Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human

(2012) Barbara Piasecka et al.   BIOINFORMATICS

Mass spectrometry-based proteomics: existing capabilities and future directions

(2012) Thomas E. Angel et al.   CHEMICAL SOCIETY REVIEWS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data

(2012) Xiaoshu Chen et al.   PLoS Computational Biology

When orthologs diverge between human and mouse

(2011) W. H. Gharib et al.   BRIEFINGS IN BIOINFORMATICS

Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development

(2011) Sharmistha Pal et al.   GENOME RESEARCH

Functional Redundancy between HumanSHOXand MouseShox2Genes in the Regulation of Sinoatrial Node Formation and Pacemaking Function

(2011) Hongbing Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

(2011) Nathan L. Nehrt et al.   PLoS Computational Biology

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication

(2010) J. Roux et al.   GENOME RESEARCH

Differential regulation of human and murine P-selectin expression and function in vivo

(2010) Zhenghui Liu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Maintenance of duplicate genes and their functional redundancy by reduced expression

(2010) Wenfeng Qian et al.   TRENDS IN GENETICS

A Problem With the Correlation Coefficient as a Measure of Gene Expression Divergence

(2009) Vini Pereira et al.   GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

How confident can we be that orthologs are similar, but paralogs differ?

(2009) Romain A. Studer et al.   TRENDS IN GENETICS

Microarray methods to identify factors determining breast cancer progression: Potentials, limitations, and challenges

(2008) B. van der Vegt et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs

(2008) Jun-ichi Takeda et al.   NUCLEIC ACIDS RESEARCH

Tissue-specific splicing factor gene expression signatures

(2008) Ana Rita Grosso et al.   NUCLEIC ACIDS RESEARCH