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Results: 13

1.

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.

PMID:
23742238
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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, Iii DL, 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.

PMID:
23731509
[PubMed - as supplied by publisher]
Free PMC Article
3.

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
[PubMed - indexed for MEDLINE]
4.

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. Epub 2011 Nov 22.

PMID:
22113082
[PubMed - indexed for MEDLINE]
Free Article
5.

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. Epub 2011 Sep 7. 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.

PMID:
21915294
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
21827656
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
21794110
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
21496274
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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. Epub 2010 Aug 5.

PMID:
20691772
[PubMed - indexed for MEDLINE]
10.

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
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
18691400
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Comparing segmentations by applying randomization techniques.

Haiminen N, Mannila H, Terzi E.

BMC Bioinformatics. 2007 May 23;8:171.

PMID:
17521423
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Discovering isochores by least-squares optimal segmentation.

Haiminen N, Mannila H.

Gene. 2007 Jun 1;394(1-2):53-60. Epub 2007 Feb 16.

PMID:
17389148
[PubMed - indexed for MEDLINE]

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