boldface: members of Benos’ lab; *equal contribution; †corresponding author; #senior author.
“Convergent and divergent immune aberrations in COVID-19, post-COVID-19-Interstitial Lung Disease and Idiopathic Pulmonary Fibrosis”
B. Tourki , M. Jia , T. Karampitsakos, I.M. Vera, A. Arsenault, Z. Fatima, C.Y. Perrot, D. Allen, F. Farsaei, D. Rutenberg, D. Bandyopadhyay, R. Restrepo-Jaramillo, M.R. Qureshi, K. Patel, A. Tzouvelekis , M. Kapetanaki, B. Juan-Guardela, K. Kim, P.V. Benos, J.D. Herazo-Maya
Am J Physiol Cell Physiol (2024) accepted.
“Pre-vaccination transcriptomic profiles of immune responders to the MUC1 peptide vaccine for colon cancer prevention”
C.M. Cameron*, V. Raghu*, B. Richardson*, L.L. Zagore , B. Tamilselvan , J. Golden , M. Cartwright, R.E. Schoen, O.J. Finn#, P.V. Benos#, Mark J. Cameron#
Frontiers in Immunology (2024) 15:1437391.
[Abstract] [Article] [medRxiv]
“Learning Identifiable Factorized Causal Representations of Cellular Responses”
H. Mao, R. Lopez, K. Liu, J.-C. Huetter, D. Richmond, P.V. Benos, L. Qiu
OpenReview (2024). Proceedings of NeurIPS 2024.
“Identification of Factors Directly Linked to Incident Chronic Obstructive Pulmonary Disease: A Causal Graph Modeling Study”
R.W. Gregg, C.M. Karoleski, E.K. Silverman, F.C. Sciurba, D.L. DeMeo, P.V. Benos
PLoS Medicine (2024) 21:e1004444.
“Development and validation of a mortality risk prediction model for chronic obstructive pulmonary disease: a cross-sectional study using probabilistic graphical modelling”
T.C. Lovelace, M.H. Ryu, M. Jia, P. Castaldi, F.C. Sciurba, C.P. Hersh, P.V. Benos
eClinicalMedicine (2024) 75:102786.
[Abstract] [Article] [medRxiv]
“A plasma peptidomic signature reveals extracellular matrix remodeling and predicts prognosis in alcohol-related hepatitis”
K. Sayed*, C.E. Dolin*, D.W. Wilkey, J. Li, T. Sato, J.I. Beier, J. Argemi, V. Vatsalya, C.J. McClain, R. Bataller, A.S. Wahed, Michael L Merchant#, P.V. Benos#, G.E Arteel#
Hepatology Communications (2024) 8:e0510.
[Abstract] [Article] [medRxiv]
“Longitudinal Multicompartment Characterization of Host-Microbiota Interactions in Patients with Acute Respiratory Failure”
G.D. Kitsios, K. Sayed, A. Fitch, H. Yang, N. Britton, F. Shah, W. Bain, J.W. Evankovich, S. Qin, X. Wang, K. Li, A. Patel, Y. Zhang, J. Radder, C. Dela Cruz, D.A. Okin, C.‐Y. Huang, D. van Tyne, P.V. Benos, B. Methé, P. Lai, A. Morris, B.J. McVerry
Nature Communications (2024) 15:4708.
“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.
“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. Sayed, P.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) 70:379-391.
“CellularPotts.jl: Simulating Multi-scale Cellular Models in Julia”
R.W. Gregg, P.V. Benos
Bioinformatics (2024) 40:btad773. [Applications Note]
“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]
“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]
“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.
“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.
“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.
“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.
“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. Mora†, P.V. Benos†, M. Rojas†
Aging Cell (2023) 22:e13969.
“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.
“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. Rojas†, P.V. Benos†
Respiratory Research (2023) 24:116.
[Abstract] [Article] [bioRxiv]
“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. Buschur, 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) 2:899655.
]