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It takes glue to tango: MeDICi integration framework's data-intensive computing pipeline

Scientific Computing 2008年第7期25卷 16-19页

作者： Gorton, Ian Oehmen, Christopher S. McDermott, Hason E. PNNL's Data Intensive Computing Program United States Laboratory's Bioinformatics and Computational Biology Group Fundamental and Computational Sciences Directorate United States

Researchers at the Department of Energy's (DOE) Pacific Northwest National Laboratory (PNNL) in Richland, WA, are creating computing environments for biologists that seamlessly integrate collections of data and computational resources. MeDICi is an evolving middleware platform for building complex, high-performance analytical applications. MIF components are constructed using Java programming interfaces that support inter-component communication using asynchronous messaging. Local components execute inside the MIF container. Remote components create distributed solutions and integrate with non-Java code. Mule provides the MIF container environment. MIF extends the Mule interface to make component and pipeline construction easier and to create an encapsulation device for component creation. The MIF interface is agnostic of the underlying Java messaging platform. This allows deployments to configure MIF applications using technologies that meet individual quality-of-service requirements.

关键词： Containers

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Grappling with the Gulf

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Science 2009年第5911期323卷 210页

作者： Dov Greenbaum Mark Gerstein Mcdermott Will and Emory LLP 3150 Porter Drive Palo Alto CA 94304 USA. Department of Molecular Biophysics and Biochemistry Program in Computational Biology and Bioinformatics and Department of Computer Science Yale University New Haven CT 06520 USA.

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Volumetric, cortical thickness and grey matter density changes on MRI over 12 months: Relationship to conversion status in the ADNI cohort

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Alzheimer's & Dementia 2009年第4期5卷 P200-P200页

作者： Shannon L. Risacher Andrew J. Saykin Li Shen John D. West Sungeun Kim Brenna C. McDonald Center for Neuroimaging Division of Imaging Sciences Department of Radiology Indiana University School of Medicine Indianapolis IN USA Medical Neuroscience Program Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN USA Indiana Alzheimer Disease Center Indianapolis IN USA Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN USA

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Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement

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Journal of bioinformatics and computational biology 2008年第2期6卷 283-300页

作者： Cui, Feng Jernigan, Robert Wu, Zhijun Laboratory of Cell Biology National Cancer Institute National Institutes of Health Bethesda MD 20892 United States Program on Bioinformatics and Computational Biology Iowa State University Ames IA 50011 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50011 United States Department of Mathematics Iowa State University Ames IA 50011 United States

Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints - NOE, torsion angle, or knowledge-based constraints - or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter. © 2008 Imperial College Press.

关键词： Knowledge-based distance constraints NMR structure refinement NOE distance constraints Precision and accuracy of NMR structures Torsion angle constraints

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Developmental systems biology flourishing on new technologies

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Journal of Genetics and Genomics 2008年第10期35卷 577-584页

作者： Jing-Dong J. Han Yi Liu Huiling Xue Kai Xia Hong Yu Shanshan Zhu Zhang Chen Wei Zhang Zheng Huang Chunyu Jin Bo Xian Jing Li Lei Hou Yixing Han Chaoqun Niu Timothy C. Alcon Chinese Academy of Sciences Key Laboratory of Molecular Developmental Biology Center for Molecular Systems Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Key Laboratory of Machine Perception （Ministry of Education） Peking University Beijing 100871 China Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA 50011-1040 USA

Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.

关键词： developmental systems biology new technologies symposium

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13th Pacific Symposium on Biocomputing, PSB 2008

作者： Lee, Jae-Hyung Hamilton, Michael Gleeson, Colin Caragea, Cornelia Zaback, Peter Sander, Jeffry D. Li, Xue Wu, Feihong Terribilini, Michael Honavar, Vasant Dobbs, Drena Bioinformatics and Computational Biology Program L.H. Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames IA 50010 United States Dept. of Genetics Development and Cell Biology Discovery Iowa State University Ames IA 50010 United States Dept. of Computer Science Iowa State University Ames IA 50010 United States Artificial Intelligence Research Lab Center for Computational Intelligence Learning and Discovery Iowa State University Ames IA 50010 United States Dept. of Computer Science Colorado State University Fort Collins CO 80523 United States Dept. of Biological Sciences Univ. of Illinois Chicago IL 60607 United States

ISBN: (纸本)9812776087

Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA repeat sequences to the ends of linear chromosomes. The enzyme plays pivotal roles in cellular senescence and aging, and because it provides a telomere maintenance mechanism for ∼90% of human cancers, it is a promising target for cancer therapy. Despite its importance, a high-resolution structure of the telomerase enzyme has been elusive, although a crystal structure of an N-terminal domain (TEN) of the telomerase reverse transcriptase subunit (TERT) from Tetrahymena has been reported. In this study, we used a comparative strategy, in which sequence-based machine learning approaches were integrated with computational structural modeling, to explore the potential conservation of structural and functional features of TERT in phylogenetically diverse species. We generated structural models of the N-terminal domains from human and yeast TERT using a combination of threading and homology modeling with the Tetrahymena TEN structure as a template. Comparative analysis of predicted and experimentally verified DNA and RNA binding residues, in the context of these structures, revealed significant similarities in nucleic acid binding surfaces of Tetrahymena and human TEN domains. In addition, the combined evidence from machine learning and structural modeling identified several specific amino acids that are likely to play a role in binding DNA or RNA, but for which no experimental evidence is currently available. © 2008 World Scientific Publishing Co. Pte. Ltd.

关键词： Enzymes

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Unexpected failure rates for modular assembly of engineered zinc fingers (vol 5, pg 374, 2008)

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NATURE METHODS 2008年第6期5卷 575-575页

作者： Ramirez, Cherie L. Foley, Jonathan E. Wright, David A. Mueller-Lerch, Felix Rahman, Shamim H. Cornu, Tatjana I. Winfrey, Ronnie J. Sander, Jeffry D. Fu, Fengli Townsend, Jeffrey A. Cathomen, Toni Voytas, Daniel F. Joung, J. Keith These authors contributed equally to this work. These authors contributed equally to this work. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Interdepartmental Graduate Program in Bioinformatics and Computational Biology 2114 Molecular Biology Building Iowa State University Ames Iowa 50011 USA. Interdepartmental Graduate Program in Bioinformatics and Computational Biology 2114 Molecular Biology Building Iowa State University Ames Iowa 50011 USA. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Department of Pathology Harvard Medical School Boston Massachusetts 02115 USA.

A letter to the editor is presented in response to an article on zinc fingers in a previous issue.

关键词： LETTERS to the editor ZINC

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Large-scale analysis of human heavy chain V(D)J recombination patterns

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Immunome Research 2008年第1期4卷 3-3页

作者： Volpe, Joseph M Kepler, Thomas B Center for Computational Immunology Duke University Durham NC United States Department of Immunology Duke Univeristy Medical Center Durham NC United States Department of Biostatistics and Bioinformatics Duke Univeristy Medical Center Durham NC United States Institute of Statistics and Decision Sciences Duke Univeristy Durham NC United States Computational Biology and Bioinformatics Graduate Program Institute for Genome Sciences and Policy Duke Univeristy Durham NC United States

Background. The processes involved in the somatic assembly of antigen receptor genes are unique to the immune system and are driven largely by random events. Subtle biases, however, may exist and provide clues to the molecular mechanisms involved in their assembly and selection. Large-scale efforts to provide baseline data about the genetic characteristics of immunoglobulin (Ig) genes and the mechanisms involved in their assembly have recently become possible due to the rapid growth of genetic databases. Results. We gathered and analyzed nearly 6,500 productive human Ig heavy chain genes and compared them with 325 non-productive Ig genes that were originally rearranged out of frame and therefore incapable of being biased by selection. We found evidence for differences in n-nucleotide tract length distributions which have interesting interpretations for the mechanisms involved in n-nucleotide polymerization. Additionally, we found striking statistical evidence for pairing preferences among D and J segments. We present a statistical model to support our hypothesis that these pairing biases are due to multiple sequential D-to-J rearrangements. Conclusion. We present here the most precise estimates of gene segment usage frequencies currently available along with analyses regarding n-nucleotide distributions and D-J segment pair preferences. Additionally, we provide the first statistical evidence that sequential D-J recombinations occur at the human heavy chain locus during B-cell ontogeny with an approximate frequency of 20%.

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Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

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Molecular Systems biology 2008年第1期4卷 198页

作者： Kunin, Victor Raes, Jeroen Harris, J. Kirk Spear, John R. Walker, Jeffrey J. Ivanova, Natalia Von Mering, Christian Bebout, Brad M. Pace, Norman R. Bork, Peer Hugenholtz, Philip Microbial Ecology Program DOE Joint Genome Institute Walnut Creek CA United States Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany Department of Pediatrics University of Colorado Denver Aurora CO United States Division of Environmental Science and Engineering Colorado School of Mines Golden CO United States Department of Molecular Cellular and Developmental Biology University of Colorado Boulder CO United States Genome Biology Program DOE Joint Genome Institute Walnut Creek CA United States Institute of Molecular Biology Swiss Institute of Bioinformatics University of Zurich Zurich Switzerland Microbial Ecology/Biogeochemistry Research Laboratory Exobiology Branch NASA Ames Research Center Moffett Field CA United States Microbial Ecology Program DOE Joint Genome Institute Walnut Creek CA 94598 2800 Mitchell Drive United States

To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-identical and acid-shifted isoelectric point profiles due to a molecular convergence of amino-acid usage, indicating that hypersalinity enforces an overriding selective pressure on the mat community. © 2008 EMBO and Nature Publishing Group All rights reserved.

关键词： Fine-scale Hypersalinity Metagenomics Microbial ecology Salt-in

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Refinement of under-determined loops of human prion protein by database-derived distance constraints

Refinement of under-determined loops of human prion protein ...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Feng Cui Kriti Mukhopadhyay Won-Bin Young Robert L. Jernigan Zhijun Wu Program on Bioinformatics and Computational Biology Department of Mathematics USA University Research Park Ames IA USA Department of Biochemistry Biophysics and Molecular Biology Iowa State University USA Program on Bioinformatics and Computational Biology USA

computational simulations of the conversion from the normal cellular prion (PrP c ) to the scrapie prion (PrP Sc ) are usually based on the structures determined by NMR because of the difficulties in crystallizing prion protein. Due to insufficient experimental restraints, a biologically critical loop region in PrP c (residues 167-171), which is a potential binding site for Protein X, is under-determined in most mammalian species. Here, we show that by adding information about distance constraints derived from a database of high-resolution protein structures, this under-determined loop as well as other secondary structural elements of the E200K variant of human prion protein (hPrP c ), a disease-related isoform, can be refined into more realistic structures in the structural ensemble with improved quality and increased accuracy. In particular, the ensemble becomes more compact after the refinement and the percentage of residues in the most favourable region of the Ramachandran diagram is increased to about 90% in the refined structures from the 80 to 85% range in the previously reported structures. Our results not only provide significantly improved structures of the prion protein and hence would facilitate insights into its conversion in the spongiform encephalopathies, but also demonstrate the strong potential for using databases of known protein structures for structure determination and refinement.

关键词： Humans Proteins Databases Diseases Nuclear magnetic resonance Genetic mutations computational biology Brain Pathogens Amino acids

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