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Results: 1 to 20 of 105

1.

Genome characterization through dichotomic classes: an analysis of the whole chromosome 1 of A. thaliana.

Properzi E, Giannerini S, Gonzalez DL, Rosa R.

Math Biosci Eng. 2013 Feb;10(1):199-219. doi: 10.3934/mbe.2013.10.199.

PMID:
23311369
[PubMed - indexed for MEDLINE]
2.

On dichotomic classes and bijections of the genetic code.

Fimmel E, Danielli A, Strüngmann L.

J Theor Biol. 2013 Nov 7;336:221-30. doi: 10.1016/j.jtbi.2013.07.027. Epub 2013 Aug 26.

PMID:
23988795
[PubMed - in process]
3.

Strong short-range correlations and dichotomic codon classes in coding DNA sequences.

Gonzalez DL, Giannerini S, Rosa R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Nov;78(5 Pt 1):051918. Epub 2008 Nov 19.

PMID:
19113166
[PubMed - indexed for MEDLINE]
4.

DNA, dichotomic classes and frame synchronization: a quasi-crystal framework.

Giannerini S, Gonzalez DL, Rosa R.

Philos Trans A Math Phys Eng Sci. 2012 Jun 28;370(1969):2987-3006. doi: 10.1098/rsta.2011.0387.

PMID:
22615472
[PubMed - indexed for MEDLINE]
5.

The word landscape of the non-coding segments of the Arabidopsis thaliana genome.

Lichtenberg J, Yilmaz A, Welch JD, Kurz K, Liang X, Drews F, Ecker K, Lee SS, Geisler M, Grotewold E, Welch LR.

BMC Genomics. 2009 Oct 8;10:463. doi: 10.1186/1471-2164-10-463.

PMID:
19814816
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing.

Feng J, Naiman DQ, Cooper B.

Mol Biosyst. 2009 Dec;5(12):1679-87. doi: 10.1039/b903031j. Epub 2009 Apr 30.

PMID:
19452047
[PubMed - indexed for MEDLINE]
7.

A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection.

Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH.

Genome Res. 2007 May;17(5):632-40. Epub 2007 Mar 29.

PMID:
17395691
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction.

Mathé C, Peresetsky A, Déhais P, Van Montagu M, Rouzé P.

J Mol Biol. 1999 Feb 5;285(5):1977-91.

PMID:
9925779
[PubMed - indexed for MEDLINE]
9.

The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides.

Unseld M, Marienfeld JR, Brandt P, Brennicke A.

Nat Genet. 1997 Jan;15(1):57-61.

PMID:
8988169
[PubMed - indexed for MEDLINE]
10.

On models of the genetic code generated by binary dichotomic algorithms.

Gumbel M, Fimmel E, Danielli A, Strüngmann L.

Biosystems. 2014 Dec 18;128C:9-18. doi: 10.1016/j.biosystems.2014.12.001. [Epub ahead of print]

PMID:
25530514
[PubMed - as supplied by publisher]
11.

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens.

Rensing SA, Fritzowsky D, Lang D, Reski R.

BMC Genomics. 2005 Mar 22;6:43.

PMID:
15784153
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The genome sequence and structure of rice chromosome 1.

Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T.

Nature. 2002 Nov 21;420(6913):312-6.

PMID:
12447438
[PubMed - indexed for MEDLINE]
13.

Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome.

Wu C, Wang S, Zhang HB.

Genomics. 2006 Oct;88(4):394-406. Epub 2006 Jun 27.

PMID:
16806804
[PubMed - indexed for MEDLINE]
Free Article
14.
15.

Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models.

Shepard SS, McSweeny A, Serpen G, Fedorov A.

Nucleic Acids Res. 2012 Jun;40(11):4765-73. doi: 10.1093/nar/gks154. Epub 2012 Feb 16.

PMID:
22344692
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Characterization of 954 bovine full-CDS cDNA sequences.

Harhay GP, Sonstegard TS, Keele JW, Heaton MP, Clawson ML, Snelling WM, Wiedmann RT, Van Tassell CP, Smith TP.

BMC Genomics. 2005 Nov 23;6:166.

PMID:
16305752
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Large-scale genomic correlations in Arabidopsis thaliana relate to chromosomal structure.

Kendal WS, Suomela BP.

BMC Genomics. 2005 Jun 2;6:82.

PMID:
15932642
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A comprehensive characterization of single-copy T-DNA insertions in the Arabidopsis thaliana genome.

Forsbach A, Schubert D, Lechtenberg B, Gils M, Schmidt R.

Plant Mol Biol. 2003 May;52(1):161-76.

PMID:
12825697
[PubMed - indexed for MEDLINE]
19.

Using MZEF to find internal coding exons.

Zhang MQ.

Curr Protoc Bioinformatics. 2002 Aug;Chapter 4:Unit 4.2. doi: 10.1002/0471250953.bi0402s00. Review.

PMID:
18792940
[PubMed - indexed for MEDLINE]
20.

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana.

Song D, Yang Y, Yu B, Zheng B, Deng Z, Lu BL, Chen X, Jiang T.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S36. doi: 10.1186/1471-2105-10-S1-S36.

PMID:
19208137
[PubMed - indexed for MEDLINE]
Free PMC Article

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