Fall Conference next week!

Posted on by

Hello,

We are pleased to announce the 2021 Center for Quantitative Life Sciences (CQLS) Fall Conference.  This will be a full day online event on Friday, September 17, 2021 (apologies for those who did not receive a notice about this previously. There was an issue with the list serve).  In celebration of our recent name change, the theme for this year is “Frontiers at the Intersection of the Life & Quantitative Sciences.” Because this is our first conference since our name change (and because the event is fully online this year) the conference this year is completely free for all attendees. We hope you will join us.

We strongly encourage all participants to submit a poster for the online poster session. Registered posters will be judged for cash prizes in three categories; Undergraduate Student, Graduate Student, and Post-Doctoral Fellow/Trainee. Since the event is online, a physical poster does not need to be printed. Rather, you will need to submit in advance a high-quality pdf and a stable internet connection. Lightning Talks will be limited to 5 minutes and no more than 5 slides.  Registered lighting talks will also be eligible for a cash prize.

Register in Advance

Or copy and paste the URL below into your internet browser:
https://oregonstate.qualtrics.com/jfe/form/SV_2tcSPOyfnG3beJw


On behalf of the organizing committee:

  • Kevin Brown, Pharmaceutical Sciences, OSU/OHSU
  • Molly Burke, Integrative Biology, OSU
  • Maude David, Microbiology & Pharmaceutical Sciences, OSU
  • Patrick De Leenheer, Mathematics, OSU
  • Perry Hystad, Public Health and Human Science, OSU
  • Natalia Shulzhenko, Immunology, OSU

CQLS Seminar Series 2021-2022

Posted on by
Fall Term 2021
September 29, 2021Chris Plaisier
Arizona State University
Finding new therapies for mesothelioma
October 13, 2021TRACE
Oregon State University
TRACE COVID Community Surveillance Project
October 27, 2021David Garcia
University of Oregon
Prion-based forms of RNA-modifying enzymes
November 10, 2021Ya-chieh Hsu
Harvard University
Deep: Stem Cells at the Nexus of the Niche, Physiology, and the External Environment
Winter Term 2022
January 5, 2022TBD
January 19, 2022Carrie Hanna
Oregon Health and Science University
Using genome editing technology to create biomedical models in the nonhuman primate
February 2, 2022Jennifer Nemhauser
University of Washington
Babbage’s Cabbage: The Logic of Information Processing In Plants
February 16, 2022Yanming Di
Oregon State University
What is a replicate?
March 2, 2022Dr. Shobhan Gaddameedhi
North Carolina State University
Environmental Regulation of Genomic Stability and Human Health through the Circadian Clock
Spring Term 2022
March 30, 2022Mike Harms
University of Oregon
Ensembles, epistasis, and evolution: how biophysics shapes evolutionary outcomes
April 13, 2022Andrew Gentles
Stanford University
Atlas of Clinically Distinct Cell States and Cellular Ecosystems Across Human Solid Tumors
April 27, 2022CANCELLED – Yehenew Agazie
West Virginia University
TBD
May 18, 2022 (rescheduled for Fall2022)Elias Fernandez
University of Tennessee
TBD
June 1, 2022 (rescheduled for Fall2022)Sourav Ghosh
Yale School of Medicine
TBD

CGRB is Hiring

Posted on by

Genomics Lab Technician opening in the Center for Genome Research and Biocomputing

The Center for Genome Research and Biocomputing at Oregon State University is searching for a lab technician for its genomics core facility. The appointee will be conduct services for Center collaborators spanning DNA and RNA extraction, DNA sequencing, genotyping, high throughput sequencing, and PCR assays as needed. A significant portion of the work will involve viral detection and sequencing. The position is a full-time 1 year appointment. Minimum qualifications include a relevant undergraduate degree and at least 12 months’ experience working in a molecular biology research or service laboratory. For more information, and to apply for the position go to jobs.oregonstate.edu and search for posting P04217UF.

The Center for Genome Research and Biocomputing at Oregon State University collaborates with and assists life scientists of all levels in their research using cutting-edge genomics, informatics and computational techniques. An important component of the CGRB’s activities is the molecular biology and genomics laboratory.

To ensure full consideration, applications must be received by March 18, 2021. Applications will continue to be accepted until March 25, 2021. The closing date is subject to change without notice to applicants. For questions, contact Brett Tyler brett.tyler@oregonstate.edu

OSU commits to inclusive excellence by advancing equity and diversity in all that we do. We are an Affirmative Action/Equal Opportunity employer, and particularly encourage applications from members of historically underrepresented racial/ethnic groups, women, individuals with disabilities, veterans, LGBTQ community members, and others who demonstrate the ability to help us achieve our vision of a diverse and inclusive community.

Congratulations, Matthew!

Posted on by
Matthew Peterson

Congratulations to our very own Matthew Peterson, who has been appointed a 2021 Trusted CI Fellow. Trusted CI is a National Science Foundation (NSF) Cybersecurity Center of Excellence. The Trusted CI Fellows program empowers members of the scientific community with knowledge of cybersecurity and trains fellows to serve as cybersecurity liaisons to their respective communities. Six fellows are selected across the nation each year. To read more about Trusted CI and the other five fellows for 2021, check out the Trusted CI blog post about the 2021 fellows.

Register for Winter Courses!

Posted on by

INTRODUCTION TO PYTHON

Introduction to Python I:
This module introduces programming concepts, driven by examples of biological data analysis, in the Python programming language. Topics covered will include variables and data types (including strings, integers and floats, dictionaries and lists), control flow (loops, conditionals, and
some boolean logic), variable scope and its proper use, basic usage of regular expressions, functions, file input and output, and interacting
with the larger Unix/Linux environment.

Introduction to Python II:
Part II expands on basic programming and explores using ‘objects’ (and their blueprints: classes) in encapsulating functionality into easily used blocks of code that more closely match the biological concepts at hand. Other topics include APIs, syntactic sugar, and creating and using packages such as BioPython.

January 4 – March 12

Monday/Wednesday 2:00-2:50 PM, BDS 599 (CRN:38557 and 38558) or as a workshop
Instructor: Matthew Peterson, matthew@cgrb.oregonstate.edu
for more information, email the instructor or visit: https://cgrb.oregonstate.edu/training/workshops

ENVIRONMENTAL SEQUENCE ANALYSIS

Gain practical experience with, 16s rRNA amplicon sequencing and shotgun metagenomics. No command line / R-studio experience required! Starting with raw FASTQ files, learn how to 1) profile rRNA sequences and 2) determine the taxonomy and functional composition of metagenomics samples!

January 4 – March 12

Tuesday/Thursday 10:00-10:50 AM, BDS 599 (CRN 38546) or as a workshop
Instructor: Andrew Black, andrew@cgrb.oregonstate.edu
For more information, email the instructor or visit: https://cgrb.oregonstate.edu/training/workshops

OSU Trace Program Comes to Eugene

Posted on by

NOVEMBER 12, 2020

Photo courtesy of The Corvallis Advocate

From The Corvallis Advocate: “Oregon State University brought its TRACE Community COVID-19 testing program to Eugene, sending three-member teams – one OSU student, one UO student and one professional –to city neighborhoods to collect nasal-swab samples from hundreds of residents and sewage samples from around Eugene and Springfield. This will further expand TRACE’s coverage, which includes five similar sweeps in Corvallis, as well as some study in Bend, Hermiston and Newport. TRACE will be working in tandem with UO’s Monitoring and Assessment Program (MAP).” See the full article for more information.

CGRB Seminar Series 2020-2021

Posted on by
Fall Term 2020
September 30, 2020Liang Huang
Oregon State University
Fighting COVID-19 with RNA Folding and RNA Design
October 14, 2020Mak 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, 2020Scott Doney
University of Virginia
Host: Kim Halsey
Developing models of marine planktonic systems
November 18, 2020A. 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, 2020Katherine 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, 2021Maria Clara Franco (Maca)
Oregon State University
Host: Michael Freitag
The relevance of oxidatively-modified proteins as therapeutic tumor-directed targets
February 3, 2021Bruce Hungate
Northern Arizona University
Host: David Myrold
Frontiers in ecosystem science: microbial ecology to biogeochemistry
February 17, 2021Yuanchao Wang
Nanjing Agricultural University
Host: Brett Tyler
The story of XEG1: From a core effector to broad spectrum resistance
March 3, 2021Francesca Marassi
Sanford Burnham Prebys Medical Discovery Institute
Host: Elisar Barbar
Spring Term 2021
March 31, 2021Martin 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, 2021Clare Bird
University of Stirling
Host: Jennifer Fehrenbacher
The microbiomes of single cells
April 28, 2021Zachary Lippman
Cold Spring Harbor Laboratory
Host: Steven Strauss
Dissecting and exploiting mechanisms of quantitative trait variation in pl
May 12, 2021Xiangshu Xiao
Oregon Health & Science University
Host: Siva Kolluri
Cancer Drug Discovery Targeting Transcription and DNA Repair
May 26, 2021Peter Ralph
University of Oregon
Host: Aaron Liston

Data Science for the Public Good Symposium

Posted on by

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 PMIntroduction 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 PMTri-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 PMBreak
Presentations
2:00 PMMeasuring Economic and Social Infrastructure: Intergenerational Poverty in Page County, VA
2:15 PMWintertime air quality health impacts in Oakridge and Westfir
2:30 PMMapping Iowa’s Substance Use Care Infrastructure
2:45 PMImpacts of dam water release policy on Deschutes River health and recreation
3:00 PMBarriers to Health Care Access and Use in Patrick County, VA
3:15 PMForecasting tools for cost analysis of water and wastewater facilities in Oregon small towns and cities
3:30 PMEconomic Mobility Baseline and Comparative Analysis for the South Wasco County School District Area, Oregon
3:45 PMRegulatory impacts on economic development in the Eastern Oregon border region
4:00 PMWater 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

Posted on by

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