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Items: 1 to 50 of 308

1.

Clinical and Molecular Analysis of Pathologic Fracture-associated Osteosarcoma: MicroRNA profile Is Different and Correlates with Prognosis.

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.

Clin Orthop Relat Res. 2019 Sep;477(9):2114-2126. doi: 10.1097/CORR.0000000000000867.

PMID:
31389890
2.

The kinetic requirements of extreme qPCR.

Millington AL, Houskeeper JA, Quackenbush JF, Trauba JM, Wittwer CT.

Biomol Detect Quantif. 2019 Mar 13;17:100081. doi: 10.1016/j.bdq.2019.100081. eCollection 2019 Mar.

3.

Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting.

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.

Cancer Causes Control. 2019 Aug;30(8):799-811. doi: 10.1007/s10552-019-01177-z. Epub 2019 May 8. Review.

PMID:
31069578
4.

Identification of differentially expressed gene sets using the Generalized Berk-Jones statistica.

Gaynor SM, Sun R, Lin X, Quackenbush J.

Bioinformatics. 2019 May 7. pii: btz277. doi: 10.1093/bioinformatics/btz277. [Epub ahead of print]

PMID:
31062858
5.

Correction: 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. 2019 Apr 15;79(8):2084. doi: 10.1158/0008-5472.CAN-19-0678. No abstract available.

PMID:
30987980
6.

Estimating Sample-Specific Regulatory Networks.

Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K.

iScience. 2019 Apr 26;14:226-240. doi: 10.1016/j.isci.2019.03.021. Epub 2019 Mar 28.

7.

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.

8.

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. Erratum in: Cancer Res. 2019 Apr 15;79(8):2084.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

Exploring regulation in tissues with eQTL networks.

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

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7841-E7850. doi: 10.1073/pnas.1707375114. Epub 2017 Aug 29.

28.

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma.

Qiu W, Guo F, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG.

J Allergy Clin Immunol. 2018 Apr;141(4):1250-1258. doi: 10.1016/j.jaci.2017.05.052. Epub 2017 Jul 20.

29.

Biomarker correlation network in colorectal carcinoma by tumor anatomic location.

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.

BMC Bioinformatics. 2017 Jun 17;18(1):304. doi: 10.1186/s12859-017-1718-5.

30.

Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer.

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.

Cancer Res. 2017 Jul 15;77(14):3922-3930. doi: 10.1158/0008-5472.CAN-17-0122. Epub 2017 May 31.

31.

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets.

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.

J Hematol Oncol. 2017 May 15;10(1):107. doi: 10.1186/s13045-017-0465-4.

32.

Challenges and emerging directions in single-cell analysis.

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.

Genome Biol. 2017 May 8;18(1):84. doi: 10.1186/s13059-017-1218-y. Review.

33.

Estimating gene regulatory networks with pandaR.

Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J.

Bioinformatics. 2017 Jul 15;33(14):2232-2234. doi: 10.1093/bioinformatics/btx139.

34.

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue.

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.

Sci Rep. 2017 Mar 13;7:44232. doi: 10.1038/srep44232.

35.

Plasma Exosome Profiling of Cancer Patients by a Next Generation Systems Biology Approach.

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.

Sci Rep. 2017 Feb 20;7:42741. doi: 10.1038/srep42741.

36.

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue.

Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A.

PLoS One. 2017 Feb 2;12(2):e0170181. doi: 10.1371/journal.pone.0170181. eCollection 2017.

37.

Proceedings of the third international molecular pathological epidemiology (MPE) meeting.

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.

Cancer Causes Control. 2017 Feb;28(2):167-176. doi: 10.1007/s10552-016-0845-z. Epub 2017 Jan 17. Review.

38.

Safikhani et al. reply.

Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.

Nature. 2016 Nov 30;540(7631):E2-E4. doi: 10.1038/nature19839. No abstract available.

PMID:
27905430
39.

Safikhani et al. reply.

Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.

Nature. 2016 Nov 30;540(7631):E11-E12. doi: 10.1038/nature20581. No abstract available.

PMID:
27905423
40.

Safikhani et al. reply.

Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.

Nature. 2016 Nov 30;540(7631):E6-E8. doi: 10.1038/nature20172. No abstract available.

PMID:
27905416
41.

Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation.

Berrios C, Padi M, Keibler MA, Park DE, Molla V, Cheng J, Lee SM, Stephanopoulos G, Quackenbush J, DeCaprio JA.

PLoS Pathog. 2016 Nov 23;12(11):e1006020. doi: 10.1371/journal.ppat.1006020. eCollection 2016 Nov.

42.

PyPanda: a Python package for gene regulatory network reconstruction.

van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML.

Bioinformatics. 2016 Nov 1;32(21):3363-3365. Epub 2016 Jul 10.

43.

Respiratory Muscle Training and Exercise Endurance at Altitude.

Helfer S, Quackenbush J, Fletcher M, Pendergast DR.

Aerosp Med Hum Perform. 2016 Aug;87(8):704-11. doi: 10.3357/AMHP.4405.2016.

PMID:
27634605
44.

Bipartite Community Structure of eQTLs.

Platig J, Castaldi PJ, DeMeo D, Quackenbush J.

PLoS Comput Biol. 2016 Sep 12;12(9):e1005033. doi: 10.1371/journal.pcbi.1005033. eCollection 2016 Sep.

45.

Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors.

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.

JCI Insight. 2016 Aug 18;1(13). pii: e87988.

46.

DNA methylation profiling in human lung tissue identifies genes associated with COPD.

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.

Epigenetics. 2016 Oct 2;11(10):730-739. doi: 10.1080/15592294.2016.1226451. Epub 2016 Nov 1.

47.

BatchQC: interactive software for evaluating sample and batch effects in genomic data.

Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE.

Bioinformatics. 2016 Dec 15;32(24):3836-3838. Epub 2016 Aug 18.

48.

Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa.

Vargas AJ, Quackenbush J, Glass K.

Genomics. 2016 Oct;108(3-4):126-133. doi: 10.1016/j.ygeno.2016.08.001. Epub 2016 Aug 11.

49.

Assessment of pharmacogenomic agreement.

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.

F1000Res. 2016 May 9;5:825. doi: 10.12688/f1000research.8705.1. eCollection 2016.

50.

Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis.

Kusko RL, Brothers JF 2nd, 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.

Am J Respir Crit Care Med. 2016 Oct 15;194(8):948-960.

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