[HTML][HTML] Proteogenomics: concepts, applications and computational strategies

AI Nesvizhskii - Nature methods, 2014 - nature.com
Proteogenomics is an area of research at the interface of proteomics and genomics. In this
approach, customized protein sequence databases generated using genomic and …

[HTML][HTML] Towards environmental systems biology of Shewanella

JK Fredrickson, MF Romine, AS Beliaev… - Nature Reviews …, 2008 - nature.com
Bacteria of the genus Shewanella are known for their versatile electron-accepting
capacities, which allow them to couple the decomposition of organic matter to the reduction …

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

International Wheat Genome Sequencing Consortium … - Science, 2014 - science.org
An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum)
genome has been produced by sequencing isolated chromosome arms. We have annotated …

[HTML][HTML] Proteomics: a pragmatic perspective

P Mallick, B Kuster - Nature biotechnology, 2010 - nature.com
The evolution of mass spectrometry–based proteomic technologies has advanced our
understanding of the complex and dynamic nature of proteomes while concurrently …

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

S Kim, N Gupta, PA Pevzner - Journal of proteome research, 2008 - ACS Publications
A key problem in computational proteomics is distinguishing between correct and false
peptide identifications. We argue that evaluating the error rates of peptide identifications is …

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

SP Schrimpf, M Weiss, L Reiter, CH Ahrens… - PLoS …, 2009 - journals.plos.org
The nematode Caenorhabditis elegans is a popular model system in genetics, not least
because a majority of human disease genes are conserved in C. elegans. To generate a …

False discovery rates of protein identifications: a strike against the two-peptide rule

N Gupta, PA Pevzner - Journal of proteome research, 2009 - ACS Publications
Most proteomics studies attempt to maximize the number of peptide identifications and
subsequently infer proteins containing two or more peptides as reliable protein …

[图书][B] DNA and RNA modification enzymes: structure, mechanism, function and evolution

H Grosjean - 2009 - taylorfrancis.com
This volume is a timely and comprehensive description of the many facets of DNA and RNA
modification-editing processes and to some extent repair mechanisms. Each chapter offers …

[HTML][HTML] Bioinformatics analysis of mass spectrometry-based proteomics data sets

C Kumar, M Mann - FEBS letters, 2009 - Elsevier
Proteomics has made tremendous progress, attaining throughput and comprehensiveness
so far only seen in genomics technologies. The consequent avalanche of proteome level …

Protein identification using top-down spectra

X Liu, Y Sirotkin, Y Shen, G Anderson, YS Tsai… - Molecular & cellular …, 2012 - ASBMB
In the last two years, because of advances in protein separation and mass spectrometry, top-
down mass spectrometry moved from analyzing single proteins to analyzing complex …