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John Quackenbush, PhD

Publications

  • Quackenbush J.Learning to share.Sci Am. 2014 Jul;311(1):S22.
    24974706
  • Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin P.Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.Nat Commun. 2014;5:4006.
    24892406
  • Quackenbush J.Perspective: Learning to share.Nature. 2014 May 29;509(7502):S68.
    24870827
  • Ferrari G, Quackenbush J, Strobeck J, Hu L, Johnson CK, Mak A, Shaw RE, Sayles K, Brizzio ME, Zapolanski A, Grau JB.Comparative genome-wide transcriptional analysis of human left and right internal mammary arteries.Genomics. 2014 May 20.
    24858532
  • Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J.Inference and validation of predictive gene networks from biomedical literature and gene expression data.Genomics. 2014 Mar 29.
    24691108
  • Lee JW, Norden AD, Ligon KL, Golby AJ, Beroukhim R, Quackenbush J, Wells W, Oelschlager K, Maetzold D, Wen PY.Tumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: A gene expression imaging study.Epilepsy Res. 2014 Mar 12.
    24690158
  • Sharron Lin X, Hu L, Sandy K, Correll M, Quackenbush J, Wu CL, Scott McDougal W.Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: Applying RNA-sequencing analysis on archived specimens.Urol Oncol. 2014 Apr;32(3):327-36.
    24055427
  • Adamia S, Haibe-Kains B, Pilarski PM, Bar-Natan M, Pevzner S, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Burke J, Galinsky I, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, Deangelo DJ, Quackenbush J, Stone R, Griffin JD.A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets.Clin Cancer Res. 2014 Mar 1;20(5):1135-45.
    24284058
  • Adamia S, Bar-Natan M, Haibe-Kains B, Pilarski PM, Bach C, Pevzner S, Calimeri T, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Galinsky I, Mathews S, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, Deangelo DJ, Quackenbush J, Tenen DG, Stone RM, Griffin JD.NOTCH2 and FLT3 gene mis-splicing are common events in patients with acute myeloid leukemia (AML): new potential targets in AML.Blood. 2014 Feb 26.
    24574459
  • Li WQ, Han J, Widlund HR, Correll M, Wang YE, Quackenbush J, Mihm MC, Canales AL, Wu S, Golub T, Hoshida Y, Hunter DJ, Murphy G, Kupper TS, Qureshi AA.CXCR4 pathway associated with family history of melanoma.Cancer Causes Control. 2014 Jan;25(1):125-32.
    24158781
  • Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J.Inconsistency in large pharmacogenomic studies.Nature. 2013 Dec 19;504(7480):389-93.
    24284626
  • Merritt MA, Bentink S, Schwede M, Iwanicki MP, Quackenbush J, Woo T, Agoston ES, Reinhardt F, Crum CP, Berkowitz RS, Mok SC, Witt AE, Jones MA, Wang B, Ince TA.Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes.PLoS ONE. 2013;8(11):e80314.
    24303006
  • Lam HC, Cloonan SM, Bhashyam AR, Haspel JA, Singh A, Sathirapongsasuti JF, Cervo M, Yao H, Chung AL, Mizumura K, An CH, Shan B, Franks JM, Haley KJ, Owen CA, Tesfaigzi Y, Washko GR, Quackenbush J, Silverman EK, Rahman I, Kim HP, Mahmood A, Biswal SS, Ryter SW, Choi AM.Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction.J Clin Invest. 2013 Dec 2;123(12):5212-30.
    24200693
  • Portal D, Zhou H, Zhao B, Kharchenko PV, Lowry E, Wong L, Quackenbush J, Holloway D, Jiang S, Lu Y, Kieff E.Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18537-42.
    24167291
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC.Passing messages between biological networks to refine predicted interactions.PLoS ONE. 2013;8(5):e64832.
    23741402
  • Correll M, Johnson CK, Ferrari G, Brizzio M, Mak AW, Quackenbush J, Shaw RE, Zapolanski A, Grau JB.Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting.Genomics. 2013 Feb 24.
    23462555
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC.A tiered hidden Markov model characterizes multi-scale chromatin states.Genomics. 2013 Apr 6.
    23570996
  • Zhou X, Qiu W, Sathirapongsasuti JF, Cho MH, Mancini JD, Lao T, Thibault DM, Litonjua AA, Bakke PS, Gulsvik A, Lomas DA, Beaty TH, Hersh CP, Anderson C, Geigenmuller U, Raby BA, Rennard SI, Perrella MA, Choi AM, Quackenbush J, Silverman EK.Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells.Genomics. 2013 May;101(5):263-72.
    23459001
  • De Rienzo A, Richards WG, Yeap BY, Coleman MH, Sugarbaker PE, Chirieac LR, Wang YE, Quackenbush J, Jensen RV, Bueno R.Sequential Binary Gene Ratio Tests Define a Novel Molecular Diagnostic Strategy for Malignant Pleural Mesothelioma.Clin Cancer Res. 2013 Apr 18.
    23493352
  • Kelly AD, Hill KE, Correll M, Hu L, Wang Y, Rubio R, Duan S, Quackenbush J, Spentzos D.Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Preliminary assessment of cross-platform concordance.Genomics. 2013 Apr 3.
    23562991
  • Schwede M, Spentzos D, Bentink S, Hofmann O, Haibe-Kains B, Harrington D, Quackenbush J, Culhane AC.Stem Cell-Like Gene Expression in Ovarian Cancer Predicts Type II Subtype and Prognosis.PLoS ONE. 2013;8(3):e57799.
    23536770
  • Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B.RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.Bioinformatics. 2013 Mar 1;29(5):666-8.
    23297033
  • Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B.Significance analysis of prognostic signatures.PLoS Comput. Biol. 2013 Jan;9(1):e1002875.
    23365551
  • Papillon-Cavanagh S, De Jay N, Hachem N, Olsen C, Bontempi G, Aerts HJ, Quackenbush J, Haibe-Kains B.Comparison and validation of genomic predictors for anticancer drug sensitivity.J Am Med Inform Assoc. 2013 Jan 26.
    23355484
  • Kelly AD, Haibe-Kains B, Janeway KA, Hill KE, Howe E, Goldsmith J, Kurek K, Perez-Atayde AR, Francoeur N, Fan JB, April C, Schneider H, Gebhardt MC, Culhane A, Quackenbush J, Spentzos D.MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.Genome Med. 2013 Jan 22;5(1):2.
    23339462
  • Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS, Parmigiani G, Huttenhower C.Expression Profiling of Archival Tumors for Long-term Health Studies.Clin Cancer Res. 2012 Nov 15;18(22):6136-6146.
    23136189
  • Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, Defazio A, Quackenbush J, Berkowitz RS, Iglehart JD, Bowtell DD, , Matulonis UA.Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome.Clin Cancer Res. 2012 Oct 15;18(20):5806-5815.
    22912389
  • Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC.iBBiG: iterative binary bi-clustering of gene sets.Bioinformatics. 2012 Oct 1;28(19):2484-92.
    22789589
  • Fountzilas E, Kelly AD, Perez-Atayde AR, Goldsmith J, Konstantinopoulos PA, Francoeur N, Correll M, Rubio R, Hu L, Gebhardt MC, Quackenbush J, Spentzos D.A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study.BMC Genomics. 2012;13:332.
    22823907
  • Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M.Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.Nature. 2012 Jul 26;487(7408):491-5.
    22810586
  • Gulbahce N, Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rozenblatt-Rosen O, Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Simonis N, Huh KW, Hellner K, Grace M, Chen A, Rubio R, Marto JA, Christakis NA, Kieff E, Roth FP, Roecklein-Canfield J, Decaprio JA, Cusick ME, Quackenbush J, Hill DE, Münger K, Vidal M, Barabási AL.Viral perturbations of host networks reflect disease etiology.PLoS Comput. Biol. 2012;8(6):e1002531.
    22761553
  • Skiadas CC, Duan S, Correll M, Rubio R, Karaca N, Ginsburg ES, Quackenbush J, Racowsky C.Ovarian reserve status in young women is associated with altered gene expression in membrana granulosa cells.Molecular Human Reproduction. 2012 Mar 9.
    22355044
  • Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes C.nEASE: a method for gene ontology subclassification of high-throughput gene expression data.Bioinformatics. 2012 Mar 1;28(5):726-728.
    22247278
  • Milbury CA, Correll M, Quackenbush J, Rubio R, Makrigiorgos GM.COLD-PCR Enrichment of Rare Cancer Mutations prior to Targeted Amplicon Resequencing.Clin Chem. 2012 Mar;58(3):580-9.
    22194627
  • Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C.A three-gene model to robustly identify breast cancer molecular subtypes.Journal of the National Cancer Institute. 2012 Feb 22;104(4):311-25.
    22262870
  • Bentink S, Haibe-Kains B, Risch T, Fan JB, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Culhane A, Drapkin R, Quackenbush J, Matulonis UA.Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer.PLoS ONE. 2012;7(2):e30269.
    22348002
  • Desmedt C, Majjaj S, Kheddoumi N, Singhal SK, Haibe-Kains B, El Ouriaghli F, Chaboteaux C, Michiels S, Lallemand F, Journe F, Duvillier H, Loi S, Quackenbush J, Dekoninck S, Blanpain C, Lagneaux L, Houhou N, Delorenzi M, Larsimont D, Piccart M, Sotiriou C.Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment.Clin Cancer Res. 2012 Feb 15;18(4):1004-14.
    22235100
  • Gewurz BE, Towfic F, Mar JC, Shinners NP, Takasaki K, Zhao B, Cahir-McFarland ED, Quackenbush J, Xavier RJ, Kieff E.Genome-wide siRNA screen for mediators of NF-κB activation.Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2467-72.
    22308454
  • Bontempi G, Haibe-Kains B, Desmedt C, Sotiriou C, Quackenbush J.Multiple-input multiple-output causal strategies for gene selection.BMC Bioinformatics. 2011;12:458.
    22118187
  • Cannon EK, Birkett SM, Braun BL, Kodavali S, Jennewein DM, Yilmaz A, Antonescu V, Antonescu C, Harper LC, Gardiner JM, Schaeffer ML, Campbell DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, Lawrence CJ.POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.Int J Plant Genomics. 2011;2011:923035.
    22253616
  • Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J.Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.Nucleic Acids Res. 2012 Jan;40(Database issue):D866-75.
    22096235
  • Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J.GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.Nucleic Acids Res. 2012 Jan;40(Database issue):D1060-6.
    22110038
  • Mar JC, Matigian NA, Quackenbush J, Wells CA.attract: A method for identifying core pathways that define cellular phenotypes.PLoS ONE. 2011;6(10):e25445.
    22022396
  • Howe EA, Sinha R, Schlauch D, Quackenbush J.RNA-Seq Analysis in MeV.Bioinformatics. 2011 Oct 5.
    21976420
  • Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.Bioinformatics. 2011 Oct 1;27(19):2648-2654.
    21828086
  • Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B.survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.Bioinformatics. 2011 Sep 7.
    21903630
  • Zhao B, Zou J, Wang H, Johannsen E, Peng CW, Quackenbush J, Mar JC, Morton CC, Freedman ML, Blacklow SC, Aster JC, Bernstein BE, Kieff E.Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth.Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14902-7.
    21746931
  • Mar JC, Matigian NA, Mackay-Sim A, Mellick GD, Sue CM, Silburn PA, McGrath JJ, Quackenbush J, Wells CA.Variance of gene expression identifies altered network constraints in neurological disease.PLoS Genet. 2011 Aug;7(8):e1002207.
    21852951
  • Marko NF, Quackenbush J, Weil RJ.Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data.PLoS ONE. 2011;6(7):e20826.
    21829433
  • Gewurz BE, Mar JC, Padi M, Zhao B, Shinners NP, Takasaki K, Bedoya E, Zou JY, Cahir-McFarland E, Quackenbush J, Kieff E.Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation.J Virol. 2011 Jul;85(13):6764-73.
    21543491
  • Jirawatnotai S, Hu Y, Michowski W, Elias JE, Becks L, Bienvenu F, Zagozdzon A, Goswami T, Wang YE, Clark AB, Kunkel TA, van Harn T, Xia B, Correll M, Quackenbush J, Livingston DM, Gygi SP, Sicinski P.A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers.Nature. 2011 Jun 9;474(7350):230-4.
    21654808
  • Konstantinopoulos PA, Cannistra SA, Fountzilas H, Culhane A, Pillay K, Rueda B, Cramer D, Seiden M, Birrer M, Coukos G, Zhang L, Quackenbush J, Spentzos D.Integrated analysis of multiple microarray datasets identifies a reproducible survival predictor in ovarian cancer.PLoS ONE. 2011;6(3):e18202.
    21479231
  • Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA.Data standards for omics data: the basis of data sharing and reuse.Methods Mol Biol. 2011;719:31-69.
    21370078
  • Liu F, White JA, Antonescu C, Gusenleitner D, Quackenbush J.GCOD - GeneChip Oncology Database.BMC Bioinformatics. 2011;12:46.
    21291543
  • Mar JC, Wells CA, Quackenbush J.Defining an Informativeness Metric for Clustering Gene Expression Data.Bioinformatics. 2011 Feb 16.
    21330289
  • Chittenden TW, Pak J, Rubio R, Cheng H, Holton K, Prendergast N, Glinskii V, Cai Y, Culhane A, Bentink S, Schwede M, Mar JC, Howe EA, Aryee M, Sultana R, Lanahan AA, Taylor JM, Holmes C, Hahn WC, Zhao JJ, Iglehart JD, Quackenbush J.Therapeutic implications of GIPC1 silencing in cancer.PLoS ONE. 2010;5(12):e15581.
    21209904
  • Zhao B, Mar JC, Maruo S, Lee S, Gewurz BE, Johannsen E, Holton K, Rubio R, Takada K, Quackenbush J, Kieff E.Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines.Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):337-42.
    21173222
  • Tanaka N, Huttenhower C, Nosho K, Baba Y, Shima K, Quackenbush J, Haigis KM, Giovannucci E, Fuchs CS, Ogino S.Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer.Am J Pathol. 2010 Dec;177(6):2731-40.
    21037082
  • Tseveleki V, Rubio R, Vamvakas SS, White J, Taoufik E, Petit E, Quackenbush J, Probert L.Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes.Genomics. 2010 Aug;96(2):82-91.
    20435134
  • Colak D, Chishti MA, Al-Bakheet AB, Al-Qahtani A, Shoukri MM, Goyns MH, Ozand PT, Quackenbush J, Park BH, Kaya N.Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old.Mol Cancer. 2010;9:146.
    20540791
  • Antonescu C, Antonescu V, Sultana R, Quackenbush J.Using the DFCI gene index databases for biological discovery.Curr Protoc Bioinformatics. 2010 Mar;Chapter 1:Unit1.6.1-36.
    20205187
  • Quackenbush J.Data reporting standards: making the things we use better.Genome Med. 2009;1(11):111.
    19939294
  • Aryee MJ, Gutiérrez-Pabello JA, Kramnik I, Maiti T, Quackenbush J.An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).BMC Bioinformatics. 2009;10:409.
    20003283
  • Mar JC, Quackenbush J.Decomposition of gene expression state space trajectories.PLoS Comput. Biol. 2009 Dec;5(12):e1000626.
    20041215
  • Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J.GeneSigDB--a curated database of gene expression signatures.Nucleic Acids Res. 2010 Jan;38(Database issue):D716-25.
    19934259
  • Chen DT,Nasir A,Culhane A,Venkataramu C,Fulp W,Rubio R,Wang T,Agrawal D,McCarthy SM,Gruidl M,Bloom G,Anderson T,White J,Quackenbush J,Yeatman T.Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue.Breast Cancer Res Treat. 2010 Jan;119(2):335-46.
    19266279
  • April C, Klotzle B, Royce T, Wickham-Garcia E, Boyaniwsky T, Izzo J, Cox D, Jones W, Rubio R, Holton K, Matulonis U, Quackenbush J, Fan JB.Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.PLoS ONE. 2009;4(12):e8162.
    19997620
  • Santagata S, Maire CL, Idbaih A, Geffers L, Correll M, Holton K, Quackenbush J, Ligon KL.CRX is a diagnostic marker of retinal and pineal lineage tumors.PLoS ONE. 2009;4(11):e7932.
    19936203
  • Speers C, Tsimelzon A, Sexton K, Herrick AM, Gutierrez C, Culhane A, Quackenbush J, Hilsenbeck S, Chang J, Brown P.Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer.Clin Cancer Res. 2009 Oct 15;15(20):6327-40.
    19808870
  • Culhane AC, Quackenbush J.Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".Cancer Res. 2009 Sep 15;69(18):7480-5.
    19723662
  • Hellner K, Mar J, Fang F, Quackenbush J, Münger K.HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition.Virology. 2009 Aug 15;391(1):57-63.
    19552933
  • Colak D,Kaya N,Al-Zahrani J,Al Bakheet A,Muiya P,Andres E,Quackenbush J,Dzimiri N.Left ventricular global transcriptional profiling in human end-stage dilated cardiomyopathy.Genomics. 2009 Jul;94(1):20-31.
    19332114
  • Suzuki H,Forrest AR,van Nimwegen E,Daub CO,Balwierz PJ,Irvine KM,Lassmann T,Ravasi T,Hasegawa Y,de Hoon MJ,Katayama S,Schroder K,Carninci P,Tomaru Y,Kanamori-Katayama M,Kubosaki A,Akalin A,Ando Y,Arner E,Asada M,Asahara H,Bailey T,Bajic VB,Bauer D,Beckhouse AG,Bertin N,Bjorkegren J,Brombacher F,Bulger E,Chalk AM,Chiba J,Cloonan N,Dawe A,Dostie J,Engstrom PG,Essack M,Faulkner GJ,Fink JL,Fredman D,Fujimori K,Furuno M,Gojobori T,Gough J,Grimmond SM,Gustafsson M,Hashimoto M,Hashimoto T,Hatakeyama M,Heinzel S,Hide W,Hofmann O,Hornquist M,Huminiecki L,Ikeo K,Imamoto N,Inoue S,Inoue Y,Ishihara R,Iwayanagi T,Jacobsen A,Kaur M,Kawaji H,Kerr MC,Kimura R,Kimura S,Kimura Y,Kitano H,Koga H,Kojima T,Kondo S,Konno T,Krogh A,Kruger A,Kumar A,Lenhard B,Lennartsson A,Lindow M,Lizio M,Macpherson C,Maeda N,Maher CA,Maqungo M,Mar J,Matigian NA,Matsuda H,Mattick JS,Meier S,Miyamoto S,Miyamoto-Sato E,Nakabayashi K,Nakachi Y,Nakano M,Nygaard S,Okayama T,Okazaki Y,Okuda-Yabukami H,Orlando V,Otomo J,Pachkov M,Petrovsky N,Plessy C,Quackenbush J,Radovanovic A,Rehli M,Saito R,Sandelin A,Schmeier S,Schonbach C,Schwartz AS,Semple CA,Sera M,Severin J,Shirahige K,Simons C,St Laurent G,Suzuki M,Suzuki T,Sweet MJ,Taft RJ,Takeda S,Takenaka Y,Tan K,Taylor MS,Teasdale RD,Tegner J,Teichmann S,Valen E,Wahlestedt C,Waki K,Waterhouse A,Wells CA,Winther O,Wu L,Yamaguchi K,Yanagawa H,Yasuda J,Zavolan M,Hume DA,Arakawa T,Fukuda S,Imamura K,Kai C,Kaiho A,Kawashima T,Kawazu C,Kitazume Y,Kojima M,Miura H,Murakami K,Murata M,Ninomiya N,Nishiyori H,Noma S,Ogawa C,Sano T,Simon C,Tagami M,Takahashi Y,Kawai J,Hayashizaki Y.The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.Nat Genet. 2009 May;41(5):553-62.
    19377474
  • Mar JC,Kimura Y,Schroder K,Irvine KM,Hayashizaki Y,Suzuki H,Hume D,Quackenbush J.Data-driven normalization strategies for high-throughput quantitative RT-PCR.BMC Bioinformatics. 2009;10:110.
    19374774
  • Fedorov VB,Goropashnaya AV,Toien O,Stewart NC,Gracey AY,Chang C,Qin S,Pertea G,Quackenbush J,Showe LC,Showe MK,Boyer BB,Barnes BM.Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).Physiol Genomics. 2009 Apr 10;37(2):108-18.
    19240299
  • Gorgun G,Ramsay AG,Holderried TA,Zahrieh D,Le Dieu R,Liu F,Quackenbush J,Croce CM,Gribben JG.E(mu)-TCL1 mice represent a model for immunotherapeutic reversal of chronic lymphocytic leukemia-induced T-cell dysfunction.Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6250-5.
    19332800
  • Parker JS,Mullins M,Cheang MC,Leung S,Voduc D,Vickery T,Davies S,Fauron C,He X,Hu Z,Quackenbush JF,Stijleman IJ,Palazzo J,Marron JS,Nobel AB,Mardis E,Nielsen TO,Ellis MJ,Perou CM,Bernard PS.Supervised risk predictor of breast cancer based on intrinsic subtypes.J Clin Oncol. 2009 Mar 10;27(8):1160-7.
    19204204
  • Bateman A,Quackenbush J.Bioinformatics for next generation sequencing.Bioinformatics. 2009 Feb 15;25(4):429.
    19202193
  • Nosho K,Irahara N,Shima K,Kure S,Kirkner GJ,Schernhammer ES,Hazra A,Hunter DJ,Quackenbush J,Spiegelman D,Giovannucci EL,Fuchs CS,Ogino S.Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample.PLoS ONE. 2008;3(11):e3698.
    19002263
  • Dutta B,Kanani H,Quackenbush J,Klapa MI.Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures.Biotechnol Bioeng. 2009 Jan 1;102(1):264-79.
    18958862
  • Kahvejian A,Quackenbush J,Thompson JF.What would you do if you could sequence everything?.Nat Biotechnol. 2008 Oct;26(10):1125-33.
    18846086
  • Kitami T,Rubio R,O'Brien W,Quackenbush J,Nadeau JH.Gene-environment interactions reveal a homeostatic role for cholesterol metabolism during dietary folate perturbation in mice.Physiol Genomics. 2008 Oct 8;35(2):182-90.
    18697859
  • Taylor CF,Field D,Sansone SA,Aerts J,Apweiler R,Ashburner M,Ball CA,Binz PA,Bogue M,Booth T,Brazma A,Brinkman RR,Michael Clark A,Deutsch EW,Fiehn O,Fostel J,Ghazal P,Gibson F,Gray T,Grimes G,Hancock JM,Hardy NW,Hermjakob H,Julian RK Jr,Kane M,Kettner C,Kinsinger C,Kolker E,Kuiper M,Le Novere N,Leebens-Mack J,Lewis SE,Lord P,Mallon AM,Marthandan N,Masuya H,McNally R,Mehrle A,Morrison N,Orchard S,Quackenbush J,Reecy JM,Robertson DG,Rocca-Serra P,Rodriguez H,Rosenfelder H,Santoyo-Lopez J,Scheuermann RH,Schober D,Smith B,Snape J,Stoeckert CJ Jr,Tipton K,Sterk P,Untergasser A,Vandesompele J,Wiemann S.Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.Nat Biotechnol. 2008 Aug;26(8):889-96.
    18688244
  • Aryee MJ,Quackenbush J.An optimized predictive strategy for interactome mapping.J Proteome Res. 2008 Sep;7(9):4089-94.
    18642945
  • Djebbari A,Quackenbush J.Seeded Bayesian Networks: constructing genetic networks from microarray data.BMC Syst Biol. 2008;2:57.
    18601736
  • Brown LA,Hoog J,Chin SF,Tao Y,Zayed AA,Chin K,Teschendorff AE,Quackenbush JF,Marioni JC,Leung S,Perou CM,Neilsen TO,Ellis M,Gray JW,Bernard PS,Huntsman DG,Caldas C.ESR1 gene amplification in breast cancer: a common phenomenon?.Nat Genet. 2008 Jul;40(7):806-7; author reply 810-2.
    18583964
  • Boedigheimer MJ,Wolfinger RD,Bass MB,Bushel PR,Chou JW,Cooper M,Corton JC,Fostel J,Hester S,Lee JS,Liu F,Liu J,Qian HR,Quackenbush J,Pettit S,Thompson KL.Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories.BMC Genomics. 2008;9:285.
    18549499
  • Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush J.Functional classification analysis of somatically mutated genes in human breast and colorectal cancers.Genomics. 2008 Jun;91(6):508-11.
    18434084
  • Lee Y,Quackenbush J.Using the TIGR gene index databases for biological discovery.Curr Protoc Bioinformatics. 2003 Nov;Chapter 1:Unit 1.6.
    18428690
  • Taoufik E, Petit E, Divoux D, Tseveleki V, Mengozzi M, Roberts ML, Valable S, Ghezzi P, Quackenbush J, Brines M, Cerami A, Probert L.TNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injury.Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6185-90.
    18413601
  • Bastien R, Lewis TB, Hawkes JE, Quackenbush JF, Robbins TC, Palazzo J, Perou CM, Bernard PS.High-throughput amplicon scanning of the TP53 gene in breast cancer using high-resolution fluorescent melting curve analyses and automatic mutation calling.Hum Mutat. 2008 May;29(5):757-64.
    18348286
  • Cheng AS, Culhane AC, Chan MW, Venkataramu CR, Ehrich M, Nasir A, Rodriguez BA, Liu J, Yan PS, Quackenbush J, Nephew KP, Yeatman TJ, Huang TH.Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.Cancer Res. 2008 Mar 15;68(6):1786-96.
    18339859
  • Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).Nat Biotechnol. 2008 Mar;26(3):305-12.
    18327244
  • Chan AP,Rabinowicz PD,Quackenbush J,Buell CR,Town CD.Plant database resources at The Institute for Genomic Research.Methods Mol Biol. 2007;406:113-36.
    18287690
  • Hollingsworth JW,Whitehead G,Berman KG,Tekippe EM,Gilmour MI,Larkin JE,Quackenbush J,Schwartz DA.Genetic basis of murine antibacterial defense to streptococcal lung infection.Immunogenetics. 2007 Sep;59(9):713-24.
    17701033
  • Mullins M, Perreard L, Quackenbush JF, Gauthier N, Bayer S, Ellis M, Parker J, Perou CM, Szabo A, Bernard PS.Agreement in Breast Cancer Classification between Microarray and Quantitative Reverse Transcription PCR from Fresh-Frozen and Formalin-Fixed, Paraffin-Embedded Tissues.Clin Chem. 2007 Jul;53(7):1273-9.
    17525107
  • Raj JU, Aliferis C, Caprioli RM, Cowley AW Jr, Davies PF, Duncan MW, Erle DJ, Erzurum SC, Finn PW, Ischiropoulos H, Kaminski N, Kleeberger SR, Leikauf GD, Loyd JE, Martin TR, Matalon S, Moore JH, Quackenbush J, Sabo-Attwood T, Shapiro SD, Schnitzer JE, Schwartz DA, Schwiebert LM, Sheppard D, Ware LB, Weiss ST, Whitsett JA, Wurfel MM, Matthay MA.Genomics and proteomics of lung disease: conference summary.Am J Physiol Lung Cell Mol Physiol. 2007 Jul;293(1):L45-51.
    17468134
  • Danley PD,Mullen SP,Liu F,Nene V,Quackenbush J,Shaw KL.A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution.BMC Genomics. 2007;8:109.
    17459168
  • Quackenbush J.Extracting biology from high-dimensional biological data.J Exp Biol. 2007 May;210(Pt 9):1507-17.
    17449816
  • Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X.Microarray blob-defect removal improves array analysis.Bioinformatics. 2007 Apr 15;23(8):966-71.
    17332024
  • Mar JC,Rubio R,Quackenbush J.Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples.Genome Biol. 2006;7(12):R119.
    17169148
  • Frith MC,Bailey TL,Kasukawa T,Mignone F,Kummerfeld SK,Madera M,Sunkara S,Furuno M,Bult CJ,Quackenbush J,Kai C,Kawai J,Carninci P,Hayashizaki Y,Pesole G,Mattick JS.Discrimination of non-protein-coding transcripts from protein-coding mRNA.RNA Biol. 2006 Jan-Mar;3(1):40-8.
    17114936
  • Maher EA, Brennan C, Wen PY, Durso L, Ligon KL, Richardson A, Khatry D, Feng B, Sinha R, Louis DN, Quackenbush J, Black PM, Chin L, DePinho RA.Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities.Cancer Res. 2006 Dec 1;66(23):11502-13.
    17114236
  • Quackenbush J.Weighing our measures of gene expression.Mol Syst Biol. 2006;2:63.
    17102808
  • 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, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.BMC Bioinformatics. 2006;7:489.
    17087822
  • Chan VS, Chau SY, Tian L, Chen Y, Kwong SK, Quackenbush J, Dallman M, Lamb J, Tam PK.Sonic hedgehog promotes CD4+ T lymphocyte proliferation and modulates the expression of a subset of CD28-targeted genes.Int Immunol. 2006 Dec;18(12):1627-36.
    17005629
  • Saeed AI,Bhagabati NK,Braisted JC,Liang W,Sharov V,Howe EA,Li J,Thiagarajan M,White JA,Quackenbush J.TM4 microarray software suite.Methods Enzymol. 2006;411:134-93. Review.
    16939790
  • Quackenbush J, Irizarry RA.Response to Shields: 'MIAME, we have a problem'.Trends Genet. 2006 Sep;22(9):471-2.
    16859802
  • Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J.Uneven chromosome contraction and expansion in the maize genome.Genome Res. 2006 Oct;16(10):1241-51.
    16902087
  • Brooksbank C, Quackenbush J.Data standards: a call to action.OMICS. 2006 Summer;10(2):94-9. Review.
    16901212
  • Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).OMICS. 2006 Summer;10(2):205-8. Review.
    16901227
  • Quackenbush J.From 'omes to biology.Anim Genet. 2006 Aug;37 Suppl 1:48-56.
    16887002
  • Quackenbush J, Salzberg SL.It is time to end the patenting of software.Bioinformatics. 2006 Jun 15;22(12):1416-7.
    16766564
  • Quackenbush J.Microarray analysis and tumor classification.N Engl J Med. 2006 Jun 8;354(23):2463-72. Review.
    16760446
  • Quackenbush J.Standardizing the standards.Mol Syst Biol. 2006;2:2006.0010.
    16738556
  • Hu VW,Frank BC,Heine S,Lee NH,Quackenbush J.Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes.BMC Genomics. 2006;7:118.
    16709250
  • Maeda N,Kasukawa T,Oyama R,Gough J,Frith M,Engstrom PG,Lenhard B,Aturaliya RN,Batalov S,Beisel KW,Bult CJ,Fletcher CF,Forrest AR,Furuno M,Hill D,Itoh M,Kanamori-Katayama M,Katayama S,Katoh M,Kawashima T,Quackenbush J,Ravasi T,Ring BZ,Shibata K,Sugiura K,Takenaka Y,Teasdale RD,Wells CA,Zhu Y,Kai C,Kawai J,Hume DA,Carninci P,Hayashizaki Y.Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.PLoS Genet. 2006 Apr;2(4):e62.
    16683036
  • Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.Top-down standards will not serve systems biology.Nature. 2006 Mar 2;440(7080):24.
    16511469
  • Walker JK, Ahumada A, Frank B, Gaspard R, Berman K, Quackenbush J, Schwartz DA.Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsiveness.Am J Respir Cell Mol Biol. 2006 Jun;34(6):711-8.
    16474097
  • Hackl H,Burkard TR,Sturn A,Rubio R,Schleiffer A,Tian S,Quackenbush J,Eisenhaber F,Trajanoski Z.Molecular processes during fat cell development revealed by gene expression profiling and functional annotation.Genome Biol. 2005;6(13):R108.
    16420668
  • Malek RL,Wang HY,Kwitek AE,Greene AS,Bhagabati N,Borchardt G,Cahill L,Currier T,Frank B,Fu X,Hasinoff M,Howe E,Letwin N,Luu TV,Saeed A,Sajadi H,Salzberg SL,Sultana R,Thiagarajan M,Tsai J,Veratti K,White J,Quackenbush J,Jacob HJ,Lee NH.Physiogenomic resources for rat models of heart, lung and blood disorders.Nat Genet. 2006 Feb;38(2):234-9.
    16415889
  • Stoeckert C,Ball C,Brazma A,Brinkman R,Causton H,Fan L,Fostel J,Fragoso G,Heiskanen M,Holstege F,Morrison N,Parkinson H,Quackenbush J,Rocca-Serra P,Sansone SA,Sarkans U,Sherlock G,Stevens R,Taylor C,Taylor R,Whetzel P,White J.Wrestling with SUMO and bio-ontologies.Nat Biotechnol. 2006 Jan;24(1):21-2; author reply 23.
    16404382
  • Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J.TM4 microarray software suite.Methods Enzymol. 2006;411:134-193.
  • Quackenbush J.Computational approaches to analysis of DNA microarray data.Methods Inf Med. 2006;45 Supp 1:91-103.
  • Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS.Discrimination of Non-Protein-Coding Transcripts from Protein-Coding mRNA.RNA Biol. 2006;3(1):in press.
  • Chan AP,Pertea G,Cheung F,Lee D,Zheng L,Whitelaw C,Pontaroli AC,SanMiguel P,Yuan Y,Bennetzen J,Barbazuk WB,Quackenbush J,Rabinowicz PD.The TIGR Maize Database.Nucleic Acids Res. 2006 Jan 1;34(Database issue):D771-6.
    16381977
  • Quackenbush J.Meeting the Challenges of Functional Genomics: From the Laboratory to the Clinic.Preclinica. 2005 Dec 30;2:313-316.
  • Cui L,Fan Q,Hu Y,Karamycheva SA,Quackenbush J,Khuntirat B,Sattabongkot J,Carlton JM.Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages.Mol Biochem Parasitol. 2005 Nov;144(1):1-9.
    16085323
  • Quackenbush J.Extracting meaning from functional genomics experiments.Toxicol Appl Pharmacol. 2005 Sep 1;207(2 Suppl):195-9.
    16002114
  • Kwong KY,Bloom GC,Yang I,Boulware D,Coppola D,Haseman J,Chen E,McGrath A,Makusky AJ,Taylor J,Steiner S,Zhou J,Yeatman TJ,Quackenbush J.Synchronous global assessment of gene and protein expression in colorectal cancer progression.Genomics. 2005 Aug;86(2):142-58.
    15951154
  • Djebbari A,Karamycheva S,Howe E,Quackenbush J.MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.Bioinformatics. 2005 Aug 1;21(15):3324-6.
    15919728
  • Eschrich S,Yang I,Bloom G,Kwong KY,Boulware D,Cantor A,Coppola D,Kruhoffer M,Aaltonen L,Orntoft TF,Quackenbush J,Yeatman TJ.Molecular staging for survival prediction of colorectal cancer patients.J Clin Oncol. 2005 May 20;23(15):3526-35.
    15908663
  • Margolin AA,Greshock J,Naylor TL,Mosse Y,Maris JM,Bignell G,Saeed AI,Quackenbush J,Weber BL.CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.Bioinformatics. 2005 Aug 1;21(15):3308-11.
    15905276
  • Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J.Independence and reproducibility across microarray platforms.Nat Methods. 2005 May;2(5):337-44.
    15846360
  • 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,Martinez-Murillo F,Morsberger L,Lee H,Petersen D,Quackenbush J,Scott A,Wilson M,Yang Y,Ye SQ,Yu W.Multiple-laboratory comparison of microarray platforms.Nat Methods. 2005 May;2(5):345-50.
    15846361
  • Marko NF,Frank B,Quackenbush J,Lee NH.A robust method for the amplification of RNA in the sense orientation.BMC Genomics. 2005;6(1):27.
    15740627
  • Liu F,Vantoai T,Moy LP,Bock G,Linford LD,Quackenbush J.Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis.Plant Physiol. 2005 Mar;137(3):1115-29.
    15734912
  • Bergman NH,Passalacqua KD,Gaspard R,Shetron-Rama LM,Quackenbush J,Hanna PC.Murine macrophage transcriptional responses to Bacillus anthracis infection and intoxication.Infect Immun. 2005 Feb;73(2):1069-80.
    15664951
  • Stanley Kim H,Yu Y,Snesrud EC,Moy LP,Linford LD,Haas BJ,Nierman WC,Quackenbush J.Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome.Plant J. 2005 Jan;41(2):212-20.
    15634198
  • Ball C,Brazma A,Causton H,Chervitz S,Edgar R,Hingamp P,Matese JC,Icahn C,Parkinson H,Quackenbush J,Ringwald M,Sansone SA,Sherlock G,Spellman P,Stoeckert C,Tateno Y,Taylor R,White J,Winegarden N.An open letter on microarray data from the MGED Society.Microbiology. 2004 Nov;150(Pt 11):3522-4.
    15528642
  • Nene V,Lee D,Kang'a S,Skilton R,Shah T,de Villiers E,Mwaura S,Taylor D,Quackenbush J,Bishop R.Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva.Insect Biochem Mol Biol. 2004 Oct;34(10):1117-28.
    15475305
  • Ball C,Brazma A,Causton H,Chervitz S,Edgar R,Hingamp P,Matese JC,Parkinson H,Quackenbush J,Ringwald M,Sansone SA,Sherlock G,Spellman P,Stoeckert C,Tateno Y,Taylor R,White J,Winegarden N.Standards for microarray data: an open letter.Environ Health Perspect. 2004 Aug;112(12):A666-7.
    15345376
  • Ball CA,Brazma A,Causton H,Chervitz S,Edgar R,Hingamp P,Matese JC,Parkinson H,Quackenbush J,Ringwald M,Sansone SA,Sherlock G,Spellman P,Stoeckert C,Tateno Y,Taylor R,White J,Winegarden N.Submission of microarray data to public repositories.PLoS Biol. 2004 Sep;2(9):E317.
    15340489
  • Cook DN,Wang S,Wang Y,Howles GP,Whitehead GS,Berman KG,Church TD,Frank BC,Gaspard RM,Yu Y,Quackenbush J,Schwartz DA.Genetic regulation of endotoxin-induced airway disease.Genomics. 2004 Jun;83(6):961-9.
    15177550
  • Ghedin E,Pumfery A,de la Fuente C,Yao K,Miller N,Lacoste V,Quackenbush J,Jacobson S,Kashanchi F.Use of a multi-virus array for the study of human viral and retroviral pathogens: gene expression studies and ChIP-chip analysis.Retrovirology. 2004;1:10.
    15169557
  • Cronin M,Ghosh K,Sistare F,Quackenbush J,Vilker V,O'Connell C.Universal RNA reference materials for gene expression.Clin Chem. 2004 Aug;50(8):1464-71.
    15155546
  • 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 Biol. 2004;5(5):R34.
    15128448
  • Larkin JE,Frank BC,Gaspard RM,Duka I,Gavras H,Quackenbush J.Cardiac transcriptional response to acute and chronic angiotensin II treatments.Physiol Genomics. 2004 Jul 8;18(2):152-66.
    15126644
  • Quackenbush J.Data standards for 'omic' science.Nat Biotechnol. 2004 May;22(5):613-4.
    15122299
  • Sharov V,Kwong KY,Frank B,Chen E,Hasseman J,Gaspard R,Yu Y,Yang I,Quackenbush J.The limits of log-ratios.BMC Biotechnol. 2004 Mar 8;4:3.
    15113428
  • Imanishi T,Itoh T,Suzuki Y,O'Donovan C,Fukuchi S,Koyanagi KO,Barrero RA,Tamura T,Yamaguchi-Kabata Y,Tanino M,Yura K,Miyazaki S,Ikeo K,Homma K,Kasprzyk A,Nishikawa T,Hirakawa M,Thierry-Mieg J,Thierry-Mieg D,Ashurst J,Jia L,Nakao M,Thomas MA,Mulder N,Karavidopoulou Y,Jin L,Kim S,Yasuda T,Lenhard B,Eveno E,Suzuki Y,Yamasaki C,Takeda J,Gough C,Hilton P,Fujii Y,Sakai H,Tanaka S,Amid C,Bellgard M,Bonaldo Mde F,Bono H,Bromberg SK,Brookes AJ,Bruford E,Carninci P,Chelala C,Couillault C,de Souza SJ,Debily MA,Devignes MD,Dubchak I,Endo T,Estreicher A,Eyras E,Fukami-Kobayashi K,Gopinath GR,Graudens E,Hahn Y,Han M,Han ZG,Hanada K,Hanaoka H,Harada E,Hashimoto K,Hinz U,Hirai M,Hishiki T,Hopkinson I,Imbeaud S,Inoko H,Kanapin A,Kaneko Y,Kasukawa T,Kelso J,Kersey P,Kikuno R,Kimura K,Korn B,Kuryshev V,Makalowska I,Makino T,Mano S,Mariage-Samson R,Mashima J,Matsuda H,Mewes HW,Minoshima S,Nagai K,Nagasaki H,Nagata N,Nigam R,Ogasawara O,Ohara O,Ohtsubo M,Okada N,Okido T,Oota S,Ota M,Ota T,Otsuki T,Piatier-Tonneau D,Poustka A,Ren SX,Saitou N,Sakai K,Sakamoto S,Sakate R,Schupp I,Servant F,Sherry S,Shiba R,Shimizu N,Shimoyama M,Simpson AJ,Soares B,Steward C,Suwa M,Suzuki M,Takahashi A,Tamiya G,Tanaka H,Taylor T,Terwilliger JD,Unneberg P,Veeramachaneni V,Watanabe S,Wilming L,Yasuda N,Yoo HS,Stodolsky M,Makalowski W,Go M,Nakai K,Takagi T,Kanehisa M,Sakaki Y,Quackenbush J,Okazaki Y,Hayashizaki Y,Hide W,Chakraborty R,Nishikawa K,Sugawara H,Tateno Y,Chen Z,Oishi M,Tonellato P,Apweiler R,Okubo K,Wagner L,Wiemann S,Strausberg RL,Isogai T,Auffray C,Nomura N,Gojobori T,Sugano S.Integrative annotation of 21,037 human genes validated by full-length cDNA clones.PLoS Biol. 2004 Jun;2(6):e162.
    15103394
  • Agrawal D,Chen T,Irby R,Quackenbush J,Chambers AF,Szabo M,Cantor A,Coppola D,Yeatman TJ.Osteopontin identified as colon cancer tumor progression marker.C R Biol. 2003 Oct-Nov;326(10-11):1041-3.
    14744111
  • Klapa MI,Quackenbush J.The quest for the mechanisms of life.Biotechnol Bioeng. 2003 Dec 30;84(7):739-42.
    14708113
  • Bloom G,Yang IV,Boulware D,Kwong KY,Coppola D,Eschrich S,Quackenbush J,Yeatman TJ.Multi-platform, multi-site, microarray-based human tumor classification.Am J Pathol. 2004 Jan;164(1):9-16.
    14695313
  • Brentani H,Caballero OL,Camargo AA,da Silva AM,da Silva WA Jr,Dias Neto E,Grivet M,Gruber A,Guimaraes PE,Hide W,Iseli C,Jongeneel CV,Kelso J,Nagai MA,Ojopi EP,Osorio EC,Reis EM,Riggins GJ,Simpson AJ,de Souza S,Stevenson BJ,Strausberg RL,Tajara EH,Verjovski-Almeida S,Acencio ML,Bengtson MH,Bettoni F,Bodmer WF,Briones MR,Camargo LP,Cavenee W,Cerutti JM,Coelho Andrade LE,Costa dos Santos PC,Ramos Costa MC,da Silva IT,Estecio MR,Sa Ferreira K,Furnari FB,Faria M Jr,Galante PA,Guimaraes GS,Holanda AJ,Kimura ET,Leerkes MR,Lu X,Maciel RM,Martins EA,Massirer KB,Melo AS,Mestriner CA,Miracca EC,Miranda LL,Nobrega FG,Oliveira PS,Paquola AC,Pandolfi JR,Campos Pardini MI,Passetti F,Quackenbush J,Schnabel B,Sogayar MC,Souza JE,Valentini SR,Zaiats AC,Amaral EJ,Arnaldi LA,de Araujo AG,de Bessa SA,Bicknell DC,Ribeiro de Camaro ME,Carraro DM,Carrer H,Carvalho AF,Colin C,Costa F,Curcio C,Guerreiro da Silva ID,Pereira da Silva N,Dellamano M,El-Dorry H,Espreafico EM,Scattone Ferreira AJ,Ayres Ferreira C,Fortes MA,Gama AH,Giannella-Neto D,Giannella ML,Giorgi RR,Goldman GH,Goldman MH,Hackel C,Ho PL,Kimura EM,Kowalski LP,Krieger JE,Leite LC,Lopes A,Luna AM,Mackay A,Mari SK,Marques AA,Martins WK,Montagnini A,Mourao Neto M,Nascimento AL,Neville AM,Nobrega MP,O'Hare MJ,Otsuka AY,Ruas de Melo AI,Paco-Larson ML,Guimaraes Pereira G,Pereira da Silva N,Pesquero JB,Pessoa JG,Rahal P,Rainho CA,Rodrigues V,Rogatto SR,Romano CM,Romeiro JG,Rossi BM,Rusticci M,Guerra de Sa R,Sant' Anna SC,Sarmazo ML,Silva TC,Soares FA,Sonati Mde F,de Freitas Sousa J,Queiroz D,Valente V,Vettore AL,Villanova FE,Zago MA,Zalcberg H.The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13418-23.
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  • Quackenbush J.Genomics. Microarrays--guilt by association.Science. 2003 Oct 10;302(5643):240-1.
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  • Quackenbush J.Open-source software accelerates bioinformatics.Genome Biol. 2003;4(9):336.
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  • Chen T,Yang I,Irby R,Shain KH,Wang HG,Quackenbush J,Coppola D,Cheng JQ,Yeatman TJ.Regulation of caspase expression and apoptosis by adenomatous polyposis coli.Cancer Res. 2003 Aug 1;63(15):4368-74.
    12907606
  • Kasukawa T,Furuno M,Nikaido I,Bono H,Hume DA,Bult C,Hill DP,Baldarelli R,Gough J,Kanapin A,Matsuda H,Schriml LM,Hayashizaki Y,Okazaki Y,Quackenbush J.Development and evaluation of an automated annotation pipeline and cDNA annotation system.Genome Res. 2003 Jun;13(6B):1542-51.
    12819153
  • Wells CA,Ravasi T,Sultana R,Yagi K,Carninci P,Bono H,Faulkner G,Okazaki Y,Quackenbush J,Hume DA,Lyons PA.Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage.Genome Res. 2003 Jun;13(6B):1360-5.
    12819134
  • Merrick JM,Osman A,Tsai J,Quackenbush J,LoVerde PT,Lee NH.The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences.J Parasitol. 2003 Apr;89(2):261-9.
    12760639
  • Abulencia JP,Gaspard R,Healy ZR,Gaarde WA,Quackenbush J,Konstantopoulos K.Shear-induced cyclooxygenase-2 via a JNK2/c-Jun-dependent pathway regulates prostaglandin receptor expression in chondrocytic cells.J Biol Chem. 2003 Aug 1;278(31):28388-94.
    12743126
  • Dudoit S,Gentleman RC,Quackenbush J.Open source software for the analysis of microarray data.Biotechniques. 2003 Mar;Suppl:45-51.
    12664684
  • Pertea G,Huang X,Liang F,Antonescu V,Sultana R,Karamycheva S,Lee Y,White J,Cheung F,Parvizi B,Tsai J,Quackenbush J.TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.Bioinformatics. 2003 Mar 22;19(5):651-2.
    12651724
  • Cook DN,Wang S,Howles GP,Speer M,Churchhill G,Quackenbush J,Schwartz DA.The genetics of innate immunity in the lung.Chest. 2003 Mar;123(3 Suppl):369S.
    12628980
  • Zhu Y,King BL,Parvizi B,Brunk BP,Stoeckert CJ Jr,Quackenbush J,Richardson J,Bult CJ.Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.Genome Biol. 2003;4(2):R16.
    12620126
  • Kim H,Snesrud EC,Haas B,Cheung F,Town CD,Quackenbush J.Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.Genome Res. 2003 Mar;13(3):327-40.
    12618363
  • Ronning CM,Stegalkina SS,Ascenzi RA,Bougri O,Hart AL,Utterbach TR,Vanaken SE,Riedmuller SB,White JA,Cho J,Pertea GM,Lee Y,Karamycheva S,Sultana R,Tsai J,Quackenbush J,Griffiths HM,Restrepo S,Smart CD,Fry WE,Van Der Hoeven R,Tanksley S,Zhang P,Jin H,Yamamoto ML,Baker BJ,Buell CR.Comparative analyses of potato expressed sequence tag libraries.Plant Physiol. 2003 Feb;131(2):419-29.
    12586867
  • Wang HY,Malek RL,Kwitek AE,Greene AS,Luu TV,Behbahani B,Frank B,Quackenbush J,Lee NH.Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays.Genome Biol. 2003;4(1):R5.
    12540297
  • Yuan Q,Ouyang S,Liu J,Suh B,Cheung F,Sultana R,Lee D,Quackenbush J,Buell CR.The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.Nucleic Acids Res. 2003 Jan 1;31(1):229-33.
    12519988
  • Quackenbush J.Microarray data normalization and transformation.Nat Genet. 2002 Dec;32 Suppl:496-501.
    12454644
  • Yang IV,Chen E,Hasseman JP,Liang W,Frank BC,Wang S,Sharov V,Saeed AI,White J,Li J,Lee NH,Yeatman TJ,Quackenbush J.Within the fold: assessing differential expression measures and reproducibility in microarray assays.Genome Biol. 2002 Oct 24;3(11):research0062.
    12429061
  • Ball CA,Sherlock G,Parkinson H,Rocca-Sera P,Brooksbank C,Causton HC,Cavalieri D,Gaasterland T,Hingamp P,Holstege F,Ringwald M,Spellman P,Stoeckert CJ Jr,Stewart JE,Taylor R,Brazma A,Quackenbush J.The underlying principles of scientific publication.Bioinformatics. 2002 Nov;18(11):1409.
    12424109
  • Nene V,Lee D,Quackenbush J,Skilton R,Mwaura S,Gardner MJ,Bishop R.AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum.Int J Parasitol. 2002 Nov;32(12):1447-56.
    12392910
  • Ball CA,Sherlock G,Parkinson H,Rocca-Sera P,Brooksbank C,Causton HC,Cavalieri D,Gaasterland T,Hingamp P,Holstege F,Ringwald M,Spellman P,Stoeckert CJ Jr,Stewart JE,Taylor R,Brazma A,Quackenbush J.Standards for microarray data.Science. 2002 Oct 18;298(5593):539.
    12387284
  • Malek RL,Irby RB,Guo QM,Lee K,Wong S,He M,Tsai J,Frank B,Liu ET,Quackenbush J,Jove R,Yeatman TJ,Lee NH.Identification of Src transformation fingerprint in human colon cancer.Oncogene. 2002 Oct 17;21(47):7256-65.
    12370817
  • Carlton JM,Angiuoli SV,Suh BB,Kooij TW,Pertea M,Silva JC,Ermolaeva MD,Allen JE,Selengut JD,Koo HL,Peterson JD,Pop M,Kosack DS,Shumway MF,Bidwell SL,Shallom SJ,van Aken SE,Riedmuller SB,Feldblyum TV,Cho JK,Quackenbush J,Sedegah M,Shoaibi A,Cummings LM,Florens L,Yates JR,Raine JD,Sinden RE,Harris MA,Cunningham DA,Preiser PR,Bergman LW,Vaidya AB,van Lin LH,Janse CJ,Waters AP,Smith HO,White OR,Salzberg SL,Venter JC,Fraser CM,Hoffman SL,Gardner MJ,Carucci DJ.Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.Nature. 2002 Oct 3;419(6906):512-9.
    12368865
  • Fahrenkrug SC,Smith TP,Freking BA,Cho J,White J,Vallet J,Wise T,Rohrer G,Pertea G,Sultana R,Quackenbush J,Keele JW.Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly.Mamm Genome. 2002 Aug;13(8):475-8.
    12226715
  • Sonstegard TS,Capuco AV,White J,Van Tassell CP,Connor EE,Cho J,Sultana R,Shade L,Wray JE,Wells KD,Quackenbush J.Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index.Mamm Genome. 2002 Jul;13(7):373-9.
    12140684
  • Agrawal D,Chen T,Irby R,Quackenbush J,Chambers AF,Szabo M,Cantor A,Coppola D,Yeatman TJ.Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling.Journal of the National Cancer Institute. 2002 Apr 3;94(7):513-21.
    11929952
  • Lee Y,Sultana R,Pertea G,Cho J,Karamycheva S,Tsai J,Parvizi B,Cheung F,Antonescu V,White J,Holt I,Liang F,Quackenbush J.Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).Genome Res. 2002 Mar;12(3):493-502.
    11875039
  • Sturn A,Quackenbush J,Trajanoski Z.Genesis: cluster analysis of microarray data.Bioinformatics. 2002 Jan;18(1):207-8.
    11836235