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Rafael A. Irizarry
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- affiliation: Harvard University, Cambridge, USA
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2010 – 2019
- 2016
- [i1]Stephanie C. Hicks, Rafael A. Irizarry:
A Guide to Teaching Data Science. CoRR abs/1612.07140 (2016) - 2015
- [j30]Christopher J. Mitchell, Derese Getnet, Min Sik Kim, Srinivas Manda Srikanth, Praveen Kumar, Tai-Chung Huang, Sneha M. Pinto, Nirujogi Raja Sekhar, Mio Iwasaki, Patrick G. Shaw, Xinyan Wu, Jun Zhong, Raghothama Chaerkady, Arivusudar Marimuthu, Babylakshmi Muthusamy, Nandini A. Sahasrabuddhe, Rajesh Raju, Caitlyn Bowman, Ludmila V. Danilova, Jevon Cutler, Dhanashree S. Kelkar, Charles G. Drake, T. S. Keshava Prasad, Luigi Marchionni, Peter N. Murakami, Alan F. Scott, Leming Shi, Jean Thierry-Mieg, Danielle Thierry-Mieg, Rafael A. Irizarry, Leslie Cope, Yasushi Ishihama, Charles Wang, Harsha Gowda, Akhilesh Pandey:
A multi-omic analysis of human naïve CD4+ T cells. BMC Syst. Biol. 9: 75 (2015) - 2014
- [j29]Martin J. Aryee, Andrew E. Jaffe, Héctor Corrada Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry:
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinform. 30(10): 1363-1369 (2014) - [j28]Eitan Halper-Stromberg, Jared Steranka, Kathleen H. Burns, Sarven Sabunciyan, Rafael A. Irizarry:
Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinform. 30(11): 1514-1521 (2014) - [j27]Ruijie Liu, Zhiyin Dai, Meredith Yeager, Rafael A. Irizarry, Matthew E. Ritchie:
KRLMM: an adaptive genotype calling method for common and low frequency variants. BMC Bioinform. 15: 158 (2014) - [j26]Matthew N. McCall, Harris A. Jaffee, Susan J. Zelisko, Neeraj Sinha, Guido J. E. K. Hooiveld, Rafael A. Irizarry, Michael J. Zilliox:
The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Res. 42(Database-Issue): 938-943 (2014) - [c4]Juemin Yang, Fang Han, Rafael A. Irizarry, Han Liu:
Context Aware Group Nearest Shrunken Centroids in Large-Scale Genomic Studies. AISTATS 2014: 1051-1059 - 2013
- [j25]George Wu, Jason T. Yustein, Matthew N. McCall, Michael J. Zilliox, Rafael A. Irizarry, Karen Zeller, Chi V. Dang, Hongkai Ji:
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinform. 29(9): 1182-1189 (2013) - 2012
- [j24]Matthew N. McCall, Harris A. Jaffee, Rafael A. Irizarry:
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinform. 28(23): 3153-3154 (2012) - [j23]Weiliang Shi, Grace Wahba, Rafael A. Irizarry, Héctor Corrada Bravo, Stephen J. Wright:
The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC Bioinform. 13: 98 (2012) - [j22]Héctor Corrada Bravo, Vasyl Pihur, Matthew N. McCall, Rafael A. Irizarry, Jeffrey T. Leek:
Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinform. 13: 272 (2012) - [j21]Kristof De Beuf, Joachim M. De Schrijver, Olivier Thas, Wim Van Criekinge, Rafael A. Irizarry, Lieven Clement:
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinform. 13: 303 (2012) - 2011
- [j20]Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert B. Scharpf, Chunfa Jie, Benilton S. Carvalho, Haiping Hao, Kurt N. Hetrick, Anne Jedlicka, Amanda Dziedzic, Kim Doheny, Alan F. Scott, Steve Baylin, Jonathan Pevsner, Forrest Spencer, Rafael A. Irizarry:
Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinform. 27(8): 1052-1060 (2011) - [j19]Matthew E. Ritchie, Ruijie Liu, Benilton S. Carvalho, Rafael A. Irizarry:
Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. BMC Bioinform. 12: 68 (2011) - [j18]Matthew N. McCall, Peter N. Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry:
Assessments of Affymetrix GeneChip Microarray Quality for Laboratories and Single Samples. BMC Bioinform. 12: 137 (2011) - [j17]Matthew N. McCall, Rafael A. Irizarry:
Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinform. 12: 369 (2011) - [j16]Matthew N. McCall, Karan Uppal, Harris A. Jaffee, Michael J. Zilliox, Rafael A. Irizarry:
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res. 39(Database-Issue): 1011-1015 (2011) - 2010
- [j15]Benilton S. Carvalho, Thomas A. Louis, Rafael A. Irizarry:
Quantifying uncertainty in genotype calls. Bioinform. 26(2): 242-249 (2010) - [j14]Benilton S. Carvalho, Rafael A. Irizarry:
A framework for oligonucleotide microarray preprocessing. Bioinform. 26(19): 2363-2367 (2010)
2000 – 2009
- 2009
- [j13]Matthew E. Ritchie, Benilton S. Carvalho, Kurt N. Hetrick, Simon Tavaré, Rafael A. Irizarry:
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinform. 25(19): 2621-2623 (2009) - 2008
- [j12]Henrik Bengtsson, Rafael A. Irizarry, Benilton S. Carvalho, Terence P. Speed:
Estimation and assessment of raw copy numbers at the single locus level. Bioinform. 24(6): 759-767 (2008) - [j11]Wenyi Wang, Benilton S. Carvalho, Nathaniel D. Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry:
Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models. J. Comput. Biol. 15(7): 857-866 (2008) - 2007
- [c3]Wenyi Wang, Benilton S. Carvalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, Rafael A. Irizarry:
Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models. RECOMB 2007: 137-150 - 2006
- [j10]Rafael A. Irizarry, Zhijin Wu, Harris A. Jaffee:
Comparison of Affymetrix GeneChip expression measures. Bioinform. 22(7): 789-794 (2006) - [j9]Daniel S. Yuan, Rafael A. Irizarry:
High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinform. 22(24): 3054-3060 (2006) - [j8]Simon Katz, Rafael A. Irizarry, Xue Lin, Mark Tripputi, Mark W. Porter:
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinform. 7: 464 (2006) - [j7]Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma:
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinform. 7: 489 (2006) - 2005
- [j6]Zhijin Wu, Rafael A. Irizarry:
Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays. J. Comput. Biol. 12(6): 882-893 (2005) - 2004
- [j5]Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry:
affy - analysis of Affymetrix GeneChip data at the probe level. Bioinform. 20(3): 307-315 (2004) - [j4]Leslie Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, Terence P. Speed:
A benchmark for Affymetrix GeneChip expression measures. Bioinform. 20(3): 323-331 (2004) - [c2]Zhijin Wu, Rafael A. Irizarry:
Stochastic models inspired by hybridization theory for short oligonucleotide arrays. RECOMB 2004: 98-106 - 2003
- [j3]Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed:
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinform. 19(2): 185-193 (2003) - 2000
- [j2]David R. Brillinger, Pedro Alberto Morettin, Rafael A. Irizarry, Chang Chiann:
Some wavelet-based analyses of Markov chain data. Signal Process. 80(8): 1607-1627 (2000)
1990 – 1999
- 1998
- [j1]David R. Brillinger, Rafael A. Irizarry:
An investigation of the second- and higher-order spectra of music. Signal Process. 65(2): 161-179 (1998) - [c1]Rafael A. Irizarry:
The Additive Sinusoidal Plus Residual Model: A Statistical Analysis. ICMC 1998
Coauthor Index
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