The Experts below are selected from a list of 453 Experts worldwide ranked by ideXlab platform
José B. Pereira-leal - One of the best experts on this subject based on the ideXlab platform.
-
Thousands of Rab GTPases for the Cell Biologist
PLOS Computational Biology, 2011Co-Authors: Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-cadete, Miguel C. Seabra, José B. Pereira-lealAbstract:Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB.org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology.
John Meurig Thomas - One of the best experts on this subject based on the ideXlab platform.
-
max perutz chemist molecular biologist human rights activist
Notes and Records, 2006Co-Authors: John Meurig ThomasAbstract:Tribute paid to Max Perutz before the Max Perutz Memorial Lecture given by Professor Sari Nusseibeh at The International Human Rights Network of Academics and Scholarly Societies, The Royal Society...
-
max perutz chemist molecular biologist human rights activist
Chemical Communications, 2005Co-Authors: John Meurig ThomasAbstract:Tribute paid to Max Perutz prior to the Max Perutz Memorial Lecture given by Professor Sari Nusseibeh at The International Human Rights Network of Academics and Scholarly Societies, Royal Society, London, 19 May 2005.
Yoan Diekmann - One of the best experts on this subject based on the ideXlab platform.
-
Thousands of Rab GTPases for the Cell Biologist
PLOS Computational Biology, 2011Co-Authors: Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-cadete, Miguel C. Seabra, José B. Pereira-lealAbstract:Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB.org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology.
T S Schneider - One of the best experts on this subject based on the ideXlab platform.
-
claude shannon biologist information theory used in biology
IEEE Engineering in Medicine and Biology Magazine, 2006Co-Authors: T S SchneiderAbstract:This paper discusses how Claude Shannon, the founder of information theory, came to be regarded a biologist. It was discovered that Shannon's channel capacity theorem only applied to living organisms and their products, such as communication channels and molecular machines that make choices from several possibilities. Information theory is therefore a theory about biology, which makes Shannon a biologist. Shannon's work then meant that communications systems and molecular biology are headed on a collision course. As electrical circuits approach molecular sizes, the results of molecular biologists can be used to guide designs. There may come a time when communications and biology will be treated as a single field. The codes discovered for communications potentially teach new biology if the same codes are found in biological system. On the other hand, discoveries in molecular biology about systems that have been refined by evolution for billions of years could help build new and more efficient communications systems.
Peter Parry - One of the best experts on this subject based on the ideXlab platform.
-
Biologism in Psychiatry: A Young Man’s Experience of Being Diagnosed with “Pediatric Bipolar Disorder”
MDPI AG, 2014Co-Authors: Peter ParryAbstract:Pediatric bipolar disorder is a diagnosis that arose in the mid 1990s in the USA and has mostly remained confined to that nation. In this article a young American man (under a pseudonym) describes his experience of having the diagnosis throughout his adolescent years. His story was conveyed via correspondence and a meeting with the author, an Australian child psychiatrist. The young American’s story reveals several issues that afflict contemporary psychiatry, particularly in the USA, where social and economic factors have contributed to the rise of a dominant biomedical paradigm—or “Biologism”. This focus on the “bio” to the relative exclusion of the “psychosocial” in both diagnosis and treatment can have serious consequences as this young man’s story attests. The author explores aspects of his tale to analyze how the pediatric bipolar disorder “epidemic” arose and became emblematic of a dominant Biologism. This narrative points to the need, depending on the service and country, to return to or retain/improve a balanced biopsychosocial perspective in child and adolescent mental health. Child psychiatry needs to advocate for health systems that support deeper listening to our patients. Then we can explore with them the full range of contextual factors that contribute to symptoms of individual and family distress
-
Opinion Biologism in Psychiatry: A Young Man’s Experience of Being Diagnosed with “Pediatric Bipolar Disorder”
2014Co-Authors: Peter ParryAbstract:Abstract: Pediatric bipolar disorder is a diagnosis that arose in the mid 1990s in the USA and has mostly remained confined to that nation. In this article a young American man (under a pseudonym) describes his experience of having the diagnosis throughout his adolescent years. His story was conveyed via correspondence and a meeting with the author, an Australian child psychiatrist. The young American’s story reveals several issues that afflict contemporary psychiatry, particularly in the USA, where social and economic factors have contributed to the rise of a dominant biomedical paradigm—or “Biologism”. This focus on the “bio ” to the relative exclusion of the “psychosocial ” in both diagnosis and treatment can have serious consequences as this young man’s story attests. The author explores aspects of his tale to analyze how the pediatric bipolar disorder “epidemic ” arose and became emblematic of a dominant Biologism. This narrative points to the need, depending on the service and country, to return to or retain/improve a balanced biopsychosocial perspective in child and adolescent mental health. Child psychiatry needs to advocate for health systems that support deeper listening to our patients. Then we can explore with them the full range of contextual factors that contribute to symptoms of individual and family distress