girarda « Center for Quantitative Life Sciences

Monday, April 7, 2014

Poster Award Winners

Postdoc/Trainee/Faculty: Jonathan Galazka
Grad student: Renee Bellinger
Undergrad student: Steven Hill

Program

8:00	Registration & refreshments (Poster & lightning talk slides setup)
9:00	Brett Tyler, Director, CGRB Opening Remarks
	Moderator: Glencora Borradaile
9:10	Gail Rosen, Drexel University Computational Challenges in Processing Metagenomic Data
10:00	Break (Poster & lightning talk slides setup)
10:30	Thomas Sharpton, OSU, Microbiology/Statistics From Noise to Signal: Mining Human Exome Sequences Reveals the Hunter-Gatherer Oral Microbiome
10:55	Stephen Giovannoni, OSU, Microbiology The Broad Implications of Genome Streamlining
11:20	Christopher Sullivan, OSU, CGRB Managing data across different experiments, hardware platforms and research groups
11:45	Lunch and Poster Session Turn in poster ballot envelopes to registration desk for counting by 2:00pm
	Moderator: Yuan Jiang
2:00	Arash Termehchy, OSU, Electrical Engineering and Computer Science Design Independent Data Exploration
2:25	David Hendrix, OSU, Biochemistry and Biophysics, Electrical Engineering and Computer Science Surfing the Noncoding RNA tidal wave
2:50	Stephen Ramsey, OSU, Biomedical Sciences, Electrical Engineering and Computer Science An Integrative Computational Systems Biology Approach for Mapping Gene Regulatory Networks
3:15	Break
	Moderator: Thomas Sharpton
3:50	Awards Ceremony, Brett Tyler
4:00	Sandrine Dudoit, UC Berkeley Normalization of RNA-Seq Data
4:50	Thomas Dietterich, OSU, Distinguished Professor and Director of Intelligent Systems Closing Remarks

*Fall Term 2013*
October 2, 2013	William Muller Department of Biochemistry McGill University, Quebec, Canada Oncogene-mediated signal transduction in transgenic models of breast cancer Host: Siva Kolluri
October 16, 2013	Steve DiFazio Department of Biology West Virginia University Population Genomics of Populus trichocarpa Host: Steve Strauss
October 30, 2013	Jamie Cate Department of Molecular & Cell Biology University of California, Berkeley From Neurospora to yeast: Pathways to sustainable biofuels Host: Jon Galazka
November 13, 2013	Vladimir Botchkarev Boston University Epigenetic regulation of Keratinocyte differentiation and reprogramming Host: Arup Indra
*Winter Term 2014*
January 8, 2014	Vanessa Sperandio Department of Microbiology UT Southwestern Medical Center EHEC sings: Pour some sugar on me Host: Luiz Bermudez
January 22, 2014	Trent Northen Lawrence Berkeley National Laboratory Metabolic dark matter: mass spectrometry explorations of bacterial metabolism Host: Steve Giovannoni
February 5, 2014	John Taylor Department of Plant and Microbial Biology University of California, Berkeley Population genomics of fungi: divergence, adaptation and genome wide association Host: Joey Spatafora
February 19, 2014	Nick Grishin Department of Biochemistry UT Southwestern Medical Center Is bioinformatics beyond BLAST useful? Host: Andy Karplus
March 5, 2014	Weihong Qiu Department of Physics Oregon State University Shining Light on the Mechanism of Molecular Motor Proteins
*Spring Term 2014*
April 2, 2014	Robin Buell Department of Plant Biology Michigan State University Exploring the diversity of wild and cultivated potato through genomics Host: Elizabeth Savory
April 16, 2014	Nancy Keller Department of Medical Microbiology and Immunology University of Wisconsin – Madison Insights into the fungal secondary metabolome Host: Joey Spatafora
April 30, 2014	No seminar
May 14, 2014	Eric Nielsen Molecular, Cellular, Developmental Biology University of Michigan The roles of CSLD proteins in polarized cell wall deposition in Arabidopsis Host: Valerian Dolja
May, 21, 2014Special Seminar3:30 – 4:30 pm Crop Science Bldg Room 122	Biswarup Mukhopadhyay Department of Biochemistry Virginia Bioinformatics Institute Development of biological sulfate reduction and thioredoxin systems and methanogenic archaea
May 28, 2014	Colin Johnson Department of Biochemistry & Biophysics Oregon State University The Emerging Roles of the Ferlin Family of Proteins in Membrane Trafficking and Human Disease

Monday, June 3, 2013

Program

8:00	Registration & refreshments (Poster & lightning talk slides setup)
9:00	Brett Tyler, Director, CGRB Opening Remarks
	Moderator: Molly Kile, College of Public Health & Human Sciences
9:15	Katrina Waters, Pacific Northwest National Laboratory Integration of Multiple Omics Data for Network Reconstruction of Viral Pathogenesis
10:15	Natalia Shulzhenko, OSU College of Veterinary Medicine Antibiotic-induced Changes in Microbiota and Its Host: A Multi-omics Perspective
10:35	Break (Poster & lightning talk slides setup)
11:10	Cindy Grimm, OSU Mechanical, Industrial & Manufacturing Engineering Research Analyzing Shape Change in Biological Structures
11:30	Edward Waymire, OSU Department of Mathematics Some Dynamic, Stochastic and Numerical Problems from Biology
11:55	Lunch and Poster Session Turn in poster ballot envelopes to registration desk for counting by 2:00pm
	Moderator: Yanming Di, Statistics
2:00	E. Andrés Houseman, OSU College of Public Health DNA Methylation Arrays and Cell Mixtures
2:25	Yuan Jiang, OSU Department of Statistics Identification of Differentially Expressed Genes by Adjusting the Non-Uniformity in RNA-Seq Data
2:50	Break
3:20	Molly Megraw, OSU Department of Botany & Plant Pathology Promoter Architecture in Plant Model Systems
3:45	Joe Beckman, OSU Environmental Health Sciences Center Closing remarks
4:00	Awards Ceremony

September 19-20, 2010

Program

3:00 pm	Registration & poster setup
4:00	Welcome Reception
5:00	Jim Carrington, CGRB DirectorModerator: Lynda Ciuffetti
5:10	Christopher Sulliivan, CGRB “Recent Advances within the CGRB Computational Infrastructure”
5:20	Mark Leid, Pharmaceutical Sciences“Ctip2/Bcl11b: A Top-Level Regulator of Cell Fate in Multiple Developmental Systems”
5:45	Elliot Meyerowitz, California Institute of Technology“Chemical and Physical Signals and their Interactions in Plant Stem Cell Control”
6:30-9:00	Poster Session and Sponsor Displays
8:30 am	Coffee and Pastries
9:00	Joseph Spatafora, Botany & Plant Pathology“Tolypocladium inflatum: A Home Grown Genome”
9:25	Pallavi Phatale, Botany & Plant Pathology“Genetic Studies to Uncover Rules for Centromere Inheritance”
9:50	Jay Dunlap, Dartmouth Medical School”Genetic and Molecular Dissection of a Simple Circadian System”
11:00	P. Andrew Karplus, Biochemistry and Biophysics“A Beneficial Bulge: TT-Helices and the Evolution of Proteins”
11:25	Richard Spinrad, Vice President for Research“OSU Research Now, Next, and After Next”
1:15	Award Presentation
1:20	Gary Ruvkun, Harvard Medical School“Phylogenetic Profiling of the Small RNA Pathway Genes of C. elegans”
2:05	Doug Bryant, Electrical Engineering and Computer Science“Next-Generation Hybrid Empirical-ab initio Gene Prediction”
2:30	Daniel Schafer, Statistics“Some Lessons from the Biometry of Evolution and the Evolution of Biometry”
3:30	Gene D.Kundson Lectures featuring Peter & Rosemary Grant, Princeton University“Evolution of Darwin’s Finches: The Roles of Genetics, Ecology and Behavior”
5:00	Kundson Lectures Reception

*Fall Term 2010*
October 6, 2010	Sophien Kamoun The Sainsbury Laboratory John Innes Centre Norwich, United Kingdom “The secrets of a plant killer: Evolution and function of Phytophthora effectors” Host: Niklaus Grunwald
October 20, 2010	Matteo Pellegrini Department of Molecular, Cell and Developmental Biology University of California, Los Angeles “Epigenetic and Transcriptomic Profiling using Illumina Sequencers” Host: Jim Carrington
November 3, 2010	Canceled
November 17, 2010	Judith Berman Department of Genetics, Cell Biology and Development University of Minnesota “Centromeres and neocentromeres in Candida albicans” Host: Michael Freitag
~~December 1, 2010~~ Postponed to January 26, 2011	Inder Verma Laboratory of Genetics The Salk Institute for Biological Studies “Cancer: a malady of genes” Host: Arup Indra
*Winter Term 2011*
January 12, 2011	Cancelled
January 26, 2011	Inder Verma Laboratory of Genetics The Salk Institute for Biological Studies “Cancer: a malady of genes” Host: Arup Indra
February 9, 2011	W. Kelley Thomas Hubbard Center for Genome Studies University of New Hampshire “Ultra-deep 454 sequencing of the meiofaunal biosphere: practice, promises and pitfalls” Host: Dee Denver
February 23, 2011	Cancelled
March 9, 2011 CANCELLED	Danny Schnell Biochemistry and Molecular Biology University of Massachusetts at Amherst “Studies of Chloroplast Protein Targeting and Membrane Expansion as a Model for Understanding Organelle Biogenesis and Homeostasis” Host: Valerian Dolja
*Spring Term 2011*
April 6, 2011	Ruedi Aebersold Institute of Molecular Systems Biology Eidgenössische Technische Hochschule Zürich Zürich, Switzerland “Proteomics and Systems Biology” Host: Mark Leid
April 20, 2011	Jeffrey Townsend Department of Ecology and Evolutionary Biology, Yale University “Phylogenetic and comparative transcriptomic analysis of fungal fruiting body development”Host: Joey Spatafora
Friday, April 29, 2011	Ellen Rothenberg Division of Biology California Institute of Technology“ Transcriptional control of T-cell lineage identity” Host: Mark Leid
June 1, 2011	Graham Hatfull Department of Biological Sciences University of Pittsburgh “Exploration and Exploitation of Mycobacteriophages” Hosts: Dee Denver, Theo Dreher and Barbara Taylor

September 20-21, 2009

Program

3:00 pm	Registration & poster setup
4:00	Welcome Reception
5:00	Jim Carrington, CGRB DirectorAchievements of the Computational & Genome Biology Initiative
5:20	Noah Fahlgren, MCB Graduate ProgramSmall RNA Transcriptome Profiling and Evolution
5:40	Jason Cumbie, MCB Graduate ProgramComputational and Statistical Tools for Type III Effector Transcriptome Profiling
6:00	Kristina Smith, Biochemistry & BiophysicsEvolution of Centromeres in Filamentous Fungi
6:25	Steve Jacobsen, University of California, Los AngelesDNA Methylation
7:05-9:00	Poster session; Sponsor displays
8:30 am	Coffee and Pastries
9:00	Chrissa Kioussi, College of PharmacyGoodies for the Tooth Fairy: Ctip2 and the Production of Enamel
9:25	Adrian Gombart, Linus Pauling InstituteVitamin D and Human Innate Immunity
9:50	Joseph Thornton, University of OregonEvolution of Protein Structure and Function in the Steroid Hormone Receptor Family
10:55	Pankaj Jaiswal, Botany & Plant PathologyOntologies for Plant Genomics and Phenomics
11:20	Olivier Voinnet, Institut de Biologie Moleculaire des Plantes du CNRS, StrasbourgGenomics, Mechanisms and Roles of Small Silencing RNA
1:00	Announcement of Poster Awards
1:10	Roundtable Discussion – Issues Affecting Research, Funding & Education in Molecular Biosciences at OSUPanelists: Howard Grimes, Washington State University; Sonny Ramaswamy, Oregon State University; Steve Jacobsen, UCLA; Michael Lynch, Indiana University
3:05	Michael Lynch, Indiana UniversityThe Origins of Genome Complexity
3:45	William Cresko, University of OregonPopulation Genomic Analysis of Stickleback Evolution Using Illumina-Sequenced RAD tags

Saturday & Sunday, October 4-5, 2008

Program

12:00 pm	Registration & Poster setup
1:00	Jim Carrington, Director, CGRB Introduction, CGRB update
1:10	New Technologies in CGRBMark Dasenko, Chris Sullivan, Caprice Rosato, Anne-Marie Giirard – CGRB Core Labs
1:45	Peter Dolan, Zoology, “TileQC: A System For Tile-Based Quality Control and Data Manipulation”
2:10	Patrick Chappell, Zoology “Molecular Circadian Clock Regulation of Mammalian Reproduction”
2:35	Brian Wall, Office of Technology Transfer “The OSU Venture Fund: Bridging the Research Support Gap”
3:30	Erica Bakker, Horticulture “Genome-Wide Pathogenicity Gene Discovery in Botrytis cinerea”
3:55	Detlef Weigel, Max Planck Institute for Developmental Biology “Whole-Genome Variation and its Impact on Reproductive Isolation in Arabidopsis thaliana”
4:45	Poster Session, Sponsor’s Displays and Open Bar
7:45-11:00	Entertainment, Announcement of Awards
7:30 am	Continental Breakfast
8:30	Arup Indra, College of Pharmacy “CTIP – A Novel Regulator of Skin Organogenesis”
8:55	Xiaoli Fern, Electrical Engineering & Computer Science “Ensemble and Multi-View Data Clustering”
9:20	Steven Brenner, University of California, Berkeley “Ultraconserved Nonsense: Gene Regulation by Splicing and RNA Surveillance”
10:30	Vincent Remcho, Chemistry “Materials and Methods for the Design, Fabrication, and Application of Microfluidic Tools for Chemical Analysis”
10:55	Brendan Jeffery, MCB Graduate Program “Chlamydial Biology and Genomics”
11:20	Thomas Wolpert, Botany and Plant Pathology “A Downside to Plant Disease Resistance, Good LOV Gone Bad”
11:45-1:00	Lunch

Saturday-Sunday, September 29-30, 2007

Program

12:00 pm	Registration and Poster setup
1:00	Jim Carrington, Director, CGRB Welcome, Updates and Announcements
1:20	Gary Merrill, Biochemistry and Biophysics “MCB Core Program Curriculum Revisions”
1:35	Darryl Conte, University of Massachusetts Medical Center “Dicer-Related Helicases: Defining Conserved Complexes and New RNAi-Related Pathways in C. elegans”
2:10	Tai Montgomery, MCB Graduate Program “ARGONAUTEs and Silencing Specificity”
3:05	Siva Kullori, Environmental and Molecular Toxicology “Signaling from Nucleus to Mitochondria: Nuclear Receptor Nur77 Based Cancer Therapeutics”
3:30	Michael Freitag, Biochemistry and Biophysics “Centromere Assembly and Maintenance”
3:55	Shelley Halpain, University of California, San Diego “MAPs, MARCKS, and Morphology: A Few Keys to Neuronal Development”
5:00	Poster Session, Sponsors’ Displays and Open Bar
6:45	Dinner
8:00-12:00	Entertainment, Announcement of Awards
8:45 am	Jeff Chang, Botany and Plant Pathology “Functional Genomic Screen for Type III Effectors of Mutualistic Rhizobia”
9:10	Martin Schuster, Microbiology “Social Cheating in Pseudomonas aeruginosa Quorum Sensing”
9:35	Jennifer Nemhauser, University of Washington “Manipulation and Dissection of Plant Growth Control Networks”
10:45	Valerian Dolja, Botany and Plant Pathology “Origin of Viruses and Cells in Light of Comparative Genomics”
11:10	Joe Beckman, Linus Pauling Institute “Mass Spectometry of Native Proteins from Brain: Understanding How SOD Causes ALS”
11:35	Theresa Filtz, Pharmaceutical Sciences “Lipids, Dimers, Phosphates, Calcium and Lipase: Fine Tuning the Regulation of a Common Signaling Pathway”
12:00 pm	Lunch

Friday and Saturday, September 15-16, 2006

Program

12:00 pm	Registration & Poster setup
1:15	Jim Carrington, Director, CGRB Introduction, CGRB update
1:35	Dee Denver, Assistant Professor, Zoology “Forces Shaping Genome Evolution”
2:00	Todd Mockler, Assistant Professor, Botany and Plant Pathology “Regulation of Diurnal Plant Gene Expression”
2:25	Barbara Robbertse, Postdoctoral Research Associate, Botany and Plant Pathology “A Phylogenomic Analysis of the Ascomycota”
3:15	Roundtable Discussion – Computational Biology and CGBI Initiative Scott Givan, Lead Presenter
4:15	Joe Ecker – Keynote Address, The Salk Institute “Discovery of Functional Elements in Arabidopsis Genome and Epigenome”
5:15	Poster Session and Sponsors’ Displays
7:00	Dinner
8:00-12:00	Entertainment
7:30-9:00 am	Continental Breakfast
9:00	Dan Rockey, Associate Professor, Biomedical Sciences “Genomics and Genetics of Chlamydia”
9:25	Ian Paulsen – Keynote Address, TIGR “The Ins and Outs of Membrane Transport: A Genomic View”
10:35	Announcement of Awards
10:40	Sarah Sowell, Ph.D. Student, MCB Graduate Program “Can Proteomics Reveal the Metabolic States of Marine Micro-organisms in Situ (in the Ocean)?”
11:05	Steve Strauss, Professor, Forest Sciencs “Gibberellic Acid Genes for Physiological Sculpture of Trees”
11:30	Lunch
	Post Retreat
1:10 pm	2nd Annual CGRB Golf TournamentEagle Crest Challenge Course

2006 Fall Conference

Fall Term 2012
October 3, 2012	Sean Megason Biological and Biomedical Sciences Harvard Medical School“In toto imaging and modeling reveal higher scale principles of embryonic patterning” Host: Robert Tanguay
October 17, 2012	Axel Brunger Molecular and Cellular Physiology Stanford University“Insights into the molecular mechanism of synaptic vesicle fusion”Host: Andy Karplus
October 31, 2012	Yanming Di Department of Statistics Oregon State University “Statistical methods for gene mapping with pedigree data: linkage, association and identity-by-descent (IBD)”
November 14, 2012	Dennis Carson Moores Cancer Center University of California – San Diego “Cancer stem cells as therapeutic targets” Host: Siva Kolluri
November 28, 2012	Richard Caprioli Department of Biochemistry Vanderbilt University School of Medicine “Molecular Imaging of Tissue Sections by Mass Spectrometry” Host: Craig Marcus
Winter Term 2013
January 9, 2013	Victor Nizet Skaggs School of Pharmacy and Pharmaceutical Sciences University of California – San Diego “Probing the Host-Pathogen Interface for New Therapeutic Targets“ Host: Luiz Bermudez
January 23, 2013	Iain Cheeseman Whitehead Institute for Biomedical Research “Generating a Dynamic Kinetochore-Microtubule Interface”Host: Michael Freitag
February 6, 2013	Yi Liu Physiology Univsity of Texas Southwestern Medical Center“Less is more, codon usage regulates protien expression, structure and function” Host: Michael Freitag
February 20, 2013	Mark Martindale Whitney Laboratory for Marine Bioscience University of Florida“The jelly ball genome: insights from a ctenophore, an early metazoan lineage”Host: Barbara Taylor
March 6, 2013	Eli Meyer Department of Zoology Oregon State Univeristy“2b-RAD, a cost effective method for genome-wide SNP genotyping”
March 20, 2013 Additional seminar	Yuanchao Wang Department of Plant Pathology Nanjing Agricultural University, China“Functional analysis of Phytophthora sojae RxLR effectors”
Spring Term 2013
April 3, 2013	Jeffrey Bennetzen Department of Genetics University of Georgia“Mechanisms and rates of local genome rearrangement in angiosperms”Host: Pankaj Jaiswal
April 17, 2013	Richard Hamelin Department of Forest Sciences University of British Columbia“A tale of two poplar pathogens”Host: Nik Grunwald
May 1, 2013	Vitaly Citovsky Department of Biochemistry and Cell Biology Stony Brook University“Plant-Pathogen Arms Race: How Agrobacterium Subverts Host Defense”Host: Valerian Dolja
May 15, 2013	Eric Selker The Institute of Molecular Biology University of Oregon“Genome defense, gene silencing and epigenetic dynamics in Neurospora” Host: Michael Freitag
May 29, 2013	Robbie Waugh Cell and Molecular Sciences The James Hutton Institute“Post domestication selection and adaptation in cultivated barley“ Host: Pat Hayes
May 30, 2013 11:00 – noon LPSC 402 Additional seminar	Gitta Coaker Plant Pathology University of California, Davis“Unraveling Plant Immune Perception and Signaling” Host: Jeff Chang

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