The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. Proteomic analysis for each CPTAC study is carried out independently by Proteomic Characterization Centers (PCCs) using a variety of protein fractionation techniques, instrumentation, and workflows. Mass spectrometry and...

The MicrobesOnline genome database contains over 1000 prokaryotic genomes. Genomes were last updated in late 2011 and no further database updates are planned. All genomes are analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, UCSC Blat, SwissProt, COG) and protein domains (HMMer, InterPro), to assign gene...

PATRIC (Pathosystems Resource Integration Center) is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools. PATRIC sharpens and hones the scope of available bacterial phylogenomic data from numerous sources specifically...

This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE 2.0 on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature. Maintained by the Lowe Lab, Biomolecular Engineering, University of California Santa Cruz.

Summary from the GEO: "Patients with locally advanced prostate cancer after radical prostatectomy are candidates for secondary therapy. However, this higher risk population is heterogeneous. Many cases do not metastasize even when conservatively managed. Given the limited specificity of pathological features to predict metastasis, newer risk prediction models are needed. We report a validation study...

Summary from the GEO: "Genomic DNA was extracted from tumors that developed in C57BL/6 mice fed with CD-HFD for 12 months alone or fed with CD-HFD for 12 months followed by 8 weeks of treatment with anti-PD-1. DNA extracted from five pooled tail-clips of C57BL/6 mice was used as reference DNA." Overall design from the GEO: "the tumor profiles of 9 CD-HFD only mice was compared to that of 12 CD-HFD/anti-PD1-treated...

Summary from the GEO: "Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment." Overall design from the GEO: "Small RNA samples from 11 Drosophila species." Abstract Summary: "To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit...

Summary from Dryad: "Abstract: The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace....

Summary from Dryad: "Abstract: Background: Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. Results: To enable functional analysis of human transposase-derived genes, we combined forward chemical genetic hypoxanthine-guanine...

Summary from Dryad: "Abstract: Context: Pituitary corticotroph adenomas are rare tumors that can be associated with excess adrenocorticotropic hormone (ACTH) and adrenal cortisol production, resulting in the clinically debilitating endocrine condition Cushing disease. A subset of corticotroph tumors behave aggressively, and genomic drivers behind the development of these tumors are largely unknown....