Recent Publications

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

“Protecting the lungs but hurting the kidneys: causal inference study for the risk of ventilation-induced kidney injury in ARDS”
[Abstract]      [Article]
H.  Yang, P.V. Benos, G.D. Kitsions,
Annals in Transl Med (2020) accepted. [Editorial]
“An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs”
[Abstract]      [Article]
G. Bertolazzi, P.V. Benos, M. Tumminello, C. Coronnello,
BMC Bioinformatics (2020) accepted.
“CausalMGM: An interactive web-based causal discovery tool”
[Abstract]      [Article]
X. Ge, V.K. Raghu, P.K. Chrysanthis, P.V. Benos
Nucl Acids Res (2020) 48 (Web Server Issue):W597–W602.
“The evolution of radiographic edema in ARDS and its association with clinical outcomes: a prospective cohort study in adult patients”
[Abstract]      [Article]
D. Kotok, J.W. Evankovich, W. Bain, D.G. Dunlap, F. Shah, L. Yang, Y. Zhang, D.V. Manatakis, P.V. Benos, I.J. Barbash, S.F. Rapport, J.S. Lee, A. Morris, B.J. McVerry, G.D. Kitsios, 
J Crit Care (2020) 56:222-228.
“Causal network perturbations for instance-specific analysis of single cell and disease samples”
[Abstract]      [Article]
K.L. Buschur, M. Chikina, P.V. Benos
Bioinformatics (2020) 36:2515–2521.
“COPDGene 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease”
[Abstract]      [Article]
K.E. Lowe, E.A. Regan, A. Anzueto, E. Austin, J.H.M. Austin, Beaty TH, P.V. Benos, …, E.K. Silverman, J.D. Crapo
Chronic Obstructive Pulm Dis (2019) 6:384-399.
“Host-Response Subphenotypes Offer Prognostic Enrichment in Patients With or at Risk for Acute Respiratory Distress Syndrome”
[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) 47:1724-1734.
“A dynamic regulatory model of gene expression changes in differentially affected regions of the human IPF lung”
[Abstract]      [Article]
J.E. McDonough, F. Ahangari1, Q. Li, S. Jain, S.E. Verleden, J. Herazo-Maya, M. Vukmirovic, G. Deluliis, A. Tzouvelekis, N. Tanabe, F. Chu, X. Yan, J. Verschakelen, R.J. Homer, D.V. Manatakis, J. Zhang, J. Ding, K. Maes, L. De Sadeleer, R. Vos, A. Neyrinck, P.V. Benos, Z. Bar-Joseph, D. Tantin, J.C. Hogg, B.M. Vanaudenaerde, W.A. Wuyts, N. Kaminski
JCI Insight (2019) 4:e131597.
“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) 54:1802441.
“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.
“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.
“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 (2019) 85:E284-E293.
“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.