Literature DB >> 24799088

Big data bioinformatics.

Casey S Greene1, Jie Tan, Matthew Ung, Jason H Moore, Chao Cheng.   

Abstract

Recent technological advances allow for high throughput profiling of biological systems in a cost-efficient manner. The low cost of data generation is leading us to the "big data" era. The availability of big data provides unprecedented opportunities but also raises new challenges for data mining and analysis. In this review, we introduce key concepts in the analysis of big data, including both "machine learning" algorithms as well as "unsupervised" and "supervised" examples of each. We note packages for the R programming language that are available to perform machine learning analyses. In addition to programming based solutions, we review webservers that allow users with limited or no programming background to perform these analyses on large data compendia.
© 2014 Wiley Periodicals, Inc.

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Year:  2014        PMID: 24799088      PMCID: PMC5604462          DOI: 10.1002/jcp.24662

Source DB:  PubMed          Journal:  J Cell Physiol        ISSN: 0021-9541            Impact factor:   6.384


  19 in total

Review 1.  Bioinformatics.

Authors:  Jason H Moore
Journal:  J Cell Physiol       Date:  2007-11       Impact factor: 6.384

2.  Histone modification levels are predictive for gene expression.

Authors:  Rosa Karlić; Ho-Ryun Chung; Julia Lasserre; Kristian Vlahovicek; Martin Vingron
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-01       Impact factor: 11.205

3.  ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.

Authors:  Zhengqing Ouyang; Qing Zhou; Wing Hung Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-07       Impact factor: 11.205

4.  In vivo enhancer analysis of human conserved non-coding sequences.

Authors:  Len A Pennacchio; Nadav Ahituv; Alan M Moses; Shyam Prabhakar; Marcelo A Nobrega; Malak Shoukry; Simon Minovitsky; Inna Dubchak; Amy Holt; Keith D Lewis; Ingrid Plajzer-Frick; Jennifer Akiyama; Sarah De Val; Veena Afzal; Brian L Black; Olivier Couronne; Michael B Eisen; Axel Visel; Edward M Rubin
Journal:  Nature       Date:  2006-11-05       Impact factor: 49.962

5.  Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.

Authors:  Kevin Y Yip; Chao Cheng; Nitin Bhardwaj; James B Brown; Jing Leng; Anshul Kundaje; Joel Rozowsky; Ewan Birney; Peter Bickel; Michael Snyder; Mark Gerstein
Journal:  Genome Biol       Date:  2012-09-26       Impact factor: 13.583

6.  Integrated genomic analyses of ovarian carcinoma.

Authors: 
Journal:  Nature       Date:  2011-06-29       Impact factor: 49.962

7.  PILGRM: an interactive data-driven discovery platform for expert biologists.

Authors:  Casey S Greene; Olga G Troyanskaya
Journal:  Nucleic Acids Res       Date:  2011-06-07       Impact factor: 16.971

8.  Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells.

Authors:  Chao Cheng; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2011-09-16       Impact factor: 16.971

9.  Defining cell-type specificity at the transcriptional level in human disease.

Authors:  Wenjun Ju; Casey S Greene; Felix Eichinger; Viji Nair; Jeffrey B Hodgin; Markus Bitzer; Young-Suk Lee; Qian Zhu; Masami Kehata; Min Li; Song Jiang; Maria Pia Rastaldi; Clemens D Cohen; Olga G Troyanskaya; Matthias Kretzler
Journal:  Genome Res       Date:  2013-08-15       Impact factor: 9.043

10.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

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  44 in total

1.  Metabolomics technology and bioinformatics for precision medicine.

Authors:  Rajeev K Azad; Vladimir Shulaev
Journal:  Brief Bioinform       Date:  2019-11-27       Impact factor: 11.622

Review 2.  Current Applications and Future Impact of Machine Learning in Radiology.

Authors:  Garry Choy; Omid Khalilzadeh; Mark Michalski; Synho Do; Anthony E Samir; Oleg S Pianykh; J Raymond Geis; Pari V Pandharipande; James A Brink; Keith J Dreyer
Journal:  Radiology       Date:  2018-06-26       Impact factor: 11.105

3.  Landscapes of binding antibody and T-cell responses to pox-protein HIV vaccines in Thais and South Africans.

Authors:  Lue Ping Zhao; Andrew Fiore-Gartland; Lindsay N Carpp; Kristen W Cohen; Nadine Rouphael; Llewellyn Fleurs; One Dintwe; Michael Zhao; Zoe Moodie; Youyi Fong; Nigel Garrett; Ying Huang; Craig Innes; Holly E Janes; Erica Lazarus; Nelson L Michael; Sorachai Nitayaphan; Punnee Pitisuttithum; Supachai Rerks-Ngarm; Merlin L Robb; Stephen C De Rosa; Lawrence Corey; Glenda E Gray; Kelly E Seaton; Nicole L Yates; M Juliana McElrath; Nicole Frahm; Georgia D Tomaras; Peter B Gilbert
Journal:  PLoS One       Date:  2020-01-30       Impact factor: 3.240

4.  Unsupervised feature construction and knowledge extraction from genome-wide assays of breast cancer with denoising autoencoders.

Authors:  Jie Tan; Matthew Ung; Chao Cheng; Casey S Greene
Journal:  Pac Symp Biocomput       Date:  2015

5.  A hybrid metaheuristic-deep learning technique for the pan-classification of cancer based on DNA methylation.

Authors:  Noureldin S Eissa; Uswah Khairuddin; Rubiyah Yusof
Journal:  BMC Bioinformatics       Date:  2022-07-11       Impact factor: 3.307

6.  Transcriptome marker diagnostics using big data.

Authors:  Henry Han; Ying Liu
Journal:  IET Syst Biol       Date:  2016-02       Impact factor: 1.615

7.  Rapid, accurate, and on-site detection of C. difficile in stool samples.

Authors:  Marije K Bomers; Frederik P Menke; Richard S Savage; Christina M J E Vandenbroucke-Grauls; Michiel A van Agtmael; James A Covington; Yvo M Smulders
Journal:  Am J Gastroenterol       Date:  2015-03-31       Impact factor: 10.864

Review 8.  Genetics of Food Allergy.

Authors:  Elisabet Johansson; Tesfaye B Mersha
Journal:  Immunol Allergy Clin North Am       Date:  2021-03-26       Impact factor: 3.479

9.  Simulation-derived best practices for clustering clinical data.

Authors:  Caitlin E Coombes; Xin Liu; Zachary B Abrams; Kevin R Coombes; Guy Brock
Journal:  J Biomed Inform       Date:  2021-04-20       Impact factor: 8.000

Review 10.  Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry.

Authors:  Jayanta Gupta; Elisabet Johansson; Jonathan A Bernstein; Ranajit Chakraborty; Gurjit K Khurana Hershey; Marc E Rothenberg; Tesfaye B Mersha
Journal:  J Allergy Clin Immunol       Date:  2016-06-11       Impact factor: 10.793

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