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Results: 1 to 20 of 172

1.

Reference-assisted chromosome assembly.

Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA, Ma J.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1785-90. doi: 10.1073/pnas.1220349110. Epub 2013 Jan 10.

PMID:
23307812
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Desai A, Marwah VS, Yadav A, Jha V, Dhaygude K, Bangar U, Kulkarni V, Jere A.

PLoS One. 2013 Apr 12;8(4):e60204. doi: 10.1371/journal.pone.0060204. Print 2013.

PMID:
23593174
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404. doi: 10.1186/1471-2164-9-404.

PMID:
18755037
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

TIGER: tiled iterative genome assembler.

Wu XL, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J.

BMC Bioinformatics. 2012;13 Suppl 19:S18. doi: 10.1186/1471-2105-13-S19-S18. Epub 2012 Dec 19.

PMID:
23281792
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.

Baxter SW, Davey JW, Johnston JS, Shelton AM, Heckel DG, Jiggins CD, Blaxter ML.

PLoS One. 2011 Apr 26;6(4):e19315. doi: 10.1371/journal.pone.0019315.

PMID:
21541297
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.

PMID:
23815503
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A new strategy for better genome assembly from very short reads.

Ji Y, Shi Y, Ding G, Li Y.

BMC Bioinformatics. 2011 Dec 30;12:493. doi: 10.1186/1471-2105-12-493.

PMID:
22208765
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

Palmer LE, Dejori M, Bolanos R, Fasulo D.

BMC Bioinformatics. 2010 Jan 15;11:33. doi: 10.1186/1471-2105-11-33.

PMID:
20078885
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Efficient high-throughput sequencing of a laser microdissected chromosome arm.

Seifertova E, Zimmerman LB, Gilchrist MJ, Macha J, Kubickova S, Cernohorska H, Zarsky V, Owens ND, Sesay AK, Tlapakova T, Krylov V.

BMC Genomics. 2013 May 28;14:357. doi: 10.1186/1471-2164-14-357.

PMID:
23714049
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Optimization of de novo transcriptome assembly from next-generation sequencing data.

Surget-Groba Y, Montoya-Burgos JI.

Genome Res. 2010 Oct;20(10):1432-40. doi: 10.1101/gr.103846.109. Epub 2010 Aug 6.

PMID:
20693479
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome.

Philippe R, Choulet F, Paux E, van Oeveren J, Tang J, Wittenberg AH, Janssen A, van Eijk MJ, Stormo K, Alberti A, Wincker P, Akhunov E, van der Vossen E, Feuillet C.

BMC Genomics. 2012 Jan 30;13:47. doi: 10.1186/1471-2164-13-47.

PMID:
22289472
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes.

Dias Z, Dias U, Setubal JC.

BMC Bioinformatics. 2012 May 14;13:96. doi: 10.1186/1471-2105-13-96.

PMID:
22583530
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals.

Kai W, Kikuchi K, Tohari S, Chew AK, Tay A, Fujiwara A, Hosoya S, Suetake H, Naruse K, Brenner S, Suzuki Y, Venkatesh B.

Genome Biol Evol. 2011;3:424-42. doi: 10.1093/gbe/evr041. Epub 2011 Jun 1.

PMID:
21551351
[PubMed - indexed for MEDLINE]
Free Article
14.

The sequence of the human genome.

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51. Erratum in: Science 2001 Jun 5;292(5523):1838.

PMID:
11181995
[PubMed - indexed for MEDLINE]
15.

A duck RH panel and its potential for assisting NGS genome assembly.

Rao M, Morisson M, Faraut T, Bardes S, Fève K, Labarthe E, Fillon V, Huang Y, Li N, Vignal A.

BMC Genomics. 2012 Sep 28;13:513. doi: 10.1186/1471-2164-13-513.

PMID:
23020625
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. doi: 10.1073/pnas.1017351108. Epub 2010 Dec 27.

PMID:
21187386
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Advances in plant chromosome genomics.

Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Simková H.

Biotechnol Adv. 2014 Jan-Feb;32(1):122-36. doi: 10.1016/j.biotechadv.2013.12.011. Epub 2014 Jan 7.

PMID:
24406816
[PubMed - in process]
Free Article
18.

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J.

Nat Biotechnol. 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.2727. Epub 2013 Nov 3.

PMID:
24185095
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT, Durbin R.

Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111. Epub 2011 Dec 7.

PMID:
22156294
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map.

Wang C, Deakin JE, Rens W, Zenger KR, Belov K, Marshall Graves JA, Nicholas FW.

BMC Genomics. 2011 Aug 19;12:422. doi: 10.1186/1471-2164-12-422.

PMID:
21854555
[PubMed - indexed for MEDLINE]
Free PMC Article

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