Getting intimate with trypsin, the leading protease in proteomics

E Vandermarliere, M Mueller… - Mass spectrometry …, 2013 - Wiley Online Library
Nowadays, mass spectrometry‐based proteomics is carried out primarily in a bottom‐up
fashion, with peptides obtained after proteolytic digest of a whole proteome lysate as the …

Proteomics-based methods for discovery, quantification, and validation of protein–protein interactions

YV Miteva, HG Budayeva, IM Cristea - Analytical chemistry, 2013 - ACS Publications
Proteins play a fundamental role in establishing the diversity of cellular processes in health
or disease systems. This diversity is accomplished by a vast array of protein functions. In …

Punctuated evolution of prostate cancer genomes

SC Baca, D Prandi, MS Lawrence, JM Mosquera… - Cell, 2013 - cell.com
The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes,
but the spectrum of genome-wide alterations has not been profiled extensively in this …

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

AM Dulak, P Stojanov, S Peng, MS Lawrence, C Fox… - Nature …, 2013 - nature.com
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years.
With a 5-year survival rate of∼ 15%, the identification of new therapeutic targets for EAC is …

FunGene: the functional gene pipeline and repository

JA Fish, B Chai, Q Wang, Y Sun, CT Brown… - Frontiers in …, 2013 - frontiersin.org
Ribosomal RNA genes have become the standard molecular markers for microbial
community analysis for good reasons, including universal occurrence in cellular organisms …

The Protein Model Portal—a comprehensive resource for protein structure and model information

J Haas, S Roth, K Arnold, F Kiefer, T Schmidt… - Database, 2013 - academic.oup.com
Abstract The Protein Model Portal (PMP) has been developed to foster effective use of 3D
molecular models in biomedical research by providing convenient and comprehensive …

Integration of clinical data with a genome‐scale metabolic model of the human adipocyte

A Mardinoglu, R Agren, C Kampf, A Asplund… - Molecular systems …, 2013 - embopress.org
We evaluated the presence/absence of proteins encoded by 14 077 genes in adipocytes
obtained from different tissue samples using immunohistochemistry. By combining this with …

HBVdb: a knowledge database for Hepatitis B Virus

J Hayer, F Jadeau, G Deleage, A Kay… - Nucleic acids …, 2013 - academic.oup.com
We have developed a specialized database, HBVdb (http://hbvdb. ibcp. fr), allowing the
researchers to investigate the genetic variability of Hepatitis B Virus (HBV) and viral …

Energy barriers and driving forces in tRNA translocation through the ribosome

LV Bock, C Blau, GF Schröder, II Davydov… - Nature structural & …, 2013 - nature.com
During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites.
Here we investigate conformational motions during spontaneous translocation, using …

A guide to best practices for Gene Ontology (GO) manual annotation

R Balakrishnan, MA Harris, R Huntley, K Van Auken… - Database, 2013 - academic.oup.com
Abstract The Gene Ontology Consortium (GOC) is a community-based bioinformatics project
that classifies gene product function through the use of structured controlled vocabularies. A …