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The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository

Authors: Yu-Ning Huang, Pooja Vinod Jaiswal, Anushka Rajes, Anushka Yadav, Dottie Yu, Fangyun Liu, Grace Scheg, Emma Shih, Grigore Boldirev, Irina Nakashidze, Aditya Sarkar, Jay Himanshu Mehta, Ke Wang, Khooshbu Kantibhai Patel, Mustafa Ali Baig Mirza, Kunali Chetan Hapani…

Citation: Genome Biology 2025 26:274

Content type: Research Published on: 9 September 2025
A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer

Authors: Mike Mason, Óscar Lapuente-Santana, Anni S. Halkola, Wenyu Wang, Raghvendra Mall, Xu Xiao, Jacob Kaufman, Jingxin Fu, Jacob Pfeil, Jineta Banerjee, Verena Chung, Han Chang, Scott D. Chasalow, Hung Ying Lin, Rongrong Chai, Thomas Yu…

Citation: Journal of Translational Medicine 2024 22:190

Content type: Research Published on: 21 February 2024
A novel estimator for the two-way partial AUC

Authors: Elias Chaibub Neto, Vijay Yadav, Solveig K. Sieberts and Larsson Omberg

Citation: BMC Medical Informatics and Decision Making 2024 24:57

Content type: Research Published on: 20 February 2024
The STEPWISE study: study protocol for a smartphone-based exercise solution for people with Parkinson’s Disease (randomized controlled trial)

Authors: Sabine Schootemeijer, Nienke M. de Vries, Eric A. Macklin, Kit C.B. Roes, Hilde Joosten, Larsson Omberg, Alberto Ascherio, Michael A. Schwarzschild and Bastiaan R. Bloem

Citation: BMC Neurology 2023 23:323

Content type: Study Protocol Published on: 12 September 2023
Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease

Authors: Jake Gockley, Kelsey S. Montgomery, William L. Poehlman, Jesse C. Wiley, Yue Liu, Ekaterina Gerasimov, Anna K. Greenwood, Solveig K. Sieberts, Aliza P. Wingo, Thomas S. Wingo, Lara M. Mangravite and Benjamin A. Logsdon

Citation: Genome Medicine 2021 13:76

Content type: Research Published on: 4 May 2021
Comprehensive identification of somatic nucleotide variants in human brain tissue

Authors: Yifan Wang, Taejeong Bae, Jeremy Thorpe, Maxwell A. Sherman, Attila G. Jones, Sean Cho, Kenneth Daily, Yanmei Dou, Javier Ganz, Alon Galor, Irene Lobon, Reenal Pattni, Chaggai Rosenbluh, Simone Tomasi, Livia Tomasini, Xiaoxu Yang…

Citation: Genome Biology 2021 22:92

Content type: Research Published on: 29 March 2021
A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease

Authors: Christoph Preuss, Ravi Pandey, Erin Piazza, Alexander Fine, Asli Uyar, Thanneer Perumal, Dylan Garceau, Kevin P. Kotredes, Harriet Williams, Lara M. Mangravite, Bruce T. Lamb, Adrian L. Oblak, Gareth R. Howell, Michael Sasner, Benjamin A. Logsdon and Gregory W. Carter

Citation: Molecular Neurodegeneration 2020 15:67

Content type: Methodology Published on: 10 November 2020
Developing pathways for community-led research with big data: a content analysis of stakeholder interviews

Authors: Shira Grayson, Megan Doerr and Joon-Ho Yu

Citation: Health Research Policy and Systems 2020 18:76

Content type: Research Published on: 8 July 2020
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Authors: Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros and Justin Guinney

Citation: Genome Biology 2019 20:195

Content type: Open Letter Published on: 10 September 2019
Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Authors: Hong Wang, Yupeng Li, John W. Ryder, Justin T. Hole, Philip J. Ebert, David C. Airey, Hui-Rong Qian, Benjamin Logsdon, Alice Fisher, Zeshan Ahmed, Tracey K. Murray, Annalisa Cavallini, Suchira Bose, Brian J. Eastwood, David A. Collier, Jeffrey L. Dage…

Citation: Molecular Neurodegeneration 2018 13:65

Content type: Research article Published on: 17 December 2018
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Authors: Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend…

Citation: Genome Biology 2018 19:188

Content type: Research Published on: 6 November 2018
Valection: design optimization for validation and verification studies

Authors: Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P’ng, Kathleen E Houlahan, Cristian Caloian, Michael Fraser, Kyle Ellrott, Adam A Margolin, Robert G Bristow, Joshua M Stuart and Paul C Boutros

Citation: BMC Bioinformatics 2018 19:339

Content type: Software Published on: 25 September 2018
Probing the chemical–biological relationship space with the Drug Target Explorer

Authors: Robert J. Allaway, Salvatore La Rosa, Justin Guinney and Sara J. C. Gosline

Citation: Journal of Cheminformatics 2018 10:41

Content type: Software Published on: 20 August 2018
Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Authors: Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart and Paul C. Boutros

Citation: BMC Bioinformatics 2018 19:28

Content type: Research Article Published on: 31 January 2018
Creating a data resource: what will it take to build a medical information commons?

Authors: Patricia A. Deverka, Mary A. Majumder, Angela G. Villanueva, Margaret Anderson, Annette C. Bakker, Jessica Bardill, Eric Boerwinkle, Tania Bubela, Barbara J. Evans, Nanibaa’ A. Garrison, Richard A. Gibbs, Robert Gentleman, David Glazer, Melissa M. Goldstein, Hank Greely, Crane Harris…

Citation: Genome Medicine 2017 9:84

Content type: Correspondence Published on: 22 September 2017
Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer

Authors: Safiye Celik, Benjamin A. Logsdon, Stephanie Battle, Charles W. Drescher, Mara Rendi, R. David Hawkins and Su-In Lee

Citation: Genome Medicine 2016 8:66

Content type: Method Published on: 10 June 2016
A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits

Authors: Jun Zhu, Congying Chen, Bin Yang, Yuanmei Guo, Huashui Ai, Jun Ren, Zhiyu Peng, Zhidong Tu, Xia Yang, Qingying Meng, Stephen Friend and Lusheng Huang

Citation: BMC Genomics 2015 16:88

Content type: Research article Published on: 14 February 2015
Toward better benchmarking: challenge-based methods assessment in cancer genomics

Authors: Paul C Boutros, Adam A Margolin, Joshua M Stuart, Andrea Califano and Gustavo Stolovitzky

Citation: Genome Biology 2014 15:462

Content type: Opinion Published on: 17 September 2014
ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma

Authors: Jeanette E Eckel-Passow, Daniel J Serie, Brian M Bot, Richard W Joseph, John C Cheville and Alexander S Parker

Citation: BMC Urology 2014 14:14

Content type: Research article Published on: 31 January 2014
GSVA: gene set variation analysis for microarray and RNA-Seq data

Authors: Sonja Hänzelmann, Robert Castelo and Justin Guinney

Citation: BMC Bioinformatics 2013 14:7

Content type: Software Published on: 16 January 2013