{"id":1097,"date":"2019-01-26T15:56:03","date_gmt":"2019-01-26T15:56:03","guid":{"rendered":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1097"},"modified":"2022-08-10T17:46:20","modified_gmt":"2022-08-10T17:46:20","slug":"pubs-new","status":"publish","type":"page","link":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1097","title":{"rendered":"Recent Publications"},"content":{"rendered":"

boldface<\/strong>: members of Benos’ lab; \u00a0*<\/strong>corresponding author; \u00a0\u2020<\/strong>equal contirbution.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\u201cCausal discovery in high-dimensional, multicollinear datasets\u201d<\/td>\n<\/tr>\n
\nM. Jia\u2020<\/strong>, D. Yuan<\/strong>, T.C. Lovelace<\/strong>, M. Hu<\/strong>, P.V. Benos<\/strong>
\nFront Epidemiol<\/i><\/strong><\/i>\u00a0(2022) accepted<\/em>.<\/span><\/td>\n<\/tr>\n
\u201cEssential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets\u201d<\/td>\n<\/tr>\n
\nX. Bing\u2020<\/strong> T. Lovelace\u2020<\/strong>. F. Bunea, M. Wegkamp, S.P. Kasturi, H. Singh*, P.V. Benos*<\/strong>, J. Das*
\nPatterns<\/i><\/strong><\/i>\u00a0(2022) 3:<\/strong>100473.<\/span><\/td>\n<\/tr>\n
\u201cCritically ill COVID-19 patients 1 exhibit peripheral immune profiles predictive of mortality and reflective of SARS-CoV-2 viral burden in the lung\u201d<\/td>\n<\/tr>\n
\nA.R. Cillo, A. Somasundaram, F. Shan<\/strong>, 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<\/strong>, 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
\nCell Reports Med<\/i><\/strong><\/i>\u00a0(2021) 2:<\/strong>100476.<\/span><\/td>\n<\/tr>\n
\u201cMyofibroblast transcriptome indicates SFRP2+ fibroblast progenitors in systemic sclerosis skin\u201d<\/td>\n<\/tr>\n
\nT. Tabib, M. Huang, C. Morse, A. Papazoglou, R. Behera, M. Jia<\/strong>, M. Bulik, D. Monier, P.V. Benos<\/strong>, W. Chen, R. Domsic. R. Lafyatis
\nNature Commun<\/i><\/strong><\/i>\u00a0(2021) 12:<\/strong>4384.<\/span><\/td>\n<\/tr>\n
\u201cCompensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors\u201d<\/td>\n<\/tr>\n
\nL.M. Molina, J. Zhu, Q. Li, T. Pradhan-Sundd, K. Sayed<\/strong>, 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<\/strong>, A. Feranchak, K. Nejak-Bowen, A. Watson, A. Bell, S.P. Monga
\nCell Reports<\/i><\/strong><\/i>\u00a0(2021) 36:<\/strong>109310.<\/span><\/td>\n<\/tr>\n
\u201cPlasma 1,3-beta-D-glucan levels predict adverse clinical outcomes in critical illness\u201d<\/td>\n<\/tr>\n
\nG.D. Kitsios, D. Kotok, H. Yang<\/strong>, 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. Meth\u00e9, P.V. Benos<\/strong>, B.J. McVerry, A. Morris<\/span>
\nJCI Insight<\/i><\/strong><\/i>\u00a0(2021) 6:<\/strong>141277. \u00a0 [medRxiv<\/a>]<\/td>\n<\/tr>\n
\u201cTranscriptomics of Bronchoalveolar Lavage Cells Identifies New Molecular Endotypes of Sarcoidosis\u201d<\/td>\n<\/tr>\n
\nM. 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<\/strong>, D.R. Moller, A. Prasse, L.L. Koth, N. Kaminski<\/span>
\nEur Resp J<\/i><\/strong><\/i>\u00a0(2021) 58:<\/strong>2002950. \u00a0 [medRxiv<\/a>]<\/td>\n<\/tr>\n
\u201cNeurological Complications Acquired during Pediatric Critical Illness: Exploratory \u2018Mixed Graphical Modeling\u2019 Analysis using Serum Biomarker Levels\u201d<\/td>\n<\/tr>\n
\nV.K. Raghu<\/strong>, C.M. Horvat, P.M. Kochanek, E.L. Fink, R.S.B. Clark, P.V. Benos<\/strong>*<\/strong>, A. Au*<\/strong><\/span>
\nPediatric Crit Care Med\u00a0<\/i><\/strong>(2021) 22:<\/strong>906-914.<\/td>\n<\/tr>\n
\u201cReduced Proportion and Activity of Natural Killer Cells in the Lung of Patients with Idiopathic Pulmonary Fibrosis\u201d<\/td>\n<\/tr>\n
\nT. Cruz\u2020*, M. Jia<\/strong>\u2020<\/strong>, J.C. Sembrat, T. Tabib, D.A.A. Vignali, P. Sanchez, R. Lafyatis, A.L. Mora, P.V. Benos<\/strong>*<\/strong>, M. Rojas*<\/strong><\/span>
\nAm J Resp Crit Care Med\u00a0<\/i><\/strong>(2021) 204:<\/strong>608-610.<\/td>\n<\/tr>\n
\u201cTopographic Heterogeneity of Lung Microbiota in End-Stage Idiopathic Pulmonary Fibrosis: The Microbiome in Lung Explants-2 (MiLEs-2) Study\u201d<\/td>\n<\/tr>\n
\nE. Valenzi, H. Yang<\/strong>, 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<\/strong>, B.J. McVerry, M. Rojas, A. Morris, G.D. Kitsios\u00a0<\/span>
\nThorax\u00a0<\/i><\/strong>(2021) 76:<\/strong>239-247. \u00a0[medRxiv<\/a>]<\/td>\n<\/tr>\n
\u201cHuman ex vivo lung perfusion: A novel model to study human lung diseases\u201d<\/td>\n<\/tr>\n
\n N. C\u00e1rdenes\u2020, J. Sembrat\u2020, K. Noda\u2020, <\/span>T. Lovelace\u2020,<\/strong> D. \u00c1lvarez, H.E. Trejo Bittar, B.J. Philips, M. Nouraie,\u00a0<\/span>P.V.<\/span>\u00a0Benos,<\/span><\/strong>, P.G. S\u00e1nchez, M. Rojas<\/span>
\nScientific\u00a0<\/i><\/strong>Reports\u00a0<\/i><\/strong>(2021) 11:<\/strong>490.<\/td>\n<\/tr>\n
\u201cImproving Constraint-Based Causal Discovery from Moralized Graphs\u201d<\/td>\n<\/tr>\n
\n
\"\"<\/div>\n
A. Fuccello, D. Yuan,<\/strong>\u00a0P.V. Benos,\u00a0V.K. Raghu<\/strong>\u00a0<\/span>
\nNeurIPS 2020<\/i><\/strong>\u00a0workshop on Causality<\/i><\/i>\u00a0<\/i><\/strong>(2020) accepted<\/em>. \u00a0Presented: 11-Dec-2020.<\/td>\n<\/tr>\n
\u201cmiR-1207-5p can contribute to dysregulation of inflammatory response in COVID-19 via targeting SARS-CoV-2 RNA\u201d<\/td>\n<\/tr>\n
\nG. Bertolazzi<\/strong>, C. Cipollina, P.V. Benos<\/strong>,\u00a0M. Tumminello, C. Coronnello <\/span>
\nFrontiers in Cellular and Infection Microbiology\u00a0<\/i><\/strong>(2020) 10:<\/strong>586592.<\/td>\n<\/tr>\n
\u201cInterpretable Factors in scRNA-seq Data with Disentangled Generative Models\u201d<\/td>\n<\/tr>\n
\nH. Mao, <\/strong>, M.J. Broerman, \u00a0P.V. Benos<\/strong>,<\/span>
\n2020 IEEE BIBE<\/i><\/strong>\u00a0International Conference<\/i><\/i>\u00a0<\/i><\/strong>(2020) accepted<\/em>. \u00a0Presented: 26-Oct-2020.<\/td>\n<\/tr>\n
\u201cRespiratory Tract Dysbiosis is Associated With Worse Outcomes in Mechanically-Ventilated Patients\u201d<\/td>\n<\/tr>\n
\nG.D. Kitsios, H. Yang, <\/strong>, L. Yang, S. Qin, A. Fitch, X.-H. Wang, K. Fair, J. Evankovich, W. Bain, F Shah, K. Li, B. Meth\u00e9, P.V. Benos<\/strong>, A. Morris, B.J. McVerry,<\/span>
\nAm J Resp Crit \u00a0Care Med\u00a0<\/i><\/strong>(2020) 202:<\/strong>1666-1677.<\/td>\n<\/tr>\n
\u201cProtecting the lungs but hurting the kidneys: causal inference study for the risk of ventilation-induced kidney injury in ARDS\u201d<\/td>\n<\/tr>\n
\nH. \u00a0Yang, <\/strong>P.V. Benos<\/strong>,\u00a0G.D. Kitsios,<\/span>
\nAnnals in Transl Med\u00a0<\/i><\/strong>(2020) 8:<\/strong>985. [Editorial]<\/td>\n<\/tr>\n
\u201cAn improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs\u201d<\/td>\n<\/tr>\n
\nG. Bertolazzi, <\/strong>P.V. Benos<\/strong>,\u00a0M. Tumminello, C. Coronnello,<\/span>
\nBMC\u00a0Bioinformatics\u00a0<\/i><\/strong>(2020) 21<\/strong>(Suppl 8):363.<\/td>\n<\/tr>\n
\u201cCausalMGM: An interactive web-based causal discovery tool\u201d<\/td>\n<\/tr>\n
\nX. Ge\u2020, V.K. Raghu\u2020, <\/strong>P.K. Chrysanthis, P.V. Benos<\/strong>,\u00a0<\/span>
\nNucl Acids Res\u00a0<\/i><\/strong>(2020) 48<\/strong> (Web Server Issue):W597\u2013W602.<\/td>\n<\/tr>\n
\u201cThe evolution of radiographic edema in ARDS and its association with clinical outcomes: a prospective cohort study in adult patients\u201d<\/td>\n<\/tr>\n
\nD. Kotok, J.W. Evankovich, W. Bain, D.G. Dunlap, F. Shah, L. Yang, Y. Zhang, D.V. Manatakis, P.V. Benos<\/strong>, I.J. Barbash, S.F. Rapport, J.S. Lee, A. Morris, B.J. McVerry, G.D. Kitsios,\u00a0<\/span>
\nJ Crit Care\u00a0<\/i><\/strong>(2020) 56:<\/strong>222-228.<\/td>\n<\/tr>\n
\u201cCausal network perturbations for instance-specific analysis of single cell and disease samples\u201d<\/td>\n<\/tr>\n
\nK.L. Buschur<\/strong>, M. Chikina,\u00a0P.V. Benos<\/strong><\/span>
\nBioinformatics<\/i><\/span><\/strong>\u00a0(2020) 36:<\/strong>2515\u20132521.<\/td>\n<\/tr>\n
\u201cCOPDGene 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease\u201d<\/td>\n<\/tr>\n
\nK.E. Lowe, E.A.\u00a0Regan, A.\u00a0Anzueto, E.\u00a0Austin, J.H.M.\u00a0Austin, Beaty TH,\u00a0P.V. Benos<\/strong>, …, E.K. Silverman, J.D. Crapo<\/span>
\nChronic\u00a0Obstructive Pulm Dis<\/i><\/span><\/strong>\u00a0(2019)\u00a0<\/em>6:<\/strong>384-399.<\/td>\n<\/tr>\n
\u201cHost-Response Subphenotypes Offer Prognostic Enrichment in Patients With or at Risk for Acute Respiratory Distress Syndrome\u201d<\/td>\n<\/tr>\n
\nG.D. Kitsios, L. Yang,\u00a0D.V. Manatakis<\/strong>, 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,\u00a0P.V. Benos<\/strong>, J.S. Lee, A. Morris, B.J. McVerry<\/span>
\nCritical Care Medicine<\/span><\/strong><\/em>\u00a0(2019)\u00a0<\/em>47:<\/strong>1724-1734.<\/td>\n<\/tr>\n
\u201cA dynamic regulatory model of gene expression changes in differentially affected regions of the human IPF lung\u201d<\/td>\n<\/tr>\n
\nJ.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<\/strong>, J. Zhang<\/strong>, J. Ding, K. Maes, L. De Sadeleer, R. Vos, A. Neyrinck, P.V. Benos<\/strong>, Z. Bar-Joseph, D. Tantin, J.C. Hogg, B.M. Vanaudenaerde, W.A. Wuyts, N. Kaminski<\/span><\/span>
\nJCI Insight<\/span><\/strong><\/em>\u00a0(2019) 4:<\/strong>e131597.<\/td>\n<\/tr>\n
\u201cProliferating SPP1\/MERTK-expressing macrophages in idiopathic pulmonary fibrosis\u201d<\/td>\n<\/tr>\n
\nC. Morse, T. Tabib, J. Sembrat, K.L. Buschur<\/strong>, H.T. Bittar, E. Valenzi, Y. Jiang, D.J. Kass, K. Gibson, W. Chen, A. Mora, P.V. Benos<\/strong>, M. Rojas, R. Lafyatis<\/span>
\nEuropean Respiratory Journal<\/span><\/strong><\/em>\u00a0(2019) 54:<\/b>1802441.<\/td>\n<\/tr>\n
\u201cA pipeline for integrated theory and data-driven modeling of genomic and clinical data\u201d<\/td>\n<\/tr>\n
\nV.K. Raghu<\/strong>, X. Ge, A. Balajee, D. Shirer, I. Das<\/strong>, P.V. Benos<\/strong>, P.K. Chrysanthis<\/span>
\nBioKDD2019<\/span><\/strong><\/em>\u00a0(2019) accepted<\/em>.<\/td>\n<\/tr>\n
\u201cExpression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers\u201d<\/td>\n<\/tr>\n
\nJ. Mandel, H. Wang, D.P. Normolle, W. Chen, Q. Yan, P.C. Lucas, P.V. Benos<\/strong>, E.V. Prochownik<\/span>
\nBMC Cancer<\/span><\/strong><\/em>\u00a0(2019) 19:<\/strong>686.<\/td>\n<\/tr>\n
\u201cFeasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models\u201d<\/td>\n<\/tr>\n
\nV.K. Raghu<\/strong>, W. Zhao, J. Pu, J.K. Leader, R. Wang, J. Herman, J.-M. Yuan, P.V. Benos*<\/strong>, D.O. Wilson<\/span>
\nThorax<\/strong><\/em>\u00a0(2019)\u00a074:<\/strong>643-649.<\/td>\n<\/tr>\n
\u201cPARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy\u201d<\/td>\n<\/tr>\n
\nI. Abecassis\u2020, A.J. Sedgewick\u2020<\/strong>, M. Romkes, S. Buch, T. Nukui, M.G. Kapetanaki, A. Vogt, J.M. Kirkwood, P.V. Benos*<\/strong>, H. Tawbi*<\/span>
\nScientific Reports<\/strong><\/em>\u00a0(2019)\u00a09:<\/strong>3309.<\/td>\n<\/tr>\n
\u201cMixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis\u201d<\/td>\n<\/tr>\n
\nA.J. Sedgewick<\/strong>,\u00a0K. Buschur<\/strong>, I. Shi<\/strong>, J.D. Ramsey, V.K. Raghu<\/strong>, D.V. Manatakis<\/strong>, Y. Zhang, J. Bon, D. Chandra, C. Karoleski, F.C. Sciurba, P. Spirtes, C. Glymour, P.V. Benos<\/strong><\/span>
\nBioinformatics<\/strong><\/em>\u00a0(2019) 35:<\/strong>1204-1212.<\/td>\n<\/tr>\n
\u201cMitochondria are a substrate of cellular memory\u201d<\/td>\n<\/tr>\n
\nA. Cheikhi, C. Wallace, C.S. Croix, C. Cohen, W.Y. Tang, P. Wipf, P.V. Benos<\/strong>, F. Ambrosio, A. Barchowsky<\/span>
\nFree Radic Biol Med<\/strong><\/em>. (2019)\u00a0130:<\/strong>528-541.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

boldface: members of Benos’ lab; \u00a0*corresponding author; \u00a0\u2020equal contirbution. \u201cCausal discovery in high-dimensional, multicollinear datasets\u201d [Abstract] \u00a0 \u00a0 \u00a0[Article] M. Jia\u2020, D. Yuan, T.C. Lovelace, M. Hu, P.V. Benos Front Epidemiol\u00a0(2022) accepted. \u201cEssential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets\u201d [Abstract] \u00a0 \u00a0 \u00a0[Article] X. …<\/p>\n

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