Harvard Catalyst Profiles

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

John Quackenbush, Ph.D.

Title
Institution
Department
Address
Phone
Profile Picture
Other Positions
Title
Institution
Department

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.
Most Recent  |  List All
  1. U24CA231846 (QUACKENBUSH, JOHN) Sep 1, 2019 - Aug 31, 2024
    NIH/NCI
    WebMeV: A Robust Platform for Intuitive Genomic Data Analysis
    Role: Principal Investigator
  2. R35CA220523 (QUACKENBUSH, JOHN) Sep 1, 2018 - Aug 31, 2025
    NIH/NCI
    Unraveling the Complexities of Risk and Mechanism in Cancer
    Role: Principal Investigator
  3. T32LM012411 (QUACKENBUSH, JOHN) Apr 1, 2016 - Mar 31, 2021
    NIH/NLM
    Statistical and Quantitative Training in Big Data Health Science
    Role: Principal Investigator
  4. U24CA194354 (AERTS, HUGO) Apr 1, 2015 - Mar 31, 2020
    NIH/NCI
    Quantitative Radiomics System Decoding the Tumor Phenotype
    Role: Co-Principal Investigator
  5. U01CA190234 (AERTS, HUGO) Jan 9, 2015 - Dec 31, 2019
    NIH/NCI
    Genotype and Imaging Phenotype Biomarkers in Lung Cancer
    Role: Co-Principal Investigator

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.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
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. Morrow JD, Make B, Regan E, Han M, Hersh CP, Tal-Singer R, Quackenbush J, Choi AMK, Silverman EK, DeMeo DL. DNA Methylation Is Predictive of Mortality in Current and Former Smokers. Am J Respir Crit Care Med. 2020 May 01; 201(9):1099-1109. PMID: 31995399.
    Citations:    
  2. Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J. Molecular networks in Network Medicine: Development and applications. Wiley Interdiscip Rev Syst Biol Med. 2020 Apr 19; e1489. PMID: 32307915.
    Citations:    
  3. Lietz CE, Garbutt C, Barry WT, Deshpande V, Chen YL, Lozano-Calderon SA, Wang Y, Lawney B, Ebb D, Cote GM, Duan Z, Hornicek FJ, Choy E, Petur Nielsen G, Haibe-Kains B, Quackenbush J, Spentzos D. MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma. Sci Rep. 2020 Mar 10; 10(1):4409. PMID: 32157112.
    Citations:    
  4. Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane AC. The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer. Cancer Epidemiol Biomarkers Prev. 2020 Feb; 29(2):509-519. PMID: 31871106.
    Citations:    
  5. Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush J. Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. Br J Cancer. 2020 Feb; 122(4):569-577. PMID: 31806877.
    Citations:    
  6. St Hilaire MA, Kristal BS, Rahman SA, Sullivan JP, Quackenbush J, Duffy JF, Barger LK, Gooley JJ, Czeisler CA, Lockley SW. Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake. Sci Rep. 2019 Nov 13; 9(1):16681. PMID: 31723161.
    Citations:    
  7. Gaynor SM, Sun R, Lin X, Quackenbush J. Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic. Bioinformatics. 2019 Nov 01; 35(22):4568-4576. PMID: 31062858.
    Citations:    
  8. Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single sample network inference in R. BMC Cancer. 2019 Oct 25; 19(1):1003. PMID: 31653243.
    Citations:    
  9. Altenbuchinger M, Weihs A, Quackenbush J, Grabe HJ, Zacharias HU. Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools. Biochim Biophys Acta Gene Regul Mech. 2020 Jun; 1863(6):194418. PMID: 31639475.
    Citations:    
  10. Lozano Calderón SA, Garbutt C, Kim J, Lietz CE, Chen YL, Bernstein K, Chebib I, Nielsen GP, Deshpande V, Rubio R, Wang YE, Quackenbush J, Delaney T, Raskin K, Schwab J, Cote G, Spentzos D. Clinical and Molecular Analysis of Pathologic Fracture-associated Osteosarcoma: MicroRNA profile Is Different and Correlates with Prognosis. Clin Orthop Relat Res. 2019 Sep; 477(9):2114-2126. PMID: 31389890.
    Citations:    
  11. 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 Aug; 30(8):799-811. PMID: 31069578.
    Citations:    
  12. 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:    
  13. 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:    
  14. Millington AL, Houskeeper JA, Quackenbush JF, Trauba JM, Wittwer CT. The kinetic requirements of extreme qPCR. Biomol Detect Quantif. 2019 Mar; 17:100081. PMID: 31285997.
    Citations:    
  15. 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 01; 16(1):1-16. PMID: 30592451.
    Citations:    Fields:    
  16. 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:    
  17. 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 10 01; 78(19):5538-5547. PMID: 30275053.
    Citations: 1     Fields:    
  18. 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:    
  19. 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:    
  20. Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. Br J Cancer. 2018 05; 118(11):1492-1501. PMID: 29765148.
    Citations:    Fields:    
  21. 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 05 15; 197(10):1275-1284. PMID: 29313708.
    Citations:    Fields:    
  22. Padi M, Quackenbush J. Detecting phenotype-driven transitions in regulatory network structure. NPJ Syst Biol Appl. 2018; 4:16. PMID: 29707235.
    Citations:    
  23. 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:    
  24. Parmar C, Barry JD, Hosny A, Quackenbush J, Aerts HJWL. Data Analysis Strategies in Medical Imaging. Clin Cancer Res. 2018 08 01; 24(15):3492-3499. PMID: 29581134.
    Citations:    Fields:    
  25. 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
  26. 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
  27. 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
  28. 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:    
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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 04; 141(4):1250-1258. PMID: 28736268.
    Citations:    Fields:    
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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:    
  47. 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:    
  48. 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:    
  49. 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
  50. 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
  51. 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:    
  52. 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     
  53. 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
  54. 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
  55. 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:    
  56. 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
  57. 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
  58. 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     
  59. 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     
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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:    
  67. 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:    
  68. 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
  69. 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
  70. 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
  71. 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   &nbs