Photo of John Quackenbush,  PhD

John Quackenbush, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 582-8163
Fax: (617) 582-7760


johnq@jimmy.harvard.edu

John Quackenbush, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Professor, Biostatistics, Harvard T.H. Chan School Of Public Health
  • Professor, Biostatistics and Computational Biology, Dana-Farber Cancer Institute

DF/HCC PROGRAM AFFILIATION

Research Abstract

Two trends are driving innovation and discovery in biological sciences: technologies that allow holistic surveys of genes, proteins, and metabolites and the growing realization that analysis and interpretation of the resulting requires an understanding of the complex factors that mediate the link between genotype and phenotype. The growing body of biological and biomedical information, driven by an exponential drop in the cost of generating genomic data, provides an outstanding opportunity for leveraging what we already “know” in a systematic way to understand the problems that we are studying, including the processes that drive the development of disease phenotypes. Our group uses a variety of bioinformatics and computational approaches, biostatistical analyses, and fundamental laboratory investigation to explore fundamental questions about the nature of human disease. Our approach is based on using high-throughput assays and applying "systems" methods integrate diverse datatypes, including the genome sequence, its annotation, genetic information, phenotype, and the vast body of knowledge captured in the literature. Our goal is not only to develop our own insight into these processes, but to instantiate our methods in tools, protocols, and databases to the broader community that will accelerate research beyond our own.

Publications

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  • Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA 2015; 21:164-71. PubMed
  • Lao T, Glass K, Qiu W, Polverino F, Gupta K, Morrow J, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou X. Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Med 2015; 7:12. PubMed
  • Quackenbush J. Learning to share. Sci Am 2014; 311:S22. PubMed
  • Quackenbush J. Perspective: Learning to share. Nature 2014; 509:S68. PubMed
  • 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. PubMed
  • 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-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood 2014. PubMed
  • 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; 32:327-36. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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; 20:1135-45. PubMed
  • 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. PubMed
  • 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; 25:125-32. PubMed
  • Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J. Inconsistency in large pharmacogenomic studies. Nature 2013; 504:389-93. PubMed
  • 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; 123:5212-30. PubMed
  • 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; 110:18537-42. PubMed
  • 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; 101:263-72. PubMed
  • 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. PubMed
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics 2013. PubMed
  • 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. PubMed
  • Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B. RamiGO: an R/Bioconductor package providing an AmiGO visualize interface. Bioinformatics 2013; 29:666-8. PubMed
  • 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. PubMed
  • 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. PubMed
  • 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; 5:2. PubMed
  • 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:e57799. PubMed
  • 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:e80314. PubMed
  • Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE 2013; 8:e64832. PubMed
  • 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; 9:e1002875. PubMed
  • 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; 18:6136-6146. PubMed
  • 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; 18:5806-5815. PubMed
  • Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. Bioinformatics 2012; 28:2484-92. PubMed
  • 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; 487:491-5. PubMed
  • 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. 2012. PubMed
  • 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; 28:726-728. PubMed
  • 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; 58:580-9. PubMed
  • 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; 104:311-25. PubMed
  • 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; 18:1004-14. PubMed
  • 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-虜B activation. Proc Natl Acad Sci U S A 2012; 109:2467-72. PubMed
  • 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 2011; 40:D1060-6. PubMed
  • 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. PubMed
  • 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 2011; 40:D866-75. PubMed
  • 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:e30269. PubMed
  • 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:e1002531. PubMed
  • Howe EA, Sinha R, Schlauch D, Quackenbush J. RNA-Seq Analysis in MeV. Bioinformatics 2011. PubMed
  • 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; 27:2648-2654. PubMed
  • Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B. survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Bioinformatics 2011. PubMed
  • 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; 108:14902-7. PubMed
  • 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; 7:e1002207. PubMed
  • 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; 85:6764-73. PubMed
  • 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; 474:230-4. PubMed
  • Mar JC, Wells CA, Quackenbush J. Defining an Informativeness Metric for Clustering Gene Expression Data. Bioinformatics 2011. PubMed
  • 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; 108:337-42. PubMed
  • 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:e20826. PubMed
  • 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:e18202. PubMed
  • Liu F, White JA, Antonescu C, Gusenleitner D, Quackenbush J. GCOD - GeneChip Oncology Database. BMC Bioinformatics 2011; 12:46. PubMed
  • Bontempi G, Haibe-Kains B, Desmedt C, Sotiriou C, Quackenbush J. Multiple-input multiple-output causal strategies for gene selection. BMC Bioinformatics 2012; 12:458. PubMed
  • Mar JC, Matigian NA, Quackenbush J, Wells CA. attract: A method for identifying core pathways that define cellular phenotypes. PLoS ONE 2011; 6:e25445. PubMed
  • 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 2012; 2011:923035. PubMed
  • 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. PubMed
  • 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; 177:2731-40. PubMed
  • 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; 96:82-91. PubMed
  • Antonescu C, Antonescu V, Sultana R, Quackenbush J. Using the DFCI gene index databases for biological discovery. Curr Protoc Bioinformatics 2010; Chapter 1:Unit1.6.1-36. PubMed
  • 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. PubMed
  • 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 2009; 38:D716-25. PubMed
  • 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 2009; 119:335-46. PubMed
  • 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 2011; 5:e15581. PubMed
  • Mar JC, Quackenbush J. Decomposition of gene expression state space trajectories. PLoS Comput. Biol. 2009; 5:e1000626. PubMed
  • 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; 15:6327-40. PubMed
  • Culhane AC, Quackenbush J. Confounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Res 2009; 69:7480-5. PubMed
  • 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; 391:57-63. PubMed
  • 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; 94:20-31. PubMed
  • 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; 41:553-62. PubMed
  • 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; 106:6250-5. PubMed
  • 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; 37:108-18. PubMed
  • 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; 27:1160-7. PubMed
  • Bateman A,Quackenbush J. Bioinformatics for next generation sequencing. Bioinformatics 2009; 25:429. PubMed
  • 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:e7932. PubMed
  • 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 2010; 10:409. PubMed
  • 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 2008; 102:264-79. PubMed
  • 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. PubMed
  • 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:e8162. PubMed
  • Quackenbush J. Data reporting standards: making the things we use better. Genome Med 2010; 1:111. PubMed
  • 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; 35:182-90. PubMed
  • Kahvejian A,Quackenbush J,Thompson JF. What would you do if you could sequence everything? Nat Biotechnol 2008; 26:1125-33. PubMed
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  • Cook DN,Wang S,Howles GP,Speer M,Churchhill G,Quackenbush J,Schwartz DA. The genetics of innate immunity in the lung. Chest 2003; 123:369S. PubMed
  • 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; 13:327-40. PubMed
  • 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; 131:419-29. PubMed
  • 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:R5. PubMed
  • 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:R16. PubMed
  • 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; 31:229-33. PubMed
  • Quackenbush J. Open-source software accelerates bioinformatics. Genome Biol 2003; 4:336. PubMed
  • Quackenbush J. Microarray data normalization and transformation. Nat Genet 2002; 32 Suppl:496-501. PubMed
  • 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; 32:1447-56. PubMed
  • 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; 18:1409. PubMed
  • 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; 3:research0062. PubMed
  • 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; 298:539. PubMed
  • 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; 21:7256-65. PubMed
  • 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; 419:512-9. PubMed
  • 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; 13:475-8. PubMed
  • 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; 13:373-9. PubMed
  • 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; 94:513-21. PubMed
  • 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; 12:493-502. PubMed
  • Sturn A,Quackenbush J,Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics 2002; 18:207-8. PubMed
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