CASCI

Postdoctoral Positions at CASCI

The Complex Adaptive Systems and Computational Intelligence (CASCI) lab at the Systems Science and Industrial Engineering Department, Binghamton University (State University of New York)  is accepting applications for one or more full-time non-tenure track postdoctoral fellows to conduct interdisciplinary research in Complex Networks and Systems applied to various social, ecological, biological, medicine and health problems.

Recent projects at the lab, funded by NIH, NSF, and FCT, Include:

The appointments are full-time for 12 months, with potential to be extended an additional year subject to funding and satisfactory performance. We offer a competitive salary with generous benefits.

The postdocs will be supervised by Prof. Luis M Rocha and join a dynamic and interdisciplinary team embedded in the cross-university Center for Social and Biomedical Complexity (CSBC) and the Center for Collective Dynamics of Complex Systems (CoCo)  that includes systems scientists, biologists, computer scientists, and social scientists. Please contact him for further information.

Basic Qualifications: A PhD is required in Complex Systems, Network Science, Computer or Computational Science, Computational Biology, Applied Mathematics, Physics, Statistics, Artificial Intelligence or related field; a strong background in analysis and modeling of complex systems and networks; and solid programming skills necessary to handle big data and develop large scale simulations. ABD (all but dissertation) candidates may apply but will need the Ph.D. prior to start.

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Criticality in Biochemical Networks

J Royal Society Interface

Researchers from our center, in collaboration with State University of New York, Binghamton University and the Instituto Gulbenkian de Ciência developed a mathematical and computational framework to understand how biochemical networks contribute to the evolvability, robustness, and resilience of biological organisms.

In a paper in the journal Journal of the Royal Society InterfaceLuis Rocha, George J. Klir Professor of Systems Science, and Drs. Manuel Marques-Pita and Santosh Manicka (who earned his Ph.D. in complex networks and systems from the Luddy School), show that a large amount of redundancy exists in how genes, proteins and other biochemical components process signals. This results in much robustness to perturbations, allowing biological systems to exist in a stable or near-critical dynamical regime, despite being composed of thousands of biochemical variables which would ordinarily result in chaotic dynamics.

The measure of effective connectivity developed by Rocha and Marques-Pita captures redundancy in automata networks and is shown in the paper to be highly predictive of dynamical regime of biochemical systems ranging from flower development to breast cancer in humans. The approach thus adds empirical validity to several  well-known hypotheses in theoretical biology: 1) that canalization adds robustness to biological development put forth by C.H. Waddington, 2) that redundancy is essential for evolvability put forth by Michael Conrad, and 3) that biological organisms exist in a near-critical dynamical regime put forth by Stuart Kauffman. The new work further connects the three hypotheses by equating canalization with redundancy, providing a  measure of effective connectivity based on dynamical redundancy, and further showing that this measure very accurately predicts the dynamical regime of biochemical networks.

You can read the article following the links in reference:

Manicka Santosh, Marques-Pita Manuel and Rocha Luis M. [2022]. “Effective connectivity determines the critical dynamics of biochemical continue reading.

Congratulations to new PhD Kelly McClinton!

 

Congratulations to CASCI member Kelly McClinton for successfully defending her dissertation entitled “Computationally Modeling Roman Domestic Art and Architecture” on April 23rd 2021. Kelly was co-supervised by Luis Rocha and Bernard Frischer. She completed her PhD degree as a fellow of the NSF-NRT Interdisciplinary training in Complex networks and Systems. Dr. McClinton’s research investigates how computational models, including 3D reconstructions, mixed-media models, complex systems, and machine learning, present unique technological affordances in studying the fragmented material record of ancient Rome, focusing on domestic Roman art and architecture. In addition to Complex Networks and Systems, her dissertation contributes to the fields of virtual heritage, archaeology, and art history. Kelly is now the Assistant Director of the Virtual World Heritage Lab, and this fall, Kelly will be studying at the University of Oxford, and working on a project entitled “Elite Identity in Domestic Space in Rome. Architectural Change and Redecoration in Late Antique Houses” under the supervision of Professor Ine Jacobs… continue reading.

Uncovering the “master switches” of biochemical networks can explain the effects of drugs in the destruction of cancer cells

Researchers from our lab, in collaboration with the Luddy School of Informatics, Computing, and Engineering, the Instituto Gulbenkian de Ciência, and Northeastern University have developed a mathematical framework that increases our ability to explain and control biochemical systems, including those involved in disease.

In a paper featured on the cover of the journal Proceedings of the National Academy of Sciences (PNAS), Professor of Informatics Luis Rocha and Alexander Gates (who earned his Ph.D. in complex networks and systems from the Luddy School), introduce an effective graph that can capture nonlinear logical redundancy present in biochemical network regulation, signaling, and control.

Rion Correia (a member of the CSBC lab, who also earned his Ph.D. in complex networks and systems from the Luddy School and Xuan Wang, a current Ph.D. candidate, and member of the lab) are also working on the project. Together, the authors demonstrate the utility of the approach with computational models of human cancer cells, showing that the effective graph reveals why some cancer medications are more effective than others in killing breast cancer cells.

You can read the full details via the press releases below:

Luddy Press Release

Instituto Gulbenkian de Ciência Press Release

You can read the article here:

https://www.pnas.org/content/118/12/e2022598118

*Those interested in contacting the authors should do so directly, via the links provided above.… continue reading.

We are hiring Posdoctoral Fellows!

The Center for Social and Biomedical Complexity (CSBC) at Indiana University Bloomington is accepting applications for one or more full-time non-tenure track postdoctoral fellows to conduct interdisciplinary research in Complex Networks and Systems applied to various social, ecological, biological, medicine and health problems. The expected start date for the appointments is February 2020.

Candidates interested in conducting research in urban community-environment systems, or network science methods to analyze and visualize information relevant for epilepsy and other chronic diseases are encouraged to apply. The appointments are full-time for 12 months, with potential to be extended an additional year subject to funding and satisfactory performance. We offer a competitive salary with generous benefits.

The postdocs will join a dynamic and interdisciplinary team that includes systems scientists, biologists, computer scientists, and social scientists. The postdocs will work with Prof. Luis M Rocha and Prof. Johan Bollen.

Basic Qualifications: A PhD is required in Complex Systems, Network Science, Computer or Computational Science, Computational Biology, Applied Mathematics, Physics, Statistics, Artificial Intelligence or related field; a strong background in analysis and modeling of complex systems and networks; and solid programming skills necessary to handle big data and develop large scale simulations. ABD (all but dissertation) candidates may apply but will need the Ph.D. prior to start.

Applications received by January 29, 2020 will receive the fullest consideration. We will continue accepting applications until the positions are filled. Please review the application requirements and apply online. Questions may be sent to: luddyjob+postdoc-lr@indiana.edu or Professors Bollen and Rocha.

Indiana University is an equal employment and affirmative action employer and a provider of ADA services. All qualified applicants will receive consideration for employment without regard to age, ethnicity, color, race, religion, sex, sexual orientation, gender identity or expression, genetic information, marital status, national origin, disability status or … continue reading.

CSBC Awarded Project to develop Resilient Community-Environment Interactions in Urban Waterways

Prepared for Environmental Change LogoIn a collaboration with Professors Heather Reynolds (IU Biology) and Gabriel Filippelli (IUPUI, Center for Urban Health) of the Environmental Resilience Institute, CSBC Professors Bollen and Rocha were awarded a grant for project “A River Runs Through It: Restoring Biodiversity and Empowering Resilient Community-Environment Interactions in Urban Waterways.” This 2-year project is part  of the Prepared for Environmental Change (PfEC) Grand Challenge initiative at Indiana University.

The project integrates environmental, social, and complex adaptive systems sciences with stakeholder values to study an urban watershed in transition, developing strategies to enhance its resilience to shocks–both slow (i.e., environmental change) and rapid (i.e., sewage diversion). CSBC will develop a  socio-ecological complex adaptive system analysis to identify, visualize, and model the dynamic relationships between public and private stakeholders and watershed biophysical variables.… continue reading.