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Rafael Irizarry
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Research Profile (preview)
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Genes & Molecular Sequences
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Network (preview)
8
Boeke, Jef
7
Ye, Shui
7
Speed, Terence
7
Spencer, Forrest
7
Cope, Leslie
7
Garcia, Joe
6
Feinberg, Andrew
5
Peyser, Brian
5
Yuan, Daniel
5
Quackenbush, John
4
Wu, Zhijin
4
Minhas, Khalid
4
Bolstad, Benjamin
4
Hare, Joshua
3
Kittleson, Michelle
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All Publications
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2009: Wen Bo; Wu Hao; Shinkai Yoichi; Irizarry Rafael A; Feinberg Andrew P
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells.
Nature genetics 2009;41(2):246-50.
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2009: Irizarry Rafael A; 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; Feinberg Andrew P
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
Nature genetics 2009;41(2):178-86.
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2008: Yegnasubramanian Srinivasan; Haffner Michael C; Zhang Yonggang; Gurel Bora; Cornish Toby C; Wu Zhijin; Irizarry Rafael A; Morgan James; Hicks Jessica; DeWeese Theodore L; Isaacs William B; Bova G Steven; De Marzo Angelo M; Nelson William G
DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity.
Cancer research 2008;68(21):8954-67.
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2008: Wen Bo; Wu Hao; Bjornsson Hans; Green Roland D; Irizarry Rafael; Feinberg Andrew P
Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification.
Genome research 2008;18(11):1806-13.
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2008: McCall Matthew N; Irizarry Rafael A
Consolidated strategy for the analysis of microarray spike-in data.
Nucleic acids research 2008;36(17):e108.
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2008: Wang Wenyi; Carvalho Benilton; Miller Nathaniel D; Pevsner Jonathan; Chakravarti Aravinda; Irizarry Rafael A
Estimating genome-wide copy number using allele-specific mixture models.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(7):857-66.
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2008: Bjornsson Hans T; Sigurdsson Martin I; Fallin M Daniele; Irizarry Rafael A; Aspelund Thor; Cui Hengmi; Yu Wenqiang; Rongione Michael A; Ekström Tomas J; Harris Tamara B; Launer Lenore J; Eiriksdottir Gudny; Leppert Mark F; Sapienza Carmen; Gudnason Vilmundur; Feinberg Andrew P
Intra-individual change over time in DNA methylation with familial clustering.
JAMA : the journal of the American Medical Association 2008;299(24):2877-83.
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2008: Bjornsson Hans T; Albert Thomas J; Ladd-Acosta Christine M; Green Roland D; Rongione Michael A; Middle Christina M; Irizarry Rafael A; Broman Karl W; Feinberg Andrew P
SNP-specific array-based allele-specific expression analysis.
Genome research 2008;18(5):771-9.
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2008: Irizarry Rafael A; Ladd-Acosta Christine; Carvalho Benilton; Wu Hao; Brandenburg Sheri A; Jeddeloh Jeffrey A; Wen Bo; Feinberg Andrew P
Comprehensive high-throughput arrays for relative methylation (CHARM).
Genome research 2008;18(5):780-90.
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2008: Bengtsson H; Irizarry R; Carvalho B; Speed T P
Estimation and assessment of raw copy numbers at the single locus level.
Bioinformatics (Oxford, England) 2008;24(6):759-67.
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2008: Peyser Brian D; Irizarry Rafael; Spencer Forrest A
Statistical analysis of fitness data determined by TAG hybridization on microarrays.
Methods in molecular biology (Clifton, N.J.) 2008;416():369-81.
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2008: Meluh Pamela B; Pan Xuewen; Yuan Daniel S; Tiffany Carol; Chen Ou; Sookhai-Mahadeo Sharon; Wang Xiaoling; Peyser Brian D; Irizarry Rafael; Spencer Forrest A; Boeke Jef D
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.) 2008;416():221-47.
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2008: Rodríguez-Quiñones José F; Irizarry Rafael A; Díaz-Blanco Nitza L; Rivera-Molina Félix E; Gómez-Garzón Diana; Rodríguez-Medina José R
Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions.
BMC genomics 2008;9():34.
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2007: Zilliox Michael J; Irizarry Rafael A
A gene expression bar code for microarray data.
Nature methods 2007;4(11):911-3.
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2007: Loyo-Berríos Nilsa I; Irizarry Rafael; Hennessey Joseph G; Tao Xuguang Grant; Matanoski Genevieve
Air pollution sources and childhood asthma attacks in Catano, Puerto Rico.
American journal of epidemiology 2007;165(8):927-35.
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2007: Carvalho Benilton; Bengtsson Henrik; Speed Terence P; Irizarry Rafael A
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.
Biostatistics (Oxford, England) 2007;8(2):485-99.
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2006: Yuan Daniel S; Irizarry Rafael A
High-resolution spatial normalization for microarrays containing embedded technical replicates.
Bioinformatics (Oxford, England) 2006;22(24):3054-60.
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2006: Wheelan Sarah J; Scheifele Lisa Z; Martínez-Murillo Francisco; Irizarry Rafael A; Boeke Jef D
Transposon insertion site profiling chip (TIP-chip).
Proceedings of the National Academy of Sciences of the United States of America 2006;103(47):17632-7.
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2006: Wheelan Sarah J; Martínez-Murillo Francisco; Irizarry Rafael A; Boeke Jef D
Stacking the deck: double-tiled DNA microarrays.
Nature methods 2006;3(11):903-7.
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2006: Quackenbush John; Irizarry Rafael A
Response to Shields: 'MIAME, we have a problem'.
Trends in genetics : TIG 2006;22(9):471-2.
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2006: Takahashi Hidekazu; McCaffery J Michael; Irizarry Rafael A; Boeke Jef D
Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription.
Molecular cell 2006;23(2):207-17.
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2006: DiPietro Janet A; Caulfield Laura E; Irizarry Rafael A; Chen Ping; Merialdi Mario; Zavaleta Nelly
Prenatal development of intrafetal and maternal-fetal synchrony.
Behavioral neuroscience 2006;120(3):687-701.
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2006: Irizarry Rafael A; Wu Zhijin; Jaffee Harris A
Comparison of Affymetrix GeneChip expression measures.
Bioinformatics (Oxford, England) 2006;22(7):789-94.
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2006: Quackenbush John; Stoeckert Christian; Ball Catherine; Brazma Alvis; Gentleman Robert; Huber Wolfgang; Irizarry Rafael; Salit Marc; Sherlock Gavin; Spellman Paul; Winegarden Neil
Top-down standards will not serve systems biology.
Nature 2006;440(7080):24.
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2006: Cope Leslie; Hartman Scott M; Göhlmann Hinrich W H; Tiesman Jay P; Irizarry Rafael A
Analysis of Affymetrix GeneChip data using amplified RNA.
BioTechniques 2006;40(2):165-6, 168, 170.
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2006: Ooi Siew Loon; Pan Xuewen; Peyser Brian D; Ye Ping; Meluh Pamela B; Yuan Daniel S; Irizarry Rafael A; Bader Joel S; Spencer Forrest A; Boeke Jef D
Global synthetic-lethality analysis and yeast functional profiling.
Trends in genetics : TIG 2006;22(1):56-63.
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2006: Rayner Tim F; Rocca-Serra Philippe; Spellman Paul T; Causton Helen C; Farne Anna; Holloway Ele; Irizarry Rafael A; Liu Junmin; Maier Donald S; Miller Michael; Petersen Kjell; Quackenbush John; Sherlock Gavin; Stoeckert Christian J; White Joseph; Whetzel Patricia L; Wymore Farrell; Parkinson Helen; Sarkans Ugis; Ball Catherine A; Brazma Alvis
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
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2006: Katz Simon; Irizarry Rafael A; Lin Xue; Tripputi Mark; Porter Mark W
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database.
BMC bioinformatics 2006;7():464.
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2006: Irizarry Rafael A; Cope Leslie M; Wu Zhijin
Feature-level exploration of a published Affymetrix GeneChip control dataset.
Genome biology 2006;7(8):404.
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2006: Zeger Scott L; Irizarry Rafael; Peng Roger D
On time series analysis of public health and biomedical data.
Annual review of public health 2006;27():57-79.
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2006: Lechtzin Noah; John Majnu; Irizarry Rafael; Merlo Christian; Diette Gregory B; Boyle Michael P
Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa.
Respiration; international review of thoracic diseases 2006;73(1):27-33.
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2005: Baker Shawn C; Bauer Steven R; Beyer Richard P; Brenton James D; Bromley Bud; Burrill John; Causton Helen; Conley Michael P; Elespuru Rosalie; Fero Michael; Foy Carole; Fuscoe James; Gao Xiaolian; Gerhold David Lee; Gilles Patrick; Goodsaid Federico; Guo Xu; Hackett Joe; Hockett Richard D; Ikonomi Pranvera; Irizarry Rafael A; Kawasaki Ernest S; Kaysser-Kranich Tamma; Kerr Kathleen; Kiser Gretchen; Koch Walter H; Lee Kathy Y; Liu Chunmei; Liu Z Lewis; Lucas Anne; Manohar Chitra F; Miyada Garry; Modrusan Zora; Parkes Helen; Puri Raj K; Reid Laura; Ryder Thomas B; Salit Marc; Samaha Raymond R; Scherf Uwe; Sendera Timothy J; Setterquist Robert A; Shi Leming; Shippy Richard; Soriano Jesus V; Wagar Elizabeth A; Warrington Janet A; Williams Mickey; Wilmer Frederike; Wilson Mike; Wolber Paul K; Wu Xiaoning; Zadro Renata;
The External RNA Controls Consortium: a progress report.
Nature methods 2005;2(10):731-4.
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2005: Wu Zhijin; Irizarry Rafael A
Stochastic models inspired by hybridization theory for short oligonucleotide arrays.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(6):882-93.
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2005: Kittleson Michelle M; Minhas Khalid M; Irizarry Rafael A; Ye Shui Q; Edness Gina; Breton Elayne; Conte John V; Tomaselli Gordon; Garcia Joe G N; Hare Joshua M
Gene expression in giant cell myocarditis: Altered expression of immune response genes.
International journal of cardiology 2005;102(2):333-40.
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2005: Hansel Nadia N; Hilmer Sara C; Georas Steve N; Cope Leslie M; Guo Jia; Irizarry Rafael A; Diette Gregory B
Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma.
The Journal of laboratory and clinical medicine 2005;145(5):263-74.
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2005: Irizarry Rafael A; Warren Daniel; Spencer Forrest; Kim Irene F; Biswal Shyam; Frank Bryan C; Gabrielson Edward; Garcia Joe G N; Geoghegan Joel; Germino Gregory; Griffin Constance; Hilmer Sara C; Hoffman Eric; Jedlicka Anne E; Kawasaki Ernest; Martínez-Murillo Francisco; Morsberger Laura; Lee Hannah; Petersen David; Quackenbush John; Scott Alan; Wilson Michael; Yang Yanqin; Ye Shui Qing; Yu Wayne
Multiple-laboratory comparison of microarray platforms.
Nature methods 2005;2(5):345-50.
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2005: Kittleson Michelle M; Minhas Khalid M; Irizarry Rafael A; Ye Shui Q; Edness Gina; Breton Elayne; Conte John V; Tomaselli Gordon; Garcia Joe G N; Hare Joshua M
Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure.
Physiological genomics 2005;21(3):299-307.
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2005: Kendziorski C; Irizarry R A; Chen K-S; Haag J D; Gould M N
On the utility of pooling biological samples in microarray experiments.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(12):4252-7.
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2005: Peyser Brian D; Irizarry Rafael A; Tiffany Carol W; Chen Ou; Yuan Daniel S; Boeke Jef D; Spencer Forrest A
Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.
Nucleic acids research 2005;33(16):e140.
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2005: Yuan Daniel S; Pan Xuewen; Ooi Siew Loon; Peyser Brian D; Spencer Forrest A; Irizarry Rafael A; Boeke Jef D
Improved microarray methods for profiling the Yeast Knockout strain collection.
Nucleic acids research 2005;33(12):e103.
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2005: Grigoryev Dmitry N; Ma Shwu-Fan; Simon Brett A; Irizarry Rafael A; Ye Shui Q; Garcia Joe G N
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.
BMC genomics 2005;6(1):62.
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2004: Kittleson Michelle M; Ye Shui Q; Irizarry Rafael A; Minhas Khalid M; Edness Gina; Conte John V; Parmigiani Giovanni; Miller Leslie W; Chen Yingjie; Hall Jennifer L; Garcia Joe G N; Hare Joshua M
Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy.
Circulation 2004;110(22):3444-51.
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2004: Dipietro Janet A; Irizarry Rafael A; Costigan Kathleen A; Gurewitsch Edith D
The psychophysiology of the maternal-fetal relationship.
Psychophysiology 2004;41(4):510-20.
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2004: Wu Zhijin; Irizarry Rafael A
Preprocessing of oligonucleotide array data.
Nature biotechnology 2004;22(6):656-8; author reply 658.
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2004: Warren Cheryl D; Eckley D Mark; Lee Marina S; Hanna Joseph S; Hughes Adam; Peyser Brian; Jie Chunfa; Irizarry Rafael; Spencer Forrest A
S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion.
Molecular biology of the cell 2004;15(4):1724-35.
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2004: Cope Leslie M; Irizarry Rafael A; Jaffee Harris A; Wu Zhijin; Speed Terence P
A benchmark for Affymetrix GeneChip expression measures.
Bioinformatics (Oxford, England) 2004;20(3):323-31.
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2004: Gautier Laurent; Cope Leslie; Bolstad Benjamin M; Irizarry Rafael A
affy--analysis of Affymetrix GeneChip data at the probe level.
Bioinformatics (Oxford, England) 2004;20(3):307-15.
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2004: Cummings Derek A T; Irizarry Rafael A; Huang Norden E; Endy Timothy P; Nisalak Ananda; Ungchusak Kumnuan; Burke Donald S
Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand.
Nature 2004;427(6972):344-7.
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2004: Chen Haolin; Irizarry Rafael A; Luo Lindi; Zirkin Barry R
Leydig cell gene expression: effects of age and caloric restriction.
Experimental gerontology 2004;39(1):31-43.
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2004: Bolstad B M; Collin F; Simpson K M; Irizarry R A; Speed T P
Experimental design and low-level analysis of microarray data.
International review of neurobiology 2004;60():25-58.
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2004: Gentleman Robert C; Carey Vincent J; Bates Douglas M; Bolstad Ben; Dettling Marcel; Dudoit Sandrine; Ellis Byron; Gautier Laurent; Ge Yongchao; Gentry Jeff; Hornik Kurt; Hothorn Torsten; Huber Wolfgang; Iacus Stefano; Irizarry Rafael; Leisch Friedrich; Li Cheng; Maechler Martin; Rossini Anthony J; Sawitzki Gunther; Smith Colin; Smyth Gordon; Tierney Luke; Yang Jean Y H; Zhang Jianhua
Bioconductor: open software development for computational biology and bioinformatics.
Genome biology 2004;5(10):R80.
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2004: Grigoryev Dmitry N; Ma Shwu-Fan; Irizarry Rafael A; Ye Shui Qing; Quackenbush John; Garcia Joe G N
Orthologous gene-expression profiling in multi-species models: search for candidate genes.
Genome biology 2004;5(5):R34.
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2003: Sidransky David; Irizarry Rafael; Califano Joseph A; Li Xianbin; Ren Hening; Benoit Nicole; Mao Li
Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer patients from control subjects.
Journal of the National Cancer Institute 2003;95(22):1711-7.
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2003: Scharfstein Daniel O; Irizarry Rafael A
Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data.
Biometrics 2003;59(3):601-13.
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2003: Cappola Thomas P; Cope Leslie; Cernetich Amy; Barouch Lili A; Minhas Khalid; Irizarry Rafael A; Parmigiani Giovanni; Durrani Sarfraz; Lavoie Tera; Hoffman Eric P; Ye Shui Q; Garcia Joe G N; Hare Joshua M
Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy.
Physiological genomics 2003;14(1):25-34.
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2003: Irizarry Rafael A; Hobbs Bridget; Collin Francois; Beazer-Barclay Yasmin D; Antonellis Kristen J; Scherf Uwe; Speed Terence P
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
Biostatistics (Oxford, England) 2003;4(2):249-64.
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2003: Tankersley Clarke G; Irizarry Rafael; Flanders Susan E; Rabold Richard; Frank Robert
Unstable heart rate and temperature regulation predict mortality in AKR/J mice.
American journal of physiology. Regulatory, integrative and comparative physiology 2003;284(3):R742-50.
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2003: Irizarry Rafael A; Bolstad Benjamin M; Collin Francois; Cope Leslie M; Hobbs Bridget; Speed Terence P
Summaries of Affymetrix GeneChip probe level data.
Nucleic acids research 2003;31(4):e15.
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2003: Bolstad B M; Irizarry R A; Astrand M; Speed T P
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
Bioinformatics (Oxford, England) 2003;19(2):185-93.
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2003: Irizarry Rafael A; Ooi Siew Loon; Wu Zhijin; Boeke Jef D
Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants.
Statistical applications in genetics and molecular biology 2003;2():Article1.
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2002: Tankersley Clarke G; Irizarry Rafael; Flanders Susan; Rabold Richard
Circadian rhythm variation in activity, body temperature, and heart rate between C3H/HeJ and C57BL/6J inbred strains.
Journal of applied physiology (Bethesda, Md. : 1985) 2002;92(2):870-7.
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2001: Irizarry R A; Tankersley C; Frank R; Flanders S
Assessing homeostasis through circadian patterns.
Biometrics 2001;57(4):1228-37.
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2001: Dipietro J A; Irizarry R A; Hawkins M; Costigan K A; Pressman E K
Cross-correlation of fetal cardiac and somatic activity as an indicator of antenatal neural development.
American journal of obstetrics and gynecology 2001;185(6):1421-8.
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2001: Crone N E; Hao L; Hart J; Boatman D; Lesser R P; Irizarry R; Gordon B
Electrocorticographic gamma activity during word production in spoken and sign language.
Neurology 2001;57(11):2045-53.
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