Research articles, presentations, and other scholarship

Recent Submissions

  • The PathLinker app: Connect the dots in protein interaction networks 

    Gil, Daniel P.; Law, Jeffrey N.; Murali, T. M. (F1000Research, 2017-01-20)
    PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors ...
  • Automating the PathLinker app for Cytoscape 

    Huang, Li Jun; Law, Jeffrey N.; Murali, T. M. (F1000Research, 2018-06-12)
    PathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network ...
  • Connectivity Measures for Signaling Pathway Topologies 

    Franzese, Nicholas; Groce, Adam; Murali, T. M.; Ritz, Anna (Virginia Tech, 2019-03-30)
    Characterizing cellular responses to different extrinsic signals is an active area of research, and curated pathway databases describe these complex signaling reactions. Here, we revisit a fundamental question in signaling ...
  • Antibacterial efficacy of core-shell nanostructures encapsulating gentamicin against an in vivo intracellular Salmonella model 

    Ranjan, Ashish; Pothayee, Nikorn; Seleem, Mohammed N.; Tyler, Ronald D.; Brenseke, Bonnie; Sriranganathan, Nammalwar; Riffle, Judy S.; Kasimanickam, Ramanathan (Dove Medical Press, 2009-01-01)
    Pluronic based core-shell nanostructures encapsulating gentamicin were designed in this study. Block copolymers of (PAA(+/-)Na-b-(PEO-b-PPO-b-PEO)-b-PAA(+/-)Na) were blended with PAA(-) Na(+) and complexed with the ...
  • The assembly of integrated rat intestinal-hepatocyte cultures 

    Kothari, Anjaney; Rajagopala, Padmavathy (2019-11)
    The jejunum is the segment of the small intestine responsible for several metabolism and biotransformation functions. In this report, we have cultured rat jejunum explants in vitro and integrated them with hepatocyte ...
  • Pulmonary Exposure to Magnéli Phase Titanium Suboxides Results in Significant Macrophage Abnormalities and Decreased Lung Function 

    McDaniel, Dylan K.; Ringel-Scaia, Veronica M.; Morrison, Holly A.; Coutermarsh-Ott, Sheryl; Council-Troche, McAlister; Angle, Jonathan W.; Perry, Justin B.; Davis, Grace; Leng, Weinan; Minarchick, Valerie; Yang, Yi; Chen, Bo; Reece, Sky W.; Brown, David A.; Cecere, Thomas E.; Brown, Jared M.; Gowdy, Kymberly M.; Hochella, Michael F. Jr.; Allen, Irving C. (Frontiers, 2019-11-28)
    Coal is one of the most abundant and economic sources for global energy production. However, the burning of coal is widely recognized as a significant contributor to atmospheric particulate matter linked to deleterious ...
  • Nanoparticulate Nickel-Hosting Phases in Sulfidic Environments: Effects of Ferrous Iron and Bacterial Presence on Mineral Formation Mechanism and Solid-Phase Nickel Distribution 

    Manson, Muammar; Winkler, Christopher; Hochella, Michael F. Jr.; Xu, Jie (Frontiers, 2019-06-26)
    The precipitation of nickel with sulfide is an important process governing the bioavailability of Ni in natural waters, and this process has the potential to effectively remove aqueous Ni contaminants in near-surface ...
  • Nanotechnology in the real world: Redeveloping the nanomaterial consumer products inventory 

    Vance, Marina; Kuiken, Todd; Vejerano, Eric P.; McGinnis, Sean; Hochella, Michael F. Jr.; Rejeski, David; Hull, Matthew S. (Beilstein-Institut, 2015)
    To document the marketing and distribution of nano-enabled products into the commercial marketplace, the Woodrow Wilson International Center for Scholars and the Project on Emerging Nanotechnologies created the Nanotechnology ...
  • High-frequency irreversible electroporation is an effective tumor ablation strategy that induces immunologic cell death and promotes systemic anti-tumor immunity 

    Ringel-Scaia, Veronica M.; Beitel-White, Natalie; Lorenzo, Melvin F.; Brock, Rebecca M.; Huie, Kathleen E.; Coutermarsh-Ott, Sheryl; Eden, Kristin; McDaniel, Dylan K.; Verbridge, Scott; Rossmeisl, John H. Jr.; Oestreich, Kenneth J.; Davalos, Rafael, V.; Allen, Irving C. (2019-06)
    Background: Despite promising treatments for breast cancer, mortality rates remain high and treatments for metastatic disease are limited. High-frequency irreversible electroporation (H-FIRE) is a novel tumor ablation ...
  • Aerosol microdroplets exhibit a stable pH gradient 

    Wei, Haoran; Vejerano, Eric P.; Leng, Weinan; Huang, Qishen; Willner, Marjorie R.; Marr, Linsey C.; Vikesland, Peter J. (2018-07-10)
    Suspended aqueous aerosol droplets (< 50 mu m) are microreactors for many important atmospheric reactions. In droplets and other aquatic environments, pH is arguably the key parameter dictating chemical and biological ...
  • Continuous synthesis of Zn2Al-CO3 layered double hydroxides: a comparison of bench, pilot and industrial scale syntheses 

    Clark, Ian; Gomes, Rachel Louise; Crawshaw, C.; Neve, L.; Lodge, Rhys; Fay, Michael; Winkler, C.; Hull, Matthew S.; Lester, Ed (2019-04-01)
    Zn2Al-CO3 was produced continuously at bench (g h(-1)), pilot (100s g h -1) and industrial scale (10s kg h(-1)). Crystal domain length and BET surface area were similar at all three scales although there was a small increase ...
  • Sequence verification of synthetic DNA by assembly of sequencing reads 

    Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, Joao C.; Tyler, Brett M.; Peccoud, Jean (2013-01)
    Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the ...
  • XTALKDB: a database of signaling pathway crosstalk 

    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T. M. (2017-01-04)
    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents ...
  • Effects of internal electrode cooling on irreversible electroporation using a perfused organ model 

    O’Brien, T. J.; Bonakdar, Mohammad; Bhonsle, Suyashree P.; Neal, Robert E.; Aardema, C.H.; Robertson, John L.; Goldberg, S.N.; Davalos, Rafael V. (Taylor and Francis Ltd, 2018-05-28)
    Purpose: This study evaluates the effects of active electrode cooling, via internal fluid circulation, on the irreversible electroporation (IRE) lesion, deployed electric current and temperature changes using a perfused ...
  • Processing method for grain-oriented lead-free piezoelectric Na0.5Bi0.5TiO3—BaTiO3 ceramics exhibiting giant performance 

    Mechanical Engineering; Institute for Critical Technology and Applied Science (ICTAS); Virginia Tech Intellectual Properties, Inc.; Priya, Shashank; Maurya, Deepam (United States Patent and Trademark Office, 2017-09-26)
    Textured ceramic compositions having improved piezoelectric characteristics as compared with their random counterparts are provided. Methods of making the compositions and devices using them are also included. More ...
  • A high-energy-density sugar biobattery based on a synthetic enzymatic pathway 

    Zhu, Zhiguang; Tam, Tsz Kin; Sun, Fangfang; You, Chun; Zhang, Y. H. Percival (Springer Nature, 2014-01)
    High-energy-density, green, safe batteries are highly desirable for meeting the rapidly growing needs of portable electronics. The incomplete oxidation of sugars mediated by one or a few enzymes in enzymatic fuel cells ...
  • Giant piezoelectric voltage coefficient in grain-oriented modified PbTiO3 material 

    Yan, Yongke; Zhou, Jie E.; Maurya, Deepam; Wang, Yu U.; Priya, Shashank (Springer Nature, 2016-10-11)
    A rapid surge in the research on piezoelectric sensors is occurring with the arrival of the Internet of Things. Single-phase oxide piezoelectric materials with giant piezoelectric voltage coefficient (g, induced voltage ...
  • Abundance and Speciation of Surface Oxygen on Nanosized Platinum Catalysts and Effect on Catalytic Activity 

    Serra-Maia, Rui; Winkler, Christopher; Murayama, Mitsuhiro; Tranhuu, Kevin; Michel, F. Marc (2018-06-18)
    Oxygen at the surface of nanosized platinum has a direct effect on catalytic activity of oxidation−reduction chemical reactions. However, the abundance and speciation of oxygen remain uncertain for platinum with different ...
  • Compositionally Graded Multilayer Ceramic Capacitors 

    Song, Hyun-Cheol; Zhou, Jie E.; Maurya, Deepam; Yan, Yongke; Wang, Yu U.; Priya, Shashank (Springer Nature, 2017-09-27)
    Multilayer ceramic capacitors (MLCC) are widely used in consumer electronics. Here, we provide a transformative method for achieving high dielectric response and tunability over a wide temperature range through design of ...
  • Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models 

    Tegge, Allison N.; Rodrigues, Richard R.; Larkin, Adam L.; Vu, Lucas; Murali, T. M.; Rajagopalan, Padmavathy (Springer Nature, 2018-07-27)
    Liver homeostasis requires the presence of both parenchymal and non-parenchymal cells (NPCs). However, systems biology studies of the liver have primarily focused on hepatocytes. Using an organotypic three-dimensional (3D) ...

View more