Fall Term 2021 | |
September 29, 2021 | Chris Plaisier Arizona State University Finding new therapies for mesothelioma |
October 13, 2021 | TRACE Oregon State University TRACE COVID Community Surveillance Project |
October 27, 2021 | David Garcia University of Oregon Prion-based forms of RNA-modifying enzymes |
November 10, 2021 | Ya-chieh Hsu Harvard University Deep: Stem Cells at the Nexus of the Niche, Physiology, and the External Environment |
Winter Term 2022 | |
January 5, 2022 | TBD |
January 19, 2022 | Carrie Hanna Oregon Health and Science University Using genome editing technology to create biomedical models in the nonhuman primate |
February 2, 2022 | Jennifer Nemhauser University of Washington Babbage’s Cabbage: The Logic of Information Processing In Plants |
February 16, 2022 | Yanming Di Oregon State University What is a replicate? |
March 2, 2022 | Dr. Shobhan Gaddameedhi North Carolina State University Environmental Regulation of Genomic Stability and Human Health through the Circadian Clock |
Spring Term 2022 | |
March 30, 2022 | Mike Harms University of Oregon Ensembles, epistasis, and evolution: how biophysics shapes evolutionary outcomes |
April 13, 2022 | Andrew Gentles Stanford University Atlas of Clinically Distinct Cell States and Cellular Ecosystems Across Human Solid Tumors |
April 27, 2022 | CANCELLED – 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
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!
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!
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
NOVEMBER 12, 2020
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.
Oregon State University project to determine COVID-19 prevalence in Corvallis
April 16, 2020
CGRB partners on Oregon State University project to determine COVID-19 prevalence in Corvallis. See the full article for more information.
CGRB Seminar Series 2020-2021
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 |
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 2019 BUG Recap
Another great term of the CGRB’s Bioinformatics User Group (BUG) is in the books!
This term we had a wide range of presenters—graduate students to Principle Investigators. It was nice to get the perspective of folks who are in different parts of their careers.
A special thanks to all of our presenters:
Sept 25: Christopher Sullivan and Ken Lett (Center for Genome Research & Biocomputing)
- Title: CGRB’s new DFS for one and all!, i.e., Don’t know what a Distributed File System is? Come find out!
- Abstract: The CGRB works with researchers to provide the most robust computational infrastructure available today. Many group rely on file services at the heart of their research computing needs and the CGRB has worked for over 2 decades to provide redundant high speed file services. Over the years users have grown to expect the best solution at a very cheap price. Because of this model the CGRB spends a great deal of time evaluating the available systems to ensure we always have the best at the lowest price. In the past year the CGRB has worked to evaluate and purchase new file service hardware that will replace our existing setups. We will be explaining the pathway taken to bring the new service online and some of the new exciting features.
Oct 9: Lillian Padgitt-Cobb (David Hendrix Lab, Biochemistry & Biophysics)
- Title: A phased, diploid assembly of the hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation, i.e., Resolving functional and evolutionary mysteries of a large, complex plant genome with genomic data science
- Abstract: Hop (Humulus lupulus) is a plant valued for its use in brewing and traditional medicine. Efforts to determine how biosynthetic pathways in hop are regulated have been challenged by its complex genomic landscape. The diploid hop genome is large, repetitive, and heterozygous, which challenged early attempts at sequencing with short-reads. Advances in long-read sequencing have improved detection of repeats and heterozygous regions, revealing that the genome is nearly 78% repetitive. For our assembly, PacBio long-read sequences were assembled with FALCON and phased into haplotype assemblies with FALCON-Unzip. Using the phased, diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. The approaches we developed to analyze the phased, diploid assembly of hop have broader applicability to the study of other large, complex genomes.
- Lillian’s GitHub: https://github.com/padgittl/CascadeHopAssembly
- Hop Genome Browser: http://hopbase.org/
Oct 23: Kelly Vining (Kelly Vining Lab, Horticulture)
- Title: R/qtl, i.e., Applications and methods for analysis of quantitative traits
- Abstract: R/qtl is an R package that is used for genetic mapping and marker-trait association. This presentation will explore specific features of R/qtl applied to plant breeding populations. Data types, functions, and interpretation of results will be explored.
Nov 6: Ed Davis (Center for Genome Research & Biocomputing)
- Title: Introductory microbiome analysis using phyloseq, i.e., How to generate exploratory diversity plots and what they mean
- Abstract: Generating high quality, publication ready figures for a microbiome study can be somewhat difficult. An understanding of both the statistical tests and how to effectively use R to produce figures is required, so the learning curve can be somewhat steep. Fortunately, there are several easy-to-use packages in R that facilitate the analysis of microbiome studies using 16S amplicon data, including the phyloseq package that will be the focus of my talk. I will cover the basics of analyzing alpha and beta diversity and provide some code and example images to show how to generate publication ready figures starting from the base phyloseq output. I will also generate some exploratory charts and graphs such that one would be able to form and later test hypotheses using microbiome data. I will be happy to share the examples and code as well, so that I might catalyze the analysis of your own microbiome studies.
- Follow up blog post: https://tips.cgrb.oregonstate.edu/posts/phyloseq-bug-meeting-presentation-fall-2019/
Nov 20: Cedar Warman (John Fowler Lab, Botany & Plant Pathology)
- Title: High-throughput maize ear phenotyping with a custom-built scanner and machine learning seed detection, i.e., Computer counts corn, correctly.
- Abstract: Near-incomprehensible amounts of maize are produced each year, but our understanding of the dominant North American crop is fundamentally incomplete. Of particular interest is the seed-producing structure of maize, the ear. Here, we present a novel maize ear phenotyping system. Our system captures a video of a rotating ear, which is subsequently flattened into a projection of the ear’s surface. Seed positions and genetic markers can be quantified manually from this projection. To increase throughput, we applied deep learning-based computer vision approaches to seed and marker quantification. Our progress towards a completely automated phenotyping system will be described, in addition to challenges we continue to face adapting computer vision technology to maize ears.
- Links from Cedar’s presentation:
- Movie flattening: github.com/fowler-lab-osu/flatten_all_videos_in_pwd
- Seed distribution analysis: github.com/vischulisem/Maize_Scanner
- Also here’s a preprint describing the scanner: https://www.biorxiv.org/content/10.1101/780650v2
Dec 4: Christina Mulch (Kelly Vining Lab, Horticulture)
- Title: IsoSeq pooling and HiSeq multiplexing comparison for Rubus occidentalis samples to explore Aphid resistance, i.e., Utilizing RNA to find differences between Aphid Resistant and Susceptible plants.
- Abstract: Black raspberry (Rubus occidentalis L.) is a small specialty crop produced primarily in the Pacific Northwest of the U.S. A major challenge for its success is Black raspberry necrosis virus vectored by the Large Raspberry Aphid (Amphorophora agathonica A.). We used Pacific Biosciences IsoSeq long read sequencing technology to study the gene expression patterns in leaves following aphid inoculation. We collected samples from a segregating population for resistance to the pest. High quality RNA was extracted from 20 samples, 10 resistant (R) and 10 susceptible (S) using a modified RNA extraction protocol. Data processing was preformed using the IsoSeq3 pipeline. Alignment of each R and S pool to the latest chromosome level black raspberry reference genome used minimap2 according to recommended options for IsoSeq. Reads were filtered based on mapping quality, alignment length, and presence or absence in multiple samples. This study seeks to reveal the genetic underpinning of aphid resistance with the ultimate goal of enabling marker assisted selection.
Thank you for attending and we look forward to seeing you in 2020!
All of the slots for winter 2020 are full, but please contact us if you’re interested in presenting in the future.
Interview: Pacific Biosciences (PacBio) Sequel Service
Aaron Trippe discusses the changes and challenges of working with the PacBio Sequel since 2016. He discusses improvements in the technology since 2016 and has advice for user who would like to utilize this service.
Q1: How long have you been running the PacBio sequencing service at the CGRB?
The CGRB was one of the early adopters of the Sequel, the second phase of long read genomic sequencing technology from Pacific Biosciences. It arrived here on campus in August of 2016. Since then the technology has made significant improvements to the user-interface, and has tremendously increased read lengths and output.
Q2: You started up the PacBio sequencing service at the CGRB. What has been the most challenging aspect about developing this service?
Aside from the continually changing and evolving technology, one of the most challenging aspects of the service is getting everything you feed the machine to produce optimal results. One of the advantages of the technology is that you are sequencing native DNA, but that also makes it challenging when working with an organism that traditionally is difficult to work with and considered problematic. Finding ways to produce super clean and high molecular weight DNA from just about everything is probably the largest hurdle to working with the technology as a service provider. The keys to success are definitely within the sample quality. Having pure, high molecular weight DNA is essential to take advantage of the long read aspect of the technology, and is directly correlated to the quality of the sequencing output.
Q3: What type(s) of project(s) would you recommend to use PacBio’s long read technology?
The technology is great for just about any sequencing application. With the long reads, you have access to regions of DNA that were not previously accessible due to repetitive regions in genomic DNA. There is enough output to multiplex several microbial genomes on a single SMRT Cell. Complete sequences of multiplexed amplicons using Circular Consensus Sequencing for high fidelity reads of shorter inserts. With the read lengths exceeding that of RNA transcripts, Isoform sequencing using the Iso-seq application is also available for obtaining complete transcripts.
Q4: Favorite or most interesting project you’ve worked on?
Since managing the PacBio Sequel, I’ve gotten to work with plants, animals (vertebrates/invertebrates), fungi, bacteria, and insects for the local scientific community, and beyond. I can’t say that I have had a favorite organism, and they have all been interesting projects, but overcoming challenges with successful results always feels rewarding.
For more information please visit the CGRB website: https://cgrb.oregonstate.edu/core/pacbio
Note: We wish Aaron the best as he purses a new opportunity and are grateful he was able to develop a successful PacBio Service at the CGRB! For future sequencing inquires please contact Katie Carter.