Gabriel Thierrin

Bio: Gabriel Thierrin is an academic researcher from University of Western Ontario. The author has contributed to research in topics: Syntactic monoid & Free monoid. The author has an hindex of 17, co-authored 59 publications receiving 866 citations. Previous affiliations of Gabriel Thierrin include National Chung Hsing University & Kyoto Sangyo University.

Contextual Insertions/Deletions and Computability

Abstract: We investigate two generalizations of insertion and deletion of words, that have recently become of interest in the context of molecular computing. Given a pair of words (x, y), called a context, the (x, y)-contextual insertion of a wordvinto a worduis performed as follows. For each occurrence ofxyas a subword inu, we include in the result of the contextual insertion the words obtained by insertingvintou, betweenxandy. The (x, y)-contextual deletion operation is defined in a similar way. We study closure properties of the Chomsky families under the defined operations, contextual ins-closed and del-closed languages, and decidability of existence of solutions to equations involving these operations. Moreover, we prove that every Turing machine can be simulated by a system based entirely on contextual insertions and deletions

Disjunctive languages and codes

Abstract: * A i A + A i " X + AB = {xylx c A, y ~ B}, A = o and = u A word w ~ is i=0+ i=l called primitive if w = fn, f c X , implies n = i. A non-empty language A such that A ~ X + is called a code if XlX2...x n = ylY2...y m and xi,Y j ~ A for every i and j implies n = m and x i = Yi for all i. A code A is said to be a prefix (suffix) code if A n AX + = ~ (A n X+A=~). For any language A, the relations PA and RA defined by x E y (PA) if and only if A..x = A..y

Codes, involutions, and DNA encodings

Abstract: DNA computing as a field started in 1994 when Leonard Adleman solved a hard computational problem entirely by manipulations of DNA molecules in a test tube [1]. The premise behind DNA computing is that DNA is capable of storing information, while various laboratory techniques that operate on and modify DNA strands (called bio-operations in the sequel) can be used to perform computational steps. Most DNA computations consists of three basic stages. The first is encoding the problem using single-stranded or double-stranded DNA. Then the actual computation is performed by employing a succession of bio-operations [14]. Finally, the DNA strands representing the solution to the problem are detected and decoded. Because of the nature of the substrate in which the data is encoded, namely DNA strands, problems can occur at the encoding stage which would not occur in an electronic medium. In order to describe these problems and our attempts at solutions, we now briefly present some basic molecular biology notions and notations.

Bioinformatics Methods and Protocols

Abstract: Part 1 Sequence Analysis Packages GCG: The Wisconsin Package of Sequence Analysis Programs David D Womble Web-Based Interfaces for the GCG Sequence Analysis Programs David D Womble Omiga: A PC-Based Sequence Analysis Tool Jeffrey A Kramer MacVector: Integrated Sequence Analysis for the Macintosh Promila A Rastogi DNASTAR's Lasergene Sequence Analysis Software Timothy G Burland PepTool(TM) and GeneTool(TM): Platform-Independent Tools for Biological Sequence Analysis David S Wishart, Paul Stothard, and Gary H Van Domselaar The Staden Package, 1998 Rodger Staden, Kathryn F Beal, and James K Bonfield Building a Multiuser Sequence Analysis Facility Using Freeware Brian Fristensky Part 2 Molecular Biology Software Free Software in Molecular Biology for Macintosh and MS Windows Computers Appendix: Software Listings Don Gilbert Flexible Sequence Similarity Searching with the FASTA3 Program Package William R Pearson The Use of CLUSTAL W and CLUSTAL X for Multiple Sequence Alignment Ashok Aiyar Phylogenetic Analysis Using PHYLIP Jacques D Retief Annotating Sequence Data Using Genotator Nomi L Harris Low Cost Gel Analysis Jeffry A Reidler Part 3 Web-Based Resources Computer Resources for the Clinical and Molecular Geneticist Yuval Yaron and Avi Orr-Urtreger The NCBI: Publicly Available Tools and Resources on the Web Jack P Jenuth Resources at EBI Patricia Rodriguez-Tome Computer-Assisted Analysis of Transcription Control Regions: MatInspector and Other Programs Thomas Werner Computational Approaches for Gene Identification Gautam B Singh Primer3 on the WWW for General Users and for Biologist Programmers Steve Rozen andHelen Skaletsky Using the WWW to Supply the Molecular Biology Lab MaryAnn Labant and Roger Anderson Part 4 Computers and Molecular Biology: Issues and Constraints Network Computing: Restructuring How Scientists Use Computers and What We Get Out of Them Brian Fristensky Computing with DNA Lila Kari and Laura F Landweber Detecting Biological Patterns: The Integration of Databases, Models, and Algorithms Gautam B Singh Part 5 Teaching Bioinformatics and Keeping Up-to-Date with the Literature Design and Implementation of an Introductory Course for Computer Applications in Molecular Biology and Genetics Stephen A Krawetz The Virtual Library I: Searching MEDLINE Keir Reavie The Virtual Library II: Science Citation Index and Current Awareness Services Keir Reavie The Virtual Library III: Electronic Journals, Grants, and Funding Information Keir Reavie

Discrete Applied Mathematics

Abstract: : Significant progress has been made with solution of location problems and in preprocessing and decomposition for discrete optimization. There has also been research on the application of techniques from combinational optimization to nonlinear problems.

Codes and Automata

Abstract: Preface 1. Preliminaries 2. Codes 3. Prefix codes 4. Automata 5. Deciphering delay 6. Bifix codes 7. Circular codes 8. Factorizations of free monoids 9. Unambiguous monoids of relations 10. Synchronization 11. Groups of codes 12. Factorizations of cyclic groups 13. Densities 14. Polynomials of finite codes Solutions of exercises Appendix: Research problems References Index of notation Index.