boldface: members of Benos’ lab; *corresponding author; †equal contribution.
“Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury”
D.A. Zuppo, M.A. Missinato, L. Santana-Santos, G. Li, P.V. Benos, Michael Tsang
Development (2023) in print.
[Abstract] [Article] [preprint version]
“Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis”
K.L. Bushur, C. Riley, A. Saferali, P. Castaldi, G. Zhang, F. Aguet, K.G. Ardlie, P. Durda, W.C. Johnson, S. Kasela, Y. Liu, A. Manichaikul, S.S. Rich, J.I. Rotter, J. Smith, K.D. Taylor, R.P. Tracy, T. Lappalainen, R.G. Barr, F. Sciurba, C.P. Hersh, P.V. Benos
Respiratory Research (2023) 24:30.
“Lipidomic Signatures Align with Inflammatory Patterns and Outcomes in Critical Illness”
J. Wu, A. Cyr, D.S. Gruen, T.C. Lovelace, P.V. Benos, …, T.R. Billiar, PAMPer study group
Nature Communications (2022) 13:6789.
[Abstract] [Article] [preprint version]
“Towards cross-modal causal structure and representation learning”
H. Mao, H. Liu, J.X. Dou, P.V. Benos
PMLR (2022) 193:120–140. (Proc of the Machine Learning for Health workshop at NeurIPS 2022)
[Abstract] [Article]
“Causal discovery in high-dimensional, multicollinear datasets”
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”
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”
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”
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.
“Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors”
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”
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”
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”
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”
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”
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”
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”
A. Fuccello, D. Yuan, P.V. Benos, V.K. Raghu
NeurIPS 2020 workshop on Causality(2020) accepted. Presented: 11-Dec-2020.
[Abstract] [Article] [Supplementary]
“miR-1207-5p can contribute to dysregulation of inflammatory response in COVID-19 via targeting SARS-CoV-2 RNA”
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”
H. Mao, , M.J. Broerman, P.V. Benos,
2020 IEEE BIBE International Conference(2020) accepted. Presented: 26-Oct-2020.
[Abstract] [Article]
“Respiratory Tract Dysbiosis is Associated With Worse Outcomes in Mechanically-Ventilated Patients”
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”
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”
G. Bertolazzi, P.V. Benos, M. Tumminello, C. Coronnello,
BMC Bioinformatics (2020) 21(Suppl 8):363.
“CausalMGM: An interactive web-based causal discovery tool”
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”
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”
K.L. Buschur, M. Chikina, P.V. Benos
Bioinformatics (2020) 36:2515–2521.
“COPDGene 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease”
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”
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”
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
JJ.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”
CC. 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”
VV.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”
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.
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“Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models”
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”
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”
A.J. Sedgewick, K. 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”
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.