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Mixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis.

Sedgewick AJ, Buschur K, Shi I, Ramsey JD, Raghu VK, Manatakis DV, Zhang Y, Bon J, Chandra D, Karoleski C, Sciurba FC, Spirtes P, Glymour C, Benos PV.

Bioinformatics. 2018 Sep 5. doi: 10.1093/bioinformatics/bty769. [Epub ahead of print]


Comparison of strategies for scalable causal discovery of latent variable models from mixed data.

Raghu VK, Ramsey JD, Morris A, Manatakis DV, Sprites P, Chrysanthis PK, Glymour C, Benos PV.

Int J Data Sci Anal. 2018;6(1):33-45. doi: 10.1007/s41060-018-0104-3. Epub 2018 Feb 6.


Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients.

Kitsios GD, Fitch A, Manatakis DV, Rapport SF, Li K, Qin S, Huwe J, Zhang Y, Doi Y, Evankovich J, Bain W, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ.

Front Microbiol. 2018 Jul 10;9:1413. doi: 10.3389/fmicb.2018.01413. eCollection 2018.


Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine.

Ping P, Hermjakob H, Polson JS, Benos PV, Wang W.

Circ Res. 2018 Apr 27;122(9):1290-1301. doi: 10.1161/CIRCRESAHA.117.310967. Review.


Integrated Theory- and Data-driven Feature Selection in Gene Expression Data Analysis.

Raghu VK, Ge X, Chrysanthis PK, Benos PV.

Proc Int Conf Data Eng. 2017 Apr;2017:1525-1532. doi: 10.1109/ICDE.2017.223. Epub 2017 May 18.


Biomarker identification for statin sensitivity of cancer cell lines.

Raghu VK, Beckwitt CH, Warita K, Wells A, Benos PV, Oltvai ZN.

Biochem Biophys Res Commun. 2018 Jan 1;495(1):659-665. doi: 10.1016/j.bbrc.2017.11.065. Epub 2017 Nov 14.


Ribosomopathy-like properties of murine and human cancers.

Kulkarni S, Dolezal JM, Wang H, Jackson L, Lu J, Frodey BP, Dosunmu-Ogunbi A, Li Y, Fromherz M, Kang A, Santana-Santos L, Benos PV, Prochownik EV.

PLoS One. 2017 Aug 18;12(8):e0182705. doi: 10.1371/journal.pone.0182705. eCollection 2017.


Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection.

Pociask DA, Robinson KM, Chen K, McHugh KJ, Clay ME, Huang GT, Benos PV, Janssen-Heininger YMW, Kolls JK, Anathy V, Alcorn JF.

Am J Pathol. 2017 Apr;187(4):851-863. doi: 10.1016/j.ajpath.2016.12.012. Epub 2017 Feb 10.


Non-coding single nucleotide variants affecting estrogen receptor binding and activity.

Bahreini A, Levine K, Santana-Santos L, Benos PV, Wang P, Andersen C, Oesterreich S, Lee AV.

Genome Med. 2016 Dec 13;8(1):128.


Downregulation of estrogen receptor and modulation of growth of breast cancer cell lines mediated by paracrine stromal cell signals.

Huang J, Woods P, Normolle D, Goff JP, Benos PV, Stehle CJ, Steinman RA.

Breast Cancer Res Treat. 2017 Jan;161(2):229-243. doi: 10.1007/s10549-016-4052-0. Epub 2016 Nov 16.


Learning mixed graphical models with separate sparsity parameters and stability-based model selection.

Sedgewick AJ, Shi I, Donovan RM, Benos PV.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:175. doi: 10.1186/s12859-016-1039-0.


Regulation of alveolar septation by microRNA-489.

Olave N, Lal CV, Halloran B, Pandit K, Cuna AC, Faye-Petersen OM, Kelly DR, Nicola T, Benos PV, Kaminski N, Ambalavanan N.

Am J Physiol Lung Cell Mol Physiol. 2016 Mar 1;310(5):L476-87. doi: 10.1152/ajplung.00145.2015. Epub 2015 Dec 30.


Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells.

Chandran UR, Luthra S, Santana-Santos L, Mao P, Kim SH, Minata M, Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW.

Genom Data. 2015 Sep 1;5:333-336.


The center for causal discovery of biomedical knowledge from big data.

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R; Center for Causal Discovery team.

J Am Med Inform Assoc. 2015 Nov;22(6):1132-6. doi: 10.1093/jamia/ocv059. Epub 2015 Jul 2.


MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603.

Villaruz LC, Huang G, Romkes M, Kirkwood JM, Buch SC, Nukui T, Flaherty KT, Lee SJ, Wilson MA, Nathanson KL, Benos PV, Tawbi HA.

Clin Epigenetics. 2015 Jun 4;7:58. doi: 10.1186/s13148-015-0092-2. eCollection 2015.


T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes.

Huang GT, Tsamardinos I, Raghu V, Kaminski N, Benos PV.

Pac Symp Biocomput. 2015:431-42.


Aldosterone regulates microRNAs in the cortical collecting duct to alter sodium transport.

Edinger RS, Coronnello C, Bodnar AJ, Labarca M, Bhalla V, LaFramboise WA, Benos PV, Ho J, Johnson JP, Butterworth MB.

J Am Soc Nephrol. 2014 Nov;25(11):2445-57. doi: 10.1681/ASN.2013090931. Epub 2014 Apr 17. Erratum in: J Am Soc Nephrol. 2015 Jun;26(6):1476. J Am Soc Nephrol. 2015 Oct;26(10):2600.


Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways.

Lu TY, Lin B, Li Y, Arora A, Han L, Cui C, Coronnello C, Sheng Y, Benos PV, Yang L.

J Mol Cell Cardiol. 2013 Oct;63:146-54. doi: 10.1016/j.yjmcc.2013.07.019. Epub 2013 Aug 9.


Estrogen represses gene expression through reconfiguring chromatin structures.

Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, Lu X.

Nucleic Acids Res. 2013 Sep;41(17):8061-71. doi: 10.1093/nar/gkt586. Epub 2013 Jul 1.


ComiR: Combinatorial microRNA target prediction tool.

Coronnello C, Benos PV.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W159-64. doi: 10.1093/nar/gkt379. Epub 2013 May 22.

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