Computational Biology Department - Carnegie Mellon University

Robert F. Murphy

June 17, 2016

Murphy receives grant from new international collaboration program

Bob Murphy and his collaborator Christoph Wülfing from the University of Bristol have just received grants from a new program encouraging collaboration between U.S. and U.K. investigators.  The program, run jointly by the U.S. National Science Foundation (NSF) and the U.K. Biotechnology and Biological Sciences Research Council, allows the investigators to submit a single proposal that is reviewed by only one of the agencies: if it scores highly, the second agency simply accepts the recommendation of the first.  The project builds on their work described in a recent major paper in Science Signaling.  The project will involve analyzing fluorescence microscope movies to create spatiotemporal maps of proteins involved in signaling by T cells, a key component of the immune system.  The maps will be combined with data on cell-wide protein phosphorylation and used both to infer potential signaling complexes, and to estimate the apparent affinities and potential causal relationships amongst proteins involved in T lymphocyte signaling.

Noora Jassim Al-Muftah receives CMU-Qatar's first computational biology degree

May 2, 2016

CBD Celebrates First CMU-Qatar Computational Biology Graduate 

Noora Jassim Al-Muftah is the first graduate from Carnegie Mellon University-Qatar’s Computational Biology program, graduating with both College and University Honors for exceptional academic performance.

“Noora is very dedicated, her work has been brilliant, and we are very proud that she is our first graduate in Computational Biology,” says Valentin Ilyin, Associate Teaching Professor of Computational Biology.

Noora approached Dr. Ilyin during her freshman year to learn more about the new Computational Biology program offered at CMU-Q. The highly selective program includes coursework from both computer science and biological sciences, as well as specific classes for computational biology. Noora showed interest in research very early: in her sophomore year, she conducted an independent research project in the area of next generation sequencing (NGS) and won third place for her poster, “SNV-check: A quality control tool for familiar exome sequencing data based on the sharing of rare genetic mutations,” at Meeting of the Minds, 2014.

Noora continued to dedicate herself to research in her senior year, successfully completing a project titled, “The discovery of hidden relatedness and population structure in the 1000 Genomes Project.” 

Dean Ilkers Baybars announced that Noora has accepted an offer to attend Harvard University’s graduate program in Computational Biology.  Professor Ilyin says that the doors are open for her. “Computational biology is an emerging field: she could continue her studies on genome analysis, or go to work in areas like personalized medicine, virtual drug testing and automated imaging. Computational Biology research is now being carried out and used in almost every university, hospital, and pharmaceutical and biotech company. She has a very bright future.”

Congratulations, Noora!

Dynamic Changes RF Murphy

April 19, 2016

Study of dynamics of T cell signaling published in Science Signaling

Cells often need to respond to signals received through surface receptors, and their responses involve changes in the spatial arrangement of proteins with the cell.  For example, T cells receive signals through the T cell receptor (TCR) to indicate the presence of a particular antigen that they should respond to, and an additional signal through a costimulatory receptor (CD28) is required for them to respond fully. Changes in individual proteins within the T cell can be imaged using fluorescence microscopy, but variability from cell to cell and noise in the images make it difficult to understand the sequence of events that are occurring. In a paper published today in Science Signaling, Dr. Murphy’s group describes computational methods to address this problem. more

melissa tetrick rookie of the year founders day scs

April 12, 2016

Congratulations to  “Rookie of the Year” CBD Business Manager, Melissa Tetrick!

CBD Business Manager Melissa (“Missy”) Tetrick received the “Rookie of the Year” staff award from the School of Computer Science.  The award was presented by CBD Professor Russell Schwartz during the SCS Founders Day celebration.  “I was really surprised and grateful to be thought of. It’s an honor to be recognized for the work that you love to do,” said Missy, adding “ I love working with people from different cultural backgrounds, which is something great about working at CMU in general. And I love the Computational Biology Department because we’re a small and upcoming team. I like being a part of something that is going to take off.” In her daily life, Missy enjoys spending time with family (especially her awesome son, Benjamin!), and karate.


March 24, 2016

Pittsburgh Health Data Alliance Funds Clinical Genomics Project led by CBD Professors Kingsford and Langmead

 The Clinical Genomics Modeling Platform, a system for easily creating and deploying predictive models to help physicians make treatment decisions, is the first Carnegie Mellon University project to be funded by UPMC Enterprises under the umbrella of the Pittsburgh Health Data Alliance. UPMC's funding for the initial set of projects, including several from the University of Pittsburgh, is expected to total more than $3 million over the next six months. The Clinical Genomics Modeling Platform project is being led by CBD’s associate professors, Carl Kingsford and Christopher Langmead. It is part of CMU's Center for Machine Learning and Health, which is directed by Eric Xing, Professor of Machine Learning, Language Technologies and Computational Biology more  


March 18, 2016

Exciting Upcoming Computational Biology Lectures in March/early April at CMU

- Fri, 3/25/16 @11AM: CMU CBD’s own Andreas Pfenning to present a Joint CMU-Pitt PhD Program in Computational Biology and Computational Biology Department Seminar: “The genetic basis of brain aging and Alzheimer’s disease”

Location: GHC 4307

- Wed, 3/30/16 @1:30PM: Morgan Wirthlin, Ph.D, hosted by Andreas Pfenning, to present "Evolutionary Neurogenomics Provides Insight into the Basis of Learned Behavior”

Location: Mellon Institute Social Room

- Fri, 4/1/16 @11AM: Tim Hughes, U. of Toronto, hosted by CBD and Biological Sciences Assistant Professor Joel McManus, to present a Joint CMU-Pitt PhD Program in Computational Biology and Computational Biology Department Seminar: “Decoding Gene Regulation"

Location: GHC 4405

Naik Murphy Sullivan Kangas Robotically Driven Experimentation System

February 9, 2016

CMU CBD Scientists’ Robotically Driven System Could Reduce Cost of Discovering Drug and Target Interactions

CBD Lane Fellow Armaghan Naik, CBD Alumni Devin Sullivan and Josh Kangas, and CBD Department Head Robert F Murphy have created the first robotically driven experimentation system to determine the effects of a large number of drugs on many proteins, reducing the number of necessary experiments by 70%. The model, presented in elife, uses an approach that could lead to accurate predictions of the interactions between novel drugs and their targets, helping reduce the cost of drug discovery. more

Kingsford Bioinformatics DNA Sequences Search Techniques

February 8, 2016

CMU CBD Method Tames Giant Bioinformatics Database

Database searches for DNA sequences that can take biologists and medical researchers days can now be completed in a matter of minutes, thanks to a new search method developed by CBD Associate Professor Carl Kingsford and CBD Ph.D student, Brad Solomon. Kingsford and Solomon’s method is designed for searching so-called "short reads" — DNA and RNA sequences generated by high-throughput sequencing techniques. It relies on a new indexing data structure, called Sequence Bloom Trees (SBTs), that the researchers describe in a report published online today by the journal Nature Biotechnology. more


February 8, 2016

CBD Leads Accepted Papers at RECOMB 2016 

We are proud to announce that 7 of the 35 accepted papers at the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB) were authored by members of the Carnegie Mellon Computational Biology Department. No other institution had authors of more than 3 accepted papers. RECOMB is a highly competitive international conference and is a leading venue for publishing computational biology research. In its 20-year history, it has published some of the most influential papers on algorithms for biological problems.

• Hao Wang, Joel McManus and Carl Kingsford. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast

• Shashank Singh, Sabrina Rashid, Saket Navlakha and Ziv Bar-Joseph. Distributed Gradient Descent in Bacterial Food Search

• Meghana Kshirsagar, Jaime Carbonell, Judith Klein-Seetharaman and Keerthiram Murugesan. Multitask matrix completion for learning protein interactions across diseases

• David Pellow, Darya Filippova and Carl Kingsford. Improving Bloom filter performance on sequence data using k-mer Bloom filters

• Mingfu Shao and Bernard Moret. On Computing Pairwise Breakpoint Distances

• Emre Sefer and Ziv Bar-Joseph. Shall we dense? Comparing design strategies for time series expression experiments

• Yang Li, Shiguo Zhou, David Schwartz and Jian Ma. Allele-Specific Quantification of Structural Variations in Cancer Genomes

Suresh 3-D bioprinting

CMU President and CBD Professor Subra Suresh and his collaborators have demonstrated a a promising new method for 3-D bioprinting that could lead to new possibilities in medical research and applications.


Dr. Gregory R. Johnson

Congratulations to Dr. Gregory Johnson, who successfully defended his doctoral thesis, "Image-Derived Models of the Organization of Cellular Componenets" completed under the supervision of Dr. Robert F. Murphy.

Greg will enjoy a well-deserved week on the beach before moving to Seattle to start his new position as a Machine Learning Scientist at the Allen Institute for Cell Science.


CBD Opens Applications for Lane Fellowships

We are accepting applications for Lane Fellowships from recent PhD recipients. The Lane Fellow Program recognizes and supports scientists of outstanding intellect who are dedicated to a career at the interface of computational and biological sciences so that they can pursue postdoctoral research in the rich computational environment at Carnegie Mellon. Applications should be submitted by March 15, 2016.

Lane Fellows will be selected for a three-year appointment beginning approximately August 1, 2016. They will receive a stipend of $65,000, benefits including medical, dental, vision and life insurance, and a professional support allocation of $3,000 to cover items such as purchase of a laptop computer, travel to conferences, membership in relevant professional societies, and journal subscriptions.

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CBD Recruiting Tenture-Track Faculty

Following a very successful faculty recruiting season last year, CBD is again searching for outstanding researchers who are developing and applying rigorous computational methods in all areas of biology to fill tenure-track positions. We especially seek candidates working on automated analysis and modeling of biological and medical images, and those addressing problems in neurobiology using computational methods, although outstanding candidates from all areas will be enthusiastically considered.  We particularly encourage applications from candidates who have a demonstrated track record in mentoring and nurturing female and under-represented minority students.

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The Computational Biology Department

The Computational Biology Department at Carnegie Mellon University seeks to realize the potential of machine learning for expanding our understanding of complex biological systems. A primary goal of the department is to develop computational tools that will enable automated creation of detailed, predictive models of biological processes, including automated experiment design and data acquisition. We anticipate that these efforts will not only lead to deep biological knowledge but also to tools for individualized diagnosis and treatment of cancer and other diseases. The Computation Biology Department builds on the strong history of computational and interdisciplinary research at Carnegie Mellon.

Computational Biology Ph.D. Program

The Computational Biology Department is the administrative home on the Carnegie Mellon side for the Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology. Applications for the Fall 2016 class have closed. The online application will be available again in September 2016 for students interested in beginning study in Fall 2017.