Showing papers by "Adam Kiezun published in 2012"
TL;DR: Exome sequencing methods and their applications in studies to identify the genetic basis of human complex traits are presented and include analyses of the whole-exome sequences of 438 individuals from across several studies.
Abstract: Shamil Sunyaev and colleagues present exome sequencing methods and their applications in studies to identify the genetic basis of human complex traits. They include analyses of the whole-exome sequences of 438 individuals from across several studies.
412 citations
TL;DR: The miRviewer web-server, presented here, encompasses all known miRNAs of currently fully annotated animal genomes in a visual 'birds-eye' view representation in a graphical outlook of the current miRNA world together with sequence alignments and secondary structures of each miRNA.
Abstract: Background
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression via binding to the 3' ends of mRNAs. MiRNAs have been associated with many cellular events ascertaining their central role in gene regulation. In order to better understand miRNAs of interest it is of utmost importance to learn about the genomic conservation of these genes.
65 citations
TL;DR: It is concluded that SNIPE can enhance the utility of shotgun proteomics data to facilitate the study of poorly detected proteins in complex mixtures.
Abstract: Motivation: Proteomics presents the opportunity to provide novel insights about the global biochemical state of a tissue. However, a significant problem with current methods is that shotgun proteomics has limited success at detecting many low abundance proteins, such as transcription factors from complex mixtures of cells and tissues. The ability to assay for these proteins in the context of the entire proteome would be useful in many areas of experimental biology.
Results: We used network-based inference in an approach named SNIPE (Software for Network Inference of Proteomics Experiments) that selectively highlights proteins that are more likely to be active but are otherwise undetectable in a shotgun proteomic sample. SNIPE integrates spectral counts from paired case–control samples over a network neighbourhood and assesses the statistical likelihood of enrichment by a permutation test. As an initial application, SNIPE was able to select several proteins required for early murine tooth development. Multiple lines of additional experimental evidence confirm that SNIPE can uncover previously unreported transcription factors in this system. We conclude that SNIPE can enhance the utility of shotgun proteomics data to facilitate the study of poorly detected proteins in complex mixtures.
Availability and Implementation: An implementation for the R statistical computing environment named snipeR has been made freely available at http://genetics.bwh.harvard.edu/snipe/.
Contact: ssunyaev@rics.bwh.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
13 citations
TL;DR: It is demonstrated that a high proportion of CLL patients harbor somatic and germline variants in NF-κB pathway genes, some of which appear to be functional and pharmacological inhibition of the pathway leads to increased cancer cell death.
3 citations