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Bring your Questions, Posters, Ideas,

present them in the
Interdisciplinary Bazar of Ideas
at EvoSysBio & Modeling Madison 2015

Registration is Free
Includes Dinner

Update 25 Aug 2015
(Latest updates on this page)

Evolutionary systems biology aims to build bridges between rigorous mechanistic models in evolutionary biology, molecular systems biology, and the many disciplines between them.

EvoSysBio needs to navigate many challenges, most notably, to create a meeting place for real-world observations in the field and in the wet-lab, computational modeling, and abstract theory.

Many benefits spring from creating a cross-disciplinary dialogue capable of including many diverse fields from anthropology and abstract math to molecular ecology and zoology. For example, this would make it easier to learn and investigate many complex phenomena as seen in the metabolism of cells, cancer, antibiotics resistance evolution, or species extinction.

No discipline has all the answers. Together we might stand a chance to address the most pressing problems of our time.

If you would love to contribute to this dialogue and are in Madison, Wisconsin, on Tue, Aug 25, 2015, then you would be most welcome to join us at the Wisconsin Institute for Discovery for a lively discussion. Bring all your questions and ideas.

A particular welcome to graduate students interested in developing an interdisciplinary research program. If you think this is a good venue for your ideas, please send us an abstract and your preference for a talk or a poster (see registration).

We will discuss a broad mix of topics from gene regulatory networks to evolutionary biology, while highlighting some diverse theoretical challenges and quantitative methods that have proved useful to address them. Bring your laptop to get started with simulating a gene regulatory network. End the day by asking hard questions in the bazar of ideas. Who knows what you may learn.


Key dates

  • 20 Aug 2015 (6pm, Thur):
    Register for attendance and catering. Submit intent to present talk or poster along with registration.

  • 22 Aug 2015 (Sat):
    If you would like to revise your abstract, final versions are due
    (email Laurence Loewe).

  • 25 Aug 2015 (Tue):
    Workshop, 2pm-10pm

Invited Talk

What Makes Us Different?
A Systems Biology Perspective on Evolution

Dr. Anne-Ruxandra Carvunis
Department of Medicine,
University of California San Diego, USA (webpage)

The molecular mechanisms underlying what makes each species unique remain largely unknown. A longstanding theory has been that species evolve new traits through the natural selection of mutations occurring within the functional protein-coding regions of genes. However, this view was significantly challenged by work in recent decades showing that the number of protein-coding genes in a genome of an organism is not correlated with organismal complexity, and that organisms as different as human and chimpanzee share a nearly identical set of protein-coding genes, among other findings. The resulting, more contemporary view, is that modifications of cellular networks made of intricate physical and functional interactions among genes and gene products may be the principal drivers of phenotypic diversity. I am exploring the evolution of cellular networks and how it relates to the evolution of genomes. I will describe how protein interactions are rewired under the action of natural selection during plant evolution. I will also present ongoing work comparing the dynamics of transcriptional network rewiring across mammals, birds and insects. My observations provide evidence for a molecular clock in transcriptional network evolution.

Workshop Program

2:00pm Laurence Loewe:
Welcome to the Workshop
Evolutionary Systems Biology: Overview and Challenges.

2:30pm Invited Talk by Anne-Ruxandra Carvunis:
What makes us different?
A systems biology perspective on evolution.

3:30pm Coffee Break

4:00pm John Yin:
From Genome to Organism: A Virus-World View.

4:30pm Laurence Loewe:
Modeling a simple Gene-Regulatory Network in Evolvix and the challenge of translating between disciplines.

5:00pm Claudia Solis-Lemus:
Statistical Inference of Pylogenetic Networks

5:30pm Poster session

6pm Dinner

7:00pm Bazaar of Ideas:

Interdisciplinary approaches to Modeling
in Evolutionary Systems Biology


  • Michael Ferris (CompSci)
  • Bret Hanlon (Statistics)
  • Laurence Loewe (Genetics)
  • Anne-Ruxandra Carvunis (Systems Biology).

Open discussion comparing modeling tools, approaches and challenges. Bring your favorite tools, your latest modeling frustration, and the features you dream about.
We want to hear it all to help improve modeling in biology.

Contribute live on this Etherpad:


Additional Background on EvoSysBio

Evolution depends on molecular structures and functions, which were largely unknown when the basis for a mechanistic understanding of evolution was laid. Thus population genetics uses descriptive parameters like selection coefficients, ‘hiding’ unknown molecular functions. As resulting models are conditional on assumed values, much effort goes into estimating selection by empirical observation or inference from DNA sequences using specific evolutionary models. Results do not integrate easily the many mechanistic details known in molecular systems biology.   

Evolutionary systems biology aims to build a bridge between evolutionary biology and systems biology. Integrating rigorous models from both fields will improve our mechanistic understanding of evolution. Key aspects of fitness are affected by molecular interaction networks, which are modified by mutations that improve or degrade molecular functions. Understanding aspects of molecular networks important for fitness will boost a mechanistical understanding of mutational effects.

Workshop Organizers

Laurence Loewe
Laboratory of Genetics, University of Wisconsin-Madison,
Phone: 608-316-4324, email:

Anne-Ruxandra Carvunis
Department of Medicine, University of California San Diego,
Phone: 858 822 3555, email:

Bret Hanlon
Department of Statistics, University of Wisconsin-Madison,
Phone: 608-262-2539, email:

Michael Ferris
Computer Sciences, University of Wisconsin-Madison,
Phone: 608-316-4356, email:



Attendance, coffee and dinner at the workshop are free, but we cannot provide accomodation. Madison in summer is beautiful and there are lots of opportunities for finding accomodation. Should you need help with finding the right place, please contact Tony Pietsch (