Identifying genomic islands with deep neural networks.

Autor: Assaf, Rida¹ (AUTHOR) rida@uchicago.edu, Fangfang Xia^2,3 (AUTHOR), Stevens, Rick^2,4 (AUTHOR)

Publikováno v: BMC Genomics. 6/4/2021 Supplement 3, Vol. 22, p1-11. 11p. 1 Color Photograph, 1 Diagram, 5 Charts, 1 Graph.

Feature Transformations to Enhance Representation Learning

Autor: Assaf, Rida

Machine learning has crowned itself as a breakthrough in a number of domains, such as computer vision and natural language processing, matching and sometimes exceeding human level performance on certain supervised learning tasks.A major factor drivin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::3be2b794ad6663b8412650f4d643cec0

Identifying Operons with Deep Neural Networks

Autor: Assaf, Rida, Xia, Fangfang, Stevens, Rick

Genes in prokaryotic genomes often assemble in transcription units called operons. Detecting operons are of significant importance to help infer functionality and detect regulatory networks. Several tools have been proposed to detect such operons com

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=sharebioRxiv::0040eab38f9ee95d85547d783757d700

Monte Carlo Automatic Integration with Dynamic Parallelism in CUDA.

Autor: de Doncker, Elise, Kapenga, John, Assaf, Rida

Publikováno v: Numerical Computations with GPUs; 2014, p273-298, 26p

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.

Autor: Olson RD; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Assaf R; Department of Computer Science, American University of Beirut, Beirut, Lebanon., Brettin T; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA., Conrad N; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Cucinell C; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Davis JJ; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Dempsey DM; Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA., Dickerman A; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Dietrich EM; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Kenyon RW; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Kuscuoglu M; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA., Lefkowitz EJ; Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA., Lu J; J. Craig Venter Institute, Rockville, MD 20850, USA., Machi D; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Macken C; Department of Statistics, University of Auckland, Auckland, New Zealand., Mao C; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Niewiadomska A; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA., Nguyen M; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Olsen GJ; Department of Microbiology, University of Illinois, Urbana, IL 61801, USA., Overbeek JC; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Parrello B; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA., Parrello V; Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA., Porter JS; Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA., Pusch GD; Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA., Shukla M; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Singh I; J. Craig Venter Institute, Rockville, MD 20850, USA., Stewart L; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA., Tan G; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA., Thomas C; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., VanOeffelen M; Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA., Vonstein V; Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA., Wallace ZS; Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA.; Department of Computer Science and Engineering, University of California, San Diego, CA 92039, USA., Warren AS; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Wattam AR; University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA., Xia F; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Yoo H; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA.; Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA., Zhang Y; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA., Zmasek CM; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA., Scheuermann RH; Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA.; Department of Pathology, University of California, San Diego, CA 92093, USA.; Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.; Global Virus Network, Baltimore, MD 21201, USA., Stevens RL; Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.; Department of Computer Science, University of Chicago, Chicago, IL 60637, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2023 Jan 06; Vol. 51 (D1), pp. D678-D689.