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John Quackenbush, Ph.D.

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Research
research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
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  1. T32LM012411 (QUACKENBUSH, JOHN) Apr 1, 2016 - Mar 31, 2021
    NIH/NLM
    Statistical and Quantitative Training in Big Data Health Science
    Role: Principal Investigator
  2. U24CA194354 (AERTS, HUGO) Apr 1, 2015 - Mar 31, 2020
    NIH/NCI
    Quantitative Radiomics System Decoding the Tumor Phenotype
    Role: Co-Principal Investigator
  3. U01CA190234 (AERTS, HUGO) Jan 9, 2015 - Dec 31, 2019
    NIH/NCI
    Genotype and Imaging Phenotype Biomarkers in Lung Cancer
    Role: Co-Principal Investigator
  4. R01HL111759 (QUACKENBUSH, JOHN) Sep 1, 2012 - Jul 31, 2016
    NIH/NHLBI
    Using Networks to Assign Gene Function in Lung Disease
    Role: Principal Investigator
  5. U01CA151118 (QUACKENBUSH, JOHN) Sep 7, 2011 - Aug 31, 2016
    NIH/NCI
    MeV: Software for Next Generation Genomic Data Analysis
    Role: Principal Investigator
research resources
This researcher has shared information about their research resources in the eagle-i Network. To update or add resource records, contact eagle-i@hms.harvard.edu.
Center for Cancer Computational Biology (DFCI) - Core services (4), Databases (2), Instruments (3) and Software (2)

Bibliographic
selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Hersh CP, Adcock IM, Celedón JC, Cho MH, Christiani DC, Himes BE, Kaminski N, Mathias RA, Meyers DA, Quackenbush J, Redline S, Steiling KA, Tabor HK, Tobin MD, Wurfel MM, Yang IV, Koppelman GH. High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc. 2019 Jan; 16(1):1-16. PMID: 30592451.
    View in: PubMed
  2. Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Res. 2018 Oct 01; 78(19):5538-5547. PMID: 30275053.
    View in: PubMed
  3. Hosny A, Parmar C, Quackenbush J, Schwartz LH, Aerts HJWL. Artificial intelligence in radiology. Nat Rev Cancer. 2018 Aug; 18(8):500-510. PMID: 29777175.
    View in: PubMed
  4. Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush J. Histopathological Image QTL Discovery of Immune Infiltration Variants. iScience. 2018 Jul 27; 5:80-89. PMID: 30240647.
    View in: PubMed
  5. Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. Br J Cancer. 2018 May; 118(11):1492-1501. PMID: 29765148.
    View in: PubMed
  6. Morrow JD, Glass K, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci. Am J Respir Crit Care Med. 2018 May 15; 197(10):1275-1284. PMID: 29313708.
    View in: PubMed
  7. Padi M, Quackenbush J. Detecting phenotype-driven transitions in regulatory network structure. NPJ Syst Biol Appl. 2018; 4:16. PMID: 29707235.
    View in: PubMed
  8. Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics. 2018 Apr 01; 19(2):185-198. PMID: 29036413.
    View in: PubMed
  9. Parmar C, Barry JD, Hosny A, Quackenbush J, Aerts HJWL. Data Analysis Strategies in Medical Imaging. Clin Cancer Res. 2018 Aug 01; 24(15):3492-3499. PMID: 29581134.
    View in: PubMed
  10. Domenyuk V, Gatalica Z, Santhanam R, Wei X, Stark A, Kennedy P, Toussaint B, Levenberg S, Wang J, Xiao N, Greil R, Rinnerthaler G, Gampenrieder SP, Heimberger AB, Berry DA, Barker A, Quackenbush J, Marshall JL, Poste G, Vacirca JL, Vidal GA, Schwartzberg LS, Halbert DD, Voss A, Magee D, Miglarese MR, Famulok M, Mayer G, Spetzler D. Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes. Nat Commun. 2018 03 23; 9(1):1219. PMID: 29572535.
    View in: PubMed
  11. Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN. Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. MBio. 2018 03 06; 9(2). PMID: 29511081.
    View in: PubMed
  12. Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics. 2018 01 15; 12(1):1. PMID: 29335020.
    View in: PubMed
  13. Driesbaugh KH, Branchetti E, Grau JB, Keeney SJ, Glass K, Oyama MA, Rioux N, Ayoub S, Sacks MS, Quackenbush J, Levy RJ, Ferrari G. Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation. J Mol Cell Cardiol. 2018 Feb; 115:94-103. PMID: 29291394.
    View in: PubMed
  14. Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating drivers of cell state transitions using gene regulatory network models. BMC Syst Biol. 2017 Dec 13; 11(1):139. PMID: 29237467.
    View in: PubMed
  15. Kibbe W, Klemm J, Quackenbush J. Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research. Cancer Res. 2017 11 01; 77(21):e1-e2. PMID: 29092926.
    View in: PubMed
  16. Wang YE, Kutnetsov L, Partensky A, Farid J, Quackenbush J. WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data. Cancer Res. 2017 11 01; 77(21):e11-e14. PMID: 29092929.
    View in: PubMed
  17. Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Rep. 2017 Oct 24; 21(4):1077-1088. PMID: 29069589.
    View in: PubMed
  18. Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics. 2017 Oct 03; 18(1):437. PMID: 28974199.
    View in: PubMed
  19. Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. 2017 Sep 12; 18(1):723. PMID: 28899340.
    View in: PubMed
  20. Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proc Natl Acad Sci U S A. 2017 09 12; 114(37):E7841-E7850. PMID: 28851834.
    View in: PubMed
  21. Qiu W, Guo F, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG. Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. J Allergy Clin Immunol. 2018 Apr; 141(4):1250-1258. PMID: 28736268.
    View in: PubMed
  22. Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating gene regulatory networks with pandaR. Bioinformatics. 2017 Jul 15; 33(14):2232-2234. PMID: 28334344.
    View in: PubMed
  23. Nishihara R, Glass K, Mima K, Hamada T, Nowak JA, Qian ZR, Kraft P, Giovannucci EL, Fuchs CS, Chan AT, Quackenbush J, Ogino S, Onnela JP. Biomarker correlation network in colorectal carcinoma by tumor anatomic location. BMC Bioinformatics. 2017 Jun 17; 18(1):304. PMID: 28623901.
    View in: PubMed
  24. Rios Velazquez E, Parmar C, Liu Y, Coroller TP, Cruz G, Stringfield O, Ye Z, Makrigiorgos M, Fennessy F, Mak RH, Gillies R, Quackenbush J, Aerts HJWL. Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer. Cancer Res. 2017 07 15; 77(14):3922-3930. PMID: 28566328.
    View in: PubMed
  25. Hill KE, Kelly AD, Kuijjer ML, Barry W, Rattani A, Garbutt CC, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani MS, Cote G, Hornicek F, Choy E, Duan Z, Quackenbush J, Haibe-Kains B, Spentzos D. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. J Hematol Oncol. 2017 05 15; 10(1):107. PMID: 28506242.
    View in: PubMed
  26. Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 05 08; 18(1):84. PMID: 28482897.
    View in: PubMed
  27. Morrow JD, Zhou X, Lao T, Jiang Z, DeMeo DL, Cho MH, Qiu W, Cloonan S, Pinto-Plata V, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Choi AM, Silverman EK, Hersh CP. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Sci Rep. 2017 03 13; 7:44232. PMID: 28287180.
    View in: PubMed
  28. Domenyuk V, Zhong Z, Stark A, Xiao N, O'Neill HA, Wei X, Wang J, Tinder TT, Tonapi S, Duncan J, Hornung T, Hunter A, Miglarese MR, Schorr J, Halbert DD, Quackenbush J, Poste G, Berry DA, Mayer G, Famulok M, Spetzler D. Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach. Sci Rep. 2017 02 20; 7:42741. PMID: 28218293.
    View in: PubMed
  29. Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PLoS One. 2017; 12(2):e0170181. PMID: 28152060.
    View in: PubMed
  30. Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017 02; 28(2):167-176. PMID: 28097472.
    View in: PubMed
  31. Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature. 2016 11 30; 540(7631):E6-E8. PMID: 27905416.
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  32. Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature. 2016 11 30; 540(7631):E11-E12. PMID: 27905423.
    View in: PubMed
  33. Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature. 2016 11 30; 540(7631):E2-E4. PMID: 27905430.
    View in: PubMed
  34. Berrios C, Padi M, Keibler MA, Park DE, Molla V, Cheng J, Lee SM, Stephanopoulos G, Quackenbush J, DeCaprio JA. Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation. PLoS Pathog. 2016 Nov; 12(11):e1006020. PMID: 27880818.
    View in: PubMed
  35. Kusko RL, Brothers JF, Tedrow J, Pandit K, Huleihel L, Perdomo C, Liu G, Juan-Guardela B, Kass D, Zhang S, Lenburg M, Martinez F, Quackenbush J, Sciurba F, Limper A, Geraci M, Yang I, Schwartz DA, Beane J, Spira A, Kaminski N. Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2016 10 15; 194(8):948-960. PMID: 27104832.
    View in: PubMed
  36. Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. Revisiting inconsistency in large pharmacogenomic studies. F1000Res. 2016; 5:2333. PMID: 28928933.
    View in: PubMed
  37. Platig J, Castaldi PJ, DeMeo D, Quackenbush J. Bipartite Community Structure of eQTLs. PLoS Comput Biol. 2016 09; 12(9):e1005033. PMID: 27618581.
    View in: PubMed
  38. Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AM, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics. 2016 Aug 26; 1-10. PMID: 27564456.
    View in: PubMed
  39. Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE. BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinformatics. 2016 12 15; 32(24):3836-3838. PMID: 27540268.
    View in: PubMed
  40. Elias KM, Emori MM, Westerling T, Long H, Budina-Kolomets A, Li F, MacDuffie E, Davis MR, Holman A, Lawney B, Freedman ML, Quackenbush J, Brown M, Drapkin R. Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors. JCI Insight. 2016 Aug 18; 1(13). PMID: 27617304.
    View in: PubMed
  41. Vargas AJ, Quackenbush J, Glass K. Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. Genomics. 2016 10; 108(3-4):126-133. PMID: 27524493.
    View in: PubMed
  42. van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics. 2016 11 01; 32(21):3363-3365. PMID: 27402905.
    View in: PubMed
  43. Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B. Assessment of pharmacogenomic agreement. F1000Res. 2016; 5:825. PMID: 27408686; PMCID: PMC4926729.
    View in: PubMed, PubMed Central
  44. Wu W, Parmar C, Grossmann P, Quackenbush J, Lambin P, Bussink J, Mak R, Aerts HJ. Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology. Front Oncol. 2016; 6:71. PMID: 27064691; PMCID: PMC4811956.
    View in: PubMed, PubMed Central
  45. Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC. Toward clinical genomics in everyday medicine: perspectives and recommendations. Expert Rev Mol Diagn. 2016; 16(5):521-32. PMID: 26810587; PMCID: PMC4841021.
    View in: PubMed, PubMed Central
  46. Malleshaiah M, Padi M, Rué P, Quackenbush J, Martinez-Arias A, Gunawardena J. Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation. Cell Rep. 2016 Feb 09; 14(5):1181-1194. PMID: 26832399; PMCID: PMC4749452.
    View in: PubMed, PubMed Central
  47. Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney KT, Chen ZH, Goldklang MP, Yuan GC, Moore SC, Demeo DL, Rouault TA, D'Armiento JM, Schon EA, Manfredi G, Quackenbush J, Mahmood A, Silverman EK, Owen CA, Choi AM. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med. 2016 Feb; 22(2):163-74. PMID: 26752519.
    View in: PubMed
  48. Padi M, Quackenbush J. Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. BMC Syst Biol. 2015 Nov 14; 9:80. PMID: 26576632; PMCID: PMC4650867.
    View in: PubMed, PubMed Central
  49. De Rienzo A, Archer MA, Yeap BY, Dao N, Sciaranghella D, Sideris AC, Zheng Y, Holman AG, Wang YE, Dal Cin PS, Fletcher JA, Rubio R, Croft L, Quackenbush J, Sugarbaker PE, Munir KJ, Battilana JR, Gustafson CE, Chirieac LR, Ching SM, Wong J, Tay LC, Rudd S, Hercus R, Sugarbaker DJ, Richards WG, Bueno R. Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma. Cancer Res. 2016 Jan 15; 76(2):319-28. PMID: 26554828; PMCID: PMC4715909 [Available on 01/15/17].
    View in: PubMed, PubMed Central
  50. Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. BMC Bioinformatics. 2015 Apr 11; 16:115. PMID: 25888305; PMCID: PMC4408593.
    View in: PubMed, PubMed Central
  51. Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B. Using shRNA experiments to validate gene regulatory networks. Genom Data. 2015 Jun; 4:123-6. PMID: 26484195; PMCID: PMC4535466.
    View in: PubMed, PubMed Central
  52. 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(1):12. PMID: 25763110; PMCID: PMC4355149.
    View in: PubMed, PubMed Central
  53. 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 Feb; 21(2):164-71. PMID: 25519487; PMCID: PMC4338344.
    View in: PubMed, PubMed Central
  54. Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, Spira A, Kaminski N, Schwartz DA. Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2014 Dec 01; 190(11):1263-72. PMID: 25333685; PMCID: PMC4315819.
    View in: PubMed, PubMed Central
  55. Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol. 2014 Nov 28; 8:118. PMID: 25431000; PMCID: PMC4269917.
    View in: PubMed, PubMed Central
  56. Castaldi PJ, Cho MH, Zhou X, Qiu W, Mcgeachie M, Celli B, Bakke P, Gulsvik A, Lomas DA, Crapo JD, Beaty TH, Rennard S, Harshfield B, Lange C, Singh D, Tal-Singer R, Riley JH, Quackenbush J, Raby BA, Carey VJ, Silverman EK, Hersh CP. Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci. Hum Mol Genet. 2015 Feb 15; 24(4):1200-10. PMID: 25315895.
    View in: PubMed
  57. Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Carvalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin P. Corrigendum: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat Commun. 2014; 5:4644. PMID: 25100327.
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  58. Mason EA, Mar JC, Laslett AL, Pera MF, Quackenbush J, Wolvetang E, Wells CA. Gene expression variability as a unifying element of the pluripotency network. Stem Cell Reports. 2014 Aug 12; 3(2):365-77. PMID: 25254348; PMCID: PMC4175554.
    View in: PubMed, PubMed Central
  59. Hatzis C, Bedard PL, Birkbak NJ, Beck AH, Aerts HJ, Stem DF, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B. Enhancing reproducibility in cancer drug screening: how do we move forward? Cancer Res. 2014 Aug 01; 74(15):4016-23. PMID: 25015668; PMCID: PMC4119520.
    View in: PubMed, PubMed Central
  60. Chu JH, Hersh CP, Castaldi PJ, Cho MH, Raby BA, Laird N, Bowler R, Rennard S, Loscalzo J, Quackenbush J, Silverman EK. Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. BMC Syst Biol. 2014 Jun 25; 8:78. PMID: 24964944; PMCID: PMC4105829.
    View in: PubMed, PubMed Central
  61. Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B. Relevance of different prior knowledge sources for inferring gene interaction networks. Front Genet. 2014; 5:177. PMID: 25009552; PMCID: PMC4067568.
    View in: PubMed, PubMed Central
  62. Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Carvalho S, 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 Jun 03; 5:4006. PMID: 24892406; PMCID: PMC4059926.
    View in: PubMed, PubMed Central
  63. Quackenbush J. Perspective: Learning to share. Nature. 2014 May 29; 509(7502):S68. PMID: 24870827; PMCID: PMC4205237.
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  64. 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 Jul; 104(1):36-44. PMID: 24858532; PMCID: PMC4152843.
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  65. 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 May-Jun; 103(5-6):329-36. PMID: 24691108; PMCID: PMC4119824.
    View in: PubMed, PubMed Central
  66. 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 Jul; 108(5):843-52. PMID: 24690158; PMCID: PMC4076930.
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  67. 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 May 01; 123(18):2816-25. PMID: 24574459; PMCID: PMC4007608.
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  68. Quackenbush JF, Cassidy PB, Pfeffer LM, Boucher KM, Hawkes JE, Pfeffer SR, Kopelovich L, Leachman SA. Isolation of circulating microRNAs from microvesicles found in human plasma. Methods Mol Biol. 2014; 1102:641-53. PMID: 24259003.
    View in: PubMed
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  70. 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. PMID: 24284626.
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  71. 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 01; 20(5):1135-45. PMID: 24284058; PMCID: PMC4458245.
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  72. 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. PMID: 24303006.
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  74. 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. PMID: 24167291; PMCID: PMC3832032.
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  75. 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. PMID: 24158781; PMCID: PMC4100594.
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  76. 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. PMID: 24055427; PMCID: PMC4446054.
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  77. Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS One. 2013; 8(5):e64832. PMID: 23741402; PMCID: PMC3669401.
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  78. Fan JB, Quackenbush J, Wacek B. Accelerating genomic data publishing and sharing. Genom Data. 2013 Dec; 1:1. PMID: 26484049; PMCID: PMC4608866.
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  79. Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul; 102(1):1-7. PMID: 23570996; PMCID: PMC3676702.
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  80. Kelly AD, Hill KE, Correll M, Hu L, Wang YE, 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 Jul; 102(1):8-14. PMID: 23562991; PMCID: PMC4116671.
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  81. 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 May 01; 19(9):2493-502. PMID: 23493352; PMCID: PMC3644001.
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  82. 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. PMID: 23536770; PMCID: PMC3594231.
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  83. 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. PMID: 23459001; PMCID: PMC3659826.
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  84. 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 Jun; 101(6):313-7. PMID: 23462555; PMCID: PMC4149181.
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  85. 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 Jul-Aug; 20(4):597-602. PMID: 23355484; PMCID: PMC3721163.
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  86. 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(1):e1002875. PMID: 23365551; PMCID: PMC3554539.
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  87. 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(1):2. PMID: 23339462; PMCID: PMC3706900.
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  88. Schröder MS, Gusenleitner D, Quackenbush J, Culhane AC, Haibe-Kains B. RamiGO: an R/Bioconductor package providing an AmiGO visualize interface. Bioinformatics. 2013 Mar 01; 29(5):666-8. PMID: 23297033; PMCID: PMC3582261.
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  90. 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):5806-15. PMID: 22912389; PMCID: PMC4205235.
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  92. 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 Jul 23; 13:332. PMID: 22823907; PMCID: PMC3443663.
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  93. Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. iBBiG: iterative binary bi-clustering of gene sets. Bioinformatics. 2012 Oct 01; 28(19):2484-92. PMID: 22789589; PMCID: PMC3463116.
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  94. 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. PMID: 22761553; PMCID: PMC3386155.
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  95. 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. Mol Hum Reprod. 2012 Jul; 18(7):362-71. PMID: 22355044; PMCID: PMC3378309.
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  96. 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. PMID: 22348002; PMCID: PMC3278409.
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  97. 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. J Natl Cancer Inst. 2012 Feb 22; 104(4):311-25. PMID: 22262870; PMCID: PMC3283537.
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  98. 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-?B activation. Proc Natl Acad Sci U S A. 2012 Feb 14; 109(7):2467-72. PMID: 22308454; PMCID: PMC3289371.
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  99. 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 01; 28(5):726-8. PMID: 22247278.
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  100. 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. PMID: 22235100; PMCID: PMC4446057.
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  102. 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. PMID: 22194627; PMCID: PMC3418918.
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  103. Bontempi G, Haibe-Kains B, Desmedt C, Sotiriou C, Quackenbush J. Multiple-input multiple-output causal strategies for gene selection. BMC Bioinformatics. 2011 Nov 25; 12:458. PMID: 22118187; PMCID: PMC3323860.
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  104. 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. PMID: 22110038; PMCID: PMC3245038.
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  105. 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. PMID: 22096235; PMCID: PMC3245161.
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  106. 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. PMID: 22022396; PMCID: PMC3194807.
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  107. Howe EA, Sinha R, Schlauch D, Quackenbush J. RNA-Seq analysis in MeV. Bioinformatics. 2011 Nov 15; 27(22):3209-10. PMID: 21976420.
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  109. 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. PMID: 21852951; PMCID: PMC3154954.
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  110. 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 01; 27(19):2648-54. PMID: 21828086; PMCID: PMC3179661.
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  111. 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. PMID: 21829433; PMCID: PMC3145641.
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  112. 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 06; 108(36):14902-7. PMID: 21746931; PMCID: PMC3169132.
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  114. 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. PMID: 21543491; PMCID: PMC3126495.
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  115. 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 Mar 29; 6(3):e18202. PMID: 21479231; PMCID: PMC3066217.
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  116. Mar JC, Wells CA, Quackenbush J. Defining an informativeness metric for clustering gene expression data. Bioinformatics. 2011 Apr 15; 27(8):1094-100. PMID: 21330289; PMCID: PMC3072547.
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  117. Liu F, White JA, Antonescu C, Gusenleitner D, Quackenbush J. GCOD - GeneChip Oncology Database. BMC Bioinformatics. 2011 Feb 03; 12:46. PMID: 21291543; PMCID: PMC3045303.
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  118. 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. PMID: 21370078; PMCID: PMC4152841.
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  120. 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 04; 108(1):337-42. PMID: 21173222; PMCID: PMC3017193.
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  121. 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. PMID: 21037082; PMCID: PMC2993288.
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  122. 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 Jun 12; 9:146. PMID: 20540791; PMCID: PMC2898705.
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  123. 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. PMID: 20435134; PMCID: PMC4205236.
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  124. 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. PMID: 20205187; PMCID: PMC4205239.
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  126. 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 Dec 10; 10:409. PMID: 20003283; PMCID: PMC2801687.
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  127. 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 Dec 03; 4(12):e8162. PMID: 19997620; PMCID: PMC2780295.
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  129. 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. PMID: 19934259; PMCID: PMC2808880.
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  130. 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 Nov 20; 4(11):e7932. PMID: 19936203; PMCID: PMC2775954.
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  131. 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. PMID: 19808870; PMCID: PMC2763053.
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  132. 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. PMID: 19723662; PMCID: PMC3128918.
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  133. 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. PMID: 19552933; PMCID: PMC2728214.
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  135. 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 Apr 19; 10:110. PMID: 19374774; PMCID: PMC2680405.
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  136. 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. PMID: 19332800; PMCID: PMC2669383.
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  137. 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. PMID: 19332114; PMCID: PMC4152850.
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  138. 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. PMID: 19266279; PMCID: PMC2796276.
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  139. Fedorov VB, Goropashnaya AV, Tøien Ø, 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 04 10; 37(2):108-18. PMID: 19240299; PMCID: PMC3774579.
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  140. 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. PMID: 19204204; PMCID: PMC2667820.
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  141. Bateman A, Quackenbush J. Bioinformatics for next generation sequencing. Bioinformatics. 2009 Feb 15; 25(4):429. PMID: 19202193.
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  142. 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 01; 102(1):264-279. PMID: 18958862; PMCID: PMC4134133.
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  143. 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. PMID: 19002263; PMCID: PMC2579485.
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  144. Kahvejian A, Quackenbush J, Thompson JF. What would you do if you could sequence everything? Nat Biotechnol. 2008 Oct; 26(10):1125-33. PMID: 18846086; PMCID: PMC4153598.
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  145. 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 08; 35(2):182-90. PMID: 18697859; PMCID: PMC2575958.
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  146. 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, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère 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, 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. PMID: 18688244; PMCID: PMC2771753.
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  147. Aryee MJ, Quackenbush J. An optimized predictive strategy for interactome mapping. J Proteome Res. 2008 Sep; 7(9):4089-94. PMID: 18642945.
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  148. Djebbari A, Quackenbush J. Seeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol. 2008 Jul 04; 2:57. PMID: 18601736; PMCID: PMC2474592.
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  149. 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. PMID: 18583964; PMCID: PMC2846830.
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  150. 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 Jun 12; 9:285. PMID: 18549499; PMCID: PMC2453529.
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  151. 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. PMID: 18348286.
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  152. 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. PMID: 18434084; PMCID: PMC2492759.
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  153. 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. PMID: 18413601; PMCID: PMC2299225.
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  154. 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. PMID: 18339859; PMCID: PMC4172329.
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  155. 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, 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. PMID: 18327244; PMCID: PMC4367930.
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  156. 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. PMID: 17701033.
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  157. 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. PMID: 17525107.
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  158. Quackenbush J. Extracting biology from high-dimensional biological data. J Exp Biol. 2007 May; 210(Pt 9):1507-17. PMID: 17449816.
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  159. Raj JU, Aliferis C, Caprioli RM, Cowley AW, 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. PMID: 17468134.
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  160. 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 Apr 25; 8:109. PMID: 17459168.
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  161. 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. PMID: 17332024.
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  162. 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. PMID: 18287690.
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  163. Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol. 2007; 8(5):R76. PMID: 17493263; PMCID: PMC1929138.
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  164. 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 01; 66(23):11502-13. PMID: 17114236.
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  165. Quackenbush J. Weighing our measures of gene expression. Mol Syst Biol. 2006; 2:63. PMID: 17102808; PMCID: PMC1682020.
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  166. 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 Nov 06; 7:489. PMID: 17087822; PMCID: PMC1687205.
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  167. 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. PMID: 16902087; PMCID: PMC1581433.
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  168. Quackenbush J. From 'omes to biology. Anim Genet. 2006 Aug; 37 Suppl 1:48-56. PMID: 16887002.
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  171. Quackenbush J. Microarray analysis and tumor classification. N Engl J Med. 2006 Jun 08; 354(23):2463-72. PMID: 16760446.
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  172. 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 May 18; 7:118. PMID: 16709250; PMCID: PMC1525191.
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  173. Hu Z, Fan C, Oh DS, Marron JS, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, Nobel A, Parker J, Ewend MG, Sawyer LR, Wu J, Liu Y, Nanda R, Tretiakova M, Ruiz Orrico A, Dreher D, Palazzo JP, Perreard L, Nelson E, Mone M, Hansen H, Mullins M, Quackenbush JF, Ellis MJ, Olopade OI, Bernard PS, Perou CM. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics. 2006 Apr 27; 7:96. PMID: 16643655; PMCID: PMC1468408.
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  174. Perreard L, Fan C, Quackenbush JF, Mullins M, Gauthier NP, Nelson E, Mone M, Hansen H, Buys SS, Rasmussen K, Orrico AR, Dreher D, Walters R, Parker J, Hu Z, He X, Palazzo JP, Olopade OI, Szabo A, Perou CM, Bernard PS. Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay. Breast Cancer Res. 2006; 8(2):R23. PMID: 16626501; PMCID: PMC1557722.
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  175. 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. PMID: 17114936.
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  177. 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 02; 440(7080):24. PMID: 16511469.
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  179. 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. PMID: 16474097; PMCID: PMC2644233.
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  180. 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. PMID: 16415889.
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  181. Brooksbank C, Quackenbush J. Data standards: a call to action. OMICS. 2006; 10(2):94-9. PMID: 16901212.
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  182. 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 01; 34(Database issue):D771-6. PMID: 16381977; PMCID: PMC1347435.
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  183. 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, 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; 10(2):205-8. PMID: 16901227.
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  184. 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. PMID: 16404382.
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  185. 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. PMID: 16939790.
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  186. 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. PMID: 17169148; PMCID: PMC1794432.
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  187. Quackenbush J. Computational approaches to analysis of DNA microarray data. Yearb Med Inform. 2006; 91-103. PMID: 17051302.
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  188. 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. PMID: 16420668; PMCID: PMC1414107.
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  189. 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. PMID: 16085323.
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  192. Pinent M, Bladé MC, Salvadó MJ, Arola L, Hackl H, Quackenbush J, Trajanoski Z, Ardévol A. Grape-seed derived procyanidins interfere with adipogenesis of 3T3-L1 cells at the onset of differentiation. Int J Obes (Lond). 2005 Aug; 29(8):934-41. PMID: 15917849.
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  194. 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 01; 21(15):3324-6. PMID: 15919728.
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  195. Eschrich S, Yang I, Bloom G, Kwong KY, Boulware D, Cantor A, Coppola D, Kruhøffer 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. PMID: 15908663.
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  196. 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 01; 21(15):3308-11. PMID: 15905276.
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  198. 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, Martínez-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. PMID: 15846361.
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  199. Guerrero FD, Miller RJ, Rousseau ME, Sunkara S, Quackenbush J, Lee Y, Nene V. BmiGI: a database of cDNAs expressed in Boophilus microplus, the tropical/southern cattle tick. Insect Biochem Mol Biol. 2005 Jun; 35(6):585-95. PMID: 15857764.
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  200. Marko NF, Frank B, Quackenbush J, Lee NH. A robust method for the amplification of RNA in the sense orientation. BMC Genomics. 2005 Mar 01; 6:27. PMID: 15740627; PMCID: PMC554769.
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  201. 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. PMID: 15734912; PMCID: PMC1065411.
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  202. 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. PMID: 15664951; PMCID: PMC547061.
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  203. Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J. The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D71-4. PMID: 15608288; PMCID: PMC540018.
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  204. 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. PMID: 15528642.
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  205. 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. PMID: 15475305.
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  207. 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. PMID: 15345376.
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  208. Szabo A, Perou CM, Karaca M, Perreard L, Palais R, Quackenbush JF, Bernard PS. Statistical modeling for selecting housekeeper genes. Genome Biol. 2004; 5(8):R59. PMID: 15287981; PMCID: PMC507884.
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  209. 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 08; 18(2):152-66. PMID: 15126644.
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  210. 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. PMID: 15177550.
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  211. 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. PMID: 15155546.
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  212. Quackenbush J. Data standards for 'omic' science. Nat Biotechnol. 2004 May; 22(5):613-4. PMID: 15122299.
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  214. 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. PMID: 15103394; PMCID: PMC393292.
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  215. 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 08; 4:3. PMID: 15113428; PMCID: PMC400743.
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  216. 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. PMID: 14695313; PMCID: PMC1602228.
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  217. Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J. Enrichment of gene-coding sequences in maize by genome filtration. Science. 2003 Dec 19; 302(5653):2118-20. PMID: 14684821.
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  218. Lee Y, Quackenbush J. Using the TIGR gene index databases for biological discovery. Curr Protoc Bioinformatics. 2003 Nov; Chapter 1:Unit 1.6. PMID: 18428690.
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  223. 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 01; 63(15):4368-74. PMID: 12907606.
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  224. 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. PMID: 12819153; PMCID: PMC403710.
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  225. 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. PMID: 12819134; PMCID: PMC403663.
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  226. 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 01; 278(31):28388-94. PMID: 12743126.
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  227. 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. PMID: 12760639.
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  228. 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. PMID: 12651724.
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  229. 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. PMID: 12618363; PMCID: PMC430289.
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  230. Dudoit S, Gentleman RC, Quackenbush J. Open source software for the analysis of microarray data. Biotechniques. 2003 Mar; Suppl:45-51. PMID: 12664684.
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  232. Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert CJ, 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. PMID: 12620126; PMCID: PMC151306.
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  236. 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. PMID: 12540297; PMCID: PMC151289.
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  237. 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 01; 31(1):229-33. PMID: 12519988; PMCID: PMC165506.
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  238. Rexroad CE, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res. 2003; 102(1-4):347-54. PMID: 14970727.
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  239. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 05; 420(6915):563-73. PMID: 12466851.
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  242. 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. PMID: 12392910.
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  245. 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. PMID: 12370817.
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  246. 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 03; 419(6906):512-9. PMID: 12368865.
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  247. Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J. Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. Biotechniques. 2002 Oct; 33(4):924-30. PMID: 12398202.
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  248. 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. PMID: 12226715.
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  249. 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. PMID: 12140684.
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  250. Andersson T, Unneberg P, Nilsson P, Odeberg J, Quackenbush J, Lundeberg J. Monitoring of representational difference analysis subtraction procedures by global microarrays. Biotechniques. 2002 Jun; 32(6):1348-50, 1352, 1354-6, 1358. PMID: 12074166.
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  251. 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. J Natl Cancer Inst. 2002 Apr 03; 94(7):513-21. PMID: 11929952.
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  252. 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. PMID: 11875039; PMCID: PMC155294.
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  253. Sturn A, Quackenbush J, Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics. 2002 Jan; 18(1):207-8. PMID: 11836235.
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  254. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001 Dec; 29(4):365-71. PMID: 11726920.
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  255. Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, Quackenbush J. Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray. Cancer Res. 2001 Nov 01; 61(21):7792-7. PMID: 11691794.
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  256. Kappe SH, Gardner MJ, Brown SM, Ross J, Matuschewski K, Ribeiro JM, Adams JH, Quackenbush J, Cho J, Carucci DJ, Hoffman SL, Nussenzweig V. Exploring the transcriptome of the malaria sporozoite stage. Proc Natl Acad Sci U S A. 2001 Aug 14; 98(17):9895-900. PMID: 11493695; PMCID: PMC55549.
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  257. Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T. Effects of ischemia on gene expression. J Surg Res. 2001 Aug; 99(2):222-7. PMID: 11469890.
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  258. Quackenbush J. Computational analysis of microarray data. Nat Rev Genet. 2001 Jun; 2(6):418-27. PMID: 11389458.
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  259. Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW. Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res. 2001 Apr; 11(4):626-30. PMID: 11282978; PMCID: PMC311058.
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  260. Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR. Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol. 2001 Mar; 125(3):1166-74. PMID: 11244096; PMCID: PMC1539370.
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  261. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y. Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 08; 409(6821):685-90. PMID: 11217851.
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  262. Tsai J, Sultana R, Lee Y, Pertea G, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J. RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol. 2001; 2(11):SOFTWARE0002. PMID: 16173164; PMCID: PMC138985.
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  263. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 2001 Jan 01; 29(1):159-64. PMID: 11125077; PMCID: PMC29813.
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  264. Yuan Q, Liang F, Hsiao J, Zismann V, Benito MI, Quackenbush J, Wing R, Buell R. Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic Acids Res. 2000 Sep 15; 28(18):3636-41. PMID: 10982886.
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  265. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. An optimized protocol for analysis of EST sequences. Nucleic Acids Res. 2000 Sep 15; 28(18):3657-65. PMID: 10982889; PMCID: PMC110731.
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  266. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J. Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet. 2000 Jun; 25(2):239-40. PMID: 10835646.
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  267. Quackenbush J, Liang F, Holt I, Pertea G, Upton J. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 2000 Jan 01; 28(1):141-5. PMID: 10592205; PMCID: PMC102391.
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  268. Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van Vugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fuji C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 1997 Dec 11; 390(6660):580-6. PMID: 9403685.
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  269. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 1997 Nov 27; 390(6658):364-70. PMID: 9389475.
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  270. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997 Aug 07; 388(6642):539-47. PMID: 9252185.
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  271. Stewart EA, McKusick KB, Aggarwal A, Bajorek E, Brady S, Chu A, Fang N, Hadley D, Harris M, Hussain S, Lee R, Maratukulam A, O'Connor K, Perkins S, Piercy M, Qin F, Reif T, Sanders C, She X, Sun WL, Tabar P, Voyticky S, Cowles S, Fan JB, Mader C, Quackenbush J, Myers RM, Cox DR. An STS-based radiation hybrid map of the human genome. Genome Res. 1997 May; 7(5):422-33. PMID: 9149939.
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  272. Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, Chu A, Clee C, Cowles S, Day PJ, Dibling T, Drouot N, Dunham I, Duprat S, East C, Edwards C, Fan JB, Fang N, Fizames C, Garrett C, Green L, Hadley D, Harris M, Harrison P, Brady S, Hicks A, Holloway E, Hui L, Hussain S, Louis-Dit-Sully C, Ma J, MacGilvery A, Mader C, Maratukulam A, Matise TC, McKusick KB, Morissette J, Mungall A, Muselet D, Nusbaum HC, Page DC, Peck A, Perkins S, Piercy M, Qin F, Quackenbush J, Ranby S, Reif T, Rozen S, Sanders C, She X, Silva J, Slonim DK, Soderlund C, Sun WL, Tabar P, Thangarajah T, Vega-Czarny N, Vollrath D, Voyticky S, Wilmer T, Wu X, Adams MD, Auffray C, Walter NA, Brandon R, Dehejia A, Goodfellow PN, Houlgatte R, Hudson JR, Ide SE, Iorio KR, Lee WY, Seki N, Nagase T, Ishikawa K, Nomura N, Phillips C, Polymeropoulos MH, Sandusky M, Schmitt K, Berry R, Swanson K, Torres R, Venter JC, Sikela JM, Beckmann JS, Weissenbach J, Myers RM, Cox DR, James MR, Bentley D, Deloukas P, Lander ES, Hudson TJ. A gene map of the human genome. Science. 1996 Oct 25; 274(5287):540-6. PMID: 8849440.
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  273. Quackenbush J, Davies C, Bailis JM, Khristich JV, Diggle K, Marchuck Y, Tobin J, Clark SP, Rodkins A, Marcano S, et al. An STS content map of human chromosome 11: localization of 910 YAC clones and 109 islands. Genomics. 1995 Sep 20; 29(2):512-25. PMID: 8666402.
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  274. Kupfer K, Smith MW, Quackenbush J, Evans GA. Physical mapping of complex genomes by sampled sequencing: a theoretical analysis. Genomics. 1995 May 01; 27(1):90-100. PMID: 7665188.
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  275. Khristich JV, Bailis J, Diggle K, Rodkins A, Romo A, Quackenbush J, Evans GA. Large-scale screening of yeast artificial chromosome libraries using PCR. Biotechniques. 1994 Sep; 17(3):498-501. PMID: 7818903.
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  276. Selleri L, Giovannini M, Hermanson GG, Romo A, Quackenbush J, Penny L, Khristich JV, Evans GA. Yeast artificial chromosome cloning of 3.2 megabases within chromosomal band 11q24 closely linking c-ets 1 and Fli-1 and encompassing the Ewing sarcoma breakpoint. Genomics. 1994 Jul 01; 22(1):137-47. PMID: 7959760.
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©2019 President and Fellows of Harvard College
Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.