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The Fourth q-bio Summer School on Cellular Information Processing

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The Fourth q-bio Summer School is sponsored by the New Mexico Center for Systems Biology, the Center for Nonlinear Studies at Los Alamos National Laboratory, and the Los Alamos Institute for Advanced Studies. Participants will attend daily lectures about theory and modeling of cellular regulatory systems and networks. They will work in small teams on open-ended projects under the guidance of the summer school faculty. The summer school is designed for graduate students, postdocs, or anyone with a quantitative background who is new to modeling cellular regulatory systems and networks. After the summer school, students will participate in the Fourth q-bio Conference in Santa Fe, NM, August 10-14, 2010. Summer School applications are due on February 26th, 2010 and can be found at http://cnls.lanl.gov/q-bio/summer_school.html.

The q-bio Summer School is not affiliated with arXiv.q-bio.

Contents

Logistics

School Themes

Quote

“If I was a senior in college or a first-year graduate student trying to figure out what area to work in, I would be a computational biologist.” - Francis Collins (Director, National Institutes of Health)

Participants

Schedule Overview

Unless otherwise noted, the school schedule will consist of approximately 3 hours of lectures in the morning. A typical schedule will look like

  • 9:00-10:45 -- Lecture One
  • 10:45-11:00 -- Break
  • 11:00-12:45 -- Lecture Two

Afternoons will be left for other activities, such as ad hoc lectures, student talks (please come prepared to give an informal talk about your research), discussions, and study sessions, work on homework projects, continuation of the participants' regular academic work, and recreation. A classroom with wireless internet access will be reserved for the school participants for all afternoons during the school program. Additionally, we expect the students to spend some of the afternoons with the school faculty, most of whom are scientists at LANL, familiarizing themselves with the workings of the research institution and potentially starting collaborative research with the faculty.

Detailed schedule

July 25 - Sunday
Arrive in Los Alamos

Week 1

July 26 - Monday
Opening remarks - 8:00 AM
Lecture 1, Ruy Ribeiro, Dynamics of CD4+ T cells in HIV-1 infection
Lecture 2, Brian Munsky, Stochastic effects in systems biology: theoretical foundations and experimental results (part 1) Slides--Part1
Lunch discussion with lecturers
Student Talk 1 - Christoph Zimmer
July 27 - Tuesday
Lecture 3, S. 'Gnana' Gnanakaran, How multiscale modeling approaches have been applied to study a wide variety of biological problems
Lecture 4, William S. Hlavacek, Rule-based modeling (slides)
Lunch discussion with lecturers
Student Talk 2 - Erin Rivera
14:00-15:00, Jasmin Fisher, Microsoft Research Cambridge -- q-bio seminar talk.
Student Talk 3 - Kentaro Hayashi
Student Talk 4 - Abhinav Tiwari
July 28 - Wednesday
Lecture 5, Tanmoy Bhattacharya, Phylogenetics (slides)
Lecture 6, Brian Munsky, Stochastic effects in systems biology: theoretical foundations and experimental results (part 2) Slides--Part2
Lunch discussion with lecturers
Student Talk 5 - Anat Burger
Student Talk 6 - Erwin Schoof
Student Talk 7 - Paolo Cazzaniga
Student Talk 8 - Dario Pescini
July 29 - Thursday
Lecture 7, Alan S. Perelson, How to model a viral infection
Lecture 8, Bridget S. Wilson, Protein clustering
Lunch discussion with lecturers
Student Talk 9 - Sam Schwartz
Student Talk 10 - Duncan Wadsworth
Student Talk 11 - Jean Hausser
Student Talk 12 - Jiankui He
July 30 - Friday
Lecture 9, Bette Korber, HIV vaccine design
Lecture 10, Anurag Sethi, Molecular dynamics and network theory approaches with special emphasis on signaling and intrinsically disordered proteins
Lunch discussion with lecturers
Student Talk 13 - Michael Nip
Student Talk 14 - Michael de Freitas
Student Talk 15 - Julio Belmonte
Student Talk 16 - Maria Mateescu
July 31 and August 1 (Saturday and Sunday)
Ideas for weekend activities -- TBA

Week 2

August 2 - Monday
Lecture 11, Cynthia Reichhardt, Computational Modeling of Directed Motion in Self-Driven Systems such as Bacteria and Cells
Lecture 12, Helen Wearing, University of New Mexico
Lunch discussion with lecturers
Guest Lecture - Ramit Mehr (slides)
Student Talk 17 - Alvin Tamsir
Student Talk 18 - Barak Peleg
August 3 - Tuesday
Lecture 13a, Arjun Raj, Measuring cell-to-cell variability with fluorescence microscopy and single molecule Fluorescence In Situ Hybridization (FISH) techniques.
Lecture 13b, Babs Marrone, Measuring cell-to-cell variability with flow cytometry and fluorescence activated cell sorting. (slides)
Lecture 14, Thomas Leitner, Molecular evolution: tracing HIV epidemics and the origin of the domestic dog
Lunch discussion with lecturers
Student Talk 22 - Rosemary Braun
Student Talk 23 - Antoine Delmotte
14:00-15:00, Arjun Raj, University of Pennsylvania -- q-bio seminar talk A single molecule view of cell fate: FISHing for worm guts
August 4 - Wednesday
Lecture 15, Partha Ramakrishnan, Quantum mechanical and molecular modeling approaches with special emphasis on molecular recognition during host-pathogen and nanomaterial-protein Interactions
Lecture 16A, Jim Werner, Fluorescence Correlation Spectroscopy (FCS) and 3 Dimensional Molecule Tracking:
Lecture 16B, Brian Munsky, Using single-cell variability data (FISH and Flow Cytometry) to identify parameters and mechanisms of gene regulatory systems.
Lunch discussion with lecturers
Lecture 17, Arthur D. Lander, Biological Pattern and Growth: Mechanism and Control
Student Talk 24 - Xiaojing Yang
Student Talk 25 - Chunbo Lou
August 5 - Thursday
Lecture 18, Ryan Gutenkunst, Inferring population history and natural selection from genomic data
Lecture 19, Giovanni Bellesia, Coarse-grained and statistical mechanical approaches with special emphasis on biofuels and membrane physics
Lunch discussion with lecturers
"Guest Lecture" - Ramit Mehr
Student Talk 26 - Eyal Ben Isaac
Special Talk - Mac Hyman, Tulane/Los Alamos, Good choices for great careers (this talk will start at 4 PM) (slides)
August 6 - Friday
Lecture 20, Ilya Nemenman, Signal processing in biochemical networks, Part 1.
Lecture 21, Ilya Nemenman, Signal processing in biochemical networks, Part 2.
Lunch discussion with lecturers
Student Talk 27 - Paul Bogdan
Student Talk 28 - Arfu Guo
Student Talk 29 - Jonghyeon Shin
Student Talk 30 - Sheng Wu
August 7 and 8 (Saturday and Sunday)
Ideas for weekend activities -- TBA

Week 3

August 9 - Monday
Lecture 22, Anton Zilman, History of Stochastic Modeling in Physics.
Lecture 23, Anton Zilman, Advanced stochastic analyses: Fokker Planck equation, Moment Generating Functions, etc...
Lunch - Panel discussion on the Necessary Complexity of Biological Models: Tanmoy Bhattacharya, Gnanakaran, S, Byron Goldstein, Ryan Gutenkunst, Ilya Nemenman
Lecture 24, Elaine L. Bearer, Cellular dynamics: inside and outside
Student Talk 34 - Mario Paz
Student Talk 35 - Kimberly Kanigel-Winner
August 10 - Tuesday
Lecture 25, James R. Faeder, University of Pittsburgh School of Medicine
Lecture 26, Christopher A. Voigt, CANCELLED - Replacement 1/2 talk to be given by Alvin Tamsir. Synthetic biology
Lunch discussion with lecturers
14:00-15:00, Chris Bystroff, Rensselaer Polytechnic Institute -- q-bio seminar talk (this talk will take place in Room 203A/B of the Los Alamos Research Park building)
Lecture 27, Tomasz Lipniacki, Polish Academy of Sciences
August 11 - Wednesday
Depart to Santa Fe for the q-bio Conference -- Students will take a NM Park & Ride bus to Santa Fe in the morning ($3 exact change is required); organizers will arrange for separate transport of luggage to the conference site. A van will be waiting with an organizer at the school hotel at 8:15 am for transport of luggage to the site of the conference.
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