Title of thesis: GENOME ASSEMBLY TECHNIQUES

[1]  David R. Kelley,et al.  A whole-genome assembly of the domestic cow, Bos taurus , 2009, Genome Biology.

[2]  S. Kurtz,et al.  A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes , 2008, BMC Genomics.

[3]  Yufeng Shen,et al.  Bos taurus genome assembly , 2009, BMC Genomics.

[4]  C. Nusbaum,et al.  ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.

[5]  P. Pevzner,et al.  An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[6]  D. Matula k-Components, Clusters and Slicings in Graphs , 1972 .

[7]  Mihai Pop,et al.  Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..

[8]  Stephen J O'Brien,et al.  Every genome sequence needs a good map. , 2009, Genome research.

[9]  Albert J. Vilella,et al.  Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis , 2010, PLoS biology.

[10]  Michel Chein,et al.  Minimally 2-edge connected graphs , 1979, J. Graph Theory.

[11]  Carsten Thomassen,et al.  Nonseparating cycles in K-Connected graphs , 1981, J. Graph Theory.

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

[13]  Jerzy Tiuryn,et al.  Identification of functional modules from conserved ancestral protein-protein interactions , 2007, ISMB/ECCB.

[14]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[15]  Xiuwei Zhang,et al.  Refining transcriptional regulatory networks using network evolutionary models and gene histories , 2010, Algorithms for Molecular Biology.

[16]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[17]  E. Mauceli,et al.  Whole-genome sequence assembly for mammalian genomes: Arachne 2. , 2003, Genome research.

[18]  E. Ziv,et al.  Inferring network mechanisms: the Drosophila melanogaster protein interaction network. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[19]  J. Schwartz,et al.  Annotating large genomes with exact word matches. , 2003, Genome research.

[20]  Elhanan Borenstein,et al.  Topological Signatures of Species Interactions in Metabolic Networks , 2009, J. Comput. Biol..

[21]  G. Weinstock,et al.  The Atlas genome assembly system. , 2004, Genome research.

[22]  R. Solé,et al.  Evolving protein interaction networks through gene duplication. , 2003, Journal of theoretical biology.

[23]  Dana Randall Efficient Generation of Random Nonsingular Matrices , 1993, Random Struct. Algorithms.

[24]  Bonnie Berger,et al.  Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology , 2007, RECOMB.

[25]  Michael Roberts,et al.  A Preprocessor for Shotgun Assembly of Large Genomes , 2004, J. Comput. Biol..

[26]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[27]  Jotun Hein,et al.  A stochastic model for the evolution of metabolic networks with neighbor dependence , 2009, Bioinform..

[28]  Timothy P. L. Smith,et al.  Development and Characterization of a High Density SNP Genotyping Assay for Cattle , 2009, PloS one.

[29]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[30]  Lior Pachter,et al.  An introduction to reconstructing ancestral genomes , 2006, q-bio/0612046.

[31]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[32]  E. Steinitz,et al.  Vorlesungen über die Theorie der Polyeder unter Einfluss der Elemente der Topologie , 1934 .

[33]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[34]  E. Myers,et al.  Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence , 2002, Genome Biology.

[35]  Carsten Thomassen,et al.  Non-separating induced cycles in graphs , 1981, J. Comb. Theory, Ser. B.

[36]  Jonathan L. Gross,et al.  Graph Theory and Its Applications, Second Edition (Discrete Mathematics and Its Applications) , 2005 .

[37]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Sergei Maslov,et al.  Computational architecture of the yeast regulatory network , 2005, Physical biology.

[39]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[40]  J. Gross,et al.  Graph Theory and Its Applications , 1998 .

[41]  S. Teichmann,et al.  Gene regulatory network growth by duplication , 2004, Nature Genetics.

[42]  David R. Kelley,et al.  Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.

[43]  M. Feldman,et al.  Large-scale reconstruction and phylogenetic analysis of metabolic environments , 2008, Proceedings of the National Academy of Sciences.

[44]  Emmanuel D Levy,et al.  Evolution and dynamics of protein interactions and networks. , 2008, Current opinion in structural biology.

[45]  Alexander J. Stewart,et al.  Degree dependence in rates of transcription factor evolution explains the unusual structure of transcription networks , 2009, Proceedings of the Royal Society B: Biological Sciences.

[46]  Carl Kingsford,et al.  Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions , 2010, PLoS Comput. Biol..

[47]  Giorgio Valle,et al.  BIOINFORMATICS ORIGINAL PAPER Sequence analysis RAP: a new computer program for de novo identification of repeated sequences in whole genomes , 2004 .

[48]  B. Birren,et al.  Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[49]  D V Foster,et al.  Network growth models and genetic regulatory networks. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[50]  M. Schatz,et al.  Assembly of large genomes using second-generation sequencing. , 2010, Genome research.

[51]  R. Don Lick Critically and minimally n-connected graphs , 1969 .

[52]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[53]  Alex Zelikovsky,et al.  Improved Steiner tree approximation in graphs , 2000, SODA '00.

[54]  A. Wagner,et al.  Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Antal F. Novak,et al.  networks Græmlin : General and robust alignment of multiple large interaction data , 2006 .

[56]  Hui Gao,et al.  Almost wait-free resizable hashtables , 2004, 18th International Parallel and Distributed Processing Symposium, 2004. Proceedings..

[57]  B. Bollobás,et al.  Extremal Graph Theory , 2013 .

[58]  Sergey Koren,et al.  Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..

[59]  Xiuwei Zhang,et al.  Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach , 2008, WABI.

[60]  Matthias Kriesell,et al.  A constructive characterization of 3-connected triangle-free graphs , 2007, J. Comb. Theory, Ser. B.

[61]  Steven J. M. Jones,et al.  A physical map of the bovine genome , 2007, Genome Biology.

[62]  Sarah A Teichmann,et al.  Evolution of protein complexes by duplication of homomeric interactions , 2007, Genome Biology.

[63]  Timothy L. Harris,et al.  Non-blocking Hashtables with Open Addressing , 2005, DISC.

[64]  Christian A. Grove,et al.  A Gene-Centered C. elegans Protein-DNA Interaction Network , 2006, Cell.

[65]  I. Ispolatov,et al.  Duplication-divergence model of protein interaction network. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[66]  David Barnette A construction of 3-connected graphs , 1994 .

[67]  Anat Kreimer,et al.  The evolution of modularity in bacterial metabolic networks , 2008, Proceedings of the National Academy of Sciences.

[68]  Debra Goldberg,et al.  Reverse Engineering the Evolution of Protein Interaction Networks , 2008, Pacific Symposium on Biocomputing.

[69]  S. Salzberg,et al.  Hierarchical scaffolding with Bambus. , 2003, Genome research.

[70]  Nir Shavit,et al.  An optimistic approach to lock-free FIFO queues , 2004, Distributed Computing.

[71]  Michael Y. Galperin,et al.  Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes , 2003, BMC Evolutionary Biology.

[72]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[73]  Richard M. Karp,et al.  Reducibility Among Combinatorial Problems , 1972, 50 Years of Integer Programming.

[74]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[75]  Maged M. Michael,et al.  Simple, fast, and practical non-blocking and blocking concurrent queue algorithms , 1996, PODC '96.

[76]  Suzanne S. Sindi,et al.  Duplication count distributions in DNA sequences. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[77]  Arnaud Lefebvre,et al.  FORRepeats: detects repeats on entire chromosomes and between genomes , 2003, Bioinform..

[78]  Brendan D. McKay,et al.  Hamiltonian cycles in cubic 3-connected bipartite planar graphs , 1985, J. Comb. Theory, Ser. B.

[79]  M. Plummer On minimal blocks , 1968 .

[80]  Katsumi Inoue,et al.  Nonseparating Induced Cycles Consisting of Contractible Edges in k-Connected Graphs , 2002, Electron. Notes Discret. Math..

[81]  Maged M. Michael,et al.  High performance dynamic lock-free hash tables and list-based sets , 2002, SPAA '02.

[82]  S. Kauffman,et al.  Robustness and evolvability in genetic regulatory networks. , 2007, Journal of theoretical biology.

[83]  Sanjay Ghemawat,et al.  MapReduce: Simplified Data Processing on Large Clusters , 2004, OSDI.

[84]  Magnus Rattray,et al.  Reconstruction of ancestral protein interaction networks for the bZIP transcription factors , 2007, Proceedings of the National Academy of Sciences.

[85]  Fan Chung Graham,et al.  Duplication Models for Biological Networks , 2002, J. Comput. Biol..

[86]  Julio Collado-Vides,et al.  RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation , 2007, Nucleic Acids Res..

[87]  Dmitrij Frishman,et al.  The MIPS mammalian protein?Cprotein interaction database , 2005, Bioinform..

[88]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[89]  Nir Shavit,et al.  Split-ordered lists: Lock-free extensible hash tables , 2006, JACM.

[90]  Eugene W. Myers,et al.  Combinatorial algorithms for DNA sequence assembly , 1995, Algorithmica.

[91]  Reinhard Diestel,et al.  Graph Theory , 1997 .

[92]  Steven Salzberg,et al.  Beware of mis-assembled genomes , 2005, Bioinform..

[93]  S. E. Dreyfus,et al.  The steiner problem in graphs , 1971, Networks.

[94]  Peter P. Chen,et al.  Generating r-regular graphs , 2003, Discret. Appl. Math..

[95]  R. Halin A theorem on n-connected graphs , 1969 .

[96]  A. Gnirke,et al.  High-quality draft assemblies of mammalian genomes from massively parallel sequence data , 2010, Proceedings of the National Academy of Sciences.