Dispersal mediated persistence: Two tales from the ecological crypt

Seminar: Mathematical and Computational Biology Seminar Series | September 2 | 2-3 p.m. | 939 Evans Hall

Speaker: Sebastian Schreiber, UC Davis

Sponsor: Mathematics, Department of

Ecologists have long recognized that movement of individuals across space can mediate persistence of interacting populations. In this talk, I will explore this theme using empirically motivated variations of two classical models: Lewontin & Cohen’s model of a population living in a temporally variable environment and May & Leonard’s model of rock-paper-scissor dynamics. For both.

SNP Association Studies with Case-Parent Trios

Seminar: Statistics and Genomics Seminar Series | September 3 | 4-5 p.m. | 1011 Evans Hall

Speaker: Ingo Ruczinski, Department of Biostatistics, Johns Hopkins University

Sponsor: Public Health, School of

While most SNP association studies are case-control based, family based designs and in particular case-parent trio designs have some very attractive features. We discuss and demonstrate those via a genome-wide and a candidate gene association study that employ case-parent trios. We also extend the logic regression methodology, originally developed for cohort and case-control...   More >

Evolutionary Bioinformatics and the RNA World

Seminar | September 9 | 12-1 p.m. | 106 Stanley Hall

Speaker/Performer: Professor Ian Holmes, Department of Bioengineering, UC Berkeley

Sponsor: Bioengineering (BioE)

Fall 2009 Seminar Series
Wednesday, September 9
12noon - 1:00pm
106 Stanley Hall, UC Berkeley

Professor Ian Holmes

Department of Bioengineering
UC Berkeley

Evolutionary Bioinformatics and the RNA World

Abstract:
Evolution makes sense of biological diversity; the "RNA World"
hypothesis is a good example. This hypothesis proposes that life based
on

Personalized medicine and global health: Genetic markers that predict risk for disease, drug efficacy and toxicity

Seminar: Related Seminars (Non-CCB) | September 9 | 12-1 p.m. | 101 Barker Hall

Speaker: Tom White, Celera Corporation

Sponsor: Molecular and Cell Biology, Department of

Questioning the T cell proliferation program

Seminar: Mathematical and Computational Biology Seminar Series | September 9 | 2-3 p.m. | 939 Evans Hall

Speaker: Peter Kim, University of Utah

Sponsor: Mathematics, Department of

The current paradigm for primary T cell responses is that each effector T cell independently commits to an autonomous developmental program. This concept is based on several experiments that have demonstrated that the dynamics of a T cell response is largely determined shortly after initial antigen exposure and does not depend greatly on the level and duration of antigen...   More >

Adjusted Bayesian inference for selected parameters

Seminar: Statistics and Genomics Seminar Series | September 10 | 4-5 p.m. | 1011 Evans Hall

Speaker: Daniel Yekutieli, Professor, Department of Statistics and Operations Research, Tel Aviv University

Sponsor: Statistics, Department of

I will address the problem of providing inference for parameters selected after viewing the data. A frequentist solution to this problem is using False Discovery Rate controlling multiple testing procedures to select the parameters and constructing False Coverage-statement Rate adjusted confidence intervals for the selected parameters.I will argue that selection also affects...   More >

IB Seminar

Seminar: Related Seminars (Non-CCB) | September 10 | 4 p.m. | 2040 Valley Life Sciences Bldg.

Speaker: David Mindell, Cal Academy of Sciences

Sponsor: Integrative Biology, Department of

Modeling Gene Regulatory Networks

Seminar: Related Seminars (Non-CCB) | September 14 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Aaron Dinner, Department of Chemistry, Univeristy of Chicago

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

A statistical framework for improved prediction of true indels in pair HMM based alignments

Seminar: Mathematical and Computational Biology Seminar Series | September 16 | 2-3 p.m. | 939 Evans Hall

Speaker: Alexander Schönhuth, UC Berkeley

Sponsor: Mathematics, Department of

Since both evolutionary origins and consequences of indels have not yet been fully understood, indels as inferred by alignment algorithms usually need further evaluation. It would be desirable to be able to more reliably distinguish between, highly likely, true evolutionary indels and “gap noise” in large-scale alignment studies. We have developed a pair HMM pased framework to...   More >

Abbott Infosession: Come learn about the Abbott Internship Program and direct hire opportunities!

Information Session: Related Seminars (Non-CCB) | September 16 | 6-8 p.m. | Faculty Club, Howard Room

Sponsor: Abbott Laboratories

Interested in getting a summer internship or a full-time job at a leading biotech company? Abbott Laboratories will be coming on campus to discuss the Abbott Internship Program and direct hire opportunities.

Target audiences: Alumni, Faculty, Staff, Students - Graduate, Students - Prospective, Students - Undergraduate

Open to audience: All Audiences

From high-density genetic interaction maps to a genome wide strategy for monitoring protein translation: New tools for probing biological systems

Seminar: Related Seminars (Non-CCB) | September 17 | 4-5 p.m. | 101 Barker Hall

Featured Speaker: Jonathan Weissman, University of California San Francisco/HHMI

Sponsor: Molecular and Cell Biology, Department of

This seminar is partially sponsored by NIH

Reconstructing Indian Population History with Genomic Data

Seminar: Related Seminars (Non-CCB) | September 17 | 4 p.m. | 2040 Valley Life Sciences Bldg.

Speaker: David Reich, Harvard University

Sponsor: Integrative Biology, Department of

India has been underrepresented in genome-wide surveys of human
variation. Here we analyze variation in 25 diverse Indian groups to provide
strong evidence for two ancient populations, genetically divergent, that are
ancestral to most groups today. One, the "Ancestral North Indians" (ANI), is
genetically close to Middle Easterners, Central Asians, and Europeans, while
the...   More >

Seminar Canceled!

Seminar: Statistics and Genomics Seminar Series | September 17 | 4-5 p.m. | 1011 Evans Hall | Canceled

Speaker: Holger Schwender, Postdoctoral Fellow, Department of Biostatistics, Johns Hopkins University

Sponsor: Statistics, Department of

A major goal of genetic association studies is the identification of SNPs (Single NucleotidePolymorphisms) and SNP interactions that are associated with the disease of interest. Aproblem concerned with this task is that SNPs often show only an effect on the disease riskwhen interacting with other SNPs so that testing each SNP individually might fail to detectsuch SNPs. This problem...   More >

Environmentally-Controlled Protein/Protein Interactions: Nature's Way of Building Biological Switches

Seminar: Related Seminars (Non-CCB) | September 21 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Kevin Gardner, Department of Biochemistry, UT Southwestern Medical Center

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Genetic clocks from engineered oscillators

Seminar: Related Seminars (Non-CCB) | September 23 | 12-1 p.m. | 106 Stanley Hall

Speaker/Performer: Professor Jeff Hasty, University of California, San Diego

Sponsor: Bioengineering (BioE)

Fall 2009 Seminar Series
Wednesday, September 23
12noon - 1:00pm
106 Stanley Hall, UC Berkeley

Professor Jeff Hasty

Departments of Molecular Biology and Bioengineering
BioCircuits Institute
University of California, San Diego

Genetic clocks from engineered oscillators

Abstract:
One defining goal of synthetic biology is the development of...   More >

The genetic architecture of maize. What you learn from mixing tremendous diversity and create 5000 lines.

Seminar: Related Seminars (Non-CCB) | September 23 | 12-1 p.m. | 101 Barker Hall

Speaker: Ed Buckler, Cornell

Sponsor: Plant and Microbial Biology, Department of

Learning models for aligning protein sequences with predicted secondary structure

Seminar: Mathematical and Computational Biology Seminar Series | September 23 | 2-3 p.m. | 939 Evans Hall

Speaker: John Kececioglu, University of Arizona

Sponsor: Mathematics, Department of

Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted secondary structure. We introduce several new models for scoring alignments of protein sequences with predicted secondary structure, which use the predictions and their confidences to modify both the...   More >

Non-coding sequences near duplicated genes evolve rapidly

Seminar: Statistics and Genomics Seminar Series | September 24 | 4-5 p.m. | 1011 Evans Hall | Note change in date

Speaker: Dennis Kostka, Gladstone Institutes, UCSF

Sponsor: Statistics, Department of

DATE CHANGE: This talk has been rescheduled for Oct. 8, 2009.

Interactions and Reactions in Model Membrane Assemblies

Seminar: Related Seminars (Non-CCB) | September 28 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Steven G. Boxer, Department of Chemistry, Stanford University

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Bayesian networks and resistance conferring mutations

Seminar: Mathematical and Computational Biology Seminar Series | September 30 | 2-3 p.m. | 939 Evans Hall

Speaker: Kristina Crona, UC Merced

Sponsor: Mathematics, Department of

It is well known that resistance conferring mutations for viruses and bacteria may be restricted in the order of occurrence. A central problem is to derive from the data the constraints on the orders in which the mutations have accumulated. We consider a Bayesian network model for mutations conferring resistance to antibiotics where both conjunctions and disjunctions are allowed as...   More >

A Bayesian Approach to Transforming Public Gene Expression Repositories into Disease Diagnosis Databases

Seminar: Related Seminars (Non-CCB) | September 30 | 4-5 p.m. | 1011 Evans Hall

Speaker: Haiyan Huang, Assistant Professor, Department of Statistics, UC Berkeley

Sponsor: Statistics, Department of

The rapid accumulation of gene expression data has offered unprecedented
opportunities to study human diseases. The NCBI Gene Expression Omnibus
(http://www.ncbi.nlm.nih.gov/geo/) is currently the largest database that
systematically documents the genome-wide molecular basis of diseases.
However, thus far, this resource has been far from fully utilized. In this
talk, I will...   More >

TumorBoost: Normalization of allele-specific tumor copy numbers in paired tumor/normal designs for genotyping microarrays

Seminar: Statistics and Genomics Seminar Series | October 1 | 4-5 p.m. | 1011 Evans Hall

Speaker: Pierre Neuvial, Postdoctoral Scholar, Department of Statistics, UC Berkeley

Sponsor: Statistics, Department of

High-throughput genotyping microarrays can be used not only to assess changes in total DNA copy number, but also changes in allele-specific copy numbers (ASCNs). Even after state of the art preprocessing methods, ASCN estimates still suffer from systematic effects that make them difficult to use effectively for downstream analyses, such as ASCN segmentation and calling in cancer...   More >

PMB Graduate Student and Post-doctoral Fellow Seminar Series

Seminar: Related Seminars (Non-CCB) | October 5 | 12-1 p.m. | 338 Koshland Hall

Speaker: Eric Lyons, UC Berkeley

Sponsor: Plant and Microbial Biology, Department of

This will be a 2-part talk:

Uncovering ancient whole genome duplication events in the Fabacaea
AND
Understanding the evolution of genomic GC content in malaria plasmodia species: does the tail wag the dog?

Structural Insights into the Dynamic Process of G Protein Coupled Receptor Activation

Seminar: Related Seminars (Non-CCB) | October 5 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Brian Kobilka, Department of Medicine and Molecular & Cellular Physiology, Stanford University

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Mass Spectrometry Base Metabolomic Approaches to Studying Cyanobacterial Metabolism

Seminar: Related Seminars (Non-CCB) | October 6 | 4-5 p.m. | Lawrence Berkeley National Laboratory, Bldg 84, room 318

Location: 1 Cyclotron Road, Berkeley, CA 94720

Speaker: Trent Northen, Ph.D., Life Sciences Division, LBNL

Sponsor: Lawrence Berkeley National Laboratory

Comp. Bio DE Seminar

Seminar: DE Student Research Seminars | October 6 | 5:30-7 p.m. | Annex Campbell Hall

Speaker: Alistair Boettiger

Sponsor: Computational Biology, Center for

Title: "Stability in Times of Change: Biophysics of Robust Gene Control"

Spike-time reliability of layered neural oscillator networks

Seminar: Mathematical and Computational Biology Seminar Series | October 7 | 2-3 p.m. | 939 Evans Hall

Speaker: Kevin Lin, University of Arizona

Sponsor: Mathematics, Department of

This talk concerns the reliability of large networks of coupled neural oscillators driven by fluctuating stimuli. Reliability means that upon repeated presentations of a given stimulus, the network gives essentially the same response each time; whether a network is reliable can impact its ability to encode information via the precise timing of spikes. I will explain how questions...   More >

Non-coding sequences near duplicated genes evolve rapidly

Seminar | October 8 | 4-5 p.m. | 1011 Evans Hall

Speaker: Dennis Kostka, Gladstone Institutes, UCSF

Sponsor: Statistics, Department of

Gene expression divergence and chromosomal rearrangements have both been put forward as major contributors to phenotypic differences between closely related species. It has also been established that duplicated genes show enhanced rates of positive selection in their amino acid sequences. If functional divergence is largely due to changes in gene expression, it follows that...   More >

Dynamics of Ribosome Assembly in Vitro and in Cells

Seminar: Related Seminars (Non-CCB) | October 12 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor James R. Williamson, Department of Chemistry & Molecular B, The Scripps Research Institute

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Fluorescent reporters of protein trafficking and interactions, and applications to imaging studies of synapse development

Seminar: Related Seminars (Non-CCB) | October 13 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Featured Speaker: Alice Ting, Massachusetts Institute of Technology, Chemistry

Sponsor: Molecular and Cell Biology, Department of

Folding@home: Pushing the boundaries of molecular simulation orders of magnitude using a combination of Bayesian statistics and large-scale distributed computing

Seminar: Mathematical and Computational Biology Seminar Series | October 14 | 2-3 p.m. | 939 Evans Hall

Speaker: Vijay Pande, Stanford

Sponsor: Mathematics, Department of

Many key problems involving molecular simulation are fundamentally limited by the timescales they can address (nanoseconds to microseconds), compared to the relevant timescales experimentally (microseconds to milliseconds to seconds). I will describe recent advances that allow for dramatic advances in the capabilities of molecular simulation driven by world-wide distributed...   More >

Time Varying Networks: reverse engineering and analyzing rewiring genetic interactions

Seminar: Related Seminars (Non-CCB) | October 14 | 4-5 p.m. | 1011 Evans Hall

Speaker: Eric Xing, Associate Professor, Department of Computer Science, Carnegie Mellon University

Sponsor: Statistics, Department of

A plausible representation of the relational information among entities
in dynamic systems such as a living cell is a stochastic network that is
topologically rewiring and semantically evolving over time. While there
is a rich literature in modeling static or temporally invariant
networks, until recently, little has been done toward modeling the
dynamic processes underlying...   More >

Charles M. and Martha Hitchcock Lectures: A Scientist Addresses Science Education

Lecture: Related Seminars (Non-CCB) | October 14 | 4:10 p.m. | International House, Chevron Auditorium

Speaker: Leon Lederman, Founder and Resident Scholar, Illinois Mathematics and Science Academy

Sponsor: Graduate Division

Nobel Laureate Leon Lederman will present two Hitchcock Lectures. His first lecture will be presented on Wednesday, October 14 and is titled "A Scientist Addresses Science Education." His second lecture will occur on Thursday, October 15 and is titled "A Sense of Wonder."

Using RNA-Seq for a global analysis of alternative splicing regulation in Drosophila melanogaster

Seminar | October 15 | 4-5 p.m. | 1011 Evans Hall

Speaker: Angela N. Brooks, Department of Molecular and Cell Biology, UC Berkeley

Sponsor: Statistics, Department of

POSTPONED to October 29

Quaternary Climatic Oscillations and Plant Evolution

Seminar: Related Seminars (Non-CCB) | October 15 | 4 p.m. | 2040 Valley Life Sciences Bldg.

Speaker: Joachim Kadereit, Johannes Gutenberg University

Sponsor: Integrative Biology, Department of

Charles M. and Martha Hitchcock Lectures: A Sense of Wonder

Lecture: Related Seminars (Non-CCB) | October 15 | 4:10 p.m. | International House, Chevron Auditorium

Speaker: Leon Lederman, Founder and Resident Scholar, Illinois Mathematics and Science Academy

Sponsor: Graduate Division

Nobel Laureate Leon Lederman will present two Hitchcock Lectures. His first lecture will be presented on Wednesday, October 14 and is titled "A Scientist Addresses Science Education." His second lecture will occur on Thursday, October 15 and is titled "A Sense of Wonder."

Northern California iGEM Jamboree: Premiere Synthetic Biology Event

Presentation | October 17 | 9 a.m.-1:30 p.m. | 105 Stanley Hall

Sponsor: QB3 - California Institute for Quantitative Biosciences

The International Genetically Engineered Machine Competition comes to UC Berkeley! iGEM teams from Berkeley, UCSF, Davis, Stanford, and San Francisco City College will present innovative Synthetic Biology projects competing in the IGEM 2009 competition. Students, faculty and community members are invited to judge the results! Free of charge.

Target audience: All Audiences

Open to audience: All Audiences

Enzymes as Escorts in Organometallic Cofactor Trafficking

Seminar: Related Seminars (Non-CCB) | October 19 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Ruma Banerjee, Department of Biological Chemistry, University of Michigan Medical Center

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Computational Data Driven Algorithms for MicroRNA prediction in Ciona: Comp Bio DE Seminar

Seminar: DE Student Research Seminars | October 20 | 5:30-7 p.m. | Campbell Hall, Campbell Annex (001)

Speaker/Performer: Dave Hendrix, Computational Biology DE

Sponsor: Computational Biology, Center for

Dave Hendrix will be speaking on "Computational Data Driven Algorithms for MicroRNA prediction in Ciona".
Dave is a post doc collaborating with the Rokhsar and Levine labs on analysis of whole genome data.

Tropical geometry and dissimilarity vectors of trees

Seminar: Mathematical and Computational Biology Seminar Series | October 21 | 2-3 p.m. | 939 Evans Hall

Speaker: Filip Cools, K.U. Leuven

Sponsor: Mathematics, Department of

I would like to talk about tropical geometry and dissimilarity vectors of trees. At first sight, these two mathematical topics seem to have no relation. However, nice connections are given by tropical Grassmannians. Indeed, for example, the space of n-trees is equal to the tropical Grassmannian G2,n (see [2, 4]). In the recent articles [1] and [3] (partially joint work with C....   More >

The DNA damage response: How four amino acids changed my life

Seminar: Related Seminars (Non-CCB) | October 21 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Featured Speaker: Stephen J. Elledge, Harvard Medical School, Department of Genetics

Sponsor: Molecular and Cell Biology, Department of

C. H. Li Memorial Lectures

Adventures in mammalian genetics: Genetic mining of the cancer genome

Seminar: Related Seminars (Non-CCB) | October 22 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Featured Speaker: Stephen J. Elledge, Harvard Medical School, Department of Genetics

Sponsor: Molecular and Cell Biology, Department of

C. H. Li Memorial Lectures

An atlas of open chromatin spanning diverse human cell types in health and disease

Seminar: Statistics and Genomics Seminar Series | October 22 | 4-5 p.m. | 1011 Evans Hall

Speaker: Jason Lieb, Associate Professor, Department of Biology, University of North Carolina, Chapel Hill

Sponsor: Statistics, Department of

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) is a simple, low-cost genomic method for the isolation and identification of nucleosome-depleted regions in eukaryotic cells. Identification of "open" chromatin regions has been one of the most accurate and robust methods to identify functional promoters, enhancers, silencers, insulators, and locus control regions in...   More >

Fast DNA Sequencing: A Physicist’s Perspective: Nano Seminar Series

Seminar: Related Seminars (Non-CCB) | October 23 | 2-3 p.m. | 390 Hearst Memorial Mining Bldg.

Speaker/Performer: Prof. Massimiliano Di Ventra, UC San Diego, Physics Department

Sponsor: Berkeley Nanosciences and Nanoengineering Institute

Fast and low-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced so that drugs could be tailored to his/her specific illnesses; doctors could know in advance patients’ likelihood to develop a given ailment; cures to major diseases could be found faster.

However, this goal of “personalized medicine” is hampered today by the..

Bioengineering Dept Seminar

Seminar: Related Seminars (Non-CCB) | October 28 | 12-1 p.m. | 106 Stanley Hall

Speaker/Performer: Professor Jay Keasling, University of California, Berkeley

Sponsor: Bioengineering (BioE)

Fall 2009 Seminar Series
Wednesday, October 28
12noon - 1:00pm
106 Stanley Hall, UC Berkeley

Professor Jay Keasling

Departments of Bioengineering and Chemical Engineering
UC Berkeley

Director, Physical Biosciences Division, LBL and Synthetic Biology Engineering Research Center

CEO, Joint BioEnergy Institute

details forthcoming

Structural variation in human and cancer genomes

Seminar: Mathematical and Computational Biology Seminar Series | October 28 | 2-3 p.m. | 939 Evans Hall

Speaker: Ben Raphael, Brown

Sponsor: Mathematics, Department of

Genome variation occurs on a continuum of scales ranging from single nucleotide differences to large structural rearrangements. In the past few years, structural variants including deletions, insertions, inversions, and translocations of large blocks of DNA sequence have been shown to be a significant fraction of the genetic differences in human populations. Structural variants...   More >

Using RNA-Seq for a global analysis of alternative splicing regulation in Drosophila melanogaster

Seminar: Statistics and Genomics Seminar Series | October 29 | 4-5 p.m. | 1011 Evans Hall

Speaker: Angela N. Brooks, Department of Molecular and Cell Biology, UC Berkeley

Sponsor: Statistics, Department of

Splicing regulators are proteins that bind to newly-transcribed pre-mRNA and guide their processing into mature mRNAs. Specifically, they regulate the removal of introns usually at a nearby splice site. They are believed to operate by inhibiting or promoting assembly of the spliceosome, a complex of proteins which is involved in splicing out intronic sequences. Splice regulators...   More >

Randomness and Predictability of Cellular Response in Bacteria

Seminar: Related Seminars (Non-CCB) | November 2 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Philippe Cluzel, Department of Molecular & Cell Biology, Harvard

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Techniques for inferring phylogenetic relationships of species from multi-locus data

Seminar: Mathematical and Computational Biology Seminar Series | November 4 | 2-3 p.m. | 939 Evans Hall

Speaker: Luay Nakhleh, Rice

Sponsor: Mathematics, Department of

Accurate inference of species phylogenies and understanding of their relationships with gene trees are two central themes in molecular and evolutionary biology. Traditionally, a species tree is inferred by sequencing a genomic region of interest from the group of species under study, reconstructing its evolutionary history, and declaring it to be estimate of the species tree....   More >

Metabolite-sensing Riboswitches: Molecular fossils from the RNA world?

Seminar: Related Seminars (Non-CCB) | November 4 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Speaker: Ronald Breaker, Yale University, Molecular, Cellular and Developmental Biology

Sponsor: Molecular and Cell Biology, Department of

Discovery and analysis of extraordinary noncoding RNAs

Seminar: Related Seminars (Non-CCB) | November 5 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Speaker: Ronald Breaker, Yale University, Molecular, Cellular and Developmental Biology

Sponsor: Molecular and Cell Biology, Department of

Combining data using Bayes factors

Seminar: Statistics and Genomics Seminar Series | November 5 | 4-5 p.m. | 1011 Evans Hall

Speaker: Robert Gentleman, Genentech

Sponsor: Statistics, Department of

Combining data from different experiments should account in some way for relative error rates in the experiments. While this is standard practice in meta-analysis it seems not to be addressed on many high throughput screens. I will focus on rotein interaction data in this talk and propose a paradigm for data integration.

The unicellular ancestry of animal development

Seminar: Related Seminars (Non-CCB) | November 10 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Featured Speaker: Nicole King , University of California at Berkeley, Dept. of Molecular and Cell Biology

Sponsor: Molecular and Cell Biology, Department of

This seminar is partially sponsored by NIH

Computational Biology DE Seminar: The Concomitant Genomic Analysis of an Obligate Pathogen-Host Interaction

Seminar: DE Student Research Seminars | November 10 | 5:30-7 p.m. | 001 Campbell Hall

Speaker: Ksenia V Krasileva

Sponsor: Computational Biology, Center for

The development of genomic tools to concomitantly study obligate
eukaryotic biotrophic pathogens interacting with their respective
hosts has been rapidly advanced by the use of high throughput next
generation deep-sequencing technologies. These technologies now allow
for the simultaneous isolation of different RNA species (mRNA or
smallRNAs) from both the pathogen and infected...   More >

Analysis of natural variation in yeast

Seminar: Related Seminars (Non-CCB) | November 12 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Featured Speaker: Barak Cohen, Washington University Medical School, Department of Genetics

Sponsor: Molecular and Cell Biology, Department of

Statmap: A utility for the principled mapping of short reads to a reference genome

Seminar: Statistics and Genomics Seminar Series | November 12 | 4-5 p.m. | 1011 Evans Hall

Speaker: Nathan Boley, UC Berkeley, Department of Statistics

Sponsor: Statistics, Department of

Next generation sequencing technologies have given rise to a host of assays that are able to quickly answer a diverse set of biological questions. These assays, which include RNA-seq, ChIP-seq, methyl-seq, Hi-C-seq, and DNase-seq are similar in that, at the end of a "*-seq" experiment, they result in a set of sequences, or 'reads', generated by the sequencing platform, and it is...   More >

IB Seminar

Seminar: Related Seminars (Non-CCB) | November 12 | 4 p.m. | 2040 Valley Life Sciences Bldg.

Speaker: Peter Vize, University of Calgary

Sponsor: Integrative Biology, Department of

Cynthia A. Chan Memorial Lecture

Seminar: Related Seminars (Non-CCB) | November 16 | 4-5 p.m. |  Berdahl Auditorium, 105 Stanley Hall

Speaker: Ronald Vale, University of California at San Francisco, Cellular and Molecular Biology

Sponsor: Molecular and Cell Biology, Department of

The Drosophila Genome: Transcriptional Profiling throughout Development

Seminar: Related Seminars (Non-CCB) | November 17 | 4-5 p.m. | Lawrence Berkeley National Laboratory, Bldg. 66 Auditorium

Speaker/Performer: Susan Celniker, Life Sciences Division, Berkeley Lab

Sponsor: Lawrence Berkeley National Laboratory

Computational Biology DE Seminar: Theory and Application of Random Forests to Genome Wide Association studies

Seminar: DE Student Research Seminars | November 17 | 5:30-7 p.m. | 001 Campbell Hall

Speaker: Ben Goldstein

Sponsor: Computational Biology, Center for

Random Forests is one of the of the few machine learning algorithms capable of handling large GWA SNP data sets. I will review the theory behind the RF algorithm and discuss some issues that arise when applying it to this type of data. I will discuss some new methods in development for selecting important variables.

Diversity in tomato fruit shape: Identifying the underlying mechanisms controlling morphological variation

Seminar: Related Seminars (Non-CCB) | November 18 | 12-1 p.m. | 101 Barker Hall

Speaker: Esther van der Knaap, Ohio State University

Sponsor: Plant and Microbial Biology, Department of

Genome rearrangements: From models to predictions

Seminar: Mathematical and Computational Biology Seminar Series | November 18 | 2-3 p.m. | 939 Evans Hall

Speaker: Max Alekseyev, University of South Carolina

Sponsor: Mathematics, Department of

Genome rearrangements are evolutionary "earthquakes" that break a genome into fragments and "glue" them in a new order. A driving force of rearrangements is one of most important unsolved mysteries in evolutionary studies. In particular, it is unclear (i) what makes a certain region a breakpoint (that is broken by a rearrangement); and (ii) whether the same breakpoint is likely to.

Detecting Rare Variants in Candidate Genes for Mitochondrial Diseases using Resequencing Microarrays

Seminar: Statistics and Genomics Seminar Series | November 19 | 4-5 p.m. | 1011 Evans Hall

Speaker: Wenyi Wang, Postdoctoral Fellow, Stanford Genome Technology Center

Sponsor: Statistics, Department of

Oligonucleotide resequencing arrays provide cost-effective approaches to identify key biomarkers in human disorders. Mitochondrial diseases are one disease family with the underlying genetic variations not yet fully understood. As a proof-of-principle study, we sequenced 39 candidate genes in healthy individuals and patients with mitochondrial diseases using custom designed...   More >

IB Seminar: Profs on Parade

Seminar: Related Seminars (Non-CCB) | November 19 | 4 p.m. | 2040 Valley Life Sciences Bldg.

Speakers: Doris Bachtrog, UC Berkeley; Cindy Looy, UC Berkeley; John Huelsenbeck, UC Berkeley

Sponsor: Integrative Biology, Department of

Surviving in the absence of air – analysis of the adaptation of Chlamydomonas to hypoxia by RNA-seq and classical approaches

Seminar: Related Seminars (Non-CCB) | November 20 | 10-11 a.m. | 338 Koshland Hall

Speaker: Anja Hemschemeier, UCLA and University of Bochum, Germany

Sponsor: Plant and Microbial Biology, Department of

Recycling Metabolic “Waste”: Moonlighting Enzymes and the Evolution of Chemodiversity in Plant Specialized Metabolic Pathways

Seminar: Related Seminars (Non-CCB) | November 23 | 4-5 p.m. | 105 Stanley Hall

Speaker: Professor Joseph P. Noel, Chemical Biology, Salk Institute for Biological Studies

Sponsor: Chemistry, Department of

Coffee & Refreshments served on lower level Stanley Hall @3:50pm-4:10pm

Long-range Gene Regulatory Architecture of the Human Genome

Seminar: Related Seminars (Non-CCB) | November 24 | 4-5 p.m. | Lawrence Berkeley National Laboratory, Bldg 66 Aud

Speaker: Job Dekker, University of Massachusetts Medical Schoo

Sponsor: Lawrence Berkeley National Laboratory

Evolutionary changes across the transcriptome during human origins

Seminar: Related Seminars (Non-CCB) | December 1 | 4-5 p.m. | 100 Genetics & Plant Biology Bldg.

Featured Speaker: Greg Wray, Duke University, Biology

Sponsor: Molecular and Cell Biology, Department of

Computational Biology DE Seminar: Berkeley PHOG: PhyloFacts Orthology Group

Seminar: DE Student Research Seminars | December 1 | 5:30-7 p.m. | 001 Campbell Hall

Speaker: Ruchira Datta

Sponsor: Computational Biology, Center for

We present a new algorithm, PHOG phylogenomic orthology prediction, which is available as a web service through the PhyloFacts Phylogenomic Encyclopedias at http://phylofacts.berkeley.edu/orthologs

Mathematical and Computational Biology Seminar

Seminar: Mathematical and Computational Biology Seminar Series | December 2 | 2-3 p.m. | 939 Evans Hall

Speaker: Ruchira Datta, UC Berkeley

Sponsor: Mathematics, Department of

Supervised topic models

Seminar: Related Seminars (Non-CCB) | December 2 | 4-5 p.m. | 1011 Evans Hall

Speaker: Jon McAuliffe, Adjunct Assistant Professor, Department of Statistics, UC Berkeley

Sponsor: Statistics, Department of

The scale of contemporary electronic text collections has led to growing
interest in statistical models based on so-called topics. Formally, a
topic is a probability distribution over a vocabulary. Informally, a
topic is intended to capture an underlying semantic theme. Most topic
models are unsupervised: only the words in the documents are modelled. I will describe...   More >

Statistics and Genomics Seminar: Oleg Mayba

Seminar: Statistics and Genomics Seminar Series | December 3 | 4-5 p.m. | 1011 Evans Hall

Speaker: Oleg Mayba, Department of Statistics, UC Berkeley

Sponsor: Statistics, Department of

Mathematical and Computational Biology Seminar

Seminar: Mathematical and Computational Biology Seminar Series | December 9 | 2-3 p.m. | 939 Evans Hall

Speaker: Chand John, Stanford

Sponsor: Mathematics, Department of

Leveraging High Throughput Interaction Screens: New Players in Iron Sulfur Cluster Biosynthesis

Seminar: Related Seminars (Non-CCB) | December 15 | 4-5 p.m. |  Lawrence Berkeley National Laboratory

Speaker: Gareth Butland, Life Sciences Division, Berkeley Lab

Sponsor: Lawrence Berkeley National Laboratory