Literature DB >> 20717155

Computational solutions to large-scale data management and analysis.

Eric E Schadt1, Michael D Linderman, Jon Sorenson, Lawrence Lee, Garry P Nolan.   

Abstract

Today we can generate hundreds of gigabases of DNA and RNA sequencing data in a week for less than US$5,000. The astonishing rate of data generation by these low-cost, high-throughput technologies in genomics is being matched by that of other technologies, such as real-time imaging and mass spectrometry-based flow cytometry. Success in the life sciences will depend on our ability to properly interpret the large-scale, high-dimensional data sets that are generated by these technologies, which in turn requires us to adopt advances in informatics. Here we discuss how we can master the different types of computational environments that exist - such as cloud and heterogeneous computing - to successfully tackle our big data problems.

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Year:  2010        PMID: 20717155      PMCID: PMC3124937          DOI: 10.1038/nrg2857

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  29 in total

1.  BLAST: at the core of a powerful and diverse set of sequence analysis tools.

Authors:  Scott McGinnis; Thomas L Madden
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  A general framework for weighted gene co-expression network analysis.

Authors:  Bin Zhang; Steve Horvath
Journal:  Stat Appl Genet Mol Biol       Date:  2005-08-12

3.  Accelerating molecular dynamic simulation on the cell processor and Playstation 3.

Authors:  Edgar Luttmann; Daniel L Ensign; Vishal Vaidyanathan; Mike Houston; Noam Rimon; Jeppe Øland; Guha Jayachandran; Mark Friedrichs; Vijay S Pande
Journal:  J Comput Chem       Date:  2009-01-30       Impact factor: 3.376

Review 4.  Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges.

Authors:  Lincoln D Stein
Journal:  Nat Rev Genet       Date:  2008-09       Impact factor: 53.242

5.  Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.

Authors:  Jun Zhu; Bin Zhang; Erin N Smith; Becky Drees; Rachel B Brem; Leonid Kruglyak; Roger E Bumgarner; Eric E Schadt
Journal:  Nat Genet       Date:  2008-06-15       Impact factor: 38.330

Review 6.  Genetic mapping in human disease.

Authors:  David Altshuler; Mark J Daly; Eric S Lander
Journal:  Science       Date:  2008-11-07       Impact factor: 47.728

7.  Genetics of gene expression and its effect on disease.

Authors:  Valur Emilsson; Gudmar Thorleifsson; Bin Zhang; Amy S Leonardson; Florian Zink; Jun Zhu; Sonia Carlson; Agnar Helgason; G Bragi Walters; Steinunn Gunnarsdottir; Magali Mouy; Valgerdur Steinthorsdottir; Gudrun H Eiriksdottir; Gyda Bjornsdottir; Inga Reynisdottir; Daniel Gudbjartsson; Anna Helgadottir; Aslaug Jonasdottir; Adalbjorg Jonasdottir; Unnur Styrkarsdottir; Solveig Gretarsdottir; Kristinn P Magnusson; Hreinn Stefansson; Ragnheidur Fossdal; Kristleifur Kristjansson; Hjortur G Gislason; Tryggvi Stefansson; Bjorn G Leifsson; Unnur Thorsteinsdottir; John R Lamb; Jeffrey R Gulcher; Marc L Reitman; Augustine Kong; Eric E Schadt; Kari Stefansson
Journal:  Nature       Date:  2008-03-16       Impact factor: 49.962

8.  Variations in DNA elucidate molecular networks that cause disease.

Authors:  Yanqing Chen; Jun Zhu; Pek Yee Lum; Xia Yang; Shirly Pinto; Douglas J MacNeil; Chunsheng Zhang; John Lamb; Stephen Edwards; Solveig K Sieberts; Amy Leonardson; Lawrence W Castellini; Susanna Wang; Marie-France Champy; Bin Zhang; Valur Emilsson; Sudheer Doss; Anatole Ghazalpour; Steve Horvath; Thomas A Drake; Aldons J Lusis; Eric E Schadt
Journal:  Nature       Date:  2008-03-16       Impact factor: 49.962

9.  High-throughput sequence alignment using Graphics Processing Units.

Authors:  Michael C Schatz; Cole Trapnell; Arthur L Delcher; Amitabh Varshney
Journal:  BMC Bioinformatics       Date:  2007-12-10       Impact factor: 3.169

10.  Mapping the genetic architecture of gene expression in human liver.

Authors:  Eric E Schadt; Cliona Molony; Eugene Chudin; Ke Hao; Xia Yang; Pek Y Lum; Andrew Kasarskis; Bin Zhang; Susanna Wang; Christine Suver; Jun Zhu; Joshua Millstein; Solveig Sieberts; John Lamb; Debraj GuhaThakurta; Jonathan Derry; John D Storey; Iliana Avila-Campillo; Mark J Kruger; Jason M Johnson; Carol A Rohl; Atila van Nas; Margarete Mehrabian; Thomas A Drake; Aldons J Lusis; Ryan C Smith; F Peter Guengerich; Stephen C Strom; Erin Schuetz; Thomas H Rushmore; Roger Ulrich
Journal:  PLoS Biol       Date:  2008-05-06       Impact factor: 8.029

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  128 in total

1.  Monte Carlo simulation of photon migration in a cloud computing environment with MapReduce.

Authors:  Guillem Pratx; Lei Xing
Journal:  J Biomed Opt       Date:  2011-12       Impact factor: 3.170

2.  Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment.

Authors:  Bowen Meng; Guillem Pratx; Lei Xing
Journal:  Med Phys       Date:  2011-12       Impact factor: 4.071

3.  Opportunities and challenges for the life sciences community.

Authors:  Eugene Kolker; Elizabeth Stewart; Vural Ozdemir
Journal:  OMICS       Date:  2012-03

Review 4.  Computational tools for discovery and interpretation of expression quantitative trait loci.

Authors:  Fred A Wright; Andrey A Shabalin; Ivan Rusyn
Journal:  Pharmacogenomics       Date:  2012-02       Impact factor: 2.533

5.  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

6.  PD-1 Blockade Expands Intratumoral Memory T Cells.

Authors:  Antoni Ribas; Daniel Sanghoon Shin; Jesse Zaretsky; Juliet Frederiksen; Andrew Cornish; Earl Avramis; Elizabeth Seja; Christine Kivork; Janet Siebert; Paula Kaplan-Lefko; Xiaoyan Wang; Bartosz Chmielowski; John A Glaspy; Paul C Tumeh; Thinle Chodon; Dana Pe'er; Begoña Comin-Anduix
Journal:  Cancer Immunol Res       Date:  2016-01-19       Impact factor: 11.151

7.  Decoding the immune response to successful influenza vaccination.

Authors:  Brian A Kidd
Journal:  Nat Immunol       Date:  2016-02       Impact factor: 25.606

8.  Comparative co-expression network analysis extracts the SlHSP70 gene affecting to shoot elongation of tomato.

Authors:  Nam Tuan Vu; Ken Kamiya; Atsushi Fukushima; Shuhei Hao; Wang Ning; Tohru Ariizumi; Hiroshi Ezura; Miyako Kusano
Journal:  Plant Biotechnol (Tokyo)       Date:  2019-09-25       Impact factor: 1.133

9.  Heart beats in the cloud: distributed analysis of electrophysiological 'Big Data' using cloud computing for epilepsy clinical research.

Authors:  Satya S Sahoo; Catherine Jayapandian; Gaurav Garg; Farhad Kaffashi; Stephanie Chung; Alireza Bozorgi; Chien-Hun Chen; Kenneth Loparo; Samden D Lhatoo; Guo-Qiang Zhang
Journal:  J Am Med Inform Assoc       Date:  2013-12-10       Impact factor: 4.497

10.  Big Data Provenance: Challenges, State of the Art and Opportunities.

Authors:  Jianwu Wang; Daniel Crawl; Shweta Purawat; Mai Nguyen; Ilkay Altintas
Journal:  Proc IEEE Int Conf Big Data       Date:  2015-12-28
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