Conference « Center for Quantitative Life Sciences

Friday, April 7, 2017

Conference Award Winners:

Lightning Talk: Zachary Foster, “Metacoder: An R package for visualization and manipulation of community taxonomic diversity data”
Poster: Khiem Lam, “Exploring the Microbiome of Cervical Cancer through Transkingdom Networks”

Program

8:00	Registration & refreshments (Poster & lightning talk slides setup)
9:00	Brett Tyler, Director, CGRB Opening Remarks
9:10	Ian Muñoz, Assistant Computational Scientist, CGRB Using Amazon Web Services (AWS) for Batch Processing
9:25	Lightning talksModerator: Stephen Ramsey, Assistant Professor, Biomedical Sciences and School of Electrical Engineering & Computer Science
10:35	Break (Poster setup)
11:00	Brent Kronmiller, Bioinformatics Analyst, CGRB Draft Genome of the North American Beaver (Castor canadensis)
11:25	Reidun Twarock, Departments of Mathematics and Biology University of York, England Solving a Viral Enigma: Discovery of a hidden code in RNA viral genomes provides a new perspective on viral evolution and anti-viral therapy
12:15	Lunch and Poster Session (Posters & Lightning Talk slides judged) Poster & lightning talk ballot envelopes will be picked up for counting right after lunch
	Moderator: Duo Jiang, Assistant Professor, Statistics
1:20	Katherine McLaughlin, Assistant Professor, Statistics Accessing Hidden Populations at High Risk for HIV/AIDS Using Respondent-Driven Sampling
1:45	Afua Nyarko, Assistant Professor, Biochemistry & Biophysics Molecular basis for regulation of the Yorkie transcription co-activator
2:10	Sharmodeep Bhattacharyya, Assistant Professor, Statistics Union-of-Intersection (UoI) methods for Data-driven Discovery and Prediction
2:35	Break
3:00	Molly Megraw, Assistant Professor, Botany & Plant Pathology Using Machine Learning Models to Determine the Principles Behind Tissue-Specific Gene Expression
3:25	Benjamin Dalziel, Assistant Professor, Integrative Biology and Mathematics Cities as natural experiments in bacterial metacommunity dynamics
3:50	Awards Ceremony, Brett Tyler
4:00	Reinhard Laubenbacher, Center for Quantitative Medicine, UConn Health Iron metabolism and its role in breast cancer
4:50	David Hendrix, Biochemistry & Biophysics and Electrical Engineering & Computer Science Closing remarks

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

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

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

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

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

Monday, April 6, 2015

Conference Award Winners

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

Program

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

8:00	Registration & refreshments (Poster & sponsor setup)
9:00	Brett Tyler, Director, CGRB Introduction, CGRB update
9:20	Shawn O’Neil, Adelaide Rhodes and Kelly Vining, CGRB CGRB Bioinformatics Training: We can help!
	Moderator: Thomas Wolpert
9:30	Sheng-Yang He, Michigan State University Bacterial pathogenesis as a probe of plant biology
10:15	Niklaus J. Grünwald, USDA –ARS/Botany & Plant Pathology Inferring pattern and process of emergence in Phytophthora pathogens
10:40	Break (Poster & sponsor setup)
11:10	Ryan Mueller, Microbiology Linking phylogenetic identity and biogeochemical function of uncultivated marine microbes with novel mass spectrometry techniques
	[Joyce Loper introduces C. Whistler]
11:35	Cheryl Whistler, University of New Hampshire Barbarians at the gate: Adaptive evolution of squid-naive Vibrio fischeri to light organ symbiosis
12:20	Lunch (Poster and Sponsor setups / displays)
	Moderator: Siva Kolluri
1:35	Michael Banks, Cooperative Institute for Marine Resource Studies (CIMRS) Enigmas Related to the Ocean Migration of Chinook Salmon
2:00	Justin Sanders, Microbiology Development of a novel vertebrate model for the cosmopolitan parasite, Toxoplasma gondii
2:25	Patrick De Leenheer, Mathematics/Integrative Biology On finding hotspots and sinks in a multipatch malaria model
2:50	Break (Poster and Sponsor setups / displays)
3:15	Prasad Kopparapu, Environmental & Molecular Toxicology Fighting Cancer with its own tools
3:40	William Bisson, Environmental & Molecular Toxicology Computer-aided cancer drug discovery and chemoprevention in the postgenomic era
4:05	Shankar Subramaniam, University of California – San Diego The Impact of “Omics” on Systems Medicine
4:50	Ron Adams, Interim Vice President of Research Closing remarks
5:00	Poster Session/Reception, Sponsor Displays

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

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

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

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