News

Congratulations to Taraz Buck, who successfully defended his thesis entitled, "Automatic construction of dynamic models of subcellular structure" on October 22nd. Taraz will be remaining in the Lane Center for a short postdoctoral stint before beginning his next position. Taraz was advised by Dr. Robert F. Murphy.

CPCB faculty member Chakra Chennubhotla is getting some press due to his recent paper reducing the thousands of odors humans can detect to only ten categories.

CPCB Director Dan Zuckerman has written an editorial for the Pittsburgh Post Gazette stressing the importance of teaching our kids programming skills and giving them an advantage in the evolving world of technology. You can read his article here.

Congratulations to Armaghan "Rumi" Naik, who successfully defended his thesis entitled, "Efficient Modeling and Active Learning of Biological Responses: Learning without Prior Knowledge" on August 28. Rumi has accepted a position as a Lane Fellow in Computational Biology at Carnegie Mellon.

Congratulations to Justin Hogg, who successfully defended his thesis entitled "Advances in Rule-based Modeling: Compartments, Energy, and Hybrid Simulation, with Application to Sepsis and Cell Signaling" on June 27. Justin has accepted a position as an iOS Text & Input Engineer with Apple. Justin was advised by Dr. James Faeder.

Tricks like ripening a green banana by placing it in a paper bag with an apple have been known for thousands of years, but two CPCB researchers were part of the team that has just figured out why this works. Assoc. Professor Ziv Bar-Joseph and his Ph.D. advisee Shan Zhong joined a team lead by investigators at the Salk Institute for Biological Sciences to help identify thousands of genes that are activated by ethylene. The discovery may lead to powerful practical applications in agriculture, including the ability to slow growth when needed, accelerate or prevent ripening, retard rotting, or make plants more resistant to disease.

CPCB training faculty member Ziv Bar-Joseph was chosen as one of only six 2013 James S. McDonnell Foundation Scholars in the area of "Studying Complex Systems". The Complex Systems program supports scholarship and research directed toward the development of theoretical and mathematical tools that can be applied to the study of complex, adaptive, nonlinear systems. Ziv's primary research focus is on development of computational methods for understanding the dynamics and conservation of complex biological regulatory networks.

CPCB student Virginia Burger (advisor: Dr. Chakra Chennubhotla) has been awarded a two-year NSF Postdoctoral Research Fellowship award in Biology, Competitive Area #2, Intersection of Biology and Math, Physical Science and Engineering. She will conduct her postdoctoral research at MIT and Vrije Universiteit Brussel. Congratulations, Virginia!

Congratulations to Cordelia Ziraldo, who successfully defended her thesis entitled "Computational Models of Inflammation and Wound Healing" on April 16. Cordelia has accepted a position as a Research Fellow in the labs of Jennifer Linderman and Denise Kirschner at the University of Michigan, where she will be studying the immune response to infection with M. tuberculosis. Cordelia was advised by Dr. Yoram Vodovotz.

Congratulations to Shan Zhong, who successfully defended his thesis entitled "Computational Study of Transcriptional Regulation - From Sequence to Expression" on April 16. Shan has accepted a position as a Bioinformatics Scientist in the Molecular Anatomic Pathology Laboratory at UPMC Presbyterian. Shan was advised by Dr. Ziv Bar-Joseph.

CPCB training faculty member Seyoung Kim was named a 2013 Sloan Research Fellow in the area of Computational and Evolutionary Molecular Biology. The Alfred P. Sloan Foundation selected "126 early-career scientists and scholars who represent the very best that science has to offer. Nominated by their fellow researchers and chosen by a distinguished panel of senior scholars, the Sloan Research Fellows represent the next generation of leaders in the natural sciences, economics, and mathematics."

CPCB student Ming-Chi Tsai was first author on a paper chosen for Best Student Paper at the ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2012. The paper was: Tsai MC, Blelloch G, Ravi R, and Schwartz R "Coalescent-based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data."

Congratulations to Joshua Kangas, who succesfully defended his thesis, entitled "Active Learning for Drug Discovery" on January 24. Dr. Kangas has accepted a position as Chief Scientific Officer at Quantitative Medicine, LLC. Joshua was advised by Dr. Robert F. Murphy.

The Society for Laboratory Automation and Screening (SLAS) named Automated Image Analysis for High-Content Screening and Analysis, authored by CPCB's Aabid Shariff, Joshua Kangas, Luis Pedro Coelho, Shannon Quinn, and Robert F. Murphy, a 2013 Author's Choice Award winner. The Author's Choice Award reflects popularity among authors (citations) throughout 2012.

The 5th Annual CPCB Retreat was held at Hidden Valley Four Seasons Resort August 24-25, 2012. In addition to fun, the retreat affords an opportunity to recognize the work of our students. The 2012 Outstanding Research Accomplishment Awards were won by Yuefeng Lin and Suvrajit Maji. The 2012 Outstanding Academic Achievement Awards went to AJ Sedgewick and Lingxue Zhang, and Andrej Savol and Lu Xie took home the 2012 Poster Awards.

Congratulations to Suvrajit Maji, who successfully defended his thesis, entitled "Generative Models for Super-Resolution Single Molecule Microscopy Images of Biological Structures" on August 23. Suvrajit has accepted a position as a Postdoctoral Associate in Judith Klein-Seetharaman's lab at the University of Pittsburgh. Suvrajit was advised by Dr. Marcel Bruchez.

Congratulations to Chao Ma, who successfully defended his thesis, entitled "Novel Algorithms and Tools for Ligand-Based Drug Design - A Machine Learning Approach for Ligand Profiling" on August 22. Chao has accepted a position as a Machine Learning Engineer at RedBeacon. Chao was advised by Dr. Xiang-Qun (Sean) Xie.

Congratulations to Kyaw Zeyar Myint, who successfully defended his thesis, entitled "QSAR Methods Development, Virtual and Experimental Screening for Cannabinoid Ligand Discovery" on August 20. Kyaw has accepted a position as a Computational Biology Specialist with MathWorks. Kyaw was advised by Dr. Xiang-Qun (Sean) Xie.

Congratulations to Jacob Joseph, who successfully defended his thesis, entitled "On the Identification and Investigation of Homologous Gene Families, with Particular Emphasis on the Accuracy of Multidomain Families" on August 1. Jacob has accepted a position as a Forensic Analyst at the Software Engineering Institute at Carnegie Mellon University. Jacob was advised by Dr. Dannie Durand.

Congratulations to Guy Zinman, who successfully defended his thesis, entitled "Analysis of High Throughput Genomic Datasets Across Species" on May 4. Guy has accepted a position as a Systems Scientist in the Lane Center for Computational Biology at Carnegie Mellon University. Guy was advised by Dr. Ziv Bar-Joseph.

Congratulations to Aabid Shariff, who successfully defended his thesis, entitled "Learning Generative Models of Microtubule Distributions" on March 19. Aabid has accepted a position as a Senior Scientist, Image Analysis and Computational Biology, at GrassRoots Biotechnology. Aabid was advised by Drs. Robert F. Murphy and Gustavo Rohde.

CPCB Training Faculty Lillian Chong has been awarded the Carnegie Science Emerging Female Scientist Award, which recognizes a female leader whose cutting-edge work inspires change in math, science, or technology.

CPCB student Guy Zinman and his advisor Ziv Bar-Joseph are among the authors of a paper in Nature that for the first time links overexpression of a gene called sirtuin 6 to increased life span in mammals, specifically mice. Researchers who study aging have been intrigued by the large family of sirtuin genes and their proteins ever since they were linked to longevity in yeast.

CPCB Training Faculty member Ziv Bar-Joseph has been awarded
the International Society for Computational Biology's Overton Prize
for outstanding accomplishment. In recognition of this award,
Bar-Joseph will give a keynote address this July at ISMB in Long Beach.
READ MORE...


Congratulations to Sabah Kadri, who successfully defended her thesis, entitled "miRNA Regulation in Development" on January 13. Sabah has accept ed a position as Associate Computational Biologist at the Broad Institute. Sabah was advised by Drs. Veronica Hinman and Takis Benos.

Congratulations to Ross E Curtis, who successfully defended his thesis, entitled "Using Visualization and Automation to Accelerate Genetics Discovery" on Dec. 19. Ross has accepted a position on the DNA Software Development team at Ancestry.com. Ross was advised by Dr. Ziv Bar-Joseph.

CPCB Training Faculty member Robert F. Murphy was appointed to a three year term on the NIH Council of Councils, established to advise the NIH Director on policies and activities of the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI), including making recommendations on research that represents important areas of emerging scientific opportunities, rising public health challenges, or knowledge gaps that deserve special emphasis or would otherwise benefit from strategic planning and coordination.

Congratulations to Rachel Brower-Sinning, who succesfully defended her thesis, entitled "On the Evolution of Microbes: The Evolution of Genomes With Respect to RNA Folding" on Oct. 31, 2011.

Congratulations to Luis Pedro Coelho, who successfully defended his thesis, entitled "Modeling the space of subcellular location patterns using images and other sources of information" on Sept. 28, 2011. Luis Pedro has accepted a position as a postdoctoral researcher at the Institute for Molecular Medicine in Lisbon in the lab of Musa Mhlanga working on host-parasite interaction.

CPCB faculty member Elodie Ghedin ahas been named a 2011 MacArthur Fellow for her work on harnessing the power of genomics to study viruses. The awards, also known as "Genius Grants" are intended to encourage people of outstanding talent to pursue their own creative, intellectual, and professional inclinations.

CPCB student Luis Pedro Coelho was named to the 2012 class of Siebel Scholars. Luis Pedro and his advisor, Dr. Robert F. Murphy, will join other Siebel Scholars in October at the Janelia Farm Research Campus of the Howard Hughes Medical Inst. to explore the science, applications, benefits, and risks of synthetic biology with world-renowned scientific, industry, ethics, and policy experts.

Congratulations to CPCB student Om Choudhary, who won an Andrew Mellon Predoctoral Fellowship for the academic year 2011-2012. The appointment covers stipend and full tuition scholarship for the period of Fellowship.

CPCB student Shannon Quinn was runner-up for Best Student Paper at the BSEC 2011 conference for his paper entitled "Novel Use of Differential Image Velocity Invariants to Categorize Ciliary Motion Defects ."

Work by team including CPCB faculty member Robert F. Murphy and CPCB student Luis Pedro Coelho featured in Nature Biotechnology article on Computational Biology breakthroughs in 2010.

In an article published in Science, a group led by CPCB faculty member Ziv Bar-Joseph solved an important problem in distributed computing using inspiration from the mechanism by which fruit flies organize their sensory hairs. Read more here.

Team including CPCB faculty member Bino John describes a novel RNA copying mechanism in human cells in the journal Nature

Congratulations to Arvind Ramanathan, who successfully defended his thesis, entitled "Internal Dynamics and Energetics During Enzyme Catalysis" on May 4. His thesis advisor was Dr. Chris Langmead. Arvind has accepted a position as a post-doctoral researcher with Dr. Pratul K. Agarwal at Oak Ridge National Laboratory.

Congratulations to Kui Shen, who successfully defended his thesis, entitled "Meta-Analysis for Pathway Enrichment Analysis and Biomarker Detection When Combining Multiple Genomic Studies" on April 5. His thesis advisor was Dr. George Tseng. Kui has accepted a position as the Bioinformatics Scientist at Precision Therapeutics, Inc.

Gustavo Rohde received his first R01 grant from the National Institutes of Health. It is entitled "Automated High-Throughput Estimation and Modeling of Protein Network Distributions." This project is to develop sophisticated high-speed computational tools for analyzing protein distribution inside living cells.

CPCB faculty member Philip LeDuc discovers new protein function that could save lives. >>

Congratulations to Ahmet Bakan, who successfully defended his thesis, entitled "Dynamics of Protein-Drug Interactions Inferred from Structural Ensemblesand Physics-Based Models" on December 3. His thesis advisor was Dr. Ivet Bahar. Ahmet plans to continue working with Dr. Bahar as a post-doctoral researcher.

CPCB faculty member Bino John's team discovers a new class of small RNAs called usRNAs. >>

CPCB faculty member Eric Xing received a USAF Young Investigator Award. Eric was one of only 38 scientists nationwide to receive this award, which is intended to support the research of young scientists who show exceptional ability and promise.>>

Congratulations to Byoungkoo Lee, the first CPCB graduate! Byoungkoo successfully defended his thesis, entitled "Stochastic Off-Lattice Simulations of Binding Chemistry in Crowded Conditions," on August 27. His thesis advisor was Dr. Russell Schwartz. Byoungkoo plans to continue working with Dr. Schwartz as a post-doctoral researcher.

Three CPCB faculty members, Ed Clarke, James Faeder, and Christopher Langmead have received a five-year, $10 million grant from the National Science Foundation to develop advanced computational methods for analyzing complex systems. The research targets 4 application domains, including Pancreatic Cancer, where Drs. Faeder and Langmead will lead a multidisciplinary team focusing on the molecular and cellular dynamics of this deadly disease. >>

Two faculty in our program received Sloan Research Fellowships in the last two years: Michael Grabe, in 2009, in molecular biology, and Eric P. Xing, in 2008, in computer science. Awards are intended to enhance the careers of the very best young faculty. Currently a total of 118 fellowships are awarded annually. >>

Our program recently received the Phase II award from the NIBIB Interfaces Initiative for Interdisciplinary Graduate Research Training (T32). Phase I of this award was received from HHMI >>

Eric P. Xing has received a Sloan Research Fellowship in computer science. Awards are intended to enhance the careers of the very best young faculty. Currently a total of 118 fellowships are awarded annually. >>

Pitt Is Ranked Among the Top 10 U.S. University Recipients of Federal Research and Development Obligations >>

For the second year, our Program was very well represented at the ISMB meeting, which was held this year in Toronto. Our program students and faculty gave 2 proceedings talks, 4 highlights talk, 1 special session talk, 1 technology track presentation, and 13 poster presentations, as well as 1 plenary talk, 1 regular talk and 2 posters at the 3DSig Satellite meeting!

Carnegie Mellon Technique Accelerates Biological Image Analysis; Will Improve Automated High-Throughput Screening Techniques >>

Pitt Team Receives $2.5 Million to Simulate and Analyze Brain, Immune System Activity and Apply Math to Medical Problems >>

HHMI Awards $10 Million for Interdisciplinary Graduate Education >>

Carnegie Mellon and University of Pittsburgh Receive Educational Grant from Howard Hughes Medical Institute >>