{"id":1219,"date":"2019-02-11T03:56:35","date_gmt":"2019-02-11T03:56:35","guid":{"rendered":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1219"},"modified":"2022-08-11T07:53:31","modified_gmt":"2022-08-11T07:53:31","slug":"pubs-test-2","status":"publish","type":"page","link":"https:\/\/csbweb.csb.pitt.edu\/Faculty\/benos\/?page_id=1219","title":{"rendered":"Publications"},"content":{"rendered":"
boldface<\/strong>: members of Benos’ lab, \u00a0\u2020equal contribution,\u00a0*(co-)corresponding authors, \u00a0PMC paper versions are freely available<\/h5>\n

Latest Trends of the Lab<\/strong><\/h3>\n
<\/span>2022<\/div>
\n
    \n
  1. Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets
    \nM. Jia\u2020<\/strong>, D. Yuan\u2020<\/strong>, T.C. Lovelace<\/strong>, M. Hu<\/strong>, P.V. Benos<\/strong>
    \nFront Epidemiol<\/strong><\/em>\u00a0(2022) <\/span>.\u00a0Accepted: 5-Aug-2022. \u00a0Advance publ date: TBD. \u00a0Final publ date: TBD.<\/span>
    \n<\/span>[Abstract] [Article<\/a>]<\/li>\n
  2. Essential Regression: A generalizable framework for inferring causal latent factors from multi-omic datasets
    \nX. Bing\u2020<\/strong>, T. Lovelace\u2020<\/strong>. F. Bunea, M. Wegkamp, S.P. Kasturi, H. Singh*, P.V. Benos*<\/strong>, J. Das*
    \nPatterns<\/strong><\/em>\u00a0(2022) 3:<\/strong>100473<\/span>.\u00a0Accepted: 1-Mar-2022. \u00a0Advance publ date: 24-Mar-2022. \u00a0Final publ date: 13-May-2022.<\/span>
    \n<\/span>[    Abstract<\/a>] [Article<\/a>]<\/li>\n<\/ol>\n<\/div><\/div>\n
    <\/span>2021<\/div>
    \n
      \n
    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
      \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<\/span>
      \nCell Rep Med<\/strong><\/em>\u00a0(2021) 2:<\/strong>100476.\u00a0Accepted: 23-Nov-2021. \u00a0Advance publ date: 2-Dec-2021. \u00a0Final publ date: 21-Dec-2021.
      \n[      Abstract<\/a>] [Article<\/a>]<\/li>\n
    2. Transcriptomics of Bronchoalveolar Lavage Cells Identifies New Molecular Endotypes of Sarcoidosis
      \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<\/strong><\/em>\u00a0(2021) 58:<\/strong>2002950. \u00a0 Accepted: 8-May-2021. \u00a0Advance publ date: 3-Jun-2021. \u00a0Final publ date: 2-Dec-2021.
      \n[      Abstract<\/a>] [Article<\/a>] [medRxiv<\/a>] (freely available)<\/li>\n
    3. Neurological Complications Acquired during Pediatric Critical Illness: Exploratory \u2018Mixed Graphical Modeling\u2019 Analysis using Serum Biomarker Levels
      \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<\/strong><\/em>\u00a0(2021) 22:<\/strong>906-914. \u00a0 Accepted: 5-Apr-2021. \u00a0Advance publ date: 1-Jun-2021. Journal publ date: 1-Oct-2021.
      \n[      Abstract<\/a>] [Article<\/a>]<\/li>\n
    4. Reduced Proportion and Activity of Natural Killer Cells in the Lung of Patients with Idiopathic Pulmonary Fibrosis
      \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. Benos<\/strong>, M. Rojas<\/span>
      \nAm J Resp Crit Care Med<\/i><\/strong>\u00a0<\/i><\/b><\/span><\/span>(2021) 204:<\/strong>608-610. \u00a0 Accepted: 17-Mar-2021. \u00a0Advance publ date: 2-Jun-2021. Journal publ date:\u00a01-Sep-2021.
      \n[      Abstract<\/a>] [Article<\/a>]<\/li>\n
    5. Plasma 1,3-beta-D-glucan levels predict adverse clinical outcomes in critical illness
      \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<\/strong><\/em>\u00a0(2021) 6:<\/strong>141277. \u00a0 Accepted: 2-Jun-2021. \u00a0Advance publ date: 15-Jun-2021. \u00a0Journal\u00a0publ date:\u00a022-Jul-2021.
      \n[      Abstract<\/a>] [Article<\/a>] [medRxiv<\/a>] (freely available)<\/li>\n
    6. Myofibroblast transcriptome indicates SFRP2+ fibroblast progenitors in systemic sclerosis skin
      \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<\/span>
      \nNature Communications<\/strong><\/em>\u00a0(2021) 12:<\/strong>4384. \u00a0 Accepted: 11-Jun-2021. \u00a0Advance publ date: 15-Jun-2021. Journal\u00a0publ date:\u00a019-Jul-2021.
      \n[      Abstract<\/a>] [Article<\/a>]<\/li>\n
    7. Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors
      \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<\/span>
      \nCell Reports<\/strong><\/em>\u00a0(2021) 36:<\/strong>109310. \u00a0Accepted: 4-Jun-2021. \u00a0 Advance publ date: 15-Jun-2021. Paper publ date:\u00a06-Jul-2021
      \n[      Abstract<\/a>] [Article<\/a>]<\/li>\n
    8. A pipeline for integrated theory and data-driven modeling of genomic and clinical data
      \nV.K. Raghu<\/strong>, X. Ge, A. Balajee, D. Shirer, I. Das<\/strong>, P.V. Benos<\/strong>, P.K. Chrysanthis<\/span>
      \nIEEE\/ACM Trans on Comput Biol and\u00a0Bioinf<\/strong><\/em>\u00a0(2021) 18:<\/strong>811-822. \u00a0 BioKDD2019 Conf presentation: 5-Aug-2019. \u00a0IEEE Early access: 25-Aug-2020. Paper publ date: 3-Jun-2021.
      \n[      Abstract<\/a>] [Article<\/a>] [arXiv version<\/a>] (freely available)<\/li>\n
    9. Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study
      \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<\/span>
      \nThorax<\/strong><\/em>\u00a0(2021) 76:<\/strong>239-247. \u00a0 Accepted: Oct-2020. \u00a0 Advance publ date: 2-Dec-2020. Paper publ date: 16-Feb-2021.
      \n[      Abstract<\/a>] [Article<\/a>] \u00a0[medRxiv<\/a>] (freely available)<\/li>\n
    10. Human ex vivo lung perfusion: A novel model to study human lung diseases
      \nN. C\u00e1rdenes\u2020, J. Sembrat\u2020, K. Noda\u2020, T. Lovelace\u2020<\/strong>, D. \u00c1lvarez, H.E. Trejo Bittar, B.J. Philips, M. Nouraie, P.V. Benos<\/strong>, P.G. S\u00e1nchez, M. Rojas<\/span>
      \nScientific Reports<\/strong>, (2021) 11:<\/strong>490. \u00a0 Accepted: 1-Dec-2020. \u00a0 Journal publ date: 12-Jan-2021.
      \n[      Abstract<\/a>] [Article<\/a>] \u00a0(freely available)<\/li>\n<\/ol>\n<\/div><\/div>\n
      <\/span>2020<\/div>
      \n
        \n
      1. Interpretable Factors in scRNA-seq Data with Disentangled Generative Models
        \nH. Mao<\/strong>, M.J. Broerman, P.V. Benos<\/strong><\/span>
        \n2020 IEEE BIBE <\/strong>(20th International Conference on Bioinformatics and Bioengineering), pp. 85-88, \u00a0(2020) accepted<\/em>. \u00a0 Conf presentation: 26-Oct-2020. \u00a0IEEE Xplore access: 16-Dec-2020.
        \n[Abstract] [        Article<\/a>] \u00a0(IEEE Xplore)<\/li>\n
      2. Respiratory Tract Dysbiosis is Associated With Worse Outcomes in Mechanically-Ventilated Patients
        \nG.D. Kitsios,\u00a0H. Yang<\/strong>, L. Yang, S. Qin, A. Fitch, X.-H. Wang, K. Fair, J. Evankovich, W. Bain, F. Shah, K. Li, B. Methe,\u00a0P.V. Benos<\/strong>, A. Morris, B.J. McVerry<\/span>
        \nAm J Respir Crit Care Med\u00a0<\/i><\/strong>(2020)\u00a0<\/i>202:<\/strong>1666-1677. \u00a0Epub: 27-Jul-2020. \u00a0Journal publ date: 15-Dec-2020.
        \n[        Abstract<\/a>] [Article<\/a>] [PMC version]<\/li>\n
      3. Improving Constraint-Based Causal Discovery from Moralized Graphs
        \nA.\u00a0Fuccello<\/strong>, D.\u00a0Yuan<\/strong>, P.V. Benos<\/strong>, V.K. Raghu<\/strong><\/span>
        \nNeurIPS 2020<\/strong> Workshop on Causal Discovery and Causality-Inspired Machine Learning, (2020) accepted<\/em>. \u00a0 Conf presentation: 11-Dec-2020.
        \n[Abstract] [        Article<\/a>] \u00a0(Workshop website)<\/li>\n
      4. miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19 via Targeting SARS-CoV-2 RNA
        \nG. Bertolazzi<\/strong>, C. Cipollina, P.V. Benos<\/strong>, M. Tumminello, C. Coronnello<\/span>
        \nFront Cell Infect Microbiol<\/strong><\/em>\u00a0(2020) 10<\/strong>:586592. \u00a0 Journal publ date: 29-Oct-2020.
        \n[        Abstract<\/a>] [Article<\/a>] \u00a0(freely available)<\/li>\n
      5. An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs
        \nG. Bertolazzi<\/strong>, P.V. Benos<\/strong>, M. Tumminello, C. Coronnello<\/span>
        \nBMC Bioinf<\/strong><\/em>\u00a0(2020) 21<\/strong>(Suppl 8):363. \u00a0 BITS2019 Conf presentation: 26-28-Jun-2019. \u00a0Journal publ date: 16-Sep-2020.
        \n[        Abstract<\/a>] [Article<\/a>] \u00a0(freely available)<\/li>\n
      6. Protecting the lungs and hurting the kidneys: causal inference study for the risk of ventilation-induced kidney injury in ARDS
        \nH. Yang<\/strong>, P.V. Benos<\/strong>, G.D. Kitsios<\/span>
        \nAnnals Transl Med\u00a0<\/i><\/strong>(2020) 8:<\/strong>985. \u00a0Epub: 20-May-2020. \u00a0Journal publ date: 8-Aug-2020.
        \n[        Abstract<\/a>] [PMC version<\/a>] [Article<\/a>] (freely available) \u00a0[Editorial]<\/li>\n
      7. CausalMGM: An interactive web-based causal discovery tool
        \nX. Ge\u2020, V.K. Raghu\u2020<\/strong>, P.K. Chrysanthis, P.V. Benos<\/strong><\/span>
        \nNucl Acids Res\u00a0<\/i><\/strong>(2020) 48<\/strong> (Web Server Issue):W597\u2013W602. Epub: 11-May-2020. \u00a0Journal publ date: 2-Jul-2020.
        \n[        Abstract<\/a>] [Article<\/a>] (freely available) \u00a0[Web tool<\/a>]<\/li>\n
      8. Causal network perturbations for instance-specific analysis of single cell and disease samples
        \nK.L. Buschur<\/strong>, M. Chikina,\u00a0P.V. Benos<\/strong><\/span>
        \nBioinformatics\u00a0<\/i><\/strong>(2020) 36:<\/strong>2515\u20132521. Epub: 24-Dec-2019. Journal publ date: 15-Apr-2020.
        \n[        Abstract<\/a>] [Article<\/a>] (freely available) \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 [Supplementary Data<\/a>] [Code and Data<\/a>]<\/li>\n
      9. The evolution of radiographic edema in ARDS and its association with clinical outcomes: a prospective cohort study in adult patients
        \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<\/span>
        \nJ Crit Care\u00a0<\/i><\/strong>(2020) 56:<\/strong>222-228. Epub: 6-Feb-2020. Journal publ date: Apr-2020.
        \n[        Abstract<\/a>] [Article<\/a>] [PMC version<\/a>]<\/li>\n<\/ol>\n<\/div><\/div>\n
        <\/span>2019<\/div>
        \n
          \n
        1. Host-Response Subphenotypes Offer Prognostic Enrichment in Patients With or at Risk for Acute Respiratory Distress Syndrome
          \nG.D. Kitsios, L. Yang, D.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, P.V. Benos<\/strong>, J.S. Lee, A. Morris, B.J. McVerry<\/span>
          \nCritical Care\u00a0<\/strong><\/em>Medicine<\/strong><\/em>\u00a0<\/i><\/b><\/span><\/span>(2019) 47:<\/strong>1724-1734. \u00a0 Epub: 18-Oct-2019. \u00a0Journal publ date: Dec-2019.
          \n[          Abstract<\/a>] [Article<\/a>] [PMC version<\/a>]<\/li>\n
        2. COPDGene 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease
          \nK.E. Lowe, E.A.\u00a0Regan, A.\u00a0Anzueto, E.\u00a0Austin, J.H.M.\u00a0Austin, T.H. Beaty,\u00a0P.V. Benos<\/strong>, …, E.K. Silverman, J.D. Crapo<\/span>
          \nChronic Obstr Pulm Dis <\/i><\/strong>(2019) 6:<\/strong>384-399. \u00a0Publ Date: 10-Nov-2019.
          \n[          Abstract<\/a>] [Article<\/a>] (freely available)<\/li>\n
        3. Transcriptional regulatory model of fibrosis progression in the human lung
          \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>
          \nJCI Insight<\/strong><\/em>\u00a0<\/i><\/b><\/span><\/span>(2019)\u00a04:<\/strong>e131597.\u00a0 \u00a0Epub: 10-Oct-2019. \u00a0Journal publ date: 4-Nov-2019.
          \n[          Abstract<\/a>] [Article<\/a>] (freely available) \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0[Supplementary Material<\/a>]<\/li>\n
        4. Proliferating SPP1\/MERTK-expressing macrophages in idiopathic pulmonary fibrosis
          \nC. Morse, T. Tabib, J. Sembrat, K. 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<\/strong><\/em>\u00a0(2019) 54:<\/strong>1802441. \u00a0 Epub: 22-Aug-2019. \u00a0Journal publ date: 22-Aug-2019.
          \n[          Abstract<\/a>] [Article<\/a>] [PMC version] \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 [Supplementary Material<\/a>]<\/li>\n
        5. A pipeline for integrated theory and data-driven modeling of genomic and clinical data
          \nV.K. Raghu<\/strong>, X. Ge, A. Balajee, D. Shirer, I. Das<\/strong>, P.V. Benos<\/strong>, P.K. Chrysanthis<\/span>
          \nBioKDD2019<\/strong><\/em>\u00a0(2019) accepted<\/em>. \u00a0 Conf presentation: 5-Aug-2019
          \n[Abstract] [          Article<\/a>] (freely available)
          \n[UPDATE 2020-08-27: An updated version of this paper was published by the IEEE\/ACM Transactions on Computational Biology and Bioinformatics<\/em>]<\/li>\n
        6. Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque
          \nE. Caparosa\u2020, A.J. Sedgewick\u2020<\/strong>, 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<\/strong>, R.M. Friedlander, <\/span>
          \nNeurosurgery<\/strong><\/em> (2019)\u00a085:<\/strong>E284-E293. \u00a0 Epub: 17-Oct-2018. \u00a0Journal publ date: 1-Aug-2019.
          \n[          Abstract<\/a>] [Article<\/a>] [PMC version] \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 [Supplementary Material<\/a>]<\/li>\n
        7. Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers
          \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>\u00a0<\/span><\/span><\/strong><\/em>(2019)\u00a019:<\/strong>686. \u00a0 Publ Date: 12-Jul-2019. \u00a0Journal publ date: 12-Jul-2019.
          \n[          Abstract<\/a>] [Article<\/a>] (freely available)<\/li>\n
        8. Feasibility of lung cancer prediction from low-dose CT scan and smoking factors using causal models
          \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) 74:<\/strong>643-649. \u00a0 Epub: 12-Mar-2019. \u00a0Journal publ date: Jul-2019.
          \n[          Abstract<\/a>] [Article<\/a>] (freely available) \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0[Supplementary Material<\/a>]<\/li>\n
        9. Mixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis
          \nA.J. Sedgewick<\/strong>, K. 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> (2019) 35:<\/strong>1204-1212. \u00a0Epub: 5-Sep-2018. \u00a0Journal publ date: 1-Apr-2019.
          \n[          Abstract<\/a>] \u00a0[Article<\/a>] [PMC version<\/a>] \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0[Supplementary Material<\/a>]\n[arXiv version<\/a>] \u00a0 Submitted: 9-Apr-2017<\/li>\n
        10. PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy
          \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. \u00a0 Publ date: 1-Mar-2019.
          \n[          Abstract<\/a>] [Article<\/a>]\u00a0(freely available) \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0[Supplementary Material<\/a>]<\/li>\n
        11. Mitochondria are a substrate of cellular memory
          \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>\u00a0(2019)\u00a0130:<\/strong>528-541. \u00a0Epub: 22-Nov-2018. \u00a0Journal publ date: Jan-2019.
          \n[          Abstract<\/a>] [Article<\/a>] (freely available)<\/li>\n<\/ol>\n<\/div><\/div>\n
          <\/span>2018<\/div>
          \n
            \n
          1. An insulin responsive sensor in the SIRT1 disordered region binds DBC1 and PACS-2 to control enzyme activity
            \nT.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<\/strong>, D.L. Marks, A.M. Gronenborn, G. Thomas<\/span>
            \nMolecular Cell<\/em><\/strong>\u00a0(2018)\u00a072:<\/strong>985-998.e7. \u00a0 Epub: 8-Nov-2018
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
          2. piMGM: Incorporating Multi-Source Priors in Mixed Graphical Models for Learning Disease Networks
            \nD.V. Manatakis\u2020<\/strong>, V.K. Raghu\u2020<\/strong>, and P.V. Benos<\/strong><\/span>
            \nBioinformatics<\/strong><\/em>\u00a0(2018)\u00a034:<\/strong>i848\u2013i856. \u00a0 (Proc ECCB 2018) \u00a0 \u00a0Publ Date: 1-Sep-2018
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>] \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0\u00a0[Supplementary Material<\/a>]<\/li>\n
          3. Evaluation of Causal Structure Learning Methods on Mixed Data Types
            \nV.K. Raghu<\/strong>, A. Poon<\/strong>, and P.V. Benos<\/strong><\/span>
            \nProc Machine Learning Research<\/strong><\/em>\u00a0(2018)\u00a092:<\/strong>48-65.
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] (freely available)<\/li>\n
          4. A pipeline for integrated theory and data-driven modeling of genomic and clinical data
            \nV.K. Raghu<\/strong>, X. Ge, A. Balajee, D. Shirer, I. Das<\/strong>, P.V. Benos<\/strong>, P.K. Chrysanthis
            \nBioKDD2019<\/strong><\/em>\u00a0(2019) accepted<\/em>. \u00a0 Conf presentation: 5-Aug-2019
            \n[Abstract] [            Article<\/a>] (freely available)
            \n[UPDATE 2020-08-27: An updated version of this paper was published by the IEEE\/ACM Transactions on Computational Biology and Bioinformatics<\/em>]<\/li>\n
          5. Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients
            \nG.D. Kitsios, A. Fitch, D.V. Manatakis<\/strong>, S. Rapport, K. Li, S. Qin, J. Huwe, Y. Zhang, Y. Doi, J. Evankovich, W. Bain, J.S. Lee, B. Methe, P.V. Benos<\/strong>, A. Morris, B. McVerry<\/span>
            \nFrontiers in Microbiology<\/strong><\/em>\u00a0(2018)\u00a0<\/em>9:<\/strong>1413. \u00a0 Publ Date: 10-Jul-2018
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
          6. Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine
            \nP. Ping, H. Hermjakob, J.S. Poison,\u00a0P.V. Benos<\/strong>, W. Wang<\/span>
            \nCirculation Research<\/strong><\/em>\u00a0(2018)\u00a0122:<\/strong>1290-1301. \u00a0 \u00a0Publ Date: 27-Apr-2018
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>] [Review]<\/li>\n
          7. Comparison of strategies for scalable causal discovery of latent variable models from mixed data
            \nV.K. Raghu<\/strong>, J.D. Ramsey, A. Morris, D.V. Manatakis<\/strong>, P. Sprites, P.K. Chrysanthis, C. Glymour, P.V. Benos<\/strong><\/span>
            \nInt J Data Sci and Analytics<\/strong><\/em>\u00a0(2018) 6:33-45. \u00a0 Epub: 6-Feb-2018
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
          8. Biomarker identification for statin sensitivity of cancer cell lines
            \nV.K. Raghu<\/strong>, C.H. Beckwitt, K. Warita, A. Wells, P.V. Benos*<\/strong>, Z.N. Oltvai*<\/span>
            \nBiochem Biophys Res Commun<\/strong><\/em>\u00a0(2018)\u00a0495:<\/strong>659-665. \u00a0Epub: 14-Nov-2017
            \n[            Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n<\/ol>\n<\/div><\/div>\n
            <\/span>2017<\/div>
            \n
              \n
            1. Ribosomopathy-like properties of murine and human cancers
              \nS. 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<\/strong>, P.V.\u00a0Benos<\/strong>, E.V. Prochownik<\/span>
              \nPLoS One<\/i><\/span><\/span><\/strong> (2017)\u00a012:<\/strong>e0182705. \u00a0 Publ Date: 18-Aug-2017
              \n[              Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
            2. Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection
              \nD.A. Pociask, K.M. Robinson, K. Chen, K.J. McHugh, M.E. Clay, G.T. Huang<\/strong>, P.V. Benos<\/strong>, Y.M.W. Janssen-Heininger, J.K. Kolls, V. Anathy, J.F. Alcorn<\/span>
              \nAm J Pathol<\/strong><\/em>\u00a0(2017)\u00a0118<\/strong>:<\/strong>851-863. \u00a0 Epub: 10-Feb-2017
              \n[              Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
            3. Downregulation of estrogen receptor and modulation of growth of breast cancer cell lines mediated by paracrine stromal cell signals
              \nJ. Huang, P. Woods, D. Normolle, J.P. Goff, P.V. Benos<\/strong>, C.J. Stehle, R.A. Steinman<\/span>
              \nBreast Cancer Res Treat<\/strong><\/em>\u00a0(2017)\u00a0118<\/strong>:<\/strong>851-863. \u00a0 Epub: 16-Nov-2016
              \n[              Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n<\/ol>\n<\/div><\/div>\n
              <\/span>2016<\/div>
              \n
                \n
              1. Non-coding single nucleotide variants affecting estrogen receptor binding and activity
                \nA. Bahreini, K. Levine, L. Santana-Santos<\/strong>, P.V. Benos<\/strong>, P. Wang, C. Andersen, S. Oesterreich, A.V. Lee<\/span>
                \nGenome Medicine<\/strong><\/em>\u00a0(2016) 8:<\/strong>128. \u00a0 Publ Date: 13-Dec-2016
                \n[                Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
              2. Learning mixed graphical models with separate sparsity parameters and stability-based model selection
                \nA.J. Sedgewick<\/strong>,\u00a0I. Shi<\/strong>, R.M. Donovan,\u00a0P.V.\u00a0Benos<\/strong>
                \nBMC Bioinformatics<\/strong><\/em>\u00a0(2016)\u00a017 Suppl 5:<\/strong>175 (Proc SMODIA2014) \u00a0 Publ Date: 6-Jun-2016
                \n[                Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
              3. Regulation of alveolar septation by microRNA-489
                \nN. Olave, C.V. Lal, B. Halloran, K. Pandit, A.C. Cuna, O.M. Faye-Petersen, D.R. Kelly, T. Nicola, P.V. Benos<\/strong>, N. Kaminski, N. Ambalavanan<\/span>
                \nAm J Physiol Lung Cell Mol Physiol<\/strong><\/em>\u00a0(2016) 10:<\/strong>L476-L487. \u00a0Epub: 30-Dec-2015
                \n[                Abstract<\/a>] [Article<\/a>] [PMC version<\/a>] \u00a0\u00a0Editor’s pick<\/em><\/li>\n<\/ol>\n<\/div><\/div>\n
                <\/span>2015<\/div>
                \n
                  \n
                1. Gene expression profiling distinguishes proneural glioma cells from mesenchymal glioma cells
                  \nU.R. Chandran, S. Luthra, L. Santana-Santos<\/strong>, P. Mao, S.H. Kim, M. Minata, J. Li, P.V. Benos<\/strong>, M. DeWang, B. Hu, S.Y. Cheng, I.B. Nakano, R.W. Sobol<\/span>
                  \nGenomics Data<\/strong><\/em> (2015)\u00a05:<\/strong>333-336. \u00a0 Epub: 14-Jul-2015
                  \n[                  Abstract<\/a>] \u00a0[Article] \u00a0[PMC version<\/a>]<\/li>\n
                2. The Center for Causal Discovery of biomedical knowledge from Big Data
                  \nG.F. Cooper, I. Bahar, M.J. Becich, P.V. Benos<\/strong>, 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<\/span>
                  \nJ Am Med Inform Assoc<\/strong><\/em>\u00a0(2015) 22:<\/strong>1132-1136. \u00a0 Epub: 2-Jul-2015
                  \n[                  Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                3. MicroRNA expression profiling predicts clinical outcome of carboplatin\/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603
                  \nL.C. Villaruz\u2020<\/strong>, G.T. Huang\u2020<\/strong>, 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<\/strong>, H.A. Tawbi<\/span>
                  \nClinical Epigenetics<\/em><\/strong>\u00a0(2015) 7:<\/strong>58. \u00a0 Publ Date: 4-Jun-2015
                  \n[                  Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                4. T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes
                  \nG.T. Huang<\/strong>, I. Tsamardinos, V. Raghu<\/strong>, N. Kaminski, P.V. Benos<\/strong><\/span>
                  \nPac Symp Biocomput<\/strong><\/em>\u00a0(2015) 20:<\/strong>431-442.
                  \n[                  Abstract<\/a>] \u00a0[Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n<\/ol>\n<\/div><\/div>\n

                  Older Publications (2002-2014)<\/strong><\/h3>\n
                  <\/span>2009-2014<\/div>
                  \n
                    \n
                  1. Aldosterone Regulates MicroRNAs in the Cortical Collecting Duct to Alter Sodium Transport
                    \nR.S. Edinger, C. Coronnello<\/strong>, A.J. Bodnar, W.A. Laframboise, P.V. Benos<\/strong>, J. Ho, J.P. Johnson, M.B. Butterworth<\/span>
                    \nJ Am Soc Nephrol<\/em><\/strong> (2014) 25:<\/strong>2445-2457
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  2. Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways
                    \nT.Y. Lu, B. Lin, Y. Li, A. Arora<\/strong>, L. Han, C. Cui, C. Coronnello<\/strong>, Y. Sheng, P.V. Benos<\/strong>, L. Yang<\/span>
                    \nJ Mol Cell<\/strong> Cardiol<\/strong><\/em>\u00a0(2013) 63:<\/strong> 146-154
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  3. Estrogen represses gene expression through reconfiguring chromatin structures
                    \nH.U. Osmanbeyoglu, K.N. Lu, S. Oesterreich, R.S. Day, P.V. Benos<\/strong>, C. Coronnello<\/strong>, X. Lu<\/span>
                    \nNucleic Acids Research<\/em><\/strong>\u00a0(2013) 41:<\/strong>8061-8071
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  4. Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3
                    \nP. Mao, K. Joshi, J. Li, L. Santana-Santos<\/strong>, S. Luthra, U.R. Chandran, P.V. Benos<\/strong>, L. Smith, M. DeWang, B. Hu, S-Y. Cheng, R.W. Sobol, I. Nakano<\/span>
                    \nProc Natl Acad Sci USA<\/em><\/strong>\u00a0(2013) 110:<\/strong> 8644-8649
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  5. ComiR: Combinatorial microRNA target prediction tool
                    \nC. Coronnello<\/strong>, P.V. Benos<\/strong><\/span>
                    \nNucleic Acids Research<\/em><\/strong>\u00a0(2013) 41:<\/strong>W159-W164
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>] \u00a0[Web tool<\/a>]<\/li>\n
                  6. Spectral clustering strategies for heterogeneous disease expression data
                    \nG.T. Huang<\/strong>, K. Cunningham<\/strong>, P.V. Benos<\/strong>, C.S. Chennubhotla<\/span>
                    \nPac Symp Biocomput<\/em><\/strong>\u00a0(2013) 212-223
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  7. Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density
                    \nC. Coronnello<\/strong>, R. Hartmaier, A. Arora<\/strong>, L. Huleihel, K.V. Pandit, A.S. Bais<\/strong>, M. Butterworth, N. Kaminski, G.D. Stormo, S. Oesterreich, P.V. Benos<\/strong><\/span>
                    \nPLoS Comput Biol<\/em><\/strong>. (2012)\u00a08:<\/strong>e1002830
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  8. Profibrotic Role of miR-154 in Pulmonary Fibrosis
                    \nJ. Milosevic, K. Pandit, M. Magister, E. Rabinovich, D.C. Ellwanger, G. Yu, L.J. Vuga, B. Weksler, P.V. Benos<\/strong>, K.F. Gibson, M. Macmillan, M. Kahn, N. Kaminski<\/span>
                    \nAm J Respir Cell Mol Biol<\/em><\/strong>. (2012)\u00a047:<\/strong>879-887
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  9. To bind or not to bind – FoxA1 determines estrogen receptor action in breast cancer
                    \nR.J. Watters, P.V. Benos<\/strong>, S. Oesterreich<\/span>
                    \nBreast Cancer Research<\/strong>\u00a0(2012) \u00a014:<\/strong>312. \u00a0(invited Viewpoint<\/em>)
                    \n[                    Abstract<\/a>] [Article<\/a>] \u00a0[PMC version<\/a>]<\/li>\n
                  10. S. Kadri<\/strong>, V. Hinman, P.V. Benos<\/strong>, \u201cRNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star\u201d, PLoS One<\/em><\/strong>, (2011), 6:<\/strong>e29217.\u00a0 PMID: 22216218<\/a>.<\/li>\n
                  11. G. Zinman, R. Brower-Sinning<\/strong>, C.H. Emeche, J. Ernst, G.T. Huang<\/strong>, S. Mahony<\/strong>, A.J. Myers, D.M. O\u2019Dee, J. L. Flynn, G.J. Nau, T.M. Ross, R.D. Salter, P.V. Benos<\/strong>, Z. Bar-Joseph, P.A. Morel, \u201cLarge scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque\u201d, PLoS One\u00a0<\/em><\/strong>(2011)\u00a06:<\/strong>e22401.\u00a0 PMID: 21789257<\/a>.<\/li>\n
                  12. Y. Zhang, D. Handley, T. Kaplan, H. Yu, A.S. Bais<\/strong>, T. Richards, K.V. Pandit, P.V. Benos<\/strong>, N. Friedman, O. Eickelberg, N. Kaminski, \u201cHigh throughput determination of TGF\u03b21\/SMAD3 targets in A549 lung epithelial cells\u201d,\u00a0PLoS One<\/em><\/strong>\u00a0(2011)\u00a06:<\/strong>e20319.<\/em>\u00a0 PMID: 21625455<\/a>.<\/li>\n
                  13. (Web tool<\/a>) G.T. Huang<\/u><\/strong>, C. Athanassiou<\/strong>,\u00a0P.V. Benos<\/strong>, \u201cmirConnX: Condition-specific mRNA-microRNA network integrator\u201d, Nucleic Acids Research<\/em><\/strong>\u00a0(2011)\u00a039:<\/strong>W416-423.<\/em>PMID: 21558324<\/a>.<\/li>\n
                  14. A.S. Bais<\/strong>, N. Kaminski, P.V. Benos,<\/strong> “Finding subtypes of transcription factor motif pairs with distinct regulatory roles”, Nucleic Acids Research<\/em><\/strong>\u00a0(2011), 39:<\/strong>e76. PMID: 21486752<\/a>.<\/li>\n
                  15. K.V. Pandit\u2020, D. Corcoran\u2020<\/strong>, 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*<\/strong>, N. Kaminski*, \u201cInhibition and role of let-7d<\/em>in idiopathic pulmonary fibrosis\u201d, Am J Respir Crit Care Med<\/em><\/strong>. (2010)\u00a0182:<\/strong>220-229.\u00a0 PMID: 20395557<\/a>.<\/li>\n
                  16. N.A. Temiz, P.V. Benos<\/strong>, 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<\/i><\/strong>\u00a0<\/i><\/b>(2010) 38:<\/b>2134-2144. \u00a0PMID:\u00a020047959<\/a>.<\/li>\n
                  17. A.B. Tchagang<\/strong>, K.V. Bui<\/strong>, T. McGinnis<\/strong>, P.V. Benos<\/strong>, \u201cExtracting Biologically Significant Patterns from Short Time Series Gene Expression Data\u201d, BMC Bioinformatics<\/i><\/strong>\u00a0<\/i><\/b>(2009), 10:<\/b>255. \u00a0PMID: 19695084<\/a>. \u00a0 \u00a0\"\"<\/a><\/li>\n
                  18. D.L. Corcoran\u2020<\/span><\/strong>, K.V. Pandit\u2020, B. Gordon, A. Bhattacharjee, N. Kaminski*, P.V. Benos*<\/strong>, “Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.” PLoS One\u00a0<\/em><\/strong>(2009)\u00a04:<\/strong>e5279.\u00a0 PMID: 19390574<\/a>.<\/li>\n
                  19. R. Brower-Sinning<\/strong>, D.M. Carter, C.J. Crevar, E. Ghedin, T.M. Ross, P.V. Benos<\/strong>, \u201cThe role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus\u201d, Genome Biology\u00a0<\/em><\/strong>(2009), 10:<\/strong>R18. PMID: 19216739<\/a>.<\/li>\n
                  20. S. Kadri<\/strong>, V. Hinman, P.V. Benos<\/strong>, \u201cHHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models\u201d, BMC Bioinformatics<\/strong><\/em>\u00a0(2009) 10<\/strong>(Supl 1):<\/strong>S35. (Proc APBC 2009)\u00a0PMID: 19208136<\/a>.<\/li>\n<\/ol>\n<\/div><\/div>\n
                    <\/span>2002-2008<\/div>
                    \n
                      \n
                    1. Y. Lu, S. Mahony<\/strong>, P.V. Benos<\/strong>, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, \u201cMultiple evidence supporting cyclic assignments\u201d, Genome Biology<\/strong>\u00a0<\/em>(2008),9:<\/strong>403 [rebattle article on Jensen et al.<\/em>, \u201cCircular reasoning rather than cyclic expression\u201d, Genome Biol<\/em><\/strong> (2008),9:<\/strong>403]. \u00a0PMID: 18598377<\/a>.<\/li>\n
                    2. A.B. Tchagang<\/strong>, A.H. Tewfik, P.V. \u00a0Benos<\/strong>, “Biological evaluation of biclustering algorithms using Gene Ontology and chIP-chip data”, IEEE ICASSP<\/strong> (2008). \u00a0[Article<\/a>]<\/li>\n
                    3. H. Feng, J.L. Taylor, P.V. Benos<\/strong>, R. Newton, R. Downing, K. Waddell, Y. Chang, P.S. Moore, \u201cSubtraction of the human transcriptome to search for human tumor viruses\u201d, J Virology <\/em><\/strong>\u00a0<\/em>(2007) 81:<\/strong>11332-11340. PMID: 17686852<\/a>.<\/li>\n
                    4. Y. Lu, S. Mahony<\/strong>, P.V. Benos<\/strong>, R. Rosenfeld, I. Simon, L. Breeden, Z. Bar-Joseph, \u201cCombined analysis reveals a core set of cycling genes\u201d, Genome Biology\u00a0<\/em><\/strong>(2007)\u00a08:<\/strong>R146. \u00a0PMID: 17650318<\/a>.<\/li>\n
                    5. S. Mahony<\/strong>, P.E. Auron and P.V. Benos<\/strong> “Inferring protein-DNA dependencies using motif alignments and mutual information.” Bioinformatics<\/em><\/strong>\u00a0(2007) 23:<\/strong>i297-i304. \u00a0(Proc ISMB 2007) \u00a0PMID:\u00a017646310<\/a>.<\/li>\n
                    6. S. Mahony<\/strong>, D.L. Corcoran<\/strong>, E. Feingold, P.V. Benos<\/strong>, \u201cRegulatory conservation of protein coding and miRNA genes in vertebrates:\u00a0 lessons from the opossum genome\u201d, Genome Biology<\/em><\/strong>\u00a0(2007) 8:<\/strong>R84. PMID: 17506886<\/a>.\u00a0 \u00a0\u00a0\"\"<\/a><\/li>\n
                    7. T.S. Mikkelsen (1), \u2026, P.V. Benos<\/strong>(18), \u2026, K. Lindblad-Toh (61), \u201cGenome of the marsupial Monodelphis domestica<\/em>reveals lineage-specific innovation in coding and non-coding sequences\u201d, Nature\u00a0<\/em><\/strong>(2007) 447:<\/strong>167-177. \u00a0PMID: 17495919<\/a>.<\/li>\n
                    8. (Web tool<\/a>)<\/strong> S. Mahony<\/strong>, P.V. Benos<\/strong>, \u201cSTAMP: a web tool for exploring DNA-binding motif similarities”, Nucleic Acids Research<\/em><\/strong>\u00a0<\/em>(2007)\u00a035:<\/strong>W253-258. \u00a0PMID: 17478497<\/a>.<\/li>\n
                    9. S. Mahony<\/strong>, P.E. Auron, P.V. Benos<\/strong>, \u201cDNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies\u201d, PLoS Comput Biol\u00a0<\/em><\/strong>(2007) 3:<\/strong>e61. PMID: 17397256<\/a>.<\/li>\n
                    10. S. Mahony<\/strong>, P.V. Benos<\/strong>, T.J. Smith, A. Golden, \u201cSelf-organizing neural networks to support the discovery of DNA-binding motifs\u201d, Neural Networks\u00a0<\/em><\/strong>(2006) 19:<\/strong>950-962. PMID: 16839740<\/a>.<\/li>\n
                    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<\/strong>, J.G.R. Cross, P.V. Benos<\/strong>, P.B. Samollow, T.P. Speed, J.A.M. Graves, R.D. Miller, \u201cReconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex\u201d, PLoS Biology\u00a0<\/em><\/strong>(2006) 4:<\/strong>e46. PMID: 16435885<\/a>.<\/li>\n
                    12. K.R. Rogulski, D.E. Cohen, D.L. Corcoran<\/strong>, P.V. Benos<\/strong> and E.V. Prochownik “Deregulation of common genes by c-Myc and its direct target, MT-MC1.” Proc Natl Acad Sci USA<\/em><\/strong>\u00a0(2005)\u00a0102:<\/strong>18968-18973. PMID:\u00a016365299<\/a>.<\/li>\n
                    13. S. Mahony<\/strong>, A. Golden, T.J. Smith and P.V. Benos<\/strong> “Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.” Bioinformatics<\/em><\/strong>\u00a0(2005) 21 Suppl:<\/strong>i283-i291. \u00a0(Proc ISMB 2005) PMID:\u00a015961468<\/a>.<\/li>\n
                    14. (Web tool)<\/strong> S. Ringquist, C. Pecoraro, C. Gilchrist, A. Styche, W. Rudert, P.V. Benos<\/strong>, and M. Trucco “SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.” Nucleic Acids Research<\/em><\/strong>\u00a0(2005) 33:<\/strong>W548-552. \u00a0PMID:\u00a015980532<\/a>.<\/li>\n
                    15. (Web tool<\/a>)<\/strong> D.L. Corcoran<\/strong>, E. Feingold, and P.V. Benos<\/strong> “FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.” Nucleic Acids Research<\/em><\/strong>\u00a0(2005) 33:<\/strong>W442-446. \u00a0PMID: 15980508<\/a>.<\/li>\n
                    16. (Web tool<\/a>)<\/strong> C.T. Workman, Y. Yin<\/strong>, D.L. Corcoran<\/strong>, T. Ideker, G.D. Stormo and P.V. Benos<\/strong>,\u00a0“EnoLOGOS: a versatile web tool for energy normalized sequence logos.” Nucleic Acids Research<\/em><\/strong>, (2005) 33:<\/strong>W389-392. \u00a0PMID:\u00a015980495<\/a>.<\/li>\n
                    17. D.L. Corcoran<\/strong>, E. Feingold, J. Dominick, M. Wright, J. Harnaha, M. Trucco, N. Giannoukakis, P.V. Benos<\/strong>, “FOOTER: a quantitative comparative genomics method for efficient recognition of cis<\/em>-regulatory elements”, Genome Research<\/em>\u00a0<\/strong>(2005) 15:<\/strong>840-847.PMID: 15930494<\/a>.<\/li>\n
                    18. A.M. Alexander, C. Pecoraro, A. Styche, W.A. Rudert, P.V. Benos,<\/strong> S. Ringquist, M. Trucco, SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing\u201d, Biotechniques\u00a0<\/em><\/strong>(2005) 38:<\/strong>87-94. PMID: 15679090<\/a>.<\/li>\n
                    19. J.K. Vries, R. Munshi, D. Tobi, J. Klein-Seetharaman, P.V. Benos<\/strong>, I. Bahar, \u201cA sequence alignment-independent method for protein classification\u201d, Applied Bioinformatics\u00a0<\/em><\/strong>(2004) 3:<\/strong>137-148. PMID: 15693739<\/a>.<\/li>\n
                    20. D.G. Peters, X.C. Zhang, P.V. Benos<\/strong>, E. Heidrich-O\u2019Hare, R.E. Ferrell, \u201cGenomic analysis of the immediate\/early response to shear stress in human coronary artery endothelial cell\u201d, Physiol. Genomics\u00a0<\/em><\/strong>(2002) 12:<\/strong>25-33.PMID: 12407183<\/a>.<\/li>\n<\/ol>\n<\/div><\/div>\n

                      Pre-Independence Publications (prior to 2002)<\/strong><\/h3>\n
                      <\/span>Post-graduate work<\/div>
                      \n
                        \n
                      1. P.V. Benos<\/strong>, M.L. Bulyk, G.D. Stormo, \u201cAdditivity on protein-DNA interactions: how good an approximation is it?\u201d, Nucleic Acids Research\u00a0<\/em><\/strong>(2002) 30:<\/strong>4442-4445. PMID: 12384591<\/a><\/li>\n
                      2. P.V. Benos<\/strong>, A.S. Lapedes and G.D. Stormo, “Probabilistic code for DNA recognition by proteins of the EGR-family”, J. Molecular Biology<\/em>,<\/strong> (2002) 323:<\/strong>701-727. \u00a0PMID: 12419259<\/a><\/li>\n
                      3. P.V. Benos<\/strong>, A.S. Lapedes, G.D. Stormo, “Is there a code for protein-DNA recognition? Probab(ilistical)ly…”, Bioessays\u00a0<\/strong>(2002) 24:<\/strong>466-475. \u00a0(Review) \u00a0PMID: 12001270<\/a>.<\/li>\n
                      4. P.V. Benos*<\/strong>, A.S. Lapedes, D.S. Fields, G.D. Stormo, “SAMIE: Statistical Algorithm for Modeling Interaction Energies”, Pac Symp Biocomput<\/em><\/strong> (2001) 6:<\/strong>115-126. \u00a0PMID:\u00a011262933<\/a>.<\/li>\n
                      5. A. Peter, P. Schoettler, M. Werner, N. Beinert, G. Dowe, P. Burkert, F. Mourkioti, L. Denzer, Y. He, P. Deak, P.V. Benos<\/strong>, 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<\/em>“,\u00a0EMBO Reports<\/em><\/strong>, (2002) 3:<\/strong>34-38.\u00a0 PMID: 11751581<\/a>.<\/li>\n
                      6. P.V. Benos<\/strong>, 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<\/em>, a comparison of two sequencing strategies”, Genome Research\u00a0<\/em><\/strong>(2001) 11:<\/strong>710-730. PMID: 11337470<\/a>.<\/li>\n
                      7. P.V. Benos<\/strong>, 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<\/em>“, Science<\/em><\/strong> (2000) 287:<\/strong>2220-2222. \u00a0PMID:\u00a010731137<\/a>.<\/li>\n
                      8. M. Adams(1), …, P.V. Benos<\/strong>(43), …, C. Venter(195), “The genome sequence of Drosophila melanogaster<\/em>“, Science\u00a0<\/em><\/strong>(2000) 287:<\/strong>2185-2195. PMID: 10731132<\/a>.<\/li>\n<\/ol>\n<\/div><\/div>\n
                        <\/span>Graduate work<\/div>
                        \n
                          \n
                        1. S. Brogna\u2020<\/strong>,\u00a0P.V. Benos\u2020<\/strong>, G. Gasperi, C. Savakis, “The\u00a0Drosophila<\/em>\u00a0alcohol dehydrogenase gene may have evolved independently of the functionally homologous medfly, olive fly and flesh fly genes”,\u00a0Molecular Biology Evolution<\/em><\/strong>, (2001)\u00a018:<\/strong>322-329. PMID:\u00a011230533<\/a>.<\/li>\n
                        2. P. Benos*<\/strong>, 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<\/em> by functional complementation in yeast”, Molecular General Genetics<\/em><\/strong>\u00a0(2000) 263:<\/strong>90-95. PMID:\u00a010732677<\/a>.<\/li>\n
                        3. R. Gessmann, P. Benos<\/strong>, H. Brueckner, M. Kokkinidis, “The crystal structures of the synthetic C-terminal Octa- and Dodecapeptides of Trichovirin”, J. Peptide Science\u00a0<\/em><\/strong>(1999) 5:<\/strong>83-95. PMID: 10100124<\/a>.<\/li>\n
                        4. P. Deak, M.M. Omar, R.D. Saunders, M. Pal, O. Komonyi, J. Szidonya, P. Maroy, Y. Zhang, M. Ashburner, P. Benos<\/strong>, 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<\/em>: correlation of physical and cytogenetic maps in chromosomal region 86E-87F”, Genetics\u00a0<\/em><\/strong>(1997) 147:<\/strong>1697-1722. PMID: 9409831<\/a>.<\/li>\n
                        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<\/strong>, V.N. Bolshakov, P. Deak, D.M. Glover, S. Herrmann, F.C. Kafatos, “One-hundred and five new potential Drosophila melanogaster<\/em>genes revealed through STS analysis”, Gene\u00a0<\/em><\/strong>(1997) 195:<\/strong>187-193. PMID: 9305763<\/a>.<\/li>\n
                        6. M. Tabler, P. Benos<\/strong>, M. Doerr, “Representation of unique sequences in libraries of randomized nucleic acids”, Nucleic Acids Research\u00a0<\/em><\/strong>(1996) 24:<\/strong>3437-3438. PMID: 8811100<\/a>.<\/li>\n
                        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<\/strong>, 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<\/em>: Cosmid contigs and sequence tagged sites”, Genetics\u00a0<\/em><\/strong>(1995) 139:<\/strong>1631-1647. PMID: 7789765<\/a>.<\/li>\n<\/ol>\n<\/div><\/div>\n

                          <\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

                          boldface: members of Benos’ lab, \u00a0\u2020equal contribution,\u00a0*(co-)corresponding authors, \u00a0PMC paper versions are freely available Latest Trends of the Lab Older Publications (2002-2014) Pre-Independence Publications (prior to 2002)<\/p>\n

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