Algorithms in Bioinformatics - 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings

[1]  Giovanna Rosone,et al.  Lightweight algorithms for constructing and inverting the BWT of string collections , 2013, Theor. Comput. Sci..

[2]  Daniel G. Brown,et al.  Towards a practical O(nlogn) phylogeny algorithm , 2012, Algorithms for Molecular Biology.

[3]  Siu-Ming Yiu,et al.  MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample , 2012, Bioinform..

[4]  Charles Semple,et al.  Bounding the maximum size of a minimal definitive set of quartets , 2012, Inf. Process. Lett..

[5]  Gonzalo Navarro,et al.  Fast, Small, Simple Rank/Select on Bitmaps , 2012, SEA.

[6]  Manolis Kellis,et al.  Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss , 2012, Bioinform..

[7]  David Fernández-Baca,et al.  Extracting conflict-free information from multi-labeled trees , 2012, Algorithms for Molecular Biology.

[8]  T. Shibuya,et al.  Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes , 2012, BMC Research Notes.

[9]  Jin-Kao Hao,et al.  Pattern-driven neighborhood search for biclustering of microarray data , 2012, BMC Bioinformatics.

[10]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[11]  Roded Sharan,et al.  Comparative analysis of protein networks , 2012, Commun. ACM.

[12]  Giovanna Rosone,et al.  Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform , 2012, Bioinform..

[13]  Mihai Pop,et al.  Exploiting sparseness in de novo genome assembly , 2012, BMC Bioinformatics.

[14]  Eran Halperin,et al.  MGMR: leveraging RNA-Seq population data to optimize expression estimation , 2012, BMC Bioinformatics.

[15]  Manolis Kellis,et al.  Unified modeling of gene duplication, loss, and coalescence using a locus tree. , 2012, Genome research.

[16]  Simon J. Puglisi,et al.  Practical Efficient String Mining , 2012, IEEE Transactions on Knowledge and Data Engineering.

[17]  M. Baker.  De novo genome assembly: what every biologist should know , 2012, Nature Methods.

[18]  Rayan Chikhi,et al.  Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer , 2012, BMC Bioinformatics.

[19]  Tandy Warnow,et al.  SuperFine: fast and accurate supertree estimation. , 2012, Systematic biology.

[20]  G. Getz,et al.  High-order chromatin architecture shapes the landscape of chromosomal alterations in cancer , 2012 .

[21]  R. Durbin,et al.  Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.

[22]  Zhi-Zhong Chen,et al.  Algorithms for Reticulate Networks of Multiple Phylogenetic Trees , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[23]  A. Tanay,et al.  Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome , 2012, Cell.

[24]  Siu-Ming Yiu,et al.  MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species , 2012, J. Comput. Biol..

[25]  N. Carter,et al.  Estimation of rearrangement phylogeny for cancer genomes. , 2012, Genome research.

[26]  E. Anderson,et al.  A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem , 2012, Molecular ecology resources.

[27]  Reza Kalhor,et al.  Genome architectures revealed by tethered chromosome conformation capture and population-based modeling , 2011, Nature Biotechnology.

[28]  Leo van Iersel,et al.  Cycle Killer...Qu'est-ce que c'est? On the Comparative Approximability of Hybridization Number and Directed Feedback Vertex Set , 2011, SIAM J. Discret. Math..

[29]  Arend Hintze,et al.  Scaling metagenome sequence assembly with probabilistic de Bruijn graphs , 2011, Proceedings of the National Academy of Sciences.

[30]  James B. Brown,et al.  Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation , 2011, Proceedings of the National Academy of Sciences.

[31]  S. De,et al.  DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes , 2011, Nature Biotechnology.

[32]  E. Eichler,et al.  Simultaneous structural variation discovery among multiple paired-end sequenced genomes. , 2011, Genome research.

[33]  Vipin Kumar,et al.  Discovery of error-tolerant biclusters from noisy gene expression data , 2011, BMC Bioinformatics.

[34]  G. McVean,et al.  De novo assembly and genotyping of variants using colored de Bruijn graphs , 2011, Nature Genetics.

[35]  M. David,et al.  Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw , 2011, Nature.

[36]  Guillaume Fertin,et al.  Pancake Flipping Is Hard , 2011, MFCS.

[37]  Mathieu Lupien,et al.  PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer , 2011, PLoS genetics.

[38]  A. Tanay,et al.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture , 2011, Nature Genetics.

[39]  Anastassis Perrakis,et al.  Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank , 2011, Bioinform..

[40]  Mathieu Blanchette,et al.  Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling , 2011, BMC Bioinformatics.

[41]  Enno Ohlebusch,et al.  Computing the longest common prefix array based on the Burrows-Wheeler transform , 2011, J. Discrete Algorithms.

[42]  R. Guan,et al.  Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica , 2011, BMC Genomics.

[43]  Hosein Mohimani,et al.  Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases. , 2011, Journal of proteome research.

[44]  Jens Stoye,et al.  Genomic distance under gene substitutions , 2011, BMC Bioinformatics.

[45]  Jean-Stéphane Varré,et al.  Genome dedoubling by DCJ and reversal , 2011, BMC Bioinformatics.

[46]  Jens Stoye,et al.  On the weight of indels in genomic distances , 2011, BMC Bioinformatics.

[47]  P. Pevzner,et al.  Efficient de novo assembly of single-cell bacterial genomes from short-read data sets , 2011, Nature Biotechnology.

[48]  Simone Linz,et al.  Quantifying Hybridization in Realistic Time , 2011, J. Comput. Biol..

[49]  Ho Sung Kang,et al.  Homeobox gene Dlx-2 is implicated in metabolic stress-induced necrosis , 2011, Molecular Cancer.

[50]  Jens Stoye,et al.  Double Cut and Join with Insertions and Deletions , 2011, J. Comput. Biol..

[51]  L. Landweber,et al.  RNA-Mediated Epigenetic Programming of Genome Rearrangements. , 2011, Annual review of genomics and human genetics.

[52]  Jens Stoye,et al.  Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation , 2011, J. Comput. Biol..

[53]  Gad Getz,et al.  High-order chromatin architecture determines the landscape of chromosomal alterations in cancer , 2011, Nature Biotechnology.

[54]  Tao Jiang,et al.  Separating metagenomic short reads into genomes via clustering , 2011, Algorithms for Molecular Biology.

[55]  Bonnie Kirkpatrick,et al.  Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values , 2011, WABI.

[56]  Dominique Lavenier,et al.  Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph , 2011, WABI.

[57]  Dan Gusfield,et al.  Constructing perfect phylogenies and proper triangulations for three-state characters , 2011, Algorithms for Molecular Biology.

[58]  Nadia El-Mabrouk,et al.  Removing Noise from Gene Trees , 2011, WABI.

[59]  Vincent Berry,et al.  Models, algorithms and programs for phylogeny reconciliation , 2011, Briefings Bioinform..

[60]  Hosein Mohimani,et al.  Sequencing cyclic peptides by multistage mass spectrometry , 2011, Proteomics.

[61]  João Meidanis,et al.  SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[62]  Pierre Baldi,et al.  Tree and Hashing Data Structures to Speed up Chemical Searches: Analysis and Experiments , 2011, Molecular informatics.

[63]  Isaac Y. Ho,et al.  Meraculous: De Novo Genome Assembly with Short Paired-End Reads , 2011, PloS one.

[64]  Huanming Yang,et al.  Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly , 2011, Nature Biotechnology.

[65]  Raj Acharya,et al.  A two-way multi-dimensional mixture model for clustering metagenomic sequences , 2011, BCB '11.

[66]  Dan Gusfield,et al.  Extensions and Improvements to the Chordal Graph Approach to the Multistate Perfect Phylogeny Problem , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[67]  Hyungwon Choi,et al.  MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. , 2011, Journal of proteome research.

[68]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[69]  Katharina T. Huber,et al.  Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[70]  Marc A. Martí-Renom,et al.  Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization , 2011, PLoS Comput. Biol..

[71]  Kang Ning,et al.  Saliva microbiomes distinguish caries-active from healthy human populations , 2011, The ISME Journal.

[72]  Robert Giegerich,et al.  Forest Alignment with Affine Gaps and Anchors , 2011, CPM.

[73]  Giovanna Rosone,et al.  Lightweight BWT Construction for Very Large String Collections , 2011, CPM.

[74]  Siu-Ming Yiu,et al.  Meta-IDBA: a de Novo assembler for metagenomic data , 2011, Bioinform..

[75]  David Fernández-Baca,et al.  A simple characterization of the minimal obstruction sets for three-state perfect phylogenies , 2011, Appl. Math. Lett..

[76]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[77]  Oliver Eulenstein,et al.  Algorithms for Rapid Error Correction for the Gene Duplication Problem , 2011, ISBRA.

[78]  V. Barbe,et al.  Structural and Content Diversity of Mitochondrial Genome in Beet: A Comparative Genomic Analysis , 2011, Genome biology and evolution.

[79]  Michel Habib,et al.  On a Conjecture about Compatibility of Multi-states Characters , 2011, WABI.

[80]  Zasha Weinberg,et al.  Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations , 2011, PLoS Comput. Biol..

[81]  Fedor V. Fomin,et al.  Subexponential parameterized algorithm for minimum fill-in , 2011, SODA.

[82]  Shamil R. Sunyaev,et al.  Assigning spectrum-specific P-values to protein identifications by mass spectrometry , 2011, Bioinform..

[83]  Pavel A. Pevzner,et al.  Multiplex De Novo Sequencing of Peptide Antibiotics , 2011, RECOMB.

[84]  Tao Jiang,et al.  IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly - (Extended Abstract) , 2011, RECOMB.

[85]  Wing-Kin Sung,et al.  Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences , 2011, RECOMB.

[86]  Dong Chen,et al.  JunD and JunB integrate prostaglandin E2 activation of breast cancer-associated proximal aromatase promoters. , 2011, Molecular endocrinology.

[87]  J. Vederas,et al.  [Drug discovery and natural products: end of era or an endless frontier?]. , 2011, Biomeditsinskaia khimiia.

[88]  Sorin Istrail,et al.  The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS , 2010, RECOMB.

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

[90]  Michael T. Hallett,et al.  Simultaneous Identification of Duplications and Lateral Gene Transfers , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[91]  Vincent Berry,et al.  Building species trees from larger parts of phylogenomic databases , 2011, Inf. Comput..

[92]  Toni Gabaldón,et al.  TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees , 2011, Nucleic acids research.

[93]  S. Tringe,et al.  Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen , 2011, Science.

[94]  Enno Ohlebusch,et al.  Fast and Lightweight LCP-Array Construction Algorithms , 2011, ALENEX.

[95]  Johannes Fischer,et al.  Inducing the LCP-Array , 2011, WADS.

[96]  R. Holt,et al.  Targeted Assembly of Short Sequence Reads , 2011, PloS one.

[97]  Ran Libeskind-Hadas,et al.  The Cophylogeny Reconstruction Problem Is NP-Complete , 2011, J. Comput. Biol..

[98]  Lawrence A. David,et al.  Rapid evolutionary innovation during an Archaean genetic expansion , 2011, Nature.

[99]  Dale Schuurmans,et al.  Linear Coherent Bi-cluster Discovery via Beam Detection and Sample Set Clustering , 2010, COCOA.

[100]  Steven Salzberg,et al.  Mugsy: fast multiple alignment of closely related whole genomes , 2010, Bioinform..

[101]  Jijun Tang,et al.  Phylogenetic reconstruction with gene rearrangements and gene losses , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

[103]  D. Huson,et al.  A Survey of Combinatorial Methods for Phylogenetic Networks , 2010, Genome biology and evolution.

[104]  Zhi-Zhong Chen,et al.  HybridNET: a tool for constructing hybridization networks , 2010, Bioinform..

[105]  Steven J. M. Jones,et al.  De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.

[106]  Hideki Tanizawa,et al.  Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation , 2010, Nucleic acids research.

[107]  Monzoorul Haque Mohammed,et al.  DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences , 2010, BMC Bioinformatics.

[108]  Marie-France Sagot,et al.  Identifying SNPs without a Reference Genome by Comparing Raw Reads , 2010, SPIRE.

[109]  Enno Ohlebusch,et al.  Computing Matching Statistics and Maximal Exact Matches on Compressed Full-Text Indexes , 2010, SPIRE.

[110]  A. Nesvizhskii.  A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. , 2010, Journal of proteomics.

[111]  Vincent Berry,et al.  An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers , 2010, RECOMB-CG.

[112]  Jens Stoye,et al.  The Solution Space of Sorting by DCJ , 2010, J. Comput. Biol..

[113]  P. Pevzner,et al.  The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search* , 2010, Molecular & Cellular Proteomics.

[114]  Daniel G. Brown,et al.  Discovering Kinship through Small Subsets , 2010, WABI.

[115]  Jens Stoye,et al.  Genomic Distance with DCJ and Indels , 2010, WABI.

[116]  Derek Y. Chiang,et al.  MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.

[117]  Dominique Lavenier,et al.  GASSST: global alignment short sequence search tool , 2010, Bioinform..

[118]  Pierre Baldi,et al.  Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors , 2010, J. Chem. Inf. Model..

[119]  Thomas C. Conway,et al.  Succinct data structures for assembling large genomes , 2010, Bioinform..

[120]  Karin Jirström,et al.  Homeobox transcription factor muscle segment homeobox 2 (Msx2) correlates with good prognosis in breast cancer patients and induces apoptosis in vitro , 2010, Breast Cancer Research.

[121]  See-Kiong Ng,et al.  An Indexing Scheme for Fast and Accurate Chemical Fingerprint Database Searching , 2010, SSDBM.

[122]  N. Perna,et al.  progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement , 2010, PloS one.

[123]  Jared T. Simpson,et al.  Efficient construction of an assembly string graph using the FM-index , 2010, Bioinform..

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

[125]  Pinar Heggernes,et al.  A Parameterized Algorithm for Chordal Sandwich , 2010, CIAC.

[126]  Zhaohui S. Qin,et al.  A Global Protein Kinase and Phosphatase Interaction Network in Yeast , 2010, Science.

[127]  Norbert Zeh,et al.  Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments , 2010, SEA.

[128]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[129]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.

[130]  Yu-Wei Wu,et al.  A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples , 2010, RECOMB.

[131]  David Fernández-Baca,et al.  Graph triangulations and the compatibility of unrooted phylogenetic trees , 2010, Appl. Math. Lett..

[132]  D. Auboeuf,et al.  NFAT3 transcription factor inhibits breast cancer cell motility by targeting the Lipocalin 2 gene , 2010, Oncogene.

[133]  M. Berriman,et al.  Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps , 2010, Genome Biology.

[134]  Juan M. Vaquerizas,et al.  Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets , 2010, Nucleic acids research.

[135]  A. Darracq,et al.  A scenario of mitochondrial genome evolution in maize based on rearrangement events , 2010, BMC Genomics.

[136]  Y. Xing,et al.  Detection of splice junctions from paired-end RNA-seq data by SpliceMap , 2010, Nucleic acids research.

[137]  W. Art Chaovalitwongse,et al.  New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers , 2010, INFORMS J. Comput..

[138]  Martine Labbé,et al.  A Class Representative Model for Pure Parsimony Haplotyping , 2010, INFORMS J. Comput..

[139]  William Stafford Noble,et al.  A Three-Dimensional Model of the Yeast Genome , 2010, Nature.

[140]  Alain Denise,et al.  Alignments of RNA Structures , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[141]  Jonathan W. Essex,et al.  Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments , 2010, J. Chem. Inf. Model..

[142]  B. Letcher,et al.  PedAgree: software to quantify error and assess accuracy and congruence for genetically reconstructed pedigree relationships , 2010, Conservation Genetics Resources.

[143]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[144]  David Fernández-Baca,et al.  Robinson-Foulds Supertrees , 2010, Algorithms for Molecular Biology.

[145]  Ran Libeskind-Hadas,et al.  Jane: a new tool for the cophylogeny reconstruction problem , 2010, Algorithms for Molecular Biology.

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

[147]  Guoliang Li,et al.  Analyzing the Fitch Method for Reconstructing Ancestral States on Ultrametric Phylogenetic Trees , 2010, Bulletin of mathematical biology.

[148]  Martin Bader,et al.  Genome rearrangements with duplications , 2010, BMC Bioinformatics.

[149]  Christophe Zimmer,et al.  Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres , 2010, Proceedings of the National Academy of Sciences.

[150]  Mihai Pop,et al.  Assembly complexity of prokaryotic genomes using short reads , 2010, BMC Bioinformatics.

[151]  Christian N. S. Pedersen,et al.  A tree-based method for the rapid screening of chemical fingerprints , 2009, Algorithms for Molecular Biology.

[152]  Roded Sharan,et al.  Network-Free Inference of Knockout Effects in Yeast , 2010, PLoS Comput. Biol..

[153]  Daniel R. Zerbino,et al.  Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler , 2009, PloS one.

[154]  M. Bernt,et al.  Gene order rearrangement methods for the reconstruction of phylogeny , 2009 .

[155]  Roland L. Dunbrack,et al.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .

[156]  Siu-Ming Yiu,et al.  Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers , 2009, BMC Bioinformatics.

[157]  Inanç Birol,et al.  De novo transcriptome assembly with ABySS , 2009, Bioinform..

[158]  Fabrizio Luccio,et al.  Compressing and indexing labeled trees, with applications , 2009, JACM.

[159]  Richard Friedberg,et al.  DCJ Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications , 2009, J. Comput. Biol..

[160]  Ujjwal Maulik,et al.  A Novel Coherence Measure for Discovering Scaling Biclusters from Gene Expression Data , 2009, J. Bioinform. Comput. Biol..

[161]  A. Gnirke,et al.  ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads , 2009, Genome Biology.

[162]  Travis Gagie,et al.  Lightweight Data Indexing and Compression in External Memory , 2009, Algorithmica.

[163]  Vincent Moulton,et al.  Inferring polyploid phylogenies from multiply-labeled gene trees , 2009, BMC Evolutionary Biology.

[164]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[165]  S. Salzberg,et al.  Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models , 2009, Nature Methods.

[166]  Pierre Baldi,et al.  An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases , 2009, J. Chem. Inf. Model..

[167]  Nuno Bandeira,et al.  Dereplication and De Novo Sequencing of Nonribosomal Peptides , 2009, Nature Methods.

[168]  Mihai Pop,et al.  Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing , 2009, J. Comput. Biol..

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

[170]  Snehit Prabhu,et al.  Overlapping Pools for High Throughput Targeted Resequencing , 2009, RECOMB.

[171]  B Dasgupta,et al.  KINALYZER, a computer program for reconstructing sibling groups , 2009, Molecular ecology resources.

[172]  Monzoorul Haque Mohammed,et al.  SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences , 2009, Bioinform..

[173]  Serita M. Nelesen,et al.  Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees , 2009, Science.

[174]  Matthias Bernt,et al.  Finding all sorting tandem duplication random loss operations , 2009, J. Discrete Algorithms.

[175]  Juha Kärkkäinen,et al.  Permuted Longest-Common-Prefix Array , 2009, CPM.

[176]  Dale Schuurmans,et al.  Linear Coherent Bi-cluster Discovery via Line Detection and Sample Majority Voting , 2009, COCOA.

[177]  Guy Perrière,et al.  Databases of homologous gene families for comparative genomics , 2009, BMC Bioinformatics.

[178]  Ying Xu,et al.  QUBIC: a qualitative biclustering algorithm for analyses of gene expression data , 2009, Nucleic acids research.

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

[180]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[181]  Dan Gusfield,et al.  The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory , 2009, RECOMB.

[182]  Nadia El-Mabrouk,et al.  New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees , 2009, RECOMB.

[183]  Gerardo Rubino,et al.  Rare Event Simulation using Monte Carlo Methods , 2009 .

[184]  Dan Gusfield,et al.  Generalizing the Splits Equivalence Theorem and Four Gamete Condition: Perfect Phylogeny on Three-State Characters , 2009, SIAM J. Discret. Math..

[185]  Kunihiko Sadakane,et al.  Fully Functional Static and Dynamic Succinct Trees , 2009, TALG.

[186]  David Sankoff,et al.  Multichromosomal median and halving problems under different genomic distances , 2009, BMC Bioinformatics.

[187]  Vladimir Kolmogorov,et al.  Blossom V: a new implementation of a minimum cost perfect matching algorithm , 2009, Math. Program. Comput..

[188]  Adam P. Arkin,et al.  FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.

[189]  J. Lagergren,et al.  Simultaneous Bayesian gene tree reconstruction and reconciliation analysis , 2009, Proceedings of the National Academy of Sciences.

[190]  Bengt Sennblad,et al.  The gene evolution model and computing its associated probabilities , 2009, JACM.

[191]  David Sankoff,et al.  Genome Halving with Double Cut and Join , 2009, APBC.

[192]  S. Salzberg,et al.  TopHat: discovering splice junctions with RNA-Seq , 2009, Bioinform..

[193]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[194]  Yun Yen,et al.  Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer , 2009, Breast Cancer Research.

[195]  B. Browning,et al.  A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. , 2009, American journal of human genetics.

[196]  Naryttza N. Diaz,et al.  TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach , 2009, BMC Bioinformatics.

[197]  Ora Schueler-Furman,et al.  Rapid Sampling of Molecular Motions with Prior Information Constraints , 2009, PLoS Comput. Biol..

[198]  Marni Mishna,et al.  Average-Case Analysis of Perfect Sorting by Reversals , 2009, Discret. Math. Algorithms Appl..

[199]  Dahlia R. Weiss,et al.  Can morphing methods predict intermediate structures? , 2009, Journal of molecular biology.

[200]  N. Go,et al.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. , 2009 .

[201]  Ran Libeskind-Hadas,et al.  On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem , 2009, J. Comput. Biol..

[202]  Simon J. Puglisi,et al.  Space-Time Tradeoffs for Longest-Common-Prefix Array Computation , 2008, ISAAC.

[203]  Johannes Fischer,et al.  Space Efficient String Mining under Frequency Constraints , 2008, 2008 Eighth IEEE International Conference on Data Mining.

[204]  Shuai Cheng Li,et al.  Fragment‐HMM: A new approach to protein structure prediction , 2008, Protein science : a publication of the Protein Society.

[205]  Peer Bork,et al.  Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes , 2008, Journal of bacteriology.

[206]  Daniel H. Huson,et al.  MetaSim—A Sequencing Simulator for Genomics and Metagenomics , 2008, PloS one.

[207]  Sarah J. Bourlat,et al.  Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom. , 2008, Molecular phylogenetics and evolution.

[208]  David Haussler,et al.  The infinite sites model of genome evolution , 2008, Proceedings of the National Academy of Sciences.

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