Transcriptome assembly strategies for precision medicine
暂无分享,去创建一个
Lipi Acharya | Changxin Bai | Lipi R. Acharya | Dongxiao Zhu | Lu Wang | Dongxiao Zhu | Lu Wang | Changxin Bai
[1] Daniel J. Gaffney,et al. A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[2] Yongsheng Bai,et al. Evaluation of de novo transcriptome assemblies from RNA-Seq data , 2014, Genome Biology.
[3] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[4] 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.
[5] F. Collins,et al. A new initiative on precision medicine. , 2015, The New England journal of medicine.
[6] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[7] B. Taylor,et al. Implementing Genome-Driven Oncology , 2017, Cell.
[8] Steven J. M. Jones,et al. De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.
[9] de Ng Dick Bruijn. A combinatorial problem , 1946 .
[10] Akhilesh K. Tyagi,et al. De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.
[11] Chittibabu Guda,et al. Classification of breast cancer patients using somatic mutation profiles and machine learning approaches , 2016, BMC Systems Biology.
[12] Xun Xu,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads , 2013, Bioinform..
[13] Eugene W. Myers,et al. Toward Simplifying and Accurately Formulating Fragment Assembly , 1995, J. Comput. Biol..
[14] Rajat K De,et al. Precision medicine with electronic medical records: from the patients and for the patients. , 2016, Annals of translational medicine.
[15] Chengying Shi,et al. Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds , 2011, BMC Genomics.
[16] Ben Ewen-Campen,et al. De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis , 2011, BMC Genomics.
[17] 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.
[18] Jeffrey S. Buguliskis. Could RNA-Seq Become the Workhorse of Precision Medicine? , 2015 .
[19] Xiuzhen Huang,et al. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data , 2015, Genome Biology.
[20] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[21] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[22] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[23] Rui Chen,et al. Promise of personalized omics to precision medicine , 2013, Wiley interdisciplinary reviews. Systems biology and medicine.
[24] Xuan Li,et al. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study , 2011, BMC Bioinformatics.
[25] M. Blaxter,et al. Comparing de novo assemblers for 454 transcriptome data , 2010, BMC Genomics.
[26] M. Fumagalli,et al. Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences , 2013, PloS one.
[27] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[28] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[29] Baohong Zhang,et al. De Novo Transcriptome Assembly and Comparative Analysis Elucidate Complicated Mechanism Regulating Astragalus chrysochlorus Response to Selenium Stimuli , 2015, PloS one.
[30] Dimitrios I. Fotiadis,et al. Machine learning applications in cancer prognosis and prediction , 2014, Computational and structural biotechnology journal.
[31] Siu-Ming Yiu,et al. SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..
[32] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[33] G. Sherlock,et al. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads , 2010, BMC Genomics.
[34] M. Yandell,et al. A beginner's guide to eukaryotic genome annotation , 2012, Nature Reviews Genetics.
[35] Anders Krogh,et al. Bayesian transcriptome assembly , 2014, Genome Biology.
[36] 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.
[37] 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.
[38] Guojun Li,et al. TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs , 2016, Genome Biology.
[39] Martin Vingron,et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..
[40] Ulrich Keilholz,et al. The combinatorial complexity of cancer precision medicine , 2014, Oncoscience.
[41] Fuhong He,et al. Modeling Transcriptome Based on Transcript-Sampling Data , 2008, PloS one.
[42] Cole Trapnell,et al. Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.