TY - JOUR AU - Baum, L. E. AU - Petrie, T. PY - 1966 DA - 1966// TI - Statistical inference for probabilistic functions of finite state Markov chains JO - Ann Math Stat VL - 37 UR - https://doi.org/10.1214/aoms/1177699147 DO - 10.1214/aoms/1177699147 ID - Baum1966 ER - TY - JOUR AU - Baum, L. E. AU - Eagon, J. A. PY - 1967 DA - 1967// TI - An inequality with applications to statistical estimation for probabilistic functions of Markov processes and to a model for ecology JO - Bull Am Math Soc VL - 73 UR - https://doi.org/10.1090/S0002-9904-1967-11751-8 DO - 10.1090/S0002-9904-1967-11751-8 ID - Baum1967 ER - TY - JOUR AU - Baum, L. E. AU - Sell, G. PY - 1968 DA - 1968// TI - Growth transformations for functions on manifolds JO - Pac J Math VL - 27 UR - https://doi.org/10.2140/pjm.1968.27.211 DO - 10.2140/pjm.1968.27.211 ID - Baum1968 ER - TY - JOUR AU - Baum, L. E. AU - Petrie, T. AU - Soules, G. AU - Weiss, N. PY - 1970 DA - 1970// TI - A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains JO - Ann Math Stat VL - 41 UR - https://doi.org/10.1214/aoms/1177697196 DO - 10.1214/aoms/1177697196 ID - Baum1970 ER - TY - JOUR AU - Baum, L. PY - 1972 DA - 1972// TI - An inequality and associated maximization technique in statistical estimation of probabilistic functions of a Markov process JO - Inequalities VL - 3 ID - Baum1972 ER - TY - STD TI - Scheffer T, Decomain C, Wrobel S. Active hidden Markov models for information extraction. In: International symposium on intelligent data analysis. Springer; 2001. p. 309–18. ID - ref6 ER - TY - JOUR AU - Lee, J. -. Y. AU - Wang, X. AU - Cui, W. AU - Sager, R. AU - Modla, S. AU - Czymmek, K. AU - Zybaliov, B. AU - Wijk, K. AU - Zhang, C. AU - Lu, H. PY - 2011 DA - 2011// TI - A plasmodesmata-localized protein mediates crosstalk between cell-to-cell communication and innate immunity in arabidopsis JO - Plant Cell VL - 23 UR - https://doi.org/10.1105/tpc.111.087742 DO - 10.1105/tpc.111.087742 ID - Lee2011 ER - TY - STD TI - Li J, Lee,J-Y, Liao L. Detecting de novo plasmodesmata targeting signals and identifying PD targeting proteins. In: International conference on computational advances in bio and medical sciences. Springer; 2019. p. 1–12. ID - ref8 ER - TY - JOUR AU - Tamposis, I. A. AU - Tsirigos, K. D. AU - Theodoropoulou, M. C. AU - Kontou, P. I. AU - Bagos, P. G. PY - 2019 DA - 2019// TI - Semi-supervised learning of hidden Markov models for biological sequence analysis JO - Bioinformatics VL - 35 UR - https://doi.org/10.1093/bioinformatics/bty910 DO - 10.1093/bioinformatics/bty910 ID - Tamposis2019 ER - TY - JOUR AU - Rabiner, L. AU - Juang, B. PY - 1986 DA - 1986// TI - An introduction to hidden Markov models JO - IEEE ASSP Mag VL - 3 UR - https://doi.org/10.1109/MASSP.1986.1165342 DO - 10.1109/MASSP.1986.1165342 ID - Rabiner1986 ER - TY - JOUR AU - Viterbi, A. PY - 1967 DA - 1967// TI - Error bounds for convolutional codes and an asymptotically optimum decoding algorithm JO - IEEE Trans Inf Theory VL - 13 UR - https://doi.org/10.1109/TIT.1967.1054010 DO - 10.1109/TIT.1967.1054010 ID - Viterbi1967 ER - TY - JOUR AU - Bagos, P. G. AU - Liakopoulos, T. D. AU - Hamodrakas, S. J. PY - 2006 DA - 2006// TI - Algorithms for incorporating prior topological information in HMMS: application to transmembrane proteins JO - BMC Bioinform VL - 7 UR - https://doi.org/10.1186/1471-2105-7-189 DO - 10.1186/1471-2105-7-189 ID - Bagos2006 ER - TY - JOUR AU - Juang, B. -. H. AU - Rabiner, L. R. PY - 1990 DA - 1990// TI - The segmental k-means algorithm for estimating parameters of hidden Markov models JO - IEEE Trans Acoust Speech Signal Process VL - 38 UR - https://doi.org/10.1109/29.60082 DO - 10.1109/29.60082 ID - Juang1990 ER - TY - JOUR AU - Käll, L. AU - Krogh, A. AU - Sonnhammer, E. L. PY - 2005 DA - 2005// TI - An hmm posterior decoder for sequence feature prediction that includes homology information JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1014 DO - 10.1093/bioinformatics/bti1014 ID - Käll2005 ER - TY - JOUR AU - Fariselli, P. AU - Martelli, P. L. AU - Casadio, R. PY - 2005 DA - 2005// TI - A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins JO - BMC Bioinform VL - 6 ID - Fariselli2005 ER - TY - JOUR AU - Kahsay, R. Y. AU - Gao, G. AU - Liao, L. PY - 2005 DA - 2005// TI - An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti303 DO - 10.1093/bioinformatics/bti303 ID - Kahsay2005 ER - TY - STD TI - Sonnhammer EL, Von Heijne G, Krogh A, et al. A hidden Markov model for predicting transmembrane helices in protein sequences; 1998. ID - ref17 ER - TY - JOUR AU - Käll, L. AU - Krogh, A. AU - Sonnhammer, E. L. PY - 2007 DA - 2007// TI - Advantages of combined transmembrane topology and signal peptide prediction—the phobius web server JO - Nucl Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm256 DO - 10.1093/nar/gkm256 ID - Käll2007 ER - TY - JOUR AU - Hayat, S. AU - Peters, C. AU - Shu, N. AU - Tsirigos, K. D. AU - Elofsson, A. PY - 2016 DA - 2016// TI - Inclusion of dyad-repeat pattern improves topology prediction of transmembrane $$\beta$$β-barrel proteins JO - Bioinformatics VL - 32 UR - https://doi.org/10.1093/bioinformatics/btw025 DO - 10.1093/bioinformatics/btw025 ID - Hayat2016 ER -