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HOME » PROGRAMS/ACTIVITIES » Annual Thematic Program
| Massachusetts Institute of Technology | |
| University of Waterloo | |
| Rutgers, The State University of New Jersey |

The functioning of living organisms is controlled by highly complex networks of interactions among genes, proteins, and small signaling molecules. These range from signal transduction networks to metabolic networks to gene regulatory networks. In each case, the signal carrier is usually protein amounts, whose robust and tight control is at the basis of most cellular processes, including the cell cycle, circadian rhythms, apoptosis, and many others. The functioning of these networks is remarkably robust and reliable, despite the influence of environmental fluctuations, intrinsic noise, and uncertain network components. This robustness might be a factor affecting resistance to chemotherapy, targeted antibodies, and small inhibitors in disease treatments. Understanding the design principles underlying the functioning of biological networks is one of the main objectives of systems biology. At the same time, a main goal of synthetic biology is to establish an engineering discipline to create functional semi-synthetic circuits in cellular chassis on the basis of a library of standard parts. What control theory techniques can be leveraged to both analyze and design biological networks? What new control theoretic tools need to be developed in order to attain the ultimate goal of untangling the complexity of biological network analysis and design? This workshop will cover recent work that addresses these questions.

| Monday | Tuesday | Wednesday | Thursday | Friday | | |||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Monday November 16, 2015 | |||||||||||||||||||||||
| 8:15am-8:45am | Coffee and Registration | Keller Hall 3-176 | |||||||||||||||||||||
| 8:45am-9:00am | Welcome and Introduction | Keller Hall 3-180 | |||||||||||||||||||||
| 9:00am-10:00am | Universal Laws and Architectures: Theory and Lessons from Brains, Nets, Hearts, Bugs, Grids, Flows, and Zombies | John Doyle (California Institute of Technology) | Keller Hall 3-180 | ||||||||||||||||||||
| 10:00am-10:30am | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 10:30am-11:30am | Cybergenetics | Mustafa Khammash (ETH Zürich) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:30am-12:30pm | Regulatory Networks in Synthetic Microbial Consortia | Matthew Bennett (Rice University) | Keller Hall 3-180 | ||||||||||||||||||||
| 12:30pm-2:30pm | Lunch | ||||||||||||||||||||||
| 2:30pm-3:30pm | Anticipators and Procrastinators: Cellular Decision Making in Multivariate Environments | Hana El-Samad (University of California, San Francisco) | Keller Hall 3-180 | ||||||||||||||||||||
| 3:30pm-4:00pm | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 4:00pm-5:00pm | Understanding Signal Propagation through Cellular Networks | Herbert Sauro (University of Washington) | Keller Hall 3-180 | ||||||||||||||||||||
| 5:00pm-6:00pm | Cell-free Transcription-translation: Prototyping Parts and Gene Circuits in Vitro | Vincent Noireaux (University of Minnesota, Twin Cities) | Keller Hall 3-180 | ||||||||||||||||||||
| 6:30pm-8:30pm | Social Hour at Stub & Herbs 227 SE Oak St Minneapolis, MN 55455 | ||||||||||||||||||||||
| Tuesday November 17, 2015 | |||||||||||||||||||||||
| 8:30am-9:00am | Coffee | Keller Hall 3-176 | |||||||||||||||||||||
| 9:00am-10:00am | Characterizing the Genotype-Phenotype Map and Its Evolution: A Radically New Strategy | Michael Savageau (University of California, Davis) | Keller Hall 3-180 | ||||||||||||||||||||
| 10:00am-10:10am | Group Photo | Keller Hall 3-180 | |||||||||||||||||||||
| 10:10am-10:30am | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 10:30am-11:30am | Control of Disease-related Signal Transduction Networks | Reka Albert (The Pennsylvania State University) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:30am-12:30pm | Excitability and other dynamic behaviors regulating motility | Pablo Iglesias (Johns Hopkins University) | Keller Hall 3-180 | ||||||||||||||||||||
| 12:30pm-2:30pm | Lunch | ||||||||||||||||||||||
| 2:30pm-3:30pm | Criticality and Adaptivity in Enzymatic Networks | Ruth Williams (University of California, San Diego) | Keller Hall 3-180 | ||||||||||||||||||||
| 3:30pm-4:00pm | Break/Poster SessionKeller Hall 3-176
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| 4:00pm-5:00pm | Mammalian Synthetic Biology: Circuit Design Principles and Therapeutic Applications | Leonidas Bleris (University of Texas at Dallas) | Keller Hall 3-180 | ||||||||||||||||||||
| 5:00pm-6:00pm | Predictability of Gene Network Evolution | Gabor Balazsi (State University of New York, Stony Brook (SUNY)) | Keller Hall 3-180 | ||||||||||||||||||||
| Wednesday November 18, 2015 | |||||||||||||||||||||||
| 8:30am-9:00am | Coffee | Keller Hall 3-176 | |||||||||||||||||||||
| 9:00am-10:00am | Inferring Genome-Wide Interaction Networks from Genomic Data | Mathukumalli Vidyasagar (University of Texas) | Keller Hall 3-180 | ||||||||||||||||||||
| 10:00am-10:30am | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 10:30am-11:30am | Identification of Predictive Dynamic Models for Systems Biology | Joerg Stelling (ETH Zürich) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:30am-12:30pm | In-vivo Feedback Real-time Control of Synthetic Gene Networks | Diego di Bernardo (Università di Napoli "Federico II") Mario di Bernardo (University of Bristol) | Keller Hall 3-180 | ||||||||||||||||||||
| 12:30pm-2:30pm | Lunch | ||||||||||||||||||||||
| 2:30pm-3:30pm | An Evolutionary Perspective of the p53 Network | Joao Hespanha (University of California, Santa Barbara) | Keller Hall 3-180 | ||||||||||||||||||||
| 3:30pm-4:00pm | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 4:00pm-5:00pm | Quantifying, Modeling and Predicting Fluctuations of Signal-Activated Gene Expression | Brian Munsky (Colorado State University) | Keller Hall 3-180 | ||||||||||||||||||||
| 5:00pm-6:00pm | Discussion: Synthetic Biology and Control Theory | Keller Hall 3-180 | |||||||||||||||||||||
| Thursday November 19, 2015 | |||||||||||||||||||||||
| 8:30am-9:00am | Coffee | Keller Hall 3-176 | |||||||||||||||||||||
| 9:00am-10:00am | Design Principles of Proliferative Control | Arthur Lander (University of California, Irvine) | Keller Hall 3-180 | ||||||||||||||||||||
| 10:00am-10:30am | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 10:30am-11:30am | Biological Networks Associated to Biological Questions | Avner Friedman (The Ohio State University) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:30am-12:30pm | Systems Describing the Tumor Microenvironment: A Geometric Optimal Control Approach | Urszula Ledzewicz (Southern Illinois University) | Keller Hall 3-180 | ||||||||||||||||||||
| 12:30pm-2:30pm | Lunch | ||||||||||||||||||||||
| 2:30pm-3:30pm | Mass Transfer of Drug Delivery and Bacterial Therapy to Tumors | Neil Forbes (University of Massachusetts) | Keller Hall 3-180 | ||||||||||||||||||||
| 3:30pm-4:00pm | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 4:00pm-5:00pm | Uncovering the Mechanisms and Physiological Roles of Non-monotonic Response Dynamics in Bacterial Stress Response and Differentiation | Oleg Igoshin (Rice University) | Keller Hall 3-180 | ||||||||||||||||||||
| 5:00pm-6:00pm | Discussion: Cancer, Immunology, and Control Theory | Keller Hall 3-180 | |||||||||||||||||||||
| Friday November 20, 2015 | |||||||||||||||||||||||
| 8:30am-9:00am | Coffee | Keller Hall 3-176 | |||||||||||||||||||||
| 8:55am-10:30am | Contributed Talks | ||||||||||||||||||||||
| 9:00am-9:15am | Optimizing Deep Brain Stimulation for Suppression of Pathological Oscillations in Parkinson's Disease | Theoden Netoff (University of Minnesota, Twin Cities) | Keller Hall 3-180 | ||||||||||||||||||||
| 9:15am-9:30am | Cell Fate Reprogramming by Control of Intracellular Network Dynamics | Jorge G. T. Zañudo (The Pennsylvania State University) | Keller Hall 3-180 | ||||||||||||||||||||
| 9:30am-9:45am | Molecular Network Control Through Boolean Canalization | David Murrugarra (University of Kentucky) | Keller Hall 3-180 | ||||||||||||||||||||
| 9:45am-10:00am | Modeling Timing Phenomena in Single-cells: From Phage-induced Lysis to Cell-Division Events | Abhyudai Singh (University of Delaware) | Keller Hall 3-180 | ||||||||||||||||||||
| 10:00am-10:15am | Performance Limitations in Autocatalytic Pathways | Milad Siami (Lehigh University) | Keller Hall 3-180 | ||||||||||||||||||||
| 10:15am-10:45am | Break | Keller Hall 3-176 | |||||||||||||||||||||
| 10:40am-12:15pm | Contributed Talks | ||||||||||||||||||||||
| 10:45am-11:00am | A Proof of the Global Attractor Conjecture for General Reaction Networks | Gheorghe Craciun (University of Wisconsin, Madison) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:00am-11:15am | Analysis and Design of Genetic Control Circuits for Metabolism | Diego Oyarzún (Imperial College London) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:15am-11:30am | Robust Control of Evolutionary Dynamics: Case studies in HIV/Antibody Therapy and Non-small Cell Lung Cancer (NSCLC) | Vanessa Jonsson (California Institute of Technology) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:30am-11:45am | Graph Theory for Systems Biology: Interval Graphs, Motifs, and Pattern Recognition | John Jungck (University of Delaware) | Keller Hall 3-180 | ||||||||||||||||||||
| 11:45am-12:00pm | Study of Emergent Transport Properties of Molecular Motor Ensemble Using Novel Computational Approach | Shreyas Bhaban (University of Minnesota, Twin Cities) | Keller Hall 3-180 | ||||||||||||||||||||
| 12:00pm-12:15pm | Stochastic Analysis of Biochemical Reaction Networks with Absolute Concentration Robustness | German Enciso (University of California, Irvine) | Keller Hall 3-180 | ||||||||||||||||||||
| 12:15pm-12:30pm | Model-guided Design of a Synthetic Signaling Switch | Casim Sarkar (University of Minnesota, Twin Cities) | Keller Hall 3-180 | ||||||||||||||||||||
| NAME | DEPARTMENT | AFFILIATION |
|---|---|---|
| Hema Achanta | University of Texas at Dallas | |
| Shin-hyung Ahn | DSO | DARPA |
| Reka Albert | The Pennsylvania State University | |
| Jordan Ang | Bioengineering | Imperial College London |
| Sergei Avdonin | Department of Mathematics and Statistics | University of Alaska |
| Marco Avila Ponce de Leon | Department of Mathematics | University of Minnesota, Twin Cities |
| Romeo Awi | Institute of Mathematics and its Applications | University of Minnesota, Twin Cities |
| Gabor Balazsi | Laufer Center for Physical & Quantitative Biology and Dept. of Biomedical Eng. | State University of New York, Stony Brook (SUNY) |
| Matthew Bennett | Department of Biosciences | Rice University |
| Shreyas Bhaban | Department of Electrical Engineering | University of Minnesota, Twin Cities |
| Leonidas Bleris | Department of Bioengineering | University of Texas at Dallas |
| Anthony Bloch | Department of Mathematics | University of Michigan |
| Mireille Broucke | Department of Electrical and Computer Engineering | University of Toronto |
| James Brunner | Department of Mathematics | University of Wisconsin, Madison |
| Eric Bullinger | Institute for Automation Engineering | Otto-von-Guericke-Universität Magdeburg |
| Yongxin Chen | Department of Electrical and Computer Engineering | University of Minnesota, Twin Cities |
| Michelle Chong | Automatic Control | Lund University |
| Juan Cockburn | Department of Computer Engineering | Rochester Institute of Technology |
| Gheorghe Craciun | Department of Mathematics | University of Wisconsin, Madison |
| Domenico D'Alessandro | Department of Mathematics | Iowa State University |
| Diego di Bernardo | Università di Napoli "Federico II" | |
| Mario di Bernardo | Centre for Applied Nonlinear Mathematics | University of Bristol |
| Wandi Ding | Department of Mathematical Sciences | Middle Tennessee State University |
| Khanh Dinh | Department of Mathematics | University of Alabama |
| Ian Dinwoodie | Department of Mathematics and Statistics | Portland State University |
| John Doyle | Department of Control and Dynamical Systems | California Institute of Technology |
| Hana El-Samad | Department of Biochemistry and Biophysics | University of California, San Francisco |
| German Enciso | Department of Mathematics | University of California, Irvine |
| Wesley Errington | Department of Biomedical Engineering | University of Minnesota, Twin Cities |
| Fariba Fahroo | DSO | DARPA |
| Neil Forbes | Department of Chemical Engineering | University of Massachusetts |
| Avner Friedman | Mathematical Biosciences Institute | The Ohio State University |
| Tryphon Georgiou | Department of Electrical Engineering | University of Minnesota, Twin Cities |
| Cheol-Min Ghim | Mathematical Bioscience Institute | The Ohio State University |
| Marcella Gomez | BioSciences | Rice University |
| Jorge G. T. Zañudo | Department of Physics | The Pennsylvania State University |
| Rohit Gupta | Aerospace Engineering | University of Michigan |
| Abdullah Hamadeh | Massachusetts Institute of Technology | |
| Zachary Hamaker | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
| Bin He | Department of Electrical Engineering | University of Minnesota, Twin Cities |
| Peng He | Department of Mathematics | University of Pittsburgh |
| J. William Helton | Department of Mathematics | University of California, San Diego |
| Joao Hespanha | Department of Electrical and Computer Engineering | University of California, Santa Barbara |
| Mary Ann Horn | Division of Mathematical Sciences | National Science Foundation |
| Weiwei Hu | Institute of Mathematics and its Applications | University of Minnesota, Twin Cities |
| Pablo Iglesias | Department of Electrical and Computer Engineering | Johns Hopkins University |
| Oleg Igoshin | Department of BioEngineering | Rice University |
| Brian Ingalls | Department of Applied Mathematics | University of Waterloo |
| Ben Frederick Intoy | School of Physics and Astronomy | University of Minnesota, Twin Cities |
| Kazufumi Ito | Department of Mathematics | North Carolina State University |
| Farhad Jafari | Department of Mathematics | University of Wyoming |
| Alexandra Jilkine | ACMS | University of Notre Dame |
| Vanessa Jonsson | Department of Computing and Mathematical Sciences | California Institute of Technology |
| Mihailo Jovanovic | Electrical and Computer Engineering | University of Minnesota, Twin Cities |
| John Jungck | Biological Sciences (Affiliated faculty: Mathematical Sciences) | University of Delaware |
| Mustafa Khammash | Department of Biosystems Science and Engineering | ETH Zürich |
| Sei Zhen Khong | Institute of Mathematics and its Applications | University of Minnesota, Twin Cities |
| Yoonsoo Kim | Department of Aerospace and System Engineering | Gyeongsang National University |
| Rahul Kumar | Department of Mathematics | University of Houston |
| Gerardo Lafferriere | Department of Mathematics and Statistics | Portland State University |
| Tri Lai | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
| Arthur Lander | Department of Developmental and Cell Biology | University of California, Irvine |
| Urszula Ledzewicz | Department of Mathematics and Statistics | Southern Illinois University |
| Jieun Lee | College of Science and Engineering | University of Minnesota, Twin Cities |
| Priscilla Macansantos | Department of Mathematics and Computer Science | University of the Philippines Baguio |
| Arnaud Marsiglietti | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
| Nikolai Matni | Department of Control and Dynamical Systems | California Institute of Technology |
| Burook Misganaw | Erik Jonsson School of Engineering & Computer Science | University of Texas at Dallas |
| Yoichiro Mori | School of Mathematics | University of Minnesota, Twin Cities |
| Brian Munsky | Department of Chemical and Biological Engineering | Colorado State University |
| David Murrugarra | Department of Mathematics | University of Kentucky |
| Humberto Naves | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
| Theoden Netoff | Department of Biomedical Engineering | University of Minnesota, Twin Cities |
| Vincent Noireaux | School of Physics and Astronomy | University of Minnesota, Twin Cities |
| Diego Oyarzún | Department of Mathematics | Imperial College London |
| Casian Pantea | Mathematics | West Virginia University |
| Keshab Parhi | University of Minnesota, Twin Cities | |
| Camelia Pop | School of Mathematics | University of Minnesota, Twin Cities |
| Thomas Prescott | Department of Engineering Science | University of Oxford |
| Sivaraman Rajaganapathy | Department of Electrical and Computer Engineering | University of Minnesota, Twin Cities |
| Anders Rantzer | Department of Automatic Control | Lund University |
| Peter Rejto | School of Mathematics | University of Minnesota, Twin Cities |
| Farrah Sadre-Marandi | Department of Mathematics | The Ohio State University |
| Ahmad Salehi | University of Minnesota, Twin Cities | |
| Ricardo Sanchez | Department of General Education | Art Institutes International Minnesota |
| Casim Sarkar | Department of Biomedical Engineering | University of Minnesota, Twin Cities |
| Herbert Sauro | Department of Bioengineering | University of Washington |
| Michael Savageau | Department of Biomedical Engineering, and Microbiology Graduate Group | University of California, Davis |
| Heinz Schaettler | School of Engineering and Applied Sciences | Washington University |
| James Scott-Brown | Department of Engineering Science | University of Oxford |
| Leili Shahriyari | Mathematical Biosciences Institute | The Ohio State University |
| Milad Siami | Department of Mechanical Engineering | Lehigh University |
| Dan Siegal | DARPA | |
| Abhyudai Singh | Department of Electrical and Computer Engineering | University of Delaware |
| Hari Sivakumar | Department of Electrical Engineering | University of California, Santa Barbara |
| Ekaterina Smirnova | Department of Statistics | University of Wyoming |
| Eduardo Sontag | Department of Mathematics | Rutgers, The State University of New Jersey |
| Joerg Stelling | Department of Biosystems Science and Engineering | ETH Zürich |
| Edward Stites | Department of Pathology and Immunology | Washington University |
| Saurav Talukdar | Department of Mechanical Engineering | University of Minnesota, Twin Cities |
| Allen Tannenbaum | Department of Computational Science | State University of New York, Stony Brook (SUNY) |
| Andrew Thaler | Institute of Mathematics and its Applications | University of Minnesota, Twin Cities |
| Mathukumalli Vidyasagar | Erik Jonsson School of Engineering & Computer Science | University of Texas |
| Huy Vo | Department of Mathematics | University of Alabama |
| Xueying Wang | Department of Mathematics | Washington State University |
| Yuh-Shyang Wang | California Institute of Technology | |
| Ruth Williams | Department of Mathematics | University of California, San Diego |
| Xiaofan Wu | Department of Electrical Engineering | University of Minnesota, Twin Cities |
| Yangyang Xu | Institute of Mathematics and its Applications | University of Minnesota, Twin Cities |
| Kaoru Yamamoto | University of Minnesota, Twin Cities | |
| Armin Zare | Department of Electrical and Computer Engineering | University of Minnesota, Twin Cities |
| Zhou Zhou | Institute of Mathematics and its Applications | University of Minnesota, Twin Cities |
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