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Items: 1 to 20 of 98

1.

A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection.

Bulla I, Schultz AK, Chesneau C, Mark T, Serea F.

BMC Bioinformatics. 2014 Jun 19;15:205. doi: 10.1186/1471-2105-15-205.

2.

Improving Hidden Markov Models for classification of human immunodeficiency virus-1 subtypes through linear classifier learning.

Bulla I, Schultz AK, Meinicke P.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(1):Article 1. doi: 10.2202/1544-6115.1680.

PMID:
22499688
3.

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.

Unterthiner T, Schultz AK, Bulla J, Morgenstern B, Stanke M, Bulla I.

BMC Bioinformatics. 2011 Apr 11;12:93. doi: 10.1186/1471-2105-12-93.

4.

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.

Schultz AK, Zhang M, Leitner T, Kuiken C, Korber B, Morgenstern B, Stanke M.

BMC Bioinformatics. 2006 May 22;7:265.

5.

A clustering approach for estimating parameters of a profile hidden Markov model.

Aghdam R, Pezeshk H, Malekpour SA, Shemehsavar S, Eslahchi C.

Int J Data Min Bioinform. 2013;8(1):66-82.

PMID:
23865165
6.

HMMEditor: a visual editing tool for profile hidden Markov model.

Dai J, Cheng J.

BMC Genomics. 2008;9 Suppl 1:S8. doi: 10.1186/1471-2164-9-S1-S8.

8.

More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs.

Truszkowski J, Brown DG.

BMC Bioinformatics. 2011 May 17;12:168. doi: 10.1186/1471-2105-12-168.

9.

Automated protein subfamily identification and classification.

Brown DP, Krishnamurthy N, Sjölander K.

PLoS Comput Biol. 2007 Aug;3(8):e160.

10.

Combined prediction of transmembrane topology and signal peptide of beta-barrel proteins: using a hidden Markov model and genetic algorithms.

Zou L, Wang Z, Wang Y, Hu F.

Comput Biol Med. 2010 Jul;40(7):621-8. doi: 10.1016/j.compbiomed.2010.04.006. Epub 2010 May 21.

PMID:
20488436
11.

Probabilistic models for biological sequences: selection and Maximum Likelihood estimation.

Ekisheva S, Borodovsky M.

Int J Bioinform Res Appl. 2006;2(3):305-24.

PMID:
18048168
12.

A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion.

Kedzierska A, Husmeier D.

Stat Appl Genet Mol Biol. 2006;5:Article27. Epub 2006 Oct 24.

PMID:
17140392
13.

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

Zhang M, Schultz AK, Calef C, Kuiken C, Leitner T, Korber B, Morgenstern B, Stanke M.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W463-5.

14.

The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin.

Gao F, Robertson DL, Morrison SG, Hui H, Craig S, Decker J, Fultz PN, Girard M, Shaw GM, Hahn BH, Sharp PM.

J Virol. 1996 Oct;70(10):7013-29.

15.

HMM Logos for visualization of protein families.

Schuster-Böckler B, Schultz J, Rahmann S.

BMC Bioinformatics. 2004 Jan 21;5:7.

16.

Detection of recombination in DNA multiple alignments with hidden Markov models.

Husmeier D, Wright F.

J Comput Biol. 2001;8(4):401-27.

PMID:
11571075
17.

Using hidden Markov models to align multiple sequences.

Mount DW.

Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.top41. doi: 10.1101/pdb.top41.

PMID:
20147223
18.

A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.

Martin DP, Posada D, Crandall KA, Williamson C.

AIDS Res Hum Retroviruses. 2005 Jan;21(1):98-102.

PMID:
15665649
20.
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