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GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome Nature Precedings
A. Bignell; A. Frankish; B. Aken; M. Diekhans; F. Kokocinski; M. Lin; M. Tress; J. Van Baren; I. Barnes; T. Hunt; D. Carvalho-Silva; C. Davidson; S. Donaldson; J. Gilbert; E. Hart; M. Kay; R. Kinsella; D. Lloyd; J. Loveland; J. E. Mudge; C. Snow; J. Vamathevan; L. Wilming; M. Brent; M. Gerstein; R. Guigó; R. Harte; M. Kellis; S. Searle; J. Harrow; T. Hubbard.
The Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute produced the manually annotated geneset for the Encyclopedia of DNA Elements (ENCODE) pilot project and, as part of the Gencode subgroup, are reprising this role in the scale up to cover the whole human genome. Our manual annotation is checked computationally and validated experimentally. Loci and transcripts predicted to be absent from the initial annotation are identified by comparison with a number of state-of-the-art algorithms for identifying exons, splice sites, transcripts and pseudogenes. Where novel features are confirmed the annotation is updated. Annotated coding transcripts are analysed to assess their coding potential by investigating...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3155/version/1
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Molecular Evaluation of exons 8 and 22 of the SHANK3 gene in Autism Spectrum Disorders Nature Precedings
A L. Bossolani-Martins; F C. Rodrigues-Lisoni; M L. Nogueira; A Barbosa-Gonçalves; E H. Tajara; A C. Fett-Conte.
Autism spectrum disorders are a group of neurodevelopmental disorders with a complex and heterogeneous etiology. Studies have shown that genetic factors play an important role in the aetiology of these diseases. Recently, de novo mutations, frameshifts and deletions have been described in the SHANK3 gene, also known as ProSAP2 gene, which encodes a synaptic scaffolding protein. All the participants of this study had normal karyotypes and underwent screening for Fragile-X syndrome. Subsequently, they were analyzed by direct sequencing of different points of exons 8 and 22 of the SHANK3 gene. None of the study participants presented with changes in these regions. These findings may be due to the fact that mutations, deletions and duplications of the SHANK3...
Tipo: Manuscript Palavras-chave: Genetics & Genomics.
Ano: 2010 URL: http://precedings.nature.com/documents/4200/version/1
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BFO/DOLCE Primitive Relation Comparison Nature Precedings
A. Patrice Seyed.
This paper examines the primitive relations (dependence, quality, and constitution) of the BFO and DOLCE upper ontologies, employed in developing domain ontologies of the biomedical sciences. The strengths in both upper ontologies are examined, which sets a framework for developing a common upper ontology that utilizes the assets of both.
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3481/version/1
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The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI Nature Precedings
Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3267/version/5
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The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI Nature Precedings
Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3267/version/3
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MR Neurography and Diffusion Tensor Imaging: Origins, History & Clinical Impact Nature Precedings
Aaron G. Filler.
Objective – Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques – MR Neurography and Diffusion Tensor Imaging – were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.

Method – In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/2877/version/1
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The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI Nature Precedings
Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3267/version/1
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MR Neurography and Diffusion Tensor Imaging: Origins, History & Clinical Impact Nature Precedings
Aaron G. Filler.
Objective – Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques – MR Neurography and Diffusion Tensor Imaging – were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.

Method – In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/2877/version/2
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MR Neurography and Diffusion Tensor Imaging: Origin, History and Impact Nature Precedings
Aaron G. Filler.
*Objective:* Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques – MR Neurography and Diffusion Tensor Imaging – were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.

*Method:* In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a variety of small...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/1932/version/2
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MR Neurography and Diffusion Tensor Imaging: Origin, History and Impact Nature Precedings
Aaron G. Filler.
Objective – Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques – MR Neurography and Diffusion Tensor Imaging – were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.

Method – In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a...
Tipo: Manuscript Palavras-chave: Neuroscience.
Ano: 2008 URL: http://precedings.nature.com/documents/1932/version/1
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The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI Nature Precedings
Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3267/version/2
Imagem não selecionada

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The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI Nature Precedings
Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009 URL: http://precedings.nature.com/documents/3267/version/4
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Successful use of axonal transport for drug delivery by synthetic molecular vehicles Nature Precedings
Aaron G. Filler; Garth Whiteside; Mark Bacon; Martyn Frederickson; Franklyn A. Howe; Miri K. Rabinowitz; Alan J. Sokoloff; Terrence Deacon; Chris Abell; Raj Munglani; John R. Griffiths; B. Anthony Bell; Andrew Lever.
We report the use of axonal transport to achieve intraneural drug delivery. We constructed a novel tripartite complex of an axonal transport facilitator conjugated to a linker molecule bearing up to a hundred reversibly attached drug molecules. The complex efficiently enters nerve terminals after intramuscular or intradermal administration and travels within axonal processes to neuron cell bodies. The tripartite agent provided 100-fold amplification of saturable neural uptake events, delivering multiple drug molecules per complex. _In vivo_, analgesic drug delivery to systemic and to non-targeted neural tissues was greatly reduced compared to existing routes of administration, thus exemplifying the possibility of specific nerve root targeting and...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2008 URL: http://precedings.nature.com/documents/2164/version/1
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A Fresh Look at Energy, Materials, and Labor in Agriculture Nature Precedings
Aaron W. Baum; Tadeusz Patzek; Martin Bender; Steve Renich; Wes Jackson.
An understanding of agriculture's energy, material, and labor requirements is essential for achieving economic and ecological sustainability, and for assessing the effectiveness of relevant policy decisions (biofuel subsidies, regulations, labeling, etc.). Previous studies of energy, materials, and labor use in farming have been based on either unverified voluntary reporting or test plots, rather than on the high-resolution measurements of mass and energy flows. Here we present a recursive analysis of 1.25 million data points describing in unprecedented detail the resource transactions on a 60 ha farm functioning for over 6 years. This analysis highlights the importance of accounting for all types of materials, as well as capital equipment,...
Tipo: Manuscript Palavras-chave: Ecology; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/4291/version/1
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YeastMed: An XML-Based System for Biological Data Integration of Yeast Nature Precedings
Abdelaali Briache; Kamar Marrakchi; Amine Kerzazi; Ismael Navas-Delgado; José F. Aldana Montes; Badr Din Rossi Hassani; Khalid Lairini.
A key goal of bioinformatics is to create database systems and software platforms capable of storing and analysing large sets of biological data. Hundreds of biological databases are now available and provide access to huge amount of biological data. SGD, Yeastract, CYGD-MIPS, BioGrid and PhosphoGrid are five of the most visited databases by the yeast community. These sources provide complementary data on biological entities. Biologists are brought systematically to query these data sources in order to analyse the results of their experiments. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned result is a complex and laborious task. To provide transparent and simultaneous access to these...
Tipo: Presentation Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5396/version/1
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Changes in Antioxidant Enzymes Activity and Oxidative Damage in Four Argania spinosa Ecotypes Under Water Stress Conditions Nature Precedings
Abdelghani Chakhchar; Abderrahim Ferradous; Mouna Lamaoui; Said Wahbi; Cherkaoui El Modafar.
_Argania spinosa_ L. Skell, a tree endemic of Morocco, grows in semiarid and arid areas. Biochemical response to drought in four ecotypes of the _A. spinosa_ was compared. Choice of ecotypes was based on evident differences in geographical features in south-west Morocco: two coastal ecotypes (Essaouira and Agadir) and two paralittorale ecotypes (Aoulouz and Lakhssas). Lipid peroxidation (malonyldialdehyde (MDA)), content of endogenous hydrogen peroxide (H2O2) and antioxidant enzyme system (Catalase (CAT), Ascorbate peroxidase (APX), Total peroxidase (POD) and Polyphenoloxidase (PPO) were measured in control (100% relative humidity (RH) at field capacity (FC)) and water-stressed plants (50 and 25% RH at FC). For all ecotypes, drought stress significantly...
Tipo: Poster Palavras-chave: Biotechnology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6189/version/1
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Ecoinformatics: where are we, where do we want to go, and how to reach there. Nature Precedings
Abhay Krishna.
Compared to other natural sciences ecological sciences has always been about seeing the bigger picture. The realization that local actions can have global impact has been the hallmark of ecological research. This integrative view is getting more and more accepted now with the recognition that whole is definitely more then sum of its parts. Advancement in computer sciences has now made it possible to comprehend the complexity arising from an integrative approach. This has given rise to a field interfacing computer science and ecological sciences called Ecoinformatics. The other popular parallel and more mature field is bioinformatics or computational biology. The presentation will take the audience on an Ecoinformatics tour touching on present status of...
Tipo: Presentation Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2018/version/1
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Web 2.0 and the ever elusive balance between information explosion and data mining Nature Precedings
Abhay Krishna.
In a fascinating tussle of perspectives in Volume 6 and issue no 3 of april 2008 Frontiers in Ecology and Evolution, Martin A Nuñez and Gregory M Crustinger enlist ways to brace up with the recent literature. They advocate that PhD students should choose a well studied system to have better chances of success. On the other side of this fascinating tussle Daniel Simberloff and Nathan J Sanders agree with there enthusiastic case and approaches for bracing up with the recent literature. However, they disagree with the play safe strategy of start-ups in ecology and evolution.

For me this tussle of perspectives is really fascinating. It underlines the story of our times. In the times of information explosion, should...
Tipo: Manuscript Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/1959/version/1
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Dissecting the Biological Motherboard (Systems Biology and Beyond) Nature Precedings
Abhay Krishna; Ajit Narayanan.
Genome-scale molecular networks, including gene pathways, gene regulatory networks and protein interactions, are central to the investigation of the nascent disciplines of systems biology and bio-complexity. Dissecting these genome-scale molecular networks in its all-possible manifestations is paramount in our quest for a genotype-input phenotype-output application which will also take environment-genome interactions into account.

Machine learning approaches are now increasingly being used for reverse engineering such networks. Our work stresses the importance of a system approach in biological research and how artificial neural networks are at the forefront of Artificial Intelligence techniques that are increasingly...
Tipo: Presentation Palavras-chave: Ecology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2003/version/1
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Systems level analysis of transgenerational spermatogenic inheritance predicts biomarkers and underlying pathways Nature Precedings
Abhay Sharma.
Transgenerational spermatogenic inheritance of adult male acquired CNS gene expression characteristics has recently been discovered using a Drosophila systems model. In this novel mode of inheritance, transcriptomic alteration induced by the neuroactive drug pentylenetetrazole (PTZ) has been found to leak to future generations. Here, the available microarray gene expression data pertaining to CNS and/or testis of exposed F0 and the resulting F1 and F2 generations has been pooled and analyzed in an unbiased manner at four levels, namely, biological processes and pathways, protein interactome networks, miRNA-targets, and microarray expression profile similarities. Enrichment for processes related to translation, energy metabolism, cell proliferation, cell...
Tipo: Manuscript Palavras-chave: Genetics & Genomics.
Ano: 2009 URL: http://precedings.nature.com/documents/3312/version/1
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