Friday, September 9, 2016

Poster Award Winners

 Postdoc/Trainee: Rodrigo Goncalves,  Functional characterization of chromo domain proteins  
 Grad student:  Martin Pearce,  Targeting therapy resistant cancer through the Bcl-2 family of proteins  
 Undergrad student:  Madeleine Duquette & Anna Co,  P. sojae revertants: return of the virulence

Program

8:00Registration & refreshments (Poster & sponsor setup) 
9:00Brett Tyler, Director, CGRB
Introduction, CGRB update
  Moderator: David Maddison, Integrative Biology
9:25Stephanie Yarwood, University of Maryland
Are Urban Centers leading to Microbial Biodiversity Loss?
10:10Carol Mallory-Smith,  Crop & Soil Science 
National Academies Report:Genetically Engineered Crops: Experiences and Prospects
10:35Break (Poster & sponsor setup / displays)
11:00Chrissa Kioussi, College of Pharmacy  
Myopathies and Metabolic Syndrome
11:25Susan Tilton, Environmental & Molecular Toxicology
Role of miRNAs in pulmonary inflammation associated with diet and smoking
11:50Laura Kubatko, Ohio State University
Genome-scale Evolutionary Inference using Site Pattern Frequencies
12:35Lunch (Poster and Sponsor setups / displays)
  Moderator: Kathy Magnusson, Biomedical Sciences
1:50Michael Wing, Forest Engineering, Resources & Management 
Natural resource phenotyping with unmanned aircraft systems (UAS) 
2:15Fuxin Li, Electrical Engineering and Computer Science
Object Recognition and Semantic Segmentation in the Deep Learning Era
2:40George Perry, University of Texas, San Antonio 
Role of Mitochondria in the Oxidative Stress of Alzheimer Disease
3:25Break (Poster and Sponsor setups / displays)
3:50Jim Strother, Integrative Biology
Unraveling neural circuits using genetically encoded probes   
4:15Patrick Chappell, Biomedical Sciences 
An in vitro exploration into the effects of estrogen and endocrine disruptors on neuroendocrine regulation of puberty and reproduction in females
4:40Roy Haggerty, Associate Vice President for Research, Office of Research
Closing remarks
5:00 – 7:30Poster Session/Reception, Sponsor Displays

Thank you to our conference committee:

David Maddison, Integrative Biology
Kathy Magnusson, Biomedical Sciences
Steven Strauss, Forest Ecosystems & Society

Thank you to our sponsors:

Applied Biosystems
Illumina
Invitrogen
Pacific Biosciences
Fall Term 2016
September 28, 2016Matthew Andrews 
Associate Dean for Strategic Initiatives and Administration
OSU, Dept of Biochemistry & Biophysics
Genes that control hibernation in mammals
October 12, 2016Zhongchi Liu
University of Maryland
Genomic approaches to identify genes and gene networks that regulate strawberry fruit development 

Host: Steve Strauss
October 26, 2016Susannah Tringe
Joint Genome Institute
Microbial communities and greenhouse gas cycling in coastal wetlands
Host: Dave Myrold
November 9, 2016William Cresko
University of Oregon
The genomic basis of stickleback evolution in 50 years
Host: Brett Tyler
December 7, 2016
 Speaker rescheduled to February 1, 2017
Winter Term 2017
January 18, 2017Keith Dunker
Indiana University
A Toolkit for Developmental Biology:
Intrinsically Disordered Protein, Alternative Splicing, and Post-translational Modification (IDP-AS-PTM)
Host: Andy Karplus 
February 1, 2017Liang Huang
OSU, Computer Science
Linear-Time Prediction of RNA Secondary Structures 
February 15, 2017Sue Biggins
Fred Hutchinson Cancer Research Center
How do cells get the right chromosomes?
Host: Michael Freitag 
March 7, 2017Special Seminar
4:00 – 5:00 pm
ALS 4001
Yuanchao Wang
Nanjing Agricultural University, China
Defense and counter-defense during Phytophthora infection
Host: Brett Tyler
March 15, 2017Aaron Wright
Pacific Northwest National Laboratory
Activity-based profiling of nutrient acquisition and metabolism in microbes and microbial communities
Host: Dave Myrold
Spring Term 2017
April 5, 2017Noah Fierer
University of Colorado Boulder
Searching for simplicity amidst the complexity of the soil microbiome
Host: Thomas Sharpton 
April 19, 2017Lisa Fauci
Tulane University
Explorations in the bio-fluid-mechanics of locomotion
Host: Juan Restrepo 
May 3, 2017John Reinitz
University of Chicago
From Drosophilidae to Sepsidae…and Back Again
Host: David Hendrix
May 17, 2017Laura Heiser
Oregon Health & Science University
An integrative systems biology approach to study therapeutic response in breast cancer
Host: Siva Kolluri
May 31, 2017June Medford
Colorado State University
Plant Synthetic Biology:  From Computational Protein Designs and Engineering Approaches comes a pathway to sustainable systems
Host: Molly Megraw

History of the Knudson Lecture Series

The Collins Pine Company established the Gene Knudson Lectures in Molecular Genetics in 1983 as a way to honor Gene Knudson for his many years of service to the company as a director. Knudson was intimately involved in the planning progress to develop programs in molecular genetics and materials science at Oregon State University. Creating this lectureship was seen by the University as a fitting way to pay tribute to Knudson and to help develop programs that would be beneficial to the entire state of Oregon.
 
Past lecturers have included:

  • Richard Lenski (2016)
  • Francis Martin (2013)  Event Poster
  • Peter and Rosemary Grant (2010) Event Poster
  • Susan Lindquist (2007)
  • Mario Capecchi (2005)
  • Victor Ambros (2003)
  • Russ Doolittle (1999)
  • Rich Roberts (1997)
  • Bud Ryan (1996)
  • Edwin Krebs (1995)
  • Sharon Long (1994)
  • Bruce Alberts (1993)
  • Nina Fedoroff (1992)
  • Paul Berg (1990)
  • Roger Beachy (1989)
  • Harold Varmus (1988)

Gene D. Knudson Biography

Gene D. Knudson was born in 1916 in Washtucna, Washington (near Pullman), to Andrew Christian and Eta Chapman Knudson. He graduated from high school in Weston, Oregon. He graduated with honors from the School of Forestry at Oregon State College in 1939 and then served in Europe as an artillery officer during the Second World War. He was awarded the Bronze Star and the French Croix de Guerre with silver star.
 
Knudson started his career in 1949 as chief forester of Willamette Valley Lumber Company, as Willamette Industries was then called. He earned successive promotions to logging manager, vice president for raw material supply, and executive vice president, and in 1970 became president and chief operating officer. He became chief executive officer in 1974, and was elected chair of Willamette’s board of directors in 1976. He retired from his position as CEO in 1981, and from the board chairship in 1984.
 
Knudson was a well-liked and respected chief. In 1984, in a letter to then-Forestry dean Carl Stoltenberg, Cathy Baldwin Dunn, corporate communications manager for Willamette Industries, wrote that Knudson was “universally loved and respected…a man of his word, a straight-shooter; extremely modest; highly intelligent yet a very practical thinker; …he likes people and knows how to manage them.” He was similarly esteemed by his peers in the wood-products industry.
 
Knudson served on the Oregon State Board of Forestry from 1961 to 1968; in 1961 he was influential in transferring the state’s forestry research program from the Department of Forestry to Oregon State University and placing it under the direction of the Dean of the College of Forestry. He was a member of the Forest Research Laboratory’s statutory Advisory Committee.
 
He served in leadership roles in many industry-related organizations, including the Oregon Logging Congress, Associated Oregon Industries and its legislative arm the Oregon Forest Industries Council, the Industrial Forestry Association, the National Forest Products Association, the Western Forestry and Conservation Association, and the Forest History Society.
 
For 25 years, he was on the board of Keep Oregon Green, a fire-prevention organization. He joined the board of Portland’s Western Forestry Center (now World Forestry Center) in 1973 and was president from 1983 to 1985. He was a member of the Society of American Foresters.
 
Knudson had strong ties to Oregon State University and built many warm relationships over the years with people at OSU. He was named a trustee of the OSU Foundation Board of Trustees in 1975 and joined the board’s fundraising committee in 1980. He served as the board’s president from 1981-83. He also served on the steering committee of the FourSight! Campaign, a major University effort to raise funds for four areas of the University including funds for materials science research programs.
 
A founding member of the OSU Presidents Club, Knudson gave generously to support several University programs including the Valley Library renovation, the OSU Research Council, and teaching and research in the College of Forestry.
 
Knudson received OSU’s Distinguished Service Award in 1985. In nominating him for this award, Dean Stoltenberg said, “Mr. Knudson has made generous and significant contributions through his behind-the-scenes sharing of managerial skills with public and non-profit organizations. And although not as widely recognized, his quiet, generous sharing of personal resources has inspired many others to give similarly…To every organization he has served, Gene Knudson brought leadership, respect, integrity, performance, and commitment.”
 
Gene Knudson passed away on April 9, 1998.

Monday, April 11, 2016

Conference Award Winners:

Lightning Talk: Christopher Gaulke, Developing the zebrafish as a high-throughput model of interactions between hosts, their microbiomes and the environment
Poster: Richard Tehan, Evolutionary Metabolomics in Tolypocladium Fungi to Guide Natural Products Discovery

Program

8:00Registration & refreshments (Poster & lightning talk slides setup) 
9:00Brett Tyler, Director, CGRB
  Opening Remarks
  Moderator: David Hendrix
9:10Elaine Ostrander, National Human Genome Research Institute
Genetics of the Domestic Dog: A tale of morphology and disease
10:00Break (Poster & lightning talk slides setup)
10:30Xiaoli Fern, Electrical Engineering & Computer Science
Learning, reasoning and planning for experimental design
10:55Kelly Vining, Horticulture
Bringing genomics to Oregon specialty crops
11:20Lightning talks   Moderator: Andy Housemen & Stephen Ramsey
12:30Lunch and Poster Session & Lightning Talk slides presentation judging 
Turn in poster & lightning talk ballot envelopes to registration desk by 1:45 pm for counting
  Moderator: Molly Megraw
1:45Emily Ho, Biological & Population Health Sciences
Cancer prevention with diet and epigenetics
2:10Harold Bae, Biological and Population Health Sciences
Associations of FOXO3A in Four Studies of Extreme Longevity
2:35Rebecca Hutchinson, Electrical Engineering & Computer Science/Fisheries & Wildlife
Fitting Occupancy Models for Rare Species with Penalized Likelihood Methods
3:00Break
3:25David Koslicki, Mathematics
Quantifying strain-level variation in metagenomic profiling with MetaPalette.
3:50Awards Ceremony, Brett Tyler
4:00Gary Stormo, Washington University
Modeling Transcription Factor Binding Sites: experimental and computational methods
4:50V. John Mathews, Department Head, Electrical Engineering & Computer Science
Closing Remarks

Friday, September 18, 2015

Poster Award Winners

Undergrad student: Nick Ames   Sensiplicity Sensor Sytem
Grad student:  Andrew Osborn   De novo synthesis of sunscreen compound in vertebrates
PostDoc/Trainer/Faculty:  Amy Klocko  RNAi of apple AGAMOUS genes leads to increased floral attractiveness and decreased fertility

Program

8:00Registration & refreshments (Poster & sponsor setup) 
9:00Brett Tyler, Director, CGRB
Introduction, CGRB update
  Moderator: David Myrold, Crop & Soil Science
9:25Ferran Garcia-Pichel, Arizona State University
Combinomics to understand biological soil crusts
10:10Kimberly Halsey, Microbiology
Phytoplankton strategies for using the energy from photosynthesis
10:35Break (Poster & sponsor setup / displays)
11:00Ryan Mehl, Biochemistry & Biophysics
Defining Roles of NitroTyrosine in Disease via Genetic Code Expansion
11:25Jeff Anderson, Botany & Plant Pathology
Regulation of Pseudomonas syringae Virulence by Host Plant-derived Metabolite Signals
11:50James Giovannoni, Cornell University
Genetic regulation of tomato fruit ripening; genes to genome
12:35Lunch (Poster and Sponsor setups / displays)
  Moderator: Laurent Deluc, Horticulture
1:50Wei Kong, Chemistry
Coherent electron diffraction of single molecules embedded in superfluid helium droplets: A possible solution to the problem of protein crystallization
2:15Patrick Hayes, Crop & Soil Science
Fun with barley: from flowering to flavor
2:40Marc Johnson, University of Missouri
How to dress your virus.  Learning how viruses select the right host membrane for proper assembly
3:25Break (Poster and Sponsor setups / displays)
  Moderator: Chrissa Kioussi, College of Pharmacy
3:50Olena Taratula, College of Pharmacy
Multifunctional Theranostic Nanoplatforms for Image-Guided Surgery and Intraoperative Therapy   
4:15Andy Jones, Botany & Plant Pathology
Intraspecific variation in drought responses of tropical tree seedlings: consequences for species distributions under climate change
4:40Cynthia Sagers, Vice President of Research
Closing remarks
5:00Poster Session/Reception, Sponsor Displays

 

Fall Term 2015
September 30, 2015Steven Henikoff
Fred Hutchinson Cancer Research Center

High-resolution mapping of epigenome dynamics
Host: Molly Megraw
October 14, 2015Bruce McDonald
Dept of Environmental Systems Science
ETH ZurichThe genetic basis of pathogen adaptation in agroecosystems

Host: Nik Grunwald
October 28, 2015Eric Gouaux
Vollum Institute
Oregon Health & Science University
Principles of signal transduction at the chemical synapses of the brain
Host: Andy Karplus
Winter Term 2016
January 6, 2016Julie Pfeiffer
UT Southwestern Medical Center
How gut microbes enhance enteric virus infectivity
Host: Natalia Shulzhenko
January 20, 2016Weihong Qiu
OSU, Dept of Physics
Single-molecule studies of plant kinesin motor proteins
February 3, 2016Nathan Swenson
Department of Biology
University of Maryland
Transcriptomic analyses of tree communities: moving beyond functional traits and phylogenetic relatedness
Host: Andy Jones
February 17, 2016Marian Waterman
UC Irvine, Cancer Research Institute
Wnt Signaling in Stem Cells and Cancer
Host:  Chris Mathews
February 22, 2016Special Seminar2:00 – 3:00 pm
ALS 4001
Eugene Koonin
National Center for Biotechnology Information, NIH
Discovery of new genome editing systems and novel viruses by genome and metagenome mining
Host: Valerian Dolja
March 2, 2016David Hendrix
OSU, Dept of Biochemistry & Biophysics
School of Electrical Engineering & Computer Science Biological Discovery Through Bioinformatics: From Deep Sequencing to Deep Learning
March 8, 2016Special Seminar3:30 – 4:30 pm
ALS 4001
Frank Kempken
Christian-Albrechts-Universität zu Kiel, Germany
Secondary metabolites from marine and terrestrial fungi – genome analysis and biological function
Host: Michael Freitag
Spring Term 2016
March 30, 2016Knudson LectureRichard Lenski
Michigan State University
Host:  Brett Tyler
April 27, 2016Matthew Revington
University of Windsor
Structural and Dynamic Studies of Proteins using NMR
Host: Elisar Barbar
May 11, 2016Sara A. Courtneidge
Oregon Health & Science University
The Control of Invasion and Metastasis
Host:  Siva Kolluri
May 25, 2016Steven Almo
Albert Einstein College of Medicine
High-throughput Approaches for Enzyme Functional Annotation and Metabolism Discovery
Host:  Stephen Giovannoni

Monday, April 6, 2015

Conference Award Winners

Lightning Talk: Andrew Brereton
Poster (Grad student): Nicole Kirchoff
Poster (Undergrad student): Kayla Stalheim

Program

8:00Registration & refreshments (Poster & lightning talk slides setup) 
9:00Brett Tyler, Director, CGRB
  Opening Remarks
  Moderator: David Hendrix
9:10Daniel Rokhsar, UC Berkeley
  Population genomics of diverse plants: you can see a lot just by looking
10:00Break (Poster & lightning talk slides setup)
10:30Sandra Loesgen, OSU, Chemistry
  New anti-infective drug leads from natural sources
10:55Weihong Qiu, OSU, Physics
   Shining light on the mechanism of kinesin autoinhibition
11:20Lightning talks   Moderator: Glencora Borradaile
12:30Lunch and Poster Session & Lightning Talk slides presentation judging 
Turn in poster & lightning talk ballot envelopes to registration desk by 1:45 pm for counting
  Moderator: Yuan Jiang
1:45Perry Hystad, OSU, Public Health and Human Sciences
  Health Effects of Air Pollution: A Global Perspective
2:10Duo Jiang, OSU, Statistics
  Statistical methods for genetic association mapping of binary traits
2:40David Hendrix, OSU, Biochemistry and Biophysics, Electrical Engineering and Computer Science
  Gene and microRNA expression changes in Human Cerebral Aneurysms
3:05Break
 Moderator: Stephen Ramsey
3:25Arup Indra, OSU, Pharmacy
  Inflammation and Cancer : Role of “Nano-environment” in disease remodeling
3:50Awards Ceremony, Brett Tyler
4:00Richard Edward Green, UC Santa Cruz
  Simple and powerful – a new assembly approach for generating or improving genome assemblies
4:50Thomas Dietterich, OSU, Electrical Engineering and Computer Science
  Closing Remarks

Friday, September 12, 2014

Poster Award Winners

PostDoc/Trainer/Faculty: Venkatesh Moktali, FungiDB: a functional genomic resource for fungal & oomycete organisms
Grad student: Rachael C. Kuintzle, RNA-Seq Reveals Age-Induced Changes in Rhythmicity in Drosophila Transcriptome
Undergrad student: Alvin Yu, Identifying candidate drugs for atherosclerosis prevention or treatment through a systems biology approach to drug repurposing

Program

8:00Registration & refreshments (Poster & sponsor setup) 
9:00Brett Tyler, Director, CGRB
Introduction, CGRB update
9:20Shawn O’Neil, Adelaide Rhodes and Kelly Vining, CGRB
CGRB Bioinformatics Training: We can help!
  Moderator: Thomas Wolpert
9:30Sheng-Yang He, Michigan State University
Bacterial pathogenesis as a probe of plant biology
10:15Niklaus J. Grünwald, USDA –ARS/Botany & Plant Pathology
Inferring pattern and process of emergence in Phytophthora pathogens
10:40Break (Poster & sponsor setup)
11:10Ryan Mueller, Microbiology
Linking phylogenetic identity and biogeochemical function of uncultivated marine microbes with novel mass spectrometry techniques
[Joyce Loper introduces C. Whistler]
11:35Cheryl Whistler, University of New Hampshire
Barbarians at the gate: Adaptive evolution of squid-naive Vibrio fischeri to light organ symbiosis
12:20Lunch (Poster and Sponsor setups / displays)
  Moderator: Siva Kolluri
1:35Michael Banks, Cooperative Institute for Marine Resource Studies (CIMRS)
Enigmas Related to the Ocean Migration of Chinook Salmon
2:00Justin Sanders, Microbiology
Development of a novel vertebrate model for the cosmopolitan parasite, Toxoplasma gondii
2:25Patrick De Leenheer, Mathematics/Integrative Biology
On finding hotspots and sinks in a multipatch malaria model
2:50Break (Poster and Sponsor setups / displays)
3:15Prasad Kopparapu, Environmental & Molecular Toxicology
Fighting Cancer with its own tools
3:40William Bisson, Environmental & Molecular Toxicology
Computer-aided cancer drug discovery and chemoprevention in the postgenomic era
4:05Shankar Subramaniam, University of California – San Diego
The Impact of “Omics” on Systems Medicine
4:50Ron Adams, Interim Vice President of Research
Closing remarks
5:00Poster Session/Reception, Sponsor Displays
Fall Term 2014
October 1, 2014Robert Cardiff
Center for Comparative Medicine
University of California, Davis
Overdiagnosis and Overtreatment in Cancer: Lessons from the Mouse
Host: Siva Kolluri
October 15, 2014John Hammer
Molecular Cell Biology Section
NIH: National Heart, Lung & Blood Institute
Using mouse coat color mutants to explore motor protein: organelle interactions
Host: Valerian Dolja
October 29, 2014Jennifer Pett-Ridge
Physical & Life Sciences Directorate
Lawrence Livermore National Laboratory
From cradle to grave: Microbial C transformations in the rhizosphere
Host: David Myrold
November 12, 2014James Van Etten
Department of Plant Pathology
University of Nebraska-Lincoln
Unusual Lifestyle of Giant Algal Viruses
Host: Thomas Wolpert
Winter Term 2015
January 21, 2015A.S.N. Reddy
Department of Biology
Colorado State University
Global analysis of targets of a splicing regulator in Arabidopsis: Implications in stress responses
Host: Sergei Filichkin
February 4, 2015Daniel Bikle
Department of Medicine & Dermatology
University of California, San Francisco
The vitamin D receptor as a tumor suppressor in skin
Host: Arup Indra
February 18, 2015Jason Stajich
Plant Pathology and Microbiology Dept
University of California, Riverside
Evolutionary and functional genomics in early diverging fungi
Host: Nik Grünwald
March 4, 2015Ilya Shmulevich
Institute for Systems Biology
Integrative Analysis of Data from The Cancer Genome Atlas
Host: Stephen Ramsey
March 10, 2015C. Titus Brown
UC Davis Genome Center
Concepts and tools for exploring very large sequencing data sets: how can we move more quickly to hypotheses?
Host:  Thomas Sharpton
Spring Term 2015
April 1, 2015Mike Waterman
National Academy of Sciences Member
Biological Sciences, Mathematics and Computer Science
University of Southern California
Using Word Counts for Alignment Free Sequence Analysis
Seminar co-sponsors:  Mathematics Department, Statistics Department,
School of Computer Science and Electrical Engineering
April 15, 2015No seminar
April 29, 2015Adam Bogdanove
Plant Pathology & Plant-Microbe Biology
Cornell University
Diversity of TAL effectors in nature in relation to their utility in genome editing and other DNA targeting applications
Host: Steve Strauss
May 13, 2015Susan Tilton
Environmental & Molecular Toxicology
Oregon State University
An integrative systems toxicology approach to understanding environmental risk factors in lung disease
May 27, 2015Adreas Bäumler
Dept of Medical Microbiology & Iummunology
University of California, Davis
How the host response feeds Enterobacteriaceae
Host: Luiz Bermudez

Monday, April 7, 2014

Poster Award Winners

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

Program

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