Recent Publications

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

“Causal discovery in high-dimensional, multicollinear datasets”
[Abstract]      [Article]
M. Jia†, D. Yuan, T.C. Lovelace, M. Hu, P.V. Benos
Front Epidemiol (2022) accepted.
“Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets”
[Abstract]      [Article]
X. Bing T. Lovelace†. F. Bunea, M. Wegkamp, S.P. Kasturi, H. Singh*, P.V. Benos*, J. Das*
Patterns (2022) 3:100473.
“Critically ill COVID-19 patients 1 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 viral burden in the lung”
[Abstract]      [Article]
A.R. Cillo, A. Somasundaram, F. Shan, C. Cardello, C.J. Workman, G.D. Kitsios, A. Ruffin, S. Kunning, C. Lampenfeld, S. Onkar, S. Grebinoski, G. Deshmukh, B. Methe, C. Liu, S. Nambulli, L. Andrews, W.P. Duprex, A.V. Joglekar, P.V. Benos, P. Ray, A. Ray, B.J. McVerry, Y. Zhang, J.S. Lee, J. Das, H. Singh, A. Morris, T.C. Bruno, D.A.A. Vignali
Cell Reports Med (2021) 2:100476.
“Myofibroblast transcriptome indicates SFRP2+ fibroblast progenitors in systemic sclerosis skin”
[Abstract]      [Article]
T. Tabib, M. Huang, C. Morse, A. Papazoglou, R. Behera, M. Jia, M. Bulik, D. Monier, P.V. Benos, W. Chen, R. Domsic. R. Lafyatis
Nature Commun (2021) 12:4384.
“Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors”
[Abstract]      [Article]
L.M. Molina, J. Zhu, Q. Li, T. Pradhan-Sundd, K. Sayed, N. Jenkins, R. Vats, S. Ko, S. Hu, M. Poddar, S.Singh, J. Tao, P. Sundd, A Singhi, S. Watkins, X. Ma, P.V. Benos, A. Feranchak, K. Nejak-Bowen, A. Watson, A. Bell, S.P. Monga
Cell Reports (2021) 36:109310.
“Plasma 1,3-beta-D-glucan levels predict adverse clinical outcomes in critical illness”
[Abstract]      [Article]
G.D. Kitsios, D. Kotok, H. Yang, M.A. Finkelman, Y. Zhang, N. Britton, X. Li, M.S. Levochkina, A.K. Wagner, C. Schaefer, J.J. Villandre, R. Guo, J.W. Evankovich, W. Bain, F. Shah, Y. Zhang, B.A. Methé, P.V. Benos, B.J. McVerry, A. Morris
JCI Insight (2021) 6:141277.   [medRxiv]
“Transcriptomics of Bronchoalveolar Lavage Cells Identifies New Molecular Endotypes of Sarcoidosis”
[Abstract]      [Article]
M. Vukmirovic, X. Yan, K.F. Gibson, M. Gulati, J.C. Schupp, G. DeIuliis, T.S. Adam, B. Hu, A. Mihaljinec, T. Woolard, H. Lynn, N. Emeagwali, E.L. Herzog, E.S. Chen, A.M. Morris, J.K. Leader, Y. Zhang, J.G.N. Garcia, L.A. Maier, R. Colman, W.P. Drake, M. Becich, H. Hochheiser, S.R. Wisniewski, P.V. Benos, D.R. Moller, A. Prasse, L.L. Koth, N. Kaminski
Eur Resp J (2021) 58:2002950.   [medRxiv]
“Neurological Complications Acquired during Pediatric Critical Illness: Exploratory ‘Mixed Graphical Modeling’ Analysis using Serum Biomarker Levels”
[Abstract]      [Article]
V.K. Raghu, C.M. Horvat, P.M. Kochanek, E.L. Fink, R.S.B. Clark, P.V. Benos*, A. Au*
Pediatric Crit Care Med (2021) 22:906-914.
“Reduced Proportion and Activity of Natural Killer Cells in the Lung of Patients with Idiopathic Pulmonary Fibrosis”
[Abstract]      [Article]
T. Cruz†*, M. Jia, J.C. Sembrat, T. Tabib, D.A.A. Vignali, P. Sanchez, R. Lafyatis, A.L. Mora, P.V. Benos*, M. Rojas*
Am J Resp Crit Care Med (2021) 204:608-610.
“Topographic Heterogeneity of Lung Microbiota in End-Stage Idiopathic Pulmonary Fibrosis: The Microbiome in Lung Explants-2 (MiLEs-2) Study”
[Abstract]      [Article]
E. Valenzi, H. Yang, J.C. Sembrat, L. Yang, S. Winters, R. Nettles, D.J. Kass, S. Qin, X. Wang, M. Myerburg, B. Methe, A. Fitch, J. Alder, P.V. Benos, B.J. McVerry, M. Rojas, A. Morris, G.D. Kitsios 
Thorax (2021) 76:239-247.  [medRxiv]
“Human ex vivo lung perfusion: A novel model to study human lung diseases”
[Abstract]      [Article]
N. Cárdenes†, J. Sembrat†, K. Noda†, T. Lovelace†, D. Álvarez, H.E. Trejo Bittar, B.J. Philips, M. Nouraie, P.V. Benos,, P.G. Sánchez, M. Rojas
Scientific Reports (2021) 11:490.
“Improving Constraint-Based Causal Discovery from Moralized Graphs”
[Abstract]      [Article]   [Supplementary]
A. Fuccello, D. Yuan, P.V. Benos, V.K. Raghu 
NeurIPS 2020 workshop on Causality (2020) accepted.  Presented: 11-Dec-2020.
“miR-1207-5p can contribute to dysregulation of inflammatory response in COVID-19 via targeting SARS-CoV-2 RNA”
[Abstract]      [Article]
G. Bertolazzi, C. Cipollina, P.V. Benos, M. Tumminello, C. Coronnello
Frontiers in Cellular and Infection Microbiology (2020) 10:586592.
“Interpretable Factors in scRNA-seq Data with Disentangled Generative Models”
[Abstract]      [Article]
H. Mao, , M.J. Broerman,  P.V. Benos,
2020 IEEE BIBE International Conference (2020) accepted.  Presented: 26-Oct-2020.
“Respiratory Tract Dysbiosis is Associated With Worse Outcomes in Mechanically-Ventilated Patients”
[Abstract]      [Article]
G.D. Kitsios, H. Yang, , L. Yang, S. Qin, A. Fitch, X.-H. Wang, K. Fair, J. Evankovich, W. Bain, F Shah, K. Li, B. Methé, P.V. Benos, A. Morris, B.J. McVerry,
Am J Resp Crit  Care Med (2020) 202:1666-1677.
“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. Kitsios,
Annals in Transl Med (2020) 8:985. [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) 21(Suppl 8):363.
“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.