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Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
The approach is tested on a corpus comprised of skeletal phenotype descriptions emerged from the Human Phenotype Ontology.  ...  The first step in this process is the segmentation of the phenotype descriptions into their atomic elements.  ...  The authors acknowledge use of computing resources from the NeCTAR research cloud (http://www.nectar.org.au).  ... 
doi:10.1186/1471-2105-13-265 pmid:23061930 pmcid:PMC3495645 fatcat:hvpmzhouvbhkpn2ebrswcu4hnq

Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID)

Ying Qiao, Eloi Mercier, Jila Dastan, Jane Hurlburt, Barbara McGillivray, Albert E Chudley, Sandra Farrell, Francois P Bernier, ME Suzanne Lewis, Paul Pavlidis, Evica Rajcan-Separovic
2014 BMC Medical Genetics  
Terminology for 34 primary (coarse) and 169 secondary (fine) phenotype features were used to categorize the abnormal phenotypes and determine the prevalence of each phenotype in patients grouped by the  ...  Methods: We evaluated the association of de novo, familial and common CNVs detected in 78 ID subjects with phenotypic abnormalities classified using the Winter-Baraitser Dysmorphology Database (WBDD) (  ...  Health Research, a CIHR New Investigator award, the Canadian Foundation for Innovation, and the National Institutes of Health (GM076990).  ... 
doi:10.1186/1471-2350-15-82 pmid:25030379 pmcid:PMC4107469 fatcat:37p4mmomkrf4lnqcpzcdd3oqqe

Abstracts for the 35th Human Genetics Society of Australasia Annual Scientific Meeting, Gold Coast, Australia July 31–August 3, 2011

2011 Twin Research and Human Genetics  
towards the understanding of these complicated and very human phenotypes.  ...  Recently, mutations in TRPV4 have been found to be responsible for these three skeletal phenotypes.  ...  Methods: A chart review of 67 patients, fully or partially tested per protocol, compared blood results to normal ranges.  ... 
doi:10.1375/twin.14.4.347 pmid:21787119 fatcat:nd3v7dx75zdjlcazhbhhlc73im

Integrative analysis of gene expression and phenotype data [article]

Min Xu
2015 arXiv   pre-print
We propose a method of automated multi-dimensional profiling which uses gene expression similarity.  ...  Using our method, we discovered cancer subtype-specific network modules, as well as the ways in which these modules coordinate.  ...  Large-scale prediction of phenotype profiles To test the general applicability of our method, we performed a large-scale analysis of 587 human microarray datasets (see the Methods section for details on  ... 
arXiv:1506.08511v1 fatcat:r2p6njcjbvho5afjnilewfmj64

Genetic Modifiers of Hereditary Neuromuscular Disorders and Cardiomyopathy

Sholeh Bazrafshan, Hani Kushlaf, Mashhood Kakroo, John Quinlan, Richard C. Becker, Sakthivel Sadayappan
2021 Cells  
the University of Cincinnati and characterized the clinical phenotype of 14 patients correlating with their next-generation sequencing data.  ...  The data were retrieved from the electronic medical records of the 14 patients included in the current study and comprised neurologic and cardiac phenotype and genetic reports which included comparative  ...  Acknowledgments: We acknowledge the Center for Health Information, Department of Biomedical Informatics, University of Cincinnati College of Medicine, for providing retrospective genetic and clinical data  ... 
doi:10.3390/cells10020349 pmid:33567613 fatcat:ituniupwxjaxzaaplrcv7c2fmy

Human genome meeting 2016

A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin (+828 others)
2016 Human Genomics  
Further, targeted quantitative analysis of a subset of discriminating metabolites using tandem mass spectrometry provided a reliable laboratory method to detect children with ASD.  ...  Objectives From the first description by Leo Kanner [1], autism has been an enigmatic neurobehavioral phenomenon.  ...  Acknowledgements Funding for research and development is acknowledged for Project: "Research Oriented Data Management and Analysis" at the Ucar Lab by The Jackson Laboratory, USA.  ... 
doi:10.1186/s40246-016-0063-5 pmid:27294413 pmcid:PMC4896275 fatcat:ycjj53ixrbauvnusibuz76y7bm

Matrix Biology Europe - July 2018 Meeting Celebrating 50 years of Federation of European Connective Tissue Societies Meetings(organised by the British Society for Matrix Biology and the University of Manchester Wellcome Trust Centre for Cell-Matrix Resear

2018 International journal of experimental pathology (Print)  
Materials and Methods: A new PA was designed in our group, and different stiffness of PA gel was obtained by introducing different concentrations of CaCl 2 .  ...  This study highlights the potential for targeting CSCs via mechanical property of tumour microenvironment as promising therapeutic strategy that inhibit tumour progression.  ...  Materials and Methods: The Human Combinatorial Antibody Library (HuCAL) was used for the screening of antibodies.  ... 
doi:10.1111/iep.12294 fatcat:tawvze6nore3vm4mwvo54y2nx4

Abstracts from the 51st European Society of Human Genetics Conference: Oral Presentations

2019 European Journal of Human Genetics  
Together these findings define a single founder gene mutation as a cause of RP in families of Pakistani descent, and strongly suggest that CLCC1 function is crucial for maintaining retinal integrity and  ...  We used imputed genotypes from genome-wide arrays and measures of high (HDL), low density lipoproteincholesterol (LDL) and triglycerides from UKHLS (N = 9,961), two isolated Greek populations from the  ...  Analysis of their phenotypes is enhancing the range of available models that are relevant for human diseases.  ... 
doi:10.1038/s41431-019-0407-4 fatcat:3d23n3msz5fulchpvpfipze6pq

Gait-level analysis of mouse open field behavior using deep learning-based pose estimation [article]

Keith Sheppard, Justin Gardin, Gautam Sabnis, Asaf Peer, Megan Darrell, Sean Deats, Brian Geuther, Cathleen M Lutz, Vivek Kumar
2020 bioRxiv   pre-print
Here, we develop a simple assay that allows adoption of the commonly used open field apparatus for gait and whole body posture analysis.  ...  These results provide one of the largest laboratory mouse gait-level data resources for the research community and show the utility of automated machine learning approaches for biological insights.  ...  For loss, we borrow the approach used in the original HRNet description [48] . For each keypoint label, we generate a 2D gaussian distribution centered on the respective keypoint.  ... 
doi:10.1101/2020.12.29.424780 fatcat:pydid6d5ijh7xfsgl2mzspml54

Abstracts from the 53rd European Society of Human Genetics (ESHG) Conference: Oral Presentations

2020 European Journal of Human Genetics  
Furthermore, Abstracts from the 53rd European Society of Human Genetics (ESHG) Conference: Oral Presentations thorough phenotype studies for seven of the genes with evidence of mutational burden were performed  ...  We here focus on seven genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN and LEO1) for detailed clinical descriptions to delineate the associated phenotypes and clinical presentation of these specific and  ...  Material and Methods: We performed exome sequencing, in vitro and in vivo studies. Clinical genetic (re)evaluation was performed using a Human Phenotype Ontology scoring list.  ... 
doi:10.1038/s41431-020-00740-6 pmid:33262484 fatcat:6bfe5kviofdd7fw5tcdr6y3cgu

Abstracts from the Human Genome Meeting 2018

2018 Human Genomics  
Acknowledgements Part of this research has been conducted using the UK Biobank Resource (application reference no. 19664).  ...  Acknowledgments We are grateful to all members of the Laboratory for Autoimmune Diseases for their expert technical assistance Acknowledgements The study was supported by the Russian Science Foundation  ...  To dissect the causal role of thyroid function in human phenome, we conducted a Mendelian randomization study of TSH and FT4 levels.  ... 
doi:10.1186/s40246-018-0138-6 fatcat:nl6xhsuchzgbxik4pjwjvbbkie

Abstracts for the 41st Human Genetics Society of Australasia Annual Scientific Meeting Brisbane, Queensland August 5–8, 2017

2017 Twin Research and Human Genetics  
for genetic counseling pre and post implementation of those guidelines; to ascertain the rate for non-attendance at genetics clinics and the rate of positive germline BRCA mutations.  ...  A total of 24% tested positive for a germline BRCA mutation. Conclusion: Referral rates increased since the implementation of the national guidelines.  ...  Initial analysis was performed for each phenotype independently, followed by a phenome approach.  ... 
doi:10.1017/thg.2017.47 pmid:28975874 fatcat:zytbdrepzvfrxio34wc3gs2nni

Single Strand Assimilation [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Skeletal Map: The skeletal map uses only microsatellite marker data.  ...  These methods apparently obviate the need for using human embryos to which moral, ethical and legal objections exist.  ...  S No human embryos are supposed to be generated for the purpose of extracting stem cells or no fertilized and unused eggs generated by the process of in vitro artificial fertilization should be used for  ... 
doi:10.1007/978-1-4020-6754-9_15672 fatcat:2x2wsjganfaznnshm5kvluxr7a

Sycamore (Platanus spp) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Skeletal Map: The skeletal map uses only microsatellite marker data.  ...  These methods apparently obviate the need for using human embryos to which moral, ethical and legal objections exist.  ...  S No human embryos are supposed to be generated for the purpose of extracting stem cells or no fertilized and unused eggs generated by the process of in vitro artificial fertilization should be used for  ... 
doi:10.1007/978-1-4020-6754-9_16470 fatcat:vd3dng4xina5piwpaioaz25tf4

Abstracts for the 32nd Human Genetics Society of Australasia Annual Scientific Meeting

2008 Twin Research and Human Genetics  
Transgenic HD mouse model studies have shown that raising mice in an enriched environment delays the onset of symptoms, leading us to consider whether premorbid lifestyle affects age-at-onset in humans  ...  This association was most apparent for passivity during the teens and in men.  ...  OMIM represents an up-to-date description of the human phenome, at least as far as monogenic diseases are concerned.  ... 
doi:10.1375/twin.11.4.431 fatcat:ph2ps27rn5bjxm5libxfqboqli
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