Forty-Four Novel Protein-Coding Loci Discovered Using a Proteomics Informed by Transcriptomics (PIT) Approach in Rat Male Germ Cells1

Integrated transcriptome analysis of mouse spermatogenesis

(2014) Gennady Margolin et al.   BMC GENOMICS

Discovery of Novel Genes and Gene Isoforms by Integrating Transcriptomic and Proteomic Profiling from Mouse Liver

(2014) Peng Wu et al.   JOURNAL OF PROTEOME RESEARCH

Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits

(2014) Hong-xia Wu et al.   Journal of Proteomics

Non-model organisms, a species endangered by proteogenomics

(2014) Jean Armengaud et al.   Journal of Proteomics

The human testis-specific proteome defined by transcriptomics and antibody-based profiling

(2014) D. Djureinovic et al.   MOLECULAR HUMAN REPRODUCTION

Activities at the Universal Protein Resource (UniProt)

(2014)   NUCLEIC ACIDS RESEARCH

VAMP7 Modulates Ciliary Biogenesis in Kidney Cells

(2014) Christina M. Szalinski et al.   PLoS One

An atlas of chromatoid body components

(2014) O. Meikar et al.   RNA

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

(2013) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

Integrative Proteomic and Transcriptomic Analyses Reveal Multiple Post-transcriptional Regulatory Mechanisms of Mouse Spermatogenesis

(2013) Haiyun Gan et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The splicing landscape is globally reprogrammed during male meiosis

(2013) Ralf Schmid et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Profiling of the Murine Testis during the First Wave of Spermatogenesis

(2013) Asta Laiho et al.   PLoS One

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

(2013) Mario Looso et al.   GENOME BIOLOGY

Transcriptome landscape of the human placenta

(2012) Jinsil Kim et al.   BMC GENOMICS

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility

(2012) Frédéric Chalmel et al.   HUMAN REPRODUCTION

De novo derivation of proteomes from transcriptomes for transcript and protein identification

(2012) Vanessa C Evans et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

(2011) C. Adamidi et al.   GENOME RESEARCH

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA in genome regulation

(2011) Tiffany Hung et al.   RNA Biology

The Role of VAMP7/TI-VAMP in Cell Polarity and Lysosomal Exocytosis in vivo

(2011) Mahito Sato et al.   TRAFFIC

Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

(2010) Qiang Gan et al.   CELL RESEARCH

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Transcription and post-transcriptional regulation of spermatogenesis

(2010) A. Bettegowda et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A VAMP7/Vti1a SNARE complex distinguishes a non-conventional traffic route to the cell surface used by KChIP1 and Kv4 potassium channels

(2009) Sarah E. Flowerdew et al.   BIOCHEMICAL JOURNAL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Multiple roles of the vesicular-SNARE TI-VAMP in post-Golgi and endosomal trafficking

(2009) Mathilde Chaineau et al.   FEBS LETTERS

CLPH, a Novel Casein Kinase 2-Phosphorylated Disordered Protein, Is Specifically Associated with Postmeiotic Germ Cells in Rat Spermatogenesis

(2009) Pierre Calvel et al.   JOURNAL OF PROTEOME RESEARCH

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology

(2008) Frédéric Chalmel et al.   BMC BIOINFORMATICS

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

(2008) Michael L Tress et al.   GENOME BIOLOGY