Publications

boldface: members of Benos’ lab,  †equal contribution, *(co-)corresponding authors,  PMC paper versions are freely available

Latest Trends of the Lab

2022
  1. Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets
    M. Jia†, D. Yuan†, T.C. Lovelace, M. Hu, P.V. Benos
    Front Epidemiol (2022) . Accepted: 5-Aug-2022.  Advance publ date: TBD.  Final publ date: TBD.
    [Abstract] [Article]
  2. 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. Accepted: 1-Mar-2022.  Advance publ date: 24-Mar-2022.  Final publ date: 13-May-2022.
    [Abstract] [Article]
2021
  1. 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 Rep Med (2021) 2:100476. Accepted: 23-Nov-2021.  Advance publ date: 2-Dec-2021.  Final publ date: 21-Dec-2021.
    [Abstract] [Article]
  2. 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.   Accepted: 8-May-2021.  Advance publ date: 3-Jun-2021.  Final publ date: 2-Dec-2021.
    [Abstract] [Article] [medRxiv] (freely available)
  3. 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.   Accepted: 5-Apr-2021.  Advance publ date: 1-Jun-2021. Journal publ date: 1-Oct-2021.
    [Abstract] [Article]
  4. 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. Benos, M. Rojas
    Am J Resp Crit Care Med (2021) 204:608-610.   Accepted: 17-Mar-2021.  Advance publ date: 2-Jun-2021. Journal publ date: 1-Sep-2021.
    [Abstract] [Article]
  5. 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.   Accepted: 2-Jun-2021.  Advance publ date: 15-Jun-2021.  Journal publ date: 22-Jul-2021.
    [Abstract] [Article] [medRxiv] (freely available)
  6. 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.   Accepted: 11-Jun-2021.  Advance publ date: 15-Jun-2021. Journal publ date: 19-Jul-2021.
    [Abstract] [Article]
  7. 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.  Accepted: 4-Jun-2021.   Advance publ date: 15-Jun-2021. Paper publ date: 6-Jul-2021
    [Abstract] [Article]
  8. A pipeline for integrated theory and data-driven modeling of genomic and clinical data
    V.K. Raghu, X. Ge, A. Balajee, D. Shirer, I. Das, P.V. Benos, P.K. Chrysanthis
    IEEE/ACM Trans on Comput Biol and Bioinf (2021) 18:811-822.   BioKDD2019 Conf presentation: 5-Aug-2019.  IEEE Early access: 25-Aug-2020. Paper publ date: 3-Jun-2021.
    [Abstract] [Article] [arXiv version] (freely available)
  9. 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.   Accepted: Oct-2020.   Advance publ date: 2-Dec-2020. Paper publ date: 16-Feb-2021.
    [Abstract] [Article]  [medRxiv] (freely available)
  10. 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.   Accepted: 1-Dec-2020.   Journal publ date: 12-Jan-2021.
    [Abstract] [Article]  (freely available)
2020
  1. Interpretable Factors in scRNA-seq Data with Disentangled Generative Models
    H. Mao, M.J. Broerman, P.V. Benos
    2020 IEEE BIBE (20th International Conference on Bioinformatics and Bioengineering), pp. 85-88,  (2020) accepted.   Conf presentation: 26-Oct-2020.  IEEE Xplore access: 16-Dec-2020.
    [Abstract] [Article]  (IEEE Xplore)
  2. 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. Methe, P.V. Benos, A. Morris, B.J. McVerry
    Am J Respir Crit Care Med (2020) 202:1666-1677.  Epub: 27-Jul-2020.  Journal publ date: 15-Dec-2020.
    [Abstract] [Article] [PMC version]
  3. Improving Constraint-Based Causal Discovery from Moralized Graphs
    A. Fuccello, D. Yuan, P.V. Benos, V.K. Raghu
    NeurIPS 2020 Workshop on Causal Discovery and Causality-Inspired Machine Learning, (2020) accepted.   Conf presentation: 11-Dec-2020.
    [Abstract] [Article]  (Workshop website)
  4. 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
    Front Cell Infect Microbiol (2020) 10:586592.   Journal publ date: 29-Oct-2020.
    [Abstract] [Article]  (freely available)
  5. 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 Bioinf (2020) 21(Suppl 8):363.   BITS2019 Conf presentation: 26-28-Jun-2019.  Journal publ date: 16-Sep-2020.
    [Abstract] [Article]  (freely available)
  6. Protecting the lungs and 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 Transl Med (2020) 8:985.  Epub: 20-May-2020.  Journal publ date: 8-Aug-2020.
    [Abstract] [PMC version] [Article] (freely available)  [Editorial]
  7. 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. Epub: 11-May-2020.  Journal publ date: 2-Jul-2020.
    [Abstract] [Article] (freely available)  [Web tool]
  8. 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. Epub: 24-Dec-2019. Journal publ date: 15-Apr-2020.
    [Abstract] [Article] (freely available)               [Supplementary Data] [Code and Data]
  9. 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. Epub: 6-Feb-2020. Journal publ date: Apr-2020.
    [Abstract] [Article] [PMC version]
2019
  1. 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.   Epub: 18-Oct-2019.  Journal publ date: Dec-2019.
    [Abstract] [Article] [PMC version]
  2. COPDGene 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease
    K.E. Lowe, E.A. Regan, A. Anzueto, E. Austin, J.H.M. Austin, T.H. Beaty, P.V. Benos, …, E.K. Silverman, J.D. Crapo
    Chronic Obstr Pulm Dis (2019) 6:384-399.  Publ Date: 10-Nov-2019.
    [Abstract] [Article] (freely available)
  3. Transcriptional regulatory model of fibrosis progression in the human 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
    JCI Insight (2019) 4:e131597.   Epub: 10-Oct-2019.  Journal publ date: 4-Nov-2019.
    [Abstract] [Article] (freely available)              [Supplementary Material]
  4. Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
    C. Morse, T. Tabib, J. Sembrat, K. 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.   Epub: 22-Aug-2019.  Journal publ date: 22-Aug-2019.
    [Abstract] [Article] [PMC version]               [Supplementary Material]
  5. A pipeline for integrated theory and data-driven modeling of genomic and clinical data
    V.K. Raghu, X. Ge, A. Balajee, D. Shirer, I. Das, P.V. Benos, P.K. Chrysanthis
    BioKDD2019 (2019) accepted.   Conf presentation: 5-Aug-2019
    [Abstract] [Article] (freely available)
    [UPDATE 2020-08-27: An updated version of this paper was published by the IEEE/ACM Transactions on Computational Biology and Bioinformatics]
  6. Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque
    E. Caparosa†, A.J. Sedgewick†, G. Zenonos, Y. Zhao, D.L. Carlisle, L. Stefaneanu, B.T. Jankowitz, P. Gardner, Y.-F. Chang, W.R. Lariviere, W.A. LaFramboise, P.V. Benos, R.M. Friedlander,
    Neurosurgery (2019) 85:E284-E293.   Epub: 17-Oct-2018.  Journal publ date: 1-Aug-2019.
    [Abstract] [Article] [PMC version]               [Supplementary Material]
  7. 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.   Publ Date: 12-Jul-2019.  Journal publ date: 12-Jul-2019.
    [Abstract] [Article] (freely available)
  8. 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.   Epub: 12-Mar-2019.  Journal publ date: Jul-2019.
    [Abstract] [Article] (freely available)               [Supplementary Material]
  9. 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.  Epub: 5-Sep-2018.  Journal publ date: 1-Apr-2019.
    [Abstract]  [Article] [PMC version]               [Supplementary Material] [arXiv version]   Submitted: 9-Apr-2017
  10. 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.   Publ date: 1-Mar-2019.
    [Abstract] [Article] (freely available)               [Supplementary Material]
  11. 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.  Epub: 22-Nov-2018.  Journal publ date: Jan-2019.
    [Abstract] [Article] (freely available)
2018
  1. An insulin responsive sensor in the SIRT1 disordered region binds DBC1 and PACS-2 to control enzyme activity
    T.C. Krzysiak, L. Thomas, Y.-J. Choi, S. Auclair, Y. Qian, S. Luan, S.M. Krasnow, L.L. Thomas, L.M.I. Koharudin, P.V. Benos, D.L. Marks, A.M. Gronenborn, G. Thomas
    Molecular Cell (2018) 72:985-998.e7.   Epub: 8-Nov-2018
    [Abstract]  [Article]  [PMC version]
  2. piMGM: Incorporating Multi-Source Priors in Mixed Graphical Models for Learning Disease Networks
    D.V. Manatakis†, V.K. Raghu†, and P.V. Benos
    Bioinformatics (2018) 34:i848–i856.   (Proc ECCB 2018)    Publ Date: 1-Sep-2018
    [Abstract]  [Article]  [PMC version]               [Supplementary Material]
  3. Evaluation of Causal Structure Learning Methods on Mixed Data Types
    V.K. Raghu, A. Poon, and P.V. Benos
    Proc Machine Learning Research (2018) 92:48-65.
    [Abstract]  [Article] (freely available)
  4. A pipeline for integrated theory and data-driven modeling of genomic and clinical data
    V.K. Raghu, X. Ge, A. Balajee, D. Shirer, I. Das, P.V. Benos, P.K. Chrysanthis
    BioKDD2019 (2019) accepted.   Conf presentation: 5-Aug-2019
    [Abstract] [Article] (freely available)
    [UPDATE 2020-08-27: An updated version of this paper was published by the IEEE/ACM Transactions on Computational Biology and Bioinformatics]
  5. Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients
    G.D. Kitsios, A. Fitch, D.V. Manatakis, S. Rapport, K. Li, S. Qin, J. Huwe, Y. Zhang, Y. Doi, J. Evankovich, W. Bain, J.S. Lee, B. Methe, P.V. Benos, A. Morris, B. McVerry
    Frontiers in Microbiology (2018) 9:1413.   Publ Date: 10-Jul-2018
    [Abstract]  [Article]  [PMC version]
  6. Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine
    P. Ping, H. Hermjakob, J.S. Poison, P.V. Benos, W. Wang
    Circulation Research (2018) 122:1290-1301.    Publ Date: 27-Apr-2018
    [Abstract]  [Article]  [PMC version] [Review]
  7. Comparison of strategies for scalable causal discovery of latent variable models from mixed data
    V.K. Raghu, J.D. Ramsey, A. Morris, D.V. Manatakis, P. Sprites, P.K. Chrysanthis, C. Glymour, P.V. Benos
    Int J Data Sci and Analytics (2018) 6:33-45.   Epub: 6-Feb-2018
    [Abstract]  [Article]  [PMC version]
  8. Biomarker identification for statin sensitivity of cancer cell lines
    V.K. Raghu, C.H. Beckwitt, K. Warita, A. Wells, P.V. Benos*, Z.N. Oltvai*
    Biochem Biophys Res Commun (2018) 495:659-665.  Epub: 14-Nov-2017
    [Abstract]  [Article]  [PMC version]
2017
  1. Ribosomopathy-like properties of murine and human cancers
    S. Kulkarni, J.M. Dolezal, H. Wang, L. Jackson, J. Lu, B.P. Frodey, A. Dosunmu-Ogunbi, Y. Li, M. Fromherz, A. Kang, L. Santana-Santos, P.V. Benos, E.V. Prochownik
    PLoS One (2017) 12:e0182705.   Publ Date: 18-Aug-2017
    [Abstract]  [Article]  [PMC version]
  2. Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection
    D.A. Pociask, K.M. Robinson, K. Chen, K.J. McHugh, M.E. Clay, G.T. Huang, P.V. Benos, Y.M.W. Janssen-Heininger, J.K. Kolls, V. Anathy, J.F. Alcorn
    Am J Pathol (2017) 118:851-863.   Epub: 10-Feb-2017
    [Abstract]  [Article]  [PMC version]
  3. Downregulation of estrogen receptor and modulation of growth of breast cancer cell lines mediated by paracrine stromal cell signals
    J. Huang, P. Woods, D. Normolle, J.P. Goff, P.V. Benos, C.J. Stehle, R.A. Steinman
    Breast Cancer Res Treat (2017) 118:851-863.   Epub: 16-Nov-2016
    [Abstract]  [Article]  [PMC version]
2016
  1. Non-coding single nucleotide variants affecting estrogen receptor binding and activity
    A. Bahreini, K. Levine, L. Santana-Santos, P.V. Benos, P. Wang, C. Andersen, S. Oesterreich, A.V. Lee
    Genome Medicine (2016) 8:128.   Publ Date: 13-Dec-2016
    [Abstract]  [Article]  [PMC version]
  2. Learning mixed graphical models with separate sparsity parameters and stability-based model selection
    A.J. Sedgewick, I. Shi, R.M. Donovan, P.V. Benos
    BMC Bioinformatics (2016) 17 Suppl 5:175 (Proc SMODIA2014)   Publ Date: 6-Jun-2016
    [Abstract]  [Article]  [PMC version]
  3. Regulation of alveolar septation by microRNA-489
    N. Olave, C.V. Lal, B. Halloran, K. Pandit, A.C. Cuna, O.M. Faye-Petersen, D.R. Kelly, T. Nicola, P.V. Benos, N. Kaminski, N. Ambalavanan
    Am J Physiol Lung Cell Mol Physiol (2016) 10:L476-L487.  Epub: 30-Dec-2015
    [Abstract] [Article] [PMC version]   Editor’s pick
2015
  1. Gene expression profiling distinguishes proneural glioma cells from mesenchymal glioma cells
    U.R. Chandran, S. Luthra, L. Santana-Santos, P. Mao, S.H. Kim, M. Minata, J. Li, P.V. Benos, M. DeWang, B. Hu, S.Y. Cheng, I.B. Nakano, R.W. Sobol
    Genomics Data (2015) 5:333-336.   Epub: 14-Jul-2015
    [Abstract]  [Article]  [PMC version]
  2. The Center for Causal Discovery of biomedical knowledge from Big Data
    G.F. Cooper, I. Bahar, M.J. Becich, P.V. Benos, J. Berg, J.U. Espino, C. Glymour, R.C. Jacobson, M. Kienholz, A.V. Lee, X. Lu, R.B. Scheines, Center for Causal Discovery team
    J Am Med Inform Assoc (2015) 22:1132-1136.   Epub: 2-Jul-2015
    [Abstract]  [Article]  [PMC version]
  3. MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603
    L.C. Villaruz†, G.T. Huang†, M. Romkes, J.M. Kirkwood, S.C. Buch, T. Nukui, K.T. Flaherty, S.J. Lee, M.A. Wilson, K.L. Nathanson, P.V. Benos, H.A. Tawbi
    Clinical Epigenetics (2015) 7:58.   Publ Date: 4-Jun-2015
    [Abstract]  [Article]  [PMC version]
  4. T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes
    G.T. Huang, I. Tsamardinos, V. Raghu, N. Kaminski, P.V. Benos
    Pac Symp Biocomput (2015) 20:431-442.
    [Abstract]  [Article]  [PMC version]

Older Publications (2002-2014)

2009-2014
  1. Aldosterone Regulates MicroRNAs in the Cortical Collecting Duct to Alter Sodium Transport
    R.S. Edinger, C. Coronnello, A.J. Bodnar, W.A. Laframboise, P.V. Benos, J. Ho, J.P. Johnson, M.B. Butterworth
    J Am Soc Nephrol (2014) 25:2445-2457
    [Abstract] [Article]  [PMC version]
  2. Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways
    T.Y. Lu, B. Lin, Y. Li, A. Arora, L. Han, C. Cui, C. Coronnello, Y. Sheng, P.V. Benos, L. Yang
    J Mol Cell Cardiol (2013) 63: 146-154
    [Abstract] [Article]  [PMC version]
  3. Estrogen represses gene expression through reconfiguring chromatin structures
    H.U. Osmanbeyoglu, K.N. Lu, S. Oesterreich, R.S. Day, P.V. Benos, C. Coronnello, X. Lu
    Nucleic Acids Research (2013) 41:8061-8071
    [Abstract] [Article]  [PMC version]
  4. Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3
    P. Mao, K. Joshi, J. Li, L. Santana-Santos, S. Luthra, U.R. Chandran, P.V. Benos, L. Smith, M. DeWang, B. Hu, S-Y. Cheng, R.W. Sobol, I. Nakano
    Proc Natl Acad Sci USA (2013) 110: 8644-8649
    [Abstract] [Article]  [PMC version]
  5. ComiR: Combinatorial microRNA target prediction tool
    C. Coronnello, P.V. Benos
    Nucleic Acids Research (2013) 41:W159-W164
    [Abstract] [Article]  [PMC version]  [Web tool]
  6. Spectral clustering strategies for heterogeneous disease expression data
    G.T. Huang, K. Cunningham, P.V. Benos, C.S. Chennubhotla
    Pac Symp Biocomput (2013) 212-223
    [Abstract] [Article]  [PMC version]
  7. Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density
    C. Coronnello, R. Hartmaier, A. Arora, L. Huleihel, K.V. Pandit, A.S. Bais, M. Butterworth, N. Kaminski, G.D. Stormo, S. Oesterreich, P.V. Benos
    PLoS Comput Biol. (2012) 8:e1002830
    [Abstract] [Article]  [PMC version]
  8. Profibrotic Role of miR-154 in Pulmonary Fibrosis
    J. Milosevic, K. Pandit, M. Magister, E. Rabinovich, D.C. Ellwanger, G. Yu, L.J. Vuga, B. Weksler, P.V. Benos, K.F. Gibson, M. Macmillan, M. Kahn, N. Kaminski
    Am J Respir Cell Mol Biol. (2012) 47:879-887
    [Abstract] [Article]  [PMC version]
  9. To bind or not to bind – FoxA1 determines estrogen receptor action in breast cancer
    R.J. Watters, P.V. Benos, S. Oesterreich
    Breast Cancer Research (2012)  14:312.  (invited Viewpoint)
    [Abstract] [Article]  [PMC version]
  10. S. Kadri, V. Hinman, P.V. Benos, “RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star”, PLoS One, (2011), 6:e29217.  PMID: 22216218.
  11. G. Zinman, R. Brower-Sinning, C.H. Emeche, J. Ernst, G.T. Huang, S. Mahony, A.J. Myers, D.M. O’Dee, J. L. Flynn, G.J. Nau, T.M. Ross, R.D. Salter, P.V. Benos, Z. Bar-Joseph, P.A. Morel, “Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque”, PLoS One (2011) 6:e22401.  PMID: 21789257.
  12. Y. Zhang, D. Handley, T. Kaplan, H. Yu, A.S. Bais, T. Richards, K.V. Pandit, P.V. Benos, N. Friedman, O. Eickelberg, N. Kaminski, “High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells”, PLoS One (2011) 6:e20319.  PMID: 21625455.
  13. (Web tool) G.T. Huang, C. Athanassiou, P.V. Benos, “mirConnX: Condition-specific mRNA-microRNA network integrator”, Nucleic Acids Research (2011) 39:W416-423.PMID: 21558324.
  14. A.S. Bais, N. Kaminski, P.V. Benos, “Finding subtypes of transcription factor motif pairs with distinct regulatory roles”, Nucleic Acids Research (2011), 39:e76. PMID: 21486752.
  15. K.V. Pandit†, D. Corcoran†, H. Yousef, M. Yarlagadda, A. Tzouvelekis, K.F. Gibson, K. Konishi, S.A. Yousem, M. Singh, D. Handley, T. Richards, M. Selman, S.C. Watkins, A. Pardo, A. Ben-Yehudah, D. Bouros, O. Eickelberg, P. Ray, P.V. Benos*, N. Kaminski*, “Inhibition and role of let-7din idiopathic pulmonary fibrosis”, Am J Respir Crit Care Med. (2010) 182:220-229.  PMID: 20395557.
  16. N.A. Temiz, P.V. Benos, C.J. Camacho, “Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains”, Nucleic Acids Research (2010) 38:2134-2144.  PMID: 20047959.
  17. A.B. Tchagang, K.V. Bui, T. McGinnis, P.V. Benos, “Extracting Biologically Significant Patterns from Short Time Series Gene Expression Data”, BMC Bioinformatics (2009), 10:255.  PMID: 19695084.    
  18. D.L. Corcoran†, K.V. Pandit†, B. Gordon, A. Bhattacharjee, N. Kaminski*, P.V. Benos*, “Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.” PLoS One (2009) 4:e5279.  PMID: 19390574.
  19. R. Brower-Sinning, D.M. Carter, C.J. Crevar, E. Ghedin, T.M. Ross, P.V. Benos, “The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus”, Genome Biology (2009), 10:R18. PMID: 19216739.
  20. S. Kadri, V. Hinman, P.V. Benos, “HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models”, BMC Bioinformatics (2009) 10(Supl 1):S35. (Proc APBC 2009) PMID: 19208136.
2002-2008
  1. Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, “Multiple evidence supporting cyclic assignments”, Genome Biology (2008),9:403 [rebattle article on Jensen et al., “Circular reasoning rather than cyclic expression”, Genome Biol (2008),9:403].  PMID: 18598377.
  2. A.B. Tchagang, A.H. Tewfik, P.V.  Benos, “Biological evaluation of biclustering algorithms using Gene Ontology and chIP-chip data”, IEEE ICASSP (2008).  [Article]
  3. H. Feng, J.L. Taylor, P.V. Benos, R. Newton, R. Downing, K. Waddell, Y. Chang, P.S. Moore, “Subtraction of the human transcriptome to search for human tumor viruses”, J Virology  (2007) 81:11332-11340. PMID: 17686852.
  4. Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, “Combined analysis reveals a core set of cycling genes”, Genome Biology (2007) 8:R146.  PMID: 17650318.
  5. S. Mahony, P.E. Auron and P.V. Benos “Inferring protein-DNA dependencies using motif alignments and mutual information.” Bioinformatics (2007) 23:i297-i304.  (Proc ISMB 2007)  PMID: 17646310.
  6. S. Mahony, D.L. Corcoran, E. Feingold, P.V. Benos, “Regulatory conservation of protein coding and miRNA genes in vertebrates:  lessons from the opossum genome”, Genome Biology (2007) 8:R84. PMID: 17506886.    
  7. T.S. Mikkelsen (1), …, P.V. Benos(18), …, K. Lindblad-Toh (61), “Genome of the marsupial Monodelphis domesticareveals lineage-specific innovation in coding and non-coding sequences”, Nature (2007) 447:167-177.  PMID: 17495919.
  8. (Web tool) S. Mahony, P.V. Benos, “STAMP: a web tool for exploring DNA-binding motif similarities”, Nucleic Acids Research (2007) 35:W253-258.  PMID: 17478497.
  9. S. Mahony, P.E. Auron, P.V. Benos, “DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies”, PLoS Comput Biol (2007) 3:e61. PMID: 17397256.
  10. S. Mahony, P.V. Benos, T.J. Smith, A. Golden, “Self-organizing neural networks to support the discovery of DNA-binding motifs”, Neural Networks (2006) 19:950-962. PMID: 16839740.
  11. K. Belov, J.E. Deakin, A.T. Papenfuss, M.L. Baker, S.D. Melman, H.V. Siddle, N. Gouin, D.L. Goode, T.J. Sargeant, M.D. Robinson, M.J. Wakefield, S. Mahony, J.G.R. Cross, P.V. Benos, P.B. Samollow, T.P. Speed, J.A.M. Graves, R.D. Miller, “Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex”, PLoS Biology (2006) 4:e46. PMID: 16435885.
  12. K.R. Rogulski, D.E. Cohen, D.L. Corcoran, P.V. Benos and E.V. Prochownik “Deregulation of common genes by c-Myc and its direct target, MT-MC1.” Proc Natl Acad Sci USA (2005) 102:18968-18973. PMID: 16365299.
  13. S. Mahony, A. Golden, T.J. Smith and P.V. Benos “Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.” Bioinformatics (2005) 21 Suppl:i283-i291.  (Proc ISMB 2005) PMID: 15961468.
  14. (Web tool) S. Ringquist, C. Pecoraro, C. Gilchrist, A. Styche, W. Rudert, P.V. Benos, and M. Trucco “SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.” Nucleic Acids Research (2005) 33:W548-552.  PMID: 15980532.
  15. (Web tool) D.L. Corcoran, E. Feingold, and P.V. Benos “FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.” Nucleic Acids Research (2005) 33:W442-446.  PMID: 15980508.
  16. (Web tool) C.T. Workman, Y. Yin, D.L. Corcoran, T. Ideker, G.D. Stormo and P.V. Benos, “EnoLOGOS: a versatile web tool for energy normalized sequence logos.” Nucleic Acids Research, (2005) 33:W389-392.  PMID: 15980495.
  17. D.L. Corcoran, E. Feingold, J. Dominick, M. Wright, J. Harnaha, M. Trucco, N. Giannoukakis, P.V. Benos, “FOOTER: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements”, Genome Research (2005) 15:840-847.PMID: 15930494.
  18. A.M. Alexander, C. Pecoraro, A. Styche, W.A. Rudert, P.V. Benos, S. Ringquist, M. Trucco, SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing”, Biotechniques (2005) 38:87-94. PMID: 15679090.
  19. J.K. Vries, R. Munshi, D. Tobi, J. Klein-Seetharaman, P.V. Benos, I. Bahar, “A sequence alignment-independent method for protein classification”, Applied Bioinformatics (2004) 3:137-148. PMID: 15693739.
  20. D.G. Peters, X.C. Zhang, P.V. Benos, E. Heidrich-O’Hare, R.E. Ferrell, “Genomic analysis of the immediate/early response to shear stress in human coronary artery endothelial cell”, Physiol. Genomics (2002) 12:25-33.PMID: 12407183.

Pre-Independence Publications (prior to 2002)

Post-graduate work
  1. P.V. Benos, M.L. Bulyk, G.D. Stormo, “Additivity on protein-DNA interactions: how good an approximation is it?”, Nucleic Acids Research (2002) 30:4442-4445. PMID: 12384591
  2. P.V. Benos, A.S. Lapedes and G.D. Stormo, “Probabilistic code for DNA recognition by proteins of the EGR-family”, J. Molecular Biology, (2002) 323:701-727.  PMID: 12419259
  3. P.V. Benos, A.S. Lapedes, G.D. Stormo, “Is there a code for protein-DNA recognition? Probab(ilistical)ly…”, Bioessays (2002) 24:466-475.  (Review)  PMID: 12001270.
  4. P.V. Benos*, A.S. Lapedes, D.S. Fields, G.D. Stormo, “SAMIE: Statistical Algorithm for Modeling Interaction Energies”, Pac Symp Biocomput (2001) 6:115-126.  PMID: 11262933.
  5. A. Peter, P. Schoettler, M. Werner, N. Beinert, G. Dowe, P. Burkert, F. Mourkioti, L. Denzer, Y. He, P. Deak, P.V. Benos, M.K. Gatt, L. Murphy, D. Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demaille, E. Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B. Minana, F.C. Kafatos, S. Bolshakov, I. Siden-Kiamos, G. Papagiannakis, L. Spanos, C. Louis, E. Madueno, B. de Pablos, J. Modolell, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders, A. Billaud, L. Pachter, R. Klapper, W. Janning, D.M. Glover, M. Ashburner, H.J. Bellen, H. Jaeckle, U. Schaefer, “Mapping and identification of essential gene functions on the X chromosome of Drosophila“, EMBO Reports, (2002) 3:34-38.  PMID: 11751581.
  6. P.V. Benos, M.K. Gatt, L. Murphy, D. Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demaille, E. Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B. Minana, F.C. Kafatos, S. Bolshakov, I. Siden-Kiamos, G. Papagiannakis, L. Spanos, C. Louis, E. Madueno, B. de Pablos, J. Modolell, A. Peter, P. Schoettler, M. Werner, F. Mourkioti, N. Beinert, G. Dowe, U. Schaefer, H. Jaeckle, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders, A. Billaud, L. Pachter, D.M. Glover, M. Ashburner, “From first base: The sequence of the tip of the X chromosome of D. melanogaster, a comparison of two sequencing strategies”, Genome Research (2001) 11:710-730. PMID: 11337470.
  7. P.V. Benos, M.K. Gatt, M. Ashburner, L. Murphy, D. Harris, B. Barrel, C. Ferraz, S. Vidal, C. Brun, J. Demailles, E. Cadieu, S. Dreano, S. Gloux, V. Lelaure, S. Mottier, F. Galibert, D. Borkova, B. Minana, F.C. Kafatos, C. Louis, I. Siden-Kiamos, S. Bolshakov, G. Papagiannakis, L. Spanos, S. Cox, E. Madueno, B. de Pablos, J. Modolell, A. Peter, P. Schoettler, M. Werner, F. Mourkioti, N. Beinert, G. Dowe, U. Schaefer, H. Jaeckle, A. Bucheton, D. Callister, L. Campbell, N.S. Henderson, P.J. Mcmillan, C. Salles, E. Tait, P. Valenti, R.D.C. Saunders and D.M. Glover, “From DNA sequence to chromosome organisation: the tip of the X chromosome of D. melanogaster“, Science (2000) 287:2220-2222.  PMID: 10731137.
  8. M. Adams(1), …, P.V. Benos(43), …, C. Venter(195), “The genome sequence of Drosophila melanogaster“, Science (2000) 287:2185-2195. PMID: 10731132.
Graduate work
  1. S. Brogna†, P.V. Benos†, G. Gasperi, C. Savakis, “The Drosophila alcohol dehydrogenase gene may have evolved independently of the functionally homologous medfly, olive fly and flesh fly genes”, Molecular Biology Evolution, (2001) 18:322-329. PMID: 11230533.
  2. P. Benos*, N. Tavernarakis, S.Brogna, G. Thireos, C. Savakis, “Acquisition of a potential marker for insect transformation: isolation of a novel alcohol dehydrogenase gene fromBactrocera oleae by functional complementation in yeast”, Molecular General Genetics (2000) 263:90-95. PMID: 10732677.
  3. R. Gessmann, P. Benos, H. Brueckner, M. Kokkinidis, “The crystal structures of the synthetic C-terminal Octa- and Dodecapeptides of Trichovirin”, J. Peptide Science (1999) 5:83-95. PMID: 10100124.
  4. P. Deak, M.M. Omar, R.D. Saunders, M. Pal, O. Komonyi, J. Szidonya, P. Maroy, Y. Zhang, M. Ashburner, P. Benos, C. Savakis, I. Siden-Kiamos, C. Louis, V.N. Bolshakov, F.C. Kafatos, E. Madueno, J. Modolell, D.M. Glover, “P-element insertion alleles of essential genes on the third chromosome of Drosophila melanogaster: correlation of physical and cytogenetic maps in chromosomal region 86E-87F”, Genetics (1997) 147:1697-1722. PMID: 9409831.
  5. C. Louis, E. Madueno, J. Modolell, M.M. Omar, G. Papagiannakis, R.D. Saunders, C. Savakis, I. Siden-Kiamos, L. Spanos, P. Topalis, Y.Q. Zhang, M. Ashburner, P. Benos, V.N. Bolshakov, P. Deak, D.M. Glover, S. Herrmann, F.C. Kafatos, “One-hundred and five new potential Drosophila melanogastergenes revealed through STS analysis”, Gene (1997) 195:187-193. PMID: 9305763.
  6. M. Tabler, P. Benos, M. Doerr, “Representation of unique sequences in libraries of randomized nucleic acids”, Nucleic Acids Research (1996) 24:3437-3438. PMID: 8811100.
  7. E. Madueno Amor, G. Papagiannakis, G. Rimmington, R.D.C. Saunders, C. Savakis, I. Siden-Kiamos, G. Skavdis, L. Spanos, J. Trennear, P. Adam, M. Ashburner, P. Benos, V. Bolshakov, D. Coulson, D.M. Glover, S. Herrmann, F.C. Kafatos, C. Louis, T. Majerus, J. Modolell, “A physical map of the X chromosome of Drosophila melanogaster: Cosmid contigs and sequence tagged sites”, Genetics (1995) 139:1631-1647. PMID: 7789765.