Meta-analysis of gut microbiome studies identifies disease-specific and shared responses von Duvallet, Claire, Gibbons, Sean M., Gurry, Thomas, Irizarry, Rafael A., Alm, Eric J.

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Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model von Townes, F William, Hicks, Stephanie C, Aryee, Martin J, Irizarry, Rafael A

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Robust decomposition of cell type mixtures in spatial transcriptomics von Cable, Dylan M., Murray, Evan, Zou, Luli S., Goeva, Aleksandrina, Macosko, Evan Z., Chen, Fei, Irizarry, Rafael A.

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A framework for oligonucleotide microarray preprocessing von Carvalho, Benilton S., Irizarry, Rafael A.

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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays von Aryee, Martin J., Jaffe, Andrew E., Corrada-Bravo, Hector, Ladd-Acosta, Christine, Feinberg, Andrew P., Hansen, Kasper D., Irizarry, Rafael A.

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Mortality in Puerto Rico after Hurricane Maria von Kishore, Nishant, Marqués, Domingo, Mahmud, Ayesha, Kiang, Mathew V, Rodriguez, Irmary, Fuller, Arlan, Ebner, Peggy, Sorensen, Cecilia, Racy, Fabio, Lemery, Jay, Maas, Leslie, Leaning, Jennifer, Irizarry, Rafael A, Balsari, Satchit, Buckee, Caroline O

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Accounting for cellular heterogeneity is critical in epigenome-wide association studies von Jaffe, Andrew E, Irizarry, Rafael A

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Stochastic Epigenetic Variation as a Driving Force of Development Evolutionary Adaptation, and Disease von Feinberg, Andrew P., Irizarry, Rafael A., Ellison, Peter T.

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Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing von Korthauer, Keegan, Chakraborty, Sutirtha, Benjamini, Yuval, Irizarry, Rafael A

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Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers von Townes, F. William, Irizarry, Rafael A.

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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions von Hansen, Kasper D, Langmead, Benjamin, Irizarry, Rafael A

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Tackling the widespread and critical impact of batch effects in high-throughput data von Irizarry, Rafael A, Leek, Jeffrey T, Scharpf, Robert B, Bravo, Héctor Corrada, Simcha, David, Langmead, Benjamin, Johnson, W. Evan, Geman, Donald, Baggerly, Keith

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methylCC: technology-independent estimation of cell type composition using differentially methylated regions von Hicks, Stephanie C, Irizarry, Rafael A

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Increased methylation variation in epigenetic domains across cancer types von Irizarry, Rafael A, Feinberg, Andrew P, Hansen, Kasper Daniel, Timp, Winston, Bravo, Héctor Corrada, Sabunciyan, Sarven, Langmead, Benjamin, McDonald, Oliver G, Wen, Bo, Wu, Hao, Liu, Yun, Diep, Dinh, Briem, Eirikur, Zhang, Kun

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Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells von Shinkai, Yoichi, Feinberg, Andrew P, Irizarry, Rafael A, Wu, Hao, Wen, Bo

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The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores von Irizarry, Rafael A, Feinberg, Andrew P, Ladd-Acosta, Christine, Wen, Bo, Wu, Zhijin, Montano, Carolina, Onyango, Patrick, Cui, Hengmi, Gabo, Kevin, Rongione, Michael, Webster, Maree, Ji, Hong, Potash, James B, Sabunciyan, Sarven

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MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens von Li, Wei, Xu, Han, Xiao, Tengfei, Cong, Le, Love, Michael I, Zhang, Feng, Irizarry, Rafael A, Liu, Jun S, Brown, Myles, Liu, X Shirley

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affy—analysis of Affymetrix GeneChip data at the probe level von Gautier, Laurent, Cope, Leslie, Bolstad, Benjamin M., Irizarry, Rafael A.

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Detection of allele-specific expression in spatial transcriptomics with spASE von Zou, Luli S, Cable, Dylan M, Barrera-Lopez, Irving A, Zhao, Tongtong, Murray, Evan, Aryee, Martin J, Chen, Fei, Irizarry, Rafael A

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Nucleocytosolic Acetyl-Coenzyme A Synthetase Is Required for Histone Acetylation and Global Transcription von Takahashi, Hidekazu, McCaffery, J. Michael, Irizarry, Rafael A., Boeke, Jef D.

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