Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

John Quackenbush, Ph.D.

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Other Positions
Title
Institution
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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. R35CA220523 (QUACKENBUSH, JOHN) Sep 1, 2018 - Aug 31, 2025
    NIH/NCI
    Unraveling the Complexities of Risk and Mechanism in Cancer
    Role: Principal Investigator
  2. T32LM012411 (QUACKENBUSH, JOHN) Apr 1, 2016 - Mar 31, 2021
    NIH/NLM
    Statistical and Quantitative Training in Big Data Health Science
    Role: Principal Investigator
  3. U24CA194354 (AERTS, HUGO) Apr 1, 2015 - Mar 31, 2020
    NIH/NCI
    Quantitative Radiomics System Decoding the Tumor Phenotype
    Role: Co-Principal Investigator
  4. U01CA190234 (AERTS, HUGO) Jan 9, 2015 - Dec 31, 2019
    NIH/NCI
    Genotype and Imaging Phenotype Biomarkers in Lung Cancer
    Role: Co-Principal Investigator
  5. R01HL111759 (QUACKENBUSH, JOHN) Sep 1, 2012 - Jul 31, 2016
    NIH/NHLBI
    Using Networks to Assign Gene Function in Lung Disease
    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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Campbell PT, Ambrosone CB, Nishihara R, Aerts HJWL, Bondy M, Chatterjee N, Garcia-Closas M, Giannakis M, Golden JA, Heng YJ, Kip NS, Koshiol J, Liu XS, Lopes-Ramos CM, Mucci LA, Nowak JA, Phipps AI, Quackenbush J, Schoen RE, Sholl LM, Tamimi RM, Wang M, Weijenberg MP, Wu CJ, Wu K, Yao S, Yu KH, Zhang X, Rebbeck TR, Ogino S. Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2019 May 08. PMID: 31069578.
    Citations:    
  2. Gaynor SM, Sun R, Lin X, Quackenbush J. Identification of differentially expressed gene sets using the Generalized Berk-Jones statistica. Bioinformatics. 2019 May 07. PMID: 31062858.
    Citations:    
  3. Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Res. 2019 Apr 15; 79(8):2084. PMID: 30987980.
    Citations:    
  4. Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. iScience. 2019 Apr 26; 14:226-240. PMID: 30981959.
    Citations:    
  5. 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.
    Citations:    Fields:    
  6. Garmire LX, Yuan GC, Fan R, Yeo GW, Quackenbush J. SINGLE CELL ANALYSIS, WHAT IS IN THE FUTURE? Pac Symp Biocomput. 2019; 24:332-337. PMID: 30864334.
    Citations:    
  7. 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.
    Citations: 1     Fields:    
  8. Hosny A, Parmar C, Quackenbush J, Schwartz LH, Aerts HJWL. Artificial intelligence in radiology. Nat Rev Cancer. 2018 08; 18(8):500-510. PMID: 29777175.
    Citations: 1     Fields:    
  9. 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.
    Citations:    
  10. 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.
    Citations:    Fields:    
  11. 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.
    Citations:    Fields:    
  12. Padi M, Quackenbush J. Detecting phenotype-driven transitions in regulatory network structure. NPJ Syst Biol Appl. 2018; 4:16. PMID: 29707235.
    Citations:    
  13. Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics. 2018 04 01; 19(2):185-198. PMID: 29036413.
    Citations: 2     Fields:    
  14. 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.
    Citations:    Fields:    
  15. 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.
    Citations: 1     Fields:    Translation:HumansCells
  16. 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.
    Citations:    Fields:    Translation:Cells
  17. 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.
    Citations:    Fields:    Translation:Humans
  18. 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 02; 115:94-103. PMID: 29291394.
    Citations:    Fields:    
  19. 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.
    Citations:    Fields:    Translation:Humans
  20. 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.
    Citations:    Fields:    Translation:Humans
  21. 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.
    Citations:    Fields:    Translation:Humans
  22. 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.
    Citations: 5     Fields:    Translation:HumansCells
  23. 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.
    Citations: 2     Fields:    Translation:Humans
  24. 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.
    Citations: 3     Fields:    Translation:HumansCells
  25. 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.
    Citations: 4     Fields:    Translation:HumansCells
  26. 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.
    Citations:    Fields:    
  27. 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.
    Citations: 1     Fields:    Translation:HumansCells
  28. 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.
    Citations:    Fields:    Translation:Humans
  29. 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.
    Citations: 6     Fields:    Translation:Humans
  30. 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.
    Citations: 1     Fields:    Translation:HumansCells
  31. 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.
    Citations: 20     Fields:    Translation:HumansAnimals
  32. 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.
    Citations: 7     Fields:    Translation:HumansAnimalsCTClinical Trials
  33. 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.
    Citations: 2     Fields:    Translation:HumansCells
  34. 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.
    Citations:    Fields:    Translation:Humans
  35. 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.
    Citations: 4     Fields:    Translation:Humans
  36. 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.
    Citations:    Fields:    
  37. 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.
    Citations:    Fields:    
  38. 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.
    Citations:    Fields:    
  39. 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.
    Citations: 6     Fields:    Translation:HumansCells
  40. 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.
    Citations: 17     Fields:    Translation:Humans
  41. Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics. 2016 Oct 02; 11(10):730-739. PMID: 27564456.
    Citations: 6     Fields:    
  42. 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.
    Citations: 3     
  43. Platig J, Castaldi PJ, DeMeo D, Quackenbush J. Bipartite Community Structure of eQTLs. PLoS Comput Biol. 2016 09; 12(9):e1005033. PMID: 27618581.
    Citations: 2     Fields:    Translation:Humans
  44. 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.
    Citations: 1     Fields:    Translation:Humans
  45. 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.
    Citations: 4     Fields:    
  46. 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.
    Citations: 2     Fields:    Translation:Humans
  47. 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.
    Citations:    Fields:    Translation:Animals
  48. 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.
    Citations: 9     
  49. 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.
    Citations: 23     
  50. 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.
    Citations: 8     Fields:    Translation:Humans
  51. 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.
    Citations: 4     Fields:    Translation:AnimalsCells
  52. 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.
    Citations: 35     Fields:    Translation:HumansAnimalsCells
  53. 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.
    Citations: 6     Fields:    Translation:HumansAnimals
  54. 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.
    Citations: 8     Fields:    Translation:Humans
  55. 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.
    Citations: 12     Fields:    Translation:Humans
  56. 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.
    Citations:    
  57. 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.
    Citations: 12     Fields:    
  58. 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.
    Citations: 4     Fields:    Translation:HumansCells
  59. 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.
    Citations: 34     Fields:    Translation:HumansCells
  60. 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.
    Citations: 11     Fields:    Translation:Humans
  61. 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.
    Citations: 13     Fields:    Translation:HumansCells
  62. 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.
    Citations:    
  63. 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.
    Citations: 9     Fields:    Translation:HumansCells
  64. 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.
    Citations: 15     Fields:    Translation:Humans
  65. 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.
    Citations: 8     Fields:    Translation:Humans
  66. 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.
    Citations: 3     
  67. 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.
    Citations: 343     Fields:    Translation:Humans
  68. Quackenbush J. Perspective: Learning to share. Nature. 2014 May 29; 509(7502):S68. PMID: 24870827.
    Citations:    Fields:    Translation:Humans
  69. 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.
    Citations: 2     Fields:    Translation:HumansCells
  70. 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.
    Citations: 8     Fields:    Translation:HumansCells
  71. 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.
    Citations: 5     Fields:    Translation:Humans
  72. 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.
    Citations: 9     Fields:    Translation:HumansCells
  73. 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.
    Citations: 13     Fields:    Translation:HumansCells
  74. Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski P. The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Cell Cycle. 2014; 13(18):2889-900. PMID: 25486477.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  75. 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.
    Citations: 121     Fields:    Translation:HumansCells
  76. 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.
    Citations: 18     Fields:    Translation:HumansCells
  77. 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.