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Spring 2014

Friday, January 17, 2014

Cancer Genomics Symposium

Conference/Symposium: Featured | January 17 | 9 a.m.-5 p.m. | 245 Li Ka Shing Center


Samuel Aparicio, BM, BCh, PhD, FRCPath, Nan & Lorraine Robertson Chair in Breast Cancer Research, and Canada Research Chair in Molecular Oncology, University of British Columbia and the BC Cancer Agency; Luis Diaz, MD, Attending Physician, Johns Hopkins Hospital; Maria Figueroa, MD, Assistant Professor of Pathology, University of Michigan; P. Andrew Futreal, PhD, Professor of Genomic Medicine, University of Texas MD Anderson Cancer Center; David Haussler, PhD, Investigator, Howard Hughes Medical Institute; UCSC Distinguished Professor of Biomolecular Engineering, University of California, Santa Cruz; Matthew Meyerson, MD, PhD, Professor of Pathology, Harvard Medical School, Dana-Farber Cancer Institute; Esther Rheinbay, PhD, Postdoctoral Researcher, Molecular Pathology Unit and Center for Cancer Research, and the Broad Institute

Center for Computational Biology


A one-day seminar on cancer genomics sponsored by the Berkeley Genomics Training Grant, the Center for Computational Biology, and QB3-Berkeley.


Admission is free but registration is required.

Registration opens November 21. Register by January 10 online.

Tuesday, January 21, 2014

From Systems to Structure: Bridging Networks and Mechanism

Seminar: Related Seminars (Non-CCB) | January 21 | 4-5 p.m. | Berkeley Lab at 717 Potter Street, Room 141 | Canceled


717 Potter Street, Berkeley, CA 94710

Nevan Krogan, Ph.D., University of California, San Francisco

Life Sciences Division, Berkeley Lab (LBNL)


Life Sciences Division Seminar, Berkeley Lab


RSVP required for non-LBNL and non-UCB attendees. RSVP by January 20 by calling Ciccina Guagliardo at 510-486-6490, or by emailing Ciccina Guagliardo at fguagliardo@lbl.gov.



Wednesday, January 22, 2014

MVZ Seminar: Michael Turelli, “Wolbachia population biology: from natural spatial spread to possible dengue control”

Seminar: Related Seminars (Non-CCB) | January 22 | 12-1 p.m. | Valley Life Sciences Building, MVZ 3101, Grinnell Miller Library


Michael Turelli, UC Davis

Museum of Vertebrate Zoology


MVZ Lunch is a graduate level seminar series based on current and recent vertebrate research. Professors, graduate students, staff and visiting researchers present on current and past research projects.

Friday, January 24, 2014

Mathematical Biology Seminar: Modeling the Dynamics of Tumor Heterogeneity

Seminar: Related Seminars (Non-CCB) | January 24 | 12:30-1:30 p.m. | 939 Evans Hall


Ruchira Datta, University of California San Francisco

Department of Mathematics


While each tumor may be descended from one mutant cell, recent studies have repeatedly shown single tumors to be comprised of multiple genomically distinct subpopulations. These subclones might be competing or neutrally coexisting. Axelrod, Axelrod, and Pienta (2006) suggested a third possibility: "Cooperation can evolve as by-product mutualism among genetically diverse tumor cells." Knowing...   More >

Monday, January 27, 2014

Novel genetic screens for mediators of metastatic reactivation

Seminar: Related Seminars (Non-CCB) | January 27 | 12:30-1:30 p.m. | 101 Life Sciences Addition


**Filippo Giancotti**, Memorial Sloan-Kettering Cancer Center

Department of Molecular and Cell Biology



HIV Capsid Assembly, Maturation and Host Cell Interaction

Seminar | January 27 | 4-5 p.m. | 106 Stanley Hall


Professor Peijun Zhang, Department of Structural Biology, University of Pittsburgh School of Medicine

Department of Chemistry


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

Tuesday, January 28, 2014

Modeling Visual Cortex V4 in Naturalistic Conditions with Invariant and Sparse Image Representations: Life Sciences Division Seminar

Seminar: Related Seminars (Non-CCB) | January 28 | 4-5 p.m. | Berkeley Lab (LBNL) at 717 Potter Street, Room 141


717 Potter Street, Berkeley, CA 94710

Bin Yu, Ph.D., University of California, Berkeley

Life Sciences Division, LBNL


RSVP by January 27 by calling Ciccina Guagliardo at 510-486-6490, or by emailing Ciccina Guagliardo at fguagliardo@lbl.gov.

Wednesday, January 29, 2014

MVZ Seminar: Hunter Fraser, "Adaptive evolution of gene expression"

Seminar: Related Seminars (Non-CCB) | January 29 | 12-1 p.m. | Valley Life Sciences Building, MVZ 3101, Grinnell Miller Library


Hunter Fraser, Professor, Stanford University

Museum of Vertebrate Zoology


MVZ Lunch is a graduate level seminar series based on current and recent vertebrate research. Professors, graduate students, staff and visiting researchers present on current and past research projects.



BioE Seminar: “High-throughput Mapping of Protein Energy Landscapes Using Novel Microfluidic Tools”

Seminar: Related Seminars (Non-CCB) | January 29 | 12-1 p.m. | 106 Stanley Hall


Polly Fordyce, Postdoctoral Researcher, University of California, San Francisco

Bioengineering (BioE)


Wednesday, January 29
12noon - 1:00pm
106 Stanley Hall, UC Berkeley

“High-throughput Mapping of Protein Energy Landscapes Using Novel Microfluidic Tools”

Polly Fordyce
Postdoctoral Researcher
University of California, San Francisco

Precise regulation of gene expression drives virtually all cellular processes. To achieve this regulation, transcription factor proteins bind to genomic...   More >



How do bacteria sense surfaces?

Seminar: Related Seminars (Non-CCB) | January 29 | 12-1 p.m. | 101 Barker Hall


Caroline Harwood, University of Washington

Department of Molecular and Cell Biology



Multiple Types and Functions of Midbrain Dopamine Neurons

Seminar: Related Seminars (Non-CCB) | January 29 | 12:30-1:30 p.m. | 101 Life Sciences Addition


**Stephan Lammel**, Stanford University

Department of Molecular and Cell Biology

Thursday, January 30, 2014

Monday, February 3, 2014

DNA Signaling

Seminar: Related Seminars (Non-CCB) | February 3 | 4-5 p.m. | 106 Stanley Hall


Professor Jacqueline K. Barton, Division of Chemistry & Chemical Engineering, Caltech

Department of Chemistry


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

Tuesday, February 4, 2014

Evolutionary Contribution of Histones to Genome Condensation: Life Sciences Division Seminar

Seminar: Related Seminars (Non-CCB) | February 4 | 4-5 p.m. | Berkeley Lab (LBNL) at 717 Potter Street, Room 141


717 Potter Street, Berkeley, CA 94710

Siavash Kurdistani, Ph.D., University of California, Los Angeles

Life Sciences Division, LBNL


RSVP by February 3 by calling Ciccina Guagliardo at 510-486-6490, or by emailing Ciccina Guagliardo at fguagliardo@lbl.gov.

Wednesday, February 5, 2014

Tumor Microenvironment: How Local Milieu Shapes Metastasis

Seminar: Related Seminars (Non-CCB) | February 5 | 12:30-1:30 p.m. | 101 Life Sciences Addition


**Qing Chen**, Memorial Sloan-Kettering Cancer Center

Department of Molecular and Cell Biology

Thursday, February 6, 2014

Outside the coding genome, microRNAs make a big difference

Seminar: Related Seminars (Non-CCB) | February 6 | 4-5 p.m. | 100 Genetics & Plant Biology Building | Note change in date


Lin He, University of California, Berkeley

Department of Molecular and Cell Biology



Understanding angiosperm diversity in both time and space

Seminar: Related Seminars (Non-CCB) | February 6 | 4-5 p.m. | 2040 Valley Life Sciences Building


Charles Bell, University of New Orleans, Department of Biological Sciences

Department of Integrative Biology

Monday, February 10, 2014

Simons Institute Open Lecture: Rates of Evolution and Accumulation of Cultural Variation

Lecture: Related Seminars (Non-CCB) | February 10 | 4 p.m. | Sutardja Dai Hall, Banatao Auditorium


Marc Feldman

Simons Institute for the Theory of Computing


We investigate the rate of evolution of such traits under different models of cultural transmission, and how these models produce different patterns of accumulation of culture, a phenomenon that is often claimed to distinguish human culture from possible analogues to culture in non-human species.

Wednesday, February 12, 2014

The molecular basis and evolution of mosquito preference for humans

Seminar: Related Seminars (Non-CCB) | February 12 | 12:30-1:30 p.m. | 101 Life Sciences Addition


**Carolyn McBride**, Rockefeller University

Department of Molecular and Cell Biology

Thursday, February 13, 2014

Using histone variants to modify the epigenetic landscape

Seminar: Related Seminars (Non-CCB) | February 13 | 12:30-1:30 p.m. | 101 Life Sciences Addition | Note change in time


**Laura Banaszynski**, The Rockefeller University

Department of Molecular and Cell Biology



Special Computational Biology Seminar: An IDP-Based Swiss-Army-Knife-LikeToolkit for Signaling Diversification

Seminar: Related Seminars (Non-CCB): Featured | February 13 | 4-5 p.m. | 1011 Evans Hall


Professor A. Keith Dunker, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine

Center for Computational Biology


Intrinsically disordered proteins (IDPs) and IDP regions commonly occur in eukaryotic cells [1] and have been strongly implicated both in protein-protein interaction networks [2] and in transcription factor structure [3]. These IDPs and IDP regions readily undergo alternative splicing [4], and posttranslational modification (PTM) [5]. Very few mutations are needed to radically alter any one or...   More >

Thursday, February 20, 2014

IB Seminar: Microbial Museums: A Global Collections-Based Approach to the Emergence of Mammalian Microorganisms

Seminar: Related Seminars (Non-CCB) | February 20 | 4-5 p.m. | 2040 Valley Life Sciences Building


Nathan Wolfe, Lorry I Lokey Consulting Professor in Human Biology at Stanford University; Founder & Director of Global Viral; Founder & CEO of Metabiota

Department of Integrative Biology

Monday, February 24, 2014

Intrinsic Noise in Nonlinear Gene Regulation Inference

Seminar: Related Seminars (Non-CCB) | February 24 | 1-2 p.m. | 1011 Evans Hall


Chao Du, Stanford University

Department of Statistics


Cellular intrinsic noise plays an essential role in the complex transcriptional regulatory interactions between genes, which, in turn, govern many fundamental cellular processes. Although a variety of quantitative methods are used to study gene regulation system, the role of intrinsic noises in regulatory mechanisms has largely been overlooked. Using the Kolmogorov forward equation (master...   More >



Translesion DNA Synthesis: Chemistry and Cancer Biology

Seminar: Related Seminars (Non-CCB) | February 24 | 4-5 p.m. | 106 Stanley Hall


Dr. Wei Yang, Laboratory of Molecular Biology, NIDDK, NIH

Department of Chemistry


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

Wednesday, February 26, 2014

Mechanisms of BAF (mSWI/SNF)-dependent Chromatin Remodeling in Tumor Suppression

Seminar: Related Seminars (Non-CCB) | February 26 | 12:30-1:30 p.m. | 101 Life Sciences Addition


**Diana Hargreaves**, Stanford University

Department of Molecular and Cell Biology

Thursday, February 27, 2014

Systems-level analysis of the vertebrate segmentation clock

Seminar: Related Seminars (Non-CCB) | February 27 | 4-5 p.m. | 101 Life Sciences Addition


**Ertugrul Ozbudak**, Albert Einstein College of Medicine Yeshiva University

Department of Molecular and Cell Biology



Friday, February 28, 2014

The rate and dynamics of complex adaptation

Seminar: Related Seminars (Non-CCB) | February 28 | 2-4 p.m. | 100E Hildebrand Hall


Dr. Daniel Weissman, Simons Institute for the Theory of Computing and QB3

College of Chemistry

Monday, March 3, 2014

Simons Institute Open Lecture: Quantum Hamiltonian Complexity

Lecture | March 3 | 4 p.m. | Sutardja Dai Hall, Banatao Auditorium


Dorit Aharonov

Simons Institute for the Theory of Computing


The title of this talk is the name of an exciting and rapidly growing subarea of quantum information science, which focuses on the interplay between condensed matter physics and the theory of computation.

Tuesday, March 4, 2014

How Can Telomeres Cause Age-Related Disease?: Charles M. and Martha Hitchcock Lectures by Carol Greider

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


Carol Greider, Daniel Nathans Professor and Director of Molecular Biology and Genetics, Johns Hopkins University

Graduate Division


Carol Greider will present the Hitchcock lectures on March 4 and March 5, 2014. The first lecture is entitled "How Can Telomeres Cause Age-Related Disease?" The lecture is free and open to the public. No tickets are required.

Wednesday, March 5, 2014

Telomeres and Telomerase: Past, Present, and Future: Charles M. and Martha Hitchcock Lectures by Carol Greider

Lecture: Related Seminars (Non-CCB) | March 5 | 4:10 p.m. | International House, Chevron Auditorium


Carol Greider, Daniel Nathans Professor and Director of Molecular Biology and Genetics, Johns Hopkins University

Graduate Division


Carol Greider will present the Hitchcock lectures on March 4 and March 5, 2014. The second lecture is entitled "Telomeres and Telomerase: Past, Present, and Future." The lecture is free and open to the public. No tickets are required.

Monday, March 10, 2014

Wednesday, March 12, 2014

MVZ Seminar: Dr. Geoff Hill, "The mitonuclear compatibility theory of sexual selection"

Seminar: Related Seminars (Non-CCB) | March 12 | 12-1 p.m. | Valley Life Sciences Building, MVZ 3101, Grinnell Miller Library


Dr. Geoffery Hill, Auburn University, Professor, Auburn University

Museum of Vertebrate Zoology


MVZ Lunch is a graduate level seminar series based on current and recent vertebrate research. Professors, graduate students, staff and visiting researchers present on current and past research projects.



Why do bacteria regulate gene expression using non-coding RNAs

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


Han Lim, University of California, Berkeley

Department of Molecular and Cell Biology

Wednesday, April 2, 2014

MVZ Seminar: Wayne Getz, "Simulating evolutionary processes in complex environments: a computational toolbox for dummies"

Seminar: Related Seminars (Non-CCB) | April 2 | 12-1 p.m. | Valley Life Sciences Building, MVZ 3101, Grinnell Miller Library


Wayne Getz, Professor, ESPM

Museum of Vertebrate Zoology


MVZ Lunch is a graduate level seminar series based on current and recent vertebrate research. Professors, graduate students, staff and visiting researchers present on current and past research projects.



Thursday, April 3, 2014

Department Colloquium: Tractable models for some discrete random processes arising in evolutionary biology

Colloquium: Related Seminars (Non-CCB) | April 3 | 4:10-5 p.m. | 60 Evans Hall


Mike Steel, University of Canterbury, NZ

Department of Mathematics


Underlying the study of evolutionary biology is a foundation that draws upon multiple branches of mathematics. In this talk, I will provide a brief overview of certain problems that can be modeled by random processes involving finite graphs. These include evolutionary tree reconstruction, speciation-extinction modeling, ancestral state reconstruction, and the emergence of autocatalytic...   More >

Monday, April 7, 2014

Simons Institute Open Lecture: Evolutionary Genetics in the Crush of Genomics

Lecture: Related Seminars (Non-CCB) | April 7 | 4 p.m. | Sutardja Dai Hall, Banatao Auditorium


Charles H. Langley

Simons Institute for the Theory of Computing


The third in the spring series of Simons Institute Open Lectures. The Open Lectures are intended for a broad scientific audience.

Light refreshments will be served before the lecture at 3:30 p.m.



Finishing Talk: Path integration in population genetics

Seminar: Related Seminars (Non-CCB) | April 7 | 4-5 p.m. | 2040 Valley Life Sciences Building


Joshua Schraiber, UCB (Slatkin Lab)

Department of Integrative Biology

Wednesday, April 9, 2014

MVZ Seminar: Graham Coop, "How geography shapes human adaptation"

Seminar: Related Seminars (Non-CCB) | April 9 | 12-1 p.m. | Valley Life Sciences Building, MVZ 3101, Grinnell Miller Library


Graham Coop, Assoc. Professor, UC Davis

Museum of Vertebrate Zoology


MVZ Lunch is a graduate level seminar series based on current and recent vertebrate research. Professors, graduate students, staff and visiting researchers present on current and past research projects.



Telomere function during the cell cycle

Seminar: Related Seminars (Non-CCB) | April 9 | 12:30-1:30 p.m. | 101 Life Sciences Addition


Jan Karlseder, Salk Institute

Department of Molecular and Cell Biology


This seminar is partially sponsored by NIH

Monday, April 14, 2014

Finishing Talk: A population genetic model for range expansions

Seminar: Related Seminars (Non-CCB) | April 14 | 4-5 p.m. | 2040 Valley Life Sciences Building


Benjamin Peter, UCB (Nielsen Lab and Slatkin Lab)

Department of Integrative Biology

Wednesday, April 16, 2014

Probability Seminar: A Fleming-Viot process for multiscale evolutionary dynamics

Seminar: Related Seminars (Non-CCB) | April 16 | 3-4 p.m. | 332 Evans Hall


Shishi Luo, Los Alamos National Laboratory

Department of Statistics


Evolution by natural selection can act at multiple biological levels, often in opposing directions. This is particularly the case for pathogen evolution, which occurs both within the host it infects and via transmission between hosts, and for the evolution of cooperative behavior, where individually advantageous strategies are disadvantageous at the group level. In mathematical terms, these are...   More >

Friday, April 18, 2014

Algebraic Statistics Seminar

Seminar: Related Seminars (Non-CCB) | April 18 | 3-6 p.m. | 736 Evans Hall


Kristina Crona, UC Merced; Benjamin Recht, UC Berkeley; Piotr Zwiernik, UC Berkeley

Department of Mathematics


3:00-4:00pm Kristina Crona (UC Merced), "Graph, polytopes and evolutionary biology".
4:00-5:00pm Benjamin Recht (UC Berkeley) "Going off the grid".
5:00-6:00pm Piotr Zwiernik (UC Berkeley), "Geometry of the Brownian motion tree model".

More information of the seminar's website.

Friday, May 2, 2014

Simons Institute Open Lecture: Why are Many-body Problems in Physics so Difficult? A Quantum Information Perspective

Lecture | May 2 | 3:30 p.m. | Calvin Laboratory (Simons Institute for the Theory of Computing), Auditorium | Note change in date and location


Ignacio Cirac

Simons Institute for the Theory of Computing


The fourth in the spring series of Simons Institute Open Lectures. The Open Lectures are intended for a broad scientific audience.

Light refreshments will be served before the lecture at 3 p.m.