Computational Biology Department - Carnegie Mellon University



Andreas Pfenning Computational Biology Youtube

August 5, 2016

CBD Releases First Video of Office Visit YouTube Series: Dr. Andreas Pfenning

We're excited to present CBD Assistant Professor Andreas Pfenning in the first video of our CBD Office Visit YouTube Series. Please subscribe to our new Youtube Channel for upcoming CBD Office Visits! 

Jian Ma Cell Systems

July 21, 2016

CBD Associate Professor Jian Ma Creates Research Tool that Identifies Interactions Involved in Genetic Changes

A new method for analyzing the scrambled genomes of cancer cells gives researchers for the first time the ability to simultaneously identify two different types of genetic changes associated with cancers and to identify connections between the two.

CBD Associate Professor Jian Ma said his new algorithm, called Weaver, could become an important tool for identifying interactions of the alterations within a cancerous cell’s DNA that drive the disease.

                 

“This work uses a rigorous and elegant approach to give a better picture of the genome changes that occur during the evolution of individual cancers,” said CBD Department Head Robert F. Murphy. “Having a clearer picture can help identify characteristics, such as responsiveness to drugs, that distinguish cancers and may contribute to developing more personalized treatments.”

 

A report on this work by Ma and his former Ph.D. student at the University of Illinois at Urbana-Champaign, Yang Li, was published online today by the journal Cell Systems.

The genetic code of a healthy cell is embodied by 23 pairs of chromosomes, “but in tumor cells, it’s completely scrambled,” Ma said. Many cancers are known to give rise to multiple copies of chromosomes, a type of mutation known as aneuploidy. Likewise, cancer cells are known to undergo another type of mutation, called structural variations, in which DNA sequences within the chromosomes get rearranged and duplicated.  Both of these genetic changes can occur within the same cell, but until now separate techniques had to be used to quantify them. Weaver, however, does these analyses simultaneously using the same input — whole genome sequencing data. 

 

The advantage of doing these analyses simultaneously is that researchers can now see how aneuploidy is affected by structural variations and vice versa. When the analyses are done separately, these interactions are difficult to identify. Weaver uses a probabilistic graphical model called Markov Random Field, which enables researchers to visualize not only the number of mutations but also how they connect with each other. 

 

“This gives us a better view of the complexity of cancer genomes,” Ma said. This may help researchers better characterize cancers or understand which combinations of genetic changes might affect cancer behavior for the same type of cancer or for different cancer types. 

 

Ma said he anticipates Weaver could provide useful perspective for studies of the Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute and the National Human Genome Research Institute that has described the genomes of tumor tissues and matched normal tissues from more than 11,000 patients. The publicly available TCGA dataset includes genomes for 33 different tumor types.

 

Ma and Li applied Weaver to whole genome sequencing data for two cancer cell lines and to ovarian cancers from the TCGA. In the case of the ovarian cancer samples, Weaver identified duplicated chromosomal regions caused by a specific type of structural variation, an association not previously reported.

 

David C. Schwartz and Shiguo Zhou of the University of Wisconsin-Madison joined Ma and Li in authoring the Cell Systems report. The National Institutes of Health and the National Science Foundation supported this research.

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Dr. Min Xu Assistant Research Professor Carnegie Mellon University Computational Biology

July 15, 2016

CBD Welcomes Min Xu, Assistant Research Professor

We are excited to announce that Dr. Min Xu joined us July 1 as the newest CBD faculty member. He recently finished postdoctoral research with Dr. Frank Alber at the Computational Biology and Bioinformatics Program at University of Southern California after completing PhD research with Dr. Xianghong Zhou in the same program. Min is currently developing methods for the structural analysis of cell systems at molecular resolution and in close-to-native states. In particular, his research focuses on extracting the structures and spatial organizations information of macromolecular complexes from cellular electron cryo-tomogram 3D images. This emerging research field aims to address fundamental biological questions using a wide range of state-of-the-art computational and mathematical techniques. Min says that he is “very excited about joining CBD at CMU since CBD is one of the leading Computational Biology programs in the nation and Pittsburgh is a major center of biomedical research.”  Welcome, Min!

Robert F Murphy Distinguished Service Award CYTO 2016

July 6, 2016

ISAC Presents Distinguished Service Award to CBD Department Head Robert F. Murphy at CYTO 2016

On June 15, 2016,  the International Society for Advancement of Cytometry (ISAC) presented Computational Biology Department Head Robert F. Murphy with the Distinguished Service Award. The award was presented by the society’s past president, John Nolan, in Seattle during the society’s annual awards ceremony at CYTO 2016 (ISAC’s annual international Congress). Nolan’s CYTO 2016 ceremony remarks regarding Dr. Murphy are below:

“The Distinguished Service Award was established to honor those individuals who served the Society in a major role, provided major support to the Society and its members, or made a significant contribution to the success of the Society. The Awards committee comprises significant individuals in science and cytometry able to assess the breadth and depth of a nominee’s contributions. The committee recognized the contribution you have made to ISAC through your years of involvement at the committee and Council level.  As President you transformed the aspirations of the Society and made its future more secure – we continue to enjoy the legacy of your leadership. In particular, your work to strengthen the society financially by forging a relationship with the Wallace H. Coulter Foundation, your work to increase the involvement of image cytometrists in ISAC, and your work to launch the ICCE certification program have been invaluable. The committee further recognized that your profile as a highly respected scientist and innovator together aligned with your long-term support of the Society have helped ISAC to pursue its mission of advancing cytometry. As a recipient you do honor both to ISAC and the Award.” 

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. 

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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.

PHDACloud

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

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cbd

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.

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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.

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RECOMB2016 RECOMB

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.

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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@CMU

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@CMU

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.