Biostatistics and Computational Biology Lab

selected publications

1. Quantifying uncertainty in genotype calls

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

   Bioinformatics Nov 2009
2. A framework for oligonucleotide microarray preprocessing

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

   Bioinformatics Aug 2010
3. 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, Oleś, Andrzej K, Pagès, Hervé, Reyes, Alejandro, Shannon, Paul, Smyth, Gordon K, Tenenbaum, Dan, Waldron, Levi, and Morgan, Martin

   Nature Methods Jan 2015
4. 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 Jan 2017
5. Distribution of Local Ancestry and Evidence of Adaptation in Admixed Populations

   Secolin, Rodrigo, Mas-Sandoval, Alex, Arauna, Lara R., Torres, Fábio R., Araujo, Tânia K., Santos, Marilza L., Rocha, Cristiane S., Carvalho, Benilton S., Cendes, Fernando, Lopes-Cendes, Iscia, and Comas, David

   Scientific Reports Sep 2019
6. 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
7. 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
8. 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
9. 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
10. 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
11. 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