XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons

[1]  Mingfeng Li,et al.  Temporal Specification and Bilaterality of Human Neocortical Topographic Gene Expression , 2014, Neuron.

[2]  Michael P Snyder,et al.  High-throughput sequencing for biology and medicine , 2013, Molecular systems biology.

[3]  C. Burge,et al.  Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues , 2012, Science.

[4]  Evgeny M. Zdobnov,et al.  OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs , 2012, Nucleic Acids Res..

[5]  David Haussler,et al.  The UCSC genome browser and associated tools , 2012, Briefings Bioinform..

[6]  Michael C. Schatz,et al.  Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score , 2012, Bioinform..

[7]  Y. Gilad,et al.  Comparative studies of gene expression and the evolution of gene regulation , 2012, Nature Reviews Genetics.

[8]  David G. Knowles,et al.  Fast Computation and Applications of Genome Mappability , 2012, PloS one.

[9]  Damian Szklarczyk,et al.  eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges , 2011, Nucleic Acids Res..

[10]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[11]  J. Kleinman,et al.  Spatiotemporal transcriptome of the human brain , 2011, Nature.

[12]  T. Gingeras,et al.  Synthetic spike-in standards for RNA-seq experiments. , 2011, Genome research.

[13]  Mark Gerstein,et al.  Bioinformatics Applications Note Gene Expression Rseqtools: a Modular Framework to Analyze Rna-seq Data Using Compact, Anonymized Data Summaries , 2022 .

[14]  Dan Wang,et al.  A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species , 2010, Nucleic Acids Res..

[15]  Na Li,et al.  Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq , 2010, PLoS Comput. Biol..

[16]  M. Stephens,et al.  Sex-specific and lineage-specific alternative splicing in primates. , 2010, Genome research.

[17]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[18]  David N. Messina,et al.  Evolutionary and Biomedical Insights from the Rhesus Macaque Genome , 2007, Science.

[19]  Jean L. Chang,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.

[20]  M. Kollmar,et al.  Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins , 2003, BMC Genomics.

[21]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[22]  M. King,et al.  Evolution at two levels in humans and chimpanzees. , 1975, Science.

[23]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[24]  A. Nieters,et al.  Differential expression analysis for sequence count data , 2011 .

[25]  David N. Messina,et al.  Evolutionary and Biomedical Insights from the Rhesus Macaque Genome , 2007 .

[26]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.