Sage Bionetworks

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

    Authors: Arimantas Lionikas, Caroline Meharg, Jonathan MJ Derry, Aivaras Ratkevicius, Andrew M Carroll, David J Vandenbergh and David A Blizard

    Citation: BMC Genomics 2012 13:592

    Content type: Research article Published on: 5 November 2012

19. Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes

    Authors: Chao Wu, Jun Zhu and Xuegong Zhang

    Citation: BMC Bioinformatics 2012 13:182

    Content type: Methodology article Published on: 28 July 2012

20. Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

    Authors: Chia-Ling Huang, John Lamb, Leonid Chindelevitch, Jarek Kostrowicki, Justin Guinney, Charles DeLisi and Daniel Ziemek

    Citation: BMC Bioinformatics 2012 13:46

    Content type: Methodology article Published on: 23 March 2012