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2. Long-term cost-effectiveness of a melanoma prevention program using genomic risk information compared with standard prevention advice in Australia

Author

Newson, Ainsley J., Morton, Rachael L., Kimlin, Michael, Keogh, Louise, Law, Matthew, Kirk, Judy, Dobbinson, Suzanne J., Kanetsky, Peter, Mann, Graham, Dawkins, Hugh, Savard, Jacqueline, Dunlop, Kate, Trevena, Lyndal, Jenkins, Mark, Allen, Martin, Butow, Phyllis, Wordsworth, Sarah, Lo, Serigne, Low, Cynthia, Smit, Amelia K., Espinoza, David, Cust, Anne E., Law, Chi Kin, Fernandez-Penas, Pablo, Nieweg, Omgo E., and Menzies, Alexander M.

Published
2023
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3. How many rare diseases are there?

Author

Haendel, Melissa, Vasilevsky, Nicole, Unni, Deepak, Bologa, Cristian, Harris, Nomi, Rehm, Heidi, Hamosh, Ada, Baynam, Gareth, Groza, Tudor, McMurry, Julie, Dawkins, Hugh, Rath, Ana, Thaxton, Courtney, Bocci, Giovanni, Joachimiak, Marcin, Köhler, Sebastian, Robinson, Peter, Mungall, Chris, and Oprea, Tudor

Subjects
Humans, Phenotype, Rare Diseases
Abstract

A lack of robust knowledge of the number of rare diseases and the number of people affected by them limits the development of approaches to ameliorate the substantial cumulative burden of rare diseases. Here, we call for coordinated efforts to more precisely define rare diseases.

Published
2020

4. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Author

Köhler, Sebastian, Carmody, Leigh, Vasilevsky, Nicole, Jacobsen, Julius OB, Danis, Daniel, Gourdine, Jean-Philippe, Gargano, Michael, Harris, Nomi L, Matentzoglu, Nicolas, McMurry, Julie A, Osumi-Sutherland, David, Cipriani, Valentina, Balhoff, James P, Conlin, Tom, Blau, Hannah, Baynam, Gareth, Palmer, Richard, Gratian, Dylan, Dawkins, Hugh, Segal, Michael, Jansen, Anna C, Muaz, Ahmed, Chang, Willie H, Bergerson, Jenna, Laulederkind, Stanley JF, Yüksel, Zafer, Beltran, Sergi, Freeman, Alexandra F, Sergouniotis, Panagiotis I, Durkin, Daniel, Storm, Andrea L, Hanauer, Marc, Brudno, Michael, Bello, Susan M, Sincan, Murat, Rageth, Kayli, Wheeler, Matthew T, Oegema, Renske, Lourghi, Halima, Della Rocca, Maria G, Thompson, Rachel, Castellanos, Francisco, Priest, James, Cunningham-Rundles, Charlotte, Hegde, Ayushi, Lovering, Ruth C, Hajek, Catherine, Olry, Annie, Notarangelo, Luigi, Similuk, Morgan, Zhang, Xingmin A, Gómez-Andrés, David, Lochmüller, Hanns, Dollfus, Hélène, Rosenzweig, Sergio, Marwaha, Shruti, Rath, Ana, Sullivan, Kathleen, Smith, Cynthia, Milner, Joshua D, Leroux, Dorothée, Boerkoel, Cornelius F, Klion, Amy, Carter, Melody C, Groza, Tudor, Smedley, Damian, Haendel, Melissa A, Mungall, Chris, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Rare Diseases, Human Genome, Networking and Information Technology R&D (NITRD), Generic health relevance, Good Health and Well Being, Biological Ontologies, Computational Biology, Congenital Abnormalities, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Humans, Internet, Knowledge Bases, Phenotype, Whole Genome Sequencing, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.

Published
2019

6. Impact of personal genomic risk information on melanoma prevention behaviors and psychological outcomes: a randomized controlled trial

Author

Smit, Amelia K., Allen, Martin, Beswick, Brooke, Butow, Phyllis, Dawkins, Hugh, Dobbinson, Suzanne J., Dunlop, Kate L., Espinoza, David, Fenton, Georgina, Kanetsky, Peter A., Keogh, Louise, Kimlin, Michael G., Kirk, Judy, Law, Matthew H., Lo, Serigne, Low, Cynthia, Mann, Graham J., Reyes-Marcelino, Gillian, Morton, Rachael L., Newson, Ainsley J., Savard, Jacqueline, Trevena, Lyndal, Wordsworth, Sarah, and Cust, Anne E.

Published
2021
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7. The Human Phenotype Ontology in 2017

Author

Köhler, Sebastian, Vasilevsky, Nicole A, Engelstad, Mark, Foster, Erin, McMurry, Julie, Aymé, Ségolène, Baynam, Gareth, Bello, Susan M, Boerkoel, Cornelius F, Boycott, Kym M, Brudno, Michael, Buske, Orion J, Chinnery, Patrick F, Cipriani, Valentina, Connell, Laureen E, Dawkins, Hugh JS, DeMare, Laura E, Devereau, Andrew D, de Vries, Bert BA, Firth, Helen V, Freson, Kathleen, Greene, Daniel, Hamosh, Ada, Helbig, Ingo, Hum, Courtney, Jähn, Johanna A, James, Roger, Krause, Roland, Laulederkind, Stanley JF, Lochmüller, Hanns, Lyon, Gholson J, Ogishima, Soichi, Olry, Annie, Ouwehand, Willem H, Pontikos, Nikolas, Rath, Ana, Schaefer, Franz, Scott, Richard H, Segal, Michael, Sergouniotis, Panagiotis I, Sever, Richard, Smith, Cynthia L, Straub, Volker, Thompson, Rachel, Turner, Catherine, Turro, Ernest, Veltman, Marijcke WM, Vulliamy, Tom, Yu, Jing, von Ziegenweidt, Julie, Zankl, Andreas, Züchner, Stephan, Zemojtel, Tomasz, Jacobsen, Julius OB, Groza, Tudor, Smedley, Damian, Mungall, Christopher J, Haendel, Melissa, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Networking and Information Technology R&D (NITRD), Human Genome, 2.6 Resources and infrastructure (aetiology), 4.5 Resources and infrastructure (detection), Generic health relevance, Good Health and Well Being, Algorithms, Biological Ontologies, Computational Biology, Genetic Association Studies, Genomics, Humans, Phenotype, Precision Medicine, Rare Diseases, Software, Translational Research, Biomedical, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Published
2017

9. The melanoma genomics managing your risk study: A protocol for a randomized controlled trial evaluating the impact of personal genomic risk information on skin cancer prevention behaviors

Author

Smit, Amelia K., Newson, Ainsley J., Morton, Rachael L., Kimlin, Michael, Keogh, Louise, Law, Matthew H., Kirk, Judy, Dobbinson, Suzanne, Kanetsky, Peter A., Fenton, Georgina, Allen, Martin, Butow, Phyllis, Dunlop, Kate, Trevena, Lyndal, Lo, Serigne, Savard, Jacqueline, Dawkins, Hugh, Wordsworth, Sarah, Jenkins, Mark, Mann, Graham J., and Cust, Anne E.

Published
2018
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10. Indigenous Genetics and Rare Diseases: Harmony, Diversity and Equity

Author

Baynam, Gareth, Molster, Caron, Bauskis, Alicia, Kowal, Emma, Savarirayan, Ravi, Kelaher, Margaret, Easteal, Simon, Massey, Libby, Garvey, Gail, Goldblatt, Jack, Pachter, Nicholas, Weeramanthri, Tarun S., Dawkins, Hugh J. S., COHEN, IRUN R., Series editor, LAJTHA, ABEL, Series editor, LAMBRIS, JOHN D., Series editor, PAOLETTI, RODOLFO, Series editor, REZAEI, NIMA, Series editor, Posada de la Paz, Manuel, editor, Taruscio, Domenica, editor, and Groft, Stephen C., editor

Published
2017
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11. Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework

Author

Baynam, Gareth, Bowman, Faye, Lister, Karla, Walker, Caroline E., Pachter, Nicholas, Goldblatt, Jack, Boycott, Kym M., Gahl, William A., Kosaki, Kenjiro, Adachi, Takeya, Ishii, Ken, Mahede, Trinity, McKenzie, Fiona, Townshend, Sharron, Slee, Jennie, Kiraly-Borri, Cathy, Vasudevan, Anand, Hawkins, Anne, Broley, Stephanie, Schofield, Lyn, Verhoef, Hedwig, Groza, Tudor, Zankl, Andreas, Robinson, Peter N., Haendel, Melissa, Brudno, Michael, Mattick, John S., Dinger, Marcel E., Roscioli, Tony, Cowley, Mark J., Olry, Annie, Hanauer, Marc, Alkuraya, Fowzan S., Taruscio, Domenica, Posada de la Paz, Manuel, Lochmüller, Hanns, Bushby, Kate, Thompson, Rachel, Hedley, Victoria, Lasko, Paul, Mina, Kym, Beilby, John, Tifft, Cynthia, Davis, Mark, Laing, Nigel G., Julkowska, Daria, Le Cam, Yann, Terry, Sharon F., Kaufmann, Petra, Eerola, Iiro, Norstedt, Irene, Rath, Ana, Suematsu, Makoto, Groft, Stephen C., Austin, Christopher P., Draghia-Akli, Ruxandra, Weeramanthri, Tarun S., Molster, Caron, Dawkins, Hugh J. S., COHEN, IRUN R., Series editor, LAJTHA, ABEL, Series editor, LAMBRIS, JOHN D., Series editor, PAOLETTI, RODOLFO, Series editor, REZAEI, NIMA, Series editor, Posada de la Paz, Manuel, editor, Taruscio, Domenica, editor, and Groft, Stephen C., editor

Published
2017
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13. A flexible computational pipeline for research analyses of unsolved clinical exome cases

Author

Lassmann, Timo, Francis, Richard W., Weeks, Alexia, Tang, Dave, Jamieson, Sarra E., Broley, Stephanie, Dawkins, Hugh J. S., Dreyer, Lauren, Goldblatt, Jack, Groza, Tudor, Kamien, Benjamin, Kiraly-Borri, Cathy, McKenzie, Fiona, Murphy, Lesley, Pachter, Nicholas, Pathak, Gargi, Poulton, Cathryn, Samanek, Amanda, Skoss, Rachel, Slee, Jennie, Townshend, Sharron, Ward, Michelle, Baynam, Gareth S., and Blackwell, Jenefer M.

Published
2020
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14. Correction to: Eight years after an international workshop on myotonic dystrophy patient registries: case study of a global collaboration for a rare disease

Author

Wood, Libby, Bassez, Guillaume, Bleyenheuft, Corinne, Campbell, Craig, Cossette, Louise, Jimenez-Moreno, Aura Cecilia, Dai, Yi, Dawkins, Hugh, Díaz-Manera, Jordi, Dogan, Celine, el Sherif, Rasha, Fossati, Barbara, Graham, Caroline, Hilbert, James, Kastreva, Kristinia, Kimura, En, Korngut, Lawrence, Kostera-Pruszczyk, Anna, Lindberg, Christopher, Lindvall, Bjorn, Luebbe, Elizabeth, Lusakowska, Anna, Mazanec, Radim, Meola, Giovani, Orlando, Liannna, Takahashi, Masanori P., Peric, Stojan, Puymirat, Jack, Rakocevic-Stojanovic, Vidosava, Rodrigues, Miriam, Roxburgh, Richard, Schoser, Benedikt, Segovia, Sonia, Shatillo, Andriy, Thiele, Simone, Tournev, Ivailo, van Engelen, Baziel, Vohanka, Stanislav, and Lochmüller, Hanns

Published
2019
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15. 3D facial analysis for rare disease diagnosis and treatment monitoring: Proof-Of-Concept plan for hereditary angioedema.

Author

Jamuar, Saumya, Palmer, Richard, Dawkins, Hugh, Lee, Dae-Wook, Helmholz, Petra, Baynam, Gareth, Jamuar, Saumya, Palmer, Richard, Dawkins, Hugh, Lee, Dae-Wook, Helmholz, Petra, and Baynam, Gareth

Abstract

Rare diseases pose a diagnostic conundrum to even the most experienced clinicians around the world. The technology could play an assistive role in hastening the diagnosis process. Data-driven methodologies can identify distinctive disease features and create a definitive diagnostic spectrum. The healthcare professionals in developed and developing nations would benefit immensely from these approaches resulting in quicker diagnosis and enabling early care for the patients. Hereditary Angioedema is one such rare disease that requires a lengthy diagnostic cascade ensuing massive patient inconvenience and cost burden on the healthcare system. It is hypothesized that facial analysis with advanced imaging and algorithmic association can create an ideal diagnostic peer to the clinician while assimilating signs and symptoms in the hospital. 3D photogrammetry has been applied to diagnose rare diseases in various cohorts. The facial features are captured at a granular level in utmost finer detail. A validated and proven algorithm-powered software provides recommendations in real-time. Thus, paving the way for quick and early diagnosis to well-trained or less trained clinicians in different settings around the globe. The generated evidence indicates the strong applicability of 3 D photogrammetry in association with proprietary Cliniface software to Hereditary Angioedema for aiding in the diagnostic process. The approach, mechanism, and beneficial impact have been sketched out appropriately herein. This blueprint for hereditary angioedema may have far-reaching consequences beyond disease diagnosis to benefit all the stakeholders in the healthcare arena including research and new drug development.

Published
2023

17. Plain-language medical vocabulary for precision diagnosis

Author

Vasilevsky, Nicole A., Foster, Erin D., Engelstad, Mark E., Carmody, Leigh, Might, Matt, Chambers, Chip, Dawkins, Hugh J. S., Lewis, Janine, Della Rocca, Maria G., Snyder, Michelle, Boerkoel, Cornelius F., Rath, Ana, Terry, Sharon F., Kent, Alastair, Searle, Beverly, Baynam, Gareth, Jones, Erik, Gavin, Pam, Bamshad, Michael, Chong, Jessica, Groza, Tudor, Adams, David, Resnick, Adam C., Heath, Allison P., Mungall, Chris, Holm, Ingrid A., Rageth, Kayli, Brownstein, Catherine A., Shefchek, Kent, McMurry, Julie A., Robinson, Peter N., Köhler, Sebastian, and Haendel, Melissa A.

Published
2018
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19. Eight years after an international workshop on myotonic dystrophy patient registries: case study of a global collaboration for a rare disease

Author

Wood, Libby, Bassez, Guillaume, Bleyenheuft, Corinne, Campbell, Craig, Cossette, Louise, Jimenez-Moreno, Aura Cecilia, Dai, Yi, Dawkins, Hugh, Manera, Jorge Alberto Diaz, Dogan, Celine, el Sherif, Rasha, Fossati, Barbara, Graham, Caroline, Hilbert, James, Kastreva, Kristinia, Kimura, En, Korngut, Lawrence, Kostera-Pruszczyk, Anna, Lindberg, Christopher, Lindvall, Bjorn, Luebbe, Elizabeth, Lusakowska, Anna, Mazanec, Radim, Meola, Giovani, Orlando, Liannna, Takahashi, Masanori P., Peric, Stojan, Puymirat, Jack, Rakocevic-Stojanovic, Vidosava, Rodrigues, Miriam, Roxburgh, Richard, Schoser, Benedikt, Segovia, Sonia, Shatillo, Andriy, Thiele, Simone, Tournev, Ivailo, van Engelen, Baziel, Vohanka, Stanislav, and Lochmüller, Hanns

Published
2018
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23. RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research

Author

Thompson, Rachel, Johnston, Louise, Taruscio, Domenica, Monaco, Lucia, Béroud, Christophe, Gut, Ivo G., Hansson, Mats G., ’t Hoen, Peter-Bram A., Patrinos, George P., Dawkins, Hugh, Ensini, Monica, Zatloukal, Kurt, Koubi, David, Heslop, Emma, Paschall, Justin E., Posada, Manuel, Robinson, Peter N., Bushby, Kate, and Lochmüller, Hanns

Published
2014
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26. The TREAT-NMD DMD Global Database: Analysis of More than 7,000 Duchenne Muscular Dystrophy Mutations

Author

Bladen, Catherine L., Salgado, David, Monges, Soledad, Foncuberta, Maria E., Kekou, Kyriaki, Kosma, Konstantina, Dawkins, Hugh, Lamont, Leanne, Roy, Anna J., Chamova, Teodora, Guergueltcheva, Velina, Chan, Sophelia, Korngut, Lawrence, Campbell, Craig, Dai, Yi, Wang, Jen, Barišić, Nina, Brabec, Petr, Lahdetie, Jaana, Walter, Maggie C., Schreiber-Katz, Olivia, Karcagi, Veronika, Garami, Marta, Viswanathan, Venkatarman, Bayat, Farhad, Buccella, Filippo, Kimura, En, Koeks, Zaïda, van den Bergen, Janneke C., Rodrigues, Miriam, Roxburgh, Richard, Lusakowska, Anna, Kostera-Pruszczyk, Anna, Zimowski, Janusz, Santos, Rosário, Neagu, Elena, Artemieva, Svetlana, Rasic, Vedrana Milic, Vojinovic, Dina, Posada, Manuel, Bloetzer, Clemens, Jeannet, Pierre-Yves, Joncourt, Franziska, Díaz-Manera, Jordi, Gallardo, Eduard, Karaduman, Ayşe A., Topaloğlu, Haluk, El Sherif, Rasha, Stringer, Angela, Shatillo, Andriy V., Martin, Ann S., Peay, Holly L., Bellgard, Matthew I., Kirschner, Jan, Flanigan, Kevin M., Straub, Volker, Bushby, Kate, Verschuuren, Jan, Aartsma-Rus, Annemieke, Béroud, Christophe, and Lochmüller, Hanns

Published
2015
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27. Mapping the differences in care for 5,000 Spinal Muscular Atrophy patients, a survey of 24 national registries in North America, Australasia and Europe

Author

Bladen, Catherine L., Thompson, Rachel, Jackson, Jacqueline M., Garland, Connie, Wegel, Claire, Ambrosini, Anna, Pisano, Paolo, Walter, Maggie C., Schreiber, Olivia, Lusakowska, Anna, Jedrzejowska, Maria, Kostera-Pruszczyk, Anna, van der Pol, Ludo, Wadman, Renske I., Gredal, Ole, Karaduman, Ayse, Topaloglu, Haluk, Yilmaz, Oznur, Matyushenko, Vitaliy, Rasic, Vedrana Milic, Kosac, Ana, Karcagi, Veronika, Garami, Marta, Herczegfalvi, Agnes, Monges, Soledad, Moresco, Angelica, Chertkoff, Lilien, Chamova, Teodora, Guergueltcheva, Velina, Butoianu, Niculina, Craiu, Dana, Korngut, Lawrence, Campbell, Craig, Haberlova, Jana, Strenkova, Jana, Alejandro, Moises, Jimenez, Alatorre, Ortiz, Genaro Gabriel, Enriquez, Gracia Viviana Gonzalez, Rodrigues, Miriam, Roxburgh, Richard, Dawkins, Hugh, Youngs, Leanne, Lahdetie, Jaana, Angelkova, Natalija, Saugier-Veber, Pascal, Cuisset, Jean-Marie, Bloetzer, Clemens, Jeannet, Pierre-Yves, Klein, Andrea, Nascimento, Andres, Tizzano, Eduardo, Salgado, David, Mercuri, Eugenio, Sejersen, Thomas, Kirschner, Jan, Rafferty, Karen, Straub, Volker, Bushby, Kate, Verschuuren, Jan, Beroud, Christophe, and Lochmüller, Hanns

Published
2014
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28. Investigating equity in access to Australian clinical genetic health services for Aboriginal and Torres Strait Islander people

Author

Luke, Joanne, primary, Dalach, Philippa, additional, Tuer, Lindsay, additional, Savarirayan, Ravi, additional, Ferdinand, Angeline, additional, McGaughran, Julie, additional, Kowal, Emma, additional, Massey, Libby, additional, Garvey, Gail, additional, Dawkins, Hugh, additional, Jenkins, Misty, additional, Paradies, Yin, additional, Pearson, Glenn, additional, Stutterd, Chloe, additional, Baynam, Gareth, additional, and Kelaher, Margaret, additional

Published
2021
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29. Additional file 2 of The IDeaS initiative: pilot study to assess the impact of rare diseases on patients and healthcare systems

Author

Tisdale, Ainslie, Cutillo, Christine M., Nathan, Ramaa, Russo, Pierantonio, Laraway, Bryan, Haendel, Melissa, Nowak, Douglas, Hasche, Cindy, Chan, Chun-Hung, Griese, Emily, Dawkins, Hugh, Shukla, Oodaye, Pearce, David A., Rutter, Joni L., and Pariser, Anne R.

Abstract

Additional file 2. Figure S1. Weighted Average Cost Formula Weighted average (wtavg) costs were calculated by taking the sum of the number of patients in each RD cohort (#ptRD1-13) and dividing it by the sum of all RD patient cohorts (sum pt), then multiplying by the sum of the PPPY costs of all RD patient cohorts (sumPPPY). Then the individual RD weighted averages were combined to create a weighted average for our total 13 RD population (wtavg RDpop) Abbreviations: WTavg, weighted average, RDPOP, total population for 13 representative RD, #pt, number of patients, sumPPPY, sum of the PPPY costs of all RD patient cohorts.

Published
2021
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30. Additional file 1 of The IDeaS initiative: pilot study to assess the impact of rare diseases on patients and healthcare systems

Author

Tisdale, Ainslie, Cutillo, Christine M., Nathan, Ramaa, Russo, Pierantonio, Laraway, Bryan, Haendel, Melissa, Nowak, Douglas, Hasche, Cindy, Chan, Chun-Hung, Griese, Emily, Dawkins, Hugh, Shukla, Oodaye, Pearce, David A., Rutter, Joni L., and Pariser, Anne R.

Abstract

Additional file 1. Table S1: ICD and CPT Codes and Descriptions.

Published
2021
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32. The TREAT-NMD Duchenne Muscular Dystrophy Registries: Conception, Design, and Utilization by Industry and Academia

Author

Bladen, Catherine L., Rafferty, Karen, Straub, Volker, Monges, Soledad, Moresco, Angélica, Dawkins, Hugh, Roy, Anna, Chamova, Teodora, Guergueltcheva, Velina, Korngut, Lawrence, Campbell, Craig, Dai, Yi, Barišić, Nina, Kos, Tea, Brabec, Petr, Rahbek, Jes, Lahdetie, Jaana, Tuffery-Giraud, Sylvie, Claustres, Mireille, Leturcq, France, Ben Yaou, Rabah, Walter, Maggie C., Schreiber, Olivia, Karcagi, Veronika, Herczegfalvi, Agnes, Viswanathan, Venkatarman, Bayat, Farhad, de la caridad Guerrero Sarmiento, Isis, Ambrosini, Anna, Ceradini, Francesca, Kimura, En, van den Bergen, Janneke C., Rodrigues, Miriam, Roxburgh, Richard, Lusakowska, Anna, Oliveira, Jorge, Santos, Rosário, Neagu, Elena, Butoianu, Niculina, Artemieva, Svetlana, Rasic, Vedrana Milic, Posada, Manuel, Palau, Francesc, Lindvall, Björn, Bloetzer, Clemens, Karaduman, Ayşe, Topaloğlu, Haluk, Inal, Serap, Oflazer, Piraye, Stringer, Angela, Shatillo, Andriy V., Martin, Ann S., Peay, Holly, Flanigan, Kevin M., Salgado, David, von Rekowski, Brigitta, Lynn, Stephen, Heslop, Emma, Gainotti, Sabina, Taruscio, Domenica, Kirschner, Jan, Verschuuren, Jan, Bushby, Kate, Béroud, Christophe, and Lochmüller, Hanns

Published
2013
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37. Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data

Author

Easteal, Simon, primary, Arkell, Ruth M., additional, Balboa, Renzo F., additional, Bellingham, Shayne A., additional, Brown, Alex D., additional, Calma, Tom, additional, Cook, Matthew C., additional, Davis, Megan, additional, Dawkins, Hugh J.S., additional, Dinger, Marcel E., additional, Dobbie, Michael S., additional, Farlow, Ashley, additional, Gwynne, Kylie G., additional, Hermes, Azure, additional, Hoy, Wendy E., additional, Jenkins, Misty R., additional, Jiang, Simon H., additional, Kaplan, Warren, additional, Leslie, Stephen, additional, Llamas, Bastien, additional, Mann, Graham J., additional, McMorran, Brendan J., additional, McWhirter, Rebekah E., additional, Meldrum, Cliff J., additional, Nagaraj, Shivashankar H., additional, Newman, Saul J., additional, Nunn, Jack S., additional, Ormond-Parker, Lyndon, additional, Orr, Neil J., additional, Paliwal, Devashi, additional, Patel, Hardip R., additional, Pearson, Glenn, additional, Pratt, Greg R., additional, Rambaldini, Boe, additional, Russell, Lynette W., additional, Savarirayan, Ravi, additional, Silcocks, Matthew, additional, Skinner, John C., additional, Souilmi, Yassine, additional, Vinuesa, Carola G., additional, and Baynam, Gareth, additional

Published
2020
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38. Correction to: Eight years after an international workshop on myotonic dystrophy patient registries: Case study of a global collaboration for a rare disease (Orphanet Journal of Rare Diseases (2018) 13 (155) DOI: 10.1186/s13023-018-0889-0)

Author

Wood, Libby, Bassez, Guillaume, Bleyenheuft, Corinne, Campbell, Craig, Cossette, Louise, Jimenez-Moreno, Aura Cecilia, Dai, Yi, Dawkins, Hugh, Harreiter, Jordi, Kautzky-Willer, Alexandra, Damm, Peter, Mathiesen, Elisabeth R., Jensen, Dorte M., Andersen, Lise Lotte T., Tanvig, Mette, Lapolla, Annunziata, Dalfra, Maria G., Bertolotto, Alessandra, Manta, Urszula, Wender-Ozegowska, Ewa, Zawiejska, Agnieszka, Hill, David J., Snoek, Frank J., Jelsma, Judith G.M., and van Poppel, Mireille

Abstract

The original version of this article [1] unfortunately included an error to an author's name. Author Jordi Díaz-Manera was erroneously presented as Jorge Alberto Diaz Manera. The correct author name has been included in the author list of this Correction article. For citation purposes the author's given name is Jordi and family name Diaz-Manera. Therefore, the correct citation of the author's details is: Diaz-Manera J.

Published
2019

40. Entropy maximization networks: an application to breast cancer prognosis

Author

Choong, Poh Lian, deSilva, Christopher J.S., Dawkins, Hugh J.S., and Sterrett, Gregory F.

Subjects
Entropy (Information theory) -- Research, Neural networks -- Research, Breast cancer -- Diagnosis, Pattern recognition -- Research, Business, Computers, Electronics, Electronics and electrical industries
Abstract

This paper describes two artificial neural network architectures for constructing maximum entropy models using multinomial distributions. The architectures presented maximize entropy in two ways: by the use of the partition function (which involves the solution of simultaneous polynomial equations) and by constrained gradient ascent. Results comparing the convergence properties of these two architectures are presented. The practical use of these two architectures as a method of inference is illustrated by an application to the prediction of metastases in early breast cancer patients. To assess the predictive accuracy of the maximum entropy models, we compared the results with those obtained by the use of the multilayer perceptron and the probabilistic neural network.

Published
1996

41. Key outcomes from stakeholder workshops at a symposium to inform the development of an Australian national plan for rare diseases

Author

Molster Caron, Youngs Leanne, Hammond Emma, and Dawkins Hugh

Subjects
National plan, Rare diseases, Stakeholder consultation, Medicine
Abstract

Abstract Background Calls have been made for governments to adopt a cohesive approach to rare diseases through the development of national plans. At present, Australia does not have a national plan for rare diseases. To progress such a plan an inaugural Australian Rare Diseases Symposium was held in Western Australia in April 2011. This paper describes the key issues identified by symposium attendees for the development of a national plan, compares these to the content of EUROPLAN and national plans elsewhere and discusses how the outcomes might be integrated for national planning. Methods The symposium was comprised of a series of plenary sessions followed by workshops. The topics covered were; 1) Development of national plans for rare diseases; 2) Patient empowerment; 3) Patient care, support and management; 4) Research and translation; 5) Networks, partnerships and collaboration. All stakeholders within the rare diseases community were invited to participate, including: people affected by rare diseases such as patients, carers, and families; clinicians and allied health practitioners; social and disability services; researchers; patient support groups; industry (e.g. pharmaceutical, biotechnology and medical device companies); regulators and policy-makers. Results All of these stakeholder groups were represented at the symposium. Workshop participants indicated the need for a national plan, a national peak body, a standard definition of ‘rare diseases’, education campaigns, lobbying of government, research infrastructure, streamlined whole-of-lifetime service provision, case co-ordination, early diagnosis, support for health professionals and dedicated funding. Conclusions These findings are consistent with frameworks and initiatives being undertaken internationally (such as EUROPLAN), and with national plans in other countries. This implies that the development of an Australian national plan could plausibly draw on frameworks for plan development that have been proposed for use in other jurisdictions. The translation of the symposium outcomes to government policy (i.e. a national plan) requires the consideration of several factors such as the under-representation of some stakeholder groups (e.g. clinicians) and the current lack of evidence required to translate some of the symposium outcomes to policy options. The acquisition of evidence provides a necessary first step in a comprehensive planning approach.

Published
2012
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42. Deep Phenotyping For Patients By Patients: A Plain-Language Medical Vocabulary For Precision Diagnosis

Author

Vasilevsky, Nicole A., Foster, Erin D., Engelstad, Mark E., Carmody, Leigh, Might, Matt, Chambers, Chip, Dawkins, Hugh J.S., Lewis, Janine, Della Rocca, Maria G., Snyder, Michelle, Boerkoel, Cornelius F., Rath, Ana, Terry, Sharon F., Kent, Alastair, Searle, Beverly, Baynam, Gareth, Jones, Erik, Gavin, Pam, Bamshad, Michael, Chong, Jessica, Groza, Tudor, Adams, David, Resnick, Adam C, Heath, Allison P, Mungall, Chris, Holmes, Ingrid, Rageth, Kayli, Brownstein, Catherine, Shefchek, Kent, McMurry, Julie A., Robinson, Peter N., Kohler, Sebastian, and Haendel, Melissa A

Subjects
ComputingMethodologies_PATTERNRECOGNITION, Human Phenotype Ontology, Rare disease, Medical Genetics
Abstract

This paper describes an effort to increase accessibility of the Human Phenotype Ontology to patients and non-medical expertsby adding lay-person synonyms and terminology.

Published
2018
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43. How many rare diseases are there?

Author

Haendel, Melissa, primary, Vasilevsky, Nicole, additional, Unni, Deepak, additional, Bologa, Cristian, additional, Harris, Nomi, additional, Rehm, Heidi, additional, Hamosh, Ada, additional, Baynam, Gareth, additional, Groza, Tudor, additional, McMurry, Julie, additional, Dawkins, Hugh, additional, Rath, Ana, additional, Thaxton, Courtney, additional, Bocci, Giovanni, additional, Joachimiak, Marcin P., additional, Köhler, Sebastian, additional, Robinson, Peter N., additional, Mungall, Chris, additional, and Oprea, Tudor I., additional

Published
2019
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48. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Author

Genetica, UMC Utrecht, Genetica Klinische Genetica, Brain, Child Health, Köhler, Sebastian, Carmody, Leigh, Vasilevsky, Nicole, Jacobsen, Julius O.B., Danis, Daniel, Gourdine, Jean Philippe, Gargano, Michael, Harris, Nomi L., Matentzoglu, Nicolas, McMurry, Julie A., Osumi-Sutherland, David, Cipriani, Valentina, Balhoff, James P., Conlin, Tom, Blau, Hannah, Baynam, Gareth, Palmer, Richard, Gratian, Dylan, Dawkins, Hugh, Segal, Michael, Jansen, Anna C., Muaz, Ahmed, Chang, Willie H., Bergerson, Jenna, Laulederkind, Stanley J.F., Yüksel, Zafer, Beltran, Sergi, Freeman, Alexandra F., Sergouniotis, Panagiotis I., Durkin, Daniel, Storm, Andrea L., Hanauer, Marc, Brudno, Michael, Bello, Susan M., Sincan, Murat, Rageth, Kayli, Wheeler, Matthew T., Oegema, Renske, Lourghi, Halima, Della Rocca, Maria G., Thompson, Rachel, Castellanos, Francisco, Priest, James, Cunningham-Rundles, Charlotte, Hegde, Ayushi, Lovering, Ruth C., Hajek, Catherine, Olry, Annie, Notarangelo, Luigi, Similuk, Morgan, Zhang, Xingmin A., Gómez-Andrés, David, Lochmüller, Hanns, Dollfus, Hélène, Rosenzweig, Sergio, Marwaha, Shruti, Rath, Ana, Sullivan, Kathleen, Smith, Cynthia, Milner, Joshua D., Leroux, Dorothée, Boerkoel, Cornelius F., Klion, Amy, Carter, Melody C., Groza, Tudor, Smedley, Damian, Haendel, Melissa A., Mungall, Chris, Robinson, Peter N., Genetica, UMC Utrecht, Genetica Klinische Genetica, Brain, Child Health, Köhler, Sebastian, Carmody, Leigh, Vasilevsky, Nicole, Jacobsen, Julius O.B., Danis, Daniel, Gourdine, Jean Philippe, Gargano, Michael, Harris, Nomi L., Matentzoglu, Nicolas, McMurry, Julie A., Osumi-Sutherland, David, Cipriani, Valentina, Balhoff, James P., Conlin, Tom, Blau, Hannah, Baynam, Gareth, Palmer, Richard, Gratian, Dylan, Dawkins, Hugh, Segal, Michael, Jansen, Anna C., Muaz, Ahmed, Chang, Willie H., Bergerson, Jenna, Laulederkind, Stanley J.F., Yüksel, Zafer, Beltran, Sergi, Freeman, Alexandra F., Sergouniotis, Panagiotis I., Durkin, Daniel, Storm, Andrea L., Hanauer, Marc, Brudno, Michael, Bello, Susan M., Sincan, Murat, Rageth, Kayli, Wheeler, Matthew T., Oegema, Renske, Lourghi, Halima, Della Rocca, Maria G., Thompson, Rachel, Castellanos, Francisco, Priest, James, Cunningham-Rundles, Charlotte, Hegde, Ayushi, Lovering, Ruth C., Hajek, Catherine, Olry, Annie, Notarangelo, Luigi, Similuk, Morgan, Zhang, Xingmin A., Gómez-Andrés, David, Lochmüller, Hanns, Dollfus, Hélène, Rosenzweig, Sergio, Marwaha, Shruti, Rath, Ana, Sullivan, Kathleen, Smith, Cynthia, Milner, Joshua D., Leroux, Dorothée, Boerkoel, Cornelius F., Klion, Amy, Carter, Melody C., Groza, Tudor, Smedley, Damian, Haendel, Melissa A., Mungall, Chris, and Robinson, Peter N.

Published
2019

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