{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:37:26Z","timestamp":1767962246303,"version":"3.49.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA expression signals detected by high-density genomic tiling microarrays contain comprehensive transcriptomic information of the target organism. Current methods for determining the RNA transcription units are still computation intense and lack the discriminative power. This article describes an efficient and accurate methodology to reveal complicated transcriptional architecture, including small regulatory RNAs, in microbial transcriptome profiles.<\/jats:p>\n               <jats:p>Results: Normalized microarray data were first subject to support vector regression to estimate the profile tendency by reducing noise interruption. A hybrid supervised machine learning algorithm, hidden Markov support vector machines, was then used to classify the underlying state of each probe to \u2018expression\u2019 or \u2018silence\u2019 with the assumption that the consecutive state sequence was a heterogeneous Markov chain. For model construction, we introduced a profile geometry learning method to construct the feature vectors, which considered both intensity profiles and changes of intensities over the probe spacing. Also, a robust strategy was used to dynamically evaluate and select the training set based only on prior computer gene annotation. The algorithm performed better than other methods in accuracy on simulated data, especially for small expressed regions with lower (&amp;lt;1) SNR (signal-to-noise ratio), hence more sensitive for detecting small RNAs.<\/jats:p>\n               <jats:p>Availability and implementation: Detail implementation steps of the algorithm and the complete result of the transcriptome analysis for a microbial genome Porphyromonas gingivalis W83 can be viewed at http:\/\/bioinformatics.forsyth.org\/mtd<\/jats:p>\n               <jats:p>Contact: \u00a0tchen@forsyth.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq162","type":"journal-article","created":{"date-parts":[[2010,4,16]],"date-time":"2010-04-16T01:09:35Z","timestamp":1271380175000},"page":"1423-1430","source":"Crossref","is-referenced-by-count":8,"title":["A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data"],"prefix":"10.1093","volume":"26","author":[{"given":"Wen-Han","family":"Yu","sequence":"first","affiliation":[{"name":"1 Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, 2 Bioinformatics Graduate Program, Boston University, Boston, MA 02118, USA and 3 Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway"},{"name":"1 Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, 2 Bioinformatics Graduate Program, Boston University, Boston, MA 02118, USA and 3 Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway"}]},{"given":"Hedda","family":"H\u00f8vik","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, 2 Bioinformatics Graduate Program, Boston University, Boston, MA 02118, USA and 3 Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway"}]},{"given":"Tsute","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Genetics, The Forsyth Institute, Boston, MA 02115, 2 Bioinformatics Graduate Program, Boston University, Boston, MA 02118, USA and 3 Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway"}]}],"member":"286","published-online":{"date-parts":[[2010,4,15]]},"reference":[{"key":"2023012507511626000_B1","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1128\/JB.00120-09","article-title":"Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions","volume":"191","author":"Akama","year":"2009","journal-title":"J. Bacteriol."},{"key":"2023012507511626000_B2","first-page":"3","article-title":"Hidden Markov support vector machines","volume-title":"Proceedings of the Twentieth International Conference on Machine Learning.","author":"Altun","year":"2003"},{"key":"2023012507511626000_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/jae.659","article-title":"Computation and analysis of multiple structural change models","volume":"18","author":"Bai","year":"2003","journal-title":"J. Appl. Econometrics"},{"key":"2023012507511626000_B4","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1126\/science.1103388","article-title":"Global identification of human transcribed sequences with genome tiling arrays","volume":"306","author":"Bertone","year":"2004","journal-title":"Science"},{"key":"2023012507511626000_B5","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.mib.2007.03.012","article-title":"Regulatory mechanisms employed by cis-encoded antisense RNAs","volume":"10","author":"Brantl","year":"2007","journal-title":"Curr. Opin. Microbiol."},{"key":"2023012507511626000_B6","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/BF00994018","article-title":"Support-vector networks","volume":"20","author":"Cortes","year":"1995","journal-title":"Mach. Learn."},{"key":"2023012507511626000_B7","doi-asserted-by":"crossref","first-page":"5320","DOI":"10.1073\/pnas.0601091103","article-title":"A high-resolution map of transcription in the yeast genome","volume":"103","author":"David","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507511626000_B8","doi-asserted-by":"crossref","first-page":"3016","DOI":"10.1093\/bioinformatics\/btl515","article-title":"A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge","volume":"22","author":"Du","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012507511626000_B9","doi-asserted-by":"crossref","first-page":"2260","DOI":"10.1128\/iai.61.5.2260-2265.1993","article-title":"Interactions of Porphyromonas gingivalis with epithelial cells","volume":"61","author":"Duncan","year":"1993","journal-title":"Infect. Immun."},{"key":"2023012507511626000_B10","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1093\/bioinformatics\/16.10.906","article-title":"Support vector machine classification and validation of cancer tissue samples using microarray expression data","volume":"16","author":"Furey","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012507511626000_B11","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1471-2105-11-82","article-title":"Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays","volume":"11","author":"Hovik","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012507511626000_B12","first-page":"1622","article-title":"Local support vector regression for financial time series prediction","volume-title":"International Joint Conference on Neural Networks.","author":"Huang","year":"2006"},{"issue":"Suppl. 1","key":"2023012507511626000_B13","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","article-title":"Variance stabilization applied to microarray data calibration and to the quantification of differential expression","volume":"18","author":"Huber","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012507511626000_B14","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1093\/bioinformatics\/btl289","article-title":"Transcript mapping with high-density oligonucleotide tiling arrays","volume":"22","author":"Huber","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012507511626000_B15","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s10994-009-5108-8","article-title":"Cutting-plane training of structural SVMs","volume":"77","author":"Joachims","year":"2009","journal-title":"Mach. Learn."},{"key":"2023012507511626000_B16","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1126\/science.1068597","article-title":"Large-scale transcriptional activity in chromosomes 21 and 22","volume":"296","author":"Kapranov","year":"2002","journal-title":"Science"},{"key":"2023012507511626000_B17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v011.i09","article-title":"Kernlab\u2013an S4 package for kernel methods in R","volume":"11","author":"Karatzoglou","year":"2004","journal-title":"J. Stat. Software"},{"issue":"Suppl. 1","key":"2023012507511626000_B18","doi-asserted-by":"crossref","first-page":"i274","DOI":"10.1093\/bioinformatics\/bti1046","article-title":"A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences","volume":"21","author":"Li","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012507511626000_B19","doi-asserted-by":"crossref","first-page":"e294","DOI":"10.1371\/journal.pone.0000294","article-title":"Global identification and characterization of transcriptionally active regions in the rice genome","volume":"2","author":"Li","year":"2007","journal-title":"PLoS One"},{"key":"2023012507511626000_B20","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/1471-2105-7-239","article-title":"A hidden Markov model approach for determining expression from genomic tiling micro arrays","volume":"7","author":"Munch","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012507511626000_B21","doi-asserted-by":"crossref","first-page":"2341","DOI":"10.1093\/bioinformatics\/btp395","article-title":"Transcriptional landscape estimation from tiling array data using a model of signal shift and drift","volume":"25","author":"Nicolas","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507511626000_B22","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/1471-2105-6-27","article-title":"A statistical approach for array CGH data analysis","volume":"6","author":"Picard","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012507511626000_B23","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.jviromet.2005.08.017","article-title":"Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus","volume":"132","author":"Purcell","year":"2006","journal-title":"J. Virol. Methods"},{"key":"2023012507511626000_B24","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1109\/5.18626","article-title":"A tutorial on hidden Markov models and selected applications in speech recognition","volume":"77","author":"Rabiner","year":"1989","journal-title":"Proc. IEEE"},{"key":"2023012507511626000_B25","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.tig.2005.06.007","article-title":"Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping","volume":"21","author":"Royce","year":"2005","journal-title":"Trends Genet."},{"key":"2023012507511626000_B26","doi-asserted-by":"crossref","first-page":"R73","DOI":"10.1186\/gb-2004-5-10-r73","article-title":"A comprehensive transcript index of the human genome generated using microarrays and computational approaches","volume":"5","author":"Schadt","year":"2004","journal-title":"Genome Biol."},{"key":"2023012507511626000_B27","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1038\/82367","article-title":"RNA expression analysis using a 30 base pair resolution Escherichia coli genome array","volume":"18","author":"Selinger","year":"2000","journal-title":"Nat. Biotechnol."},{"key":"2023012507511626000_B28","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1126\/science.1101312","article-title":"A gene expression map for the euchromatic genome of Drosophila melanogaster","volume":"306","author":"Stolc","year":"2004","journal-title":"Science"},{"key":"2023012507511626000_B29","doi-asserted-by":"crossref","first-page":"3732","DOI":"10.1093\/nar\/gkf505","article-title":"Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays","volume":"30","author":"Tjaden","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012507511626000_B30","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1126\/science.1088305","article-title":"Empirical analysis of transcriptional activity in the Arabidopsis genome","volume":"302","author":"Yamada","year":"2003","journal-title":"Science"},{"key":"2023012507511626000_B31","first-page":"527","article-title":"Transcript normalization and segmentation of tiling array data","author":"Zeller","year":"2008","journal-title":"Pac. Symp. Biocomput."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/11\/1423\/48851026\/bioinformatics_26_11_1423.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/11\/1423\/48851026\/bioinformatics_26_11_1423.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:51:39Z","timestamp":1674633099000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/11\/1423\/203205"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,15]]},"references-count":31,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2010,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq162","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,6,1]]},"published":{"date-parts":[[2010,4,15]]}}}