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  • Structure-guided selection of specificity determining positions in the human Kinome 

    Moll, Mark; Finn, Paul W; Kavraki, Lydia E (2016-08-18)
    Abstract Background The human kinome contains many important drug targets. It is well-known that inhibitors of protein kinases bind with very different selectivity profiles. ...
  • A maximum pseudo-likelihood approach for phylogenetic networks 

    Yu, Yun; Nakhleh, Luay (2015-10-02)
    Abstract Background Several phylogenomic analyses have recently demonstrated the need to account simultaneously for incomplete lineage sorting (ILS) and hybridization when ...
  • Performance Analysis and Optimization of a Hybrid Seismic Imaging Application 

    Paul, Sri Raj; Araya-Polo, Mauricio; Mellor-Crummey, John; Hohl, Detlef (2016)
    Applications to process seismic data are computationally expensive and, therefore, employ scalable parallel systems to produce timely results. Here we describe our experiences of using performance analysis tools to gain ...
  • Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent 

    Wen, Dingqiao; Yu, Yun; Nakhleh, Luay (2016)
    The multispecies coalescent (MSC) is a statistical framework that models how gene genealogies grow within the branches of a species tree. The field of computational phylogenetics has witnessed an explosion in the development ...
  • Meniscus-Mask Lithography for Fabrication of Narrow Nanowires 

    Abramova, Vera; Slesarev, Alexander S.; Tour, James M. (2015)
    We demonstrate the efficiency of meniscus-mask lithography (MML) for fabrication of precisely positioned nanowires in a variety of materials. Si, SiO2, Au, Cr, W, Ti, TiO2, and Al nanowires are fabricated and characterized. ...
  • The Mason Test: A Defense Against Sybil Attacks in Wireless Networks Without Trusted Authorities 

    Liu, Yue; Bild, David R.; Dick, Robert P.; Mao, Z. Morley; Wallach, Dan S. (2015)
    Wireless networks are vulnerable to Sybil attacks, in which a malicious node poses as many identities in order to gain disproportionate influence. Many defenses based on spatial variability of wireless channels exist, but ...
  • In situ imaging of the conducting filament in a silicon oxide resistive switch 

    Yao, Jun; Zhong, Lin; Natelson, Douglas; Tour, James M. (2012)
    The nature of the conducting filaments in many resistive switching systems has been elusive. Throughᅠin situᅠtransmission electron microscopy, we image the real-time formation and evolution of the filament in a silicon ...
  • Terahertz and Infrared Spectroscopy of Gated Large-Area Graphene 

    Ren, Lei; Zhang, Qi; Yao, Jun; Sun, Zhengzong; Kaneko, Ryosuke; Yan, Zheng; Nanot, Sébastien L.; Jin, Zhong; Kawayama, Iwao; Tonouchi, Masayoshi; Tour, James M.; Kono, Junichiro (2012)
    We have fabricated a centimeter-size single-layer graphene device with a gate electrode, which can modulate the transmission of terahertz and infrared waves. Using time-domain terahertz spectroscopy and Fourier-transform ...
  • Synthesis from Probabilistic Components 

    Nain, Sumit; Lustig, Yoad; Vardi, Moshe Y. (2014)
    Synthesis is the automatic construction of a system from its specification. In classical synthesis algorithms, it is always assumed that the system is "constructed from scratch" rather than composed from reusable components. ...
  • DINC: A new AutoDock-based protocol for docking large ligands 

    Dhanik, Ankur; McMurray, John S.; Kavraki, Lydia E. (2013)
    Background: Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard ...
  • Understanding the challenges of protein flexibility in drug design 

    Antunes, Dinler A.; Devaurs, Didier; Kavraki, Lydia E. (2015)
    Introduction: Protein–ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug discovery. Molecular docking is widely used to predict ...
  • From Error to Error: Why Voters Could not Cast a Ballot and Verify Their Vote With Helios, Prêt à Voter, and Scantegrity II 

    Acemyan, Claudia Z.; Kortum, Philip; Byrne, Michael D.; Wallach, Dan S. (2015)
    The aim of this paper is to identify user errors, and the related potential design deficiencies, that contributed to participants failing to vote cast and vote verify across three end-to-end voting systems: Helios, Prêt à ...
  • Transaction local aliasing in storage class memory 

    Giles, Ellis; Doshi, Kshitij; Varman, Peter (2015)
    This paper describes a lightweight software library to solve the challenges [6], [3], [1], [5], [2] of programming storage class memory (SCM). It provides primitives to demarcate failure-atomic code regions. SCM loads and ...
  • Non-intrusive Persistence with a Backend NVM Controller 

    Pu, Libei; Doshi, Kshitij; Giles, Ellis; Varman, Peter (2015)
    By providing instruction-grained access to vast amounts of persistent data with ordinary loads and stores, byte-addressable storage class memory (SCM) has the potential to revolutionize system architecture. We describe a ...
  • On computing minimal independent support and its applications to sampling and counting 

    Ivrii, Alexander; Malik, Sharad; Meel, Kuldeep S.; Vardi, Moshe Y. (2015)
    Constrained sampling and counting are two fundamental problems arising in domains ranging from artificial intelligence and security, to hardware and software testing. Recent approaches to approximate solutions for these ...
  • Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform 

    Chuang, Ryan; Hall, Benjamin A.; Benque, David; Cook, Byron; Ishtiaq, Samin; Piterman, Nir; Taylor, Alex; Vardi, Moshe; Koschmieder, Steffen; Gottgens, Berthold; Fisher, Jasmin (2015)
    Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing ...
  • Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments 

    Saxer, Gerda; Krepps, Michael D.; Merkley, Eric D.; Ansong, Charles; Deatherage Kaiser, Brooke L.; Valovska, Marie-Thérèse; Ristic, Nikola; Yeh, Ping T.; Prakash, Vittal P.; Leiser, Owen P.; Nakhleh, Luay; Gibbons, Henry S.; Kreuzer, Helen W.; Shamoo, You (2014)
    Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection. Adaptation to a new environment with abundant ...
  • Computational approaches to species phylogeny inference and gene tree reconciliation 

    Nakhleh, Luay (2013)
    An intricate relationship exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene ...
  • Linear Temporal Logic and Linear Dynamic Logic on Finite Traces 

    De Giacomo, Giuseppe; Vardi, Moshe Y. (2013)
    In this paper we look into the assumption of interpreting LTL over finite traces. In particular we show that LTLf, i.e., LTL under this assumption, is less expressive than what might appear at first sight, and that at ...
  • Once and For All 

    Kupferman, Orna; Pnueli, Amir; Vardi, Moshe Y. (2012)
    It has long been known that past-time operators add no expressive power to linear temporal logics. In this paper, we consider the extension of branching temporal logics with past-time operators. Two possible views regarding ...

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