HERE - Winter q-bio

Supporters of w-qbio
The organizers would like to acknowledge the
following for their generous support of this meeting:
AGENDA: SECOND ANNUAL WINTER Q-BIO MEETING
February 16-20, 2014
Website for meeting: http://w-qbio.org
Link to abstracts: http://w-qbio.org/2014abstracts.pdf
Email address for the organizers: coordinator@w-qbio.org
Venue: Hilton Waikoloa Village
425 Waikoloa Beach Drive, Waikoloa, HI 96738
Tel: (808) 886-1234
Registration in the hallway outside the Kohala Ballroom (a.k.a. Kohala Promenade)
Plenary sessions in the Kohala Ballroom
Evening contributed sessions in King’s 1 and King’s 2
Posters will be on display in the Kohala Promenade
Wireless Login for Meeting Room Internet:
Network ID: UHQB
Password: qbiology (all lower case, no spaces)
1
Sunday, February 16, 5-8PM: Opening registration and reception
Monday, February 17
8:00-9:00
Registration and Breakfast (Kohala Promenade)
8:45-9:00
Opening Remarks
9:00-9:45
Plenary talk: Steve Quake, Stanford University
Single Cell Genomics
9:45-10:30
Plenary talk: Petra Schwille, Max Planck Institute
How to position a divisome? Lessons from minimal systems
10:30–11:00 Coffee Break
11:00-11:45 Plenary talk: Aleksandra Walczak, Ecole Normale Superieure
Diversity generation in immune receptor repertoires
11:45-12:10 Xiling Shen, Cornell University
Controlling the Intestinal Stem Cell Niche in Space and Time
12:10-2:00
Lunch on own
2:00-2:45
Plenary talk: Arthur Lander, University of California, Irvine
The Challenges of Proliferative Control
2:45-3:10
Andre Levchenko, Yale University
Integrated analysis of signaling networks controlling cortical neurogenesis
3:10-3:35
Tal Danino, MIT
Programmable probiotics: Genetic circuit chaperones for non-invasive cancer detection
3:35-4:00
Coffee and Snack Break
4:00-6:00
Contributed Sessions (see page 4 for details)
Tuesday, February 18
9:00-9:45
Plenary talk: Christina Smolke, Stanford University
Title
9:45-10:30 Plenary talk: Hana El-Samad, University of California, San Francisco
How to build a stoichiometric gene expression program
10:30-11:00 Coffee Break
11:00-11:25 Alicia Jackson, DARPA
DARPA: Integrating biology with engineering to solve intractable problems
11:25-11:50 Georg Seelig, University of Washington
Nucleic acid logic gates based on nucleic acid strand exchange work in mammalian cells
11:50-12:15 Mary Teruel, Stanford University
Controlling low rates of terminal cell differentiation through noise and ultra-high feedback
12:15-2:00 Lunch on own
2:00-2:45
Plenary talk: Shigeru Kondo, Osaka University
Turing pattern formation in the skin of living fish
2:45-3:10
Thierry Mora, Ecole normale superieure and CNRS
Inferring the strongly collective motion of flocks of birds
3:10-3:35
Allyson E. Sgro, Princeton University
From single cells to fruiting bodies: Bridging scales in collective behaviors
3:35-4:00
Coffee and Snack Break
4:00-6:00
Contributed Sessions (see page 5 for details)
2
Wednesday, February 19
9:00-9:45
Plenary talk: Andrew Murray, Harvard University
The Blind Watchmaker Lives: Evolving a Circadian Oscillator in Budding Yeast
9:45-10:30 Plenary talk: Naama Barkai, Weizmann Institute of Science
title
10:30-11:00 Coffee Break
11:00-11:25 Nan Hao, University of California, San Diego
Dynamic signal processing by transcription factors
11:25-11:50 Molly Megraw, Oregon State University
Designing an optimally informative machine-learning model of gene regulatory control
11:50-12:15 Peter Karp, SRI International
A Literate Metabolic Model of E. coli K-12 MG1655 Derived From the EcoCyc Database
12:15-2:00 Lunch on own
2:00-2:45
Plenary talk: Taikjip Ha, University of Illinois, Champagne-Urbana
Super-resolution and single-molecule analysis of small RNA-based regulation in bacteria
2:45-3:10
Lee Bardwell, University of California, Irvine
Redundancy, Synergy and Interdependency in Multisite Phosphorylation
3:10-3:35
Matthew Bennett, Rice University
Constructing synthetic gene circuits with network-level robustness through protein-level
engineering
3:35-4:00
Silvia Santos, MRC-Imperial College London
Temporal control of cell division: switches, refractory periods and feedback control
4:00-6:00
Coffee and Snack Break, Poster Session (see pages 7-8 for details)
7:00
Banquet Dinner (Ocean View Terrace)
Thursday, February 20
9:00-9:45
Plenary talk: Jagesh Shah, Harvard Medical School
Chemical and Physical Determinants of Cell Orientation
9:45-10:10 Zeynep Gumus, Weill Cornell Medical College
iCAVE: immersive 3D visualization of complex biomolecular interaction networks
10:10-10:35 Michael Springer, Harvard Medical School
Yeast Respond to the Ratio of Glucose and Galactose Not to the Absolute Concentrations
of Each Nutrient
10:35-11:00 Coffee Break
11:00-11:45 Plenary talk: Zev Gartner, University of California, San Francisco
Building tissues to understand how tissues build themselves
11:45-12:10 Pranidhi Sood, UCSF
Developing Stentor coeruleus as a model to understand the transcriptional dynamics of
single-cell regeneration
12:10-2:00 Lunch on own
2:00-2:25
Rahul Kulkarni, University of Massachusetts Boston
Exact distributions for stochastic gene expression models with bursting and feedback
2:25-2:50
Thomas Kuhlman, University of Illinois, Champagne-Urbana
Growth State Dependent Intracellular Diffusion of Transcription Factors in E. coli
2:50-3:30
Coffee and Snack Break
3:30-5:15
Contributed Sessions (see page 6 for details)
5:15
Meeting Adjourns
3
Monday Contributed Talks
Contributed Session 1 (Kohala Ballroom)
4:00-4:15 May start sessions early if desired
4:15-4:30 Chinmaya Gupta, University of Houston. Delayed feedback in models of gene
regulatory networks
4:30-4:45 Kevin Axelrod, MIT. Loss of Resilience of a Phenotypic State in a Gene Regulatory
Network Preceding a Critical Transition
4:45-5:00 Liam Holt, UC Berkeley. Reconstruction of the ancestors of CMGC kinases reveals
neofunctionalization via relaxed specificity intermediates
5:00-5:15 Vanessa Jonsson, Caltech. Evolutionary Dynamics on Computationally Derived
Fitness Landscapes Predict HIV Escape from Antibody Monotherapy
5:15-5:30 Zhiyuan Li, UCSF. Mutual Antagonism and Network Balance in Cellular Fate Decisions:
Induction of Pluripotency with Lineage Specifiers
5:30-5:45 William Mather, Virginia Tech. A Queueing Theoretic Approach to Multisite Enzyme Kinetics
Contributed Session 2 (King’s 1)
4:00-4:15 Cailin O’Connor, UC Irvine. Learning generalization: Trading speed for precision
4:15-4:30 Chris Barnes, University College London Elucidating structurally robust stochastic
gene oscillators using methods from Bayesian statistics
4:30-4:45 Josh Cuperus, University of Washington. Multiplexed genome engineering
in Saccharomyces cerevisiae
4:45-5:00 Graham Anderson, Stanford. The Xenopus laevis embryo corrects perturbations
to cell division synchrony
5:00-5:15 Sergii Pochekailov, University of Washington. Universal fluorescent readout for cytochrome
P450 activity based on charge transfer between ferredoxin and a green fluorescent protein
5:15-5:30
5:30-5:45 Aaron Reinke, UCSD. Quantification of protein levels with tissue and
subcellular specificity in C. elegans
Contributed Session 3 (King’s 2)
4:00-4:15 May start sessions early if desired
4:15-4:30 Amy Herr, UC Berkeley. Single cell Western blotting
4:30-4:45 Guillaume Cambray, UC Berkeley. High-throughput experimental dissection of complex
sequence determinants of translation
4:45-5:00 Arthur Prindle, UCSD. Engineered coupling across space and time
5:00-5:15 Noam Kaplan, University of Massachusetts Medical School. High-throughput genome
scaffolding from in vivo DNA interaction frequency
5:15-5:30 Vincent Piras, Keio University. Transcriptome-wide noise patterns during
mammalian cell development
5:30-5:45 Steven Zucker, Yale University. Auxin and venation development in plants:
Global distance information via cellular-level signals
4
Tuesday Contributed Talks
Contributed Session 1 (Kohala Ballroom)
4:00-4:15 Allison Chia-Yi Wu, UCSD. A hidden regulatory role of elt-7 in C. elegans intestinal
differentiation is revealed by single-molecule gene expression data and modeling.
4:15-4:30 Andreas Hilfinger, Harvard Medical School. Fluctuation relations for complex biological systems
4:30-4:45 Fumiaki Katagiri, University of Minnesota. Signaling mechanisms underlying the robustness
and tunability of the plant immune network
4:45-5:00 Maxim Shokhirev, UCSD. Developing a multi-scale understanding of the
B cell immune response
5:00-5:15 Oguzhan Atay, Stanford. Modularity of a feedforward motif in the pheromone signaling pathway
from cell biology data using differential algebra, sensitivities & global optimizations
5:15-5:30 Varun Bhaskar Kothamachu, University of Exeter. Sigmoidality and bistability
in two component-signalling architectures
5:30-5:45 Rajat Bhatnagar, UCSF. Sensitivity and tradeoffs in adapting biochemical systems
Contributed Session 2 (King’s 1)
4:00-4:15 Jan Skotheim, Stanford. Histone titration by DNA sets the cell size threshold for the
mid-blastula transition in Xenopus.
4:15-4:30 Chang Liu, UC Irvine. An Orthogonal DNA Replication System in Yeast
4:30-4:45 Andre Brown, Medical Research Council, Imperial College. Syntax in C. elegans locomotion
4:45-5:00 Howard Salis, Penn State University. White-boxing genetic circuit modeling: Absolute
TF binding free energies from fluorescence measurements
5:00-5:15 Lendert Gelens, Stanford. Spatial randomness leads to orderly mitotic divisions
5:15-5:30 Brian H Smith, Arizona State University. Fast transduction speeds and high frequency pulse
tracking are necessary for identification and location of odor sources
5:30-5:45 Roy Dar, Gladstone Institutes, UCSF. Screening for noise in gene expression identifies
enhanced HIV-reactivation cocktails
Contributed Session 3 (King’s 2)
4:00-4:15 Joseph Davis, The Scripps Research Institute. Measuring ribosome biogenesis dynamics
in bacteria using stable isotope pulse-labeling and quantitative mass spectrometry
4:15-4:30 Elias M. Puchner, UCSF. Counting Molecules in Single Organelles: Tracking the Endosome
Maturation Trajectory with Super-Resolution Microscopy
4:30-4:45 Andras Gyorgy, MIT. Dynamics of Complex Gene Transcription Networks: From Single
Modules to Multi-Module Systems
4:45-5:00 Leonidas Bleris, University of Texas at Dallas. Versatile transcription activator-like
effector libraries for genome-wide assays
5:00-5:15 Miyako Kusano, RIKEN CSRS. A systems analysis of sink-source translocation in tomato
plants by LED light treatments
5:15-5:30 Philipp Jaeger, UCSD. Mining time-lapse genetic interaction data to construct a
telomere-maintenance network in yeast
5:30-5:45 Nicolas Innocenti, KTH, Royal Institute of Technology. A primary and processed bacterial transcriptome
in a single view — The ppRNome of the human hathogen Enterococcus Faecalis
5
Thursday Contributed Talks
Contributed Session 1 (Kohala Ballroom)
3:30-3:45 Alex Dickson, University of Michigan. Parameterizing quantitative biological models
using in silico binding simulations
3:45-4:00 Anders Hansen, Harvard. Promoter decoding of transcription factor dynamics involves a
trade-off between noise and control of gene expression
4:00-4:15 Cawas Engineer, UCSD. CO2 stress controlled signaling networks and their impingement on stomatal
development and patterning: predictive modeling of cell fate morphogens and de novo network establishment
4:15-4:30 Michael Chevalier, UCSF. Master equation and moment approaches for biochemical
systems with creation-time-dependent propensities
4:30-4:45 Olivier Cinquin, UC Irvine. Control of cell cycling speed to minimize mutation accumulation
4:45-5:00 Nicholas Butzin, Virginia Tech. Entrainment of synthetic gene oscillators by a noisy stimulus
Contributed Session 2 (King’s 1)
3:30-3:45 David Rueda, Imperial College London. Watching AID scan single-stranded and transcribed
double-stranded DNA at single-molecule resolution
3:45-4:00 Swami Iyer, Umass Boston. Large-scale identification of ceRNA network
of tumor suppressor genes by co-expression analysis
4:00-4:15 Shangying Wang, Duke University. Noise propagation in alternative splicing
4:15-4:30 Jongmin Kim, Caltech. In vivo application of an inhibitory RNA aptamer against T7 RNA polymerase
4:30-4:45 Hyung Joon Kim, Salk Institute. Quantitative phenotypes seeking in patients derived neural
stem cells using microfluidics-based in vitro assays
5:00-5:15 Cheol-Min Ghim, UNIST. Epigenetic control of two-component genetic switch in bacterial cell
Contributed Session 3 (King’s 2)
3:30-3:45 Alex Rosenberg, University of Washington. Massively parallel measurement and prediction
of alternative splicing
3:45-4:00 Matan Hofree, UCSD. Network-based stratification of tumor mutations
4:00-4:15 Adam Feist, UCSD. A model-driven quantitative metabolomics analysis of aerobic and anaerobic
metabolism in E. coli that is biochemically and thermodynamically consistent
4:15-4:30 Gene-Wei Li, UCSF. Absolute quantification of cellular translation rates reveals
principles underlying protein production
4:30-4:45 Justin Ashworth, Institute for Systems Biology. Prediction of gene regulatory architectures In new species
using structure-based prediction and comparative Systems Biology
4:45-5:00 Nathan Lord, Harvard Medical School. Memory and Modularity in a Bacterial
Cell Fate Decision
6
Wednesday Posters
1. Abdullarhaman Alatar, King Saud University. Seed germination and recovery responses of Suaeda Heterophylla to
abiotic stresses
2. Saleh Alfarraj, King Saud University. Organochlorine residues in cuttlefish from the Arabian Gulf
3. Evan Appleton, Boston University. Interactive Assembly Algorithms for Molecular Cloning
4. A. Jane Bardwell, University of Califoria, Irvine. Crosstalk between MAP kinase and Hedgehog pathways via direct
phosphorylation of Gli proteins
5. Zahedeh Bashardanesh, Department of Cell and Molecular Biology. Event driven simulation of reaction-diffusion
processes with exact leaps over fast re-bindings
6. Nathan Belliveau, California Institute of Technology. Identification of the transcriptional regulatory networks governing mechanosensitive channels for quantitative characterization in E. coli
7. Prasanna Bhogale, University of Cologne. Pinpointing mechanisms driving transitions between states in multistable
gene regulatory networks : Toward a systems biology of fluctuations
8. Bartlomiej Borek, University of California, San Diego. Turing patterns in cell populations using gene circuits with
gas-based degradation
9. Amy Chang, University of California, San Francisco. Characterizing population-level heterogeneities in eukaryotic
organelle morphology
10. Yuan-Jyue Chen, University of Washington. Molecular control circuits from DNA chemical reaction networks
11. Michael Chevalier, University of California, San Francisco. Effects of cell-to-cell global parameter variation on mutual
information transmission in biochemical networks
12. Tamuka Chidyausiku, Novartis Institutes for BioMedical Research. Exploring the activity and modulation of Nf-κBinducing Kinase (NIK)
13. Song Feng, University of Warwick. Evolve and Design signaling networks using rule-based models
14. Atsushi Fukushima, RIKEN Center for Sustainable Resource Science. Development of metabolite-profiling database
in Arabidopsis: AtMetExpress – Meta-analysis of metabolome data
15. Kun Gao Okinawa, Institute of Science and Technology. Human-chimpanzee alignment: ortholog exponentials and
paralog power-laws
16. Marcella Gomez, California Institute of Technology. Analysis of delays in transcriptional signaling networks with
time-varying temperature-dependent rate coefficients
17. Shaobin Guo, Caltech. Implementation And Simulation Of Phosphorylation-Based Insulator In Transcription-Translation
Platform
18. Tetsuhiro Hatakeyama, The University of Tokyo. Kinetic memory based on the enzyme-limited competition
19. Yusuke Himeoka, The University of Tokyo. Optimal uptake rate of nutrient for thermodynamically efficient cellular
growth
20. Swami Iyer, University of Massachusetts, Boston. A machine learning approach for identifying the PTEN non-coding
ceRNA network
21. Atsushi Kamimura, The University of Tokyo. Resource competition in protocells with a minority molecule of a catalytic
reaction network
22. Hiroshi Kori, Ochanomizu University. Uncovering the mechanism of jet lag symptoms using a multiple-cell model for
the circadian master clock
23. Ryuichi Tanimoto, Keio University. Detection and Analyses of Intracellular Distribution of Temperature
24. Graham Anderson, Stanford. The Xenopus laevis Embryo Corrects Perturbations to Cell Division Synchrony
25. Laurens Kraal, University of California, San Francisco. Synthetic Micro Ecology: Droplet-based microfluidics for
microbial community assembly
26. Kazuto Kugou, The University of Tokyo. Inducible genome shuffling technology, TAQing system, in yeast
27. Niraj Kumar, University of Massachusetts, Boston. Determination of burst parameters in stochastic models of gene
expression
28. Nicholas Leiby, Harvard University. Metabolic erosion primarily by mutation accumulation, and not tradeoffs, characterize adaptive specialization of E. coli to a stable environment
29. Yuzhe Li, Kyoto University. A model of amygdala-mPFC interaction for partial reinforcement fear conditioning
30. Micah Manary, University of California, San Diego. Computational separation of multi-clonal malaria infections with
high-throughput sequencing data
31. Charalampos (Harris) Mavromatis, King Abdullah University of Science and Technology. The co-transcriptome of
uropathogenic E. coli-Infected mouse macrophage co-cultures reveals new insights into host-pathogen interactions
32. Tadashi Miyamoto, The University of Tokyo. Dynamical-systems model of cell differentiation by epigenetic regulation
with transcription factor regulatory network
33. Quaid Morris, University of Toronto. A compendium of RNA binding motifs for inferring regulatory networks
34. Ismael Munoz, University of California, San Francisco. Understanding mitochondrial dynamics using Drosophila
Melanogaster
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35. Shinji Nakaoka, RIKEN Center for Integrative Medical Science Center. Mathematical modeling and simulation for
skin inflammatory response
36. Shigeyuki Oba, Kyoto University. False discovery control for functional connectivity of neurons based on calcium
imaging
37. Arisa Oda, the University of Tokyo. Transcriptional regulation by glucose starvation stress-induced lncRNAs in yeast
38. Fumiko Ogushi, Ochanomizu University. Reliability of cell fate decision using a simple multi-cell model with inhibitory
cell-cell interaction
39. Takeshi Oura, Osaka University. Spatially explicit nearly neutral model in ecology
40. Krzysztof Puszynski , Institute of Automatic Control, Silesian University of Technology. Analysis of ATM signaling pathway as an activator of p53 and NF-kappaB regulatory modules
41. Karthik Shekhar, MIT. Automatic cellular phenotype detection using non-linear dimensionality reduction
42. Divya Swaminathan, UC Irvine. Single particle tracking of the IP3 Receptor: Analysis and conclusions
43. Huseyin Tas, University of Illinois Urbana-Champaign. Quantitative analysis of growth state dependent spatial distribution of s-factors
44. Katsuhiro Uegaki, Kyoto University. A Model of orientational organization of microtubule in axon and dendrite during
polarization
45. Masataka Yamao, Kyoto University. Prediction of cellular movement from FRET time-lapse images of Rho GTPases
46. Enoch Yeung, California Institute of Technology. System identification of phosophorylation based insulator in an in
vitro cell-free transcription-translation system
47. Zeynep Gumus, Cornell University. Functional impact characterization of genomic mutations using stochastic optimization
8