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Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.


Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance.

Cook-Deegan R, Ankeny RA, Maxson Jones K.

Annu Rev Genomics Hum Genet. 2017 Aug 31;18:389-415. doi: 10.1146/annurev-genom-083115-022515. Epub 2017 Apr 17. Review.


Direct determination of diploid genome sequences.

Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB.

Genome Res. 2017 May;27(5):757-767. doi: 10.1101/gr.214874.116. Epub 2017 Apr 5.


Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.

Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.


Genetic variation and the de novo assembly of human genomes.

Chaisson MJ, Wilson RK, Eichler EE.

Nat Rev Genet. 2015 Nov;16(11):627-40. doi: 10.1038/nrg3933. Epub 2015 Oct 7. Review.


Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.

Nat Methods. 2015 Aug;12(8):780-6. doi: 10.1038/nmeth.3454. Epub 2015 Jun 29.


CD8(+) T cell-mediated immunity during Trypanosoma cruzi infection: a path for vaccine development?

Dos Santos Virgilio F, Pontes C, Dominguez MR, Ersching J, Rodrigues MM, Vasconcelos JR.

Mediators Inflamm. 2014;2014:243786. doi: 10.1155/2014/243786. Epub 2014 Jul 1. Review.


Genomic approaches for the discovery of genes mutated in inherited retinal degeneration.

Siemiatkowska AM, Collin RW, den Hollander AI, Cremers FP.

Cold Spring Harb Perspect Med. 2014 Jun 17;4(8). pii: a017137. doi: 10.1101/cshperspect.a017137. Review.


Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ.

G3 (Bethesda). 2013 Nov 6;3(11):2031-47. doi: 10.1534/g3.113.007153.


Overlapping of genes in the human genome.

Nakayama T, Asai S, Takahashi Y, Maekawa O, Kasama Y.

Int J Biomed Sci. 2007 Mar;3(1):14-9.


A short history of the genome-wide association study: where we were and where we are going.

Ikegawa S.

Genomics Inform. 2012 Dec;10(4):220-5. doi: 10.5808/GI.2012.10.4.220. Epub 2012 Dec 31.


Bioinformatics for the Human Microbiome Project.

Gevers D, Pop M, Schloss PD, Huttenhower C.

PLoS Comput Biol. 2012;8(11):e1002779. doi: 10.1371/journal.pcbi.1002779. Epub 2012 Nov 29. No abstract available.


QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads.

Huang A, Kantor R, DeLong A, Schreier L, Istrail S.

In Silico Biol. 2011-2012;11(5-6):193-201. doi: 10.3233/ISB-2012-0454.


Optimal reference sequence selection for genome assembly using minimum description length principle.

Wajid B, Serpedin E, Nounou M, Nounou H.

EURASIP J Bioinform Syst Biol. 2012 Nov 27;2012(1):18. doi: 10.1186/1687-4153-2012-18.


Mouse models of sarcomas: critical tools in our understanding of the pathobiology.

Post SM.

Clin Sarcoma Res. 2012 Oct 4;2(1):20. doi: 10.1186/2045-3329-2-20.


New Generations: Sequencing Machines and Their Computational Challenges.

Schwartz DC, Waterman MS.

J Comput Sci Technol. 2010 Jan 1;25(1):3-9.


GenomeView: a next-generation genome browser.

Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y.

Nucleic Acids Res. 2012 Jan;40(2):e12. doi: 10.1093/nar/gkr995. Epub 2011 Nov 18.


A human genome structural variation sequencing resource reveals insights into mutational mechanisms.

Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, Kallicki J, Kaul R, Wilson RK, Eichler EE.

Cell. 2010 Nov 24;143(5):837-47. doi: 10.1016/j.cell.2010.10.027.


Plasmodium immunomics.

Doolan DL.

Int J Parasitol. 2011 Jan;41(1):3-20. doi: 10.1016/j.ijpara.2010.08.002. Epub 2010 Sep 16. Review.

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