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Exploring Genomic Datasets

Luca Nanni, Pietro Pinoli, Arif Canakoglu, Stefano Ceri
<span title="">2018</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vxrc3vebzzachiwy3nopwi3h5u" style="color: black;">Proceedings of the 5th International Workshop on Exploratory Search in Databases and the Web - ExploreDB 2018</a> </i> &nbsp;
Genomic data management is focused on achieving high performance over big datasets using batch, cloud-based architectures; this enables the execution of massive pipelines, but hampers the capability of  ...  programming style of Python, and provides transparency of access when exploration requires integrating local and remote resources.  ...  ACKNOWLEDGEMENTS This work is supported by the ERC Advanced Grant 693174 "Data Driven Genomic Computing" (GeCo).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/3214708.3214710">doi:10.1145/3214708.3214710</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/sigmod/NanniPCC18.html">dblp:conf/sigmod/NanniPCC18</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dn5sb7uoq5bsfgecpabuupuc3m">fatcat:dn5sb7uoq5bsfgecpabuupuc3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307113304/https://re.public.polimi.it/retrieve/handle/11311/1095264/392193/Nanni.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/2a/a52af3cabd7e092e39a30fe87149a7733da09853.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/3214708.3214710"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

MyoMiner: explore gene co-expression in normal and pathological muscle

Apostolos Malatras, Ioannis Michalopoulos, Stéphanie Duguez, Gillian Butler-Browne, Simone Spuler, William J. Duddy
<span title="2020-05-11">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rbtzjpig4jcsfbjr5yo23sjnj4" style="color: black;">BMC Medical Genomics</a> </i> &nbsp;
These co-expression analyses will help investigators to delineate the tissue-, cell-, and pathology-specific elements of muscle protein interactions, cell signaling and gene regulation.  ...  the option to include linked genes from the database and (b) a comparison tool from which the users can test whether any two correlation coefficients from different conditions are significantly different  ...  Probes-to-genes mapping At the time of chip design, Affymetrix selection of probes relied on early genome and transcriptome annotation which is significantly different from our current knowledge.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-020-0712-3">doi:10.1186/s12920-020-0712-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32393257">pmid:32393257</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y764zniifjb4fjo2ceign4efwq">fatcat:y764zniifjb4fjo2ceign4efwq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201104184633/https://hal.sorbonne-universite.fr/hal-02746400/file/Malatras2020_Article_MyoMinerExploreGeneCo-expressi.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/61/0a/610aea2937c70f2f26138435bcc3f3430b6687be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-020-0712-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files [article]

Jayaram Kancherla, Yifan Yang, Hyeyun Chae, Hector Corrada Bravo
<span title="2019-12-05">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The File Server library decouples data from analysis workflows and provides an abstract interface to define computations independent of the location, format or structure of the file.  ...  AbstractGenomic data repositories like The Cancer Genome Atlas (TCGA), Encyclopedia of DNA Elements (ENCODE), Bioconductor's AnnotationHub and ExperimentHub etc., provide public access to large amounts  ...  and Epiviz (Chelaru et al. 2014) , an interactive and integrative functional genome browser to visualize and explore these datasets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/865295">doi:10.1101/865295</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/noyv6ebdu5ajphhjz55j3ealyq">fatcat:noyv6ebdu5ajphhjz55j3ealyq</a> </span>
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Guided visual exploration of genomic stratifications in cancer

Marc Streit, Alexander Lex, Samuel Gratzl, Christian Partl, Dieter Schmalstieg, Hanspeter Pfister, Peter J Park, Nils Gehlenborg
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
Guided visual exploration of genomic stratifications in cancer To the Editor: Cancer is a heterogeneous disease, and molecular profiling of tumors from large cohorts has enabled characterization of new  ...  Although we focus on cancer genomics here, StratomeX can also be applied in other disease cohorts. Thousands of patient stratifications can be derived from large cancer genomics datasets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth.3088">doi:10.1038/nmeth.3088</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25166867">pmid:25166867</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4196637/">pmcid:PMC4196637</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qojlugc57fahlanwwoel6575ei">fatcat:qojlugc57fahlanwwoel6575ei</a> </span>
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Overview of GeCo: A Project for Exploring and Integrating Signals from the Genome [chapter]

Stefano Ceri, Anna Bernasconi, Arif Canakoglu, Andrea Gulino, Abdulrahman Kaitoua, Marco Masseroli, Luca Nanni, Pietro Pinoli
<span title="">2018</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jyopc6cf5ze5vipjlm4aztcffi" style="color: black;">Communications in Computer and Information Science</a> </i> &nbsp;
We specifically focus on how the GeCo project is contributing to tertiary data analysis, by overviewing the main results of the project so far and by describing its future scenarios.  ...  In particular, tertiary data analysis is concerned with the integration of heterogeneous regions of the genome; this is an emerging and increasingly important problem of genomic computing, because regions  ...  primitives for data exploration spanning from select, sort, and discretize, to clustering, and pattern extraction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-319-96553-6_4">doi:10.1007/978-3-319-96553-6_4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/77dq3euaijdxndikozxqlcmou4">fatcat:77dq3euaijdxndikozxqlcmou4</a> </span>
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Som-Based Class Discovery Exploring the ICA-Reduced Features of Microarray Expression Profiles

Andrei Dragomir, Seferina Mavroudi, Anastasios Bezerianos
<span title="">2004</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eaz5kv6drnd7hlqjuszvrhtqnm" style="color: black;">Comparative and Functional Genomics</a> </i> &nbsp;
Gene expression datasets are large and complex, having many variables and unknown internal structure.  ...  An entropy criterion allows each gene to be assigned to multiple classes, which is closer to the biological representation.  ...  Acknowledgements The authors would like to thank the European Social Fund (ESF), the Operational Program for Educational and Vocational Training II (EPEAEK II), and particularly the Program IRAKLEITOS,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cfg.444">doi:10.1002/cfg.444</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18629176">pmid:18629176</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447468/">pmcid:PMC2447468</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2fvwy3ybv5hxjkyxk5lpltxgse">fatcat:2fvwy3ybv5hxjkyxk5lpltxgse</a> </span>
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Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata

A. A. Hill, M. Crotta, B. Wall, L. Good, S. J. O'Brien, J. Guitian
<span title="">2017</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b4xnwzxv5re5rbc2gcpilgy5iy" style="color: black;">Royal Society Open Science</a> </i> &nbsp;
genomic and epidemiological metadata.  ...  Research Cite this article: Hill AA, Crotta M, Wall B, Good L, O'Brien SJ, Guitian J. 2017 Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining  ...  The views expressed are those of the authors and not necessarily those of the Food Standards Agency, the National Health Service, the NIHR, the Department of Health or Public Health England.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsos.160721">doi:10.1098/rsos.160721</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28405360">pmid:28405360</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5383817/">pmcid:PMC5383817</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d4wxte4w6rfbphgjek5uht7kva">fatcat:d4wxte4w6rfbphgjek5uht7kva</a> </span>
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PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets

Luca Nanni, Pietro Pinoli, Arif Canakoglu, Stefano Ceri
<span title="2019-11-08">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Available software packages are suitable for analyzing experimental files from such datasets one by one, but do not scale to thousands of experiments.  ...  PyGMQL provides distribution transparency (the ability to address a remote dataset) and query outsourcing (the ability to assign processing to a remote service) in an orthogonal way.  ...  Acknowledgements We thank all the members of the Data-Driven Genomic Computing research group at Politecnico di Milano for their continuous support and useful discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-3159-9">doi:10.1186/s12859-019-3159-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31703553">pmid:31703553</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6842186/">pmcid:PMC6842186</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zajbfoyq5jgphpxg2ozyrbfhzu">fatcat:zajbfoyq5jgphpxg2ozyrbfhzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209235626/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3159-9" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/79/aa/79aa9bcae8c8deb719a027b6e79d0bf2506c615a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-3159-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842186" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Differential Gene Expression and Weighted Correlation Network Dynamics in High-Throughput Datasets of Prostate Cancer

Taj Mohammad, Prithvi Singh, Deeba Shamim Jairajpuri, Lamya Ahmed Al-Keridis, Nawaf Alshammari, Mohd. Adnan, Ravins Dohare, Md Imtaiyaz Hassan
<span title="2022-06-01">2022</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mefn5t5kjndavkrqau5bzfpaoe" style="color: black;">Frontiers in Oncology</a> </i> &nbsp;
from The Cancer Genome Atlas (TCGA).  ...  To identify novel therapeutic targets and precise biomarkers implicated with prostate cancer, we performed a state-of-the-art bioinformatics study, beginning with analyzing high-throughput genomic datasets  ...  Sample phenotype data such as age at diagnosis, weight, batch variables, and gender were also collected from Xena. Both these datasets were back log-transformed in R to obtain raw integer counts.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fonc.2022.881246">doi:10.3389/fonc.2022.881246</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35719950">pmid:35719950</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC9198298/">pmcid:PMC9198298</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/crc74hdnzzakvbztgh4xftizgy">fatcat:crc74hdnzzakvbztgh4xftizgy</a> </span>
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Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets

Yalchin Oytam, Fariborz Sobhanmanesh, Konsta Duesing, Joshua C. Bowden, Megan Osmond-McLeod, Jason Ross
<span title="2016-09-01">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
rejection and signal preservation across different studies makes it an effective alternative method to deal with batch effects in high-throughput genomic datasets.  ...  Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets.  ...  JB translated the Matlab code into C++ and also co-wrote the R package. MO conducted the experiments associated with datasets 1 and 2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1212-5">doi:10.1186/s12859-016-1212-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27585881">pmid:27585881</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5009651/">pmcid:PMC5009651</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/unfpioxcjbbndkc2rhhcpakzna">fatcat:unfpioxcjbbndkc2rhhcpakzna</a> </span>
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Heterogeneous Large Datasets Integration Using Bayesian Factor Regression

Alejandra Avalos-Pacheco, David Rossell, Richard S. Savage
<span title="">2020</span> <i title="Institute of Mathematical Statistics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lytpoddhxnfjxbb3llrtiyy45m" style="color: black;">Bayesian Analysis</a> </i> &nbsp;
The model provides a tool for data exploration via dimensionality reduction and sparse low-rank covariance estimation while correcting for a range of batch effects.  ...  Our model provides a novel approach to latent factor regression that balances sparsity with sensitivity in scenarios both with and without batch effects and is highly computationally efficient.  ...  Acknowledgments We thank Chris Yau for valuable insights and Veronika Ročková for providing the FastBFA package.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1214/20-ba1240">doi:10.1214/20-ba1240</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q2tdxx6v3vbh3ep357yl6rn6vu">fatcat:q2tdxx6v3vbh3ep357yl6rn6vu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427214100/https://projecteuclid.org/journals/bayesian-analysis/advance-publication/Heterogeneous-Large-Datasets-Integration-Using-Bayesian-Factor-Regression/10.1214/20-BA1240.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/8a/df8a56502038bf4cfc092c2b895c9a8360aab06f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1214/20-ba1240"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Federated Geometric Monte Carlo Clustering to Counter Non-IID Datasets [article]

Federico Lucchetti, Jérémie Decouchant, Maria Fernandes, Lydia Y. Chen, Marcus Völp
<span title="2022-04-23">2022</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
FedGMCC outperforms FedAvg and FedProx in terms of convergence rates on the EMNIST62 and a genomic sequence classification datasets (by up to +63%).  ...  FedGMCC yields an improved accuracy (+4%) on the genomic dataset with respect to CFL, in high non-IID feature space settings and label incongruency.  ...  back to clients.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2204.11017v1">arXiv:2204.11017v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kztwskrshrffzp7hbpe2ulryfi">fatcat:kztwskrshrffzp7hbpe2ulryfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220427222209/https://arxiv.org/pdf/2204.11017v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/a2/06a26f42624dde15ee474a3879c14cd8b4b31850.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2204.11017v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Efficient logging and querying for blockchain-based cross-site genomic dataset access audit

Shuaicheng Ma, Yang Cao, Li Xiong
<span title="2020-07-21">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rbtzjpig4jcsfbjr5yo23sjnj4" style="color: black;">BMC Medical Genomics</a> </i> &nbsp;
We demonstrate that Blockchain can be used to build a time and space efficient log and query genomic dataset audit trail.  ...  The 2018 iDASH competition first track provides us with an opportunity to design efficient logging and querying system for cross-site genomic dataset access audit.  ...  Tsung-Ting Kuo, the organizer of iDASH competition 2018 first track, for providing informative Q&A and helpful advice!  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-020-0725-y">doi:10.1186/s12920-020-0725-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32693835">pmid:32693835</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uia7f3ja4zdabjubxezmmhaofq">fatcat:uia7f3ja4zdabjubxezmmhaofq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200806201328/https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-020-0725-y" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/90/e8/90e8716afa49342adf50ecc1e508e486f7a24f22.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-020-0725-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb

Lars G. Fritsche, Lauren J. Beesley, Peter VandeHaar, Robert B. Peng, Maxwell Salvatore, Matthew Zawistowski, Sarah A. Gagliano Taliun, Sayantan Das, Jonathon LeFaive, Erin O. Kaleba, Thomas T. Klumpner, Stephanie E. Moser (+7 others)
<span title="2019-06-13">2019</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
This study was conducted using data from 30,702 unrelated, genotyped patients of recent European descent from the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort within Michigan  ...  The primary focus of this paper is to demonstrate how we can combine PRS and electronic health records data to better understand the shared and unique genetic architecture and etiology of disease subtypes  ...  Acknowledgments The authors acknowledge the University of Michigan Medical School Central Biorepository for providing biospecimen storage, management, and distribution services in support of the research  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1008202">doi:10.1371/journal.pgen.1008202</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31194742">pmid:31194742</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6592565/">pmcid:PMC6592565</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yjyb63szsrbwtmvcjyv2pfqk3q">fatcat:yjyb63szsrbwtmvcjyv2pfqk3q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191214185745/https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1008202&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/58/9f/589f572ee615858a3ae16065122739071484232e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1008202"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592565" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Chest ImaGenome Dataset for Clinical Reasoning [article]

Joy T. Wu, Nkechinyere N. Agu, Ismini Lourentzou, Arjun Sharma, Joseph A. Paguio, Jasper S. Yao, Edward C. Dee, William Mitchell, Satyananda Kashyap, Andrea Giovannini, Leo A. Celi, Mehdi Moradi
<span title="2021-07-31">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images.  ...  With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels  ...  Acknowledgements This work was supported by the Rensselaer-IBM AI Research Collaboration, part of the IBM AI Horizons Network, and the IBM-MIT Critical Data Collaboration.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2108.00316v1">arXiv:2108.00316v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lfuj6nv2znghdd2vwnfljqee6e">fatcat:lfuj6nv2znghdd2vwnfljqee6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210804135657/https://arxiv.org/pdf/2108.00316v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/c8/a0c8b2ea62f6a11f2817ae5c73a9afc4b909390e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2108.00316v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>
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