21 research outputs found
Recommended from our members
Summer 1980
Principles of Turfgrass Weed Control III. Broadleaf Weeds (page 3) To Stop Leaks, First Find Them (6) Turgrass Research Field Day (9) Gypsy Moth (10) Try Ground Covers for Low-Maintenance (13) Pesticide News (18
Recommended from our members
Summer 1979
Fertilizer Programs for Bluegrass and Ryegrasses (page 3) Turfgrass Slide Sets Available (6) Seed Extracts Repel Japanese Beetles (8) Principles of Turfgrass Weed Control (10) How Regulation is Impacting on Pesticide Research (12) UMass Turfgrass Research Fund (20) UMass Turfgrass Research Field Day (20
Recommended from our members
Spring 1979 Conference Issue
Principles of Turfgrass Weed Control Annual Grasses (page 3) Bean-Shape Islands (7) High Protein Food From Grass (8) Forty-Eighth Annual Turf Conference and Third Industrial Show Program (10) Dutch Elm Disease: Perspectives After 60 Years (13) Toro Irrigation Design Seminar (14) Ideas: New and Old (15) More Pesticide Exams (16) Disposal of Pesticides in Massachusetts (18) Moth Controls Nutsedge Weeds (19) New Pesticide Bill (20
Recommended from our members
Winter 1979
Clubhouse Plants (page 3) Massachusetts Pesticide News (6) The Alsea Report on 2,4,5-T (8) Better Pest Control (10) Acid Rain: Something Else to Worry About? (11) UMass Turfgrass Research Update (13) 1979 Preemergence Crabgrass Control Tria
Cellular dynamics of tRNAs and their genes
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/116361/1/feb2s0014579309009661.pd
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.
Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole genome mutation screening in Candida albicans and aeruginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.
Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe