The First Workshop on Modeling of Biological Systems (MoBS'13)

Austin, TX, June 2nd 2013


The First Workshop on Modeling of Biological Systems (MoBS) at DAC focuses on computational methods, algorithms, and software tools for the modeling and analysis of biological systems. For biologists, this workshop is an opportunity to showcase their work to an entirely new audience and gain exposure to a new talent pool of potential postdocs and graduate students. For EDA experts, the workshop provides an excellent opportunity to explore challenges in biology and medical research, and recognize potential for new collaborations and novel applications of methods and techniques they are familiar with.

The workshop format includes invited talks by leading researchers in computational biology, oral presentations and posters. The workshop encourages early dissemination of ideas and results highlighting important new problems in the early stages of development, without providing complete solutions.

Topics of interest include (but are not limited to):

·     biological network inference

·     optimization/learning techniques applied to biological data

·     statistical modeling of biological systems

·     CAD and visualization of biological systems

·     data-mining for bio and health-care systems

·     hybrid methods for bio-system simulation

·     bio-model validation and verification

·     sensitivity analysis for biological systems


Invited Speakers:

·     Edward Dougherty, Texas A&M

·     Dana Pe’er, Columbia

·     Josh Stuart, University of California, Santa Cruz

·     Shuichi Takayama, University of Michigan, Ann Arbor


Key Dates:

Call for abstracts published:            February 20, 2013

Abstract submission deadline:    April 15, 2013 April 25, 2013

Abstract acceptance notification:    April 25, 2013 May 7, 2013

Final version due:                              May 13, 2013


Abstract Submission:

You can submit your abstract using EasyChair. Abstracts should not exceed 500 words. The submission should indicate whether you would like your abstract considered for a poster presentation, an oral presentation, or both. Include the full names, affiliations and contact information of all authors.

Abstracts will be reviewed by the Program Committee. Those that are selected for oral and poster presentations will be distributed to workshop participants and posted on the workshop website.


Student Travel Support:

Support funds for students may be available. Please send the following to by April 15 April 25, but we will accept applications as long as funds are available:

·     Your name

·     Affiliation

·     Year in school

·     50-100 word statement detailing why you seek support.


Workshop Organizers:

Smita Krishnaswamy, Columbia (

Natasa Miskov-Zivanov, UPitt, CMU (

Subarna Sinha, Stanford (


Program Committee:

Michael Deem, Rice

Jasmin Fisher, Microsoft Research, UK

Soha Hassoun, Tufts

Alexander Hoffmann, UCSD

Sunil P Khatri, Texas A&M

Pietro Lio', Cambridge, UK

Chris J. Myers, Utah

Jaijeet Roychowdhury, UC Berkeley



Other pages:  


Like us on Facebook: MoBS workshop Facebook page


You can find MoBS abstracts here.




9:00am-9:15am:       Opening Remarks by MoBS organizers

9:15am-9:50am:       Keynote talk 1: Dana Pe'er, Columbia University

                                   Title: Visualizing and Analyzing Heterogeneity in Cancer

9:50am-10:25am:     Keynote talk 2:Shuichi Takayama, University of Michigan, Ann Arbor

                                   Title: Microfluidic Analysis of Cell Signaling

10:25am-10:45am:   Invited Talk 1: Erin Simonds, UCSF School of Medicine

                                   Title: TBD

10:45am-11:00am:   Coffee Break

11:00am-11:20am:   Invited Talk 2: Ruisheng Wang, Pennsylvania State University

                                   Title: Identification of key components in cellular networks using elementary signaling modes

11:20am-12:00pm:   Contributed Talks, Session 1

                                   Contributed talk 1: Smita Krishnaswamy, Columbia University

                                   Title: Characterizing Stochastic Signaling Interactions Through the T-Cell Maturation Process

                                   Contributed talk 2: Dan Connors, University of Colorado, Denver

                                   Title: GPU Acceleration of the Exploration of the Parameter Space of Fitting Synaptic Models to Measured Responses

12:00pm- 2:00pm:    Lunch and Poster Session

2:00pm-2:35pm:       Keynote talk 3: Josh Stuart, University of California, Santa Cruz

                                   Title: TBD

2:35pm-3:10pm:       Keynote talk 4: Edward Dougherty, Texas A&M University

                                   Title: Optimal Therapeutic Intervention in Gene Logic

3:10pm-3:30pm:       Invited Talk 3: Karen Sachs, Stanford University

                                   Title: TBD

3:30pm-3:45pm:       Coffee Break

3:45pm-4:20pm:       Keynote Talk 5: David LaPotin, IBM

                                   Title: TBD

4:20pm-5:00pm:       Contributed Talks, Session 2

                                   Contributed talk 3: Soha Hassoun, Tufts University

                                   Title: Deriving Reduced Kinetic Models for Biological Modules

                                   Contributed talk 4: Pey-Chang Lin, Texas AM University

                                   Title: Gene Predictor Ranking and Function Selection Using Zhegalkin Functions

5:00pm-5:10pm:       Break

5:10pm-5:30pm:       Invited Talk 5: Andras Gyorgy, MIT

                                   Title: Modularity in Gene Transcription Networks

5:30pm-5:50pm:       Invited Talk 6: Uri-David Akavia, Columbia University

                                   Title: Integrative and parallel approaches to uncover drivers of cancer

5:50pm-6:30pm:       Contributed Talks, Session 3

                                   Contributed talk 5: Subarna Sinha, Stanford University

                                   Title: Extracting Boolean Implication Networks from Large, Heterogeneous Genomic Data

                                   Contributed talk 6: Natasa Miskov-Zivanov, University of Pittsburgh/Carnegie Mellon University

                                   Title: Circuit design techniques for automated construction of mosquito immune response model in malaria infection

6:30pm-6:40pm:       Closing remarks




Rohit Shukla, Parmeswaran Ramanathan, Devesh Bhimsaria and Aseem Ansari. Virtual Foundry for Gene Synthesis

Janet Roveda and Dung Nguyen. Real Time Test based Yeast Circuit Design for Protein Pathway Identification

Alessandro A. Nacci, Vincenzo Rana, Francesco Bruschi, Marco D. Santambrogio, Enzo Wanke and Donatella Sciuto. NeoN: a software tool for the automatic extraction of neurons communication pattern

Goutham Makkena, Srinivas M.B and Avinash Vaidya. Approximation of Mother Wavelets using Levin Transforms for characterization of Biological data

Shogo Nakaya and Yuichi Nakamura. Adaptive Sensing of Cardiac Signals with the Help of R-R Interval Prediction



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