| Year |
Citation |
Score |
| 2020 |
Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, ... ... Irizarry RA, et al. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. PMID 32841603 DOI: 10.1016/J.Cell.2020.07.030 |
0.305 |
|
| 2020 |
Townes FW, Irizarry RA. Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers. Genome Biology. 21: 160. PMID 32620142 DOI: 10.1186/S13059-020-02078-0 |
0.36 |
|
| 2020 |
Nuzzo PV, Berchuck JE, Spisak S, Korthauer K, Nassar A, Abou Alaiwi S, Chakravarthy A, Shen SY, Bakouny Z, Boccardo F, Baca S, Lee GM, Chang SL, Waikar S, Sonpavde G, ... Irizarry RA, et al. Sensitive detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Journal of Clinical Oncology. 38: 728-728. DOI: 10.1200/Jco.2020.38.6_Suppl.728 |
0.303 |
|
| 2019 |
Townes FW, Hicks SC, Aryee MJ, Irizarry RA. Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Genome Biology. 20: 295. PMID 31870412 DOI: 10.1186/S13059-019-1861-6 |
0.342 |
|
| 2019 |
Hicks SC, Irizarry RA. methylCC: technology-independent estimation of cell type composition using differentially methylated regions. Genome Biology. 20: 261. PMID 31783894 DOI: 10.1186/S13059-019-1827-8 |
0.352 |
|
| 2019 |
McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP. A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs. Development (Cambridge, England). 146. PMID 30923056 DOI: 10.1242/Dev.175265 |
0.343 |
|
| 2018 |
Benjamini Y, Taylor J, Irizarry RA. Selection-Corrected Statistical Inference for Region Detection With High-Throughput Assays. Journal of the American Statistical Association. 114: 1351-1365. PMID 36312875 DOI: 10.1080/01621459.2018.1498347 |
0.324 |
|
| 2018 |
Korthauer K, Chakraborty S, Benjamini Y, Irizarry RA. Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing. Biostatistics (Oxford, England). PMID 29481604 DOI: 10.1093/Biostatistics/Kxy007 |
0.406 |
|
| 2017 |
Hicks SC, Townes FW, Teng M, Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics (Oxford, England). PMID 29121214 DOI: 10.1093/Biostatistics/Kxx053 |
0.373 |
|
| 2017 |
Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics (Oxford, England). PMID 29036413 DOI: 10.1093/Biostatistics/Kxx028 |
0.336 |
|
| 2017 |
Teng M, Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Research. PMID 29025895 DOI: 10.1101/Gr.220673.117 |
0.374 |
|
| 2017 |
Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biology. 18: 84. PMID 28482897 DOI: 10.1186/S13059-017-1218-Y |
0.345 |
|
| 2017 |
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods. PMID 28263959 DOI: 10.1038/Nmeth.4197 |
0.361 |
|
| 2017 |
Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, et al. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Research. PMID 28126923 DOI: 10.1093/Nar/Gkx026 |
0.379 |
|
| 2016 |
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Research. PMID 27694310 DOI: 10.1093/Nar/Gkw852 |
0.403 |
|
| 2016 |
Love MI, Hogenesch JB, Irizarry RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nature Biotechnology. PMID 27669167 DOI: 10.1038/Nbt.3682 |
0.367 |
|
| 2016 |
Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biology. 17: 74. PMID 27107712 DOI: 10.1186/S13059-016-0940-1 |
0.351 |
|
| 2016 |
Nakayama R, Williams RT, Cassel SH, Teng M, Irizarry RA, Demetri GD, Kadoch C. Abstract 2658: Genome-wide mistargeting of oncogenic SWI/SNF(BAF) complexes in SMARCB1(BAF47)-deficient sarcomas Cancer Research. 76: 2658-2658. DOI: 10.1158/1538-7445.Am2016-2658 |
0.335 |
|
| 2015 |
Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, ... ... Irizarry R, et al. A multi-omic analysis of human naïve CD4+ T cells. Bmc Systems Biology. 9: 75. PMID 26542228 DOI: 10.1186/S12918-015-0225-4 |
0.362 |
|
| 2015 |
Hicks SC, Irizarry RA. quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biology. 16: 117. PMID 26040460 DOI: 10.1186/S13059-015-0679-0 |
0.347 |
|
| 2015 |
Ogino S, Campbell PT, Nishihara R, Phipps AI, Beck AH, Sherman ME, Chan AT, Troester MA, Bass AJ, Fitzgerald KC, Irizarry RA, Kelsey KT, Nan H, Peters U, Poole EM, et al. Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes & Control : Ccc. 26: 959-72. PMID 25956270 DOI: 10.1007/S10552-015-0596-2 |
0.316 |
|
| 2015 |
Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biology. 16: 80. PMID 25886480 DOI: 10.1186/S13059-015-0644-Y |
0.326 |
|
| 2015 |
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 12: 115-21. PMID 25633503 DOI: 10.1038/Nmeth.3252 |
0.346 |
|
| 2014 |
Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology. 15: 554. PMID 25476604 DOI: 10.1186/S13059-014-0554-4 |
0.374 |
|
| 2014 |
Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Medicine. 6: 61. PMID 25191524 DOI: 10.1186/S13073-014-0061-Y |
0.312 |
|
| 2014 |
Liu R, Dai Z, Yeager M, Irizarry RA, Ritchie ME. KRLMM: an adaptive genotype calling method for common and low frequency variants. Bmc Bioinformatics. 15: 158. PMID 24886250 DOI: 10.1186/1471-2105-15-158 |
0.313 |
|
| 2014 |
Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics (Oxford, England). 30: 1514-21. PMID 24501098 DOI: 10.1093/Bioinformatics/Btu054 |
0.744 |
|
| 2014 |
Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biology. 15: R31. PMID 24495553 DOI: 10.1186/Gb-2014-15-2-R31 |
0.329 |
|
| 2014 |
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (Oxford, England). 30: 1363-9. PMID 24478339 DOI: 10.1093/Bioinformatics/Btu049 |
0.379 |
|
| 2014 |
Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT. Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics (Oxford, England). 15: 413-26. PMID 24398039 DOI: 10.1093/Biostatistics/Kxt053 |
0.389 |
|
| 2014 |
McCall MN, Jaffee HA, Zelisko SJ, Sinha N, Hooiveld G, Irizarry RA, Zilliox MJ. The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Research. 42: D938-43. PMID 24271388 DOI: 10.1093/Nar/Gkt1204 |
0.655 |
|
| 2014 |
Brebi P, Maldonado L, Noordhuis MG, Ili C, Leal P, Garcia P, Brait M, Ribas J, Michailidi C, Perez J, Soudry E, Tapia O, Guzman P, Muñoz S, Van Neste L, ... ... Irizarry R, et al. Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population. Epigenetics : Official Journal of the Dna Methylation Society. 9: 308-17. PMID 24241165 DOI: 10.4161/Epi.27120 |
0.335 |
|
| 2014 |
Kostadinov R, Scharpf R, Sabunciyan S, Magoon D, Irizarry R, Brown P. Identifying Methylation Changes Driving Evolution of Relapse in MLL-Rearranged Acute Lymphoblastic Leukemias Blood. 124: 3797-3797. DOI: 10.1182/Blood.V124.21.3797.3797 |
0.73 |
|
| 2014 |
Frazee AC, Hansen KD, Leek JT, Sabunciyan S, Irizarry RA. Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution Biostatistics. 15: 584-585. DOI: 10.1093/Biostatistics/Kxu022 |
0.316 |
|
| 2013 |
Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods. 10: 949-55. PMID 24076989 DOI: 10.1038/Nmeth.2632 |
0.376 |
|
| 2013 |
Montaño CM, Irizarry RA, Kaufmann WE, Talbot K, Gur RE, Feinberg AP, Taub MA. Measuring cell-type specific differential methylation in human brain tissue. Genome Biology. 14: R94. PMID 24000956 DOI: 10.1186/Gb-2013-14-8-R94 |
0.314 |
|
| 2013 |
Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics (Oxford, England). 29: 1182-1189. PMID 23457041 DOI: 10.1093/Bioinformatics/Btt108 |
0.672 |
|
| 2013 |
Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Science Translational Medicine. 5: 169ra10. PMID 23345608 DOI: 10.1126/Scitranslmed.3005211 |
0.357 |
|
| 2012 |
Beuf KD, Schrijver JD, Thas O, Criekinge WV, Irizarry RA, Clement L. Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. Bmc Bioinformatics. 13: 303. PMID 23151247 DOI: 10.1186/1471-2105-13-303 |
0.335 |
|
| 2012 |
Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. Gene expression anti-profiles as a basis for accurate universal cancer signatures. Bmc Bioinformatics. 13: 272. PMID 23088656 DOI: 10.1186/1471-2105-13-272 |
0.603 |
|
| 2012 |
McCall MN, Jaffee HA, Irizarry RA. fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics (Oxford, England). 28: 3153-4. PMID 23044545 DOI: 10.1093/Bioinformatics/Bts588 |
0.618 |
|
| 2012 |
Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biology. 13: R83. PMID 23034175 DOI: 10.1186/Gb-2012-13-10-R83 |
0.421 |
|
| 2012 |
Shi W, Wahba G, Irizarry RA, Bravo HC, Wright SJ. The partitioned LASSO-patternsearch algorithm with application to gene expression data. Bmc Bioinformatics. 13: 98. PMID 22587526 DOI: 10.1186/1471-2105-13-98 |
0.383 |
|
| 2012 |
Sabunciyan S, Aryee MJ, Irizarry RA, Rongione M, Webster MJ, Kaufman WE, Murakami P, Lessard A, Yolken RH, Feinberg AP, Potash JB. Genome-wide DNA methylation scan in major depressive disorder. Plos One. 7: e34451. PMID 22511943 DOI: 10.1371/Journal.Pone.0034451 |
0.376 |
|
| 2012 |
Clement L, De Beuf K, Thas O, Vuylsteke M, Irizarry RA, Crainiceanu CM. Fast wavelet based functional models for transcriptome analysis with tiling arrays. Statistical Applications in Genetics and Molecular Biology. 11: Article 4. PMID 22499683 DOI: 10.2202/1544-6115.1726 |
0.397 |
|
| 2012 |
Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. International Journal of Epidemiology. 41: 200-9. PMID 22422453 DOI: 10.1093/Ije/Dyr238 |
0.387 |
|
| 2012 |
Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C, Aryee MJ, Irizarry RA, Herbstman J, Witter FR, Goldman LR, Feinberg AP, Fallin MD. DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. International Journal of Epidemiology. 41: 188-99. PMID 22422452 DOI: 10.1093/Ije/Dyr237 |
0.381 |
|
| 2012 |
Hansen KD, Irizarry RA, Wu Z. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (Oxford, England). 13: 204-16. PMID 22285995 DOI: 10.1093/Biostatistics/Kxr054 |
0.394 |
|
| 2012 |
Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylated regions. Biostatistics (Oxford, England). 13: 166-78. PMID 21685414 DOI: 10.1093/Biostatistics/Kxr013 |
0.395 |
|
| 2011 |
Irizarry RA, Wang C, Zhou Y, Speed TP. Erratum: Gene set enrichment analysis made simple (Statistical Methods in Medical Research (2009) 18:6 (565-575)) Statistical Methods in Medical Research. 20. PMID 28862925 DOI: 10.1177/0962280211420490 |
0.303 |
|
| 2011 |
Scharpf RB, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I. Using the R Package crlmm for Genotyping and Copy Number Estimation. Journal of Statistical Software. 40: 1-32. PMID 22523482 |
0.726 |
|
| 2011 |
Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T. Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biology. 12: R93. PMID 21955804 DOI: 10.1186/Gb-2011-12-9-R93 |
0.34 |
|
| 2011 |
McCall MN, Irizarry RA. Thawing Frozen Robust Multi-array Analysis (fRMA). Bmc Bioinformatics. 12: 369. PMID 21923903 DOI: 10.1186/1471-2105-12-369 |
0.646 |
|
| 2011 |
Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nature Biotechnology. 29: 572-3. PMID 21747377 DOI: 10.1038/Nbt.1910 |
0.327 |
|
| 2011 |
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43: 768-75. PMID 21706001 DOI: 10.1038/Ng.865 |
0.336 |
|
| 2011 |
Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, De Marzo AM, Irizarry RA, Nelson WG. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. Bmc Genomics. 12: 313. PMID 21669002 DOI: 10.1186/1471-2164-12-313 |
0.741 |
|
| 2011 |
Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, et al. NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva Cancer Prevention Research. 4: 1061-1072. PMID 21558411 DOI: 10.1158/1940-6207.Capr-11-0006 |
0.328 |
|
| 2011 |
McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. Assessing affymetrix GeneChip microarray quality. Bmc Bioinformatics. 12: 137. PMID 21548974 DOI: 10.1186/1471-2105-12-137 |
0.632 |
|
| 2011 |
Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B, Hao H, Hetrick K, Jedlicka A, Dziedzic A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, ... Irizarry RA, et al. Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics (Oxford, England). 27: 1052-60. PMID 21478196 DOI: 10.1093/Bioinformatics/Btr106 |
0.786 |
|
| 2011 |
Ritchie ME, Liu R, Carvalho BS, Irizarry RA, Bahlo M, Booth DR, Broadley SA, Brown MA, Foote SJ, Griffiths LR, Kilpatrick TJ, Lechner-Scott J, Moscato P, Perreau VM, Rubio JP, et al. Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips Bmc Bioinformatics. 12. PMID 21385424 DOI: 10.1186/1471-2105-12-68 |
0.401 |
|
| 2011 |
McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Research. 39: D1011-5. PMID 21177656 DOI: 10.1093/Nar/Gkq1259 |
0.652 |
|
| 2011 |
Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S, Irizarry RA. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics (Oxford, England). 12: 197-210. PMID 20858772 DOI: 10.1093/Biostatistics/Kxq055 |
0.393 |
|
| 2011 |
Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA. A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics (Oxford, England). 12: 33-50. PMID 20625178 DOI: 10.1093/Biostatistics/Kxq043 |
0.764 |
|
| 2011 |
Scharpf RB, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I. Using the R Package crlmm for Genotyping and Copy Number Estimation. Journal of Statistical Software. 40: 1-32. DOI: 10.18637/Jss.V040.I12 |
0.74 |
|
| 2010 |
Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Medicine. 2: 87. PMID 21144010 DOI: 10.1186/Gm208 |
0.368 |
|
| 2010 |
Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T, Eiriksdottir G, Harris TB, Launer L, Gudnason V, Fallin MD. Personalized epigenomic signatures that are stable over time and covary with body mass index. Science Translational Medicine. 2: 49ra67. PMID 20844285 DOI: 10.1126/Scitranslmed.3001262 |
0.385 |
|
| 2010 |
Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews. Genetics. 11: 733-9. PMID 20838408 DOI: 10.1038/Nrg2825 |
0.357 |
|
| 2010 |
Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, Rossi DJ, Inlay MA, Serwold T, Karsunky H, Ho L, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 467: 338-42. PMID 20720541 DOI: 10.1038/Nature09367 |
0.338 |
|
| 2010 |
Carvalho BS, Irizarry RA. A framework for oligonucleotide microarray preprocessing. Bioinformatics (Oxford, England). 26: 2363-7. PMID 20688976 DOI: 10.1093/Bioinformatics/Btq431 |
0.389 |
|
| 2010 |
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, ... ... Irizarry RA, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/Nbt.1665 |
0.629 |
|
| 2010 |
Wu H, Irizarry RA, Bravo HC. Intensity normalization improves color calling in SOLiD sequencing. Nature Methods. 7: 336-7. PMID 20431543 DOI: 10.1038/Nmeth0510-336 |
0.363 |
|
| 2010 |
Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA. Performance evaluation of commercial miRNA expression array platforms. Bmc Research Notes. 3: 80. PMID 20298588 DOI: 10.1186/1756-0500-3-80 |
0.587 |
|
| 2010 |
Schafer E, Irizarry R, Negi S, McIntyre E, Small D, Figueroa ME, Melnick A, Brown P. Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting. Blood. 115: 4798-809. PMID 20215641 DOI: 10.1182/Blood-2009-09-243634 |
0.321 |
|
| 2010 |
Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. Redefining CpG islands using hidden Markov models. Biostatistics (Oxford, England). 11: 499-514. PMID 20212320 DOI: 10.1093/Biostatistics/Kxq005 |
0.398 |
|
| 2010 |
López-Romero P, González MA, Callejas S, Dopazo A, Irizarry RA. Processing of Agilent microRNA array data. Bmc Research Notes. 3: 18. PMID 20205787 DOI: 10.1186/1756-0500-3-18 |
0.36 |
|
| 2010 |
McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics (Oxford, England). 11: 242-53. PMID 20097884 DOI: 10.1093/Biostatistics/Kxp059 |
0.687 |
|
| 2010 |
Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences of the United States of America. 107: 1757-64. PMID 20080672 DOI: 10.1073/Pnas.0906183107 |
0.308 |
|
| 2010 |
Bravo HC, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics. 66: 665-74. PMID 19912177 DOI: 10.1111/J.1541-0420.2009.01353.X |
0.386 |
|
| 2010 |
Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics (Oxford, England). 26: 242-9. PMID 19906825 DOI: 10.1093/Bioinformatics/Btp624 |
0.436 |
|
| 2010 |
Guerrero-Preston RE, Soudry E, Ili-Gangas C, Brebi-Mieville P, Jaffe A, Barr C, Irizarry R, Berdasco M, Fu Y, Orera M, Acero J, Blanco A, Yang Q, Baez A, Esteller M, et al. Abstract 2924: Genome-wide microarray platforms uncover novel hypermethylated genes in an oral squamous cell carcinoma case-control study: A phase I preclinical biomarker development study Cancer Research. 70: 2924-2924. DOI: 10.1158/1538-7445.Am10-2924 |
0.412 |
|
| 2009 |
Irizarry RA, Wang C, Zhou Y, Speed TP. Gene set enrichment analysis made simple. Statistical Methods in Medical Research. 18: 565-75. PMID 20048385 DOI: 10.1177/0962280209351908 |
0.375 |
|
| 2009 |
Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nature Genetics. 41: 1350-3. PMID 19881528 DOI: 10.1038/Ng.471 |
0.304 |
|
| 2009 |
Irizarry RA, Wu H, Feinberg AP. A species-generalized probabilistic model-based definition of CpG islands. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 20: 674-80. PMID 19777308 DOI: 10.1007/S00335-009-9222-5 |
0.357 |
|
| 2009 |
Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (Oxford, England). 25: 2621-3. PMID 19661241 DOI: 10.1093/Bioinformatics/Btp470 |
0.407 |
|
| 2009 |
Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nature Genetics. 41: 246-50. PMID 19151716 DOI: 10.1038/Ng.297 |
0.331 |
|
| 2009 |
Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nature Genetics. 41: 178-86. PMID 19151715 DOI: 10.1038/Ng.298 |
0.313 |
|
| 2009 |
Schafer ES, Irizarry R, Negi S, McIntyre E, Small D, Figueroa ME, Melnick A, Brown P. Promoter Hypermethylation in MLL-r Leukemia: Biology and Therapeutic Targeting. Blood. 114: 3472-3472. DOI: 10.1182/Blood.V114.22.3472.3472 |
0.363 |
|
| 2009 |
Kittleson MM, Irizarry R, Heidecker B, Hare JM. Transcriptomics: Translation of Global Expression Analysis to Genomic Medicine Genomic and Personalized Medicine, Two-Vol Set. 143-156. DOI: 10.1016/B978-0-12-369420-1.00012-3 |
0.341 |
|
| 2009 |
Carvalho B, Irizarry RA, Scharpf RB, Carey VJ. Processing and analyzing Affymetrix SNP chips with Bioconductor Statistics in Biosciences. 1: 160-180. DOI: 10.1007/S12561-009-9015-0 |
0.739 |
|
| 2008 |
Wen B, Wu H, Bjornsson H, Green RD, Irizarry R, Feinberg AP. Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Research. 18: 1806-13. PMID 18849526 DOI: 10.1101/Gr.067587.108 |
0.414 |
|
| 2008 |
Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA. Estimating genome-wide copy number using allele-specific mixture models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 857-66. PMID 18707534 DOI: 10.1089/Cmb.2007.0148 |
0.763 |
|
| 2008 |
McCall MN, Irizarry RA. Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Research. 36: e108. PMID 18676452 DOI: 10.1093/Nar/Gkn430 |
0.646 |
|
| 2008 |
Peyser BD, Irizarry R, Spencer FA. Statistical analysis of fitness data determined by TAG hybridization on microarrays. Methods in Molecular Biology (Clifton, N.J.). 416: 369-81. PMID 18392981 DOI: 10.1007/978-1-59745-321-9_25 |
0.368 |
|
| 2008 |
Meluh PB, Pan X, Yuan DS, Tiffany C, Chen O, Sookhai-Mahadeo S, Wang X, Peyser BD, Irizarry R, Spencer FA, Boeke JD. Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. Methods in Molecular Biology (Clifton, N.J.). 416: 221-47. PMID 18392971 DOI: 10.1007/978-1-59745-321-9_15 |
0.337 |
|
| 2008 |
Lin S, Carvalho B, Cutler DJ, Arking DE, Chakravarti A, Irizarry RA. Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biology. 9: R63. PMID 18387188 DOI: 10.1186/Gb-2008-9-4-R63 |
0.721 |
|
| 2008 |
Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP. SNP-specific array-based allele-specific expression analysis. Genome Research. 18: 771-9. PMID 18369178 DOI: 10.1101/Gr.073254.107 |
0.403 |
|
| 2008 |
Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Research. 18: 780-90. PMID 18316654 DOI: 10.1101/Gr.7301508 |
0.746 |
|
| 2008 |
Bengtsson H, Irizarry R, Carvalho B, Speed TP. Estimation and assessment of raw copy numbers at the single locus level Bioinformatics. 24: 759-767. PMID 18204055 DOI: 10.1093/Bioinformatics/Btn016 |
0.751 |
|
| 2007 |
Zilliox MJ, Irizarry RA. A gene expression bar code for microarray data. Nature Methods. 4: 911-3. PMID 17906632 DOI: 10.1038/Nmeth1102 |
0.393 |
|
| 2007 |
Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (Oxford, England). 8: 485-99. PMID 17189563 DOI: 10.1093/Biostatistics/Kxl042 |
0.768 |
|
| 2007 |
Wu Z, Irizarry RA. A statistical framework for the analysis of microarray probe-level data The Annals of Applied Statistics. 1: 333-357. DOI: 10.1214/07-Aoas116 |
0.398 |
|
| 2006 |
Wheelan SJ, Scheifele LZ, MartÃnez-Murillo F, Irizarry RA, Boeke JD. Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America. 103: 17632-7. PMID 17101968 DOI: 10.1073/Pnas.0605450103 |
0.365 |
|
| 2006 |
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489 |
0.305 |
|
| 2006 |
Wheelan SJ, MartÃnez-Murillo F, Irizarry RA, Boeke JD. Stacking the deck: double-tiled DNA microarrays. Nature Methods. 3: 903-7. PMID 17060914 DOI: 10.1038/Nmeth951 |
0.411 |
|
| 2006 |
Katz S, Irizarry RA, Lin X, Tripputi M, Porter MW. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. Bmc Bioinformatics. 7: 464. PMID 17059591 DOI: 10.1186/1471-2105-7-464 |
0.359 |
|
| 2006 |
Cope L, Hartman SM, Göhlmann HW, Tiesman JP, Irizarry RA. Analysis of Affymetrix GeneChip data using amplified RNA. Biotechniques. 40: 165-6, 168, 170. PMID 16526405 DOI: 10.2144/000112057 |
0.364 |
|
| 2006 |
Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England). 22: 789-94. PMID 16410320 DOI: 10.1093/Bioinformatics/Btk046 |
0.327 |
|
| 2006 |
Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. Global synthetic-lethality analysis and yeast functional profiling. Trends in Genetics : Tig. 22: 56-63. PMID 16309778 DOI: 10.1016/J.Tig.2005.11.003 |
0.335 |
|
| 2005 |
Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD, Spencer FA. Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Research. 33: e140. PMID 16166654 DOI: 10.1093/Nar/Gni138 |
0.409 |
|
| 2005 |
Wu Z, Irizarry RA. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 882-93. PMID 16108723 DOI: 10.1089/Cmb.2005.12.882 |
0.356 |
|
| 2005 |
Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA, Boeke JD. Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Research. 33: e103. PMID 15994458 DOI: 10.1093/Nar/Gni105 |
0.353 |
|
| 2005 |
Grigoryev DN, Ma SF, Simon BA, Irizarry RA, Ye SQ, Garcia JG. In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology. Bmc Genomics. 6: 62. PMID 15871745 DOI: 10.1186/1471-2164-6-62 |
0.365 |
|
| 2005 |
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, et al. Multiple-laboratory comparison of microarray platforms. Nature Methods. 2: 345-50. PMID 15846361 DOI: 10.1038/Nmeth756 |
0.406 |
|
| 2005 |
Kittleson MM, Minhas KM, Irizarry RA, Ye SQ, Edness G, Breton E, Conte JV, Tomaselli G, Garcia JG, Hare JM. Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure. Physiological Genomics. 21: 299-307. PMID 15769906 DOI: 10.1152/Physiolgenomics.00255.2004 |
0.317 |
|
| 2005 |
Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN. On the utility of pooling biological samples in microarray experiments. Proceedings of the National Academy of Sciences of the United States of America. 102: 4252-7. PMID 15755808 DOI: 10.1073/Pnas.0500607102 |
0.389 |
|
| 2005 |
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JGN, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, et al. Erratum: Corrigendum: Multiple-laboratory comparison of microarray platforms Nature Methods. 2: 477-477. DOI: 10.1038/Nmeth0605-477B |
0.325 |
|
| 2004 |
Kittleson MM, Ye SQ, Irizarry RA, Minhas KM, Edness G, Conte JV, Parmigiani G, Miller LW, Chen Y, Hall JL, Garcia JG, Hare JM. Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation. 110: 3444-51. PMID 15557369 DOI: 10.1161/01.Cir.0000148178.19465.11 |
0.318 |
|
| 2004 |
Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Experimental Design and Low-Level Analysis of Microarray Data International Review of Neurobiology. 60: 25-58. PMID 15474586 DOI: 10.1016/S0074-7742(04)60002-X |
0.396 |
|
| 2004 |
Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nature Biotechnology. 22: 656-8; author reply . PMID 15175677 DOI: 10.1038/Nbt0604-656B |
0.325 |
|
| 2004 |
Grigoryev DN, Ma SF, Irizarry RA, Ye SQ, Quackenbush J, Garcia JG. Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biology. 5: R34. PMID 15128448 DOI: 10.1186/Gb-2004-5-5-R34 |
0.341 |
|
| 2004 |
Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England). 20: 323-31. PMID 14960458 DOI: 10.1093/Bioinformatics/Btg410 |
0.37 |
|
| 2004 |
Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (Oxford, England). 20: 307-15. PMID 14960456 DOI: 10.1093/Bioinformatics/Btg405 |
0.346 |
|
| 2004 |
Warren CD, Eckley DM, Lee MS, Hanna JS, Hughes A, Peyser B, Jie C, Irizarry R, Spencer FA. S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion. Molecular Biology of the Cell. 15: 1724-35. PMID 14742710 DOI: 10.1091/Mbc.E03-09-0637 |
0.331 |
|
| 2004 |
Chen H, Irizarry RA, Luo L, Zirkin BR. Leydig cell gene expression: effects of age and caloric restriction. Experimental Gerontology. 39: 31-43. PMID 14724062 DOI: 10.1016/J.Exger.2003.09.021 |
0.312 |
|
| 2004 |
Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays Journal of the American Statistical Association. 99: 909-917. DOI: 10.1198/016214504000000683 |
0.417 |
|
| 2003 |
Irizarry RA, Ooi SL, Wu Z, Boeke JD. Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Statistical Applications in Genetics and Molecular Biology. 2: Article1. PMID 16646779 DOI: 10.2202/1544-6115.1002 |
0.335 |
|
| 2003 |
Scharfstein DO, Irizarry RA. Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data. Biometrics. 59: 601-13. PMID 14601761 DOI: 10.1111/1541-0420.00070 |
0.317 |
|
| 2003 |
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (Oxford, England). 4: 249-64. PMID 12925520 DOI: 10.1093/Biostatistics/4.2.249 |
0.394 |
|
| 2003 |
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research. 31: e15. PMID 12582260 DOI: 10.1093/Nar/Gng015 |
0.396 |
|
| 2003 |
Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics. 19: 185-193. PMID 12538238 DOI: 10.1093/Bioinformatics/19.2.185 |
0.38 |
|
| 2001 |
Irizarry RA, Tankersley C, Frank R, Flanders S. Consultant's forum: Assessing homeostasis through circadian patterns Biometrics. 57: 1228-1237. PMID 11764264 DOI: 10.1111/J.0006-341X.2001.01228.X |
0.308 |
|
| 2000 |
Brillinger DR, Morettin PA, Irizarry RA, Chiann C. Some wavelet-based analyses of Markov chain data Signal Processing. 80: 1607-1627. DOI: 10.1016/S0165-1684(00)00097-9 |
0.323 |
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