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Computing for the DOE genomes to life program

E. Uberbacher, D. Thomassen, A. Patrinos, G. Johnson, C.E. Oliver, M. Frazier
Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003  
A key goal of the DOE Office of Science's systems biology program, Genomes to Life (GTL), is to achieve, over the next 10 to 20 years, a basic understanding of thousands of environmental microbes and microbial  ...  The vast amount of information, contained in the hundreds of genomes sequenced and the thousands to come, offers an unprecedented opportunity to capture the behavior of complex microbial systems in mathematical  ...  Abstract A key goal of the DOE Office of Science's systems biology program, Genomes to Life (GTL), is to achieve, over the next 10 to 20 years, a basic understanding of thousands of environmental microbes  ... 
doi:10.1109/csb.2003.1227298 dblp:conf/csb/UberbacherTPJOF03 fatcat:dmx3b6ney5hutkhw3n5vbz366u

Genome to Life grants awarded

Eugene Russo
2002 Genome Biology  
The grants, part of the 10-year Genome to Life Project, were announced 23 July.  ...  Just as the DOE's initial contribution to the Human Genome Project led to further funding opportunities, Thomassen said, the Genome to Life Project grants should lay the groundwork for more lucrative follow-up  ... 
doi:10.1186/gb-spotlight-20020730-01 fatcat:orpwfusy7bhrjgvw435heqkswe

US DOE presents priorities

Eugene Russo
2003 Genome Biology  
The four recommended life science-related facilities are central elements of the DOE Genomes to Lifeprogram, according to Keith Hodgson, director of the Stanford Synchrotron Radiation Laboratory and chair  ...  Michelle Buchanan, director of the Center for Molecular and Cellular Systems at the Oak Ridge National Laboratory and the principal investigator of a Genomes to Life research awardinvolving the high-throughput  ... 
doi:10.1186/gb-spotlight-20031112-01 fatcat:e5axvqv4rfg5zgrv3vwqll6f4m

Realizing the Potential of the Genome Revolution: The Genomes to Life Program

M. E. Frazier
2003 Science  
To meet this challenge, the U.S. Department of Energy has developed the Genomes to Life (GTL) program.  ...  Genomes to Life To address this challenge, over the past 3 years hundreds of scientists from universities, national laboratories, and industry have helped DOE develop a research program called Genomes  ... 
doi:10.1126/science.1084566 pmid:12690188 fatcat:axgte64qyjbenfckhlnax2wwiy

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Henrik Nordberg, Michael Cantor, Serge Dusheyko, Susan Hua, Alexander Poliakov, Igor Shabalov, Tatyana Smirnova, Igor V. Grigoriev, Inna Dubchak
2013 Nucleic Acids Research  
Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis  ...  The JGI Genome Portal (http://genome. provides unified access to all JGI genomic databases and analytical tools.  ...  ACKNOWLEDGEMENTS We are thankful to the JGI user community for using Genome Portal tools and providing valuable feedback, to Arkady Voloshin for technical assistance, to the NERSC staff for constant support  ... 
doi:10.1093/nar/gkt1069 pmid:24225321 pmcid:PMC3965075 fatcat:wm6gmnw6jzgv5d3r3omj5ldk7i

Bacteria as computers making computers

Antoine Danchin
2009 FEMS Microbiology Reviews  
However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge.  ...  Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers.  ...  In silico and in vivo experiments have been supported by the PROBACTYS programme, grant CT-2006-029104, in an effort to define genes essential for the construction of a synthetic cell, and the BioSapiens  ... 
doi:10.1111/j.1574-6976.2008.00137.x pmid:19016882 pmcid:PMC2704931 fatcat:plzhvj5wmjf4xir7vei6nuzw7a

Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students

Jennifer McQueen, Jody J. Wright, Joanne A. Fox, Fran Lewitter
2012 PLoS Computational Biology  
With the rapid pace of advancements in biological research brought about by the application of computer science and information technology, we believe the time is right for introducing genomics and bioinformatics  ...  tools and concepts to secondary school students.  ...  Acknowledgments We would like to acknowledge the secondary school students who have attended the outreach programs offered at the Michael Smith Labo-ratories and shared their enthusiasm for science with  ... 
doi:10.1371/journal.pcbi.1002636 pmid:22956895 pmcid:PMC3431290 fatcat:bzqy3hfkgjekxlp4rorym7vgq4

The biology of digital organisms

Claus O. Wilke, Christoph Adami
2002 Trends in Ecology & Evolution  
computer programs.  ...  Future research directions Digital life genetics To a human eye, the genome of an evolved digital organism appears to be a random collection of computer instructions, assembled without any planning or  ... 
doi:10.1016/s0169-5347(02)02612-5 fatcat:ucejywjwrbab3m5cpzw4qg7u7q

Will biologists become computer scientists?

Anne Condon, Hélène Kirchner, Damien Larivière, Wallace Marshall, Vincent Noireaux, Tsvi Tlusty, Eric Fourmentin
2018 EMBO Reports  
Acknowledgements The organizers are grateful to the 21 participants Conflict of interest The authors declare that they have no conflict of interest. Venter JC (2007) Genome transplantation in  ...  Like in a computer, in which a program does not run if it is not properly recognized by the machine, one cannot expect any genome transplantation to be productive.  ...  The architecture and programming of man-made computers should stimulate new questions for biologists: if the analogy holds, what does the cellular hardware do?  ... 
doi:10.15252/embr.201846628 pmid:30061101 pmcid:PMC6123653 fatcat:to45yly3urcqhf3sbgaossbknu

The GS (genetic selection) Principle

David, L. Abel
2009 Frontiers in Bioscience  
Even epigenetic and "genomic" factors such as regulation by DNA methylation, histone proteins and microRNAs are ultimately instructed by prior linear digital programming.  ...  All life depends upon literal genetic algorithms.  ...  What would be the basis of natural selection for a half-written program that does not yet compute?  ... 
doi:10.2741/3426 pmid:19273248 fatcat:zbarzxew3bfrjoyra7r7j4stcy

Scaling up synthetic biology: Do not forget the chassis

Antoine Danchin
2012 FEBS Letters  
Using comparative genomics and functional analysis, this work summarises how the cell's genome is organised, with emphasis on the importance of the cell's chassis.  ...  Subsequently, to illustrate overlooked essential functions, we show the importance of safety valves, as well as the need to cope with leftovers.  ...  Acknowledgement This work was supported by the FP7 European Union programme Microme KBBE-2007-3-2-08-222886-2 grant.  ... 
doi:10.1016/j.febslet.2011.12.024 pmid:22226636 fatcat:csurazbzvvf53bkoxz4455uu54

Integrating emerging areas of nursing science into PhD programs

Susan J. Henly, Donna O. McCarthy, Jean F. Wyman, Patricia W. Stone, Nancy S. Redeker, Ann Marie McCarthy, Anna C. Alt-White, Jacqueline Dunbar-Jacob, Marita G. Titler, Shirley M. Moore, Margaret M. Heitkemper, Yvette P. Conley
2015 Nursing Outlook  
Acknowledgments Yvonne Bryan, PhD, served as the NINR liaison for this work. Laura Smothers, MPA, Manager, Council for the Advancement of Nursing Science, provided logistical and advisory support.  ...  The University of Minnesota School of Nursing, Public Health and Systems Cooperative Unit provided phone conferencing for IFAC. Their contributions are acknowledged with appreciation.  ...  Elsevier does not grant permission for this article to be further copied/distributed or hosted elsewhere without the express permission from Elsevier. 8 The explosion of genomics knowledge since 2004  ... 
doi:10.1016/j.outlook.2015.04.010 pmid:26187080 fatcat:n2x4cevax5d2zg7ljnepsebsgq

Genome Diversity: A Grammar of Microbial Genomes

Antoine Danchin
2004 ComPlexUs  
The metaphor of the genetic program is ubiquitously used. Does it bring about a deeper insight into what cells are? In brief, computers do not make computers, but cells make cells.  ...  Pursuing the analogy in its deepest consequences we explore bacterial genome diversity as organized around core programs meant to couple the expression of the program with the architecture of the cell.  ...  Acknowledgments This work was supported by the BioSapiens program contract LSHG-CT-2003-503265.  ... 
doi:10.1159/000089983 fatcat:wrnlx5wpzneazoidcudq2dsphi

Epigenetic Regulation of the Protein Translation Machinery

Michelle L Holland
2017 EBioMedicine  
Furthermore, a recent study has also implicated rDNA as a part of the genome that is responsive to early life dietary exposures in a mouse model of developmental programming.  ...  genomic output and give rise to phenotypic variation that does not follow expected inheritance patterns.  ...  Author Disclosure The author declares no competing influences.  ... 
doi:10.1016/j.ebiom.2017.02.018 pmid:28238697 pmcid:PMC5360576 fatcat:4heyvrvbjzg4vkltltdoqos5xq

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors

Yingqian Ada Zhan, Charles Gregory Wray, Sandeep Namburi, Spencer T. Glantz, Reinhard Laubenbacher, Jeffrey H. Chuang, Francis Ouellette
2019 PLoS Computational Biology  
One significant obstacle pointed out by the Network for Integrating Bioinformatics into Life Sciences Education is the lack of faculty in the bioinformatics area.  ...  Consequently, a great number of undergraduate and graduate students do not get the chance to learn bioinformatics or computational biology skills within a structured curriculum during their education.  ...  Acknowledgments We would like to thank all the speakers and organizers. We also thank all the course attendees, who provided critical feedback and comments during each session.  ... 
doi:10.1371/journal.pcbi.1007026 pmid:31194735 pmcid:PMC6563947 fatcat:brett5zlsnb5dnf3vupstut5ea
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