Graph regularized, semi-supervised learning improves annotation of de novo transcriptomes
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Laraib Malik | Rob Patro | Shravya Thatipally | Nikhil Junneti | Laraib Malik | Robert Patro | Shravya Thatipally | Nikhil Junneti
[1] M. Robinson,et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.
[2] Peng Cui,et al. Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis , 2014, Genome Biology.
[3] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[4] Anthony T Papenfuss,et al. Analysis of the platypus genome suggests a transposon origin for mammalian imprinting , 2009, Genome Biology.
[5] Geet Duggal,et al. Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference , 2015, bioRxiv.
[6] J. Ayers,et al. De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues , 2016, BMC Genomics.
[7] Huanming Yang,et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. , 2010, Genome research.
[8] Partha Pratim Talukdar,et al. Experiments in Graph-Based Semi-Supervised Learning Methods for Class-Instance Acquisition , 2010, ACL.
[9] Cole Trapnell,et al. Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.
[10] A. Oshlack,et al. Corset: enabling differential gene expression analysis for de novo assembled transcriptomes , 2014, Genome Biology.
[11] Anne de Jong,et al. Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis , 2010, BMC Genomics.
[12] Shankar Kumar,et al. Video suggestion and discovery for youtube: taking random walks through the view graph , 2008, WWW.
[13] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[14] M. Stephens,et al. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.
[15] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[16] David G Hendrickson,et al. Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.
[17] Guiming Liu,et al. Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics , 2012, PloS one.
[18] J. Galindo,et al. Applications of next generation sequencing in molecular ecology of non-model organisms , 2011, Heredity.
[19] Robert Patro,et al. Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms , 2013, ArXiv.
[20] M. Robinson,et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. , 2015, F1000Research.
[21] Dennis C. Friedrich,et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries , 2011, Genome Biology.
[22] L. Coin,et al. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads , 2011, Genome Biology.
[23] K. Jiang,et al. Transcriptome Sequencing, De Novo Assembly and Differential Gene Expression Analysis of the Early Development of Acipenser baeri , 2015, PloS one.
[24] 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.
[25] Rob Patro,et al. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms , 2013, Nature Biotechnology.
[26] Johan A. Grahnen,et al. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery , 2010, BMC Genomics.
[27] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[28] David Sankoff,et al. Locating rearrangement events in a phylogeny based on highly fragmented assemblies , 2016, BMC Genomics.
[29] Robert Patro,et al. RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes , 2015, bioRxiv.