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Items: 1 to 20 of 124

1.

Conrad: gene prediction using conditional random fields.

DeCaprio D, Vinson JP, Pearson MD, Montgomery P, Doherty M, Galagan JE.

Genome Res. 2007 Sep;17(9):1389-98. Epub 2007 Aug 9.

2.

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.

Testa AC, Hane JK, Ellwood SR, Oliver RP.

BMC Genomics. 2015 Mar 11;16:170. doi: 10.1186/s12864-015-1344-4.

3.

Efficient decoding algorithms for generalized hidden Markov model gene finders.

Majoros WH, Pertea M, Delcher AL, Salzberg SL.

BMC Bioinformatics. 2005 Jan 24;6:16.

4.

An empirical analysis of training protocols for probabilistic gene finders.

Majoros WH, Salzberg SL.

BMC Bioinformatics. 2004 Dec 21;5:206. Erratum in: BMC Bioinformatics. 2005;6:193.

5.

Integration of relational and hierarchical network information for protein function prediction.

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED.

BMC Bioinformatics. 2008 Aug 22;9:350. doi: 10.1186/1471-2105-9-350.

6.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Kuhn A, Luthi-Carter R, Delorenzi M.

BMC Bioinformatics. 2008 Jan 17;9:26. doi: 10.1186/1471-2105-9-26.

7.

Reranking candidate gene models with cross-species comparison for improved gene prediction.

Liu Q, Crammer K, Pereira FC, Roos DS.

BMC Bioinformatics. 2008 Oct 14;9:433. doi: 10.1186/1471-2105-9-433.

8.

A comparative study of energy minimization methods for Markov random fields with smoothness-based priors.

Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C.

IEEE Trans Pattern Anal Mach Intell. 2008 Jun;30(6):1068-80. doi: 10.1109/TPAMI.2007.70844.

PMID:
18421111
9.

Global discriminative learning for higher-accuracy computational gene prediction.

Bernal A, Crammer K, Hatzigeorgiou A, Pereira F.

PLoS Comput Biol. 2007 Mar 16;3(3):e54. Epub 2007 Feb 2.

10.

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.

Liu Q, Mackey AJ, Roos DS, Pereira FC.

Bioinformatics. 2008 Mar 1;24(5):597-605. doi: 10.1093/bioinformatics/btn004. Epub 2008 Jan 10.

PMID:
18187439
11.

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.

Song J, Yuan Z, Tan H, Huber T, Burrage K.

Bioinformatics. 2007 Dec 1;23(23):3147-54. Epub 2007 Oct 17.

PMID:
17942444
12.

The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes.

Riley T, Yu X, Sontag E, Levine A.

BMC Bioinformatics. 2009 Apr 20;10:111. doi: 10.1186/1471-2105-10-111.

13.

CARSVM: a class association rule-based classification framework and its application to gene expression data.

Kianmehr K, Alhajj R.

Artif Intell Med. 2008 Sep;44(1):7-25. doi: 10.1016/j.artmed.2008.05.002. Epub 2008 Jun 30.

PMID:
18586476
14.
15.

Learning flexible features for conditional random fields.

Stewart L, He X, Zemel RS.

IEEE Trans Pattern Anal Mach Intell. 2008 Aug;30(8):1415-26. doi: 10.1109/TPAMI.2007.70790.

PMID:
18566495
16.
17.

High-precision high-coverage functional inference from integrated data sources.

Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C.

BMC Bioinformatics. 2008 Feb 25;9:119. doi: 10.1186/1471-2105-9-119.

18.

Multivariate analysis of full-term neonatal polysomnographic data.

Gerla V, Paul K, Lhotska L, Krajca V.

IEEE Trans Inf Technol Biomed. 2009 Jan;13(1):104-10. doi: 10.1109/TITB.2008.2007193.

PMID:
19129029
19.

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre.

Bennett-Lovsey RM, Herbert AD, Sternberg MJ, Kelley LA.

Proteins. 2008 Feb 15;70(3):611-25.

PMID:
17876813
20.

Robust prediction of mutation-induced protein stability change by property encoding of amino acids.

Kang S, Chen G, Xiao G.

Protein Eng Des Sel. 2009 Feb;22(2):75-83. doi: 10.1093/protein/gzn063. Epub 2008 Dec 2.

PMID:
19054789

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