Recent Publications

boldface: members of Benos’ lab;  *corresponding author;  equal contirbution.

“ARDS subphenotypes beyond ARDS: prognostic enrichment in mechanically-ventilated patients with or at risk for ARDS”
[Abstract]      [Article]
G.D. Kitsios, L. Yang, D.V. Manatakis, M. Nouraie, J. Evankovich, W. Bain, D.D. Dunlap, F. Shah, I.J Barbash, S.F. Rapport, Y. Zhang, R.S. DeSensi, N.M. Weathington, B.B. Chen, P. Ray, R.K. Mallampalli, P.V. Benos, J.S. Lee, A. Morris, B.J. McVerry
Critical Care Medicine (2019) conditionally accepted.
“Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers”
[Abstract]      [Article]
J. Mandel, H. Wang, D.P. Normolle, W. Chen, Q. Yan, P.C. Lucas, P.V. Benos, E.V. Prochownik
BMC Cancer (2019) 19:686.
“A pipeline for integrated theory and data-driven modeling of genomic and clinical data”
[Abstract]      [Article]
V.K. Raghu, X. Ge, A. Balajee, D. Shirer, I. Das, P.V. Benos, P.K. Chrysanthis
BioKDD2019 (2019) accepted.
“Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis”
[Abstract]      [Article]
C. Morse, T. Tabib, J. Sembrat, K.L. Buschur, H.T. Bittar, E. Valenzi, Y. Jiang, D.J. Kass, K. Gibson, W. Chen, A. Mora, P.V. Benos, M. Rojas, R. Lafyatis
European Respiratory Journal (2019) accepted.
“Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models”
[Abstract]      [Article]
V.K. Raghu, W. Zhao, J. Pu, J.K. Leader, R. Wang, J. Herman, J.-M. Yuan, P.V. Benos*, D.O. Wilson
Thorax (2019) 74:643-649.
“PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy”
[Abstract]      [Article]
I. Abecassis†, A.J. Sedgewick†, M. Romkes, S. Buch, T. Nukui, M.G. Kapetanaki, A. Vogt, J.M. Kirkwood, P.V. Benos*, H. Tawbi*
Scientific Reports (2019) 9:3309.
“Mixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis”
[Abstract]      [Article]
A.J. SedgewickK. Buschur, I. Shi, J.D. Ramsey, V.K. Raghu, D.V. Manatakis, Y. Zhang, J. Bon, D. Chandra, C. Karoleski, F.C. Sciurba, P. Spirtes, C. Glymour, P.V. Benos
Bioinformatics (2019) 35:1204-1212.
“Mitochondria are a substrate of cellular memory”
[Abstract]      [Article]
A. Cheikhi, C. Wallace, C.S. Croix, C. Cohen, W.Y. Tang, P. Wipf, P.V. Benos, F. Ambrosio, A. Barchowsky
Free Radic Biol Med. (2019) 130:528-541.
“An insulin responsive sensor in the SIRT1 disordered region binds DBC1 and PACS-2 to control enzyme activity”
[Abstract]     [Article]
T.C. Krzysiak, L. Thomas, Y.-J. Choi, S. Auclair, Y. Qian, S. Luan, S.M. Krasnow, L.L. Thomas, L.M.I. Koharudin, P.V. Benos, D.L. Marks, A.M. Gronenborn, G. Thomas
Molecular Cell (2018) 72:985-998.e7.
“Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque”
[Abstract]      [Article]
E. Caparosa†, A.J. Sedgewick†, G. Zenonos, Y. Zhao, D.L. Carlisle, L. Stefaneanu, B.T. Jankowitz, P. Gardner, Y.-F. Chang, W.R. Lariviere, W.A. LaFramboise, P.V. Benos, R.M. Friedlander
Neurosurgery (2018) Epub ahead of print.
“piMGM: Incorporating Multi-Source Priors in Mixed Graphical Models for Learning Disease Networks”
[Abstract]     [Article]
D.V. Manatakis†, V.K. Raghu†, P.V. Benos
Bioinformatics (2018) 34:i848–i856
(Proc 2018 ECCB, Athens, Greece)
“Evaluation of Causal Structure Learning Methods on Mixed Data Types”
[Abstract]     [Article]
V.K. Raghu, A. Poon, P.V. Benos
Proc Machine Learning Research (2018) 92:48-65
(Proc 2018 ACM SIGKDD Workshop on Causal Discovery, London, UK)
“Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients”
G.D. Kitsios, A. Fitch, D.V. Manatakis, S. Rapport, K. Li, S. Qin, J. Huwe, Y. Zhang, Y. Doi, J. Evankovich, W. Bain, J.S. Lee, B. Methe, P.V. Benos, A. Morris, B. McVerry
Frontiers in Microbiology (2018) 9:1413.
 “Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine”
[Abstract]     [Article]
P. Ping, H. Hermjakob, J.S. Poison, P.V. Benos, W. Wang
Circulation Research (2018) 122:1290-1301. (Review)
“Comparison of strategies for scalable causal discovery of latent variable models from mixed data”

[Abstract]     [Article]   [PMC version]
V.K. Raghu, J.D. Ramsey, A. Morris, D.V. Manatakis, P. Sprites, P.K. Chrysanthis, C. Glymour, P.V. Benos
Int J Data Sci and Analytics (2018) 1-13
(Proc 2017 ACM SIGKDD Workshop on Causal Discovery, Halifax, Canada)
“Biomarker identification for statin sensitivity of cancer cell lines”
V.K. Raghu, C.H. Beckwitt, K. Warita, A. Wells, P.V. Benos*, Z.N. Oltvai*
Biochem Biophys Res Commun, (2018), 495:659-665.