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Items: 16

1.

SimBA: simulation algorithm to fit extant-population distributions.

Parida L, Haiminen N.

BMC Bioinformatics. 2015 Mar 14;16:82. doi: 10.1186/s12859-015-0525-0.

2.

Comparative exomics of Phalaris cultivars under salt stress.

Haiminen N, Klaas M, Zhou Z, Utro F, Cormican P, Didion T, Jensen C, Mason CE, Barth S, Parida L.

BMC Genomics. 2014;15 Suppl 6:S18. doi: 10.1186/1471-2164-15-S6-S18.

3.

BAC sequencing using pooled methods.

Saski CA, Feltus FA, Parida L, Haiminen N.

Methods Mol Biol. 2015;1227:55-67. doi: 10.1007/978-1-4939-1652-8_3.

PMID:
25239741
4.

iXora: exact haplotype inferencing and trait association.

Utro F, Haiminen N, Livingstone D 3rd, Cornejo OE, Royaert S, Schnell RJ, Motamayor JC, Kuhn DN, Parida L.

BMC Genet. 2013 Jun 6;14:48. doi: 10.1186/1471-2156-14-48.

5.

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.

Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D 3rd, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN.

Genome Biol. 2013 Jun 3;14(6):r53. doi: 10.1186/gb-2013-14-6-r53.

6.

Discovering patterns in gene order.

Parida L, Haiminen N.

Methods Mol Biol. 2012;855:431-55. doi: 10.1007/978-1-61779-582-4_16. Review.

PMID:
22407719
7.

GenomicTools: a computational platform for developing high-throughput analytics in genomics.

Tsirigos A, Haiminen N, Bilal E, Utro F.

Bioinformatics. 2012 Jan 15;28(2):282-3. doi: 10.1093/bioinformatics/btr646.

8.

Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.

Haiminen N, Kuhn DN, Parida L, Rigoutsos I.

PLoS One. 2011;6(9):e24182. doi: 10.1371/journal.pone.0024182. Erratum in: PLoS One. 2011:6(10). doi: 10.1371/annotation/bb125f93-80d3-4dd1-adfe-03d9fb740f3b. PLoS One. 2011;6(10). doi: 10.1371/annotation/176d83be-ed67-4205-9265-7208792d3dcf.

9.

Randomization techniques for assessing the significance of gene periodicity results.

Kallio A, Vuokko N, Ojala M, Haiminen N, Mannila H.

BMC Bioinformatics. 2011 Aug 9;12:330. doi: 10.1186/1471-2105-12-330.

10.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.

Feltus FA, Saski CA, Mockaitis K, Haiminen N, Parida L, Smith Z, Ford J, Staton ME, Ficklin SP, Blackmon BP, Cheng CH, Schnell RJ, Kuhn DN, Motamayor JC.

BMC Genomics. 2011 Jul 27;12:379. doi: 10.1186/1471-2164-12-379.

11.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

Haiminen N, Feltus FA, Parida L.

BMC Genomics. 2011 Apr 15;12:194. doi: 10.1186/1471-2164-12-194.

12.

Detecting novel genes with sparse arrays.

Arvas M, Haiminen N, Smit B, Rautio J, Vitikainen M, Wiebe M, Martinez D, Chee C, Kunkel J, Sanchez C, Nelson MA, Pakula T, Saloheimo M, Penttilä M, Kivioja T.

Gene. 2010 Nov 1;467(1-2):41-51. doi: 10.1016/j.gene.2010.07.009.

13.

Evaluation of BIC and cross validation for model selection on sequence segmentations.

Haiminen N, Mannila H.

Int J Data Min Bioinform. 2010;4(6):675-700.

PMID:
21355501
14.

Determining significance of pairwise co-occurrences of events in bursty sequences.

Haiminen N, Mannila H, Terzi E.

BMC Bioinformatics. 2008 Aug 8;9:336. doi: 10.1186/1471-2105-9-336.

15.

Comparing segmentations by applying randomization techniques.

Haiminen N, Mannila H, Terzi E.

BMC Bioinformatics. 2007 May 23;8:171.

16.

Discovering isochores by least-squares optimal segmentation.

Haiminen N, Mannila H.

Gene. 2007 Jun 1;394(1-2):53-60.

PMID:
17389148
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