| Fall Term 2020 | |
| September 30, 2020 | Liang Huang Oregon State University Fighting COVID-19 with RNA Folding and RNA Design |
| October 14, 2020 | Mak Saito Woods Hole Oceanographic Institution Host: Steve Giovannoni Exploring the use of metals in biogeochemically important enzymes in the oceans, and development of the Biogeochemical AUV Clio and the Ocean Protein Portal |
| October 28, 2020 | Scott Doney University of Virginia Host: Kim Halsey Developing models of marine planktonic systems |
| November 18, 2020 | A. Murat Eren University of Chicago Host: Maude David and Steve Giovannoni High-resolution insights into the genomic dynamism of closely related gut microbial populations in unrelated humans |
| December 2, 2020 | Katherine Amato Northwestern University Host: Tom Sharpton A case for comparative research: Using primates to gain insight into the human gut microbiome |
| Winter Term 2021 | |
| January 20, 2021 | Maria Clara Franco (Maca) Oregon State University Host: Michael Freitag The relevance of oxidatively-modified proteins as therapeutic tumor-directed targets |
| February 3, 2021 | Bruce Hungate Northern Arizona University Host: David Myrold Frontiers in ecosystem science: microbial ecology to biogeochemistry |
| February 17, 2021 | Yuanchao Wang Nanjing Agricultural University Host: Brett Tyler The story of XEG1: From a core effector to broad spectrum resistance |
| March 3, 2021 | Francesca Marassi Sanford Burnham Prebys Medical Discovery Institute Host: Elisar Barbar |
| Spring Term 2021 | |
| March 31, 2021 | Martin Egan University of Arkansas Host: Weihong Qiu Forging the Rings of Power – Formation and remodeling of higher-order septin structures for plant invasion by the blast fungus |
| April 14, 2021 | Clare Bird University of Stirling Host: Jennifer Fehrenbacher The microbiomes of single cells |
| April 28, 2021 | Zachary Lippman Cold Spring Harbor Laboratory Host: Steven Strauss Dissecting and exploiting mechanisms of quantitative trait variation in pl |
| May 12, 2021 | Xiangshu Xiao Oregon Health & Science University Host: Siva Kolluri Cancer Drug Discovery Targeting Transcription and DNA Repair |
| May 26, 2021 | Peter Ralph University of Oregon Host: Aaron Liston |
Author Archives: girarda
Data Science for the Public Good Symposium
Keynote Speaker
Charisse Madlock-Brown
University of Tennessee Health Science Center
Charisse Madlock-Brown is a faculty member in Health Informatics and Information Management at the University of Tennessee Health Science Center. She received her Master’s in Library Science and Ph.D. in Health Informatics from the University of Iowa. She has expertise in data management, data mining, and visualization. She has a broad background in health informatics, with a current focus on obesity trends and multimorbidity. Other areas of interest are network analysis and emerging topic detection in biomedicine. She has authored several book chapters and journal articles and continues to keep up-to-date on data integration, data architecture, database management, and analytic methods. She runs the UTHSC Research Pipelines labs, which provide online interfaces for distributed computing and storage systems. Her lab can manage projects from data extraction and transformation to modeling and visualization for small-scale and big data projects.
| Introductions from DSPG Leaders | |
| 1:00 PM | Introduction to the Oregon State University Date Science for the Public Good Project–Brett Tyler, Director, Center for Quantitative Life Sciences, Oregon State University |
| 1:05 PM | Tri-state Data Science for the Public Good Project– Sallie Keller, Director, Social and Decision Analytics Division, University of Virginia’s Biocomplexity Institute |
| 1:10 PM | Data Science Knowledge and Resources for Extension Professionals– Lindsey Shirley, Associate Provost, Oregon State University Outreach and Engagement |
| Keynote Speaker | |
| 1:15 PM | Social determinants of health related to COVID-19: disparities between urban and rural communities– Charisse Madlock-Brown, University of Tennessee Health Science Center |
| 1:45 PM | Break |
| Presentations | |
| 2:00 PM | Measuring Economic and Social Infrastructure: Intergenerational Poverty in Page County, VA |
| 2:15 PM | Wintertime air quality health impacts in Oakridge and Westfir |
| 2:30 PM | Mapping Iowa’s Substance Use Care Infrastructure |
| 2:45 PM | Impacts of dam water release policy on Deschutes River health and recreation |
| 3:00 PM | Barriers to Health Care Access and Use in Patrick County, VA |
| 3:15 PM | Forecasting tools for cost analysis of water and wastewater facilities in Oregon small towns and cities |
| 3:30 PM | Economic Mobility Baseline and Comparative Analysis for the South Wasco County School District Area, Oregon |
| 3:45 PM | Regulatory impacts on economic development in the Eastern Oregon border region |
| 4:00 PM | Water quality requirements for fresh produce growers |
DSPG is a coalition of five public universities across three states: Oregon State University, Iowa State University, Virginia Tech, University of Virginia, and Virginia State University.
News 02/17/2020
Brent Kronmiller, Edward Davis, David Hendrix, Thomas Sharpton, Clinton Epps, Pankaj Jaiswal, Stephen Ramsey et al – Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis
Fall Conference 2019
Friday, September 20, 2019 CH2M HILL Alumni Center
Congratulations to our winners! To all the participants and presenters, another thank you for your contributions. We look forward to welcoming the CGRB Community to the 2020 Spring Conference on April 24, 2020.
Undergraduate Poster: Kelsey Shimoda “Altering metabolic gene expression in fruit flies: effects on longevity and brain aging”
Graduate Poster: Benjamin Americus “Elegant Infection Machines: Nematocyst diversification within Myxozoa”
Daniel Schneck “Phenotypic and transcriptional responses to different light regimes in allopatric populations of Tigriopus californicus”
Manoj Gurung “Lactobacilli ameliorate western diet induced diabetes by preventing hepatic mitochondrial damage”
Miranda Leek “A Biochemical and Biophysical Investigation into the Pathological Gain-of-Function of Nitrated Hsp90”
Rebecca Veitch “Exposure to Light at Night Alters DNA Methylation and Expression of Proliferative and DNA Damage Repair Genes”
Post-Doc Poster : Allie Graham “Independent losses of the Hypoxia-Inducible Factor (HIF) Pathway within Crustacea”
Lightning Talks: Eileen Chow “Daily blue light exposure accelerates aging in Drosophila melanogaster”
Raffle drawing for voting in all categories: 1st place – Miranda Leek
2nd place – Alexandre Sathler
| 8:00 | Registration & refreshments (Poster & sponsor setup) |
| 8:50 | Brett Tyler, Director, CGRB Introduction, CGRB update |
| 9:15 | Andrew Annalora, Environmental and Molecular Toxicology Exploring Splice Variant Biology in Nuclear Receptor and Cytochrome P450 Genes |
| 9:40 | Ed Kelly, University of Washington Tissue Chips for Human Disease Modeling |
| 10:20 | Break |
| 10:50 | Lightning Talks Moderated by Jeff Anderson Featuring: Martin Pearce, Stephanie Bollmann, Benjamin Americus, Evan Carpenter, Eileen Chow, Lauren Chan, Nolan Newman, Alexandra Weisberg |
| 11:35 | Felipe Barreto, Integrative Biology Genomics in the Tidepool: Functional and Population Genetics of Adaptation and Speciation in a Tiny Crustacean |
| 12:00 | Kevin Brown, Pharmaceutical Sciences and Chemical, Biological, and Environmental Engineering Adventures in Complex Systems |
| 12:25 | Lunch |
| 1:25 | Afua Nyarko, Biochemistry & Biophysics Selectivity and Specificity in Cancer Regulatory Proteins |
| 1:50 | Daniel Liefwalker, Oregon Health and Science University Therapeutic strategies targeting c-MYC |
| 2:30 | Lightning Talks Moderated by Jeff Anderson Featuring: Armando Alcazar Magana, Christine Tataru, Sarah Alto, Anh Ha, Heather Forsythe, Kayla Jara, Rebecca France, Rachel Franklin |
| 3:15 | Break |
| 3:45 | Morgan Giers, Chemical, Biological, and Environmental Engineering Regenerating the Intervertebral Disc: Developing Effective Therapies in a Nutrient Limited Environment |
| 4:10 | Doris Taylor, Texas Heart Institute Building Solutions for Heart Disease: A 2019 Update |
| 5:00-7:30 | Poster Session Reception, Sponsor Displays |
THANK YOU TO OUR 2019 FALL CONFERENCE COMMITTEE:
Jaga Giebultowicz, Department of Integrative Biology
Craig Marcus, Environmental and Molecular Toxicology
Jeff Anderson, Department of Botany and Plant Pathology
Viviana Perez, Department of Biochemistry and Biophysics
CGRB Seminar Series 2019-2020
| Fall Term 2019 | |
| October 9, 2019 | Marilyn Roossinck The Pennsylvania State University Lessons in Virus Ecology from Forty Years of Research Host: Jerri Bartholomew |
| October 23, 2019 | Ran Blekhman The University of Minnesota Population and Functional Genomics of Host-Microbiome Interactions Host: Tom Sharpton |
| November 6, 2019 | Mark Farman UC Davis Telomeric transposons: major drivers of fungal genome evolution and guards against genome change Host: Michael Freitag |
| December 4, 2019 | Carolina Tropini The University of British Columbia Physical perturbations to the gut microbiota during health and disease Host: Natalia Shulzhenko |
| Winter Term 2020 | |
| January 8, 2020 | Chris Hittinger University of Wisconsin-Madison Host: Joey Spatafora Genomic and metabolic evolution across budding yeasts |
| January 22, 2020 | Audrey Gasch University of Wisconsin-Madison Host: Michael Freitag The genetic basis of aneuploidy tolerance in wild yeast |
| February 19, 2020 | Jill Banfield UC Berkeley Host: Steve Giovannoni |
| March 4, 2020 | Josh Cuperus University of Washington Host: Molly Megraw, John Fowler |
| Spring Term 2020 | |
| April 1, 2020 | Pankaj Kapahi USC Leonard Davis Host: Jaga Giebultowicz |
| April 15, 2020 | Jose Dinneny Stanford University Host: John Fowler |
| May 13, 2020 | TBD |
| May 27, 2020 | TBD |
Fall Conference 2018
Friday, October 12, 2018
Poster Award Winners
Undergraduate student: Michaela Buchanan, Computer Sci/Biochemistry & Biophysics Using GPUs to Classify Oceans of Data
Graduate student: Courtney Armour, MCB A Metagenomic Meta-Analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
Postdoc/Trainer: T. William O’Neill, Biomedical Sciences Creating 3-Dimensional Models from Serial Histologic Sections Using Open-Source Software
| 8:00 | Registration & refreshments (Poster & sponsor setup) |
| 9:00 | Brett Tyler, Director, CGRB Introduction |
| 9:30 | Helen Poynton, University of Massachusetts The Toxicogenome of Hyalella Azteca, building genomic resources for healthy ecosystems |
| 10:20 | Break (Poster & sponsor setup / displays) |
| 10:45 | Gerrad Jones, Biological & Ecological Engineering Environmental Change Drives Global Soil Element Fluxes |
| 11:15 | James Watson, College of Earth, Ocean & Atmospheric Science Manifold Learning of Multi-scale Dynamics in Complex Systems |
| 11:45 | Joe Christison, Office of Commercialization & Corporate Development Patenting and Commercializing University Discoveries |
| 12:10 | Lunch (Poster and Sponsor setups / displays) |
| 1:15 | Daniel Coleman, OHSU Targeting BET Bromodomain Proteins in Castration-Resistant Prostate Cancer |
| 2:10 | Maria Franco, Biochemistry & Biophysics Role of Redox Signaling in Tumor Metabolic Reprogramming |
| 2:40 | James Strother, Integrative Biology Elucidation of neural circuit structures through imaging, optogenetics, and behavior |
| 3:05 | Break |
| 3:30 | Maude David, Depts of Microbiology & Pharmacy Children with autism and their typically-developing siblings differ in exact sequence variants and predicted functions of stool-associated microbes |
| 4:00 | Vladimir Shulaev, University of North Texas Neuroprotective effect of 17β-Estradiol (E2) on rat brain |
| 4:50 | Closing remarks |
| 5:00 – 7:30 | Poster Session/Reception, Sponsor Displays |
Thank you to our conference committee:
Jared LeBoldus, Assistant Professor, Botany & Plant Pathology
Claudia Maier, Professor, Chemistry
Natalia Shulzhenko, Assistant Professor, Vet Biomedical Science
CGRB Seminar Series 2018-2019
| Fall Term 2018 | |
| September 26, 2018 | Andrew Cato Karlsruhe Institutue of Technology, Germany Development of Bag-1L as a Therapeutic Target in Androgen Receptor-Dependent Prostate Cancer Host: Siva Kolluri |
| October 10, 2018 | Samara Reck-Peterson UC San Diego Molecular mechanisms of microtubule-based motors: how teams of motors work Host: Michael Freitag |
| October 24, 2018 | Siobhan Brady UC Davis From networks to switches: systems approaches to unravel the control of biological processes necessary for plant life Host: John Fowler/Molly Megraw |
| November 7, 2018 | Fitnat Yildiz UC Santa Clara Mechanisms and regulation of biofilm formation in Vibrio cholerae Host: Claudia Hase |
| Winter Term 2019 | |
| Feruary 8, 2019 | William Hersh OHSU Three amazing ideas about microbial biogeography that will blow your mind Host: Denise Hynes |
| March 6, 2019 | Nadja Cech University of North Carolina – Greensboro Anti-Virulence Strategies Against Drug Resistant Superbugs Host: Sandra Loesgen |
| Spring Term 2019 | |
| April 3, 2019 | Chris Marx University of Idaho Phenotypic heterogeneity between genetically identical cells permits growth with letal levels of formaldehyde stress Host: Patrick de Leenheer |
| April 17,. 2019 | Melissa Haendel OHSU/OSU The Yellow Brick Road of Open Science: Barriers to bringing data to its highest valued use Host: Brett Tyler |
| May 1, 2019 | Kristine Alpi OHSU Host: Melissa Haendel |
| May 15, 2019 | Lucia Carbone OHSU Host: Tom Sharpton |
| May 29, 2019 | Andrew Kern University of Oregon Putting the HAL in Haldane: leveraging supervised machine learning for population genetics Host: Aaron Liston |
Spring Conference 2018
Friday, April 27, 2018
Conference Award Winners
Lightning Talk: Ellie Bors, Population genomics of rapid range expansion during marine invasions
Poster: Lilian Padgitt-Cobb, Toward a phased, diploid assembly of the hop genome
Program
| 8:00 – 9:00 | Registration & refreshments (Poster & lightning talk slides setup) |
| 9:00 – 9:10 | Chris Sullivan, Assistant Director for Biocomputing, CGRB Opening Remarks |
| Moderator: Duo Jiang, Assistant Professor, Statistics | |
| 9:10 – 10:00 | Haiyan Huang, UC Berkeley Inferring Gene Interactions and Functional Modules Beyond Standard Statistical Models |
| 10:00 – 10:25 | Break,time for poster setup |
| 10:25 – 10:50 | David Hendrix, Assistant Professor, Biochemistry & Biophysics, EECS Large-scale Automated Annotation and Analysis of RNA Secondary Structure |
| 10:50 – 12:15 | Lightning talks Moderator: Molly Megraw, Assistant Professor, Botany & Plant Pathology |
| 12:15 – 1:20 | Lunch and Poster Session (Poster & Lightning Talk slides judged) Poster & lightning talk ballot envelopes will be picked up for counting right after lunch |
| Moderator: Rebecca Hutchinson, Assistant Professor, Fisheries & Wildlife, EECS | |
| 1:20 – 1:45 | Susan Tilton, Assistant Professor, Environmental & Molecular Toxicology A 3D Vitro Respiratory Model for Predicting Chemical Toxicity |
| 1:45 – 2:10 | Stephen Ramsey, Assistant Professor, Biomedical Sciences, EECS Machine-Learning for Identifying Functional Noncoding SNPs |
| 2:10 – 2:35 | Clinton Epps, Associate Professor, Fisheries & Wildlife, CAS Genetic applications in the Conservation and Management of Bighorn Sheep |
| 2:35 – 3:00 | Break |
| 3:00 – 3:50 | Fei Fang, Carnegie Mellon Machine Learning and Game Theory for Biodiversity Conservation |
| 3:50 – 4:00 | Vrushali Bokil, Associate Professor, Mathematics Awards and Closing Remarks |
Thank you to our conference committee:
Vrushali Bokil – Associate Professor, Mathematics
Rebecca Hutchinson – Assistant Professor, EECS, Fisheries & Wildlife
Duo Jiang – Assistant Professor, Statistics
Molly Megraw – Assistant Professor, Botany & Plant Pathology
Fall Conference 2017
Friday, September 8, 2017
Poster Award Winners
Postdoc/Trainee: Fadi El-Rami, Subcellular proteomics of the 2016 WHO Neisseria gonorrhoeae reference strains for identification of vaccine candidates and antibiotic resistance signatures
Grad student: Aayushi Manchanda, Loss of otoferlin alters the transcriptome profile and ribbon synapse architecture of sensory hair cells
Undergrad student: Ryan Kitchen, CASSA: The new fast GPU DNA Sequence Aligner
Program
| 8:00 | Registration & refreshments (Poster & sponsor setup) |
| 9:00 | Brett Tyler, Director, CGRB Introduction, CGRB update |
| Moderator: Aleksandra Sikora, Pharmaceutical Sciences | |
| 9:25 | Caroline Attardo Genco, Tufts University Sex as a variable: Distinct Neisseria gonorrhoeae gene expression signatures expressed during mucosal infection in men and women |
| 10:10 | Break (Poster & sponsor setup / displays) |
| 10:30 | Nathan Campbell, Columbia River Inter-Tribal Fish Commission Genotyping in Thousands by sequencing: A low cost, high-throughput, targeted SNP genotyping method |
| 11:15 | Olena Taratula, College of Pharmacy A Tumor-Activatable Theranostic Nanomedicine Platform for NIR Fluorescence-Guided Surgery and Phototherapy |
| 11:40 | Posy Busby, Botany & Plant Pathology Host genetic structuring of leaf endophyte communities in Populus and Maize |
| 12:05 | Lunch (Poster and Sponsor setups / displays) |
| Moderator: Brent Kronmiller, CGRB | |
| 1:20 | Melissa Haendel, OHSU Crossing the chasm of semantic despair: ontologies to unify genomics and phenomics |
| 2:05 | Brett Tyler, Botany & Plant Pathology Does the pathogen always win – the co-evolutionary struggle between soybean and its oomycete pathogen Phytophthora sojae |
| 2:30 | Molly Burke, Integrative Biology Genomic lessons from laboratory evolution experiments |
| 2:55 | Break |
| 3:15 | Marian Waterman, UC Irvine WNT signaling and tumor heterogeneity |
| 4:00 | Maria Clara Franco, Biochemistry & Biophysics The Two Faces of Nitrated Proteins: Neurodegeneration and Cancer |
| 4:25 | David Myrold, Crop & Soil Science Glimpses into the microbial communities of Oregon soils |
| 4:50 | Janine Trempy, Associate Vice Provost for Academic Affairs Closing remarks |
| 5:00 – 7:30 | Poster Session/Reception, Sponsor Displays |
Thank you to our conference committee:
Pankaj Jaiswal, Botany & Plant Pathology
Ryan Mehl, Biochemistry & Biophysics
Aleksandra Sikora, Pharmaceutical Sciences
CGRB Seminar Series 2017-2018
| Fall Term 2017 | |
| September 27, 2017 | Geoffrey Wahl The Salk Institute Understanding Intra-tumoral heterogeneity using a developmental lens Host: Arup Indra |
| October 11, 2017 | David Thomas Biochemistry, Molecular Biology and Biophysics University of Minnesota Muscle Protein Structural Dynamics and Therapeutic Discovery Host: Weihong Qiu |
| October 25, 2017 Cosponsored by the Departments of Microbiology and Chemistry ROOM CHANGE **Withycombe 109** | Paul Jensen Center for Marine Biotechnology & Biomedicine UC San Diego Ecological and evolutionary perspectives on secondary metabolism in marine actinobacteria Host: Sandra Loesgen |
| November 8, 2017 | Brenna Henn Stony Brook University What do we gain by studying African genomes? : Examples from human evolution Host: Thomas Sharpton |
| December 6, 2017 | Pat Schloss University of Michigan Understanding Disease through the Lens of the Microbiome Host: Thomas Sharpton |
| Winter Term 2018 | |
| February 7, 2018 | Scott Landfear Dept of Molecular Microbiology & Immunology OHSU Critical Roles for Glucose Transporters in Parasitic Protozoa: From Cell Biology to Drug Discovery Host: Sandra Loesgen |
| February 21, 2018 | Jason Slot Fungal Evolutionary Genomics The Ohio State University Investigating fungal chemical ecology with evolutionary genomics Host: Michael Freitag |
| March 7, 2018 | Rosalie Sears Molecular and Medical Genetics OHSU Modeling and targeting intra-tumor phenotypic heterogeneity and cellular plasticity Host: Siva Kolluri |
| Spring Term 2018 | |
| April 4, 2018 | John Taylor UC Berkeley The species problem for fungi in the era of genomics Host: Nik Grünwald |
| April 18, 2018 | Catherine Royer Biological Sciences Rensselaer Polytechnic Institute Pressure-based mapping of protein conformational landscapes Host: Elisar Barbar |
| May 2, 2018 | Maret Traber Linus Pauling Institute Oregon State University Ferroptosis, Mechanism of Cell Death in Vitamin E Deficiency During Embryogenesis? |
| May 16, 2018 | Steve Reichow Chemistry Portland State University Native Lens Gap Junctions Visualized at Near-Atomic Resolution by CryoEM Host: Elisar Barbar |
| May 29, 2018 NOTE: Date change Tuesday, May 29 3:30-4:30 ALS 4001 | Rebecca Fry Environmental Sciences and Engineering UNC Chapel Hill The placental epigenome as a driver of early and later life health effects Host: Molly Kile |