News
February 2012
Ph.D. 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.
January 2012
The International Society for Computational Biology (ISCB) has awarded its Overton Prize for outstanding accomplishment to Ziv Bar-Joseph, associate professor in Carnegie Mellon University’s Lane Center for Computational Biology and Machine Learning Department.
The Overton Prize is awarded annually to an early- to mid-career scientist who has made a significant contribution to the field of computational biology. In recognition of the award, Bar-Joseph will give a keynote address this July at the annual International Conference on Intelligent Systems for Molecular Biology (ISMB) in Long Beach, Calif.
Bar-Joseph applies machine learning, statistical algorithms and signal processing techniques to the analysis of high-throughput biological data. He has led international research efforts that have identified genes important to human cell division, including a subset associated with cancer cells, which have uncovered new insights into gene regulatory networks.
January 2012
Lane Center Faculty Team With Ion Torrent to Develop Open Source Software to Interpret Personal Genomic Information
Ion Torrent announced a new generation of sequencing instrument that will enable sequencing of a personal genome for $1,000. This will dramatically increase the number of individual genomes available for finding associations between sequence and disease, and Ion Torrent also announced that they are sponsoring a collaborative effort with the Lane Center to develop open-source software to help clinicians interpret personal genome sequences. Collaborators at Baylor College of Medicine and Yale Medical School will obtain genome sequences and clinical parameters to help train the system.
“The huge variation in human genome sequence between individuals has always been an obstacle to understanding how to use sequence information to improve human health,” said Dr. Robert F. Murphy, director of the Lane Center for Computational Biology in Carnegie Mellon’s School of Computer Science, who will lead the multidisciplinary CMU team. “We believe new machine learning approaches will enable interpretation of personal genome sequences to help doctors diagnose and guide treatment in the near future.”
December 2011
Lane Center Director 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.
September 2011
Lane Center student Luis Pedro Coelho was named to the 2012 class of Siebel Scholars. Luis Pedro and his advisor, Dr. Robert F. Murphy, joined other Siebel Scholars in October at the Janelia Farm Research Campus of the Howard Hughes Medical Institute to explore the science, applications, benefits, and risks of synthetic biology with world-renowned scientific, industry, ethics, and policy experts.
September 2011
Two Lane Fellows have received tenure-track faculty positions.Dr. Arvind Rao has begun as a tenure-track Assistant Professor in the University of Texas M.D. Anderson Cancer Center in Houston. He plans for the focus of his group's research to be on the mechanisms underlying oncogenesis using bioinformatics and bio-imaging approaches.
Dr. Le Song has begun as a tenure-track Assistant Professor in the College of Computing at Georgia Institute of Technology. He plans for the focus of his group's research to be on using machine learning for analyzing gene expression data from cancer patients, and for analyzing images and text.
We are proud of both Lane Fellows, and look forward to seeing the great work they do in the years to come!
August 2011
Prof. Seyoung Kim has been selected to receive a 2011 Okawa Founation Research Grant. These are highly selective small grants primarily intended to recognize outstanding investigators in the early stages of their careers. Dr. Kim joins an illustrious list of past winners from the Carnegie Mellon School of Computer Science such as James Kuffner (2005), Nancy Pollard (2006), Alexei Efros (2007), Srinivasa Narasimhan (2008), Ryan O'Donnell (2009), and Adrien Treuille (2010).
July 2011
The paper by Eric Xing's group "TREEGL: Reverse Engineering Tree-evolving Gene Networks Underlying Developing Biological Lineages" by A. Parikh, W. Wu, R. Curtis and E.P. Xing was selected as Best Paper in Translational Bioinformatics at ISMB 2011, the top conference in bioinformatics. This paper was selected from more than 100 accepted to the proceeding and highlight tracks, and one award is given every year.
June 2011
Lane Fellow Marcel Schulz won a 2010 Otto Hahn medal, awarded by the Max Planck Society to young scientists and researchers for outstanding scientific achievement. Marcel received the medal for his Ph.D. thesis entitled "Data structures and algorithms for analysis of alternative splicing with RNA-seq data." Only 26 medals were awarded this year, representing the top 3% of all Ph.D students from 2010 among the nearly eighty Max Planck Institutes. Marcel joined the Lane Center in September 2010 and is working with Prof. Ziv Bar-Joseph on dynamic regulatory networks integrating post-transcriptional regulation.
April 2011
Professor William Cohen has been elected the next President of the International Machine Learning Society. The IMLS is the professional society that organizes the annual International Conference on Machine Learning (ICML).
April 2011
Lane Faculty member Ziv Bar-Joseph led a team whose work was published as a Featured Article in this month's Nucleic Acids Research. Featured Articles represent the top 5% of papers in terms of originality, significance and scientific excellence. You can read the paper here.
January 26, 2011
Nature Biotechnology recently asked leading computational biology researchers to nominate papers of particular interest published in 2010 that influenced the direction of their research. Work from Bob Murphy's group was chosen as one of four papers highlighted in the resulting article. The featured work, originally described in papers in the Proceedings of the National Academy of Sciences, U.S.A. and Bioinformatics, was the first to provide an automated means of estimating from microscope images how much of a protein (or other marker) is present in different subcellular organelles. The research involved a collaboration with scientists Ghislain Bonamy, Daniel R. Rines, and Sumit K. Chanda from the Genomics Institute of the Novartis Research Foundation in San Diego, and was carried out by graduate students Tao Peng and Luis Pedro Coelho and postdoctoral fellow Estelle Glory-Afshar.
January 14, 2011
In an article published in Science, a group led by Ziv Bar-Joseph, associate professor of computational biology and machine learning, solve an important problem in distributed computing using inspiration from the mechanism by which fruit flies organize their sensory hairs. You can read more here. The Association for Computing Machinery highlighted this and other Bar-Joseph work in this article.
January 2011
Lane Faculty member Ziv Bar-Joseph led a team whose work was published as a Featured Article in this month's Nucleic Acids Research. Featured Articles represent the top 5% of papers in terms of originality, significance and scientific excellence. You can read the paper here.
September 1, 2010
Prof. Ge Yang received an Emerging Frontier collaborative grant from NSF entitled “Biological shape spaces: transforming shape into knowledge”. The project is to develop computational tools to characterize mitochondrial dynamics in neurons and to analyze the underlying regulatory mechanisms.
July 1, 2010
Ziv Bar-Joseph received an NSF award entitled "Cross species analysis of biological systems using expression data." This project is to develop and implement algorithms and software tools for the analysis of gene expression experiments that study the same biological system in multiple species.
June 24, 2010
Lane Fellow Le Song was the first author on the Best Paper at this year's International Conference on Machine Learning. The paper, "Hilbert Space Embeddings of Hidden Markov Models," was coauthored by Byron Boots, Sajid Siddiqi, Geoffrey Gordon, and Alex Smola.
May 4, 2010
Arvind Ramanathan successfully defended his thesis entitled "Internal Dynamics and Energetics During Enzyme Catalysis." Arvind will join the Computational BIology Institute at Oak Ridge National Laboratory as a Postdoctoral Fellow.
May 1, 2010
Lane Center faculty will teach a new course, 02-750 Automation of Biological Research, in Fall 2010. Interested students can find out more by clicking here.
April 2, 2010
Kris Dahl received an NSF CAREER award entitled "Genome Regulation and Nuclear Rheology"
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.
January 12, 2010
Lane Center's Philip LeDuc Discovers New Protein Function That Could Save Lives
December 22, 2009
Drs Ivet Bahar and Robert F. Murphy, founding directors of the Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology (CPCB), passed leadership of the program to former Associate Directors, Drs. Panayiotis (Takis) Benos and Russell Schwartz, effective December 2009.
Both Professors Schwartz and Benos have been heavily involved with the program since its inception and their work has been critical to the success of the program.
Drs. Bahar and Murphy leave their positions as directors will full confidence that the program will continue to be a success under its new leadership!
December 21, 2009
The Lane Center is pleased to welcome Dr. Karen Thickman as an Assistant Teaching Professor! Dr. Thickman will join us in September 2010 to teach graduate and undergraduate courses and will supervise our automated experimentation facilities.
October 26, 2009
Lane Center faculty member, Eric Xing, receives USAF Young Investigator Award
August 27, 2009
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.
June 28, 2009
Lane Center faculty member Christopher Langmead led a group that recently won the Best Contribution award at the 2009 3Dsig meeting on Structural Bioinformatics and Computational Biophysics for their paper “A Graphical Model Approach for Predicting Free Energies of Association for Protein-Protein Interactions Under Backbone and Side-chain Flexibility”. The paper, co-authored by Computer Science graduate student Hetunandan Kamisetty and Prof. Chris Bailey-Kellogg of Dartmouth College, introduces a powerful new method for investigating the physics governing molecular interactions. Their breakthrough result will lead to new methods for designing drugs, and for designing new proteins that can be used to produce alternative sources of energy.
September 20, 2007
Opening of Lane Center