Research Topics
Genomes and GenesSpecies  logicSummarySummary: The science that investigates the principles governing correct or reliable inference and deals with the canons and criteria of validity in thought and demonstration. This system of reasoning is applicable to any branch of knowledge or study. (Random House Unabridged Dictionary, 2d ed & Sippl, Computer Dictionary, 4th ed) Top Publications

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Publications
 Li T, Zhang L, Ai J, Dong S, Wang E. Iontuned DNA/Ag fluorescent nanoclusters as versatile logic device. ACS Nano. 2011;5:63348 pubmed publisherA novel kind of versatile logic device has been constructed utilizing iontuned DNA/Ag fluorescent nanoclusters, with K(+) and H(+) as two inputs...
 Amir L, Tam T, Pita M, Meijler M, Alfonta L, Katz E. Biofuel cell controlled by enzyme logic systems. J Am Chem Soc. 2009;131:82632 pubmed publisherAn enzymebased biofuel cell with a pHswitchable oxygen electrode, controlled by enzyme logic operations processing in situ biochemical input signals, has been developed...
 Umesono Y, Tasaki J, Nishimura Y, Hrouda M, Kawaguchi E, Yazawa S, et al. The molecular logic for planarian regeneration along the anteriorposterior axis. Nature. 2013;500:736 pubmed publisher..Thus, we have confirmed the broad outline of Morgan's hypothesis, and refined it on the basis of our proposed default property of planarian stem cells. ..
 Wang B, Buck M. Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol. 2012;20:37684 pubmed publisher..Here, we summarize the current stateoftheart of engineering synthetic genetic logic circuits to customize cellular signaling behaviors, and discuss their promising applications in biocomputing, ..
 Silva Rocha R, De Lorenzo V. Implementing an ORNOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli. Mol Biosyst. 2011;7:238996 pubmed publisherWhether biological or electronic, manengineered computation is based on logic circuits assembled with binary gates that are interconnected to perform Boolean operations...
 Katsos N, Roqueta C, Estevan R, Cummins C. Are children with Specific Language Impairment competent with the pragmatics and logic of quantification?. Cognition. 2011;119:4357 pubmed publisher..The implications of these findings for SLI, linguistic theory, and clinical practice are discussed. ..
 Shamim M, Enam S, Qidwai U. Fuzzy Logic in neurosurgery: predicting poor outcomes after lumbar disk surgery in 501 consecutive patients. Surg Neurol. 2009;72:56572; discussion 572 pubmed publisher..We have used Fuzzy Logicbased fuzzy inference system (FIS) for identifying patients unlikely to improve after disk surgery and explored ..
 Gaber R, Lebar T, Majerle A, Ster B, Dobnikar A, Bencina M, et al. Designable DNAbinding domains enable construction of logic circuits in mammalian cells. Nat Chem Biol. 2014;10:2038 pubmed publisherElectronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function...
 Sprinzak E, Cokus S, Yeates T, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multiprotein complexes using logic analysis of gene expression. BMC Syst Biol. 2009;3:115 pubmed publisher..We detect coordinated regulation of multiple protein complexes using logic analysis of gene expression data...
 Cui J, Deluca T, Jung J, Wall D. Phylogenetically informed logic relationships improve detection of biological network organization. BMC Bioinformatics. 2011;12:476 pubmed publisher..Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses...
 Chen S, Guo Z, Zhu S, Shi W, Zhu W. A multiaddressable photochromic bisthienylethene with sequencedependent responses: construction of an INHIBIT logic gate and a keypad lock. ACS Appl Mater Interfaces. 2013;5:56239 pubmed publisher..Furthermore, an INHIBIT logic gate and a keypad lock with three inputs are constructed with the unimolecular platform by employing an absorption ..
 Piran R, Halperin E, Guttmann Raviv N, Keinan E, Reshef R. Algorithm of myogenic differentiation in higherorder organisms. Development. 2009;136:383140 pubmed publisher..Specifically, we applied the ?ukasiewicz logic to a diffusible protein system that leads to myogenesis...
 Yu W, Li Z, Zhou H, Chen Y, Wang Y, Huang Y, et al. Vertically stacked multiheterostructures of layered materials for logic transistors and complementary inverters. Nat Mater. 2013;12:24652 pubmed publisher..interest for future electronics, but the absence of a bandgap limits its direct applicability in transistors and logic devices...
 Pasotti L, Quattrocelli M, Galli D, De Angelis M, Magni P. Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. Biotechnol J. 2011;6:78495 pubmed publisher..Herein, two modular biological systems that could mimic multiplexing and demultiplexing logic functions are proposed and discussed...
 Scott D, Das U, Tang Y, Roy S. Mechanistic logic underlying the axonal transport of cytosolic proteins. Neuron. 2011;70:44154 pubmed publisher..We propose a model where cytosolic proteins are transported by dynamically assembling into multiprotein complexes that are directly/indirectly conveyed by motors. ..
 Friedrich R, Friederici A. Mathematical logic in the human brain: syntax. PLoS ONE. 2009;4:e5599 pubmed publisher..This seems to imply that despite structural analogies of common and current formal languages, at the neural level, mathematics and natural language are processed differently, in principal. ..
 Bernardes J, Carbone A, Zaverucha G. A discriminative method for familybased protein remote homology detection that combines inductive logic programming and propositional models. BMC Bioinformatics. 2011;12:83 pubmed publisher..From this, Inductive Logic Programming (ILP) finds the most frequent patterns (motifs) and uses them to train propositional models, such as ..
 Liu X, Aizen R, Freeman R, Yehezkeli O, Willner I. Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations. ACS Nano. 2012;6:355363 pubmed publisher..detection of DNA, aptamersubstrate complexes, and for the integration of predesigned DNA constructs that activate logic gate operations...
 Zhou J, Arugula M, Halámek J, Pita M, Katz E. Enzymebased NAND and NOR logic gates with modular design. J Phys Chem B. 2009;113:1606570 pubmed publisherThe logic gates NAND/NOR were mimicked by enzyme biocatalyzed reactions activated by sucrose, maltose and phosphate...
 Zhou M, Du Y, Chen C, Li B, Wen D, Dong S, et al. Aptamercontrolled biofuel cells in logic systems and used as selfpowered and intelligent logic aptasensors. J Am Chem Soc. 2010;132:21724 pubmed publisherThis communication demonstrates for the first time the controlled power release of biofuel cells (BFCs) by aptamer logic systems processed according to the Boolean logic operations "programmed" into the biocomputing systems...
 Ausländer S, Ausländer D, Müller M, Wieland M, Fussenegger M. Programmable singlecell mammalian biocomputers. Nature. 2012;487:1237 pubmed publisher..designer networks that execute inputtriggered genetic instructions with precision, robustness and computational logic reminiscent of electronic circuits...
 Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, et al. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics. 2013;29:23206 pubmed publisherb>Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phosphoproteomics data...
 Daisley J, Vallortigara G, Regolin L. Logic in an asymmetrical (social) brain: Transitive inference in the young domestic chick. Soc Neurosci. 2010;5:30919 pubmed publisher..Results demonstrate that chicks with lateralized brain hemispheres show greater inference, and this is under right hemisphere control: the brain hemisphere that is dominant in social interactions. ..
 Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, et al. Distributed biological computation with multicellular engineered networks. Nature. 2011;469:20711 pubmed publisher..design of electronic circuits, are limited by the difficulties arising from wiring the basic computational units (logic gates) through the appropriate connections, each one to be implemented by a different molecule...
 Moon T, Lou C, Tamsir A, Stanton B, Voigt C. Genetic programs constructed from layered logic gates in single cells. Nature. 2012;491:24953 pubmed publisher..These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the ..
 Privman V, Halámek J, Arugula M, Melnikov D, Bocharova V, Katz E. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic. J Phys Chem B. 2010;114:141039 pubmed publisher..process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs...
 Choi J, Lee J, Shin T, Song H, Kim E, Cheon J. Selfconfirming "AND" logic nanoparticles for faultfree MRI. J Am Chem Soc. 2010;132:110157 pubmed publisher..not only possesses superior MR contrast effects but also has the unique capability of displaying "AND" logic signals in both the T1 and T2 modes...
 Terfve C, Cokelaer T, Henriques D, MacNamara A, Gonçalves E, Morris M, et al. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol. 2012;6:133 pubmed publisher..Here we present CellNOptR, an opensource R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically ..
 Orbach R, Remacle F, Levine R, Willner I. Logic reversibility and thermodynamic irreversibility demonstrated by DNAzymebased Toffoli and Fredkin logic gates. Proc Natl Acad Sci U S A. 2012;109:2122833 pubmed publisherThe Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits...
 Sternberg M, Tamaddoni Nezhad A, Lesk V, Kay E, Hitchen P, Cootes A, et al. Gene function hypotheses for the Campylobacter jejuni glycome generated by a logicbased approach. J Mol Biol. 2013;425:18697 pubmed publisher..Here, we demonstrate the power of a logicbased machine learning approach to propose hypotheses for gene function integrating information from two diverse ..

..These representations are then manipulated by mental operations that are not based on the neural mechanisms of natural language. This article is part of a Special Issue entitled "The Cognitive Neuroscience". ..
 Ran T, Kaplan S, Shapiro E. Molecular implementation of simple logic programs. Nat Nanotechnol. 2009;4:6428 pubmed publisher..Biomolecular implementations of finite automata and logic gates have already been developed...
 Chuang C, Lin C, Chang Y, Jennawasin T, Chen P. Design of synthetic biological logic circuits based on evolutionary algorithm. IET Syst Biol. 2013;7:89105 pubmed publisherThe construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology...
 Valencia Palomo G, Rossiter J. Programmable logic controller implementation of an autotuned predictive control based on minimal plant information. ISA Trans. 2011;50:92100 pubmed publisher..Hence, it describes how the constrained control algorithm is embedded in an industrial programmable logic controller (PLC) using the IEC 611313 programming standard...
 Brousselle A, Champagne F. Program theory evaluation: Logic analysis. Eval Program Plann. 2011;34:6978 pubmed publisher..This article describes a particular type of program theory evaluationlogic analysisthat allows us to test the plausibility of a program's theory using scientific knowledge...
 Xia F, Zuo X, Yang R, White R, Xiao Y, Kang D, et al. Labelfree, dualanalyte electrochemical biosensors: a new class of molecularelectronic logic gates. J Am Chem Soc. 2010;132:85579 pubmed publisherAn "XOR" gate built using labelfree, dualanalyte electrochemical sensors and the activation of this logic gate via changing concentrations of cocaine and the relevant cDNA as inputs are described.
 Guerra D, Bulsara A, Ditto W, Sinha S, Murali K, Mohanty P. A noiseassisted reprogrammable nanomechanical logic gate. Nano Lett. 2010;10:116871 pubmed publisherWe present a nanomechanical device, operating as a reprogrammable logic gate, and performing fundamental logic functions such as AND/OR and NAND/NOR. The logic function can be programmed (e.g...
 Miyamoto T, Razavi S, DeRose R, Inoue T. Synthesizing biomoleculebased Boolean logic gates. ACS Synth Biol. 2013;2:7282 pubmed..The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices...
 Morris M, Saez Rodriguez J, Sorger P, Lauffenburger D. Logicbased models for the analysis of cell signaling networks. Biochemistry. 2010;49:321624 pubmed publisher..Here we review recent advances in applying logicbased modeling to mammalian cell biology...
 MacPhee M. Developing a practiceacademic partnership logic model. Nurs Outlook. 2009;57:1437 pubmed publisherThis article will describe a testable logic model for practiceacademic partnerships. The model can be used to build collaborative practice capacity between academic and practice partners...

..Here, we demonstrate how coupled threshold oscillators may be used to perform binary logic in a manner entirely consistent with modern computer architectures...
 Acerbi A, Ghirlanda S, Enquist M. The logic of fashion cycles. PLoS ONE. 2012;7:e32541 pubmed publisher..We also establish that alternative theories, that fashions result from individuals signaling their social status, or from individuals randomly copying each other, do not satisfactorily reproduce these empirical observations. ..
 Hayes H, Parchman M, Howard R. A logic model framework for evaluation and planning in a primary care practicebased research network (PBRN). J Am Board Fam Med. 2011;24:57682 pubmed publisher..The purpose of this article is to describe the development of a logic model and how the framework has been used for planning and evaluation in a primary care PBRN...
 Steinhauer K, Drury J, Portner P, Walenski M, Ullman M. Syntax, concepts, and logic in the temporal dynamics of language comprehension: evidence from eventrelated potentials. Neuropsychologia. 2010;48:152542 pubmed publisherb>Logic has been intertwined with the study of language and meaning since antiquity, and such connections persist in present day research in linguistic theory (formal semantics) and cognitive psychology (e.g., studies of human reasoning)...
 Ma D, Kwan M, Chan D, Lee P, Yang H, Ma V, et al. Crystal violet as a fluorescent switchon probe for imotif: labelfree DNAbased logic gate. Analyst. 2011;136:26926 pubmed publisher..This interaction has been exploited to develop a labelfree DNAbased "OR" logic gate for potassium and hydrogen ions.
 Tamsir A, Tabor J, Voigt C. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature. 2011;469:2125 pubmed publisher..We construct a simple NOR logic gate in Escherichia coli by arranging two tandem promoters that function as inputs to drive the transcription of a ..
 Sakhanenko N, Galas D. Markov logic networks in the analysis of genetic data. J Comput Biol. 2010;17:1491508 pubmed publisher..We chose to use the most general such approach, Markov Logic Networks (MLNs), for combining deterministic knowledge with statistical analysis...
 Govaerts P, Vaerenberg B, De Ceulaer G, Daemers K, De Beukelaer C, Schauwers K. Development of a software tool using deterministic logic for the optimization of cochlear implant processor programming. Otol Neurotol. 2010;31:90818 pubmed publisher..An intelligent agent, Fitting to Outcomes eXpert, was developed to optimize and automate Cochlear implant (CI) programming. The current article describes the rationale, development, and features of this tool...
 Helikar T, Kowal B, Madrahimov A, Shrestha M, Pedersen J, Limbu K, et al. Biologic builder: a nontechnical tool for building dynamical, qualitative models. PLoS ONE. 2012;7:e46417 pubmed publisher..To help address this issue, we have developed a webbased tool, BioLogic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) ..
 Fino E, Packer A, Yuste R. The logic of inhibitory connectivity in the neocortex. Neuroscientist. 2013;19:22837 pubmed publisher..In a last section, the authors describe briefly the link between dense inhibitory networks and different interneuron functions described in the neocortex. ..
 Bonnet J, Yin P, Ortiz M, Subsoontorn P, Endy D. Amplifying genetic logic gates. Science. 2013;340:599603 pubmed publisher..Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes...
 Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011;7:e1002180 pubmed publisher..For each case we apply a new method, called NetworkGuided Forests, to identify predictive modules together with logic functions which tie the activity of each module to the activity of its component genes...
 Seelig G, Soloveichik D, Zhang D, Winfree E. Enzymefree nucleic acid logic circuits. Science. 2006;314:15858 pubmed..To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation...