Literature DB >> 31022372

Strategies for Network GWAS Evaluated Using Classroom Crowd Science.

Samson H Fong1, Daniel E Carlin2, Kivilcim Ozturk3, Trey Ideker4.   

Abstract

Biological networks can substantially boost power to identify disease genes in genome-wide association studies. To explore different network GWAS methods, we challenged students of a UC San Diego graduate level bioinformatics course, Network Biology and Biomedicine, to explore and improve such algorithms during a four-week-long classroom competition. Here, we report the many creative solutions and share our experiences in conducting classroom crowd science as both a research and pedagogical tool.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Mesh:

Year:  2019        PMID: 31022372      PMCID: PMC6764759          DOI: 10.1016/j.cels.2019.03.013

Source DB:  PubMed          Journal:  Cell Syst        ISSN: 2405-4712            Impact factor:   10.304


  24 in total

1.  GWAB: a web server for the network-based boosting of human genome-wide association data.

Authors:  Jung Eun Shim; Changbae Bang; Sunmo Yang; Tak Lee; Sohyun Hwang; Chan Yeong Kim; U Martin Singh-Blom; Edward M Marcotte; Insuk Lee
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

2.  Chromosome conformation elucidates regulatory relationships in developing human brain.

Authors:  Hyejung Won; Luis de la Torre-Ubieta; Jason L Stein; Neelroop N Parikshak; Jerry Huang; Carli K Opland; Michael J Gandal; Gavin J Sutton; Farhad Hormozdiari; Daning Lu; Changhoon Lee; Eleazar Eskin; Irina Voineagu; Jason Ernst; Daniel H Geschwind
Journal:  Nature       Date:  2016-10-19       Impact factor: 49.962

3.  NDEx, the Network Data Exchange.

Authors:  Dexter Pratt; Jing Chen; David Welker; Ricardo Rivas; Rudolf Pillich; Vladimir Rynkov; Keiichiro Ono; Carol Miello; Lyndon Hicks; Sandor Szalma; Aleksandar Stojmirovic; Radu Dobrin; Michael Braxenthaler; Jan Kuentzer; Barry Demchak; Trey Ideker
Journal:  Cell Syst       Date:  2015-10-28       Impact factor: 10.304

4.  Genome-wide association study identifies five new schizophrenia loci.

Authors: 
Journal:  Nat Genet       Date:  2011-09-18       Impact factor: 38.330

Review 5.  10 Years of GWAS Discovery: Biology, Function, and Translation.

Authors:  Peter M Visscher; Naomi R Wray; Qian Zhang; Pamela Sklar; Mark I McCarthy; Matthew A Brown; Jian Yang
Journal:  Am J Hum Genet       Date:  2017-07-06       Impact factor: 11.025

6.  Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.

Authors:  Mark D M Leiserson; Fabio Vandin; Hsin-Ta Wu; Jason R Dobson; Jonathan V Eldridge; Jacob L Thomas; Alexandra Papoutsaki; Younhun Kim; Beifang Niu; Michael McLellan; Michael S Lawrence; Abel Gonzalez-Perez; David Tamborero; Yuwei Cheng; Gregory A Ryslik; Nuria Lopez-Bigas; Gad Getz; Li Ding; Benjamin J Raphael
Journal:  Nat Genet       Date:  2014-12-15       Impact factor: 38.330

7.  Examination of all type 2 diabetes GWAS loci reveals HHEX-IDE as a locus influencing pediatric BMI.

Authors:  Jianhua Zhao; Jonathan P Bradfield; Haitao Zhang; Kiran Annaiah; Kai Wang; Cecilia E Kim; Joseph T Glessner; Edward C Frackelton; F George Otieno; James Doran; Kelly A Thomas; Maria Garris; Cuiping Hou; Rosetta M Chiavacci; Mingyao Li; Robert I Berkowitz; Hakon Hakonarson; Struan F A Grant
Journal:  Diabetes       Date:  2009-11-23       Impact factor: 9.461

8.  Network-based stratification of tumor mutations.

Authors:  Matan Hofree; John P Shen; Hannah Carter; Andrew Gross; Trey Ideker
Journal:  Nat Methods       Date:  2013-09-15       Impact factor: 28.547

Review 9.  A review of post-GWAS prioritization approaches.

Authors:  Lin Hou; Hongyu Zhao
Journal:  Front Genet       Date:  2013-12-09       Impact factor: 4.599

10.  Understanding multicellular function and disease with human tissue-specific networks.

Authors:  Casey S Greene; Arjun Krishnan; Aaron K Wong; Emanuela Ricciotti; Rene A Zelaya; Daniel S Himmelstein; Ran Zhang; Boris M Hartmann; Elena Zaslavsky; Stuart C Sealfon; Daniel I Chasman; Garret A FitzGerald; Kara Dolinski; Tilo Grosser; Olga G Troyanskaya
Journal:  Nat Genet       Date:  2015-04-27       Impact factor: 38.330

View more
  1 in total

1.  A Fast and Flexible Framework for Network-Assisted Genomic Association.

Authors:  Daniel E Carlin; Samson H Fong; Yue Qin; Tongqiu Jia; Justin K Huang; Bokan Bao; Chao Zhang; Trey Ideker
Journal:  iScience       Date:  2019-05-24
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.