Category Archives: CASCI

New Ph.D. Graduate

Congratulations to Alexander Gates for successfully defending his dissertation entitled “The anatomical and effective structure of complex systems” on April 3rd 2017, co-supervised by Randy beer and Luis Rocha. Alex completed a dual-PhD degree in the Complex Systems track of the Informatics PhD Program as well as the Cognitive Science program at Indiana University. Alex has accepted a postdoctoral position at Northeastern University at the Center for Complex Network Research.

Art-Science Installation Musical Morphogenesis

Musical Morphogenesis’ is an interactive installation that translates to sound, movement and lights the dynamics behind the development of petals in a flower. It is a collaborative piece developed by designers, architects, musicians and scientists in Luis Rocha‘s CASCI group. The control of this robotic “macroscope” is an implementation of the gene regulatory network of the Thaliana Arabidopsis flower. The installation provides a sensorial exploration of the dynamics between genes and proteins that leads to organ formation in plants, namely sepals, stamen, and petals. The genetic network provides an interactive “genetic soundtrack” that allows visitors to control the development of the plant towards its wild-type or mutant states. The installation has been on display at various museums such as the Science Museum in Lisbon, Gulbenkian Foundation, and the Belém ArtFest. This week it will be displayed at Dia D Ligações – Gulbenkian Foundation.

CASCI alumnus makes Fast Company’s most creative list

Ahmed Abdeen Hamed

Congratulations to CASCI alumnus Dr. Ahmed Abdeen Hamed who was recognized by FastCompany magazine, among the most creative people in the world, in 2016, for his research publication entitled: Twitter K-H networks in action: Advancing biomedical literature for drug search.Dr. Hamed completed his Computer Science MS degree at Indiana University in May 2005 and joined our Complex Networks & Systems track of the PhD in Informatics in the Fall of 2008. For personal reasons, he finished his PhD at the University of Vermont, but started his research in biomedical text mining with the CASCI group.

Control of Complex Networks

Control of the eukaryotic cell cycle of budding yeast Saccharomyces cerevisiae (from Nature.com, click for details)

Network science has allowed us to understand the organization of complex systems across disciplines. However, there is a need to understand how to control them; for example, to identify strategies to revert a diseased cell to a healthy state in cancer treatment. Recent work in the field—based on linear control theory—suggests that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics. Such graph-based approaches have been used, for instance, to suggest that biological systems are harder to control and have appreciably different control profiles than social or technological systems. The methodology has also been increasingly used in many applications from financial to biochemical networks.

In work published today in Nature Scientific Reports, CNetS graduate student Alexander Gates and Professor Luis Rocha demonstrate that such graph-based methods fail to characterize controllability when dynamics are introduced. The study computed the control profiles of large ensembles of multivariate systems as well as existing Systems Biology models of biochemical regulation in various organisms.

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Artemy Kolchinsky, recent Postdoc at the Santa Fe Institute

Artemy Kolchinsky
Artemy Kolchinsky

Recent CASCI Complex Systems & Networks Phd program graduate Artemy Kolchinsky, is now a postdoc at the Santa Fe Institute. While at SFI, Kolchinsky is working with “David Wolpert on several projects related to optimal use of information and prediction. One is the problem of modeling and analyzing complicated dynamical systems that require large amounts of time and computational power to simulate. […] Another project investigates connections
between information processing and statistical physics. […] The two are [also] beginning to work on understanding why different social groups develop different organizations, whether the group is a prehistoric tribe or a business firm.” More details on the SFI update newsletter.

Rocha Receives Fulbright Scholarship

Luis Rocha
Luis M. Rocha

Congratulations to Luis Rocha, who has been awarded a Fulbright Scholarship devoted to developing Complex Systems methodologies for the Life Sciences. The 12-month sabbatical is to be pursued under the Fulbright program for educational exchanges between the United States and Portugal. It will focus on studying collective behavior and control in biochemical and social networks. The broader goal is to advance our ability to predict and control the dynamics of complex networks in three domain areas: biochemical, neurodyamic, and social systems. The scholarship will also be used to facilitate the design of a new doctoral program on complex networks and systems for the life sciences.

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CNETS Team Uses Instagram to monitor Drug Interactions and Adverse Reactions

Subnetwork of symptoms and drugs associated with Psoriasis and Epilepsy
Subnetwork of symptoms and drugs associated with Psoriasis and Epilepsy

Update: On March 21st, 2016 the paper described below (PMC4720984) was highlighted by Russ Altman from Stanford University in his yearly review as one of 30 important papers of the year in translational bioinformatics.

Using complex networks analysis and social media mining, CNETS researchers from the CASCI team have found that Instagram, a growing social media platform among teens, can be used “to uncover drug-drug interactions (DDI) and adverse drug reactions (ADR).” The work shows that this popular social media service is “a very powerful source of data with great promise in the public-health domain”. The study, “Monitoring Potential Drug Interactions and Reactions via Network Analysis of Instagram User Timelines,” supported by an R01 grant from the National Institutes of Health as well as a gift from Persistent Inc., was recently published and presented at the Pacific Symposium on Biocomputing (PSB 2016), in Hawaii. (PubMed, arXiv). The results are based on almost 7.000 user timelines associated with depression drugs which combined have 5+ million posts.

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CNetS team studies generalized modularity in complex networks & Systems

mediumModularity in complex systems can be observed in networks and across dynamical states, time scales, and in response to different kinds of perturbations. In a paper published in Physical Review E (Rapid Communication), Kolchinsky, Gates & Rocha propose a principled alternative to detecting communities in static and dynamical networks. The method demonstrates that standard modularity measures on static networks can be seen as a special case of measuring the spread of perturbations in dynamical systems. Thus, the new method offers a powerful tool for exploring the modular organization of complex dynamical systems.