Dr. Anne-Ruxandra Carvunis to join the department

3834452We are happy to announce that Dr. Anne-Ruxandra Carvunis has accepted our offer and will be joining the Department in October!

Anne has her Ph.D. in Bioinformatics from the Université Joseph Fourier, Grenoble, France.

She was a Postdoctoral research fellow in Dr. Marc Vidal’s group at the Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute, Harvard Medical School. She worked on modeling de novo gene birth in S. cerevisiae through transitory “proto-genes” and also computational analyses of human protein interaction network maps.

She is currently a Postdoctoral research fellow in Dr. Trey Ideker’s group at the University of California San Diego, where she works on modeling the evolution of molecular networks using bioinformatics and yeast genetics.

We look forward to welcoming her to our department! Please join us in congratulating her.

New Seminar on Causal Discovery to be offered by CMU in Fall, 2015

A new seminar on causal discovery is to be offered by Carnegie Mellon University in Fall, 2015 (Course #80-516 for undergraduate level;  Course #80-816 for graduate level;  Section A for both levels).  The instructor will be Kun Zhang, a new faculty member in CMU’s Philosophy Department.  Pitt students can register now through the Pitt cross-registration process.

Click here for the announcement and syllabus


Causal connections are usually more interesting or helpful than purely associational information. This course is mainly concerned with systematic approaches to discovering causal connections from data in various scenarios and the question why causation plays an important role in science, i.e., how it is helpful in understanding,  decision making, and prediction in complex environments.

We will study the difference between causal and non-causal systems and make an attempt to characterize a causal system. Apart from identification of causal effects, we will explore two causality-related areas. One is causal discovery, i.e., going beyond the observational data to the underlying causal information. It is well known that “correlation does not imply causality,” but we will make this statement more precise by asking what information in the data and what assumptions enable us to discover causal information from purely observed data. This will cover constraint-based causal discovery, causal discovery based on structural equation models, causal discovery from time series, difficulties in practical causal discovery, causality in neuroscience, causality in biology, and causality in economics and finance. More importantly, we will have the opportunity to solve problems in various fields from a causal perspective: participants may bring any causal problems they are interested in, and we will work together to find potential solutions. The other is how to properly make use of causal information. This includes counterfactual reasoning, improving machine learning in light of causal knowledge, and forecasting in nonstationary unseen environments.

Overall, this course aims to provide fundamentals of causal discovery and inference, review emerging methods for causal discovery, report their applications, find practical causal problems in various fields, and work out potential solutions.


Research Highlight: Clark Lab


Their model species, Pieris rapae

The Clark Lab, alongside the Morehouse Lab (Department of Biological Sciences), have been using the the bursa copulatrix as a model to research the mechanisms that equip an entire organ with its characteristic physiological functions.

Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions

Camille Meslin1, Melissa S. Plakke2, Aaron B. Deutsch2, Brandon S. Small1, Nathan I. Morehouse2*, Nathan L. Clark1*
1 Department of Computational and Systems Biology, University of Pittsburgh, PA, USA
2 Department of Biological Sciences, University of Pittsburgh, PA, USA

Abstract: “The origin of novel organismal traits is a critical question in evolutionary biology. While different studies have revealed mechanisms by which novel morphological or physiological traits have evolved, the mechanisms that equip an entire organ with its characteristic physiological functions are relatively unknown. We have addressed this question by using the bursa copulatrix as a model. The bursa copulatrix is a very unique organ within the female reproductive tract in butterflies and moths that processes the male spermatophore, a nuptial gift that provides the female with nutrition. Using gene expression from 9 tissues across 2 developmental stages and phylogenetic analyses, we revealed that the bursa borrowed genes from non-reproductive tissues to gain muscular and digestive functions, transforming it into a stomach-like organ within the reproductive tract. We also showed the bursa responds to spermatophore deposition by altering its gene expression pattern. Finally, we identified bursa-specific genes that may provide novel bursa-specific functions. Overall, our work provides critical insight into female reproductive traits and genetic mechanisms that may be used to equip an organ with its physiological functions.”

Celebrating the 10th Anniversary of our Department

DSC_0114The department celebrated 10 years of Computational and Systems Biology this past month at the Mansions on Fifth.

Computational biology was established as a research discipline at the University of Pittsburgh with the vision of the Senior Vice Chancellor and Dean of the School of Medicine, Dr. Arthur S. Levine, who recruited Dr. Bahar to create a new Center for Computational Biology and Bioinformatics in March 2001, which soon became a highly visible center. The creation of the Department of Computational Biology within the School of Medicine followed in October 2004, later becoming Computational and Systems Biology in 2010.

Thank you for helping us celebrate 10 years of research, education accomplishments, collaborations, hard work, and memorable events.

To view pictures of the event, click here.

Dr. Clark receives Charles E. Kaufman Foundation Grant

ClarkDr. Nathan L. Clark received a grant of $150,000 in the New Investigator Research category from the Charles E. Kaufman Foundation for research on “Co-evolutionary Signatures as a Novel Approach to Gene Discovery”. Their project will use signals of co-evolutionary interactions to identify novel gene network components in humans and model organisms. One of their specific experimental goals is to assign human cardiac muscle proteins to their trafficking modifiers.

In 2011, the Foundation and its Supporting Organizations awarded more than $41.1 million in grants to a vast array of nonprofit organizations, students through scholarships, and medical researchers, based on donor interests and specific purposes of individual funds.

Since 1945, The Pittsburgh Foundation has been connecting its generous donors with the critical needs of our community. Donors who have established funds through the Foundation can support virtually any area of charitable interest in Pittsburgh, or anywhere in the United States. Because the Foundation is a public charity, donors benefit from significant tax advantages.

Endowment funds held by the Foundation range from $10,000 to $40 million, created by individuals and organizations with a passion for Pittsburgh and a deep commitment to their community. More than 1,000 individuals, families and organizations have established funds at The Pittsburgh Foundation, which exists in perpetuity – growing each year – to provide an ever-increasing resource to benefit the community.

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