Now showing items 1-20 of 37

    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 (2014-06-12)
      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. ...
    • Mapping Network Motif Tunability and Robustness in the Design of Synthetic Signaling Circuits 

      Iadevaia, Sergio; Nakhleh, Luay K.; Azencott, Robert; Ram, Prahlad T. (2014-03-18)
      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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks 

      Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay (2013-11-07)
      The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each ...
    • Evolution After Whole-genome Duplication: A Network Perspective 

      Zhu, Yun; Lin, Zhenguo; Nakhleh, Luay (2013-09-18)
      Gene duplication plays an important role in the evolution of genomes and interactomes. Elucidating how evolution after gene duplication interplays at the sequence and network level is of great interest. In this paper, ...
    • 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, ...
    • SIMS: A Hybrid Method for Rapid Conformational Analysis 

      Gipson, Bryant; Moll, Mark; Kavraki, Lydia E. (2013-07-23)
      Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a ...
    • An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data 

      Berestovsky, Natalie; Nakhleh, Luay (2013-06-21)
      Regulatory networks play a central role in cellular behavior and decision making. Learning these regulatory networks is a major task in biology, and devising computational methods and mathematical models for this task is ...
    • Boosting forward-time population genetic simulators through genotype compression 

      Ruths, Troy; Nakhleh, Luay (2013-06-14)
      Background: Forward-time population genetic simulations play a central role in deriving and testing evolutionary hypotheses. Such simulations may be data-intensive, depending on the settings to the various param- eters ...
    • Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome 

      Bryant, Drew H.; Moll, Mark; Finn, Paul W.; Kavraki, Lydia E. (2013-06-06)
      The protein kinases are a large family of enzymes that play fundamental roles in propagating signals within the cell. Because of the high degree of binding site similarity shared among protein kinases, designing drug ...