Now showing items 10-29 of 30

  • Gene Duplicability-Connectivity-Complexity across Organisms and a Neutral Evolutionary Explanation 

    Zhu, Yun; Du, Peng; Nakhleh, Luay (2012-09-11)
    Gene duplication has long been acknowledged by biologists as a major evolutionary force shaping genomic architectures and characteristics across the Tree of Life. Major research has been conducting on elucidating the fate ...
  • 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. ...
  • 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, ...
  • Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria 

    Park, Hyun Jung; Nakhleh, Luay (2012)
    Background: Maximum likelihood has been widely used for over three decades to infer phylogenetic trees from molecular data. When reticulate evolutionary events occur, several genomic regions may have conflicting evolutionary ...
  • Iterative Temporal Motion Planning for Hybrid Systems in Partially Unknown Environments 

    Maly, Matthew R.; Lahijanian, Morteza; Kavraki, Lydia E.; Kress-Gazit, Hadas; Vardi, Moshe Y. (2013)
    This paper considers the problem of motion planning for a hybrid robotic system with complex and nonlinear dynamics in a partially unknown environment given a temporal logic specification. We employ a multi-layered ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • ncDNA and drift drive binding site accumulation 

    Ruths, Troy; Nakhleh, Luay (2012)
    Background: The amount of transcription factor binding sites (TFBS) in an organism’s genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise ...
  • Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology 

    Ruths, Troy; Nakhleh, Luay (2013-04)
    Cis-regulatory networks (CRNs) play a central role in cellular decision making. Like every other biological system, CRNs undergo evolution, which shapes their properties by a combination of adaptive and nonadaptive ...
  • 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 ...
  • Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting 

    Yu, Yun; Barnett, R. Matthew; Nakhleh, Luay (2013-06-04)
    Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, ...
  • Publication Culture in Computing Research 

    Mehlhorn, Kurt; Vardi, Moshe Y.; Herbstritt, Marc (2012)
    The dissemination of research results is an integral part of research and hence a crucial component for any scientific discipline. In the area of computing research, there have been raised concerns recently about its ...
  • Regular Real Analysis 

    Chaudhuri, Swarat; Sankaranarayanan, Sriram; Vardi, Moshe Y. (2013)
    We initiate the study of regular real analysis, or the analysis of real functions that can be encoded by automata on infinite words. It is known that ω-automata can be used to represent {relations} between real ...
  • Relentful Strategic Reasoning in 1 Alternating-Time Temporal Logic 

    Mogavero, Fabio; Murano, Aniello; Vardi, Moshe Y. (2012-11-27)
    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 ...
  • 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 ...
  • Solving Partial-Information Stochastic Parity Games 

    Nain, Sumit; Vardi, Moshe Y. (2013)
    We study one-sided partial-information 2-player concurrent stochastic games with parity objectives. In such a game, one of the players has only partial visibility of the state of the game, while the other player has complete ...