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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2009年 5877 LNCS卷

作者： Deaton, Russell Suyama, Akira Dept. of Computer Science and Computer Engineering JBHT - CSCE 504 1 University of Arkansas Fayetteville AR 72701 United States Department of Life Science Graduate School of Arts and Sciences University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan

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Toward molecular programming with dna

Toward molecular programming with DNA

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13th international conference on Architectural Support for programming Languages and Operating Systems, ASPLOS XIII

作者： Winfree, Erik California Institute of Technology Pasadena CA United States Department of Computer Science Computation and Neural Systems and Bioengineering Caltech MIT AI Lab.

ISBN: (纸本)9781595939586

关键词： dna

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Toward molecular programming with dna

Toward molecular programming with DNA

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Proceedings of the 13th international conference on Architectural support for programming languages and operating systems

作者： Erik Winfree California Institute of Technology Pasadena CA

ISBN: (纸本)9781595939586

Biological organisms are beautiful examples of programming. the program and data are stored in biological molecules such as dna, RNA, and proteins; the algorithms are carried out by molecular and biochemical processes; and the end result is the creation and function of an organism. If we understood how to program molecular systems, what could we create? Lifelike technologies whose basic operations are chemical reactions? the fields of chemistry, physics, biology, and computer science are converging as we begin to synthesize molecules, molecular machines, and molecular systems of ever increasing complexity, leading to subdisciplines such as dna nanotechnology, dna computing, and synthetic biology. Having demonstrated simple devices and systems -- self-assembled structures, molecular motors, chemical logic gates -- researchers are now turning to the question of how to create large-scale integrated systems. To do so, we must learn how to manage complexity: how to efficiently specify the structure and behavior of intricate molecular systems, how to compile such specifications down to the design of molecules to be synthesized in the lab, and how to ensure that such systems function robustly. these issues will be illustrated for chemical logic circuits based on cascades of dna hybridization *** Erik Winfree is an Associate Professor in Computer Science, Computation & Neural Systems, and Bioengineering at Caltech. Winfree is the recipient of the Feynman Prize for Nanotechnology (2006), the NSF PECASE/CAREER Award (2001), the ONR Young Investigators Award (2001), a MacArthur Fellowship (2000), and MIT Technology Review's first TR100 list of "top young innovators" (1999). Prior to joining the faculty at Caltech in 2000, Winfree was a Lewis thomas Postdoctoral Fellow in molecular Biology at Princeton, and a Visiting Scientist at the MIT AI Lab. Winfree received a B.S. in Mathematics w/ Computer Science from the University of Chicago in 1991, and a Ph.D. in Computati

关键词： molecular programming dna

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Protein evolution driven by symmetric structural repeats

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BMC BIOINFORMATICS 2008年第s10期9卷 P3-P3页

作者： Abraham, Anne-Laure Pothier, Joel Rocha, Eduardo P. C. Univ Paris 06 F-75005 Paris France Inst Pasteur CNRS URA2171 F-75015 Paris France

Background Duplications play a major role in the evolution of genomes by creating and modifying molecular functions. Repeats are created at the dna level, but when they are intragenic they affect protein sequence and structure. Moreover, as sequences evolve faster than 3D structures, some ancient repeats cannot be detected at the sequence level. therefore, an understanding of the evolutionary and functional role of repeats requires tracking them at the three levels. Materials and methods For this task we have developed a program (SWELFE) to find repeats in dna, amino acid sequences and 3D protein structures (available at http://***/ swelfe). Repeats were searched independently at all three levels using dynamic programming (SIM algorithm) and we adapted scoring matrices for each level. 3D structures were encoded as strings of α angles (dihedral angle between four consecutive Cα) so that the same algorithm can be used at the three levels. We verified the validity of our approach by superimposing the 3D repeats. We made a statistical evaluation of the repeats we found. As there is currently no connection between 3D structures and the corresponding dna sequences, we built a databank where we associate a PDB structure with its best match among the genes in TREMBL. the databank has 85 845 entries corresponding to ~85% of the unique chains of the PDB databank after removing entries with very small peptides or many undefined residues. We could then compare directly the results of repeat identification at the three levels. Results In our analyses we were surprised to find that many of the large structural repeats are symmetrical (2-fold symmetry): one copy of the repeat can be superimposed with the other copy by a simple rotation of 180° around an axis (some repeats have 3-fold symmetry or higher). An example of a symmetrical repeat is shown on Figure 1. then structures containing such repeats resemble to homodimers combined into one unit. [ABSTRACT FROM

关键词： Dynamic programming Dihedral Angle Combinatorial Library Small Peptide Protein Evolution

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Modeling gene regulation and spatial organization of sequence based motifs

Modeling gene regulation and spatial organization of sequenc...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Jochen Supper Claas aufm Kampe Dierk Wanke Kenneth W. Berendzen Klaus Harter Richard Bonneau Andreas Zell Center for Bioinfonnatics Tiibingen (ZBIT) University of Tubingen Germany Center for Plant Molecular Biology (ZMBP) University of Tubingen Germany New York University New York NY US

Reconstructing and modeling regulatory networks is an active area of research in bioinformatics and systems biology. Hence, various computational methods have been published, often successfully modeling one aspect of regulatory control. Gene regulation, however, is a process that depends on many different components such as transcription factors (TFs), cis-regulatory motifs and their temporal and spatial coordination. Accordingly, a promising new direction for computational analysis is the incorporation of multiple data types to discover, for instance, cluster membership, the spatial organization of cis-regulatory motifs and TFs that bind to these motifs. Here, we present such a data-driven framework, comprising four stages, to infer gene regulatory networks (GRNs) by modeling: 1. Motif presence in the promoter; 2. Spatial motif arrangement in co-regulated genes; 3. TFs that bind the respective motifs, and: 4. Dynamic properties of the GRN. A novel method is presented in stage 2, where we optimize for the spatial motif properties: orientation, occurrence of multiple motifs, relative distance between two motifs and distance to the transcription start site (TSS). To find optimal distance based properties in efficient time we describe a dynamic programming approach. To combine multiple motif properties that are shared by genes with similar expression profiles a Hill-climber is employed. Subsequently, in stage 3 and 4, we infer GRNs by assigning TFs to the derived motifs and model time-dependent regulatory relationships between them with the inferelator approach. None of the stages require the user to manually adjust any parameter, and thus derived properties can be analyzed without the bias introduced by parametrization. We applied this approach to S. cerevisiae data and obtained insight into individual and general properties of the spatial assembly of regulatory elements and inferred the corresponding GRN.

关键词： Bioinformatics Systems biology Proteins Sequences Genomics Biological system modeling Biology computing dna RNA Data analysis

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New methods for detecting lineage-specific selection

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10th Annual international conference on Research in Computational molecular Biology

作者： Siepel, Adam Pollard, Katherine S. Haussler, David Univ Calif Santa Cruz Ctr Biomol Sci & Engn Santa Cruz CA 95064 USA Univ Calif Santa Cruz Howard Hughes Med Inst Santa Cruz CA 95064 USA

ISBN: (纸本)3540332952

So far, most methods for identifying sequences tinder selection based on comparative sequence data have either assumed selectional pressures are the same across all branches of a phylogeny, or have focused on changes in specific lineages of interest. Here, we introduce a more general method that detects sequences that have either come under selection, or begun to drift, on any lineage. the method is based on a phylogenetic hidden Markov model (phylo-HMM), and does not require element boundaries to be determined a prion, making it particularly useful for identifying noncoding sequences. Insertions and deletions (indels) are incorporated into the phylo-HMM by a simple strategy that uses a separately reconstructed "indel history." To evaluate the statistical significance of predictions, we introduce a novel method for computing P-values based on prior and posterior distributions of the number of substitutions that have occurred in the evolution of predicted elements. We derive efficient dynamic-programming algorithms for obtaining these distributions, given a model of neutral evolution. Our methods have been implemented as computer programs called DLESS (Detection of LinEage-Specific Selection) and phyloP (phylogenetic P-values). We discuss results obtained with these programs on both real and simulated data sets.

关键词： dna sequences

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K-group A* for multiple sequence alignment with quasi-natural gap costs

K-group A* for multiple sequence alignment with quasi-natura...

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international conference on Tools for Artificial Intelligence (ICTAI)

作者： Rong Zhou E.A. Hansen Department of Computer Science and Engineering Mississippi State University MS USA

Alignment of multiple protein or dna sequences is an important problem in bioinformatics. Previous work has shown that the A* search algorithm can find optimal alignments for up to several sequences, and that a K-group generalization of A* can find approximate alignments for much larger numbers of sequences [T. Ikeda et al. (1999)]. In this paper, we describe the first implementation of K-group A* that uses quasinatural gap costs, the cost model used in practice by biologists. We also introduce a new method for computing gap-opening costs in profile alignment. Our results show that K-group A* can efficiently find optimal or close-to-optimal alignments for small groups of sequences, and, for large numbers of sequences, it can find higher-quality alignments than the widely-used CLUSTAL family of approximate alignment tools. this demonstrates the benefits of A* in aligning large numbers of sequences, as typically compared by biologists, and suggests that K-group A* could become a practical tool for multiple sequence alignment.

关键词： Costs Sequences Iterative algorithms dna Bioinformatics Dynamic programming State-space methods Computer science Protein engineering Biological system modeling

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Invited talk: injecting life with computers 04

Invited talk: injecting life with computers

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Proceedings of the 6th ACM SIGPLAN international conference on Principles and practice of declarative programming

作者： Ehud Shapiro Weizmann Institute of Science Rehovot Israel

ISBN: (纸本)9781581138191

Although electronic computers are the only "computer species" we are accustomed to, the mathematical notion of a programmablecomputer has nothing to do with wires and logic gates. In fact, Alan Turing's notional computer, which marked in 1936 the birth of modern computer science and still stands at its heart, has greater similarity to natural biomolecular machines such as the ribosome and polymerases than to electronic computers. Recently, a new "computer species" made of biological molecules has emerged. these simple molecular computers inspired by the Turing machine, of which a trillion can fit into a microliter, do not compete with electronic computers in solving complex computational problems; their potential lies elsewhere. their molecular scale and their ability to interact directly with the biochemical environment in which they operate suggest that in the future they may be the basis of a new kind of "smart drugs": molecular devices equipped with the medical knowledge to perform disease diagnosis and therapy inside the living body. they would detect and diagnose molecular disease symptoms and, when necessary, administer the requisite drug molecules to the cell, tissue or organ in which they operate. In the talk we review this new research direction and report on preliminary steps carried out in our lab towards realizing its vision.

关键词： molecular computers computer diagnosis and therapy autonomous computers dna computing

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6th international Workshop on dna-Based Computers, dna 2000

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6th international Workshop on dna-Based Computers, dna 2000

ISBN: (纸本)3540420762

the proceedings contain 18 papers. the special focus in this conference is on dna computing. the topics include: Engineered communications for microbial robotics;solution of a satisfiability problem on a gel-based dna computer;Diophantine equations and splicing;a new demonstration of the generative capability of h systems;about time-varying distributed h systems;string tile models for dna computing by self-assembly;from molecular computing to molecular programming;graph replacement chemistry for dna processing;molecular computing with generalized homogeneous p-systems;computationally inspired biotechnologies;improved dna synthesis and associative search using error-correcting codes and vector-quantization;challenges and applications for self-assembled dna nanostructures;a dna-based random walk method for solving k-sat;solving computational learning problems of Boolean formulae on dna computers;the fidelity of annealing-ligation;dna implementation of a royal road fitness evaluation and steady flow micro-reactor module for pipelined dna computations.

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Steady flow micro-reactor module for pipelined dna computations 1

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6th international Workshop on dna-Based Computers, dna 2000

作者： McCaskill, John S. Penchovsky, Robert Gohlke, Marlies Ackermann, Jörg Rücker, thomas GMD-National Research Center for Information Technology Schloß Birlinghoven St Augustin53754 Germany

ISBN: (数字)9783540449928

ISBN: (纸本)3540420762

Microflow reactors provide a means of implementing dna computing as a whole, not just individual steps. Contrary to surface based dna Chips[1], microflow reactors with active components in closed flow systems can be used to integrate complete dna computations[2]. Microreactors allow complicated flow topologies to be realized which can implement a dataflowlike architecture for the processing of dna. A technologically feasible scalable approach with many reaction chambers however requires constant hydrodynamic flows. In this work, the experimental construction of a basic constant flow module for dna processing in such a context is addressed. Limited diffusional exchange in parallel flows is used to establish spatio-temporal segregation of reaction conditions which can be crossed by magnetic beads without barriers. As previously outlined[2], linked up with an optical programming technology, this will enable dna selection to be programmed and complex population selection to be performed. the basic first experimental step in the realization of this program is described here: the establishment of a stable hydrodynamic flow pattern which is scalable to many reactors in parallel and the demonstration of a scalable and synchronous clocking of magnetic beadbased processing. First results with fluorescently-labeled dna transfer will also be presented at the conference. the way in which this module may be integrated to solve the maximal clique problem has been proposed elsewhere[2]. © Springer-Verlag Berlin Heidelberg 2001.

关键词： dna

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