This week’s Animal Behavior Graduate Group seminar:
Dr. Edwin Lewis, Departments of Entomology and Nematology, UC Davis
Infection behaviors of parasitic nematodes: The story of the slithering herd
Friday, May 4th, 12:10 in 194 Young Hall
Coffee and cookies will be available
Dr. Lewis’ website: http://nematology.ucdavis.edu/faculty/lewis/
My research program is wide-ranging in the scope of the questions asked and in the taxa that are studied. There is, however, a common thread to the work that takes place in my laboratory; we seek to understand why and how organisms find, recognize, assess and exploit resources. We ask questions about how insects and nematodes make decisions about resource utilization and what the fitness outcomes of the decisions are. To answer these kinds of questions, we engage in studies of behavior, population ecology, community ecology and evolutionary biology with several groups of insects, nematodes and bacteria. There are also intentional links to more practical pursuits including biological control of crop pests, predicting the impact of crop management on pest and beneficial organisms and restoration ecology. I see no difference between what is traditionally called “basic” and “applied” research, thus the links of nearly all of the work in the laboratory to agricultural or environmental concerns is explicit.
CPB Seminar Series: Spring 2012
When: Tuesdays, 4:10 – 5:30PM
Where: 1022 Life Sciences Building
May 1: Kyle Edwards, Postdoctoral Research Associate Michigan State University
Title: “Predicting the structure and dynamics of phytoplankton communities with functional traits”
Interested in presenting a seminar? Please contact email@example.com.
Additional seminar information: http://cpb.ucdavis.edu/Seminars.html.
MIC 291: Selected Topics in Microbiology
Hosted by MGG students
Dr. Ned Ruby
Professor, Medical Microbiology and Immunology
University of Wisconsin, Madison
“The squid-vibrio symbiosis: thinking about bacteria as individuals”
Wednesday, May 2, 2012
1022 Life Sciences
Interdisciplinary Graduate and Professional Student Symposium,
entitled The Future of Academic Publishing. We’ll here from a variety of perspectives on existing and emerging models of publishing and what the future might hold.
- Don Strong, Editor in Chief of the journal of Ecology
- Meredith Niles, PhD student in Ecology and Evolution and Science Lobbyist in Sacramento and DC,
- William Gunn, Director of Outreach for Mendeley Research Networks
- Karthik Ram, Postdoctoral scholar at UC Berkeley and Open Science advocate
- Colin Cunliff, PhD student in Physics
From Noon to 1pm in the ARC ballroom
Machine learning methods for protein function and structure prediction
Berkeley Phylogenomics Group
University of California, Berkeley
May 1, 2012, 12:00 p.m.
1005 GBSF Auditorium
Abstract: Theodosius Dobzhansky, the noted geneticist and evolutionary biologist, is famous for having said “Nothing makes sense except in the light of evolution.” In this talk, I will discuss the explicit use of evolution as a fundamental principle in bioinformatics, using machine learning methods in combination with information from protein structure and evolution to improve the power and specificity of a number of bioinformatics tasks, including prediction of protein structure and function, ortholog identification, functional site prediction, and simultaneous estimation of multiple sequence alignments and protein superfamily phylogenies. Because many of these methods require expertise and/or computational resources not available to most experimental biologists, we provide pre-calculated
phylogenetic trees for gene families in the PhyloFacts database. PhyloFacts 3.0 is a phylogenomic database of gene families across the Tree of Life. Each PhyloFacts family contains a multiple sequence alignment, phylogenetic tree, predicted orthologs, predicted pathway associations and experimental and other annotation data. As of April 26, 2012, PF 3.0 contains >7.3M protein sequences from >99K unique taxa (including strains) across >92K families.
Finally, I will describe our work on a fully automated system for high-throughput functional annotation of genomes and for taxonomic and functional annotation of metagenome (environmental sample) datasets. This system, which we call FAT-CAT (for Fast Approximate Tree Classification) uses hidden Markov models placed at internal nodes of PhyloFacts trees to classify sequences to different levels of functional hierarchies. Subtree nodes are annotated automatically using data available for sequences descending from those nodes, allowing both functional and taxonomic inference for sequences classified to those nodes. The PhyloFacts Phylogenomic Database is available at http://phylogenomics.berkeley.edu/phylofacts/.
“Population genomics of Batrachochytrium dendrobatidis, a fungal pathogen of amphibians”
Speaker: Dr. Jason Stajich
University of California, Riverside | Department Plant Pathology and Microbiology
Monday, April 23, 2012
1022 Life Sciences
BGI@UC Davis – Information on partnership capabilities and sample submission
Presented by: Bart Weimer, Ph.D.
Professor, Department of Population Health and Reproduction, School of Veterinary Medicine
Co-director of BGI@UCDavis
Dates/Locations: Wednesday, May 2
Davis: Genome Center, Auditorium, Rm. 1005
Thursday, May 3
Sacramento: Education Building, Lecture Hall 2222
Abstract: Dr. Weimer will be presenting an information seminar to all interested researchers regarding the BGI@UC Davis partnership. Through BGI, campus researchers will have access to the capabilities and expertise of one of the world’s premier genomics and bioinformatics institutes, while BGI researchers will have the ability to collaborate with UC Davis researchers, thereby benefiting from the university’s diverse resources and expertise, especially in biology, medical sciences, agriculture, the environment and education. There will be two seminars available, one in Sacramento and one in Davis – everyone is welcome.
DEPARTMENT OF EVOLUTION AND ECOLOGY
EVOLUTION OF ORGANISMAL DIVERSITY
Department of Biological Sciences
University of Idaho
“Detecting the signature of species interactions in the tree of life”
Thursday, April 19th, 2012
1022 Life Sciences Building
Faculty Host: Professor Michael Turelli, Department of Evolution and Ecology
Harmon Seminar Flyer.doc