A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
R. Myers, J. Stamatoyannopoulos, M. Snyder
et al.
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.
1064 sitasi
en
Medicine, Biology
Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry
B. Searle, Lindsay K. Pino, Jarrett D. Egertson
et al.
Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20–25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone. Data-independent acquisition (DIA)-based proteomics often relies on mass spectrum libraries from data-dependent acquisition experiments. Here, the authors present a method to generate DIA-based chromatogram libraries, enabling DIA-only workflows and detecting more peptides than with spectrum libraries alone.
454 sitasi
en
Medicine, Computer Science
Encyclopedia of Biological Invasions
D. Simberloff, M. Rejmánek
This pioneering encyclopedia illuminates a topic at the forefront of global ecology - biological invasions, or organisms that come to live in the wrong place. Written by leading scientists from around the world, "Encyclopedia of Biological Invasions" addresses all aspects of this subject at a global level - including invasions by animals, plants, fungi, and bacteria - in succinct, alphabetically arranged articles. Scientifically uncompromising, yet clearly written and free of jargon, the volume encompasses fields of study including biology, demography, geography, ecology, evolution, sociology, and natural history. Featuring many cross-references, suggestions for further reading, illustrations, an appendix of the world's worst 100 invasive species, a glossary, and more, this is an essential reference for anyone who needs up-to-date information on this important topic. "Encyclopedia of Biological Invasions" features articles on: well-known invasive species such the zebra mussel, chestnut blight, cheatgrass, gypsy moth, Nile perch, giant African snail, and Norway rat; regions with especially large numbers of introduced species including the Great Lakes, Mediterranean Sea, Hawaiian Islands, Australia, and New Zealand; conservation, ecological, economic, and human and animal health impacts of invasions around the world; the processes and pathways involved in invasion; and, management of introduced species.