Recent Publications

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

Lancet Rheumatol Figure

“The novel Florida Scoring System for stratifying children suspected of Sjögren’s disease: findings from the first data-driven cross-sectional study applied to a rare pediatric cohort”

W. Zeng, A. Thatayatikom, N. Winn, T.C. Lovelace, I. Bhattacharyya, T. Schrepfer, A. Shah, R. Gonik, P.V. Benos#, S. Cha#
Lancet Rheumatology (2024) 6:e279-e290. 

[Abstract] [Article]

AJRCMB Figure 2024

“Lung epithelium releases growth differentiation factor 15 in response to pathogen-mediated injury”

F.A. Shah, H. Bahudhanapati, M. Jiang, M. Tabary, R. van der Geest, N.J. Tolman, M. Kochin, Z. Xiong, N. Al-Yousif, K. SayedP.V. Benos, K. Raffensperger, J. Evankovich, M.D. Neal, M.E. Snyder, O. Eickelberg, P. Ray, C. Dela Cruz, J. Bon, B.J. McVerry, A.C. Straub, M.J. Jurczak, T.l. Suber, Y. Zhang, K. Chen, G.D. Kitsios, J.S. Lee, J.K. Alder, W.G. Bain
AJRCMB (2024) accepted

[Abstract] [Article]

“CellularPotts.jl: Simulating Multi-scale Cellular Models in Julia”

R.W. Gregg, P.V. Benos
Bioinformatics (2024) 40:btad773. [Applications Note]

[Abstract] [Article]

Placenta 2023 paper figure

“Defining trophoblast injury patterns in the transcriptomes of dysfunctional placentas”

O. Barak*, T. Lovelace*, T. Chua, Z. Caoa , E. Sadovskya , J.-F. Mouillet, Y. Ouyang, P.V. Benos, Y. Sadovsky
Placenta (2023) 143:87-90. [Short Communication]

[Abstract] [Article]

LEF1 paper - graphical abstract

“LEF1 isoforms regulate cellular senescence and aging”

M. Jia*, K. Sayed*, M G. Kapetanaki*, W. Dion, L. Rosas, S. Irfan, E. Valenzi, A.L. Mora, R.A. Lafyatis, M. Rojas, B. Zhu, P.V. Benos
Aging Cell (2023) 22:e14024.

[Abstract] [Article] [bioRxiv]

BMC Med figure

“Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes”

O. Barak*, T. Lovelace*, S, Piekos, T. Chu, Z. Cao, E. Sadovsky, J.-F. Mouillet, Y. Ouyang, W.T. Parks, L. Hood, N.D. Price, P.V. Benos, Y. Sadovsky
BMC Medicine (2023) 21:349.

[Abstract] [Article]  

Sci Immunol 2023

“Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells”

F. Shan, A.R. Cillo, C. Cardello, D.Y. Yuan, S.R. Kunning, J. Cui, C. Lampenfeld, A.M. Williams, A.P. McDonough, R.L. Ferris, T.C. Bruno, C.J. Workman, P.V. Benos, D.A.A. Vignali
Science Immunology (2023) 8:adf6717.

[Abstract] [Article]  

“The plasma degradome reflects later development of NASH fibrosis after liver transplant”

J. Li, T. Sato, M. Hernández-Tejero, J.I. Beier, K. Sayed, P.V. Benos, D.W. Wilkey, A. Humar, M.L. Merchant, A. Duarte-Rojo, G.E. Arteel
Scientific Reports (2023) 13:9965.

[Abstract]   [Article]  

AJRCCM 2023 Figure

“Early Evidence of COPD Obscured by Race-Specific Prediction Equations”

A. Regan, M.E. Lowe, B.J. Make, J.L. Curtis, Q. Chen, J.L. Crooks, , C. Wilson, G.R. Oates, R.W. Gregg, A.K. Baldomero, S.P. Bhatt, A.A. Diaz, P.V. Benos, J.K. O’Brien, K.A. Young, G.L. Kinney, D.J. Conrad, K.E. Lowe, D.L. DeMeo, A. Non, M.H. Cho, J. Kallet , M.G. Foreman, G.E. Westney, K.F. Hoth, N.R. MacIntyre, N. Hanania, A. Wolfe, H. Amaza, M. Han, T.H. Beaty, N.N. Hansel, M.C. McCormack, A. Balasubramanian, J.D. Crapo, E.K. Silverman, R. Casaburi, R.A. Wise
Am J Resp Crit Care Med (2023) 209:59-69.

[Abstract] [Article]  

Aging Cell Fig.

“Transcriptional Changes of the Aging Lung”

M. Jia*, P.A. Agudelo Garcia, J.A. Ovando-Ricardez, T. Tabib, H.T. Bittar, R.A. Lafyatis, A.L. MoraP.V. Benos, M. Rojas
Aging Cell (2023) 22:e13969.

[Abstract] [Article]

Kitsios iScience 2023 figure

“The upper and lower respiratory tract microbiome in severe aspiration pneumonia”

G.D. Kitsios, V.D. Nguyen, K. Sayed, N. Al-Yousif, C. Schaefer, F.A. Shah, W. Bain, H. Yang, A. Fitch, K. Li, X. Wang, S. Qin, H. Gentry, Y. Zhang, J. Varon, A.A. Rubio, J.A. Englert, R.M. Baron, J.S. Lee, B Methé, P.V. Benos, A. Morris, B.J. McVerry
iScience (2023) 26:106832.

[Abstract]   [Article]  

IPF fibroblast paper

“Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis”

Minxue Jia*, L. Rosas*, M.G. Kapetanaki, T. Tabib, J. Sebrat, T. Cruz, A. Bondonese, A.L. Mora, R. Lafyatis, M. RojasP.V. Benos
Respiratory Research (2023) 24:116.

[Abstract]   [Article]   [bioRxiv]

ISMB 2023 image

“An intrinsically interpretable neural network architecture for sequence to function learning”

A.T. Balci, M.M. Ebeid, P.V. Benos, D. Kostka, M. Chikina
Bioinformatics (2023) 39 (Suppl 1):i413-i422. (Proc ISMB 2023)

[Abstract]   [Article] [bioRxiv]

“Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury”

D.A. Zuppo, M.A. Missinato, L. Santana-Santos, G. Li, P.V. Benos, M. Tsang
Development (2023) 150:dev201163.

[Abstract]   [Article] [bioRxiv]

“Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis”

K.L. BuschurC. 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.

[Abstract]      [Article]

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 Communications (2022) 13:6789.

[Abstract]   [Article] [preprint version]

ML4H paper figure

“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]


Fig from the Frontiers Epic paper

“Causal discovery in high-dimensional, multicollinear datasets”

M. Jia*D. Yuan*T.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]

Presentation Image

“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”

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 Communications (2021) 12:4384

[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]

Kitsios JCI_Insight figure

“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.

[Abstract]      [Article]   [medRxiv]

Presentation Image

“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.

[Abstract]      [Article] [medRxiv]

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]

Presentation Image

“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]

Presentation Image

“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.

[Abstract]      [Article]  [medRxiv]

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]


“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]


“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]


“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]


“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]


“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]