Another seminar at #UCDavis 1/11 – Evan Eichler – #TooManyChoices

Well, this is going to be awkward.  I really really want to hear this upcoming talk by Evan Eichler.  But alas, Jane Lubchenco – head of NOAA – is talking at the same time.  And sorry Evan, but Jane wins – this time (never heard her speak before).

UC Davis M.I.N.D. Institute’s 2011-2012 Distinguished Lecturer Series

SPEAKER:        Evan E. Eichler, Ph.D.
TOPIC:  Copy Number Variation, Exome Sequencing and Autism
DATE:            Wednesday, January 11, 2012
TIME:            4:30 pm – 6:00 pm
LOCATION:        M.I.N.D. Institute Auditorium (2825 50th Street, Sacramento)

Biographical / Presentation Information (attached and pasted below):

Evan E. Eichler, Ph.D., is a Professor and Howard Hughes Medical Institute Investigator in the Department of Genome Sciences, University of Washington School of Medicine. Dr. Eichler is a leader in an effort to identify and sequence normal and disease-causing structural variation in the human genome. His research group provided the first genome-wide view of segmental duplications within human and other primate genomes. The long-term goal of his research is to understand the evolution and mechanisms of recent gene duplication and its relationship to copy number variation and human disease. A graduate in biology of the University of Saskatchewan, Canada, he received his Ph.D. in 1995 from the Department of Molecular and Human Genetics at Baylor College of Medicine, Houston. After a Hollaender post-doctoral fellowship at Lawrence Livermore National Laboratory, he joined the faculty of Case Western Reserve University in 1997 and later the Department of Genome Sciences at the University of Washington in 2004. He was a March of Dimes Basil O’Connor Scholar (1998-2001), appointed as an HHMI Investigator (2005), and awarded an AAAS Fellowship (2006) and the American Society of Human Genetics Curt Stern Award (2008). He is an editor of Genome Research and has served on various scientific advisory boards for both NIH and NSF.

Copy Number Variation, Exome Sequencing and Autism.
It has become apparent that genetic structural variation contributes significantly to both neurocognitive and neuropsychiatric disease. I will present a detailed study of the genomes of children with developmental delay compared to adult controls and show that as much as 14% of pediatric disease, including autism, epilepsy and intellectual disability, is caused by deletions and duplications of large segments of the genome involving multiple genes. These mutations can be either inherited or found in the parents of children depending on the size of the event. I will present evidence from exome sequencing of over 200 parent-child trios with sporadic autism and show how these data may be used to pinpoint novel genes underlying CNV (copy number variation) burden, as well as provide insight into new pathways. We find that some of the same disease-causing mutations can manifest very differently and in particular be more severe if they occur on a background of other compounding mutations. We predict that the overall burden of rare and private severe mutations will correlate with different outcomes ranging from autism, intellectual disability and epilepsy. We propose that the early development of the brain is particularly sensitive to the timing and expression of many different genes and that multiple genetic perturbations within specific pathways can lead to disease with varying severity.

Two seminars from Jane Lubchenco at #UCDavis – fun, fun and fun

Another cool seminar speaker at UC Davis. This time we get to hear from Jane Lubchenco – Director of NOAA brought to Davis as part of the Storer Seminar Series. She will be giving two seminars
January 11
ARC Ballroom A 4:10 PM – “Public Lecture”

Sustaining the Beauty and the Bounty of Oceans: Grand Challenges for Science and Society

January 12
2 Wellman, 4:10 PM
Cutting-edge but relevant science: Whose responsibility is it?

Today at UC Davis – Joe Derisi "A Seminar in Two Acts: Honey bees and Malaria"

So psyched for today’s talk by the one and only Joe Derisi (who I have written about here before).

Monday, January 09th, 2011 in the Genome Center auditorium 1005 starting at 10 a.m. on two different genomics stories, entitled “A Seminar in Two Acts: Honey bees and Malaria”.

Charles Vest Seminar "The 21st century university: Purpose, problems & promise" wrap up

Here is a wrap up, via my twitter posts and responses to them, of the seminar yesterday by Charles M. Vest, ex head of MIT and current head of the National Academy of Engineering. I know it is a bit lazy not to rewrite a summary but I think the tweets do an OK job …

UPDATE – some new links regarding the talk

Here are my tweets:

phylogenomics
Awaiting seminar by CHarles Vest, Pres. of US Natl. Acad. Engineering, past pres. of MIT #UCDavis
11/30/11 4:07 PM

phylogenomics
Vest seminar “The 21st Century Research University Purpose, Problems and Promise” #UCDavis
11/30/11 4:08 PM
phylogenomics
Charles Vest http://t.co/NlxrgeeE says Linda Katehi is an admired educational leader throughout the country #UCDavis
11/30/11 4:10 PM
phylogenomics
Charles Vest: two main challenges for universities now are globalization and access (i.e., access to education)
11/30/11 4:13 PM
phylogenomics
Charles Vest: currently trend to “brain interaction” across the globe, but need to work on how to connect people & computers better
11/30/11 4:14 PM
phylogenomics
Vest: FoldIt tool is evidence for “collective intelligence” – the researchers involved weren’t just integrating computers but brains
11/30/11 4:15 PM
phylogenomics
Vest discussing book A New Culture of Learning by Douglas Thomas and John Seely Brown “www.newcultureoflearning.com/”
11/30/11 4:16 PM
phylogenomics
Vest says location of universities still matter for many reasons incl. people need to be together and universities are embedded in cultures
11/30/11 4:17 PM
phylogenomics
Vest: purpose of research universities is “to create opportunity” (1) for graduates, (2) for business/industry (3) nations/regions
11/30/11 4:19 PM
phylogenomics
Vest: though research universities have many purposes, must be patient b/c hard to predict when benefits will occur
11/30/11 4:20 PM
phylogenomics
Vest: MIT and Stanford work very well b/c research is side by side w/ applications
11/30/11 4:21 PM
phylogenomics
Vest: few people understand that research universities are central to innovation (e.g., computing, laser, internet, gennomics)
11/30/11 4:22 PM
phylogenomics
Note – I might disagree with Vest’s claim that Universities drove genomic innovation
11/30/11 4:23 PM
phylogenomics
Vest: virtually every job in America depends on one or more university based innovations
11/30/11 4:23 PM
phylogenomics
Vest six lessons including (1) teaching and research must be intimately intertwined and are inseparable
11/30/11 4:24 PM
phylogenomics
Vest lesson 2: quality of research university is determined by quality of its faculty
11/30/11 4:25 PM

oldivory
@phylogenomics I’ve quit telling kids to interview the faculty when applying to colleges. Parents don’t get it either. Ah, well.
11/30/11 4:29 PM

phylogenomics
@oldivory good idea …
11/30/11 4:30 PM
phylogenomics
Vest: need in particular young faculty to grow up through rising w/in university
11/30/11 4:26 PM
phylogenomics
Vest lesson 3: science can flourish only in an open environment #herehere
11/30/11 4:26 PM
phylogenomics
Vest lesson 4: young faculty must be free to study and teach what they believe is important (e.g., should not be assistants to Sr. faculty)
11/30/11 4:27 PM

KSBruno9
@phylogenomics so not the European model.
11/30/11 5:11 PM
phylogenomics
Vest lesson 5: competition engenders excellence in universities (drives improvement in research, teaching, ideas, facilities, etc)
11/30/11 4:28 PM

rmtakata
@phylogenomics @carloshotta Mild competition. Wild competition could lead to cheating, forgery, distrust, sabotage…
11/30/11 4:32 PM

phylogenomics
@rmtakata @carloshotta he did not say it was perfect, just that it can be useful
11/30/11 4:34 PM
phylogenomics
Vest Lesson 6: fundamental scholarship and research must be equal w/ applied research and innovation
11/30/11 4:29 PM
phylogenomics
Vest: there is a danger in focus on applied issues that we ignore search for truth – must not be too utilitarian
11/30/11 4:30 PM

phylogenomics
Vest says “never in his lifetime has it been so hard to hang onto his optimism” b/c Washington is broken
11/30/11 4:32 PM

tjsharpton
As a young researcher, this concerns me RT @phylogenomics Vest says “never in his lifetime has it been so har… (cont) http://t.co/eZwvMurX
11/30/11 5:23 PM
phylogenomics
Vest: v. concerned w/ financial pressures on universities especially as it affects access & this started even before recent financial issues
11/30/11 4:33 PM
phylogenomics
Vest: in the last decade real per student state appropriations have dropped >20% while costs have risen
11/30/11 4:35 PM
phylogenomics
Vest: response to financial issues will be cut back on low demand classes, fewer low/middle $$ students, decr. in merit based aid & all bad
11/30/11 4:36 PM
phylogenomics
Vest: the favorite solution to State university financial problems is to seek out of state students; this spirals out of control
11/30/11 4:37 PM
phylogenomics
Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man”
11/30/11 4:37 PM

jim_croft
nice… but also woman? RT @phylogenomics: Vest: cites U. Michigan slogan from 19th century “an uncommon education for the common man”
11/30/11 4:43 PM

phylogenomics
@jim_croft I was not endorsing – just reporting
11/30/11 4:44 PM

jim_croft
@phylogenomics of course – the sentiment is perfect, the wording is excellent, for its time, just a little dated in some circles today.
11/30/11 4:49 PM
phylogenomics
Vest references Vannevar Bush’s vision “Science The Endless Frontier” for research & for access http://t.co/9n1Q0LAF
11/30/11 4:39 PM
phylogenomics
Vest references Vannevar Bush Quote on education access http://t.co/LmE1bTF7
11/30/11 4:42 PM
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Vest: we must be good citizens of the world and contribute to and learn from increasing globalization of education
11/30/11 4:43 PM
phylogenomics
Vest: all regions of the world are more/more linked/integrated w/ shared environment, challenges, resources, knowledge, humanity
11/30/11 4:45 PM
phylogenomics
Vest: modern research universities concept was developed from Humboldt University in Germany in 1800s -> JHU in US -> others in US -> global
11/30/11 4:46 PM
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Vest says he has a hard time contemplating scale of educational expansion in China and India
11/30/11 4:46 PM
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Vest: the Yin and Yang of Universities are Competition and Collaboration
11/30/11 4:47 PM
phylogenomics
Vest: people everywhere need opportunity from universities and thus MIT developed “Open Courseware” for anyone to use anywhere/anytime
11/30/11 4:48 PM

phylogenomics
Vest: Open Courseware movement has spread globally – and it (and related initiatives) are a revolution
11/30/11 4:49 PM

mikedelic
@phylogenomics I’ve taken free courses from Stanford and MIT that imwoudlnt have been able to back in the day. Love open source education
11/30/11 5:07 PM

mikedelic
@phylogenomics my favorite was Robert sapolsky’s behavioral biology course from Stanford
11/30/11 5:08 PM
phylogenomics
Vest: openness is the true spirit of education, democratization and empowerment
11/30/11 4:49 PM
phylogenomics
Vest refs: “Unlocking the Gates” and “Abelard to Apple” – books about open education
11/30/11 4:50 PM
phylogenomics
Vest: in 21st century we are observing the early emergence of a “Meta University” via open materials and platforms
11/30/11 4:51 PM
phylogenomics
Vest: must rekindle spirit of research university as provider of opportunity while also promoting openness
11/30/11 4:52 PM
phylogenomics
Here is more form Charles Vest on the “meta university” http://t.co/tJ0fNSqo
11/30/11 4:53 PM
phylogenomics
Vest: analog of Tip ONeil’s “all politics is local” need outreach to get people locally to understand importance of research universities
11/30/11 5:03 PM
phylogenomics
Questioner asks Vest how to best export notion of democracy/ access
11/30/11 5:09 PM
phylogenomics
Vest in response to question expresses dismay at how anyone could support the “Dream Act” http://t.co/FpwekBzu
11/30/11 5:09 PM


(NOTE – I GOT THIS WRONG SOMEHOW – HE CLEARLY SEEMS LIKE THE TYPE WHO WOULD SUPPORT THE ACT). SEE OTHER POSTS …)

lukedones
@phylogenomics Dismay that anyone would *support* the DREAM Act? Why?
11/30/11 5:12 PM

phylogenomics
@lukedones do you mean why would anyone be dismayed that some support the act?
11/30/11 5:15 PM

lukedones
@phylogenomics Yes. Just wondering whether he gave a reason.
11/30/11 5:21 PM

phylogenomics
@lukedones not that I remember
11/30/11 5:21 PM

phylogenomics
@lukedones sorry – in looking at the Dream Act I am wondering if he misspoke and meant he supported it … no longer sure what he said
11/30/11 6:24 PM

VoteBothell
@phylogenomics why no support for Dream Act?
11/30/11 7:01 PM


phylogenomics
Sorry all; MAJOR error tweeting Charles Vest talk; I wrote he was against Dream Act; I think he/I got that backwards & must be for it
11/30/11 7:19 PM

phylogenomics
@VoteBothell sorry – I think he must be for it – so either he or I got it backwards
11/30/11 7:20 PM

VoteBothell
@phylogenomics Great, got it. Enjoy your tweets. I’ve been following you since the pepper spray. My support and thoughts are with UC Davis.
11/30/11 7:22 PM
lukedones
@phylogenomics Thanks – I expected an academic would be for the Dream Act.
11/30/11 7:26 PM
phylogenomics
Vest: we need more experimentation with how research is funded to try to find other ways
11/30/11 5:21 PM
phylogenomics
Vest: should keep systems at basic science agencies but should try new approaches like ARPA-E
11/30/11 5:22 PM
phylogenomics
Vest views Open Courseware as a new form of publication not really as “classes” per se, b/c not interactive
11/30/11 5:25 PM

Coming up on http://phyloseminar.org Jason Stajich (aka @hyphaltip) #fungi #genomics

Upcoming seminar on Phyloseminar.Org

Jason Stajich speaks Wednesday, June 29th at noon PST on “Fungal phylogenomics: Getting lost in the moldy forest.”
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.

Japan 04:00 (04:00 AM) on Thursday, June 30
New Zealand 07:00 (07:00 AM) on Thursday, June 30
West Coast USA 12:00 (12:00 PM) on Wednesday, June 29
East Coast USA 15:00 (03:00 PM) on Wednesday, June 29
England 20:00 (08:00 PM) on Wednesday, June 29
France 21:00 (09:00 PM) on Wednesday, June 29

Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can’t make it, don’t fret– you can always watch the recording

Phyloseminar.Org 3/29 Streaming talk by Jens Lagergren on Gene Family evolution

Just got his email from the organizer of Phyloseminar.Org:

On March 29th, phyloseminar.org will present Jens Lagergren speaking

on “Probabilistic analysis of gene families with respect with gene

duplication, gene loss, and lateral gene transfer.” Abstract below.

NOTE: the seminar will begin at 10h PST, which is three hours earlier

than the previous seminars.

This is 13h Eastern Standard Time, 19h Central European Time, and 6h

in Christchurch and Auckland!

Here’s the abstract:

Incongruences between gene trees and corresponding species trees are

common. Gene duplication, gene loss, and lateral gene transfer are

three types of evolutionary events that can cause such incongruences.

I will first describe a probabilistic process that contains standard

models of nucleotide substitutions (i.e., such that underly

probabilistic methods for phylogenetic tree reconstruction) as well as

gene duplication and gene loss. This process takes place in a given

species tree and can be used to reconstruct a gene tree for a gene

family of interest and simultaneously reconcile the gene tree with the

species tree. I will describe the algorithms available for this model

and also describe how they perform on biological data compared to

competing methods. Finally, I will describe an extension of this model

that also contains lateral gene transfer and show how it performs on

synthetic data.

Hope to see you there!