Seminar: Ed Lewis Friday at 12 #UCDavis “Infection behaviors of parasitic nematodes: The story of the slithering herd”

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:

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 May 1 “Predicting the structure & dynamics of phytoplankton communities w/ functional traits”

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

Additional seminar information:

MIC 291 – Dr. Ned Ruby – May 2, 2012

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
4:10 pm
1022 Life Sciences
Ruby 5-2-12.pdf

Future of Academic Publishing Panel discussion tomorrow at Noon – 1pm

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.

  1. Don Strong, Editor in Chief of the journal of Ecology
  2. Meredith Niles, PhD student in Ecology and Evolution and Science Lobbyist in Sacramento and DC,
  3. William Gunn, Director of Outreach for Mendeley Research Networks
  4. Karthik Ram, Postdoctoral scholar at UC Berkeley and Open Science advocate
  5. Colin Cunliff, PhD student in Physics

From Noon to 1pm in the ARC ballroom

Kimmen Sjolander talk, May 1st, 12pm, 1005 GBSF

Machine learning methods for protein function and structure prediction

Kimmen Sjölander
Associate Professor
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

Kimmen Flyer.pdf

Stajich seminar today on fungal population genomics

Genetics Seminar

“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

4:10 PM

1022 Life Sciences

BGI@UC Davis: Researcher Information Seminars May 2 and May 3

***Informational Seminar***

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

3:00-3:45 pm

Thursday, May 3

Sacramento: Education Building, Lecture Hall 2222

4:00-4:45 pm

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.

Ilkka Hanski seminars 4/25 & 4/26 at #UCDavis: Environmental biodiversity, human microbiota and allergy

Public Lecture:

Title: “Environmental biodiversity, human microbiota and allergy”
Time: Wednesday, April 25, 4:10 to 5:30 pm

Place: 1005 Genome

Evolution & Ecology Seminar:

Title: “Eco-evolutionary spatial dynamics”
Time: Thursday, April 26, 4:10 to 5:30 pm

Place: 1003 Giedt


Professor Hanski was awarded the Crafoord Prize in Biosciences by Royal Swedish Academy of Sciences in 2011 “for his pioneering studies on how spatial variation affects the dynamics of animal and plant populations”. He has established himself, in his more than 30-year career, as one of the world´s most eminent ecologists for developing a range of new analytical methods and mathematical models in ecology. Today, these are widely used to help scientists investigate how animal and plant species are affected when their habitats undergo splitting owing, for example, to urbanization, deforestation and climate change. Further, Hanski is recognized as a tireless advocate of the translational application of his research to public issues involving nature and biodiversity through his popular writings and public speaking. Among his many other honors, he is an elected Fellow of the Finnish Academy of Science and Letters, and a Foreign Member of the Royal Society (UK), the American Academy of Arts and Sciences and the National Academy of Sciences (US).

EVE Faculty Recruitment Seminar – Luke Harmon – Thursday, April 19th




Luke Harmon

Assistant Professor

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

Genetics Seminar on April 9, 2012: Dr. Brandon S. Gaut

Genetics Seminar

“The molecular diversity of adaptive convergence in E. Coli”
Speaker: Dr. Brandon S. Gaut

University of California, Irvine | Professor and Chair, Ecology and Evolutionary Biology

Monday, April 9, 2012
4:10 PM

1022 Life Sciences

Host: Jeffrey Ross- Ibarra