Now showing items 1-20 of 46

    • 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. ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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. ...
    • 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. ...
    • Mapping Network Motif Tunability and Robustness in the Design of Synthetic Signaling Circuits 

      Iadevaia, Sergio; Nakhleh, Luay K.; Azencott, Robert; Ram, Prahlad T. (2014)
      Cellular networks are highly dynamic in their function, yet evolutionarily conserved in their core network motifs or topologies. Understanding functional tunability and robustness of network motifs to small perturbations ...
    • 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 ...
    • Mechanism of Graphene Oxide Formation 

      Dimiev, Ayrat M.; Tour, James M. (2014)
      Despite intensive research, the mechanism of graphene oxide (GO) formation remains unclear. The role of interfacial interactions between solid graphite and the liquid reaction medium, and transport of the oxidizing agent ...
    • Towards accurate characterization of clonal heterogeneity based on structural variation 

      Fan, Xian; Zhou, Wanding; Chong, Zechen; Nakhleh, Luay; Chen, Ken (2014)
      Recent advances in deep digital sequencing have unveiled an unprecedented degree of clonal heterogeneity within a single tumor DNA sample. Resolving such heterogeneity depends on accurate estimation of fractions of alleles ...
    • An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes 

      Liu, Kevin J.; Dai, Jingxuan; Truong, Kathy; Song, Ying; Kohn, Michael H.; Nakhleh, Luay (2014)
      One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. ...
    • Relentful Strategic Reasoning in 1 Alternating-Time Temporal Logic 

      Mogavero, Fabio; Murano, Aniello; Vardi, Moshe Y. (2014)
      Temporal logics are a well investigated formalism for the specification, verification, and synthesis of reactive systems. Within this family, Alternating-Time Temporal Logic (ATL , for short) has been introduced as a ...
    • How To Build an Undervoting Machine: Lessons from an Alternative Ballot Design 

      Greene, Kristen K.; Byrne, Michael D.; Goggin, Stephen N. (2013-08)
      Despite the importance of usability in ensuring election integrity, it remains an under-studied aspect of voting systems. Voting computers (a.k.a. DREs) offer the opportunity to present ballots to voters in novel ways, yet ...