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Items: 7

1.

The impact of Docker containers on the performance of genomic pipelines.

Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C.

PeerJ. 2015 Sep 24;3:e1273. doi: 10.7717/peerj.1273. eCollection 2015.

2.

Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing.

Mack SJ, Milius RP, Gifford BD, Sauter J, Hofmann J, Osoegawa K, Robinson J, Groeneweg M, Turenchalk GS, Adai A, Holcomb C, Rozemuller EH, Penning MT, Heuer ML, Wang C, Salit ML, Schmidt AH, Parham PR, Müller C, Hague T, Fischer G, Fernandez-Viňa M, Hollenbach JA, Norman PJ, Maiers M.

Hum Immunol. 2015 Dec;76(12):954-62. doi: 10.1016/j.humimm.2015.09.011. Epub 2015 Sep 25.

3.

Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string.

Milius RP, Mack SJ, Hollenbach JA, Pollack J, Heuer ML, Gragert L, Spellman S, Guethlein LA, Trachtenberg EA, Cooley S, Bochtler W, Mueller CR, Robinson J, Marsh SG, Maiers M.

Tissue Antigens. 2013 Aug;82(2):106-12. doi: 10.1111/tan.12150.

4.

BioJava: an open-source framework for bioinformatics in 2012.

Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.

Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494. Epub 2012 Aug 9.

5.

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N.

Cancer Discov. 2012 May;2(5):401-4. doi: 10.1158/2159-8290.CD-12-0095. Erratum in: Cancer Discov. 2012 Oct;2(10):960.

6.

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM.

Nucleic Acids Res. 2010 Apr;38(6):1767-71. doi: 10.1093/nar/gkp1137. Epub 2009 Dec 16. Review.

7.

Databases and information integration for the Medicago truncatula genome and transcriptome.

Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EK, Dwan C, Lamblin AF, Vasdewani J, Mudge J, Cook A, Gish J, Cheung F, Kenton S, Kunau TM, Brown D, May GD, Kim D, Cook DR, Roe BA, Town CD, Young ND, Retzel EF.

Plant Physiol. 2005 May;138(1):38-46.

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