Recent Publications

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



NatComm figure

“Lipidomic Signatures Align with Inflammatory Patterns and Outcomes in Critical Illness”

J. Wu, A. Cyr, D.S. Gruen, T.C. LovelaceP.V. Benos, …, T.R. Billiar, PAMPer study group
Nature Commun (2022) accepted.

[Abstract]      [Article]


ML4H paper figure

“Towards cross-modal causal structure and representation learning”

H. Mao, H. Liu, J.X. Dou, P.V. Benos
Proc Machine Learning for Health (2022) accepted.

[Abstract]      [Article]


Fig from the Frontiers Epic paper

“Causal discovery in high-dimensional, multicollinear datasets”

M. Jia†D. YuanT.C. LovelaceM. HuP.V. Benos
Front Epidemiol (2022) accepted.

[Abstract]      [Article]


Presentation Image

“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.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]


Publications Image

“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.

[Abstract]      [Article]


Presentation Image

“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.

[Abstract]      [Article]


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“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]

[Abstract]      [Article]


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“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]

[Abstract]      [Article]


Presentation Image

“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.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]


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“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]

[Abstract]      [Article]


Presentation Image

“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.

[Abstract]      [Article]


Presentation Image

“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]


Graph

“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.

[Abstract]      [Article]


Graph

“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]


Blue Journal - Haopu

“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.

[Abstract]      [Article]


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“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]

[Abstract]      [Article]


BMC Bioinf paper - Giorgio

“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.

[Abstract]      [Article]


NAR paper (web server) - Vineet

“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.

[Abstract]      [Article]


graph

“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.

[Abstract]      [Article]


Graph

“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.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]


Presentation Image

“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.

[Abstract]      [Article]


Presentation Image

“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. ManatakisJ. 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.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]


Presentation Image

“A pipeline for integrated theory and data-driven modeling of genomic and clinical data”

VV.K. Raghu, X. Ge, A. Balajee, D. Shirer, I. DasP.V. Benos, P.K. Chrysanthis
BioKDD2019 (2019) accepted.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]


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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.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]


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“Mixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis”

A.J. SedgewickK. BuschurI. Shi, J.D. Ramsey, V.K. RaghuD.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.

[Abstract]      [Article]


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“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.

[Abstract]      [Article]