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Items: 1 to 50 of 76

1.

Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers.

Mandel J, Wang H, Normolle DP, Chen W, Yan Q, Lucas PC, Benos PV, Prochownik EV.

BMC Cancer. 2019 Jul 12;19(1):686. doi: 10.1186/s12885-019-5851-6.

2.

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis.

Morse C, Tabib T, Sembrat J, Buschur K, Bittar HT, Valenzi E, Jiang Y, Kass DJ, Gibson K, Chen W, Mora A, Benos PV, Rojas M, Lafyatis R.

Eur Respir J. 2019 Jun 20. pii: 1802441. doi: 10.1183/13993003.02441-2018. [Epub ahead of print]

PMID:
31221805
3.

Evaluation of Causal Structure Learning Methods on Mixed Data Types.

Raghu VK, Poon A, Benos PV.

Proc Mach Learn Res. 2018 Aug;92:48-65.

4.

Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models.

Raghu VK, Zhao W, Pu J, Leader JK, Wang R, Herman J, Yuan JM, Benos PV, Wilson DO.

Thorax. 2019 Jul;74(7):643-649. doi: 10.1136/thoraxjnl-2018-212638. Epub 2019 Mar 12.

5.

PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy.

Abecassis I, Sedgewick AJ, Romkes M, Buch S, Nukui T, Kapetanaki MG, Vogt A, Kirkwood JM, Benos PV, Tawbi H.

Sci Rep. 2019 Mar 1;9(1):3309. doi: 10.1038/s41598-019-39542-2.

6.

Mitochondria are a substrate of cellular memory.

Cheikhi A, Wallace C, St Croix C, Cohen C, Tang WY, Wipf P, Benos PV, Ambrosio F, Barchowsky A.

Free Radic Biol Med. 2019 Jan;130:528-541. doi: 10.1016/j.freeradbiomed.2018.11.028. Epub 2018 Nov 22.

PMID:
30472365
7.

ECCB 2018: The 17th European Conference on Computational Biology.

ECCB 2018 Steering Committee, Hatzigeorgiou AG, Bagos P, Benos PV, Nikolaou C, Moreau Y, Kavakiotis I.

Bioinformatics. 2018 Sep 1;34(17):i595-i598. doi: 10.1093/bioinformatics/bty740. No abstract available.

PMID:
30423102
8.

piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks.

Manatakis DV, Raghu VK, Benos PV.

Bioinformatics. 2018 Sep 1;34(17):i848-i856. doi: 10.1093/bioinformatics/bty591.

PMID:
30423087
9.

An Insulin-Responsive Sensor in the SIRT1 Disordered Region Binds DBC1 and PACS-2 to Control Enzyme Activity.

Krzysiak TC, Thomas L, Choi YJ, Auclair S, Qian Y, Luan S, Krasnow SM, Thomas LL, Koharudin LMI, Benos PV, Marks DL, Gronenborn AM, Thomas G.

Mol Cell. 2018 Dec 20;72(6):985-998.e7. doi: 10.1016/j.molcel.2018.10.007. Epub 2018 Nov 8.

PMID:
30415949
10.

Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque.

Caparosa EM, Sedgewick AJ, Zenonos G, Zhao Y, Carlisle DL, Stefaneanu L, Jankowitz BT, Gardner P, Chang YF, Lariviere WR, LaFramboise WA, Benos PV, Friedlander RM.

Neurosurgery. 2019 Aug 1;85(2):E284-E293. doi: 10.1093/neuros/nyy470.

PMID:
30335165
11.

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. 2019 Apr 1;35(7):1204-1212. doi: 10.1093/bioinformatics/bty769.

PMID:
30192904
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3.

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

Proc Natl Acad Sci U S A. 2013 May 21;110(21):8644-9. doi: 10.1073/pnas.1221478110. Epub 2013 May 6.

32.

Expression of regulatory platelet microRNAs in patients with sickle cell disease.

Jain S, Kapetanaki MG, Raghavachari N, Woodhouse K, Yu G, Barge S, Coronnello C, Benos PV, Kato GJ, Kaminski N, Gladwin MT.

PLoS One. 2013 Apr 12;8(4):e60932. doi: 10.1371/journal.pone.0060932. Print 2013.

33.

Spectral clustering strategies for heterogeneous disease expression data.

Huang GT, Cunningham KI, Benos PV, Chennubhotla CS.

Pac Symp Biocomput. 2013:212-23.

34.

Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density.

Coronnello C, Hartmaier R, Arora A, Huleihel L, Pandit KV, Bais AS, Butterworth M, Kaminski N, Stormo GD, Oesterreich S, Benos PV.

PLoS Comput Biol. 2012;8(12):e1002830. doi: 10.1371/journal.pcbi.1002830. Epub 2012 Dec 20.

35.

Profibrotic role of miR-154 in pulmonary fibrosis.

Milosevic J, Pandit K, Magister M, Rabinovich E, Ellwanger DC, Yu G, Vuga LJ, Weksler B, Benos PV, Gibson KF, McMillan M, Kahn M, Kaminski N.

Am J Respir Cell Mol Biol. 2012 Dec;47(6):879-87. doi: 10.1165/rcmb.2011-0377OC. Epub 2012 Oct 4.

36.

To bind or not to bind--FoxA1 determines estrogen receptor action in breast cancer progression.

Watters RJ, Benos PV, Oesterreich S.

Breast Cancer Res. 2012 Jun 19;14(3):312.

37.

RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star.

Kadri S, Hinman VF, Benos PV.

PLoS One. 2011;6(12):e29217. doi: 10.1371/journal.pone.0029217. Epub 2011 Dec 28.

38.

Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque.

Zinman G, Brower-Sinning R, Emeche CH, Ernst J, Huang GT, Mahony S, Myers AJ, O'Dee DM, Flynn JL, Nau GJ, Ross TM, Salter RD, Benos PV, Bar Joseph Z, Morel PA.

PLoS One. 2011;6(7):e22401. doi: 10.1371/journal.pone.0022401. Epub 2011 Jul 18.

39.

High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells.

Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q, Benos PV, Friedman N, Eickelberg O, Kaminski N.

PLoS One. 2011;6(5):e20319. doi: 10.1371/journal.pone.0020319. Epub 2011 May 20.

40.

mirConnX: condition-specific mRNA-microRNA network integrator.

Huang GT, Athanassiou C, Benos PV.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W416-23. doi: 10.1093/nar/gkr276. Epub 2011 May 10.

41.

Finding subtypes of transcription factor motif pairs with distinct regulatory roles.

Bais AS, Kaminski N, Benos PV.

Nucleic Acids Res. 2011 Jun;39(11):e76. doi: 10.1093/nar/gkr205. Epub 2011 Apr 12.

42.

Inhibition and role of let-7d in idiopathic pulmonary fibrosis.

Pandit KV, Corcoran D, Yousef H, Yarlagadda M, Tzouvelekis A, Gibson KF, Konishi K, Yousem SA, Singh M, Handley D, Richards T, Selman M, Watkins SC, Pardo A, Ben-Yehudah A, Bouros D, Eickelberg O, Ray P, Benos PV, Kaminski N.

Am J Respir Crit Care Med. 2010 Jul 15;182(2):220-9. doi: 10.1164/rccm.200911-1698OC. Epub 2010 Apr 15.

43.

Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.

Temiz AN, Benos PV, Camacho CJ.

Nucleic Acids Res. 2010 Apr;38(7):2134-44. doi: 10.1093/nar/gkp1132. Epub 2010 Jan 4.

44.

Extracting biologically significant patterns from short time series gene expression data.

Tchagang AB, Bui KV, McGinnis T, Benos PV.

BMC Bioinformatics. 2009 Aug 20;10:255. doi: 10.1186/1471-2105-10-255.

45.

Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.

Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV.

PLoS One. 2009;4(4):e5279. doi: 10.1371/journal.pone.0005279. Epub 2009 Apr 23.

46.

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models.

Kadri S, Hinman V, Benos PV.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S35. doi: 10.1186/1471-2105-10-S1-S35.

47.

The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.

Brower-Sinning R, Carter DM, Crevar CJ, Ghedin E, Ross TM, Benos PV.

Genome Biol. 2009 Feb 12;10(2):R18. doi: 10.1186/gb-2009-10-2-r18.

48.

Web-based identification of evolutionary conserved DNA cis-regulatory elements.

Benos PV, Corcoran DL, Feingold E.

Methods Mol Biol. 2007;395:425-36.

PMID:
17993689
49.

Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma.

Feng H, Taylor JL, Benos PV, Newton R, Waddell K, Lucas SB, Chang Y, Moore PS.

J Virol. 2007 Oct;81(20):11332-40. Epub 2007 Aug 8.

50.

Combined analysis reveals a core set of cycling genes.

Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z.

Genome Biol. 2007;8(7):R146.

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