Category: Seminars and Talks

:Noah Fierer from the University of Colorado Boulder
"Exploring terra incognita: the biogeography of soil microorganisms", will be on Thursday, January 10 at 4:10pm in 1003 Giedt Hall.

A few of his publications include:

• Fierer, N., C.M. McCain, P. Meir, M. Zimmermann, J.M. Rapp, M.R. Silman, R. Knight. 2011. Microbial elevational diversity does not follow the biogeographical trends of plants and animals. Ecology. 92: 797-804.
• Fierer, N., J.W. Leff, B.J. Adams, U.N. Nielsen, S.T. Bates, C.L. Lauber, S. Owens, J.A. Gilbert, D.A. Wall, J.G. Caporaso. in press. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS (available online)
• Fierer, N., S. Ferrenberg, G.E. Flores, A. Gonzalez, J. Kueneman, T. Legg, R.C. Lynch, D. McDonald, J.R. Mihaljevic, S.P. O’Neill, M.E. Rhodes, S. Song, W.A. Walters. 2012. From animalcules to an ecosystem: application of ecological concepts to the human microbiome. Annual Review of Ecology, Evolution, and Systematics. 43:137-155.
• Hulcr, J., J.B. Henley, N.R. Rountree, N. Fierer, A. Lucky, M.D. Lowman, A.M. Latimer, R.R. Dunn. 2012. A jungle in there: bacteria in belly buttons are highly diverse, but predictable. PLoS One. 7(11): e47712.
• Craine, J.M., N. Fierer, K. McLauchlan, A. Elmore. in press. Reduction of the temperature sensitivity of soil organic matter decomposition with sustained temperature increase. Biogeochemistry (available online)
• Fierer, N., C.L. Lauber, N. Zhou, D. McDonald, E.K. Costello, R. Knight. 2010. Forensic identification using skin bacterial communities. PNAS 107: 6477-6481.

More about his research is here.

CPB Seminar Series: Fall 2012

When: Tuesdays, 4:10 – 5:30PM

Where: 1022 Life Sciences Building

November 27: James Mallet, Distinguished Lecturer

Department of Organismic and Evolutionary Biology, Harvard University

Title: “Hybridization and speciation in Amazonian butterflies: rainforest genomics”

Host: Rick Grosberg

Abstract:
It is a seductive idea that species are independent evolutionary units. Natural hybridization is rare in nature on a per-individual basis, but it may affect many species. Brightly-coloured Heliconius butterflies engage in Müllerian mimicry of other species. Although most of this mimicry is due to adaptive reconstruction of similar patterns, we’ve long suspected that colour patterns are exchanged among some closely related species that hybridize occasionally in nature. We have recently shown that genomic regions that determine mimicry have been exchanged repeatedly among species to form new, adaptive combinations. Through their joint effects on mating behaviour and signalling to predators, these novel colour patterns are also involved in triggering evolution of new species.

Talk Title:

One-step Bacterial Genome Closure with Single-molecule Hybrid Assembly

Abstract:

Emerging single-molecule sequencing instruments can generate multi-kilobase sequences with the potential to dramatically improve genome and transcriptome assembly. However, the high error rate of single-molecule reads is challenging, and has limited their use to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that utilizes shorter, high identity sequences to correct the error in single-molecule sequences. We present an assembly recipe combining long high-error sequences and short high-idenitity sequences that can generate near-finished bacterial genomes. We demonstrate the utility of this approach on several bacterial genomes: in the best examples, producing automatically closed bacterial chromosomes without the use of paired ends.

Speaker:

Sergey Koren, Ph.D.

Bioinformatics Scientist, Genomics

National Biodefense Analysis and Countermeasures Center

Affiliations:

Center for Bioinformatics and Computational Biology

University of Maryland

Email: sergek

Reference Publication:

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, and Phillippy AM.

Nature Biotechnology 30(7):693-700 2012

http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt.2280.html

Location and Time: 4202 GBSF 11am-12pm Thursday, November 15th

[seminars]

Plant Pathology 290 Graduate Seminar Series

Plant Pathology

UC Davis

“Evolution of the Virus World”

Dr. Valerian Dolja

Professor, Department of Botany and Plant Pathology,

Oregon State University

Monday, November 5, 2012

9:00-9:50 a.m.

115 Hutchison

V. Dolja Flier.doc

Just got this:

** PLEASE DISTRIBUTE – Special Seminar: Dr. Huanming (Henry) Yang, BGI; November 9 from 4:10-5:00pm, Genome Center Auditorium #1005, Reception to follow at UC Davis

On behalf of Vice Chancellor Lewin and Professor Yilma, we are pleased to announce a special seminar by Dr. Huanming (Henry) Yang, chairman of BGI. Please distribute the following seminar announcement to others who may be interested. If you have any questions, please contact ocr@ucdavis.edu.

** Special Seminar Announcement **

Dr. Huanming (Henry) Yang

Chairman, BGI

Genomics Cannot be Done Alone:

Working together for a better world

Friday, November 9, 4:10 – 5:00 pm

1005 GBSF, Genome Center Auditorium, UC Davis

reception to follow

Hosted by the Office of Research and

The Department of Medical Microbiology & Immunology

This presentation by Huanming Yang, Ph.D., co-founder and chairman of BGI—formerly known as the Beijing Genomics Institute—provides an overview of the past, present, and future of BGI. Dr. Yang reviews the origins of BGI with the sequencing of 1% of the Human Genome Project at a time when China was unrecognized in genomic sciences. He describes the significant impact that BGI’s first-ever sequencing and sharing of the entire rice genome had on advancing rice research and its potential impact on global health. Additional breakthrough sequencing projects completed by BGI, many conducted in collaboration with the global research community, are presented. Professor Yang emphasizes BGI’s mission of sharing its extensive next-generation sequencing capacity and bioinformatics capabilities with the goal of promoting the advancement and application of global genomics.
2012Nov9-HuanmingYang-BGI.pdf.pdf

PBGG Seminar

“Messages from the Arctic: Transcriptome analysis of an Arctic mustard flower color polymorphism”

Speaker: Dr. Justen Whittall

Santa Clara University

Friday, October 19, 2012

12:10 – 1:00 PM

1022 Life Sciences

Host: Daniel Fulop

CPB Seminar Series: Fall 2012

When: Tuesdays, 4:10 – 5:30PM

Where: 1022 Life Sciences Building

• October 2: Susan Lott, Assistant Professor
  Department of Evolution and Ecology, UC Davis
  Title: “Genomic approaches to robustness and constraint in the evolution of developmental traits in Drosophila”

• October 9: Thomas Claverie, Postdoctoral Research Associate
  Department of Evolution and Ecology, UC Davis
  Title: TBA

• October 16: Johanna Schmitt, Professor
  Department of Evolution and Ecology, UC Davis
  Title: TBA

• October 23: David Plachetzki, Postdoctoral Research Associate
  Center for Population Biology, UC Davis
  Title: TBA

• October 30: Louis Pitelka – Senior Visiting Scientist
  NEON, Inc.
  Title: “The National Ecological Observatory Network (NEON): From Petals to Petabytes”
  Host: Alan Hastings

• November 6: Tracy Heath, Postdoctoral Research Associate
  Department of Integrative Biology, UC Berkeley
  Title: TBA
  Hosts: Brian Moore and Luke Mahler

• November 13: Carl Boettiger, Doctoral Candidate, Exit Seminar
  Title: “Regime Shifts in Ecology and Evolution”

• November 20: TBA

• November 27: James Mallet, Distinguished Lecturer
  Department of Organismic and Evolutionary Biology, Harvard University
  Title: TBA
  Host: Rick Grosberg

• December 4: Rebecca Best, Doctoral Candidate, Exit Seminar
  Title: TBA

CPB Seminar Series Fall 2012.pdf