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by Vogel, John P and Garvin, David F and Mockler, Todd C and Schmutz, Jeremy and Rokhsar, Dan and Bevan, Michael W and Barry, Kerrie and Lucas, Susan and Harmon-Smith, Miranda and Lail, Kathleen and Tice, Hope and Grimwood, Jane and McKenzie, Neil and Huo, Naxin and Gu, Yong Q and Lazo, Gerard R and Anderson, Olin D and You, Frank M and Luo, Ming-Cheng and Dvorak, Jan and Wright, Jonathan and Febrer, Melanie and Idziak, Dominika and Hasterok, Robert and Lindquist, Erika and Wang, Mei and Fox, Samuel E and Priest, Henry D and Filichkin, Sergei A and Givan, Scott A and Bryant, Douglas W and Chang, Jeff H and Wu, Haiyan and Wu, Wei and Hsia, An-Ping and Schnable, Patrick S and Kalyanaraman, Anantharaman and Barbazuk, Brad and Michael, Todd P and Hazen, Samuel P and Bragg, Jennifer N and Laudencia-Chingcuanco, Debbie and Weng, Yiqun and Haberer, Georg and Spannagl, Manuel and Mayer, Klaus and Rattei, Thomas and Mitros, Therese and Lee, Sang-Jik and Rose, Jocelyn K. C and Mueller, Lukas A and York, Thomas L and Wicker, Thomas and Buchmann, Jan P and Tanskanen, Jaakko and Schulman, Alan H and Gundlach, Heidrun and Beven, Michael and Costa De Oliveira, Antonio and Da C. Maia, Luciano and Belknap, William and Jiang, Ning and Lai, Jinsheng and Zhu, Liucun and Ma, Jianxin and Sun, Cheng and Pritham, Ellen and Salse, Jerome and Murat, Florent and Abrouk, Michael and Bruggmann, Remy and Messing, Joachim and Fahlgren, Noah and Sullivan, Christopher M and Carrington, James C and Chapman, Elisabeth J and May, Greg D and Zhai, Jixian and Ganssmann, Matthias and Gurazada, Sai Guna Ranjan and German, Marcelo and Meyers, Blake C and Green, Pamela J and Tyler, Ludmila and Wu, Jiajie and Thomson, James and Chen, Shan and Scheller, Henrik V and Harholt, Jesper and Ulvskov, Peter and Kimbrel, Jeffrey A and Bartley, Laura E and Cao, Peijian and Jung, Ki-Hong and Sharma, Manoj K and Vega-Sanchez, Miguel and Ronald, Pamela and Dardick, Christopher D and De Bodt, Stefanie and Verelst, Wim and ... and Int Brachypodium Initiative and International Brachypodium Initiative and The International Brachypodium Initiative and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
Nature, ISSN 0028-0836, 02/2010, Volume 463, Issue 7282, pp. 763 - 768
Journal Article
Foundations and Trends in Electronic Design Automation, ISSN 1551-3939, 2016, Volume 10, Issue 3, pp. 145 - 247
Graph representations are pervasive in scientific and social computing. They serve as vital tools to model the interplay among different interacting entities.... 
Networks | Architecture | Computation | Communities | Organizations | Graphs | Graphical representations | Trends
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 06/2003, Volume 31, Issue 11, pp. 2963 - 2974
Clustering expressed sequence tags (ESTs) is a powerful strategy for gene identification, gene expression studies and identifying important genetic variations... 
SEQUENCES | BIOCHEMISTRY & MOLECULAR BIOLOGY | Arabidopsis - genetics | Consensus Sequence | Sequence Alignment | Algorithms | Plants - genetics | Time Factors | Computer Simulation | Software | Genome, Plant | Cluster Analysis | Expressed Sequence Tags | Quality Control | Index Medicus
Journal Article
Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, 04/2006, Volume 4, Issue 2, pp. 197 - 216
Journal Article
IEEE Transactions on Parallel and Distributed Systems, ISSN 1045-9219, 10/2012, Volume 23, Issue 10, pp. 1923 - 1933
Journal Article
Bioinformatics, ISSN 1367-4803, 11/2011, Volume 27, Issue 21, pp. 3072 - 3073
A MapReduce-based implementation called MR-MSPolygraph for parallelizing peptide identification from mass spectrometry data is presented. The underlying serial... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Sequence Analysis, Protein | Software | Peptides - chemistry | Mass Spectrometry - methods | Databases, Protein | Index Medicus | Applications Note
Journal Article
2014 21st International Conference on High Performance Computing (HiPC), ISSN 1094-7256, 12/2014, pp. 1 - 11
In an era when power constraints and data movement are proving to be significant barriers for the application of high-end computing, the Tilera many-core... 
Image color analysis | Multicore processing | Communities | Layout | parallel | many-core | Resource management | Tilera | community detection | Convergence | graph algorithms
Conference Proceeding
2016 45th International Conference on Parallel Processing (ICPP), ISSN 0190-3918, 08/2016, Volume 2016-, pp. 506 - 515
Vector extensions, such as SSE, have been part of the x86 since the 1990s, with applications in graphics, signal processing, and scientific applications.... 
Algorithm design and analysis | Databases | Heuristic algorithms | Signal processing algorithms | Dynamic programming | Registers | Bioinformatics
Conference Proceeding
Journal Article
2010 39th International Conference on Parallel Processing, ISSN 0190-3918, 09/2010, pp. 333 - 342
Protein sequence homology detection is a fundamental problem in computational molecular biology, with a pervasive application in nearly all analyses that aim... 
Image edge detection | Heuristic algorithms | Oceans | hierarchical master-worker paradigm | Parallel protein sequence homology detection | Protein sequence | parallel sequence graph construction | Indexes | Parallel algorithms | Parallel sequence graph construction | Hierarchical master-worker paradigm
Conference Proceeding
Journal of bioinformatics and computational biology, ISSN 0219-7200, 04/2006, Volume 4, Issue 2, pp. 197 - 216
LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for... 
Sequence Alignment - methods | Algorithms | Base Sequence | Chromosome Mapping - methods | Molecular Sequence Data | Software | Sequence Analysis, DNA - methods | Terminal Repeat Sequences - genetics | Retroelements - genetics
Journal Article
by John P.,Vogel and David F.,Garvin and Todd C.,Mockler and Jeremy,Schmutz and Dan,Rokhsar and Michael W.,Bevan and Kerrie,Barry and Susan,Lucas and Miranda,Harmon-Smith and Kathleen,Lail and Hope,Tice and Jeremy,Schmutz and Jane,Grimwood and Neil,McKenzie and Naxin,Huo and Yong Q.,Gu and Gerard R.,Lazo and Olin D.,Anderson and John P.,Vogel and Frank M.,You and Ming-Cheng,Luo and Jan,Dvorak and Jonathan,Wright and Melanie,Febrer and Dominika,Idziak and Robert,Hasterok and Erika,Lindquist and Mei,Wang and Samuel E.,Fox and Henry D.,Priest and Sergei A.,Filichkin and Scott A.,Givan and Douglas W.,Bryant and Jeff H.,Chang and Todd C.,Mockler and Haiyan,Wu and Wei,Wu and An-Ping,Hsia and Patrick S.,Schnable and Anantharaman,Kalyanaraman and Brad,Barbazuk and Todd P.,Michael and Samuel P.,Hazen and Jennifer N.,Bragg and Debbie,Laudencia-Chingcuanco and Yiqun,Weng and Georg,Haberer and Manuel,Spannagl and Klaus,Mayer and Thomas,Rattei and Therese,Mitros and Sang-Jik,Lee and Jocelyn K. C.,Rose and Lukas A.,Mueller and Thomas L.,York and Thomas,Wicker and Jan P.,Buchmann and Jaakko,Tanskanen and Alan H.,Schulman and Heidrun,Gundlach and Michael,Bevan and Antonio,Costa de Oliveira and Luciano,da C. Maia and William,Belknap and Ning,Jiang and Jinsheng,Lai and Liucun,Zhu and Jianxin,Ma and Cheng,Sun and Ellen,Pritham and Jerome,Salse and Florent,Murat and Michael,Abrouk and Klaus,Mayer and Remy,Bruggmann and Joachim,Messing and Noah,Fahlgren and Christopher M.,Sullivan and James C.,Carrington and Elisabeth J.,Chapman and Greg D.,May and Jixian,Zhai and Matthias,Ganssmann and Sai,Guna Ranjan Gurazada and Marcelo,German and Blake C.,Meyers and Pamela J.,Green and Ludmila,Tyler and Jiajie,Wu and James,Thomson and Shan,Chen and Henrik V.,Scheller and Jesper,Harholt and Peter,Ulvskov and Jeffrey A.,Kimbrel and Laura E.,Bartley and Peijian,Cao and Ki-Hong,Jung and Manoj K,Sharma and Miguel,Vega-Sanchez and ... and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 02/2010, Volume 463, Issue 7282
Journal Article
by John P.,Vogel and David F.,Garvin and Todd C.,Mockler and Jeremy,Schmutz and Dan,Rokhsar and Michael W.,Bevan and Kerrie,Barry and Susan,Lucas and Miranda,Harmon-Smith and Kathleen,Lail and Hope,Tice and Jeremy,Schmutz and Jane,Grimwood and Neil,McKenzie and Naxin,Huo and Yong Q.,Gu and Gerard R.,Lazo and Olin D.,Anderson and John P.,Vogel and Frank M.,You and Ming-Cheng,Luo and Jan,Dvorak and Jonathan,Wright and Melanie,Febrer and Dominika,Idziak and Robert,Hasterok and Erika,Lindquist and Mei,Wang and Samuel E.,Fox and Henry D.,Priest and Sergei A.,Filichkin and Scott A.,Givan and Douglas W.,Bryant and Jeff H.,Chang and Todd C.,Mockler and Haiyan,Wu and Wei,Wu and An-Ping,Hsia and Patrick S.,Schnable and Anantharaman,Kalyanaraman and Brad,Barbazuk and Todd P.,Michael and Samuel P.,Hazen and Jennifer N.,Bragg and Debbie,Laudencia-Chingcuanco and Yiqun,Weng and Georg,Haberer and Manuel,Spannagl and Klaus,Mayer and Thomas,Rattei and Therese,Mitros and Sang-Jik,Lee and Jocelyn K. C.,Rose and Lukas A.,Mueller and Thomas L.,York and Thomas,Wicker and Jan P.,Buchmann and Jaakko,Tanskanen and Alan H.,Schulman and Heidrun,Gundlach and Michael,Bevan and Antonio,Costa de Oliveira and Luciano,da C. Maia and William,Belknap and Ning,Jiang and Jinsheng,Lai and Liucun,Zhu and Jianxin,Ma and Cheng,Sun and Ellen,Pritham and Jerome,Salse and Florent,Murat and Michael,Abrouk and Klaus,Mayer and Remy,Bruggmann and Joachim,Messing and Noah,Fahlgren and Christopher M.,Sullivan and James C.,Carrington and Elisabeth J.,Chapman and Greg D.,May and Jixian,Zhai and Matthias,Ganssmann and Sai,Guna Ranjan Gurazada and Marcelo,German and Blake C.,Meyers and Pamela J.,Green and Ludmila,Tyler and Jiajie,Wu and James,Thomson and Shan,Chen and Henrik V.,Scheller and Jesper,Harholt and Peter,Ulvskov and Jeffrey A.,Kimbrel and Laura E.,Bartley and Peijian,Cao and Ki-Hong,Jung and Manoj K,Sharma and Miguel,Vega-Sanchez and ... and Joint Bioenergy Institute (JBEI)
Nature, ISSN 0028-0836, 02/2010, Volume 463, Issue 7282
Journal Article
by John P.,Vogel and David F.,Garvin and Todd C.,Mockler and Jeremy,Schmutz and Dan,Rokhsar and Michael W.,Bevan and Kerrie,Barry and Susan,Lucas and Miranda,Harmon-Smith and Kathleen,Lail and Hope,Tice and Jeremy,Schmutz and Jane,Grimwood and Neil,McKenzie and Naxin,Huo and Yong Q.,Gu and Gerard R.,Lazo and Olin D.,Anderson and John P.,Vogel and Frank M.,You and Ming-Cheng,Luo and Jan,Dvorak and Jonathan,Wright and Melanie,Febrer and Dominika,Idziak and Robert,Hasterok and Erika,Lindquist and Mei,Wang and Samuel E.,Fox and Henry D.,Priest and Sergei A.,Filichkin and Scott A.,Givan and Douglas W.,Bryant and Jeff H.,Chang and Todd C.,Mockler and Haiyan,Wu and Wei,Wu and An-Ping,Hsia and Patrick S.,Schnable and Anantharaman,Kalyanaraman and Brad,Barbazuk and Todd P.,Michael and Samuel P.,Hazen and Jennifer N.,Bragg and Debbie,Laudencia-Chingcuanco and Yiqun,Weng and Georg,Haberer and Manuel,Spannagl and Klaus,Mayer and Thomas,Rattei and Therese,Mitros and Sang-Jik,Lee and Jocelyn K. C.,Rose and Lukas A.,Mueller and Thomas L.,York and Thomas,Wicker and Jan P.,Buchmann and Jaakko,Tanskanen and Alan H.,Schulman and Heidrun,Gundlach and Michael,Bevan and Antonio,Costa de Oliveira and Luciano,da C. Maia and William,Belknap and Ning,Jiang and Jinsheng,Lai and Liucun,Zhu and Jianxin,Ma and Cheng,Sun and Ellen,Pritham and Jerome,Salse and Florent,Murat and Michael,Abrouk and Klaus,Mayer and Remy,Bruggmann and Joachim,Messing and Noah,Fahlgren and Christopher M.,Sullivan and James C.,Carrington and Elisabeth J.,Chapman and Greg D.,May and Jixian,Zhai and Matthias,Ganssmann and Sai,Guna Ranjan Gurazada and Marcelo,German and Blake C.,Meyers and Pamela J.,Green and Ludmila,Tyler and Jiajie,Wu and James,Thomson and Shan,Chen and Henrik V.,Scheller and Jesper,Harholt and Peter,Ulvskov and Jeffrey A.,Kimbrel and Laura E.,Bartley and Peijian,Cao and Ki-Hong,Jung and Manoj K,Sharma and Miguel,Vega-Sanchez and ... and Great Lakes Bioenergy Research Center (GLBRC)
Nature, ISSN 0028-0836, 02/2010, Volume 463, Issue 7282
Journal Article
01/2006, ISBN 9780542831911
The explosive growth in biological sequence data coupled with the design and deployment of increasingly high throughput sequencing technologies has created a... 
Computer science | Bioinformatics
Dissertation
2018 IEEE High Performance extreme Computing Conference (HPEC), 09/2018, pp. 1 - 7
Graph clustering, popularly known as community detection, is a fundamental graph operation used in many applications related to network analysis and... 
Heuristic algorithms | Color | Approximation algorithms | Partitioning algorithms | Compaction | Parallel algorithms | Convergence
Conference Proceeding
2017 IEEE High Performance Extreme Computing Conference (HPEC), 09/2017, pp. 1 - 6
Graph clustering, popularly known as community detection, is a fundamental kernel for several applications of relevance to the Defense Advanced Research... 
Image color analysis | Heuristic algorithms | Image edge detection | Approximate computing | Clustering algorithms | Approximation algorithms | Partitioning algorithms
Conference Proceeding
Proceedings - 2018 IEEE 32nd International Parallel and Distributed Processing Symposium, IPDPS 2018, 08/2018, pp. 885 - 895
Conference Proceeding
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