Data mining

Content tagged with Data mining

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DRSC/TRiP and DRSC-BTRR Office Hours

News
New this fall: Online office hours! Do you have questions about modifying Drosophila cell lines with CRISPR or performing large-scale cell screens? Questions about in vivo RNAi with TRiP fly stocks or CRISPR knockout or activation with our sgRNA fly...

New publications from the DRSC bioinformatics team

News
The DRSC bioinformatics team, led by Dr. Claire Yanhui Hu, has recently published two new papers. One reports development of BioLitMine, an advanced literature mining resource. The other provides an overview of our online resources, which can be grouped...

DRSC Bioinformatics launches iProteinDB and BioLitMine

News
We have two new online tools available: iProteinDB and BioLitMine. Both continue our series of resources aimed at integrating existing information in new ways to facilitate data mining and development of new hypotheses. In addition, iProteinDB includes a...

Missed us at ADRC 2018? View our workshop slides!

News
Thank you to all those who attended our workshop at last week's Annual Drosophila Research Conference in Philadelphia, PA, USA. It was great to talk fly stocks, cell screens, and bioinformatics with the community. We are here to help and look forward to...

Pooled-format CRISPR screens in Drosophila cells

News
The DRSC/TRiP-FGR is pleased to support collaborations on pooled CRISPR screens using the method recently, reported in eLife by Viswanatha et al. (PDF download file below). From the abstract: "... Here, we developed a site-specific integration strategy...

DRSC & TRiP Workshop at ADRC

Event
The DRSC & TRiP will be hosting a workshop at the Annual Drosophila Research Conference in Philadelphia, PA. The workshop is scheduled for Friday, April 13th from 1:45 to 3:45 PM. Come hear from DRSC & TRiP leaders Norbert Perrimon, Jonathan Zirin...

Bibliographic References tagged with Data mining

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Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim, Mujeeb Qadiri, Chenxi Gao, Jonathan Zirin, Stephanie E Mohr, and Norbert Perrimon. 2024. “FlyRNAi.Org 2025 Update-Expanded Resources for New Technologies and Species.”. Nucleic Acids Research. doi:10.1093/nar/gkae917
Yanhui Hu, Aram Comjean, Jonathan Rodiger, Weihang Chen, Ah-Ram Kim, Mujeeb Qadiri, Chenxi Gao, Jonathan Zirin, Stephanie E Mohr, and Norbert Perrimon. 2024. “FlyRNAi.Org 2025 Update-Expanded Resources for New Technologies and Species.”. Nucleic Acids Research. doi:10.1093/nar/gkae917
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, and Erica Larschan. 2021. “TIMEOR: A Web-Based Tool to Uncover Temporal Regulatory Mechanisms from Multi-Omics Data”. Nucleic Acids Res, 49, W1, Pp. W641-W653. doi:10.1093/nar/gkab384
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, and Erica Larschan. 2021. “TIMEOR: A Web-Based Tool to Uncover Temporal Regulatory Mechanisms from Multi-Omics Data”. Nucleic Acids Res, 49, W1, Pp. W641-W653. doi:10.1093/nar/gkab384
Yanhui Hu, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yue Gao, Corey Forman, Grace Kim, Jonathan Rodiger, Irene Papatheodorou, Gilberto Dos Santos, Stephanie Mohr, and Norbert Perrimon. 2021. “DRscDB: A Single-Cell RNA-Seq Resource for Data Mining and Data Comparison across Species”. Comput Struct Biotechnol J, 19, Pp. 2018-26. doi:10.1016/j.csbj.2021.04.021
Yanhui Hu, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yue Gao, Corey Forman, Grace Kim, Jonathan Rodiger, Irene Papatheodorou, Gilberto Dos Santos, Stephanie Mohr, and Norbert Perrimon. 2021. “DRscDB: A Single-Cell RNA-Seq Resource for Data Mining and Data Comparison across Species”. Comput Struct Biotechnol J, 19, Pp. 2018-26. doi:10.1016/j.csbj.2021.04.021
A.M. Conard, N. Goodman, Hu Y, N. Perrimon, R. Singh, C. Lawrence, and E. Larschan. 2020. “TIMEOR: A Web-Based Tool to Uncover Temporal Regulatory Mechanisms from Multi-Omics Data [NOTE: A Modified Final Version Was Published in NAR and Is Now Available]”. BioRxiv
A.M. Conard, N. Goodman, Hu Y, N. Perrimon, R. Singh, C. Lawrence, and E. Larschan. 2020. “TIMEOR: A Web-Based Tool to Uncover Temporal Regulatory Mechanisms from Multi-Omics Data [NOTE: A Modified Final Version Was Published in NAR and Is Now Available]”. BioRxiv
Yanhui Hu, Aram Comjean, Jonathan Rodiger, Yifang Liu, Yue Gao, Verena Chung, Jonathan Zirin, Norbert Perrimon, and Stephanie Mohr. 2020. “FlyRNAi.Org-the Database of the Drosophila RNAi Screening Center and Transgenic RNAi Project: 2021 Update”. Nucleic Acids Res. doi:10.1093/nar/gkaa936
Yanhui Hu, Aram Comjean, Jonathan Rodiger, Yifang Liu, Yue Gao, Verena Chung, Jonathan Zirin, Norbert Perrimon, and Stephanie Mohr. 2020. “FlyRNAi.Org-the Database of the Drosophila RNAi Screening Center and Transgenic RNAi Project: 2021 Update”. Nucleic Acids Res. doi:10.1093/nar/gkaa936
Yanhui Hu, Verena Chung, Aram Comjean, Jonathan Rodiger, Fnu Nipun, Norbert Perrimon, and Stephanie Mohr. 2020. “BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms”. G3 (Bethesda). doi:10.1534/g3.120.401775
Yanhui Hu, Verena Chung, Aram Comjean, Jonathan Rodiger, Fnu Nipun, Norbert Perrimon, and Stephanie Mohr. 2020. “BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms”. G3 (Bethesda). doi:10.1534/g3.120.401775
Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie Mohr, and Norbert Perrimon. 2017. “Molecular Interaction Search Tool (MIST): An Integrated Resource for Mining Gene and Protein Interaction Data”. Nucleic Acids Res, 46, D1, Pp. D567-D574. doi:10.1093/nar/gkx1116
Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie Mohr, and Norbert Perrimon. 2017. “Molecular Interaction Search Tool (MIST): An Integrated Resource for Mining Gene and Protein Interaction Data”. Nucleic Acids Res, 46, D1, Pp. D567-D574. doi:10.1093/nar/gkx1116
Julia Wang, Rami Al-Ouran, Yanhui Hu, Seon-Young Kim, Ying-Wooi Wan, Michael Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Aram Comjean, Stephanie Mohr, Undiagnosed Diseases Network, Norbert Perrimon, Zhandong Liu, and Hugo Bellen. 2017. “MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome”. Am J Hum Genet, 100, 6, Pp. 843-53. doi:10.1016/j.ajhg.2017.04.010
Julia Wang, Rami Al-Ouran, Yanhui Hu, Seon-Young Kim, Ying-Wooi Wan, Michael Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Aram Comjean, Stephanie Mohr, Undiagnosed Diseases Network, Norbert Perrimon, Zhandong Liu, and Hugo Bellen. 2017. “MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome”. Am J Hum Genet, 100, 6, Pp. 843-53. doi:10.1016/j.ajhg.2017.04.010
Yanhui Hu, Aram Comjean, Stephanie Mohr, The FlyBase Consortium, and Norbert Perrimon. 2017. “Gene2Function: An Integrated Online Resource for Gene Function Discovery”. G3 (Bethesda). doi:10.1534/g3.117.043885
Yanhui Hu, Aram Comjean, Stephanie Mohr, The FlyBase Consortium, and Norbert Perrimon. 2017. “Gene2Function: An Integrated Online Resource for Gene Function Discovery”. G3 (Bethesda). doi:10.1534/g3.117.043885
AJ Copeland, Comjean, Perrimon, and SE Mohr. 2017. “Online View of High-Content Image Data Generated in the Genome-Wide Screen Described in Neumüller et Al. 2013, ‘Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses,’ Made Possible Using OMERO at HMS”
AJ Copeland, Comjean, Perrimon, and SE Mohr. 2017. “Online View of High-Content Image Data Generated in the Genome-Wide Screen Described in Neumüller et Al. 2013, ‘Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses,’ Made Possible Using OMERO at HMS”