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Online Training of New Curators

Marc Gillespie, Bijay Jassal
2009 Nature Precedings  
doi:10.1038/npre.2009.3420.1 fatcat:t3lx2whqfbb5xckk3nfqemqmam

Gene expression analysis

Felicia I. Carvalho, Christopher Johns, Marc E. Gillespie
2012 Biochemistry and Molecular Biology Education  
In the past decade rapid advances of microarray technologies have made it possible to monitor the expression profiles of thousands of genes under various experimental conditions. The requirements for methods to handle such amounts of data have arisen. These massive source of information extracted from the genome project contain the keys to address fundamental problems relating to the prevention and cure of diseases, biological evolution mechanisms and the understanding of particular functional
more » ... lements in the human organism. The knowledge of the coding sequences of virtually every gene in an organism is an exciting opportunity to develop methods to study the role of a gene in a specific organism or biological function. One of such methods consists of the monitoring of the level of expression of a gene. It has been shown that specific patterns of gene expression occur during different biological states such as cell development and during normal physiological responses in tissues and cells. There are many data mining techniques which help to analyze the gene expression data. This paper discusses some of these methods adopted by different researchers.
doi:10.1002/bmb.20588 pmid:22615226 fatcat:hdb3jwf4gbebhkxj4hgt7fl4qu

Recursion to food plants by free-ranging Bornean elephant

Megan English, Graeme Gillespie, Benoit Goossens, Sulaiman Ismail, Marc Ancrenaz, Wayne Linklater
2015 PeerJ  
. • Graeme Gillespie conceived and designed the experiments, contributed reagents/ materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper. • Benoit Goossens and Marc Ancrenaz  ... 
doi:10.7717/peerj.1030 pmid:26290779 pmcid:PMC4540050 fatcat:bfh5r7myezcjhiunlwgly5fmku

Foraging site recursion by forest elephantsElephas maximus borneensis

Megan English, Marc Ancrenaz, Graeme Gillespie, Benoit Goossens, Sen Nathan, Wayne Linklater
2014 Current Zoology  
Recursion by herbivores is the repeated use of the same site or plants. Recursion by wild animals is rarely investigated but may be ubiquitous. Optimal foraging theory predicts site recursion as a function of the quality of the site, extent of its last use, and time since its last use because these influence site resource status and recovery. We used GPS collars, behaviour and site sampling to investigate recursion to foraging sites for two elephant Elephas maximus borneensis herds in the Lower
more » ... Kinabatangan Wildlife Sanctuary, Borneo, over a 12 month period. Recursion occurred to 48 out of 87 foraging sites and was most common within 48 hours or between 151-250 days, indicating two different types of recursion. Recursion was more likely to occur if the site had previously been occupied for longer. Moreover, the time spent at a site at recursion was the same as the time spent at the site on the first occasion. The number of days that had passed between the first visit and recursion was also positively correlated with how much time was spent at the site at recursion. Habitat type also influenced the intensity of site-use, with more time spent at recursion within riverine/open grass areas along forest margins compared to other habitat types. Recursion is a common behaviour used by the elephants and its pattern suggests it may be a foraging strategy for revisiting areas of greater value. The qualities of recursion sites might usefully be incorporated into landscape management strategies for elephant conservation in the area [Current Zoology 60 (4): 551-559, 2014].
doi:10.1093/czoolo/60.4.551 fatcat:gdyvntbk3natzirw5pitazo3gm

SNARE complex-mediated degranulation in mast cells

Joseph R. Woska, Marc E. Gillespie
2012 Journal of Cellular and Molecular Medicine  
Mast cell function and dysregulation is important in the development and progression of allergic and autoimmune disease. Identifying novel proteins involved in mast cell function and disease progression is the first step in the design of new therapeutic strategies. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of proteins demonstrated to mediate the transport and fusion of secretory vesicles to the membrane in mast cells, leading to the subsequent
more » ... elease of the vesicle cargo through an exocytotic mechanism. The functional role[s] of specific SNARE family member complexes in mast cell degranulation has not been fully elucidated. Here, we review recent and historical data on the expression, formation and localization of various SNARE proteins and their complexes in murine and human mast cells. We summarize the functional data identifying the key SNARE family members that appear to participate in mast cell degranulation. Furthermore, we discuss the utilization of RNA interference (RNAi) methods to validate SNARE function and the use of siRNA as a therapeutic approach to the treatment of inflammatory disease. These studies provide an overview of the specific SNARE proteins and complexes that serve as novel targets for the development of new therapies to treat allergic and autoimmune disease.
doi:10.1111/j.1582-4934.2011.01443.x pmid:21880114 pmcid:PMC3822836 fatcat:6bu6nuex4bggzpm5aorccmhazq

Human and chicken TLR pathways: manual curation and computer-based orthology analysis

Marc Gillespie, Veronica Shamovsky, Peter D'Eustachio
2010 Mammalian Genome  
The innate immune responses mediated by Toll-like receptors (TLR) provide an evolutionarily well-conserved first line of defense against microbial pathogens. In the Reactome Knowledgebase we previously integrated annotations of human TLR molecular functions with those of over 4000 other human proteins involved in processes such as adaptive immunity, DNA replication, signaling, and intermediary metabolism, and have linked these annotations to external resources, including PubMed, UniProt,
more » ... ene, Ensembl, and the Gene Ontology to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. We have now used a combination of manual expert curation and computer-based orthology analysis to generate a set of annotations for TLR molecular function in the chicken (Gallus gallus). Mammalian and avian lineages diverged approximately 300 million years ago, and the avian TLR repertoire consists of both orthologs and distinct new genes. The work described here centers on the molecular biology of TLR3, the host receptor that mediates responses to viral and other doubledstranded polynucleotides, as a paradigm for our approach to integrated manual and computationally based annotation and data analysis. It tests the quality of computationally generated annotations projected from human onto other species and supports a systems biology approach to analysis of virus-activated signaling pathways and identification of clinically useful antiviral measures.
doi:10.1007/s00335-010-9296-0 pmid:21052677 pmcid:PMC3035812 fatcat:h5tfkubcvvb7lfaick5fwdfzdu

Dates and rates of arid region geomorphic processes

Kyle K. Nichols, Paul R. Bierman, W. Ross Foniri, Alan R. Gillespie, Marc Caffee, Robert Finkel
2006 GSA Today  
Alternatively, the valleys and peaks of the Alabama Hills may be inherited features, and the isolation of the inselbergs from erosion catalysts, such as soil moisture and wildfire (Bierman and Gillespie  ...  avoid, or account for, nuclide inheritance, then exhumation of boulders through landform erosion and/or the loss of mass from boulder surfaces complicates the interpretation of boulder ages (Bierman and Gillespie  ... 
doi:10.1130/gsat01608.1 fatcat:3hy4xh7f4rcolcbqg2ndn6bdvq

Effective anti-tuberculosis therapy correlates with plasma small RNA

Isobella Honeyborne, Marc C. Lipman, Clare Eckold, Dimitrios Evangelopoulos, Stephen H. Gillespie, Alexander Pym, Timothy D. McHugh
2015 European Respiratory Journal  
Gillespie 3 , Alexander Pym 4 and Timothy D.  ...  @ERSpublications Plasma small RNA concentration declines in response to anti-tuberculosis therapy and is independent of HIV-status http://ow.ly/IxOaD Isobella Honeyborne 1 , Marc C.  ... 
doi:10.1183/09031936.00221214 pmid:25745052 fatcat:4peo2troqnd6fej2vz6dymeyqq

REACTOME: A KNOWLEDGEBASE OF BIOLOGICAL PATHWAYS

Lincoln Stein, Peter D'Eustachio, Gopal Gopinathrao, Marc Gillespie, Lisa Matthews, Guanming Wu, Imre Vastrik, Esther Schmidt, Bernard de Bono, Bijay Jassal, David Croft, Ewan Birney (+1 others)
2006 Computational Systems Bioinformatics  
Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory
more » ... and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.
doi:10.1142/9781860947575_0009 fatcat:yk445f4ienairev4uebdmrgaca

Call to action to prevent venous thromboembolism

Thomas W. Wakefield, Robert B. McLafferty, Joann M. Lohr, Joseph A. Caprini, David L. Gillespie, Marc A. Passman
2009 Journal of Vascular Surgery  
Caprini, MD, Marc A. Passman, MD, David L. Gillespie, MD, Robert B. McLafferty, MD, and Thomas W. Wakefield, MD (Fig 2) .  ...  Fig 2 . 2 Picture of all the representatives from the AVF (from left to right); Robert McLafferty, David Gillespie, Thomas Wakefield, Joann Lohr, Joseph Caprini, Marc Passman.What follows is a summary  ... 
doi:10.1016/j.jvs.2009.01.058 pmid:19497526 fatcat:5dj33rdkxrauzl2xp77pjgqcbu

Reactome – a knowledgebase of human biological pathways

Peter D'Eustachio, Lisa Matthews, Ewan Birney, Lincoln Stein, Esther Schmidt, Imre Vastrik, Guanming Wu, David Croft, Bernard de Bono, Gopal Gopinath, Suzanna Lewis, Marc Gillespie (+1 others)
2007 Nature Precedings  
doi:10.1038/npre.2007.1281.1 fatcat:ux3n3qxu3zalho3t65cp4jh3mm

Reactome – a knowledgebase of human biological pathways

Peter D'Eustachio, Peter D'Eustachio, David Croft, Bernard de Bono, Gopal Gopinath, Marc Gillespie, Bijay Jassal, Lisa Matthews, Esther Schmidt, Imre Vastrik, Guanming Wu, Suzanna Lewis (+2 others)
2007 Nature Precedings  
doi:10.1038/npre.2007.1281 fatcat:h4zqjdvisbculp7mhzpcljzruu

Standardized Patients in Preparedness Education: In-Person and Online Training

Elizabeth Kachur, Marc Triola, Adina Kalet, Sondra Zabar, Marian Anderson, Henry Feldman, Colleen Gillespie, Mack Lipkin
2005 Prehospital and Disaster Medicine  
Standardized Patients in Preparedness Education: In- Person and Online Training Elizabeth Kachur; Marc Triola; Adina Kalet; Sondra Zabar; Marian Anderson; Henry Feldman; Colleen Gillespie; Mack Lipkin  ... 
doi:10.1017/s1049023x00015545 fatcat:qa7nqydwzjfj3adw5yidllk5lu

Teaching Risk Communication and Media Management: Lessons Learned

Elizabeth Kachur, Jane Praeger, Mack Lipkin, Marc Triola, Sondra Zabar, Henry Feldman, Adina Kalet, Colleen Gillespie, Marian Anderson, Richard Freeman, Michael Yedida
2005 Prehospital and Disaster Medicine  
doi:10.1017/s1049023x00015557 fatcat:qiykfyj62zc2vern34ul5yakhu

Reactome – A Knowledgebase of Biological Pathways [chapter]

Esther Schmidt, Ewan Birney, David Croft, Bernard de Bono, Peter D'Eustachio, Marc Gillespie, Gopal Gopinath, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Lincoln Stein, Imre Vastrik (+1 others)
2006 Lecture Notes in Computer Science  
Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory
more » ... and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.
doi:10.1007/11915034_95 fatcat:mhi75mdnrzhddiaccuq6viyebq
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