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Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience?

Ahmed A.

Front Microbiol. 2016 Jul 26;7:1061. doi: 10.3389/fmicb.2016.01061. eCollection 2016.


Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E.

Gigascience. 2016 Jun 7;5:26. doi: 10.1186/s13742-016-0132-7. Review.


Novel bioinformatic developments for exome sequencing.

Lelieveld SH, Veltman JA, Gilissen C.

Hum Genet. 2016 Jun;135(6):603-14. doi: 10.1007/s00439-016-1658-6. Epub 2016 Apr 13. Review.


A case study for cloud based high throughput analysis of NGS data using the globus genomics system.

Bhuvaneshwar K, Sulakhe D, Gauba R, Rodriguez A, Madduri R, Dave U, Lacinski L, Foster I, Gusev Y, Madhavan S.

Comput Struct Biotechnol J. 2014 Nov 7;13:64-74. doi: 10.1016/j.csbj.2014.11.001. eCollection 2015.


Long Read Alignment with Parallel MapReduce Cloud Platform.

Al-Absi AA, Kang DK.

Biomed Res Int. 2015;2015:807407. doi: 10.1155/2015/807407. Epub 2015 Dec 29.


NEAT: a framework for building fully automated NGS pipelines and analyses.

Schorderet P.

BMC Bioinformatics. 2016 Feb 1;17:53. doi: 10.1186/s12859-016-0902-3.


Applying computation biology and "big data" to develop multiplex diagnostics for complex chronic diseases such as osteoarthritis.

Ren G, Krawetz R.

Biomarkers. 2015;20(8):533-9. doi: 10.3109/1354750X.2015.1105499. Epub 2016 Jan 26.


Light-RCV: a lightweight read coverage viewer for next generation sequencing data.

Chang CW, Lee WB, Chen-Deng A, Liu T, Tseng JT, Chang DT.

BMC Bioinformatics. 2015;16 Suppl 18:S11. doi: 10.1186/1471-2105-16-S18-S11. Epub 2015 Dec 9.


Exploiting Linkage Disequilibrium for Ultrahigh-Dimensional Genome-Wide Data with an Integrated Statistical Approach.

Carlsen M, Fu G, Bushman S, Corcoran C.

Genetics. 2016 Feb;202(2):411-26. doi: 10.1534/genetics.115.179507. Epub 2015 Dec 12.


VariantSpark: population scale clustering of genotype information.

O'Brien AR, Saunders NF, Guo Y, Buske FA, Scott RJ, Bauer DC.

BMC Genomics. 2015 Dec 10;16:1052. doi: 10.1186/s12864-015-2269-7.


The sequence of sequencers: The history of sequencing DNA.

Heather JM, Chain B.

Genomics. 2016 Jan;107(1):1-8. doi: 10.1016/j.ygeno.2015.11.003. Epub 2015 Nov 10. Review.


Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Afgan E, Sloggett C, Goonasekera N, Makunin I, Benson D, Crowe M, Gladman S, Kowsar Y, Pheasant M, Horst R, Lonie A.

PLoS One. 2015 Oct 26;10(10):e0140829. doi: 10.1371/journal.pone.0140829. eCollection 2015.


Big Data: the challenge for small research groups in the era of cancer genomics.

Noor AM, Holmberg L, Gillett C, Grigoriadis A.

Br J Cancer. 2015 Nov 17;113(10):1405-12. doi: 10.1038/bjc.2015.341. Epub 2015 Oct 22. Review.


Secure Genomic Computation through Site-Wise Encryption.

Zhao Y, Wang X, Tang H.

AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:227-31. eCollection 2015.


Experiences with workflows for automating data-intensive bioinformatics.

Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, Schönherr S, Siretskiy A, Vassilev D.

Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8.


Sealer: a scalable gap-closing application for finishing draft genomes.

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.

BMC Bioinformatics. 2015 Jul 25;16:230. doi: 10.1186/s12859-015-0663-4.


Achieving human and machine accessibility of cited data in scholarly publications.

Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak LL, Haendel M, Herman I, Hodson S, Hourclé J, Kratz JE, Lin J, Nielsen LH, Nurnberger A, Proell S, Rauber A, Sacchi S, Smith A, Taylor M, Clark T.

PeerJ Comput Sci. 2015;1. pii: e1.


Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

Duarte AM, Psomopoulos FE, Blanchet C, Bonvin AM, Corpas M, Franc A, Jimenez RC, de Lucas JM, Nyrönen T, Sipos G, Suhr SB.

Front Genet. 2015 Jun 23;6:197. doi: 10.3389/fgene.2015.00197. eCollection 2015.


Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS.

PLoS One. 2015 Jun 26;10(6):e0131166. doi: 10.1371/journal.pone.0131166. eCollection 2015.


SeedsGraph: an efficient assembler for next-generation sequencing data.

Wang C, Guo M, Liu X, Liu Y, Zou Q.

BMC Med Genomics. 2015;8 Suppl 2:S13. doi: 10.1186/1755-8794-8-S2-S13. Epub 2015 May 29.

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