Literature DB >> 25032990

Data integration in the era of omics: current and future challenges.

David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam-Rudloff, Ana Conesa, Jesper Tegnér.   

Abstract

To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.

Entities:  

Mesh:

Year:  2014        PMID: 25032990      PMCID: PMC4101704          DOI: 10.1186/1752-0509-8-S2-I1

Source DB:  PubMed          Journal:  BMC Syst Biol        ISSN: 1752-0509


  62 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms.

Authors:  Orly Alter; Patrick O Brown; David Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-11       Impact factor: 11.205

3.  RNAcentral: A vision for an international database of RNA sequences.

Authors:  Alex Bateman; Shipra Agrawal; Ewan Birney; Elspeth A Bruford; Janusz M Bujnicki; Guy Cochrane; James R Cole; Marcel E Dinger; Anton J Enright; Paul P Gardner; Daniel Gautheret; Sam Griffiths-Jones; Jen Harrow; Javier Herrero; Ian H Holmes; Hsien-Da Huang; Krystyna A Kelly; Paul Kersey; Ana Kozomara; Todd M Lowe; Manja Marz; Simon Moxon; Kim D Pruitt; Tore Samuelsson; Peter F Stadler; Albert J Vilella; Jan-Hinnerk Vogel; Kelly P Williams; Mathew W Wright; Christian Zwieb
Journal:  RNA       Date:  2011-09-22       Impact factor: 4.942

4.  Alzheimer's disease: From big data to mechanism.

Authors:  Vivek Swarup; Daniel H Geschwind
Journal:  Nature       Date:  2013-07-24       Impact factor: 49.962

Review 5.  Epigenome-wide association studies for common human diseases.

Authors:  Vardhman K Rakyan; Thomas A Down; David J Balding; Stephan Beck
Journal:  Nat Rev Genet       Date:  2011-07-12       Impact factor: 53.242

6.  TRANSFAC: a database on transcription factors and their DNA binding sites.

Authors:  E Wingender; P Dietze; H Karas; R Knüppel
Journal:  Nucleic Acids Res       Date:  1996-01-01       Impact factor: 16.971

7.  Data integration in genetics and genomics: methods and challenges.

Authors:  Jemila S Hamid; Pingzhao Hu; Nicole M Roslin; Vicki Ling; Celia M T Greenwood; Joseph Beyene
Journal:  Hum Genomics Proteomics       Date:  2009-01-12

8.  The sequence of the human genome.

Authors:  J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal:  Science       Date:  2001-02-16       Impact factor: 47.728

9.  Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Authors:  Ali Mortazavi; Shirley Pepke; Camden Jansen; Georgi K Marinov; Jason Ernst; Manolis Kellis; Ross C Hardison; Richard M Myers; Barbara J Wold
Journal:  Genome Res       Date:  2013-10-29       Impact factor: 9.043

10.  Integrated genomic characterization of endometrial carcinoma.

Authors:  Cyriac Kandoth; Nikolaus Schultz; Andrew D Cherniack; Rehan Akbani; Yuexin Liu; Hui Shen; A Gordon Robertson; Itai Pashtan; Ronglai Shen; Christopher C Benz; Christina Yau; Peter W Laird; Li Ding; Wei Zhang; Gordon B Mills; Raju Kucherlapati; Elaine R Mardis; Douglas A Levine
Journal:  Nature       Date:  2013-05-02       Impact factor: 49.962

View more
  102 in total

1.  A literature mining-based approach for identification of cellular pathways associated with chemoresistance in cancer.

Authors:  Jung Hun Oh; Joseph O Deasy
Journal:  Brief Bioinform       Date:  2015-07-27       Impact factor: 11.622

Review 2.  Methods for biological data integration: perspectives and challenges.

Authors:  Vladimir Gligorijević; Nataša Pržulj
Journal:  J R Soc Interface       Date:  2015-11-06       Impact factor: 4.118

3.  NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.

Authors:  Jianguo Xia; Erin E Gill; Robert E W Hancock
Journal:  Nat Protoc       Date:  2015-05-07       Impact factor: 13.491

4.  Novel multivariate methods for integration of genomics and proteomics data: applications in a kidney transplant rejection study.

Authors:  Oliver P Günther; Heesun Shin; Raymond T Ng; W Robert McMaster; Bruce M McManus; Paul A Keown; Scott J Tebbutt; Kim-Anh Lê Cao
Journal:  OMICS       Date:  2014-11

5.  SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses.

Authors:  Adriana Tomic; Ivan Tomic; Yael Rosenberg-Hasson; Cornelia L Dekker; Holden T Maecker; Mark M Davis
Journal:  J Immunol       Date:  2019-06-14       Impact factor: 5.422

6.  Perspective: Advancing Understanding of Population Nutrient-Health Relations via Metabolomics and Precision Phenotypes.

Authors:  Stephanie Andraos; Melissa Wake; Richard Saffery; David Burgner; Martin Kussmann; Justin O'Sullivan
Journal:  Adv Nutr       Date:  2019-11-01       Impact factor: 8.701

7.  SCALEUS: Semantic Web Services Integration for Biomedical Applications.

Authors:  Pedro Sernadela; Lorena González-Castro; José Luís Oliveira
Journal:  J Med Syst       Date:  2017-02-18       Impact factor: 4.460

8.  Disease-Specific Integration of Omics Data to Guide Functional Validation of Genetic Associations.

Authors:  Maya Shumyatcher; Rui Hong; Jessica Levin; Blanca E Himes
Journal:  AMIA Annu Symp Proc       Date:  2018-04-16

Review 9.  Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities.

Authors:  Rajesh Kumar Pathak; Mamta Baunthiyal; Dinesh Pandey; Anil Kumar
Journal:  3 Biotech       Date:  2018-10-19       Impact factor: 2.406

10.  Computational challenges in modeling gene regulatory events.

Authors:  Abhijeet Pataskar; Vijay K Tiwari
Journal:  Transcription       Date:  2016-07-08
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.