Transcriptome and proteome quantification of a tumor model provides novel insights into post‐transcriptional gene regulation

An insight into iTRAQ: where do we stand now?

(2012) Caroline Evans et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Drosophila neuroblasts: a model for stem cell biology

(2012) C. C. F. Homem et al.   DEVELOPMENT

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

(2012) Mohan Babu et al.   NATURE

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi

(2011) Ralph A. Neumüller et al.   Cell Stem Cell

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

(2011) Eric J. Foss et al.   PLOS BIOLOGY

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Cancer metabolism: The Warburg effect today

(2010) Leonardo M.R. Ferreira   EXPERIMENTAL AND MOLECULAR PATHOLOGY

Addressing Accuracy and Precision Issues in iTRAQ Quantitation

(2010) Natasha A. Karp et al.   MOLECULAR & CELLULAR PROTEOMICS

PeptideClassifier for protein inference and targeted quantitative proteomics

(2010) Ermir Qeli et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

A New Probabilistic Database Search Algorithm for ETD Spectra

(2009) Rovshan G. Sadygov et al.   JOURNAL OF PROTEOME RESEARCH

High Precision Quantitative Proteomics Using iTRAQ on an LTQ Orbitrap: A New Mass Spectrometric Method Combining the Benefits of All

(2009) Thomas Köcher et al.   JOURNAL OF PROTEOME RESEARCH

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

The Mcm Complex: Unwinding the Mechanism of a Replicative Helicase

(2009) M. L. Bochman et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Cancer Cell Metabolism: Warburg and Beyond

(2008) Peggy P. Hsu et al.   CELL

Centrosome Dysfunction in Drosophila Neural Stem Cells Causes Tumors that Are Not Due to Genome Instability

(2008) Elisabeth Castellanos et al.   CURRENT BIOLOGY

Neural stem cells: balancing self-renewal with differentiation

(2008) C. Q. Doe   DEVELOPMENT

Drosophilaneuroblast asymmetric divisions: cell cycle regulators, asymmetric protein localization, and tumorigenesis: Figure 1.

(2008) William Chia et al.   JOURNAL OF CELL BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH

Coupling and coordination in gene expression processes: a systems biology view

(2007) Suzanne Komili et al.   NATURE REVIEWS GENETICS