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Items: 1 to 20 of 246

1.

High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report.

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.

Ann Am Thorac Soc. 2019 Jan;16(1):1-16. doi: 10.1513/AnnalsATS.201810-716WS.

PMID:
30592451
2.

Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.

Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J.

Cancer Res. 2018 Oct 1;78(19):5538-5547. doi: 10.1158/0008-5472.CAN-18-0454.

PMID:
30275053
3.

Histopathological Image QTL Discovery of Immune Infiltration Variants.

Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush J.

iScience. 2018 Jul 27;5:80-89. doi: 10.1016/j.isci.2018.07.001. Epub 2018 Jul 6.

4.

Artificial intelligence in radiology.

Hosny A, Parmar C, Quackenbush J, Schwartz LH, Aerts HJWL.

Nat Rev Cancer. 2018 Aug;18(8):500-510. doi: 10.1038/s41568-018-0016-5. Review.

5.

Cancer subtype identification using somatic mutation data.

Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J.

Br J Cancer. 2018 May;118(11):1492-1501. doi: 10.1038/s41416-018-0109-7. Epub 2018 May 16.

6.

Detecting phenotype-driven transitions in regulatory network structure.

Padi M, Quackenbush J.

NPJ Syst Biol Appl. 2018 Apr 19;4:16. doi: 10.1038/s41540-018-0052-5. eCollection 2018.

7.

Data Analysis Strategies in Medical Imaging.

Parmar C, Barry JD, Hosny A, Quackenbush J, Aerts HJWL.

Clin Cancer Res. 2018 Aug 1;24(15):3492-3499. doi: 10.1158/1078-0432.CCR-18-0385. Epub 2018 Mar 26. Review.

PMID:
29581134
8.

Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes.

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.

Nat Commun. 2018 Mar 23;9(1):1219. doi: 10.1038/s41467-018-03631-z.

9.

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface.

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.

MBio. 2018 Mar 6;9(2). pii: e02333-17. doi: 10.1128/mBio.02333-17.

10.

Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease.

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.

Hum Genomics. 2018 Jan 15;12(1):1. doi: 10.1186/s40246-018-0132-z.

11.

Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci.

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.

Am J Respir Crit Care Med. 2018 May 15;197(10):1275-1284. doi: 10.1164/rccm.201707-1434OC.

PMID:
29313708
12.

Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation.

Driesbaugh KH, Branchetti E, Grau JB, Keeney SJ, Glass K, Oyama MA, Rioux N, Ayoub S, Sacks MS, Quackenbush J, Levy RJ, Ferrari G.

J Mol Cell Cardiol. 2018 Feb;115:94-103. doi: 10.1016/j.yjmcc.2017.12.014. Epub 2017 Dec 30.

PMID:
29291394
13.

Estimating drivers of cell state transitions using gene regulatory network models.

Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J.

BMC Syst Biol. 2017 Dec 13;11(1):139. doi: 10.1186/s12918-017-0517-y.

14.

WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data.

Wang YE, Kutnetsov L, Partensky A, Farid J, Quackenbush J.

Cancer Res. 2017 Nov 1;77(21):e11-e14. doi: 10.1158/0008-5472.CAN-17-0802.

15.

Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research.

Kibbe W, Klemm J, Quackenbush J.

Cancer Res. 2017 Nov 1;77(21):e1-e2. doi: 10.1158/0008-5472.CAN-17-2212. No abstract available.

16.

Understanding Tissue-Specific Gene Regulation.

Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML.

Cell Rep. 2017 Oct 24;21(4):1077-1088. doi: 10.1016/j.celrep.2017.10.001.

17.

Smooth quantile normalization.

Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC.

Biostatistics. 2018 Apr 1;19(2):185-198. doi: 10.1093/biostatistics/kxx028.

PMID:
29036413
18.

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J.

BMC Bioinformatics. 2017 Oct 3;18(1):437. doi: 10.1186/s12859-017-1847-x.

19.

Revisiting inconsistency in large pharmacogenomic studies.

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.

Version 3. F1000Res. 2016 Sep 16 [revised 2017 Jan 1];5:2333. doi: 10.12688/f1000research.9611.3. eCollection 2016.

20.

Regulatory network changes between cell lines and their tissues of origin.

Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K.

BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x.

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