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Items: 1 to 50 of 299

1.

Artificial intelligence in radiology.

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

Nat Rev Cancer. 2018 May 17. doi: 10.1038/s41568-018-0016-5. [Epub ahead of print] Review.

PMID:
29777175
2.

Cancer subtype identification using somatic mutation data.

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

Br J Cancer. 2018 May 16. doi: 10.1038/s41416-018-0109-7. [Epub ahead of print]

PMID:
29765148
3.

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.

4.

Data Analysis Strategies in Medical Imaging.

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

Clin Cancer Res. 2018 Mar 26. doi: 10.1158/1078-0432.CCR-18-0385. [Epub ahead of print] Review.

PMID:
29581134
5.

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.

6.

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.

7.

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.

8.

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
9.

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
10.

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.

11.

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.

PMID:
29092929
12.

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.

PMID:
29092926
13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

PMID:
28736268
20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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
30.

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
31.

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
32.

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.

33.

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.

34.

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
35.

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.

36.

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.

37.

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 AM, Quackenbush J, Silverman EK, DeMeo DL.

Epigenetics. 2016 Aug 26:1-10. [Epub ahead of print]

38.

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.

39.

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.

40.

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.

41.

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.

42.

Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology.

Wu W, Parmar C, Grossmann P, Quackenbush J, Lambin P, Bussink J, Mak R, Aerts HJ.

Front Oncol. 2016 Mar 30;6:71. doi: 10.3389/fonc.2016.00071. eCollection 2016.

43.

Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation.

Malleshaiah M, Padi M, Rué P, Quackenbush J, Martinez-Arias A, Gunawardena J.

Cell Rep. 2016 Feb 9;14(5):1181-1194. doi: 10.1016/j.celrep.2015.12.101. Epub 2016 Jan 28.

44.

Toward clinical genomics in everyday medicine: perspectives and recommendations.

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.

Expert Rev Mol Diagn. 2016;16(5):521-32. doi: 10.1586/14737159.2016.1146593. Epub 2016 Feb 24.

45.

Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice.

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.

Nat Med. 2016 Feb;22(2):163-74. doi: 10.1038/nm.4021. Epub 2016 Jan 11.

46.

Respiratory Muscle Training and Cognitive Function Exercising at Altitude.

Quackenbush J, Duquin A, Helfer S, Pendergast DR.

Aerosp Med Hum Perform. 2016 Jan;87(1):18-25. doi: 10.3357/AMHP.4420.2016.

PMID:
26735229
47.

Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators.

Padi M, Quackenbush J.

BMC Syst Biol. 2015 Nov 14;9:80. doi: 10.1186/s12918-015-0228-1.

48.

Gender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma.

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.

Cancer Res. 2016 Jan 15;76(2):319-28. doi: 10.1158/0008-5472.CAN-15-0751. Epub 2015 Nov 10.

49.

Using shRNA experiments to validate gene regulatory networks.

Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B.

Genom Data. 2015 Apr 1;4:123-6. doi: 10.1016/j.gdata.2015.03.011. eCollection 2015 Jun.

50.

A network model for angiogenesis in ovarian cancer.

Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC.

BMC Bioinformatics. 2015 Apr 11;16:115. doi: 10.1186/s12859-015-0551-y.

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