Tag Archives: Seminars of Interest Around Davis

1/25 at #UCDavis: Monica Borucki – Recovering Viral Population Diversity to Improve Biosurveillance and Predict Viral Emergence

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. Monica Borucki


“Recovering Viral Population Diversity to Improve Biosurveillance and Predict Viral Emergence”

Wednesday, January 25, 2017

4:10 pm

1022 Life Sciences

Abstract: RNA viruses constantly evolve to optimize interactions with their hosts and potentially expand host range. Understanding the role of quasispecies in viral evolution is a necessary step toward optimizing detection of emergent viruses, developing effective countermeasures, and ultimately predicting the potential impact of emerging or novel viruses. Deep Illumina sequencing and computational analysis of viral quasispecies was used to define the role intra-host viral diversity plays in the adaptation of viruses to new host environments, with a focus on viral families of medical significance that exhibit the propensity for cross species transmission. Analysis of samples from a naturally occurring rabies host jump, and from in vitro and in vivo passage of a coronavirus and a paramyxovirus indicate that viral diversity plays a pivotal role in viral adaptation. In each case the genetic changes that characterized the emergent genotype were present as rare variants in the virus population prior to selection. These results suggest that recovering the full genetic diversity could improve biosurveillance by building a knowledge base of mutations that may play a role in viral emergence. Similarly, the presence of ancestral genotypes as rare members of the population may provide insights useful for forensic studies and outbreak investigation.

Dr. Borucki is a Biomedical Scientist in the Biosciences and Biotechnology Division of LLNL. Her research focuses on the mechanisms of viral evolution and emergence, biosurveillance, and viral forensics. Before coming to LLNL, she served as a Research Geneticist at USDA-ARS and adjunct faculty at Washington State University where she investigated the epidemiology and virulence of food pathogen, Listeria monocytogenes.

Borucki 1-25-17.doc

1/15 at #UCDavis: Tandy Warnow: New methods for species tree estimation in the presence of gene tree heterogeneity

Special Seminar:

Tandy Warnow

The University of Illinois at Urbana-Champaign

New methods for species tree estimation in the

presence of gene tree heterogeneity

Friday, January 15, 2016

1:30 PM

GBSF 1005


Estimating the Tree of Life will likely involve a two-step procedure, where in the first step trees are estimated on many genes, and then the gene trees are combined into a tree on all the taxa. However, the true gene trees may not agree with the species tree due to biological processes such as deep coalescence, gene duplication and loss, and horizontal gene transfer. Statistically consistent methods based on the multi-species coalescent model have been developed to estimate species trees in the presence of incomplete lineage sorting; however, the relative accuracy of these methods compared to the usual “concatenation” approach is a matter of substantial debate within the research community.

I will present results showing that coalescent-based estimation methods are impacted by gene tree estimation error, so that they can be less accurate than concatenation in many cases. I will also present two new methods, ASTRAL (Mirarab et al., Bioinformatics 2014) and statistical binning (Mirarab et al., Science 2014, Bayzid et al., PLOS One 2015) for estimating species trees in the presence of gene tree conflict due to ILS.  Statistical binning and weighted statistical binning are used to improve gene tree estimation, while ASTRAL is a coalescent-based method that is provably statistically consistent and that can construct very accurate large species trees. Finally, I will present theoretical results investigating whether statistically consistent accurate species tree estimation is possible when gene trees have estimation error, and discuss the controversy about statistical binning (Liu and Edwards, Science 2015, Mirarab et al. Science 2015).

See Dr. Warnow’s home page for more information on her work: http://tandy.cs.illinois.edu

Host: Jonathan Eisen



10/19 in #DavisCA: 1st Quarterly Food and Agriculture Roundtable

For those in or near Davis, CA

Block the date – this will be awesome

October 19, 2015

1:00 to 3:00pm

Student Community Center, Multipurpose Room

Jonathan Eisen

1st Quarterly Food and Agriculture Roundtable

Discussion of Microbes in Food and Agriculture
including a discussion of glyphosate and microbiomes

Eisen Roundtable Flyer .pdf

Free workshop at #UCDavis: “Microbial genomics and transcriptomics hands-on”, Sep 24-25

Was informed of this by Titus Brown, one of the instructors.  Info copied from here.

Microbial genomics and transcriptomics hands-on, Sep 24-25

Who: Ben Johnson (Michigan State University); Tracy Teal (Data Carpentry); C. Titus Brown (UC Davis).

Host: C. Titus Brown

When: Sep 24 and 25, 2015

Times: 9am-3pm on both days

Where: TBD (UC Davis campus).

Cost: there is no fee.

This workshop is open to everyone, including graduate students, postdocs, staff, faculty, and community members. We have extra space for UC Davis VetMed affiliates; contact the host if you are an SVM affiliate.

> Register here <


This two-day hands-on workshop will introduce biologists to microbial genomics and transcriptomics. The primary focus will be on genome assembly and annotation, and subsequent transcriptome analysis, of bacteria.

We will be analyzing a stock data set, and we will be using the Amazon cloud.

Topics overview

  • Logging into the Amazon Cloud
  • Short read quality and trimming
  • Genome assembly (with SPAdes or MEGAHIT)
  • Genome annotation (with Prokka)
  • RNAseq analysis
  • Differential expression analysis

Computer requirements

Attendees will need to bring a computer with a Web browser, an Internet connection, and an ssh client; Windows users should install MobaXterm before the workshop.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons – 0 License (CC0)fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

La Biology and Mathematics in the Bay Area (BaMBA) at #UCDavis 11/22

Got this in the old email tubes (note – I spoke at BaBMA a few years back – great meeting).

Dear Colleagues,

The Biology and Mathematics in the Bay Area (BaMBA) Day is an annual meeting aimed at creating a fairly informal atmosphere to explore the role of mathematics in biology. Going beyond traditional applied mathematics, the topics include sophisticated computational methods, biophysical methods, discrete mathematics and topological methods. Our goal is to encourage dialogue between researchers and students from different disciplines in an atmosphere that promotes the open exchange of ideas and viewpoints to discuss the role of mathematics in modern molecular biology. Please join us for a day full of enticing discussions!

BaMBA 9 will be held 9am-6pm on Saturday, November 22nd, in 1002 Geidt Hall on the UC Davis campus. The talks by keynote speakers will be followed by a poster session. Continue reading La Biology and Mathematics in the Bay Area (BaMBA) at #UCDavis 11/22