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The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools

Ivo D. Dinov, Petros Petrosyan, Zhizhong Liu, Paul Eggert, Alen Zamanyan, Federica Torri, Fabio Macciardi, Sam Hobel, Seok Woo Moon, Young Hee Sung, Zhiguo Jiang, Jennifer Labus (+6 others)
2013 Brain Imaging and Behavior  
These are implemented as graphical workflow protocols in the context of analyzing imaging (sMRI, fMRI, DTI), phenotypic (demographic, clinical), and genetic (SNP) data.  ...  In this paper, we demonstrate several advanced computational neuroimaging and genetics case-studies, and end-to-end pipeline solutions.  ...  Some of the data processed in this study was partly funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904).  ... 
doi:10.1007/s11682-013-9248-x pmid:23975276 pmcid:PMC3933453 fatcat:4ghlkgwe4vbo3jndkg56nz3r7y

Neurological imaging: statistics behind the pictures

Ivo D Dinov
2011 Imaging in Medicine  
The diverse phenotypes and significant normal and pathological brain variability demand reliable and efficient statistical methodologies to model, analyze and interpret raw neurological images and derived  ...  This greatly facilitates the processes of algorithm development, mathematical modeling and testing of novel computational techniques for analyzing multimodal neuroimaging data.  ...  protocols, incorporating modern Grid and Cloud computing infrastructures, and supports the engagement of multidisciplinary investigators in such translational studies.  ... 
doi:10.2217/iim.11.37 pmid:22180753 pmcid:PMC3237637 fatcat:ftwdvp25mjgxliasbaduaylkdm

Large-scale analysis of neuroimaging data on commercial clouds with content-aware resource allocation strategies

Massimo Minervini, Cristian Rusu, Mario Damiano, Valter Tucci, Angelo Bifone, Alessandro Gozzi, Sotirios A Tsaftaris
2014 The international journal of high performance computing applications  
as "mouse brain phenotyping".  ...  In this paper we use a commercial cloud platform for brain neuroimaging and analysis.  ...  ACKNOWLEDGEMENTS The authors would like to thank Alberto Galbusera for assistance with data collection and PiCloud Inc., particularly Ken Elkabany, for providing technical assistance.  ... 
doi:10.1177/1094342013519483 fatcat:qtchpzss2fhjtikjjfebg5kjmu

Neuropathophysiology, Genetic Profile, and Clinical Manifestation of Mucolipidosis IV—A Review and Case Series

Aleksandra Jezela-Stanek, Elżbieta Ciara, Karolina M. Stepien
2020 International Journal of Molecular Sciences  
This review aims to outline the pathophysiology and genetic defects of this condition with a focus on the genotype–phenotype correlation amongst cases published in the literature.  ...  The authors will present their own clinical observations and long-term outcomes in adult MLIV cases.  ...  cerebellar disease in the MLIV mouse model (but has not yet been tested in humans) [5] Molecular analysis is the most effective diagnostic test, because it allows determination of the cause of the disease  ... 
doi:10.3390/ijms21124564 pmid:32604955 pmcid:PMC7348969 fatcat:zevuz4sxd5aq5d345k7tgqxixi

OpenNeuro: An open resource for sharing of neuroimaging data [article]

Christopher J Markiewicz, Krzysztof Jacek Gorgolewski, Franklin Feingold, Ross Blair, Yaroslav O Halchenko, Eric Miller, Nell Hardcastle, Joe Wexler, Oscar Esteban, Mathias Goncalves, Anita S Jwa, Russell Poldrack
2021 bioRxiv   pre-print
The sharing of research data is essential to ensure reproducibility and maximize the impact of public investments in scientific research.  ...  The impact of the shared data is evident in a growing number of published reuses, currently totalling more than 150 publications.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1101/2021.06.28.450168 fatcat:oeaxuspnubdydmj5fyfgych7dy

Automated Landmarking via Multiple Templates [article]

Chi Zhang, Arthur Porto, Sara Rolfe, Altan Kocatulum, A. Murat Maga
2022 bioRxiv   pre-print
Geometric morphometrics based on landmark data has been increasingly used in biomedical and biological researchers for quantifying complex phenotypes.  ...  This K-means method uses an approximation of the total morphological variation in the dataset to suggest samples within the population to be used as landmark templates.  ...  In our sample, this leads reference point clouds with 791 and 674 points for mouse and ape datasets respectively. 3) For each point in the reference point cloud, the point closest to the target model is  ... 
doi:10.1101/2022.01.04.474967 fatcat:3n6rspio4bfcpf7vzandrj3ql4

RIKEN MetaDatabase

Norio Kobayashi, Satoshi Kume, Kai Lenz, Hiroshi Masuya
2018 International Journal on Semantic Web and Information Systems (IJSWIS)  
The platform was released in April 2015, and 113 databases, including mammalian, plant, bioresource and image databases, with 26 ontologies have been published using this platform as of January 2017.  ...  Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly.  ...  be generated in the RIKEN Cloud Service.  ... 
doi:10.4018/ijswis.2018010106 fatcat:o3bx674wtrgplb23tumhj3c7ia

Graphical neuroimaging informatics: Application to Alzheimer's disease

John Darrell Van Horn, Ian Bowman, Shantanu H. Joshi, Vaughan Greer
2013 Brain Imaging and Behavior  
In this article, we illustrate the utility of INVIZIAN for simultaneous exploration and mining a large collection of extracted cortical surface data arising in clinical neuroimaging studies of patients  ...  Users can fluidly interact with an entire collection of cortical surfaces using only their mouse.  ...  Acknowledgments The authors wish to thank the faculty and staff of the Institute of Neuroimaging and Informatics of the University of Southern California and the Laboratory of Neuro Imaging (LONI) at the  ... 
doi:10.1007/s11682-013-9273-9 pmid:24203652 pmcid:PMC4012008 fatcat:ws5vsn5sizb53kkzdspyri3vru

Neuropathology of brain and spinal malformations in a case of monosomy 1p36

Naoko Shiba, Ray AM Daza, Lisa G Shaffer, A Barkovich, William B Dobyns, Robert F Hevner
2013 Acta Neuropathologica Communications  
Neuroimaging studies suggest that monosomy 1p36 is associated with brain malformations including polymicrogyria and nodular heterotopia, but the histopathology of these lesions is unknown.  ...  Neuroimaging studies suggest that monosomy 1p36 is associated with brain malformations including polymicrogyria and nodular heterotopia, but the histopathology of these lesions is unknown.  ...  Table 1 1 Genes related to development and function of nervous system within region of 1p36.21-1p36.33 deletion Symbol Description Locus Site Mouse ortholog Human diseases Null mouse phenotype  ... 
doi:10.1186/2051-5960-1-45 pmid:24252393 pmcid:PMC3893467 fatcat:yuat54ahgbe5zdcufirfurprta

Cerebrovascular Disease Knowledge Portal

Katherine M. Crawford, Cristina Gallego-Fabrega, Christina Kourkoulis, Laura Miyares, Sandro Marini, Jason Flannick, Noel P. Burtt, Marcin von Grotthuss, Benjamin Alexander, Maria C. Costanzo, Neil H. Vaishnav, Rainer Malik (+4 others)
2018 Stroke  
Acknowledgments We would like to recognize all members of the technical teams at the Broad Institute and American Heart Association Institute for Cardiovascular Precision Medicine.  ...  Commands contained in these scripts are submitted to the cloud computing system, where they are executed in parallel using the appropriate kernels.  ...  Once access to the data is granted, users are able to analyze data in the secure cloud-based computational workspace provided by the PMP.  ... 
doi:10.1161/strokeaha.117.018922 pmid:29335331 pmcid:PMC5780219 fatcat:psk5tf3wbbe7bpm5ejym5z2ujm

Common variants of NRXN1, LRP1B and RORA are associated with increased ventricular volumes in psychosis - GWAS findings from the B-SNIP deep phenotyping study [article]

Ney Alliey-Rodriguez, Tamar A. Grey, Rebecca Shafee, Jaya Padmanabhan, Neeraj Tandon, Madeline Klinger, Jonathan Spring, Lucas Coppes, Katherine Reis, Matcheri S. Keshavan, Diane Gage, Steven McCarroll (+18 others)
2017 bioRxiv   pre-print
This is the first report of common genetic variants associated with these intermediate phenotypes.  ...  Significant associations were observed with two cerebrospinal fluid volumes: the temporal horn of left lateral ventricle was associated with NRXN1, and the volume of the cavum septum pellucidum was associated  ...  The Bionimbus PDC allows users authorized by NIH to compute over human genomic data in a secure compliant fashion. The Bionimbus PDC is part of the OSDC ecosystem.  ... 
doi:10.1101/175489 fatcat:u6me2ksb5felzczmvj7u75ppdq

Affective, neurocognitive and psychosocial disorders associated with traumatic brain injury and post-traumatic epilepsy

Bridgette D. Semple, Akram Zamani, Genevieve Rayner, Sandy R. Shultz, Nigel C. Jones
2018 Neurobiology of Disease  
To drive the field forward towards improved treatment strategies, it is imperative that both seizures and neurobehavioral outcomes are assessed in parallel after TBI, both in patient populations and preclinical  ...  Clinical studies in this arena are often challenged by the confounding effects of anti-seizure medications, while preclinical studies have rarely examined an adequately extended time course to fully capture  ...  Acknowledgements The authors acknowledge funding from the National Institutes of HealthRFA-NS-16-012 -Epilepsy Bioinformatics Study for Antiepileptogenic Therapy (EpiBioS4Rx) project; the National Health  ... 
doi:10.1016/j.nbd.2018.07.018 pmid:30059725 pmcid:PMC6348140 fatcat:fafdxefm3zc35k6grbvkd3owyy

A web-based brain atlas of the vervet monkey, Chlorocebus aethiops

Roger P. Woods, Scott C. Fears, Matthew J. Jorgensen, Lynn A. Fairbanks, Arthur W. Toga, Nelson B. Freimer
2011 NeuroImage  
The averaged MRI atlas is also available as a volume in Neuroimaging Informatics Technology Initiative format.  ...  Despite the extended time period since their divergence, the major sulcal and subcortical landmarks in vervets are highly conserved relative to those described in macaques.  ...  Acquisition of the cryomacrotome data was supported in part by the United States Department of Energy contract DE-FC03-87-ER60615.  ... 
doi:10.1016/j.neuroimage.2010.09.070 pmid:20923706 pmcid:PMC3008312 fatcat:lunvhd3yrbca5prht7viu76nga

NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures

Rivka Colen, Ian Foster, Robert Gatenby, Mary Ellen Giger, Robert Gillies, David Gutman, Matthew Heller, Rajan Jain, Anant Madabhushi, Subha Madhavan, Sandy Napel, Arvind Rao (+4 others)
2014 Translational Oncology  
goals in cancer research.  ...  The first workshop focused on clinical and scientific requirements, exploring our knowledge of phenotypic characteristics of cancer biological properties to determine whether the field is sufficiently  ...  This newer approach to integrated cross-species testing, termed coclinical trials, involves concurrent assessment of novel drug combinations in mouse and human-in-mouse models of tumors, and in patients  ... 
doi:10.1016/j.tranon.2014.07.007 pmid:25389451 pmcid:PMC4225695 fatcat:mmc4hxums5b2ppttzd37ffsoxi

Fragile X Syndrome: A Model of Gene-Brain-Behavior Relationships

Randi J Hagerman, Paul J Hagerman
2001 Molecular Genetics and Metabolism  
The larger head height is likely related to the larger brains seen by neuroimaging in patients with FXS compared to controls (57-59).  ...  Early studies of the knockout mouse suggested an enhanced number of dendritic connections that have also been seen in three humans with FXS (23,24,26).  ...  Background Genes Influence the Phenotype The knockout mouse models brought our attention to the influence of background gene effects on the fragile X phenotype.  ... 
doi:10.1006/mgme.2001.3225 pmid:11592806 fatcat:sq7h4p55tndwrnltcczmcnxq7a
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