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  • 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 ...
  • 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 ...
  • 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 ...
  • 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 (2014-06-12)
    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. ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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, ...
  • 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 ...

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