News
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03/2021
Working with Yale and Pitt on the PF connectome We are leading the computational analysis and modeling efforts for a new project focused on Pulmonary Fibrosis (PF). Together with Yale and Pitt we are working on developing computational methods to model disease progression at the single cell level and match drugs to different disease stages to improve personalized treatment of PF. See the news story for more details.
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10/2020
Chieh's thesis awarded SCS Honorable Mention Chieh's Lin PhD thesis, 'Probabilistic Single Cell Lineage Tracing', is one of 5 from the School of Computer Science at CMU selected for a PhD thesis award. Chieh is the second student from our group to receive this honor. Last year, Sabrina Rashid's thesis was also selected for a honorable mention (see news item below from 11/19). Given the large number of PhD students at SCS and the amazing work they all do, this is a great honor! Congratulations to Chieh.
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06/2020
c3.ai award to develop AI methods for predicting cocktail treatments for SARS-COV-2. Our proposed project was one of a handful of proposal selected for funding by the C3.ai Digital Transformation Institute. Our project focuses on using machine learning methods to model the dynamic signaling and regulatory networks that are activated lung cells following infection with SARS-COV-2. Once such networks are reconstructed they will be analyzed to identify top proteins that can lead to reduction in viral loads. Next we will identify potential drugs to target combinations of these key proteins and test these on our recently constructed iPSC lung cell lines. This is joint work with our long time collaborator Darrell Kotton from Boston University and with Profs. Regina Barzilai and Tommi Jaakkola at MIT. See the c3.ai press release, the CMU story and a story in Pittsburgh Post-Gazette.
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06/2020
LinTIMaT integrate CRISPR and single cell expression data to improve lineage tree reconstruction. In a new paper in Nature Communications we presented LinTIMaT a new computational method that combines both CRISPR mutations and single cell expression to infer developmental lineages. The method was applied to data from model organisms including zebrafish and was able to significantly improve on current methods that only rely on the sequence mutation data. Hamim Zafar (former postdoc and Lane fellow) and Chieh Lin (former PhD student) are first authors on this paper. You can read more about the methods and its importance in a press release that Hamim prepared.
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12/2019
Deep learning for gene interaction prediction paper published in PNAS We presented a new method for encoding gene expression data as an image like input. As we showed, using such encoding we can utilize the power of convolutional neural networks for several tasks related to inferring gene interactions. The new method, termed CNNC, has already been applied to identify new partners for genes, reconstruct pathways based on these interactions and assign new function to genes. In all cases the new encoding helps the method outperform all prior methods for these important tasks. You can read the full paper in PNAS and view the press release issued by CMU to discuss the importance of the work.
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11/2019
Sabrina's thesis awarded SCS Honorable Mention Sabrina Rashid's PhD thesis, 'Distributed Computing in Nature', is one of 5 from the School of Computer Science at CMU selected for a PhD thesis award. Given the large number of PhD students at SCS and the amazing work they all do, this is a great honor! Congratulations to Sabrina.
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10/2019
HuBMAP paper published in Nature The HuBMAP perspective paper, is published in Nature. The paper presents the vision and goals and the HuBMAP consortium. We are leading a large group of researchers at Carnegie Mellon, the University of California Santa Cruz and the Sanger Institute in the UK which is in charge of the computational tools and pipeline development for HuBMAP. See the SCS press release which includes a quote from Matt Ruffalo who is leading the development team.
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09/2019
Hamim Zafar accepts Assistant Prof. Position Hamim Zafar, who joined us in 2018 as a Lane Fellow, has accepted a faculty position as an Assistant Professor In one of Indias top schools: IIT Kanpur. Hamim is joining the computer science department and will continue his work on computational biology. Congratulations and good luck!
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08/2019
Best Poster Award at ISMB 2019 Congratulations to Hamim Zafar (Lane Fellow) and Chie (Jessica) Lin for winning the F1000 best poster award at the most recent ISMB meeting in . The poster presented their new method, LinTIMaT, which was developed for integrating CRISPR-Cas9 mutation data with scRNA-Seq data for constructing linage trees. ISMB is the largest computational biology conference and included hundreds of posters of which only 5 were selected for an award.
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05/2019
Bacteria tumbling paper published in PNAS Our most recent Algorithms in Nature work, which focuses on how bacteria navigates obstacle courses by adjusting its tumbling rate has been published in PNAS. In that paper we show both simulations and experimentally that by adaptively changing their tumbling rates as they encounter obstacles bacteria greatly improves their food search time. Application of the same idea to robot swarms indicates that it can be used to improve efficient search in constrained environments. More information can be found in CMUs press release, in a report by the NSF in a news and views piece in Nature Reviews Microbiology and in a great podcast interview by the Naked Scientist with Sabrina Rashid (the lead author).
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04/2019
Sabrina defends her PhD Sabrina Rashid successfully defended her PhD thesis titled Distributed Computing in Nature. Sabrina accepted a position as a research scientists in AI Therapeutics a biotechnology startup in Connecticut. Congratulations and good luck!
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09/2018
We are leading the HuBMAP Computational Tools Center The Human BioMolecular Atlas Program (HuBMAP) is a large, national effort to develop a 3D map of the human body. As part of this program the NIH has funded 15 centers to collected new data, develop new technologies and develop computational methods for the analysis of the data. We are heading one of these centers, which is a part of the HuBMAP Integration, Visualization & Engagement (HIVE) effort. Our center will focus on the development of computational methods for the processing, analysis, modeling and retrieval of the HuBMAP data and on the interactions between users and the MAP. In addition to 4 investigators from CMU our center also includes co-PIs for UCSC and the UK and investigators from Google Brain. See CMU Press Release , Post-Gazette story , and KDKA radio story
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02/2018
Matt awarded NIH Postdoctoral Fellowship Matt Ruffalo received a NIH postdoctoral fellowship grant from the NCI. Matt has been a postdoc in our group since 2016. Matt works on the analysis of cancer genomics data and his proposal focused on methods for integrating genomics data from several different sources to predict survival and drug response. Congratulations Matt!
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12/2017
Bar-Joseph receives FORE Systems Professorship. In a ceremony attended by some of the FORE Systems founders, Ziv Bar-Joseph has been awarded the FORE Systems chair in computational biology and machine learning. While the chair is a great personal honor, it is in large part due to the amazing work over the years by all the students and postdocs in our group!
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10/2017
Sid defends and accepts a new postdoc position. Siddhartha (Sid) Jain successfully defended his PhD thesis titled 'Inferring Temporal Signaling Pathways and Regulatory Mechanisms from High-Throughput Data'. Sid has accepted a postdoc position with Prof. David Gifford at MIT and will start there shortly. Congratulations Sid, and good luck!
- 08/2017
CPCB directorship. Ziv is replacing Russell Schwartz as the director of the joint CMU-Pitt Computational Biology Ph.D Program .
- 08/2017
CMLH fellowship. Congratulations to Sabrina Rashid for receiving a Fellowships in Digital Health from the Center for Machine Learning and Health (CMLH) at CMU. Sabrina spent the summer as an intern in Microsoft Research and would start the fellowship on 9/2017.
- 11/2016
New paper in Science. Collaborating with the Ecker lab at the Salk Institute we have used computational methods to model Arabidopsis response to stress. The Science paper presents models that allowed our team to identify molecular conductors, top regulators of this response and have also led to the identification of new transcription factors that play a role in plant response to hormone and salt. See the CMU press release for more details.
- 04/2016
Best paper award at RECOMB 2016! Our paper 'Shall we dense? Comparing design strategies for time series expression experiments' has won the 'Best Paper Award' in this years '20th International Conference on Research in Computational Molecular Biology (RECOMB)'. RECOMB is one of the two most important conferences in the general area of computational biology. The journal version of the paper has been published in the Journal Cell Systems, accompanied by a nice commentary which discusses the work. Congratulations to Emre and Michael.
- 11/2015
CURE cancer grant. We received a large grant from the PA Department of Health to improve the usage of 'Big Data' for cancer. The grant will establish a new center, Big Data For Better Health (BD4BH) which will be co-directed by Bar-Joseph and Greg Cooper from the University of Pittsburgh. The main focus would be on developing better methods for integrating, analyzing and modeling large volumes of diverse data on cancer patients. The goal is to produce more accurate predictions of patient outcomes and to enable clinicians to tailor care for each patient. See the press release from CMU for more details.
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07/2015
Neuroscience-based algorithms make for better networks. A new paper we published in PLoS Computational Biology shows that the methods used by the brain to optimize the topology of neural networks (termed pruning) lead to effective and robust computational networks as well. As part of this work, we have experimentally characterized the pruning rates in developing mice and showed that using similar rates to construct computer communication networks improves their ability to efficiently route messages. This paper further expands the set of Algorithms in Nature we have been working on for the last 5 years. The work has been highlighted by a CMU press release , a press release from the Salk Institute, and a few other venues (for example, Tech Times )
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07/2015
Ercument Cicek accepts new faculty position. Ercument, who is a postdoc in our group since 2013 (also a Lane fellow co-advised by Kathryn Roeder) has accepted a faculty position in the Computer Science department at Bilkent University, one of the leading research universities in Turkey. We wish him good luck on this exciting new appointment!
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01/2015
CACM publishes a new paper from our group. Communication of the ACM (CACM), the top and most widely read computer science journal publishes a paper we wrote on biological distributed computing as the cover story for their first issue of 2015. The paper summarizes several recent studies by us and others in this area. With the success of the BDA workshop we recently organized it seems that this idea is catching up and more and more people are looking into biological systems to gain insights into the design of complex distributed networks and systems. See also an interview CACM recorded with co-author Saket Navlakha discussing the area and the paper.
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06/2014
Three group members accept new faculty positions. Current group members Saket Navlakha (postdoc MLD) and Xin He (Lane fellow and postdoc, co advised with K. Roeder) and former group member Tony Gitter (PhD 2012) will start as Assistant Prof. in the Fall. Saket is joining the Salk Institute for Biological Studies in San Diego. Xin will join the Human Genetics department at the Universtiy of Chicago and Tony will be joining Department of Biostatistics & Medical Informatics and the Morgridge Institute for Research at the University of Wisconsin, Madison. The diversity in terms of types of the departments each is joining indicates the growing importance of computational biology across areas ranging from basic science to clinical studies to statistics and computer science. Congratulations and good luck to all!
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05/2014
Yeast networks provide insights for improving computational network security . In a new paper in the journal Proceeding of the Royal Society Interface we discuss how lessons from yeast and other biological networks can be used to design and evaluate secure communication networks. The work has been highlighted by a CMU press release and a few other venues ( dataconomy , Campus Technology )
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11/2013
SDREM selected as a top systems biology paper. The RECOMB/ISCB Conference on Regulatory and Systems Genomics, selected the Top Ten Papers in the field of Regulatory and Systems Genomics for 2013. We were happy to see that our SDREM paper, that appeared in 2013 in Genome Research is part of that list. Congratulations to Tony!
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10/2013
ExpressionBlast mines large expression datasets. We report in a new paper in Nature Methods on a new web based tool, ExpressionBlast, that can be used to compare expression experiments, within and across species, to hundreds of thousands of arrays deposited in large databases. The tool provides an easy to use GUI and has already been used to successfully study improtant mammalian genes. ExpressionBlast is available online with documentation and support. See the CMU press release and CMU's front page coverage. The method was also highlighted by a number of news outlets including Bio-IT World.
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09/2013
mirDREM reconstructs development and disease networks. A new paper by Lane fellow Marcel Schulz was just published in the Proceedings of the National Academy of Science (PNAS). The paper introduces a new method for reconstructing dynamic regulatory networks that are co-regulated by transcription factors and microRNAs. The paper was featured on the cover of PNAS. In addition, PNAS published a very nice commentary explaining the importance of the method and application. The paper has also been highlighted in a number of news outlets including Nature's SciBX and GenomeWeb . The method can be downloaded from the supporting website.
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07/2013
Ziv Bar-Joseph receives a Scholars Award from the James S. McDonnell Foundation. Bar-Joseph is among six recipients of the 2013 James S. McDonnell Foundation Scholars Award in Studying Complex Systems.
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07/2013
Yanjun Qi accepts faculty position. Yanjun Qi who completed her PhD in our group in 2008, joins the Department of Computer Science at the University of Virginia as an Assistant Professor. Congratulations and good luck!
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05/2013
Hai-Son and Shan defend PhD thesis Hai-Son Le and Shan Zhong successfully defended their PhD thesis. Hai-Son's thesis focused on gene expression and molecular interactions while Shan focused on regulatory interactions and networks. Both will receive their PhD degrees during the 2013 commencement. Hai-Son is joining a hedge fund in Chicago while Shan will be running a clinical genomics lab for UPMC. Congratulations Hai-Son and Shan, and good luck!
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05/2013
Marcel accepts new faculty position Marcel Schulz, A Lane Fellow and postdoc in our group is joining the Computer Science department at Saarland University as an Assistant Prof. starting in June. He would also be affiliated with the Max-Planck-Institute for Informatics. Congratulations Marcel, and good luck!
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04/2013
Three ISMB papers This year, the International Conference on Intelligent Systems for Molecular Biology (ISMB) has been extremely selective, with only 40 of roughly 250 submission accepted (~15% rate). We were very fortunate that three of these papers are from our group. You can check them out at the ISMB Proceedings website.
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03/2013
Jason Ernst wins Sloan Fellowship Jason Ernst (PhD 2008) won the prestigious Sloan Fellowship for 2013 for his computational biology work. Congratulations!
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06/2012
News Article and Keynote Video A news article in the journal PLoS Computational Biology discusses work in our group and our contributions to the computational and systems biology field. The article accompanies the 2012 Overton Prize. As part of the award Prof. Bar-Joseph gave a keynote talk at the 2012 ISMB conference in Long Beach CA. The video of that talk is available here.
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05/2012
Two students defend PhD thesis Anthony (Tony) Gitter and Guy Zinman successfully defended their PhD thesis. Both received the PhD degree during the 2012 commencement. Tony has joined Microsoft Research New England as postdoc while Guy is staying at the Lane center for computational biology as a project scientists in charge of the 'Dr. In a Box' project.
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01/2012
Overton Prize Ziv Bar-Joseph has been named the Overton Prize winner for 2012. The Overton Prize is awarded annually by the International Society For Computational Biology (ISCB) for outstanding accomplishment by a mid-career faculty member (up to 10 years from PhD). You can read more about the award and our work in the CMU press release and this Post-Gazette article.
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11/2011
Algorithms in Nature we created a new website to collect references related to algorithmic work that was inspired by biological systems and, simultaneously, led to new biological insights. The website accompanies our recent Nature MSB Perspective article which discusses such bi-directional studies leadingthe convergence of computational thinking and systems biology.
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06/2011
Communications of the ACM featured a long article covering our work on biology-inspired networking and computing. The story discusses our recent MSB and Science papers which provide examples of bi-directional studies that attempts to understand biological systems while at the same time help improve networking and distributed computing algorithms.
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05/2011
Group member Marcel Schulz is the winner the 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 carried out under the supervision of Prof. Martin Vingron, entitled 'Data structures and algorithms for analysis of alternative splicing with RNA-seq data.' 26 medals representing the top 3% of all Ph.D students from 2010 among the nearly eighty Max Planck Institutes were awarded this year. Marcel is a Lane follow in our group.
- 03/2011
Henry (Tienho) Lin defends his thesis and earns a PhD degree! Henry joined the eScience Research Group at Microsoft Research as a postdoc.
- 01/2011
In a new paper in the journal Science we have shown that by studying in details a biological process in the developing fruit fly we can develop a new distributed computing algorithms that improves upon current solutions to a problem that has been studied for almost three decades. The work has attracted considerable media attention. Here are some examples: CMU release, SCS release, Pittsburgh Post-Gazette, Discovery news, MIT Technology Review, MSNBC, Popular Science.
- 12/2010
Work on orienting edges in biological interaction networks selected as a Featured Article by the editors of Nucleic Acids Research. According to the journals website: Featured articles represent the top 5% of papers in terms of originality, significance and scientific excellence. See also news on the Lane center website.
- 06/2009
New research from our group solves a biological mystery. In a paper published in the journal Nature Molecular and Systems Biology we show that the disagreement between the results of two complementary experiments is due to backup in gene regulatory networks. See the press release issued by CMU
- 05/2009
A letter to Science regarding the delays in release of the NRC graduate rankings.
- 08/2008 - Yanjun Qi, Jason Ernst and Yong Lu defend their PhD thesis's! Yanjun joined NEC research focusing on machine learning and computational biology. Jason is now a postdoc with Manolis Kellis at MIT and Yong is a postdoc with Fritz Roth at Harvard. See the People page for their new contact info and webpages.
- 05/2008
Of the roughly 100 papers to be presented at this years ISMB 2008, the largest and most selective computational biology conference, 4 are from our group. These include two regular track papers (by Yanjun Qi and Henry Lin) and two highlight track papers: Our Genome Biology paper on the analysis of cycling genes in four species and our PNAS paper on human cycling genes.
- 01/2008
A new paper we published in PNAS about the set of cell cycle genes in healthy and cancer human cells attracted national and local attention. The following are a few notable places reporting on our work: CMU press release , US News and World Report , Forbes.com , Pittsburgh Post-Gazette (front page story) , Channel 4 (local ABC affiliate).
- 9/2007
Jason Ernst is awarded the Siebel Scholarship. The Scholars Program recognizes the most talented students who have demonstrated academic and leadership excellence at the world's leading graduate schools of business and computer science.
- 7/2007
Our paper Reconstructing dynamic regulatory maps is selected as a highlight paper at ISMB the largest and most selective computational biology conference. The paper and associated software (DREM) have also received some nice blog coverage during the conference.
- 9/2006
Matlab releases the new Bioinformatics toolbox. This toolbox includes a new function implementing the optimal leaf ordering algorithm developed by our group.
- 1/2006
Our new software, STEM: Short Time-series Expression Miner, is featured in: CMU Tech Transfer Annual Report 2005 (page 14).
- 11/2005
Our recent Nature Biotechnology paper presenting a CheckSum method for determining the quality of time-series expression profiles is featured in: CMU press release , Pittsburgh Post Gazette , Drug Discovery & Development , Bio-IT World,Red Herring.
- 10/2005
We are part of the new NIH funded Center for Modeling Pulmonary Immunity: University of Pittsburgh press release, Pittsburgh Post Gazette .
- 7/2005
- 11/2004
Yanjun Qi wins Merck Graduate Fellowship for 2004-2005.