Le cluster Algorithmes - Logiciel
001D35 (2014) | Lilian Janin [Royaume-Uni] ; Ole Schulz-Trieglaff [Royaume-Uni] ; Anthony J. Cox [Royaume-Uni] | BEETL-fastq: a searchable compressed archive for DNA reads. |
000A92 (2018) | Swati C. Manekar [Inde] ; Shailesh R. Sathe [Inde] | A benchmark study of k-mer counting methods for high-throughput sequencing |
000C32 (2017) | Roman V. Briskine ; Kentaro K. Shimizu [Japon] | Positional bias in variant calls against draft reference assemblies |
000D40 (2017) | David Pellow ; Darya Filippova ; Carl Kingsford | Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters |
001186 (2016) | Abdullah-Al Mamun [États-Unis] ; Soumitra Pal [États-Unis] ; Sanguthevar Rajasekaran [États-Unis] | KCMBT: a k-mer Counter based on Multiple Burst Trees. |
001583 (2015) | Ramin Karimi ; Andras Hajdu | SRIdent: A novel pipeline for real-time identification of species from high-throughput sequencing reads in Metagenomics and clinical diagnostic assays. |
001605 (2015) | Guillaume Marçais ; James A. Yorke ; Aleksey Zimin | QuorUM: An Error Corrector for Illumina Reads |
002229 (2012) | Berat Z. Haznedaroglu [États-Unis] ; Darryl Reeves [États-Unis] ; Hamid Rismani-Yazdi [États-Unis] ; Jordan Peccia [États-Unis] | Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms |
002256 (2012) | Chengxi Ye [États-Unis] ; Zhanshan Sam Ma ; Charles H. Cannon [États-Unis] ; Mihai Pop [États-Unis] ; Douglas W. Yu | Exploiting sparseness in de novo genome assembly |
002485 (2011) | Xiaotu Ma ; Ashwinikumar Kulkarni ; Zhihua Zhang ; Zhenyu Xuan ; Robert Serfling [États-Unis] ; Michael Q. Zhang [République populaire de Chine] | A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information |
002486 (2011) | Guillaume Marçais [États-Unis] ; Carl Kingsford | A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. |
005408 (????) | Tony Pan ; Patrick Flick ; Chirag Jain ; Yongchao Liu ; Srinivas Aluru | Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. |
005438 (????) | Atif Rahman [États-Unis] ; Ingileif Hallgrímsd Ttir [États-Unis] ; Michael Eisen [États-Unis] ; Lior Pachter [États-Unis] | Association mapping from sequencing reads using k-mers |
000429 (2019) | Akio Miyao [Japon] ; Jianyu Song Kiyomiya [Japon] ; Keiko Iida [Japon] ; Koji Doi [Japon] ; Hiroshi Yasue [Japon] | Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data |
000587 (2019) | Kui Hua [République populaire de Chine] ; Xuegong Zhang [République populaire de Chine] | Estimating the total genome length of a metagenomic sample using k-mers |
000804 (2018) | Prashant Pandey [États-Unis] ; Michael A. Bender [États-Unis] ; Rob Johnson [États-Unis] ; Rob Patro [États-Unis] ; Bonnie Berger | Squeakr: an exact and approximate k-mer counting system. |
000A69 (2018) | Chen Sun [États-Unis] ; Robert S. Harris [États-Unis] ; Rayan Chikhi [France] ; Paul Medvedev [États-Unis] | AllSome Sequence Bloom Trees. |
000B53 (2017) | Meznah Almutairy ; Eric Torng | The effects of sampling on the efficiency and accuracy of k−mer indexes: Theoretical and empirical comparisons using the human genome |
000C11 (2017) | Jad Abbass [Royaume-Uni] ; Jean-Christophe Nebel | Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta. |
000C34 (2017) | Maxime Déraspe [Canada] ; Frédéric Raymond [Canada] ; Sébastien Boisvert [Canada] ; Alexander Culley [Canada] ; Paul H. Roy [Canada] ; François Laviolette [Canada] ; Jacques Corbeil [Canada] | Phenetic Comparison of Prokaryotic Genomes Using k-mers |
000C51 (2017) | Yaron Orenstein [États-Unis] ; Robert Puccinelli [États-Unis] ; Ryan Kim [États-Unis] ; Polly Fordyce [États-Unis] ; Bonnie Berger [États-Unis] | Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping. |
000C97 (2017) | André Müller ; Christian Hundt ; Andreas Hildebrandt ; Thomas Hankeln [Allemagne] ; Bertil Schmidt | MetaCache: context-aware classification of metagenomic reads using minhashing. |
000D85 (2017) | Fanny-Dhelia Pajuste [Estonie] ; Lauris Kaplinski [Estonie] ; M Rt Möls [Estonie] ; Tarmo Puurand [Estonie] ; Maarja Lepamets [Estonie] ; Maido Remm [Estonie] | FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads |
000E30 (2017) | Yaron Orenstein [États-Unis] ; David Pellow [Israël] ; Guillaume Marçais [États-Unis] ; Ron Shamir [Israël] ; Carl Kingsford [États-Unis] | Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing |
001145 (2016) | Samuele Girotto [Italie] ; Cinzia Pizzi [Italie] ; Matteo Comin [Italie] | MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures. |
001286 (2016) | Soumitra Pal [États-Unis] ; Peng Xiao [États-Unis] ; Sanguthevar Rajasekaran [États-Unis] | Efficient sequential and parallel algorithms for finding edit distance based motifs |
001389 (2016) | Leena Salmela [Finlande] ; Riku Walve [Finlande] ; Eric Rivals [France] ; Esko Ukkonen [Finlande] | Accurate self-correction of errors in long reads using de Bruijn graphs |
001729 (2015) | Benjamin P. Vandervalk [Canada] ; Chen Yang [Canada] ; Zhuyi Xue [Canada] ; Karthika Raghavan [Canada] ; Justin Chu [Canada] ; Hamid Mohamadi [Canada] ; Shaun D. Jackman [Canada] ; Readman Chiu [Canada] ; René L. Warren [Canada] ; Inanç Birol [Canada] | Konnector v2.0: pseudo-long reads from paired-end sequencing data |
001732 (2015) | Sebastian Deorowicz [Pologne] ; Marek Kokot [Pologne] ; Szymon Grabowski [Pologne] ; Agnieszka Debudaj-Grabysz [Pologne] | KMC 2: fast and resource-frugal k-mer counting. |
001747 (2015) | Tomasz Kowalski [Pologne] ; Szymon Grabowski [Pologne] ; Sebastian Deorowicz [Pologne] | Indexing Arbitrary-Length k-Mers in Sequencing Reads |
001797 (2015) | Ruichang Zhang [République populaire de Chine] ; Zhanzhan Cheng [République populaire de Chine] ; Jihong Guan [République populaire de Chine] ; Shuigeng Zhou [République populaire de Chine] | Exploiting topic modeling to boost metagenomic reads binning |
001B03 (2014) | Philipp Koch ; Matthias Platzer ; Bryan R. Downie | RepARK—de novo creation of repeat libraries from whole-genome NGS reads |
001B11 (2014) | Zhaojun Zhang [États-Unis] ; Wei Wang [États-Unis] | RNA-Skim: a rapid method for RNA-Seq quantification at transcript level |
001C73 (2014) | Marius Nicolae [États-Unis] ; Sanguthevar Rajasekaran [États-Unis] | Efficient sequential and parallel algorithms for planted motif search |
001D50 (2014) | Evandro A. Marucci [Brésil] ; Geraldo F. D. Zafalon [Brésil] ; Julio C. Momente [Brésil] ; Leandro A. Neves [Brésil] ; Carlo R. Valêncio [Brésil] ; Alex R. Pinto [Brésil] ; Adriano M. Cansian [Brésil] ; Rogeria C. G. De Souza [Brésil] ; Yang Shiyou [République populaire de Chine] ; José M. Machado [Brésil] | An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method |
002198 (2012) | Jung Ho Ahn | ccTSA: A Coverage-Centric Threaded Sequence Assembler |
002216 (2012) | Giorgio Gonnella [Allemagne] ; Stefan Kurtz [Allemagne] | Readjoiner: a fast and memory efficient string graph-based sequence assembler |
002225 (2012) | Qiang Yu ; Hongwei Huo ; Yipu Zhang ; Hongzhi Guo | PairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search |
002228 (2012) | Svetlana Frenkel ; Valery Kirzhner ; Abraham Korol | Organizational Heterogeneity of Vertebrate Genomes |
002250 (2012) | Yu Peng [Hong Kong] ; Henry C M. Leung ; S M Yiu ; Francis Y L. Chin | IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. |
002282 (2012) | Alberto Castellini [Italie] ; Giuditta Franco [Italie] ; Vincenzo Manca [Italie] | A dictionary based informational genome analysis |
002441 (2011) | Nicolas Philippe [France] ; Mikaël Salson [France] ; Thierry Lecroq [France] ; Martine Léonard [France] ; Thérèse Commes [France] ; Eric Rivals [France] | Querying large read collections in main memory: a versatile data structure |
002469 (2011) | Páll Melsted [États-Unis] ; Jonathan K. Pritchard [États-Unis] | Efficient counting of k-mers in DNA sequences using a bloom filter |
002608 (2010) | Kana Shimizu ; Koji Tsuda [Japon] | SlideSort: all pairs similarity search for short reads |
002641 (2010) | Xiaohong Zhao [États-Unis] ; Lance E. Palmer ; Randall Bolanos ; Cristian Mircean ; Dan Fasulo ; Gayle M. Wittenberg | EDAR: an efficient error detection and removal algorithm for next generation sequencing data. |
002936 (2008) | Daniel R. Zerbino [Royaume-Uni] ; Ewan Birney | Velvet: algorithms for de novo short read assembly using de Bruijn graphs. |
002D06 (2006) | Eugene Fratkin [États-Unis] ; Brian T. Naughton ; Douglas L. Brutlag ; Serafim Batzoglou | MotifCut: regulatory motifs finding with maximum density subgraphs. |
003344 (2002) | Jeong-Hyeon Choi [Corée du Sud] ; Hwan-Gue Cho | Analysis of common k-mers for whole genome sequences using SSB-tree. |
000482 (2019) | Nathan Lapierre [États-Unis] ; Serghei Mangul [États-Unis] ; Mohammed Alser [Suisse] ; Igor Mandric [États-Unis] ; Nicholas C. Wu ; David Koslicki [États-Unis] ; Eleazar Eskin [États-Unis] | MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples |
000507 (2019) | Sebastian Deorowicz [Pologne] ; Adam Gudys [Pologne] ; Maciej Dlugosz [Pologne] ; Marek Kokot [Pologne] ; Agnieszka Danek [Pologne] | Kmer-db: instant evolutionary distance estimation. |
000698 (2019) | Umberto Ferraro Petrillo [Italie] ; Mara Sorella [Italie] ; Giuseppe Cattaneo [Italie] ; Raffaele Giancarlo [Italie] ; Simona E. Rombo [Italie] | Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics |
000739 (2019) | V. Swaminathan [Inde] ; Gangothri Rajaram [Inde] ; V. Abhishek [Inde] ; Boosi Shashank Reddy [Inde] ; K. Kannan [Inde] | A Novel Hypergraph-Based Genetic Algorithm (HGGA) Built on Unimodular and Anti-homomorphism Properties for DNA Sequencing by Hybridization. |
000756 (2018) | Md Rafsan Jani [Bangladesh] ; Md Toha Khan Mozlish [Bangladesh] ; Sajid Ahmed [Bangladesh] ; Niger Sultana Tahniat [Bangladesh] ; Dewan Md Farid [Bangladesh] ; Swakkhar Shatabda [Bangladesh] | iRecSpot-EF: Effective sequence based features for recombination hotspot prediction. |
000820 (2018) | Jie Lin [République populaire de Chine] ; Jing Wei [République populaire de Chine] ; Donald Adjeroh [États-Unis] ; Bing-Hua Jiang ; Yue Jiang [République populaire de Chine] | SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform |
000837 (2018) | Lisa K. Johnson [États-Unis] ; Harriet Alexander [États-Unis] ; C Titus Brown [États-Unis] | Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes |
000859 (2018) | Samuel M D. Seaver [États-Unis] ; Claudia Lerma-Ortiz [États-Unis] ; Neal Conrad [États-Unis] ; Arman Mikaili [États-Unis] ; Avinash Sreedasyam [États-Unis] ; Andrew D. Hanson [États-Unis] ; Christopher S. Henry [États-Unis] | PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency. |
000904 (2018) | Yasunobu Okamura ; Kengo Kinoshita | Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data |
000929 (2018) | Yaron Orenstein ; Yun William Yu ; Bonnie Berger | Joker de Bruijn: Covering k-Mers Using Joker Characters |
000A96 (2018) | Erki Aun [Estonie] ; Age Brauer [Estonie] ; Veljo Kisand [Estonie] ; Tanel Tenson [Estonie] ; Maido Remm [Estonie] | A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria |
000B09 (2017) | Hamid Mohamadi [Canada] ; Hamza Khan [Canada] ; Inanc Birol [Canada] | ntCard: a streaming algorithm for cardinality estimation in genomics data |
000B14 (2017) | Abedalrhman Alkhateeb ; Luis Rueda | Zseq: An Approach for Preprocessing Next-Generation Sequencing Data |
000B82 (2017) | Elizabeth S. Allman [États-Unis] ; John A. Rhodes [États-Unis] ; Seth Sullivant [États-Unis] | Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction. |
000D25 (2017) | Marek Kokot [Pologne] ; Maciej Dlugosz [Pologne] ; Sebastian Deorowicz [Pologne] | KMC 3: counting and manipulating k-mer statistics. |
000D39 (2017) | Guillaume Marçais [États-Unis] ; David Pellow [Israël] ; Daniel Bork [États-Unis] ; Yaron Orenstein [États-Unis] ; Ron Shamir [Israël] ; Carl Kingsford [États-Unis] | Improving the performance of minimizers and winnowing schemes |
000D84 (2017) | Roye Rozov [Israël] ; Gil Goldshlager [États-Unis] ; Eran Halperin [États-Unis] ; Ron Shamir [Israël] | Faucet: streaming de novo assembly graph construction |
000E05 (2017) | Yuan Jiang [République populaire de Chine] ; Jun Wang [République populaire de Chine] ; Dawen Xia [République populaire de Chine] ; Guoxian Yu [République populaire de Chine] | EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST |
000E36 (2017) | Jérôme Audoux [France] ; Nicolas Philippe [France] ; Rayan Chikhi [France] ; Mikaël Salson [France] ; Mélina Gallopin [France] ; Marc Gabriel [France] ; Jérémy Le Coz [France] ; Emilie Drouineau [France] ; Thérèse Commes [France] ; Daniel Gautheret [France] | DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition |
000E63 (2017) | You Li [États-Unis, République populaire de Chine] ; Tayla B. Heavican [États-Unis] ; Neetha N. Vellichirammal [États-Unis] ; Javeed Iqbal [États-Unis] ; Chittibabu Guda [États-Unis] | ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data |
000E71 (2017) | Pegah Tootoonchi Afshar [États-Unis] ; Wing Hung Wong [États-Unis] | COSINE: non-seeding method for mapping long noisy sequences |
000E95 (2017) | Guillaume Bernard [Australie] ; Cheong Xin Chan [Australie] ; Yao-Ban Chan [Australie] ; Xin-Yi Chua [Australie] ; Yingnan Cong [Australie] ; James M. Hogan [Australie] ; Stefan R. Maetschke [Australie] ; Mark A. Ragan [Australie] | Alignment-free inference of hierarchical and reticulate phylogenomic relationships |
000F38 (2016) | Hamid Mohamadi ; Justin Chu ; Benjamin P. Vandervalk ; Inanc Birol | ntHash: recursive nucleotide hashing |
001044 (2016) | Rong Wang [République populaire de Chine] ; Yong Xu [République populaire de Chine] ; Bin Liu [République populaire de Chine] | Recombination spot identification Based on gapped k-mers |
001080 (2016) | Qiang Yu [République populaire de Chine] ; Hongwei Huo [République populaire de Chine] ; Dazheng Feng [République populaire de Chine] | PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets |
001177 (2016) | Sara El-Metwally [Égypte] ; Magdi Zakaria [Égypte] ; Taher Hamza [Égypte] | LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads. |
001188 (2016) | Katrin Sameith [Allemagne] ; Juliana G. Roscito [Allemagne] ; Michael Hiller [Allemagne] | Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly |
001240 (2016) | Haoyang Zeng ; Tatsunori Hashimoto ; Daniel D. Kang ; David K. Gifford [États-Unis] | GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. |
001307 (2016) | Troy Hernandez [République populaire de Chine] ; Jie Yang | Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses. |
001395 (2016) | Josep Basha Gutierrez [Japon] ; Kenta Nakai [Japon] | A study on the application of topic models to motif finding algorithms |
001402 (2016) | Yingnan Cong [Australie] ; Yao-Ban Chan [Australie] ; Mark A. Ragan [Australie] | A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF |
001604 (2015) | Simon H. Tausch [Allemagne] ; Bernhard Y. Renard [Allemagne] ; Andreas Nitsche [Allemagne] ; Piotr Wojciech Dabrowski [Allemagne] | RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data |
001721 (2015) | Kévin Vervier ; Pierre Mahé ; Maud Tournoud ; Jean-Baptiste Veyrieras ; Jean-Philippe Vert | Large-scale machine learning for metagenomics sequence classification |
001781 (2015) | Lauris Kaplinski [Estonie] ; Maarja Lepamets [Estonie] ; Maido Remm [Estonie] | GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists. |
001819 (2015) | Junwei Luo [République populaire de Chine] ; Jianxin Wang [République populaire de Chine] ; Weilong Li [République populaire de Chine] ; Zhen Zhang [République populaire de Chine] ; Fang-Xiang Wu [Canada] ; Min Li [République populaire de Chine] ; Yi Pan [États-Unis] | EPGA2: memory-efficient de novo assembler. |
001A35 (2014) | Rajat Shuvro Roy [États-Unis] ; Debashish Bhattacharya [États-Unis] ; Alexander Schliep [États-Unis] | Turtle: identifying frequent k-mers with cache-efficient algorithms. |
001A48 (2014) | Qingpeng Zhang [États-Unis] ; Jason Pell [États-Unis] ; Rosangela Canino-Koning [États-Unis] ; Adina Chuang Howe [États-Unis] ; C. Titus Brown [États-Unis] | These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure |
001A54 (2014) | Juan Esteban Gallo [Colombie] ; José Fernando Mu Oz [Colombie] ; Elizabeth Misas [Colombie] ; Juan Guillermo Mcewen [Colombie] ; Oliver Keatinge Clay [Colombie] | The complex task of choosing a de novo assembly: lessons from fungal genomes. |
001B32 (2014) | Emanuel Weitschek [Italie] ; Daniele Santoni [Italie] ; Giulia Fiscon [Italie] ; Maria Cristina De Cola [Italie] ; Paola Bertolazzi [Italie] ; Giovanni Felici [Italie] | Next generation sequencing reads comparison with an alignment-free distance |
001B42 (2014) | Nung Kion Lee [Malaisie] ; Pui Kwan Fong [Malaisie] ; Mohd Tajuddin Abdullah [Malaisie] | Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region. |
001B43 (2014) | Xiaolei Wang ; Hiroyuki Kuwahara ; Xin Gao | Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels |
001C06 (2014) | Páll Melsted [Islande] ; Bjarni V. Halld Rsson [Islande] | KmerStream: streaming algorithms for k-mer abundance estimation. |
001C08 (2014) | Peter Audano ; Fredrik Vannberg | KAnalyze: a fast versatile pipelined K-mer toolkit |
001C09 (2014) | Jia Wen [Hong Kong] ; Raymond H F. Chan [Hong Kong] ; Shek-Chung Yau [Hong Kong] ; Rong L. He [États-Unis] ; Stephen S T. Yau [République populaire de Chine] | K-mer natural vector and its application to the phylogenetic analysis of genetic sequences. |
001C58 (2014) | Sohan Seth [Finlande] ; Niko V Lim Ki [Finlande] ; Samuel Kaski [Finlande] ; Antti Honkela [Finlande] | Exploration and retrieval of whole-metagenome sequencing samples |
002010 (2013) | Sebastian Deorowicz [Pologne] ; Agnieszka Debudaj-Grabysz [Pologne] ; Szymon Grabowski [Pologne] | Disk-based k-mer counting on a PC |
002019 (2013) | Yaron Orenstein ; Ron Shamir | Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers |
002022 (2013) | Guillaume Rizk [France] ; Dominique Lavenier ; Rayan Chikhi | DSK: k-mer counting with very low memory usage. |
002208 (2012) | Roy Ronen ; Christina Boucher [États-Unis] ; Hamidreza Chitsaz [États-Unis] ; Pavel Pevzner [États-Unis] | SEQuel: improving the accuracy of genome assemblies |
002233 (2012) | Yi Wang ; Henry C. M. Leung ; S. M. Yiu ; Francis Y. L. Chin | MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample |
002614 (2010) | Xiao Yang [États-Unis] ; Karin S. Dorman ; Srinivas Aluru | Reptile: representative tiling for short read error correction. |
002832 (2009) | Shea N. Gardner [États-Unis] ; Amy L. Hiddessen [États-Unis] ; Peter L. Williams [États-Unis] ; Christine Hara [États-Unis] ; Mark C. Wagner [États-Unis] ; Bill W. Colston [États-Unis] | Multiplex primer prediction software for divergent targets |
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