Algorithmic Contributions to Computational Molecular Biology

Nous presentons ici nos resultats de recherche depuis 2001 sur l'algorithmique des graphes lineaires, la recherche de motif (avec ou sans topologie) dans les graphes, et la genomique comparative.

[1]  Valiente Feruglio,et al.  On the maximum common embedded subtree problem for ordered trees , 2003 .

[2]  Frank Harary,et al.  Graph Theory , 2016 .

[3]  Nikola Ruskuc,et al.  Pattern Avoidance Classes and Subpermutations , 2005, Electron. J. Comb..

[4]  Christian N. S. Pedersen,et al.  RNA Pseudoknot Prediction in Energy-Based Models , 2000, J. Comput. Biol..

[5]  Jaroslav Nesetril,et al.  Graphs and homomorphisms , 2004, Oxford lecture series in mathematics and its applications.

[6]  Michael R. Fellows,et al.  Parameterized Complexity , 1998 .

[7]  D. R. Fulkerson,et al.  Incidence matrices and interval graphs , 1965 .

[8]  David Sankoff,et al.  Genome rearrangement with gene families , 1999, Bioinform..

[9]  A. Stöhr,et al.  Gelöste und ungelöste Fragen über Basen der natürlichen Zahlenreihe. II. , 1955 .

[10]  Guillaume Fertin,et al.  On the Approximability of Comparing Genomes with Duplicates , 2008, J. Graph Algorithms Appl..

[11]  Guillaume Fertin,et al.  Extracting constrained 2-interval subsets in 2-interval sets , 2007, Theor. Comput. Sci..

[12]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[13]  R. Karp,et al.  From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .

[14]  Heikki Mannila,et al.  Ordered and Unordered Tree Inclusion , 1995, SIAM J. Comput..

[15]  Reuven Bar-Yehuda,et al.  A Local-Ratio Theorem for Approximating the Weighted Vertex Cover Problem , 1983, WG.

[16]  Mathieu Raffinot,et al.  Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs , 2005, ESA.

[17]  Christos H. Papadimitriou,et al.  Algorithmic aspects of protein structure similarity , 1999, 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039).

[18]  Shuai Cheng Li,et al.  On the Complexity of the Crossing Contact Map Pattern Matching Problem , 2006, WABI.

[19]  David R. Karger,et al.  On approximating the longest path in a graph , 1997, Algorithmica.

[20]  Guillaume Fertin,et al.  How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation , 2006, Comparative Genomics.

[21]  Magnús M. Halldórsson,et al.  Strip Graphs: Recognition and Scheduling , 2006, WG.

[22]  Tatsuya Akutsu,et al.  Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots , 2000, Discret. Appl. Math..

[23]  Sebastian Wernicke,et al.  Efficient Detection of Network Motifs , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[24]  Albert Y. Zomaya,et al.  Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications , 2011 .

[25]  Guillaume Fertin,et al.  What Makes the Arc-Preserving Subsequence Problem Hard? , 2005, Trans. Comp. Sys. Biology.

[26]  Alexander Russell,et al.  Minimum Multicolored Subgraph Problem in Multiplex PCR Primer Set Selection and Population Haplotyping , 2006, International Conference on Computational Science.

[27]  G. Blin,et al.  The breakpoint distance for signed sequences , 2005 .

[28]  Guillaume Fertin,et al.  On the S-Labeling problem , 2009, Electron. Notes Discret. Math..

[29]  Reuven Bar-Yehuda,et al.  A Linear-Time Approximation Algorithm for the Weighted Vertex Cover Problem , 1981, J. Algorithms.

[30]  Gábor Tardos,et al.  Excluded permutation matrices and the Stanley-Wilf conjecture , 2004, J. Comb. Theory, Ser. A.

[31]  Tao Jiang,et al.  On the Complexity of Comparing Evolutionary Trees , 1996, Discret. Appl. Math..

[32]  Walter F. Tichy,et al.  The string-to-string correction problem with block moves , 1984, TOCS.

[33]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[34]  Michael R. Fellows,et al.  On the parameterized complexity of multiple-interval graph problems , 2009, Theor. Comput. Sci..

[35]  Paul D. Seymour,et al.  Graph Minors. II. Algorithmic Aspects of Tree-Width , 1986, J. Algorithms.

[36]  Guillaume Blin,et al.  Querying Protein-Protein Interaction Networks , 2009, ISBRA.

[37]  Satish Rao,et al.  On the tandem duplication-random loss model of genome rearrangement , 2006, SODA '06.

[38]  D. Sankoff,et al.  Comparative Genomics: "Empirical And Analytical Approaches To Gene Order Dynamics, Map Alignment And The Evolution Of Gene Families" , 2000 .

[39]  Frank Harary,et al.  On double and multiple interval graphs , 1979, J. Graph Theory.

[40]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[41]  P. Bonsma.  Complexity results for restricted instances of a paint shop problem , 2003 .

[42]  Stéphane Vialette,et al.  Bounded list injective homomorphism for comparative analysis of protein-protein interaction graphs , 2004, J. Discrete Algorithms.

[43]  Jijun Tang,et al.  Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content , 2003, WADS.

[44]  Minghui Jiang,et al.  On the parameterized complexity of some optimization problems related to multiple-interval graphs , 2010, Theor. Comput. Sci..

[45]  Jeremy P. Spinrad,et al.  Modular decomposition and transitive orientation , 1999, Discret. Math..

[46]  F. McMorris,et al.  Topics in Intersection Graph Theory , 1987 .

[47]  Guillaume Fertin,et al.  Combinatorics of Genome Rearrangements , 2009, Computational molecular biology.

[48]  L. Bergroth,et al.  A survey of longest common subsequence algorithms , 2000, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000.

[49]  Thomas Zichner,et al.  Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection , 2007, APBC.

[50]  Riccardo Dondi,et al.  Weak pattern matching in colored graphs: Minimizing the number of connected components , 2007, ICTCS.

[51]  Stéphane Vialette,et al.  Packing of (0, 1)-matrices , 2006, RAIRO Theor. Informatics Appl..

[52]  George M. Church,et al.  yMGV: a cross-species expression data mining tool , 2004, Nucleic Acids Res..

[53]  R. P. Dilworth,et al.  A DECOMPOSITION THEOREM FOR PARTIALLY ORDERED SETS , 1950 .

[54]  Tao Jiang,et al.  On the Approximation of Shortest Common Supersequences and Longest Common Subsequences , 1994, SIAM J. Comput..

[55]  Andrew D. King,et al.  Bounding χ in terms of ω and Δ for quasi-line graphs , 2008 .

[56]  Jörg Flum,et al.  Parameterized Complexity Theory , 2006, Texts in Theoretical Computer Science. An EATCS Series.

[57]  Walter Gilbert,et al.  The limited universe of exons , 1991, Current Biology.

[58]  Roded Sharan,et al.  QPath: a method for querying pathways in a protein-protein interaction network , 2006, BMC Bioinformatics.

[59]  Douglas B. West,et al.  The interval number of a planar graph: Three intervals suffice , 1983, J. Comb. Theory, Ser. B.

[60]  Stéphane Vialette.  Two-Interval Pattern Problems , 2008, Encyclopedia of Algorithms.

[61]  Maxwell Young,et al.  Nonnegative integral subset representations of integer sets , 2007, Inf. Process. Lett..

[62]  B. Peyton,et al.  An Introduction to Chordal Graphs and Clique Trees , 1993 .

[63]  Bonnie Berger,et al.  A Parameterized Algorithm for Protein Structure Alignment , 2007, J. Comput. Biol..

[64]  Bin Fu,et al.  Non-breaking Similarity of Genomes with Gene Repetitions , 2007, CPM.

[65]  P. Uetz,et al.  What do we learn from high-throughput protein interaction data? , 2004, Expert review of proteomics.

[66]  Sylvain Guillemot,et al.  D S ] 5 N ov 2 01 5 Pattern matching in ( 213 , 231 )-avoiding permutations Both , 2009 .

[67]  Robert E. Tarjan,et al.  Simple Linear-Time Algorithms to Test Chordality of Graphs, Test Acyclicity of Hypergraphs, and Selectively Reduce Acyclic Hypergraphs , 1984, SIAM J. Comput..

[68]  AilonNir,et al.  Aggregating inconsistent information , 2008 .

[69]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[70]  Maw-Shang Chang,et al.  Efficient Algorithms for the Maximum Weight Clique and Maximum Weight Independent Set Problems on Permutation Graphs , 1992, Inf. Process. Lett..

[71]  Michael R. Fellows,et al.  Algorithms and complexity for annotated sequence analysis , 1999 .

[72]  I. S. Gál.  On the Representation of 1, 2, . . . , N by Differences , 2004 .

[73]  Guillaume Fertin,et al.  A General Framework for Computing Rearrangement Distances between Genomes with Duplicates , 2007 .

[74]  Michel Habib,et al.  Revisiting T. Uno and M. Yagiura's Algorithm , 2005, ISAAC.

[75]  Blair J R S,et al.  Introduction to Chordal Graphs and Clique Trees, in Graph Theory and Sparse Matrix Computation , 1997 .

[76]  Stéphane Vialette,et al.  On the computational complexity of 2-interval pattern matching problems , 2004, Theor. Comput. Sci..

[77]  Alexander Tiskin.  Longest Common Subsequences in Permutations and Maximum Cliques in Circle Graphs , 2006, CPM.

[78]  Prosenjit Bose,et al.  Pattern Matching for Permutations , 1993, WADS.

[79]  Sylvain Guillemot.  Parameterized Complexity and Approximability of the SLCS Problem , 2008, IWPEC.

[80]  Riccardo Dondi,et al.  Maximum Motif Problem in Vertex-Colored Graphs , 2009, CPM.

[81]  René Schott,et al.  On the tree inclusion problem , 1993, Acta Informatica.

[82]  Venkatesan Guruswami,et al.  A New Multilayered PCP and the Hardness of Hypergraph Vertex Cover , 2005, SIAM J. Comput..

[83]  Paul D. Seymour,et al.  The structure of claw-free graphs , 2005, BCC.

[84]  A. Brandstädt,et al.  Graph Classes: A Survey , 1987 .

[85]  Winfried Hochstättler,et al.  Complexity results on a paint shop problem , 2004, Discret. Appl. Math..

[86]  Giorgio Gambosi,et al.  Complexity and approximation: combinatorial optimization problems and their approximability properties , 1999 .

[87]  Guillaume Fertin,et al.  A Pseudo-boolean Programming Approach for Computing the Breakpoint Distance Between Two Genomes with Duplicate Genes , 2007, RECOMB-CG.

[88]  Guillaume Blin,et al.  Comparing RNA Structures with Biologically Relevant Operations Cannot Be Done without Strong Combinatorial Restrictions , 2010, WALCOM.

[89]  Rolf Niedermeier,et al.  Pattern matching for arc-annotated sequences , 2006, TALG.

[90]  Reuven Bar-Yehuda,et al.  Scheduling split intervals , 2002, SODA '02.

[91]  Susan R. Wilson.  INTRODUCTION TO COMPUTATIONAL BIOLOGY: MAPS, SEQUENCES AND GENOMES. , 1996 .

[92]  B. Mohar,et al.  Graph Minors , 2009 .

[93]  Romeo Rizzi,et al.  Pattern Matching in Protein-Protein Interaction Graphs , 2007, FCT.

[94]  Reuven Bar-Yehuda,et al.  One for the Price of Two: a Unified Approach for Approximating Covering Problems , 1998, Algorithmica.

[95]  Daniel S. Hirschberg,et al.  Algorithms for the Longest Common Subsequence Problem , 1977, JACM.

[96]  N. Alon.  The linear arboricity of graphs , 1988 .

[97]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[98]  Joseph Y.-T. Leung,et al.  Efficient algorithms for interval graphs and circular-arc graphs , 1982, Networks.

[99]  N. Moran,et al.  From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria , 2003, PLoS biology.

[100]  Ron Y. Pinter,et al.  Alignment of metabolic pathways , 2005, Bioinform..

[101]  Simon de Givry,et al.  Searching RNA motifs and their intermolecular contacts with constraint networks , 2020 .

[102]  Moshe Lewenstein,et al.  Optimization problems in multiple-interval graphs , 2007, SODA '07.

[103]  Juan A. Rodríguez-Velázquez,et al.  Global defensive k-alliances in graphs , 2009, Discret. Appl. Math..

[104]  Louis Ibarra.  Finding Pattern Matchings for Permutations , 1997, Inf. Process. Lett..

[105]  Mike D. Atkinson,et al.  Algorithms for Pattern Involvement in Permutations , 2001, ISAAC.

[106]  Refael Hassin,et al.  The Set Cover with Pairs Problem , 2005, FSTTCS.

[107]  Jean Néraud.  Elementariness of a finite set of words is co-NP-complete , 1990, RAIRO Theor. Informatics Appl..

[108]  Weimin Chen,et al.  More Efficient Algorithm for Ordered Tree Inclusion , 1998, J. Algorithms.

[109]  Hans L. Bodlaender,et al.  A Tourist Guide through Treewidth , 1993, Acta Cybern..

[110]  Paul Dent,et al.  MAPK pathways in radiation responses , 2003, Oncogene.

[111]  Minghui Jiang.  A PTAS for the Weighted 2-Interval Pattern Problem over the Preceding-and-Crossing Model , 2007, COCOA.

[112]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[113]  Douglas B. West,et al.  Extremal Values of the Interval Number of a Graph , 1980, SIAM J. Matrix Anal. Appl..

[114]  Guillaume Fertin,et al.  Finding Exact and Maximum Occurrences of Protein Complexes in Protein-Protein Interaction Graphs , 2005, MFCS.

[115]  Frank Gurski,et al.  Polynomial algorithms for protein similarity search for restricted mRNA structures , 2007, Inf. Process. Lett..

[116]  M. Bouvel,et al.  The longest common pattern problem for two permutations , 2006 .

[117]  Zhi-Zhong Chen,et al.  The longest common subsequence problem for sequences with nested arc annotations , 2002, J. Comput. Syst. Sci..

[118]  Ronald D. Dutton,et al.  Security in graphs , 2007, Discret. Appl. Math..

[119]  Alexandr V. Kostochka,et al.  Upper bounds on the chromatic number of graphs , 1988 .

[120]  Haim Kaplan,et al.  The greedy algorithm for edit distance with moves , 2006, Inf. Process. Lett..

[121]  Cristina G. Fernandes,et al.  Motif Search in Graphs: Application to Metabolic Networks , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[122]  Guillaume Fertin,et al.  The ExemplarBreakpointDistancefor Non-trivial Genomes Cannot Be Approximated , 2009, WALCOM.

[123]  R. Ravi,et al.  Non-Overlapping Local Alignments (Weighted Independent Sets of Axis Parallel Rectangles) , 1995, WADS.

[124]  Cédric Chauve,et al.  An Edit Distance Between RNA Stem-Loops , 2005, SPIRE.

[125]  Patricia A. Evans.  Finding Common Subsequences with Arcs and Pseudoknots , 1999, CPM.

[126]  Roded Sharan,et al.  Torque: topology-free querying of protein interaction networks , 2009, Nucleic Acids Res..

[127]  Roded Sharan,et al.  Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks , 2006, J. Comput. Biol..

[128]  L. Moser.  On the representation of 1,2,..., n by sums , 1960 .

[129]  Thomas G. Szymanski,et al.  A fast algorithm for computing longest common subsequences , 1977, CACM.

[130]  Serge A. Hazout,et al.  Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms , 2006, Bioinform..

[131]  Guillaume Fertin,et al.  Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes , 2008, J. Comput. Biol..

[132]  David B. Shmoys,et al.  Recognizing graphs with fixed interval number is NP-complete , 1984, Discret. Appl. Math..

[133]  Guillaume Fertin,et al.  Finding occurrences of protein complexes in protein-protein interaction graphs , 2009, J. Discrete Algorithms.

[134]  Jens Stoye,et al.  Finding All Common Intervals of k Permutations , 2001, CPM.

[135]  Andrzej Ehrenfeucht,et al.  Elementary Homomorphisms and a Solution of the D0L Sequence Equivalence Problem , 1978, Theor. Comput. Sci..

[136]  Mathilde Bouvel,et al.  Longest Common Separable Pattern between Permutations , 2007, ArXiv.

[137]  C. Jacq,et al.  Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria , 2003, Genome Biology.

[138]  Petr Kolman,et al.  Minimum Common String Partition Problem: Hardness and Approximations , 2004, Electron. J. Comb..

[139]  Anton J. Enright,et al.  Detection of functional modules from protein interaction networks , 2003, Proteins.

[140]  Shuai Cheng Li,et al.  On two open problems of 2-interval patterns , 2009, Theor. Comput. Sci..

[141]  P. Pevzner,et al.  Colored de Bruijn Graphs and the Genome Halving Problem , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[142]  Philippe Gambette,et al.  On Restrictions of Balanced 2-Interval Graphs , 2007, WG.

[143]  Paul S. Bonsma,et al.  Complexity results on restricted instances of a paint shop problem for words , 2006, Discret. Appl. Math..

[144]  Wayne Goddard,et al.  Offensive alliances in graphs , 2004, Discuss. Math. Graph Theory.

[145]  D. R. Fulkerson,et al.  COMBINATORICS OF INTERVALS PRELIMINARY VERSION , 2003 .

[146]  H. Varmus,et al.  Characterization of ribosomal frameshifting in HIV-1 gag-pol expression , 1988, Nature.

[147]  Dimitrios M. Thilikos,et al.  Invitation to fixed-parameter algorithms , 2007, Comput. Sci. Rev..

[148]  C. Jacq,et al.  In Saccharomyces cerevisiae, ATP2 mRNA sorting to the vicinity of mitochondria is essential for respiratory function , 2002, The EMBO journal.

[149]  Christian Komusiewicz,et al.  Parameterized Algorithms and Hardness Results for Some Graph Motif Problems , 2008, CPM.

[150]  R. Stanley.  Enumerative Combinatorics: Volume 1 , 2011 .

[151]  Minghui Jiang.  A 2-approximation for the preceding-and-crossing structured 2-interval pattern problem , 2007, J. Comb. Optim..

[152]  Todd Wareham,et al.  Exact Algorithms for Computing Pairwise Alignments and 3-Medians From Structure-Annotated Sequences (Extended Abstract) , 2001, Pacific Symposium on Biocomputing.

[153]  Dror Rawitz,et al.  The Minimum Substring Cover problem , 2007, Inf. Comput..

[154]  Rolf Niedermeier,et al.  Computing the similarity of two sequences with nested arc annotations , 2004, Theor. Comput. Sci..

[155]  Andreas Björklund,et al.  Fourier meets möbius: fast subset convolution , 2006, STOC '07.

[156]  Bin Ma,et al.  The Longest Common Subsequence Problem for Arc-Annotated Sequences , 2000, CPM.

[157]  Stefan Felsner,et al.  Trapezoid Graphs and Generalizations, Geometry and Algorithms , 1994, Discret. Appl. Math..

[158]  Minghui Jiang.  Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[159]  Xin Chen,et al.  Assignment of orthologous genes via genome rearrangement , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[160]  Ronald D. Dutton.  On a graph's security number , 2009, Discret. Math..

[161]  Mam Riess Jones.  Color Coding , 1962, Human factors.

[162]  H. Varmus,et al.  Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. , 1985, Science.

[163]  Guillaume Fertin,et al.  Common Structured Patterns in Linear Graphs: Approximation and Combinatorics , 2007, CPM.

[164]  Hauz Khas,et al.  A Note on the Postage Stamp Problem , 2006 .

[165]  P. Erdos-L Lovász.  Problems and Results on 3-chromatic Hypergraphs and Some Related Questions , 2022 .

[166]  R. Backofen,et al.  Protein similarity search under mRNA structural constraints: application to targeted selenocysteine insertion. , 2002, In silico biology.

[167]  D. West.  Multitrack Interval Graphs , 1995 .

[168]  Derick Wood,et al.  A survey of adaptive sorting algorithms , 1992, CSUR.

[169]  Takeaki Uno,et al.  Fast Algorithms to Enumerate All Common Intervals of Two Permutations , 1997, Algorithmica.

[170]  Rolf Niedermeier,et al.  Compression-based fixed-parameter algorithms for feedback vertex set and edge bipartization , 2006, J. Comput. Syst. Sci..

[171]  David S. Johnson,et al.  Approximation algorithms for combinatorial problems , 1973, STOC.

[172]  Charalambos A. Charalambides,et al.  Enumerative combinatorics , 2018, SIGA.

[173]  A. Stöhr,et al.  Gelöste und ungelöste Fragen über Basen der natürlichen Zahlenreihe. I. , 1955 .

[174]  Silvio Micali,et al.  An O(v|v| c |E|) algoithm for finding maximum matching in general graphs , 1980, 21st Annual Symposium on Foundations of Computer Science (sfcs 1980).

[175]  Stephan Eidenbenz,et al.  On the Complexity of Variations of Equal Sum Subsets , 2008, Nord. J. Comput..

[176]  Tero Harju,et al.  Combinatorics on Words , 2004 .

[177]  David Sankoff,et al.  Power Boosts for Cluster Tests , 2005, Comparative Genomics.

[178]  Frank Harary,et al.  Covering and packing in graphs IV: Linear arboricity , 1981, Networks.

[179]  Romeo Rizzi,et al.  Complexity issues in color-preserving graph embeddings , 2010, Theor. Comput. Sci..

[180]  Moni Naor,et al.  Rank aggregation methods for the Web , 2001, WWW '01.

[181]  Roded Sharan,et al.  Topology-Free Querying of Protein Interaction Networks , 2009, RECOMB.

[182]  Maxime Crochemore,et al.  Finding the median of three permutations under the Kendall-tau distance , 2009 .

[183]  R. Möhring.  Algorithmic graph theory and perfect graphs , 1986 .

[184]  Guillaume Fertin,et al.  Fixed-parameter algorithms for protein similarity search under mRNA structure constraints , 2005, J. Discrete Algorithms.

[185]  Michael R. Fellows,et al.  Sharp Tractability Borderlines for Finding Connected Motifs in Vertex-Colored Graphs , 2007, ICALP.

[186]  Guillaume Blin,et al.  GraMoFoNe: a Cytoscape Plugin for Querying Motifs without Topology in Protein-Protein Interactions Networks , 2010, BICoB.

[187]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[188]  Hao Yuan,et al.  Improved algorithms for largest cardinality 2-interval pattern problem , 2005, J. Comb. Optim..

[189]  Maxime Crochemore,et al.  Algorithms on strings , 2007 .

[190]  Vasek Chvátal,et al.  A Greedy Heuristic for the Set-Covering Problem , 1979, Math. Oper. Res..

[191]  Rolf Backofen,et al.  Computational Design of New and Recombinant Selenoproteins , 2004, CPM.

[192]  Derek G. Corneil,et al.  Complexity of finding embeddings in a k -tree , 1987 .

[193]  T. Ideker,et al.  Modeling cellular machinery through biological network comparison , 2006, Nature Biotechnology.

[194]  Guillaume Fertin,et al.  Comparing Genomes with Duplications: A Computational Complexity Point of View , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[195]  Serafim Batzoglou,et al.  A computational model for RNA multiple structural alignment , 2004, Theor. Comput. Sci..

[196]  Niklas Sörensson,et al.  Translating Pseudo-Boolean Constraints into SAT , 2006, J. Satisf. Boolean Model. Comput..

[197]  Rolf Niedermeier,et al.  Towards Optimally Solving the LONGEST COMMON SUBSEQUENCE Problem for Sequences with Nested Arc Annotations in Linear Time , 2002, CPM.

[198]  Roded Sharan,et al.  Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data , 2004, J. Comput. Biol..

[199]  Timothy J. Purcell.  Sorting and searching , 2005, SIGGRAPH Courses.

[200]  Guillaume Fertin,et al.  On Finding Small 2-Generating Sets , 2009, COCOON.

[201]  Kaizhong Zhang,et al.  Simple Fast Algorithms for the Editing Distance Between Trees and Related Problems , 1989, SIAM J. Comput..

[202]  W. F. Lunnon.  A postage stamp problem , 1969, Comput. J..

[203]  Miklós Bóna,et al.  Combinatorics of permutations , 2022, SIGA.

[204]  Siu-Ming Yiu,et al.  Predicting RNA secondary structures with arbitrary pseudoknots by maximizing the number of stacking pairs , 2001, Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001).

[205]  Guillaume Fertin,et al.  Comparing RNA Structures: Towards an Intermediate Model Between the Editand the LapcsProblems , 2007, BSB.

[206]  Michael R. Fellows,et al.  Parameterized complexity analysis in computational biology , 1995, Comput. Appl. Biosci..

[207]  V. Popov.  The Longest Common Subsequence Problem for Arc-Annotated Sequences , 2011 .

[208]  Alexandr V. Kostochka,et al.  Covering and coloring polygon-circle graphs , 1997, Discret. Math..

[209]  G. Szekeres,et al.  A combinatorial problem in geometry , 2009 .

[210]  László Patthy,et al.  Exons – original building blocks of proteins? , 1991, BioEssays : news and reviews in molecular, cellular and developmental biology.

[211]  Ting Chen,et al.  An approximation algorithm for haplotype inference by maximum parsimony , 2005, SAC '05.

[212]  Romeo Rizzi,et al.  Approximation of RNA multiple structural alignment , 2006, J. Discrete Algorithms.

[213]  Zdenek Ryjácek,et al.  Claw-free graphs - A survey , 1997, Discret. Math..

[214]  Ran Raz,et al.  A sub-constant error-probability low-degree test, and a sub-constant error-probability PCP characterization of NP , 1997, STOC '97.

[215]  Hendrik W. Lenstra,et al.  Integer Programming with a Fixed Number of Variables , 1983, Math. Oper. Res..

[216]  Roded Sharan,et al.  QNet: A Tool for Querying Protein Interaction Networks , 2007, RECOMB.

[217]  Gad M. Landau,et al.  Approximating the 2-interval pattern problem , 2005, Theor. Comput. Sci..

[218]  Stéphan Thomassé.  A quadratic kernel for feedback vertex set , 2009, SODA.

[219]  Jiong Guo,et al.  Exact Algorithms for the Longest Common Subsequence Problem for Arc-Annotated Sequences , 2002 .

[220]  Carlos Eduardo Ferreira,et al.  Repetition-free longest common subsequence , 2008, Electron. Notes Discret. Math..

[221]  D. Bryant.  The Complexity of Calculating Exemplar Distances , 2000 .

[222]  Stefan Arnborg,et al.  Linear time algorithms for NP-hard problems restricted to partial k-trees , 1989, Discret. Appl. Math..

[223]  Dorit S. Hochbaum,et al.  Approximation Algorithms for the Set Covering and Vertex Cover Problems , 1982, SIAM J. Comput..

[224]  R. Karp,et al.  Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[225]  Dirk Bongartz.  Some Notes on the Complexity of Protein Similarity Search under mRNA Structure Constraints , 2004, SOFSEM.

[226]  Noga Alon,et al.  The Probabilistic Method , 2015, Fundamentals of Ramsey Theory.

[227]  Bin Fu,et al.  The Approximability of the Exemplar Breakpoint Distance Problem , 2006, AAIM.

[228]  Vijay V. Vazirani,et al.  Approximation Algorithms , 2001, Springer Berlin Heidelberg.

[229]  Grzegorz Rozenberg,et al.  The mathematical theory of L systems , 1980 .

[230]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[231]  Stéphane Vialette,et al.  MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states , 2004, BMC Bioinformatics.

[232]  David S. Johnson,et al.  Some Simplified NP-Complete Graph Problems , 1976, Theor. Comput. Sci..