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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 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
5.

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.

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.

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.

10.

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
11.

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
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.

Introduction to Hidden Markov Models and Its Applications in Biology.

Vijayabaskar MS.

Methods Mol Biol. 2017;1552:1-12. doi: 10.1007/978-1-4939-6753-7_1.

PMID:
28224487
14.

Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.

Dialdestoro K, Sibbesen JA, Maretty L, Raghwani J, Gall A, Kellam P, Pybus OG, Hein J, Jenkins PA.

Genetics. 2016 Apr;202(4):1449-72. doi: 10.1534/genetics.115.177931. Epub 2016 Feb 8.

15.

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
16.

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
17.

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
18.

HMM Logos for visualization of protein families.

Schuster-Böckler B, Schultz J, Rahmann S.

BMC Bioinformatics. 2004 Jan 21;5:7.

19.

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.

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