Maser: one-stop platform for NGS big data from analysis to visualization
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Kazuho Ikeo | Takashi Gojobori | Junichi Imoto | Sonoko Kinjo | Norikazu Monma | Sadahiko Misu | Norikazu Kitamura | Kazutoshi Yoshitake | T. Gojobori | K. Ikeo | K. Yoshitake | Norikazu Monma | Sadahiko Misu | Norikazu Kitamura | S. Kinjo | Junichi Imoto
[1] Matthew D. Young,et al. Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.
[2] S. Yajima,et al. Molecular basis of wax-based color change and UV reflection in dragonflies , 2019, eLife.
[3] Kamal Kishore,et al. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions , 2016, Front. Genet..
[4] François Laviolette,et al. Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies , 2010, J. Comput. Biol..
[5] K. Maruyama,et al. Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury , 2014, BMC Genomics.
[6] Colin N. Dewey,et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.
[7] Anton Nekrutenko,et al. NGS analyses by visualization with Trackster , 2012, Nature Biotechnology.
[8] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[9] Alexander F. Auch,et al. MEGAN analysis of metagenomic data. , 2007, Genome research.
[10] Piero Carninci,et al. Detecting expressed genes using CAGE. , 2014, Methods in molecular biology.
[11] Gordon Robertson,et al. An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq , 2011, PloS one.
[12] Xuegong Zhang,et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data , 2010, Bioinform..
[13] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[14] Todd H. Oakley,et al. Luciferase gene of a Caribbean fireworm (Syllidae) from Puerto Rico , 2019, Scientific Reports.
[15] F. Miura,et al. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging , 2012, Nucleic acids research.
[16] Burkhard Morgenstern,et al. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources , 2006, BMC Bioinformatics.
[17] A. Nekrutenko,et al. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.
[18] M. Furuno,et al. CCT2 Mutations Evoke Leber Congenital Amaurosis due to Chaperone Complex Instability , 2016, Scientific Reports.
[19] Y. Hayashizaki,et al. Bone Marrow Adipocytes Facilitate Fatty Acid Oxidation Activating AMPK and a Transcriptional Network Supporting Survival of Acute Monocytic Leukemia Cells. , 2017, Cancer research.
[20] K. Ikeo,et al. Identification of Novel Mutations in the LRR-Cap Domain of C21orf2 in Japanese Patients With Retinitis Pigmentosa and Cone-Rod Dystrophy. , 2016, Investigative ophthalmology & visual science.
[21] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[22] Jing Chen,et al. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource , 2010, Nucleic Acids Res..
[23] David G Hendrickson,et al. Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.
[24] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[25] S. Yajima,et al. Extraordinary diversity of visual opsin genes in dragonflies , 2015, Proceedings of the National Academy of Sciences.
[26] Sumio Sugano,et al. 5′-end SAGE for the analysis of transcriptional start sites , 2004, Nature Biotechnology.
[27] L. Pachter,et al. Streaming fragment assignment for real-time analysis of sequencing experiments , 2012, Nature Methods.
[28] Y. Qi,et al. Tor Signaling Regulates Transcription of Amino Acid Permeases through a GATA Transcription Factor Gaf1 in Fission Yeast , 2015, PloS one.
[29] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[30] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[31] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[32] T. Kitano,et al. Evolution of the RH gene family in vertebrates revealed by brown hagfish (Eptatretus atami) genome sequences. , 2017, Molecular phylogenetics and evolution.
[33] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[34] Pablo Cingolani,et al. © 2012 Landes Bioscience. Do not distribute. , 2022 .
[35] Timothy L. Bailey,et al. Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data , 2011 .
[36] Thomas Wetter,et al. Genome Sequence Assembly Using Trace Signals and Additional Sequence Information , 1999, German Conference on Bioinformatics.
[37] Martin C. Frith,et al. Discovering Sequence Motifs with Arbitrary Insertions and Deletions , 2008, PLoS Comput. Biol..
[39] Tetsuya Hayashi,et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads , 2014, Genome research.
[40] W. Ludwig,et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.
[41] Y. Furukawa,et al. Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis , 2016, Scientific Reports.
[42] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[43] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[44] Leping Li,et al. GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery , 2009, J. Comput. Biol..
[45] Matko Bosnjak,et al. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.
[46] Graziano Pesole,et al. WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences , 2007, BMC Bioinformatics.
[47] Piero Carninci,et al. RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE) , 2014, BMC Genomics.
[48] J. Kawai,et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[49] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[50] Felix Krueger,et al. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..
[51] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.