{ritchie_2009_rbioconductor,
  author = {Ritchie, M. E. and Carvalho, B. S. and Hetrick, K. N. and Tavare, S. and Irizarry, R. A.},
  month = {08},
  pages = {2621-2623},
  title = {R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips},
  doi = {10.1093/bioinformatics/btp470},
  urldate = {2020-03-14},
  volume = {25},
  year = {2009},
  journal = {Bioinformatics}
}

@article{carvalho_2009_quantifying,
  author = {Carvalho, Benilton S. and Louis, Thomas A. and Irizarry, Rafael A.},
  month = {11},
  pages = {242-249},
  title = {Quantifying uncertainty in genotype calls},
  doi = {10.1093/bioinformatics/btp624},
  urldate = {2020-05-07},
  volume = {26},
  year = {2009},
  journal = {Bioinformatics},
  selected = {true}
}

@article{carvalho_2010_a,
  author = {Carvalho, Benilton S. and Irizarry, Rafael A.},
  month = {08},
  pages = {2363-2367},
  title = {A framework for oligonucleotide microarray preprocessing},
  doi = {10.1093/bioinformatics/btq431},
  urldate = {2020-05-07},
  volume = {26},
  year = {2010},
  journal = {Bioinformatics},
  selected = {true}
}

@article{ritchie_2011_comparing,
  author = {Ritchie, Matthew E. and Liu, Ruijie and Carvalho, Benilton S. and Australia and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene) and Irizarry, Rafael A.},
  month = {03},
  pages = {68},
  title = {Comparing Genotyping Algorithms for Illumina's Infinium whole-genome SNP BeadChips},
  doi = {10.1186/1471-2105-12-68},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/21385424},
  urldate = {2022-02-07},
  volume = {12},
  year = {2011},
  journal = {BMC Bioinformatics}
}

@article{carvalho_2013_the,
  author = {Carvalho, Benilton S. and Rustici, Gabriella},
  month = {09},
  pages = {538–547},
  title = {The Challenges of Delivering Bioinformatics Training in the Analysis of high-throughput Data},
  doi = {10.1093/bib/bbt018},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/23543353},
  urldate = {2022-02-07},
  volume = {14},
  year = {2013},
  journal = {Briefings in Bioinformatics}
}

@article{huber_2015_orchestrating,
  author = {Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S and Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian and Hansen, Kasper D and Irizarry, Rafael A and Lawrence, Michael and Love, Michael I and MacDonald, James and Obenchain, Valerie and Oleś, Andrzej K and Pagès, Hervé and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin},
  month = {01},
  pages = {115-121},
  title = {Orchestrating high-throughput Genomic Analysis with Bioconductor},
  doi = {10.1038/nmeth.3252},
  urldate = {2020-05-06},
  volume = {12},
  year = {2015},
  journal = {Nature Methods},
  selected = {true}
}

@article{wajnberg_2015_combined,
  author = {Wajnberg, Gabriel and Carvalho, Benilton S. and Ferreira, Carlos G. and Passetti, Fabio},
  pages = {902419},
  title = {Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma},
  doi = {10.1155/2015/902419},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/26185765},
  urldate = {2022-02-07},
  volume = {2015},
  year = {2015},
  journal = {BioMed Research International}
}

@article{carvalho_2016_working,
  author = {Carvalho, Benilton S.},
  pages = {145-159},
  title = {Working with Oligonucleotide Arrays},
  doi = {10.1007/978-1-4939-3578-9_7},
  url = {https://rd.springer.com/protocol/10.1007%2F978-1-4939-3578-9_7},
  urldate = {2019-11-29},
  volume = {1418},
  year = {2016},
  journal = {Methods in Molecular Biology}
}

@article{silvaalves_2017_a,
  author = {Silva-Alves, Mariana S. and Secolin, Rodrigo and Carvalho, Benilton S. and Yasuda, Clarissa L. and Bilevicius, Elizabeth and Alvim, Marina K. M. and Santos, Renato O. and Maurer-Morelli, Claudia V. and Cendes, Fernando and Lopes-Cendes, Iscia},
  pages = {e0169214},
  title = {A Prediction Algorithm for Drug Response in Patients with Mesial Temporal Lobe Epilepsy Based on Clinical and Genetic Information},
  doi = {10.1371/journal.pone.0169214},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/28052106},
  urldate = {2022-02-07},
  volume = {12},
  year = {2017},
  journal = {PloS One}
}

@article{avansini_2017_microrna,
  author = {Avansini, Simoni H. and de Sousa Lima, Beatriz Pereira and Secolin, Rodrigo and Santos, Marilza L. and Coan, Ana Carolina and Vieira, André S. and Torres, Fábio R. and Carvalho, Benilton S. and Alvim, Marina K. M. and Morita, Márcia E. and Yasuda, Clarissa L. and Pimentel-Silva, Luciana R. and Dogini, Danyella B. and Rogerio, Fabio and Cendes, Fernando and Lopes-Cendes, Iscia},
  pages = {e0173060},
  title = {MicroRNA hsa-miR-134 Is a Circulating Biomarker for Mesial Temporal Lobe Epilepsy},
  doi = {10.1371/journal.pone.0173060},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/28384161},
  urldate = {2022-02-07},
  volume = {12},
  year = {2017},
  journal = {PloS One}
}

@article{robertson_2017_comprehensive,
  author = {Robertson, A Gordon and Kim, Jaegil and Al-Ahmadie, Hikmat and Bellmunt, Joaquim and Guo, Guangwu and Cherniack, Andrew D and Hinoue, Toshinori and Laird, Peter W and Hoadley, Katherine A and Akbani, Rehan and Castro, Mauro A A and Gibb, Ewan A and Kanchi, Rupa S and Gordenin, Dmitry A and Shukla, Sachet A and Sanchez-Vega, Francisco and Hansel, Donna E and Czerniak, Bogdan A and Reuter, Victor E and Su, Xiaoping and de Sa Carvalho, Benilton and Chagas, Vinicius S and Mungall, Karen L and Sadeghi, Sara and Pedamallu, Chandra Sekhar and Lu, Yiling and Klimczak, Leszek J and Zhang, Jiexin and Choo, Caleb and Ojesina, Akinyemi I and Bullman, Susan and Leraas, Kristen M and Lichtenberg, Tara M and Wu, Catherine J and Schultz, Nicholaus and Getz, Gad and Meyerson, Matthew and Mills, Gordon B and McConkey, David J and TCGA Research Network,  and Weinstein, John N and Kwiatkowski, David J and Lerner, Seth P},
  pages = {540-556.e25},
  title = {Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer},
  doi = {10.1016/j.cell.2017.09.007},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/28988769},
  urldate = {2020-01-30},
  volume = {171},
  year = {2017},
  journal = {Cell},
  selected = {true}
}

@article{avansini_2018_dysregulation,
  author = {Avansini, Simoni H. and Torres, Fábio R. and Vieira, André S. and Dogini, Danyella B. and Rogerio, Fabio and Coan, Ana C. and Morita, Marcia E. and Guerreiro, Marilisa M. and Yasuda, Clarissa L. and Secolin, Rodrigo and Carvalho, Benilton S. and Borges, Murilo G. and Almeida, Vanessa S. and Araújo, Patrícia A. O. R. and Queiroz, Luciano and Cendes, Fernando and Lopes-Cendes, Iscia},
  month = {03},
  pages = {623–635},
  title = {Dysregulation of NEUROG2 Plays a Key Role in Focal Cortical Dysplasia},
  doi = {10.1002/ana.25187},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/29461643},
  urldate = {2022-02-07},
  volume = {83},
  year = {2018},
  journal = {Annals of Neurology}
}

@article{gonsales_2019_multimodal,
  author = {Gonsales, Marina C. and Montenegro, Maria Augusta and Preto, Paula and Guerreiro, Marilisa M. and Coan, Ana Carolina and Quast, Monica Paiva and Carvalho, Benilton S. and Lopes-Cendes, Iscia},
  pages = {289},
  title = {Multimodal Analysis of SCN1A Missense Variants Improves Interpretation of Clinically Relevant Variants in Dravet Syndrome},
  doi = {10.3389/fneur.2019.00289},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/31001185},
  urldate = {2022-02-07},
  volume = {10},
  year = {2019},
  journal = {Frontiers in Neurology}
}

@article{rodriguesperes_2019_copy,
  author = {Rodrigues-Peres, Raquel M. and de S Carvalho, Benilton and Anurag, Meenakshi and Lei, Jonathan T. and Conz, Livia and Gonçalves, Rodrigo and Cardoso Filho, Cássio and Ramalho, Susana and de Paiva, Geisilene R. and Derchain, Sophie F. M. and Lopes-Cendes, Iscia and Ellis, Matthew J. and Sarian, Luis O.},
  month = {07},
  pages = {e00750},
  title = {Copy Number Alterations Associated with Clinical Features in an Underrepresented Population with Breast Cancer},
  doi = {10.1002/mgg3.750},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/31099189},
  urldate = {2022-02-07},
  volume = {7},
  year = {2019},
  journal = {Molecular Genetics & Genomic Medicine}
}

@article{secolin_2019_distribution,
  author = {Secolin, Rodrigo and Mas-Sandoval, Alex and Arauna, Lara R. and Torres, Fábio R. and de Araujo, Tânia K. and Santos, Marilza L. and Rocha, Cristiane S. and Carvalho, Benilton S. and Cendes, Fernando and Lopes-Cendes, Iscia and Comas, David},
  month = {09},
  pages = {13900},
  title = {Distribution of Local Ancestry and Evidence of Adaptation in Admixed Populations},
  doi = {10.1038/s41598-019-50362-2},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/31554886},
  urldate = {2022-02-07},
  volume = {9},
  year = {2019},
  journal = {Scientific Reports},
  selected = {true}
}

@article{docanto_2020_laser,
  author = {do Canto, Amanda M. and Vieira, André S. and H B Matos, Alexandre and Carvalho, Benilton S. and Henning, Barbara and Norwood, Braxton A. and Bauer, Sebastian and Rosenow, Felix and Gilioli, Rovilson and Cendes, Fernando and Lopes-Cendes, Iscia},
  month = {03},
  pages = {4412},
  title = {Laser microdissection-based Microproteomics of the Hippocampus of a Rat Epilepsy Model Reveals Regional Differences in Protein Abundances},
  doi = {10.1038/s41598-020-61401-8},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/32157145},
  urldate = {2022-02-07},
  volume = {10},
  year = {2020},
  journal = {Scientific Reports}
}

@article{borges_2020_methodological,
  author = {Borges, Murilo G. and Rocha, Cristiane S. and Carvalho, Benilton S. and Lopes-Cendes, Iscia},
  pages = {e20190270},
  title = {Methodological Differences Can Affect Sequencing Depth with a Possible Impact on the Accuracy of Genetic Diagnosis},
  doi = {10.1590/1678-4685-GMB-2019-0270},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/32343762},
  urldate = {2022-02-07},
  volume = {43},
  year = {2020},
  journal = {Genetics and Molecular Biology}
}

@article{garciarosa_2020_blood,
  author = {Garcia-Rosa, Sheila and Carvalho, Benilton S. and Guest, Paul C. and Steiner, Johann and Martins-de-Souza, Daniel},
  month = {07},
  pages = {103813},
  title = {Blood plasma proteomic modulation induced by olanzapine and risperidone in schizophrenia patients},
  doi = {10.1016/j.jprot.2020.103813},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/32464195},
  urldate = {2022-02-07},
  volume = {224},
  year = {2020},
  journal = {Journal of Proteomics}
}

@article{loureno_2020_inherited,
  author = {Lourenço, Gustavo Jacob and Oliveira, Cristiane and Carvalho, Benilton Sá and Torricelli, Caroline and Silva, Janet Keller and Gomez, Gabriela Vilas Bôas and Rinck-Junior, José Augusto and Oliveira, Wesley Lima and Vazquez, Vinicius Lima and Serrano, Sergio Vicente and Moraes, Aparecida Machado and Lima, Carmen Silvia Passos},
  month = {07},
  pages = {12129},
  title = {Inherited Variations in Human pigmentation-related Genes Modulate Cutaneous Melanoma Risk and Clinicopathological Features in Brazilian Population},
  doi = {10.1038/s41598-020-68945-9},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/32699307},
  urldate = {2022-02-07},
  volume = {10},
  year = {2020},
  journal = {Scientific Reports}
}

@article{canto_2021_multiomics,
  author = {Canto, Amanda M. and Matos, Alexandre H. B. and Godoi, Alexandre B. and Vieira, André S. and Aoyama, Beatriz B. and Rocha, Cristiane S. and Henning, Barbara and Carvalho, Benilton S. and Pascoal, Vinicius D. B. and Veiga, Diogo F. T. and Gilioli, Rovilson and Cendes, Fernando and Lopes-Cendes, Iscia},
  month = {02},
  pages = {122–139},
  title = {Multi-omics Analysis Suggests Enhanced Epileptogenesis in the Cornu Ammonis 3 of the Pilocarpine Model of Mesial Temporal Lobe Epilepsy},
  doi = {10.1002/hipo.23268},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/33037862},
  urldate = {2022-02-07},
  volume = {31},
  year = {2021},
  journal = {Hippocampus}
}

@article{rocha_2020_the,
  author = {Rocha, Cristiane S. and Secolin, Rodrigo and Rodrigues, Maíra R. and Carvalho, Benilton S. and Lopes-Cendes, Iscia},
  month = {10},
  pages = {1–7},
  title = {The Brazilian Initiative on Precision Medicine (BIPMed): Fostering Genomic data-sharing of Underrepresented Populations},
  doi = {10.1038/s41525-020-00149-6},
  url = {https://www.nature.com/articles/s41525-020-00149-6},
  urldate = {2021-12-06},
  volume = {5},
  year = {2020},
  journal = {npj Genomic Medicine},
  selected = {true}
}

@article{silveira_2021_molecular,
  author = {Silveira, Karina C. and Kanazawa, Thatiane Y. and Silveira, Cynthia and Lacarrubba-Flores, Maria D. J. and Carvalho, Benilton S. and Cavalcanti, Denise P.},
  month = {09},
  pages = {396–408},
  title = {Molecular Diagnosis in a Cohort of 114 Patients with Rare Skeletal Dysplasias},
  doi = {10.1002/ajmg.c.31937},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/34529350},
  urldate = {2022-02-07},
  volume = {187},
  year = {2021},
  journal = {American Journal of Medical Genetics. Part C, Seminars in Medical Genetics}
}

@article{way_2021_a,
  author = {Way, Gregory P. and Greene, Casey S. and Carninci, Piero and Carvalho, Benilton S. and de Hoon, Michiel and Finley, Stacey D. and Gosline, Sara J. C. and Lȇ Cao, Kim-Anh and Lee, Jerry S. H. and Marchionni, Luigi and Robine, Nicolas and Sindi, Suzanne S. and Theis, Fabian J. and Yang, Jean Y. H. and Carpenter, Anne E. and Fertig, Elana J.},
  month = {10},
  pages = {e3001419},
  title = {A Field Guide to Cultivating Computational Biology},
  doi = {10.1371/journal.pbio.3001419},
  url = {https://www.ncbi.nlm.nih.gov/pubmed/34618807},
  urldate = {2022-02-07},
  volume = {19},
  year = {2021},
  journal = {PLoS biology},
  selected = {true}
}

@article{hounkpe_2020_identification,
  author = {Hounkpe, Bidossessi Wilfried and Benatti, Rafaela de Oliveira and Carvalho, Benilton de Sá and De Paula, Erich Vinicius},
  pages = {e0235501},
  title = {Identification of Common and Divergent Gene Expression Signatures in Patients with Venous and Arterial Thrombosis Using Data from Public Repositories},
  doi = {10.1371/journal.pone.0235501},
  url = {https://pubmed.ncbi.nlm.nih.gov/32780732/},
  urldate = {2022-02-07},
  volume = {15},
  year = {2020},
  journal = {PloS One}
}

@article{corbi_2020_circulating,
  author = {Corbi, Sâmia C. T. and de Vasconcellos, Jaira F. and Bastos, Alliny S. and Bussaneli, Diego Girotto and da Silva, Bárbara Roque and Santos, Raquel Alves and Takahashi, Catarina S. and de S Rocha, Cristiane and Carvalho, Benilton de Sá and Maurer-Morelli, Cláudia V. and Orrico, Silvana R. P. and Barros, Silvana P. and Scarel-Caminaga, Raquel M.},
  month = {05},
  pages = {8145},
  title = {Circulating Lymphocytes and Monocytes Transcriptomic Analysis of Patients with Type 2 Diabetes mellitus, Dyslipidemia and Periodontitis},
  doi = {10.1038/s41598-020-65042-9},
  url = {https://pubmed.ncbi.nlm.nih.gov/32424199/},
  urldate = {2022-02-07},
  volume = {10},
  year = {2020},
  journal = {Scientific Reports}
}

@article{maruyama_2019_blood,
  author = {Maruyama, Sandra R. and Carvalho, Benilton and González-Porta, Mar and Rung, Johan and Brazma, Alvis and Gustavo Gardinassi, Luiz and Ferreira, Beatriz R. and Banin, Tamy M. and Veríssimo, Cecília J. and Katiki, Luciana M. and de Miranda-Santos, Isabel K. F.},
  pages = {53},
  title = {Blood Transcriptome Profile Induced by an Efficacious Vaccine Formulated with Salivary Antigens from Cattle Ticks},
  doi = {10.1038/s41541-019-0145-1},
  url = {https://pubmed.ncbi.nlm.nih.gov/31871773/},
  urldate = {2022-02-07},
  volume = {4},
  year = {2019},
  journal = {npj Vaccines}
}

@article{barbalho_2016_cyclooxygenase1,
  author = {Barbalho, Patrícia Gonçalves and Carvalho, Benilton de Sá and Lopes-Cendes, Iscia and Maurer-Morelli, Claudia Vianna},
  pages = {200},
  title = {Cyclooxygenase-1 as a Potential Therapeutic Target for Seizure Suppression: Evidences from Zebrafish Pentylenetetrazole-Seizure Model},
  doi = {10.3389/fneur.2016.00200},
  url = {https://pubmed.ncbi.nlm.nih.gov/27895618/},
  urldate = {2022-02-07},
  volume = {7},
  year = {2016},
  journal = {Frontiers in Neurology}
}

@article{deandrade_2016_micrornas424,
  author = {de Andrade, Helen M. T. and de Albuquerque, Milena and Avansini, Simoni H. and de S Rocha, Cristiane and Dogini, Danyella B. and Nucci, Anamarli and Carvalho, Benilton and Lopes-Cendes, Iscia and França, Marcondes C.},
  month = {09},
  pages = {19–24},
  title = {MicroRNAs-424 and 206 Are Potential Prognostic Markers in Spinal Onset Amyotrophic Lateral Sclerosis},
  doi = {10.1016/j.jns.2016.06.046},
  url = {https://pubmed.ncbi.nlm.nih.gov/27538595/},
  urldate = {2022-02-07},
  volume = {368},
  year = {2016},
  journal = {Journal of the Neurological Sciences}
}

@article{opdahl_2014_reply,
  author = {Opdahl, Anders and Ambale Venkatesh, Bharath and Fernandes, Veronica R. S. and Wu, Colin O. and Nasir, Khurram and Choi, Eui-Young and Almeida, Andre L. C. and Rosen, Boaz and Carvalho, Benilton and Edvardsen, Thor and Bluemke, David A. and Lima, João A. C.},
  month = {07},
  pages = {422},
  title = {Reply: Resting Heart rate: an Independent Predictor of Congestive Heart Failure},
  doi = {10.1016/j.jacc.2014.05.017},
  url = {https://pubmed.ncbi.nlm.nih.gov/25060383/},
  urldate = {2022-02-07},
  volume = {64},
  year = {2014},
  journal = {Journal of the American College of Cardiology}
}

@article{weaver_2014_ordering,
  author = {Weaver, Jamie M J and Ross-Innes, Caryn S and Shannon, Nicholas and Lynch, Andy G and Forshew, Tim and Barbera, Mariagnese and Murtaza, Muhammed and Ong, Chin-Ann J and Lao-Sirieix, Pierre and Dunning, Mark J and Smith, Laura and Smith, Mike L and Anderson, Charlotte L and Carvalho, Benilton and O'Donovan, Maria and Underwood, Timothy J and May, Andrew P and Grehan, Nicola and Hardwick, Richard and Davies, Jim and Oloumi, Arusha and Aparicio, Sam and Caldas, Carlos and Eldridge, Matthew D and Edwards, Paul A W and Rosenfeld, Nitzan and Tavaré, Simon and Fitzgerald, Rebecca C},
  month = {06},
  pages = {837-843},
  title = {Ordering of Mutations in Preinvasive Disease Stages of Esophageal Carcinogenesis},
  doi = {10.1038/ng.3013},
  urldate = {2021-02-12},
  volume = {46},
  year = {2014},
  journal = {Nature Genetics},
  selected = {true}
}

@article{opdahl_2014_resting,
  author = {Opdahl, Anders and Ambale Venkatesh, Bharath and Fernandes, Veronica R. S. and Wu, Colin O. and Nasir, Khurram and Choi, Eui-Young and Almeida, Andre L. C. and Rosen, Boaz and Carvalho, Benilton and Edvardsen, Thor and Bluemke, David A. and Lima, João A. C.},
  month = {04},
  pages = {1182–1189},
  title = {Resting Heart Rate as Predictor for Left Ventricular Dysfunction and Heart failure: MESA (Multi-Ethnic Study of Atherosclerosis)},
  doi = {10.1016/j.jacc.2013.11.027},
  url = {https://pubmed.ncbi.nlm.nih.gov/24412444/},
  urldate = {2022-02-07},
  volume = {63},
  year = {2014},
  journal = {Journal of the American College of Cardiology}
}

@article{scharpf_2011_using,
  author = {Scharpf, Robert B. and Irizarry, Rafael A. and Ritchie, Matthew E. and Carvalho, Benilton and Ruczinski, Ingo},
  month = {05},
  pages = {1–32},
  title = {Using the R Package crlmm for Genotyping and Copy Number Estimation},
  url = {https://pubmed.ncbi.nlm.nih.gov/22523482/},
  urldate = {2022-02-07},
  volume = {40},
  year = {2011},
  journal = {Journal of Statistical Software},
  selected = {true}
}

@article{yegnasubramanian_2011_chromosomewide,
  author = {Yegnasubramanian, Srinivasan and Wu, Zhijin and Haffner, Michael C. and Esopi, David and Aryee, Martin J. and Badrinath, Raghav and He, Tony L. and Morgan, James D. and Carvalho, Benilton and Zheng, Qizhi and De Marzo, Angelo M. and Irizarry, Rafael A. and Nelson, William G.},
  month = {06},
  pages = {313},
  title = {Chromosome-wide Mapping of DNA Methylation Patterns in Normal and Malignant Prostate Cells Reveals Pervasive Methylation of gene-associated and Conserved Intergenic Sequences},
  doi = {10.1186/1471-2164-12-313},
  url = {https://pubmed.ncbi.nlm.nih.gov/21669002/},
  urldate = {2022-02-07},
  volume = {12},
  year = {2011},
  journal = {BMC Genomics}
}

@article{halperstromberg_2011_performance,
  author = {Halper-Stromberg, Eitan and Frelin, Laurence and Ruczinski, Ingo and Scharpf, Robert and Jie, Chunfa and Carvalho, Benilton and Hao, Haiping and Hetrick, Kurt and Jedlicka, Anne and Dziedzic, Amanda and Doheny, Kim and Scott, Alan F. and Baylin, Steve and Pevsner, Jonathan and Spencer, Forrest and Irizarry, Rafael A.},
  month = {04},
  pages = {1052–1060},
  title = {Performance Assessment of Copy Number Microarray Platforms Using a spike-in Experiment},
  doi = {10.1093/bioinformatics/btr106},
  url = {https://pubmed.ncbi.nlm.nih.gov/21478196/},
  urldate = {2022-02-07},
  volume = {27},
  year = {2011},
  journal = {Bioinformatics (Oxford, England)}
}

@article{scharpf_2010_a,
  author = {Scharpf, R. B. and Ruczinski, I. and Carvalho, B. and Doan, B. and Chakravarti, A. and Irizarry, R. A.},
  month = {07},
  pages = {33-50},
  title = {A Multilevel Model to Address Batch Effects in Copy Number Estimation Using SNP Arrays},
  doi = {10.1093/biostatistics/kxq043},
  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006124/},
  urldate = {2019-11-29},
  volume = {12},
  year = {2010},
  journal = {Biostatistics}
}

@article{wang_2008_estimating,
  author = {Wang, Wenyi and Carvalho, Benilton and Miller, Nathaniel D. and Pevsner, Jonathan and Chakravarti, Aravinda and Irizarry, Rafael A.},
  month = {09},
  pages = {857-866},
  title = {Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models},
  doi = {10.1089/cmb.2007.0148},
  urldate = {2021-10-22},
  volume = {15},
  year = {2008},
  journal = {Journal of Computational Biology}
}

@article{tuefferd_2008_genomewide,
  author = {Tuefferd, Marianne and De Bondt, An and Van Den Wyngaert, Ilse and Talloen, Willem and Verbeke, Tobias and Carvalho, Benilton and Clevert, Djork-Arne and Alifano, Marco and Raghavan, Nandini and Amaratunga, Dhammika and Göhlmann, Hinrich and Broët, Philippe and Camilleri-Broët, Sophie},
  month = {11},
  pages = {957–964},
  title = {Genome-wide Copy Number Alterations Detection in Fresh Frozen and Matched FFPE Samples Using SNP 6.0 Arrays},
  doi = {10.1002/gcc.20599},
  url = {https://pubmed.ncbi.nlm.nih.gov/18663747/},
  urldate = {2022-02-07},
  volume = {47},
  year = {2008},
  journal = {Genes, Chromosomes & Cancer}
}

@article{lin_2008_validation,
  author = {Lin, Shin and Carvalho, Benilton and Cutler, David J. and Arking, Dan E. and Chakravarti, Aravinda and Irizarry, Rafael A.},
  month = {04},
  pages = {R63},
  title = {Validation and Extension of an Empirical Bayes Method for SNP Calling on Affymetrix Microarrays},
  doi = {10.1186/gb-2008-9-4-r63},
  url = {https://pubmed.ncbi.nlm.nih.gov/18387188/},
  urldate = {2022-02-07},
  volume = {9},
  year = {2008},
  journal = {Genome Biology}
}

@article{irizarry_2008_comprehensive,
  author = {Irizarry, R. A. and Ladd-Acosta, C. and Carvalho, B. and Wu, H. and Brandenburg, S. A. and Jeddeloh, J. A. and Wen, B. and Feinberg, A. P.},
  month = {02},
  pages = {780-790},
  title = {Comprehensive high-throughput Arrays for Relative Methylation (CHARM)},
  doi = {10.1101/gr.7301508},
  urldate = {2020-12-18},
  volume = {18},
  year = {2008},
  journal = {Genome Research},
  selected = {true}
}

@article{fernandes_2007_the,
  author = {Fernandes, Verônica Rolim and Edvardsen, Thor and Rosen, Boaz and Carvalho, Benilton and Campos, Orlando and Cordeiro, Marco and Kronmal, Richard and Bluemke, David and Lima, João},
  month = {11},
  pages = {921-930},
  title = {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},
  doi = {10.1080/10976640701693824},
  urldate = {2019-12-04},
  volume = {9},
  year = {2007},
  journal = {Journal of Cardiovascular Magnetic Resonance}
}

@article{fernandes_2008_arterial,
  author = {Fernandes, Verônica Rolim S. and Polak, Joseph F. and Cheng, Susan and Rosen, Boaz D. and Carvalho, Benilton and Nasir, Khurram and McClelland, Robyn and Hundley, Gregory and Pearson, Greg and O'Leary, Daniel H. and Bluemke, David A. and Lima, João A. C.},
  month = {01},
  pages = {194–201},
  title = {Arterial Stiffness Is Associated with Regional Ventricular Systolic and Diastolic dysfunction: the Multi-Ethnic Study of Atherosclerosis},
  doi = {10.1161/ATVBAHA.107.156950},
  url = {https://pubmed.ncbi.nlm.nih.gov/17962621/},
  urldate = {2022-02-07},
  volume = {28},
  year = {2008},
  journal = {Arteriosclerosis, Thrombosis, and Vascular Biology}
}

@article{carvalho_2006_exploration,
  author = {Carvalho, B. and Bengtsson, H. and Speed, T. P. and Irizarry, R. A.},
  month = {12},
  pages = {485-499},
  title = {Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data},
  doi = {10.1093/biostatistics/kxl042},
  urldate = {2020-04-06},
  volume = {8},
  year = {2006},
  journal = {Biostatistics},
  selected = {true}
}

@article{fernandes_2006_subclinical,
  author = {Fernandes, Verônica R. S. and Polak, Joseph F. and Edvardsen, Thor and Carvalho, Benilton and Gomes, Antoinette and Bluemke, David A. and Nasir, Khurram and O'Leary, Daniel H. and Lima, João A. C.},
  month = {06},
  pages = {2420–2428},
  title = {Subclinical Atherosclerosis and Incipient Regional Myocardial Dysfunction in Asymptomatic individuals: the Multi-Ethnic Study of Atherosclerosis (MESA)},
  doi = {10.1016/j.jacc.2005.12.075},
  url = {https://pubmed.ncbi.nlm.nih.gov/16781369/},
  urldate = {2022-02-07},
  volume = {47},
  year = {2006},
  journal = {Journal of the American College of Cardiology}
}