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John Quackenbush, PhD

Publications

  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC.A tiered hidden Markov model characterizes multi-scale chromatin states.Genomics. 2013 Apr 6.
    23570996
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Brooksbank C, Quackenbush J.Data standards: a call to action.OMICS. 2006 Summer;10(2):94-9. Review.
    16901212
  • 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
  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J.Independence and reproducibility across microarray platforms.Nat Methods. 2005 May;2(5):337-44.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • 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.
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  • Klapa MI,Quackenbush J.The quest for the mechanisms of life.Biotechnol Bioeng. 2003 Dec 30;84(7):739-42.
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  • 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.
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  • 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.
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  • 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.
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