Sequence Analysis
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Andrey D. Prjibelski | Anton I. Korobeynikov | Alla L. Lapidus | A. Lapidus | A. Korobeynikov | A. Prjibelski
[1] Baozhen Shan,et al. De novo peptide sequencing by deep learning , 2017, Proceedings of the National Academy of Sciences.
[2] P. Pevzner,et al. metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.
[3] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[4] K. Vyatkina. De Novo Sequencing of Top-Down Tandem Mass Spectra: A Next Step towards Retrieving a Complete Protein Sequence , 2017, Proteomes.
[5] Minoru Kanehisa,et al. KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..
[6] B. Tian,et al. RNA‐Seq methods for transcriptome analysis , 2017, Wiley interdisciplinary reviews. RNA.
[7] Ryan R. Wick,et al. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.
[8] Elena Bushmanova,et al. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies , 2016, Bioinform..
[9] Sarah C. Ayling,et al. The Ensembl gene annotation system , 2016, Database J. Biol. Databases Curation.
[10] Lior Pachter,et al. Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.
[11] Niranjan Nagarajan,et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap , 2016, Nature Communications.
[12] Dmitry Antipov,et al. hybridSPAdes: an algorithm for hybrid assembly of short and long reads , 2016, Bioinform..
[13] B. Chain,et al. The sequence of sequencers: The history of sequencing DNA , 2016, Genomics.
[14] Heng Li,et al. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences , 2015, Bioinform..
[15] Minoru Kanehisa,et al. KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..
[16] Ana Conesa,et al. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data , 2015, Bioinform..
[17] Haixu Tang,et al. Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis , 2015, Bioinform..
[18] Rahul Singh,et al. Global multiple protein-protein interaction network alignment by combining pairwise network alignments , 2015, BMC Bioinformatics.
[19] Kimberly R. Kukurba,et al. RNA Sequencing and Analysis. , 2015, Cold Spring Harbor protocols.
[20] Andrey D. Prjibelski,et al. Assembling short reads from jumping libraries with large insert sizes , 2015, Bioinform..
[21] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[22] S. Kelly,et al. TransRate: reference-free quality assessment of de novo transcriptome assemblies , 2015, bioRxiv.
[23] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[24] Han Zhao,et al. Global network alignment in the context of aging , 2015, TCBB.
[25] Kunihiko Sadakane,et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..
[26] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[27] Alexandre Lomsadze,et al. Identification of protein coding regions in RNA transcripts , 2014, BCB.
[28] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[29] Ole Schulz-Trieglaff,et al. NxTrim: optimized trimming of Illumina mate pair reads , 2014, bioRxiv.
[30] R. K. De,et al. A Comprehensive View on Metabolic Pathway Analysis Methodologies , 2014 .
[31] P. Pevzner,et al. De novo protein sequencing by combining top-down and bottom-up tandem mass spectra. , 2014, Journal of proteome research.
[32] Yongsheng Bai,et al. Evaluation of de novo transcriptome assemblies from RNA-Seq data , 2014, Genome Biology.
[33] Alla Lapidus,et al. ExSPAnder: a universal repeat resolver for DNA fragment assembly , 2014, Bioinform..
[34] Siu-Ming Yiu,et al. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information , 2014, RECOMB.
[35] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[36] Andrés Marzal,et al. Statistical Significance of Normalized Global Alignment , 2014, J. Comput. Biol..
[37] Evan Bolton,et al. Database resources of the National Center for Biotechnology Information , 2001, Nucleic Acids Res..
[38] Susumu Goto,et al. Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..
[39] Xun Xu,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads , 2013, Bioinform..
[40] C. H. Poskar,et al. High-throughput data pipelines for metabolic flux analysis in plants. , 2014, Methods in molecular biology.
[41] LC-MALDI-TOF/TOF for shotgun proteomics. , 2014, Methods in molecular biology.
[42] Dmitry Antipov,et al. Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products , 2013, J. Comput. Biol..
[43] M. Berriman,et al. REAPR: a universal tool for genome assembly evaluation , 2013, Genome Biology.
[44] Steven Salzberg,et al. GAGE-B: an evaluation of genome assemblers for bacterial organisms , 2013, Bioinform..
[45] Alexey A. Gurevich,et al. QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..
[46] Inanç Birol,et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.
[47] Sean R. Eddy,et al. Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..
[48] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[49] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[50] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[51] Sara Sheehan,et al. Telescoper: de novo assembly of highly repetitive regions , 2012, Bioinform..
[52] Wei Li,et al. RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..
[53] Bernard Henrissat,et al. Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome , 2012, PLoS Comput. Biol..
[54] Siu-Ming Yiu,et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..
[55] M. Schatz,et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.
[56] Pablo Cingolani,et al. © 2012 Landes Bioscience. Do not distribute. , 2022 .
[57] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[58] R. Durbin,et al. Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.
[59] M. Schatz,et al. Algorithms Gage: a Critical Evaluation of Genome Assemblies and Assembly Material Supplemental , 2008 .
[60] Susumu Goto,et al. KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..
[61] Nuno A. Fonseca,et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. , 2011, Genome research.
[62] S. Salzberg,et al. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts , 2011, Genome Biology.
[63] Bernard P. Puc,et al. An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.
[64] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[65] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[66] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[67] Steven J. M. Jones,et al. De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.
[68] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[69] Wendy S. Schackwitz,et al. One Bacterial Cell, One Complete Genome , 2010, PloS one.
[70] Paul D. Shaw,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[71] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[72] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[73] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[74] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[75] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[76] Björn H. Junker,et al. Computational Models of Metabolism: Stability and Regulation in Metabolic Networks , 2008 .
[77] Steven M. Johnson,et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.
[78] Alejandro A. Schäffer,et al. Database indexing for production MegaBLAST searches , 2008, Bioinform..
[79] Alexander Souvorov,et al. Splign: algorithms for computing spliced alignments with identification of paralogs , 2008, Biology Direct.
[80] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[81] Yoshihiro Yamanishi,et al. KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..
[82] Peter F. Hallin,et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.
[83] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[84] J. Shendure,et al. Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .
[85] Thomas D. Wu,et al. GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..
[86] Eugene W. Myers,et al. The fragment assembly string graph , 2005, ECCB/JBI.
[87] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[88] Volker Brendel,et al. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing , 2004, Genome Biology.
[89] Yazhu Chen,et al. A Brief Review of Computational Gene Prediction Methods , 2004, Genomics, proteomics & bioinformatics.
[90] Gonzalo Navarro,et al. An Alphabet-Friendly FM-Index , 2004, SPIRE.
[91] Dong Xu,et al. Protein Databases on the Internet , 2004, Current protocols in molecular biology.
[92] Rajeev K. Azad,et al. Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory , 2004, Briefings Bioinform..
[93] Vladimir A. Kulyukin,et al. Generalized Hamming Distance , 2002, Information Retrieval.
[94] David L. Wheeler,et al. GenBank: update , 2004, Nucleic Acids Res..
[95] Inna Dubchak,et al. Glocal alignment: finding rearrangements during alignment , 2003, ISMB.
[96] H. Jörnvall,et al. C‐Terminal Sequence Analysis , 2003, Current protocols in protein science.
[97] S. Turner,et al. Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations , 2003, Science.
[98] Paul D. Shaw,et al. Plant snoRNA database , 2003, Nucleic Acids Res..
[99] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[100] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[101] 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.
[102] B. Chait,et al. ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. , 2000, Analytical chemistry.
[103] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[104] Rolf Apweiler,et al. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..
[105] D. N. Perkins,et al. Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.
[106] S. Salzberg,et al. Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.
[107] M. Borodovsky,et al. GeneMark.hmm: new solutions for gene finding. , 1998, Nucleic acids research.
[108] W. C. Barker,et al. The PIR-International Protein Sequence Database. , 1998, Nucleic acids research.
[109] S. Salzberg,et al. Microbial gene identification using interpolated Markov models. , 1998, Nucleic acids research.
[110] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[111] R F Doolittle,et al. Progressive alignment of amino acid sequences and construction of phylogenetic trees from them. , 1996, Methods in enzymology.
[112] R S Johnson,et al. Sherpa: a Macintosh-based expert system for the interpretation of electrospray ionization LC/MS and MS/MS data from protein digests. , 1996, Rapid communications in mass spectrometry : RCM.
[113] P. Pevzner,et al. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals , 1995, STOC '95.
[114] Sudhir Kumar,et al. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers , 1994, Comput. Appl. Biosci..
[115] S. Henikoff,et al. Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[116] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[117] O. Gotoh. An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.
[118] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[119] M. O. Dayhoff. A model of evolutionary change in protein , 1978 .
[120] H. Niall. [36] Automated edman degradation: The protein sequenator , 1973 .
[121] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[122] F. Sanger,et al. The disulphide bonds of insulin. , 1955, The Biochemical journal.
[123] P. Edman,et al. A method for the determination of amino acid sequence in peptides. , 1949, Archives of biochemistry.