128 related articles for article (PubMed ID: 21586147)
1. More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs.
Truszkowski J; Brown DG
BMC Bioinformatics; 2011 May; 12():168. PubMed ID: 21586147
[TBL] [Abstract][Full Text] [Related]
2. jpHMM: improving the reliability of recombination prediction in HIV-1.
Schultz AK; Zhang M; Bulla I; Leitner T; Korber B; Morgenstern B; Stanke M
Nucleic Acids Res; 2009 Jul; 37(Web Server issue):W647-51. PubMed ID: 19443440
[TBL] [Abstract][Full Text] [Related]
3. 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; 7():265. PubMed ID: 16716226
[TBL] [Abstract][Full Text] [Related]
4. 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; 34(Web Server issue):W463-5. PubMed ID: 16845050
[TBL] [Abstract][Full Text] [Related]
5. jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.
Schultz AK; Bulla I; Abdou-Chekaraou M; Gordien E; Morgenstern B; Zoaulim F; Dény P; Stanke M
Nucleic Acids Res; 2012 Jul; 40(Web Server issue):W193-8. PubMed ID: 22600739
[TBL] [Abstract][Full Text] [Related]
6. 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. PubMed ID: 20488436
[TBL] [Abstract][Full Text] [Related]
7. Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory.
Churbanov A; Winters-Hilt S
BMC Bioinformatics; 2008 Apr; 9():224. PubMed ID: 18447951
[TBL] [Abstract][Full Text] [Related]
8. The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs.
Keibler E; Arumugam M; Brent MR
Bioinformatics; 2007 Mar; 23(5):545-54. PubMed ID: 17237054
[TBL] [Abstract][Full Text] [Related]
9. Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER.
Ferreira M; Roma N; Russo LM
BMC Bioinformatics; 2014 May; 15():165. PubMed ID: 24884826
[TBL] [Abstract][Full Text] [Related]
10. 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; 15():205. PubMed ID: 24946781
[TBL] [Abstract][Full Text] [Related]
11. A post-decoding re-ranking algorithm for predicting interacting residues in proteins with hidden Markov models incorporating long-distance information.
Kern C; Liao L
Comput Biol Chem; 2016 Dec; 65():21-28. PubMed ID: 27718452
[TBL] [Abstract][Full Text] [Related]
12. A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.
Fariselli P; Martelli PL; Casadio R
BMC Bioinformatics; 2005 Dec; 6 Suppl 4(Suppl 4):S12. PubMed ID: 16351738
[TBL] [Abstract][Full Text] [Related]
13. Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory.
Azad RK; Borodovsky M
Brief Bioinform; 2004 Jun; 5(2):118-30. PubMed ID: 15260893
[TBL] [Abstract][Full Text] [Related]
14. VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays.
Allred AF; Renshaw H; Weaver S; Tesh RB; Wang D
Bioinformatics; 2012 Nov; 28(22):2922-9. PubMed ID: 23044542
[TBL] [Abstract][Full Text] [Related]
15. Identifying the important HIV-1 recombination breakpoints.
Archer J; Pinney JW; Fan J; Simon-Loriere E; Arts EJ; Negroni M; Robertson DL
PLoS Comput Biol; 2008 Sep; 4(9):e1000178. PubMed ID: 18787691
[TBL] [Abstract][Full Text] [Related]
16. Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models.
Husmeier D
Bioinformatics; 2005 Sep; 21 Suppl 2():ii166-72. PubMed ID: 16204097
[TBL] [Abstract][Full Text] [Related]
17. Accurate detection of recombinant breakpoints in whole-genome alignments.
Westesson O; Holmes I
PLoS Comput Biol; 2009 Mar; 5(3):e1000318. PubMed ID: 19300487
[TBL] [Abstract][Full Text] [Related]
18. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.
Kosakovsky Pond SL; Posada D; Stawiski E; Chappey C; Poon AF; Hughes G; Fearnhill E; Gravenor MB; Leigh Brown AJ; Frost SD
PLoS Comput Biol; 2009 Nov; 5(11):e1000581. PubMed ID: 19956739
[TBL] [Abstract][Full Text] [Related]
19. HMM sampling and applications to gene finding and alternative splicing.
Cawley SL; Pachter L
Bioinformatics; 2003 Oct; 19 Suppl 2():ii36-41. PubMed ID: 14534169
[TBL] [Abstract][Full Text] [Related]
20. Reliable genotyping of recombinant genomes using a robust hidden Markov model.
Campos-Martin R; Schmickler S; Goel M; Schneeberger K; Tresch A
Plant Physiol; 2023 May; 192(2):821-836. PubMed ID: 36946207
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]