Public Comment on OMB Draft Risk Assessment Bulletin

The OIRA draft Risk Assessment Bulletin has worthy intentions and has stimulated useful review and discussion.; Most previous major documents in the development of the risk assessment field have been cited and used appropriately. In general, the formulation is too broad. The Revision should clarify the place of risk assessment as distinguished from hazard identification and from risk management.The category of "influential risk assessment" is unnecessary and confusing, and should be deleted. A single set of six standards would suffice, without the additional nine special standards for "influential risk assessments". Greater transparency within the EOP is desirable to give this process credibility and meet one of the explicit aims of the Bulletin. Finally, several omissions should be addressed: proactive engagement of stakeholders, public health context, deceptive use of quantitation, exclusion for research agencies, interagency steering committee and symmetry of risk assessment guidance for manufacturers as well as regulatory agencies.

The human eye proteome project

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/99592/1/pmic7517.pd

A landmark systems analysis of prion disease of the brain

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102674/1/msb200912.pd

Prognostic Factors in Cancer, 3 rd edition. By M. K. Gospodarowicz, B. O'Sullivan, L. H. Sobin (Eds.)

No abstracts.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55917/1/6385_ftp.pd

Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109787/1/pmic7911.pd

Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.

Tens of thousands of splice isoforms of proteins have been catalogued as predicted sequences from transcripts in humans and other species. Relatively few have been characterized biochemically or structurally. With the extensive development of protein bioinformatics, the characterization and modeling of isoform features, isoform functions, and isoform-level networks have advanced notably. Here we present applications of the I-TASSER family of algorithms for folding and functional predictions and the IsoFunc, MIsoMine, and Hisonet data resources for isoform-level analyses of network and pathway-based functional predictions and protein-protein interactions. Hopefully, predictions and insights from protein bioinformatics will stimulate many experimental validation studies

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

<p>Abstract</p> <p>Background</p> <p>Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched.</p> <p>Results</p> <p>We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events.</p> <p>Conclusion</p> <p>Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.</p

Highlights of B/D‐HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106985/1/pmic7698.pd