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1. Full Text Special Issue on Data-Intensive Scalable Computing Systems
by Roth, Philip C and Canon, R. Shane and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Parallel Computing, ISSN 0167-8191, 01/2017, Volume 61, Issue C, pp. 1 - 2
Traditional high performance computing (HPC) systems were designed from a compute-centric perspective, with an emphasis on high floating point performance. As... 
COMPUTER SCIENCE, THEORY & METHODS | MATHEMATICS AND COMPUTING
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2. Full Text Structure, function and diversity of the healthy human microbiome
by Huttenhower, Curtis and Gevers, Dirk and Knight, Rob and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Creasy, Heather H and Earl, Ashlee M and Fitzgerald, Michael G and Fulton, Robert S and Giglio, Michelle G and Hallsworth-Pepin, Kymberlie and Lobos, Elizabeth A and Madupu, Ramana and Magrini, Vincent and Martin, John C and Mitreva, Makedonka and Muzny, Donna M and Sodergren, Erica J and Versalovic, James and Wollam, Aye M and Worley, Kim C and Wortman, Jennifer R and Young, Sarah K and Zeng, Qiandong and Aagaard, Kjersti M and Abolude, Olukemi O and Allen-Vercoe, Emma and Alm, Eric J and Alvarado, Lucia and Andersen, Gary L and Anderson, Scott and Appelbaum, Elizabeth and Arachchi, Harindra M and Armitage, Gary and Arze, Cesar A and Ayvaz, Tulin and Baker, Carl C and Begg, Lisa and Belachew, Tsegahiwot and Bhonagiri, Veena and Bihan, Monika and Blaser, Martin J and Bloom, Toby and Bonazzi, Vivien and Paul Brooks, J and Buck, Gregory A and Buhay, Christian J and Busam, Dana A and Campbell, Joseph L and Canon, Shane R and Cantarel, Brandi L and Chain, Patrick S. G and Chen, I-Min A and Chen, Lei and Chhibba, Shaila and Chu, Ken and Ciulla, Dawn M and Clemente, Jose C and Clifton, Sandra W and Conlan, Sean and Crabtree, Jonathan and Cutting, Mary A and Davidovics, Noam J and Davis, Catherine C and Desantis, Todd Z and Deal, Carolyn and Delehaunty, Kimberley D and Dewhirst, Floyd E and Deych, Elena and Ding, Yan and Dooling, David J and Dugan, Shannon P and Michael Dunne, Wm and Scott Durkin, A and Edgar, Robert C and Erlich, Rachel L and Farmer, Candace N and Farrell, Ruth M and Faust, Karoline and Feldgarden, Michael and Felix, Victor M and Fisher, Sheila and Fodor, Anthony A and Forney, Larry J and Foster, Leslie and Di Francesco, Valentina and Friedman, Jonathan and Friedrich, Dennis C and Fronick, Catrina C and Fulton, Lucinda L and Gao, Hongyu and Garcia, Nathalia and Giannoukos, Georgia and Giblin, Christina and Giovanni, Maria Y and Goldberg, Jonathan M and Goll, Johannes and Gonzalez, Antonio and Griggs, Allison and ... and Human Microbiome Project Consortiu and Human Microbiome Project Consortium and The Human Microbiome Project Consortium and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2012, Volume 486, Issue 7402, pp. 207 - 214
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and... 
IDENTIFICATION | BACTERIA | MULTIDISCIPLINARY SCIENCES | Metagenomics | Health | Humans | Male | Biodiversity | Bacteria - genetics | Young Adult | Phenotype | Ecosystem | Adolescent | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Adult | Female | Metabolic Networks and Pathways - physiology | Metagenome | Microbiota (Symbiotic organisms) | Research | Biological diversity | Microbiology | Disease | Habitats | Taxonomy | Data processing | Skin | Life sciences | Genomes
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3. Full Text A framework for human microbiome research
by Methé, Barbara A and Nelson, Karen E and Pop, Mihai and Creasy, Heather H and Giglio, Michelle G and Huttenhower, Curtis and Gevers, Dirk and Petrosino, Joseph F and Abubucker, Sahar and Badger, Jonathan H and Chinwalla, Asif T and Earl, Ashlee M and Fitzgerald, Michael G and Fulton, Robert S and Hallsworth-Pepin, Kymberlie and Lobos, Elizabeth A and Madupu, Ramana and Magrini, Vincent and Martin, John C and Mitreva, Makedonka and Muzny, Donna M and Sodergren, Erica J and Versalovic, James and Wollam, Aye M and Worley, Kim C and Wortman, Jennifer R and Young, Sarah K and Zeng, Qiandong and Aagaard, Kjersti M and Abolude, Olukemi O and Allen-Vercoe, Emma and Alm, Eric J and Alvarado, Lucia and Andersen, Gary L and Anderson, Scott and Appelbaum, Elizabeth and Arachchi, Harindra M and Armitage, Gary and Arze, Cesar A and Ayvaz, Tulin and Baker, Carl C and Begg, Lisa and Belachew, Tsegahiwot and Bhonagiri, Veena and Bihan, Monika and Blaser, Martin J and Bloom, Toby and Bonazzi, Vivien R and Brooks, Paul and Buck, Gregory A and Buhay, Christian J and Busam, Dana A and Campbell, Joseph L and Canon, Shane R and Cantarel, Brandi L and Chain, Patrick S and Chen, I-Min A and Chen, Lei and Chhibba, Shaila and Chu, Ken and Ciulla, Dawn M and Clemente, Jose C and Clifton, Sandra W and Conlan, Sean and Crabtree, Jonathan and Cutting, Mary A and Davidovics, Noam J and Davis, Catherine C and Desantis, Todd Z and Deal, Carolyn and Delehaunty, Kimberley D and Dewhirst, Floyd E and Deych, Elena and Ding, Yan and Dooling, David J and Dugan, Shannon P and Michael Dunne, W and Scott Durkin, A and Edgar, Robert C and Erlich, Rachel L and Farmer, Candace N and Farrell, Ruth M and Faust, Karoline and Feldgarden, Michael and Felix, Victor M and Fisher, Sheila and Fodor, Anthony A and Forney, Larry and Foster, Leslie and Di Francesco, Valentina and Friedman, Jonathan and Friedrich, Dennis C and Fronick, Catrina C and Fulton, Lucinda L and Gao, Hongyu and Garcia, Nathalia and Giannoukos, Georgia and Giblin, Christina and Giovanni, Maria Y and Goldberg, Jonathan M and ... and Human Microbiome Project Consortiu and Human Microbiome Project Consortium and The Human Microbiome Project Consortium and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 06/2012, Volume 486, Issue 7402, pp. 215 - 221
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The... 
MULTIDISCIPLINARY SCIENCES | CATALOG | Young Adult | Reference Standards | Humans | Adolescent | Metagenomics - methods | RNA, Ribosomal, 16S - genetics | Adult | Female | Male | Statistics as Topic | Bacteria - genetics | Metagenome | Genetic research | Microbiological research | Genomes | Research | Microbiota (Symbiotic organisms) | Studies | Medicine | Microbiology | Publications | Taxonomy | Genomics | Data processing | Manuscripts
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4. Full Text Evaluating Interconnect and Virtualization Performance forHigh Performance Computing
by Ramakrishnan, Lavanya and Canon, R. Shane and Muriki, Krishna and Sakrejda, Iwona and Wright, Nicholas J
ACM SIGMETRICS Performance Evaluation Review, ISSN 0163-5999, 10/2012, Volume 40, Issue 2, p. 55
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5. Full Text Cori: A pre-exascale supercomputer for big data and HPC applications
by Wright, Nicholas J and Dosanjh, Sudip S and Andrews, Allison K and Antypas, Katerina B and Draney, Brent and Canon, R. Shane and Cholia, Shreyas and Daley, Christopher S and Fagnan, Kirsten M and Gerber, Richard A and Gerhardt, Lisa and Pezzaglia, Larry and Prabhat, A and Schafer, Karen H and Srinivasan, Jay
Advances in Parallel Computing, ISSN 0927-5452, 2015, Volume 26, pp. 82 - 100
Exascale computing | materials science | high energy physics | extreme data science | genomics | climate
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6. Full Text I/O performance of virtualized cloud environments
by Ghoshal, Devarshi and Canon, Richard and Ramakrishnan, Lavanya
Proceedings of the second international workshop on data intensive computing in the clouds, 11/2011, pp. 71 - 80
The scientific community is exploring the suitability of cloud infrastructure to handle High Performance Computing (HPC) applications. The goal of Magellan, a... 
cloud | I/O benchmarking | virtual environments | Virtual environments | Cloud
Conference Proceeding
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7. Full Text Empirical Analysis of a Large-Scale Hierarchical Storage System
by Yu, Weikuan and Oral, H Sarp and Canon, R Shane and Vetter, Jeffrey S and Sankaran, Ramanan
2008, Lecture Notes in Computer Science, ISBN 3540854509, Volume 5168
To prepare for future peta- or exa-scale computing, it is important to gain a good understanding on what impacts a hierarchical storage system would have on... 
Computer Systems Organization and Communication Networks | Software Engineering | Computer Science | Database Management | Numeric Computing | Theory of Computation | System Performance and Evaluation
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8. Full Text Evaluating interconnect and virtualization performance for high performance computing
by Ramakrishnan, Lavanya and Canon, Richard and Muriki, Krishna and Sakrejda, Iwona and Wright, Nicholas
Proceedings of the second international workshop on performance modeling, benchmarking and simulation of high performance computing systems, 11/2011, pp. 1 - 2
Scientists are increasingly considering cloud computing platforms to satisfy their computational needs. Previous work has shown that virtualized cloud... 
cloud | performance | interconnects | virtualization | Performance | Interconnects | Virtualization | Cloud
Conference Proceeding
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9. Full Text Exploiting Lustre File Joining for Effective Collective IO
by Weikuan Yu and Vetter, J and Canon, R.S and Song Jiang
Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07), 05/2007, pp. 267 - 274
Lustre is a parallel file system that presents high aggregated IO bandwidth by striping file extents across many storage devices. However, our experiments... 
Degradation | Software libraries | File systems | Scalability | Laboratories | Prototypes | Bandwidth | Writing | Biology computing | Application software
Conference Proceeding
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10. Full Text OPAL: An Open-Source MPI-IO Library over Cray XT
by Weikuan Yu and Vetter, J.S and Canon, R.S
Fourth International Workshop on Storage Network Architecture and Parallel I/Os (SNAPI 2007), 09/2007, pp. 41 - 46
Parallel I/O over Cray XT is supported by a vendor-supplied MPI-IO package. This package contains a proprietary ADIO implementation built on top of the sysio... 
Software maintenance | Software libraries | File systems | Operating systems | Linux | Laboratories | Packaging | File servers | Kernel | Open source software
Conference Proceeding
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11. Full Text KBase: The United States department of energy systems biology knowledgebase
by Arkin, Adam P and Cottingham, Robert W and Henry, Christopher S and Harris, Nomi L and Stevens, Rick L and Maslov, Sergei and Dehal, Paramvir and Ware, Doreen and Perez, Fernando and Canon, Shane and Sneddon, Michael W and Henderson, Matthew L and Riehl, William J and Murphy-Olson, Dan and Chan, Stephen Y and Kamimura, Roy T and Kumari, Sunita and Drake, Meghan M and Brettin, Thomas S and Glass, Elizabeth M and Chivian, Dylan and Gunter, Dan and Weston, David J and Allen, Benjamin H and Baumohl, Jason and Best, Aaron A and Bowen, Ben and Brenner, Steven E and Bun, Christopher C and Chandonia, John-Marc and Chia, Jer-Ming and Colasanti, Ric and Conrad, Neal and Davis, James J and Davison, Brian H and Dejongh, Matthew and Devoid, Scott and Dietrich, Emily and Dubchak, Inna and Edirisinghe, Janaka N and Fang, Gang and Faria, José P and Frybarger, Paul M and Gerlach, Wolfgang and Gerstein, Mark and Greiner, Annette and Gurtowski, James and Haun, Holly L and He, Fei and Jain, Rashmi and Joachimiak, Marcin P and Keegan, Kevin P and Kondo, Shinnosuke and Kumar, Vivek and Land, Miriam L and Meyer, Folker and Mills, Marissa and Novichkov, Pavel S and Oh, Taeyun and Olsen, Gary J and Olson, Robert and Parrello, Bruce and Pasternak, Shiran and Pearson, Erik and Poon, Sarah S and Price, Gavin A and Ramakrishnan, Srividya and Ranjan, Priya and Ronald, Pamela C and Schatz, Michael C and Seaver, Samuel M.D and Shukla, Maulik and Sutormin, Roman A and Syed, Mustafa H and Thomason, James and Tintle, Nathan L and Wang, Daifeng and Xia, Fangfang and Yoo, Hyunseung and Yoo, Shinjae and Yu, Dantong and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Nature Biotechnology, ISSN 1087-0156, 07/2018, Volume 36, Issue 7, pp. 566 - 569
The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand... 
DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Technology application | Usage | Databases | Genomics | Government agencies | Energy policy | Knowledge base | KNOWLEDGE MANAGEMENT AND PRESERVATION | BASIC BIOLOGICAL SCIENCES | MATHEMATICS AND COMPUTING
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12. Full Text A non-randomized dose-escalation Phase I trial of a protein-based immunotherapeutic for the treatment of breast cancer patients with HER2-overexpressing tumors
by Limentani, Steven A and Campone, Mario and Dorval, Thierry and Curigliano, Giuseppe and de Boer, Richard and Vogel, Charles and White, Shane and Bachelot, Thomas and Canon, Jean-Luc and Disis, Mary and Awada, Ahmad and Berlière, Martine and Amant, Frédéric and Levine, Ellis and Burny, Wivine and Callegaro, Andrea and de Sousa Alves, Pedro Miguel and Louahed, Jamila and Brichard, Vincent and Lehmann, Frédéric F
Breast Cancer Research and Treatment, ISSN 0167-6806, 4/2016, Volume 156, Issue 2, pp. 319 - 330
This Phase I dose-escalation study (NCT00058526) assessed the safety and immunogenicity of an anti-cancer immunotherapeutic (recombinant HER2 protein (dHER2)... 
Oncology | Cancer immunotherapeutic | Vaccine | dHER2 protein | Medicine & Public Health | HER2-overexpressing breast cancer | SURVIVAL | CLINICAL-TRIAL | TRASTUZUMAB | HER-2/NEU PROTEIN | VACCINATION | T-CELL | PERTUZUMAB | IMMUNIZATION | ONCOLOGY | HER2 | METASTATIC BREAST | Up-Regulation | Drug Administration Schedule | Humans | Middle Aged | Gene Expression Regulation, Neoplastic | Immunologic Factors - administration & dosage | Receptor, ErbB-2 - metabolism | Treatment Outcome | Recombinant Proteins - administration & dosage | Breast Neoplasms - metabolism | Breast Neoplasms - therapy | Dose-Response Relationship, Drug | Drug Dosage Calculations | Recombinant Proteins - immunology | Immunotherapy | Survival Analysis | Adult | Female | Aged | Immunologic Factors - adverse effects | Receptor, ErbB-2 - immunology | Viral antibodies | Cancer patients | Care and treatment | Clinical trials | Antibodies | Breast cancer | Drug therapy | Cancer | Index Medicus
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13. Full Text RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer
by Rao, Shuan and Sigl, Verena and Wimmer, Reiner Alois and Novatchkova, Maria and Jais, Alexander and Wagner, Gabriel and Handschuh, Stephan and Uribesalgo, Iris and Hagelkruys, Astrid and Kozieradzki, Ivona and Tortola, Luigi and Nitsch, Roberto and Cronin, Shane J and Orthofer, Michael and Branstetter, Daniel and Canon, Jude and Rossi, John and D’Arcangelo, Manolo and Botling, Johan and Micke, Patrick and La Fleur, Linnea and Edlund, Karolina and Bergqvist, Michael and Ekman, Simon and Lendl, Thomas and Popper, Helmut and Takayanagi, Hiroshi and Kenner, Lukas and Hirsch, Fred R and Dougall, William and Penninger, Josef M and Medicinska fakulteten and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för immunologi, genetik och patologi and Uppsala universitet and Klinisk och experimentell patologi
Genes and Development, ISSN 0890-9369, 10/2017, Volume 31, Issue 20, pp. 2099 - 2111
Lung cancer is the leading cause of cancer deaths. Besides smoking, epidemiological studies have linked female sex hormones to lung cancer in women; however,... 
Energy homeostasis | Lung cancer stem-like cells | RANK | Lung cancer | PROGESTERONE-RECEPTORS | DENOSUMAB | TUMOR | DEVELOPMENTAL BIOLOGY | CELL BIOLOGY | lung cancer | lung cancer stem-like cells | K-RAS | GENETICS & HEREDITY | ESTROGEN | BONE | energy homeostasis | OSTEOCLAST DIFFERENTIATION | EXPRESSION | PROGRESSION | MAMMARY-GLAND | Lung Neoplasms - drug therapy | Receptor Activator of Nuclear Factor-kappa B - antagonists & inhibitors | Proto-Oncogene Proteins p21(ras) - genetics | Humans | Lung Neoplasms - metabolism | Cells, Cultured | Homeostasis | Male | Alveolar Epithelial Cells - metabolism | Mitochondria - metabolism | Receptor Activator of Nuclear Factor-kappa B - physiology | Gonadal Steroid Hormones - physiology | Animals | Cell Respiration | Energy Metabolism | Neoplastic Stem Cells - metabolism | Receptor Activator of Nuclear Factor-kappa B - genetics | Female | Lung - metabolism | Mice | Receptor Activator of Nuclear Factor-kappa B - metabolism | Respiratory Mucosa - metabolism | Genetic aspects | Research | Risk factors | Cancer cells | Research Paper | Clinical Medicine | Medical and Health Sciences | Medicin och hälsovetenskap | Cancer and Oncology | Klinisk medicin | Cancer och onkologi
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