Early bird registration ends on March 20th

IEEE SY-Bio Workshop to Address Topics in Systems and Synthetic Biology

The IEEE Life Sciences Technical Community (LSTC) will host a Sy-Bio Workshop on March 25-26, 2015 at the
Erik Jonsson School of Engineering and Computer Science at the University of Texas at Dallas. The workshop will bring together leading researchers working at the biology-engineering interface, to present original, cutting-edge work in the areas of pharmaceutical engineering, personalized medicine, synthetic biology, and systems biology.

The workshop will address important topics in Systems and Synthetic Biology task, with an aim to exploit systems engineering tools in unraveling complex cellular and tissue-scale behavior, using both "reverse engineering" and "forward engineering" approaches that combine quantitative experiment and computational modeling, ranging from the manipulation of cell behavior in bacterial populations all the way to multivariate genetic or biochemical modulations in mammalian tissues.

The presentations in the workshop will be threaded by the set of research challenges associated with increasing the scale and scope of both systems biology and synthetic biology capabilities beyond the current state of the art. Potential applications include tools for analyzing and understanding complex networked systems whose elements are dynamic and stochastic in nature, as well as development of new technologies for materials production, biofuel synthesis, environmental diagnostics and remediation, and medical diagnostics and therapeutics using engineered biological systems.

Schedule

3/25, Wednesday
12:00p.m. - 1:30p.m.	Lunch at the UT Dallas Dining Room (Not included in the registration)
1:30p.m. - 2:00p.m.	Topic: "The Evolutionary "Design" of Proteins" Speaker: Rama Ranganathan, UT Southwestern
2:00p.m. - 2:30p.m.	Topic: "Investigation of the cRaf interactome and steady-state multiplicity in Retinoic Acid Induced Differentiation of HL-60 cells" Speaker: Jeffrey Varner, Cornell
2:30p.m. - 3:00p.m.	Topic: "SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis" Speaker: Cory Funk
3:00p.m. - 3:30p.m.	Coffee Break
3:30p.m. - 4:00p.m.	Topic: "libSBOLj 2.0: A Java Library to Support SBOL 2.0" Speaker: Chris Myers, Utah
4:00p.m. - 4:30p.m.	Topic: "Towards Personalized Medicine: Beyond Pharmacogenomics" Speaker: Doraiswami Ramkrishna, Purdue
4:30p.m. - 5:00p.m.	Topic: "Tumor Heterogeneity in Cancer" Speaker: Michael White, UT Southwestern
5:00p.m. - 6:00p.m.	Poster presentations
6:00p.m. - 7:00p.m.	Social Hour
7:00p.m. - 9:00p.m.	Workshop Banquet (open to students and included in the registration)
3/26, Thursday
9:00a.m. - 9:30a.m.	Topic: "Searching for Drug Targets in the Noisy Circadian Clock" Speaker: Francis J. Doyle III, UC Santa Barbara
9:30a.m. - 10:00a.m.	Topic: "Theoretical Analysis of Temperature-Induced Nucleation in Dual Impinging Jet Mixers" Speaker: Richart Braatz, MIT
10:00a.m. - 10:30a.m.	Topic: "SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers" Speaker: Michael Zhang, UT Dallas
10:30a.m. - 11:00a.m.	Coffee Break
11:00a.m. - 11:30a.m.	Topic: "Biased excitable networks and directed migration" Speaker: Pablo Iglesias, Johns Hopkins
11:30a.m. - 12:00p.m.	Topic: "Cellular Economy and Emergent Interaction Networks in Gene Circuits" Speaker: Domitilla Del Vecchio, MIT
12:00p.m. - 12:30p.m.	Topic: "Circadian Gating of the Mammalian Cell Cycle Restriction Point: A Mathematical Analysis" Speaker: Mike Henson, U. Massachusetts
12:30p.m. - 1:30p.m.	Lunch Break (included in the registration)
1:30p.m. - 2:00p.m.	Topic: "Engineering a simple genetic half-adder in E. coli" Speaker: David McMillen, Toronto
2:00p.m. - 2:30p.m.	Topic: "Elimination of bacterial plasmids by engineered unilateral incompatibility" Speaker: Brian Ingalls, Waterloo
2:30p.m. - 3:00p.m.	Topic: "Resolving the Pattern of AKT Activation by Variational Parameter Estimation" Speaker: Daniel Kaschek, Freiberg (Germany)
3:00p.m. - 3:30p.m.	Coffee Break
3:30p.m. - 4:00p.m.	Topic: "A Synthetic System for Pattern Formation by Lateral Inhibition" Speaker: Murat Arcak, UC Berkeley
4:00p.m. - 4:30p.m.	Topic: "TBA" Speaker: Zoltan Nagy, Purdue
4:30p.m. - 5:00p.m.	Topic: "Engineering genetic systems for smart therapeutics" Speaker: Leonidas Bleris, UT Dallas

Poster Presentations

The University of Texas at Dallas

• Burook Misganaw and Mathukumalli Vidyasagar, "Exploiting Ordinal Class Structure in Multi-Class Classification: Application to Ovarian Cancer"
• Nitin Singh, Hema K. Achanta, and Mathukumalli Vidyasagar, "Pearson Correlation Coefficient With Perturbed Samples and the Role of Randomness in Cancer Incidence"
• Mehmet Ahsen and Mathukumalli Vidyasagar, "A New Algorithm for Sparse Regression Exhibiting Both Near-Ideal Behavior and the Grouping Effect"
• Kristina Ehrhardt, Michael T. Guinn, Tyler Quarton, Michael Zhang, and Leonidas Bleris, "Genetic circuits and test-strip interface for endogenous signal detection, processing and in-situ reporting"
• Michael Guinn and Leonidas Bleris, "Biological 2-Input Decoder Circuit in Human Cells"
• Taek Kang, Taplin Moore, Yi Li, Eduardo Sontag, and Leonidas Bleris, "Unraveling the Properties of Direct and Indirect Connectivities Using Synthetic Gene Networks"
• Taplin Moore, et. al., Leonidas Bleris, "CRISPR-based self-cleaving mechanism for controllable gene delivery in human cells."
• Lagnajeet Pradhan and Hyun-Joo Nam, "A Novel Screening System for Cardiac Transcription Factor Complex Targets"
• Riccardo Ziraldo and Lan Ma, "Mechanistic dissection of Drosophila apoptotic switch"
• Olalekan P. Ogunmolu and Nicholas Gans, "?"
• Ashwinikumar Kulkarni, Chantelle Sephton, Gang Yu, Michael Zhang, "Broken Heart: Cardiac Muscle Remodeling by FUS"
• Deepa Sethuraman, et. al., Hyuntae Yoo, "Cancer-specific production of N-acetylaspartate in non-small cell lung cancer detectable in tumor and blood of patients"
• Adwait Sathe, Yong Chen, Dr. Hyuntae Yoo, Michael Zhang, "Lineage Analysis of tumorigenesis caused by mutated genes in Lung Cancer"
• Yi Li, et. al., Leonidas Bleris, "Assembly and Validation of Versatile Transcription Activator-like Effector Libraries"
• Rita Bhui, Heather N. Hayenga, "A feasible multiscale model to capture the main events during atherogenesis"

University of Texas at Arlington

• Bilal Khan, Nathan Hervey, George Alexandrakis, "Enhancing Motor Performance Improvement by Personalizing Non-invasive Cortical Stimulation with Concurrent Functional Near-Infrared Spectroscopy and Multi-modal Motor Measurements"

Monterrey

• Ilse Patricia Rivas-Valdez, et. al., Mario Moises Álvarez, "Monoclonal antibodies production by CHO cells using continuous mini bioreactor with zein foam as scaffold for cell retention"

University of California, San Diego

• James T. Yurkovich, Daniel C. Zielinski, Bernhard Ø. Palsson, "Constraint-based analysis of the biophysically-feasible metabolite concentration space"

Submission of Abstracts for Poster Session:

• Speaking at the workshop is by invitation only. However, a provision has been made for a poster session.
• Please submit an abstract of one page or less in .pdf format to: [email protected] with copy to [email protected].
• The deadline is March 13, 2015 and acceptances will be informed by March 20, 2015.
• Accepted posters should be printed on a 3 feet by 4 feet sheet. The organizers will provide boards to which the posters can be pinned up
• Abstracts of accepted posters will be included in the SY-BIO workshop web site.

Further Information:

M. Vidyasagar, [email protected]
Leonidas Bleris, [email protected]
Kathryn Owens, [email protected]