{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T21:25:21Z","timestamp":1792185921631,"version":"4.4.0"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T00:00:00Z","timestamp":1741392000000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["2019-05247"],"award-info":[{"award-number":["2019-05247"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Memorial University School of Graduate Studies"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>A terminator is a DNA region that ends the transcription process. Currently, multiple computational tools are available for predicting bacterial terminators. However, these methods are specialized for certain bacteria or terminator type (i.e. intrinsic or factor-dependent). In this work, we developed BacTermFinder using an ensemble of convolutional neural networks (CNNs) receiving as input four different representations of terminator sequences. To develop BacTermFinder, we collected roughly 41\u00a0000\u00a0bacterial terminators (intrinsic and factor-dependent) of 22 species with varying GC-content (from 28% to 71%) from published studies that used RNA-seq technologies. We evaluated BacTermFinder\u2019s performance on terminators of five bacterial species (not used for training BacTermFinder) and two archaeal species. BacTermFinder\u2019s performance was compared with that of four other bacterial terminator prediction tools. Based on our results, BacTermFinder outperforms all other four approaches in terms of average recall without increasing the number of false positives. Moreover, BacTermFinder identifies both types of terminators (intrinsic and factor-dependent) and generalizes to archaeal terminators. Additionally, we visualized the saliency map of the CNNs to gain insights on terminator motif per species. BacTermFinder is publicly available at https:\/\/github.com\/BioinformaticsLabAtMUN\/BacTermFinder.<\/jats:p>","DOI":"10.1093\/nargab\/lqaf016","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T15:22:16Z","timestamp":1739460136000},"source":"Crossref","is-referenced-by-count":15,"title":["BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble"],"prefix":"10.1093","volume":"7","author":[{"given":"Seyed\u00a0Mohammad\u00a0Amin","family":"Taheri\u00a0Ghahfarokhi","sequence":"first","affiliation":[{"name":"Department of Computer Science, Memorial University of Newfoundland , St. John\u2019s, Newfoundland A1B 3X5 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0643-2547","authenticated-orcid":false,"given":"Lourdes","family":"Pe\u00f1a-Castillo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Memorial University of Newfoundland , St. John\u2019s, Newfoundland A1B 3X5 ,","place":["Canada"]},{"name":"Department of Biology, Memorial University of Newfoundland , St. John\u2019s, Newfoundland A1B 3X9 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,3,8]]},"reference":[{"key":"2025030817161764200_B1","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-biochem-060815-014844","article-title":"Mechanisms of bacterial transcription termination: all good things must end","volume":"85","author":"Ray-Soni","year":"2016","journal-title":"Annu Rev Biochem"},{"key":"2025030817161764200_B2","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/nrmicro2560","article-title":"Termination and antitermination: RNA polymerase runs a stop sign","volume":"9","author":"Santangelo","year":"2011","journal-title":"Nat Rev Microbiol"},{"key":"2025030817161764200_B3","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.ygeno.2009.04.004","article-title":"Occurrence, divergence and evolution of intrinsic terminators across eubacteria","volume":"94","author":"Mitra","year":"2009","journal-title":"Genomics"},{"key":"2025030817161764200_B4","doi-asserted-by":"publisher","first-page":"1663","DOI":"10.1038\/s41467-022-29321-5","article-title":"Rho-dependent transcription termination proceeds via three routes","volume":"13","author":"Song","year":"2022","journal-title":"Nat Commun"},{"key":"2025030817161764200_B5","doi-asserted-by":"publisher","first-page":"R22","DOI":"10.1186\/GB-2007-8-2-R22\/FIGURES\/5","article-title":"Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake","volume":"8","author":"Kingsford","year":"2007","journal-title":"Genome Biol"},{"key":"2025030817161764200_B6","doi-asserted-by":"publisher","first-page":"aad9822","DOI":"10.1126\/science.aad9822","article-title":"Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria","volume":"352","author":"Dar","year":"2016","journal-title":"Science"},{"key":"2025030817161764200_B7","doi-asserted-by":"publisher","first-page":"1907","DOI":"10.1038\/S41564-019-0500-Z","article-title":"Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria","volume":"4","author":"Ju","year":"2019","journal-title":"Nat Microbiol"},{"key":"2025030817161764200_B8","doi-asserted-by":"publisher","first-page":"3676","DOI":"10.1038\/S41467-018-05997-6","article-title":"SMRT-Cappable-seq reveals complex operon variants in bacteria","volume":"9","author":"Yan","year":"2018","journal-title":"Nat Commun"},{"key":"2025030817161764200_B9","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1016\/j.cell.2018.03.007","article-title":"Evolutionary convergence of pathway-specific enzyme expression stoichiometry","volume":"173","author":"Lalanne","year":"2018","journal-title":"Cell"},{"key":"2025030817161764200_B10","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/NMETH.3313","article-title":"Simultaneous generation of many RNA-seq libraries in a single reaction","volume":"12","author":"Shishkin","year":"2015","journal-title":"Nat Methods"},{"key":"2025030817161764200_B11","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/J.MIB.2014.06.010","article-title":"Differential RNA-seq: the approach behind and the biological insight gained","volume":"19","author":"Sharma","year":"2014","journal-title":"Curr Opin Microbiol"},{"key":"2025030817161764200_B12","doi-asserted-by":"publisher","first-page":"e1010240","DOI":"10.1371\/JOURNAL.PCBI.1010240","article-title":"Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators","volume":"18","author":"Brandenburg","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2025030817161764200_B13","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1093\/bioinformatics\/bty827","article-title":"iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators","volume":"35","author":"Feng","year":"2019","journal-title":"Bioinformatics"},{"key":"2025030817161764200_B14","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1186\/s12859-019-2704-x","article-title":"RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases","volume":"20","author":"Di","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2025030817161764200_B15","article-title":"National Center for Biotechnology Information (NCBI) PubMed 1988\u20132023","author":"NCBI"},{"key":"2025030817161764200_B16","article-title":"National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) 1999\u20132023","author":"NCBI"},{"key":"2025030817161764200_B17","first-page":"87","article-title":"Jupyter Notebooks\u2014a publishing format for reproducible computational workflows","volume-title":"Positioning and Power in Academic Publishing: Players, Agents and Agendas","author":"Kluyver","year":"2016"},{"key":"2025030817161764200_B18","unstructured":"The pandas development team \u00a0pandas-dev\/pandas: Pandas. 2020; Zenodo10.5281\/zenodo.3509134."},{"key":"2025030817161764200_B19","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/BIOINFORMATICS\/BTQ033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025030817161764200_B20","doi-asserted-by":"publisher","first-page":"3583","DOI":"10.1093\/nar\/29.17.3583","article-title":"Prediction of rho-independent transcriptional terminators in Escherichia coli","volume":"29","author":"Lesnik","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B21","doi-asserted-by":"publisher","first-page":"D133","DOI":"10.1093\/NAR\/GKV1156","article-title":"RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond","volume":"44","author":"Gama-Castro","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B22","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1093\/NAR\/29.1.278","article-title":"DBTBS: a database of Bacillus subtilis promoters and transcription factors","volume":"29","author":"Ishii","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B23","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1099\/MGEN.0.000524","article-title":"BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access","volume":"7","author":"Geissler","year":"2021","journal-title":"Microb Genom"},{"key":"2025030817161764200_B24","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1186\/S13059-021-02514-9\/TABLES\/10","article-title":"Promotech: a general tool for bacterial promoter recognition","volume":"22","author":"Chevez-Guardado","year":"2021","journal-title":"Genome Biol"},{"key":"2025030817161764200_B25","doi-asserted-by":"publisher","first-page":"bbab434","DOI":"10.1093\/BIB\/BBAB434","article-title":"MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors","volume":"23","author":"Bonidia","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025030817161764200_B26","doi-asserted-by":"publisher","first-page":"e60","DOI":"10.1093\/NAR\/GKAB122","article-title":"iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization","volume":"49","author":"Chen","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B27","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1093\/BIOINFORMATICS\/BTU820","article-title":"repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects","volume":"31","author":"Liu","year":"2015","journal-title":"Bioinformatics"},{"key":"2025030817161764200_B28","doi-asserted-by":"crossref","first-page":"2522","DOI":"10.1038\/s42256-019-0138-9","article-title":"From local explanations to global understanding with explainable AI for trees","volume":"2","author":"Lundberg","year":"2020","journal-title":"Nat Mach Intell"},{"key":"2025030817161764200_B29","article-title":"LightGBM: a highly efficient gradient boosting decision tree","volume-title":"Advances in Neural Information Processing Systems","author":"Ke","year":"2017"},{"key":"2025030817161764200_B30","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1038\/nature14539","article-title":"Deep Learning","volume":"521","author":"LeCun","year":"2015","journal-title":"Nature"},{"key":"2025030817161764200_B31","article-title":"Why do tree-based models still outperform deep learning on typical tabular data?","author":"Grinsztajn"},{"key":"2025030817161764200_B32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0169-7439(00)00122-2","article-title":"Monte Carlo cross validation","volume":"56","author":"Xu","year":"2001","journal-title":"Chemom Intell Lab Syst"},{"key":"2025030817161764200_B33","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1038\/s41592-021-01205-4","article-title":"DOME: recommendations for supervised machine learning validation in biology","volume":"18","author":"Walsh","year":"2021","journal-title":"Nat Methods"},{"key":"2025030817161764200_B34","doi-asserted-by":"publisher","first-page":"106465","DOI":"10.1016\/j.isci.2023.106465","article-title":"Premature termination of transcription is shaped by Rho and translated uORFS in Mycobacterium tuberculosis","volume":"26","author":"D\u2019Halluin","year":"2023","journal-title":"iScience"},{"key":"2025030817161764200_B35","first-page":"11","article-title":"Rho-dependent transcription termination: more questions than answers","volume":"44","author":"Banerjee","year":"2006","journal-title":"J Microbiol"},{"key":"2025030817161764200_B36","doi-asserted-by":"publisher","first-page":"7843","DOI":"10.1038\/s41467-023-43534-2","article-title":"TRS: a method for determining transcript termini from RNAtag-seq sequencing data","volume":"14","author":"Bar","year":"2023","journal-title":"Nat Commun"},{"key":"2025030817161764200_B37","doi-asserted-by":"publisher","first-page":"e62438","DOI":"10.7554\/ELIFE.62438","article-title":"Regulatory roles of Escherichia coli 5\u2032 UTR and ORF-internal RNAs detected by 3\u2032 end mapping","volume":"10","author":"Adams","year":"2021","journal-title":"eLife"},{"key":"2025030817161764200_B38","doi-asserted-by":"crossref","first-page":"e01013-20","DOI":"10.1128\/mSystems.01013-20","article-title":"Elucidating the regulatory elements for transcription termination and posttranscriptional processing in the Streptomyces clavuligerus genome","volume":"6","author":"Hwang","year":"2021","journal-title":"mSystems"},{"key":"2025030817161764200_B39","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1016\/j.jmb.2011.03.036","article-title":"Bacterial transcription terminators: the RNA 3\u2032-end chronicles","volume":"412","author":"Peters","year":"2011","journal-title":"J Mol Biol"},{"key":"2025030817161764200_B40","doi-asserted-by":"publisher","first-page":"D37","DOI":"10.1093\/nar\/gkn597","article-title":"DiProDB: a database for dinucleotide properties","volume":"37","author":"Friedel","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B41","doi-asserted-by":"publisher","first-page":"14719","DOI":"10.1021\/bi9809425","article-title":"Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson\u2013Crick base pairs","volume":"37","author":"Xia","year":"1998","journal-title":"Biochemistry"},{"key":"2025030817161764200_B42","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1016\/j.biochi.2023.07.018","article-title":"INTERPIN: a repository for intrinsic transcription termination hairpins in bacteria","volume":"214(Pt B)","author":"Gupta","year":"2023","journal-title":"Biochimie"},{"key":"2025030817161764200_B43","first-page":"1","article-title":"Statistical comparisons of classifiers over multiple data sets","volume":"7","author":"Dem\u0161ar","year":"2006","journal-title":"J Mach Learn Res"},{"key":"2025030817161764200_B44","doi-asserted-by":"publisher","first-page":"2044","DOI":"10.1016\/j.ins.2009.12.010","article-title":"Advanced nonparametric tests for multiple comparisons in the design of experiments in computational intelligence and data mining: experimental analysis of power","volume":"180","author":"Garc\u00eda","year":"2010","journal-title":"Inform Sci"},{"key":"2025030817161764200_B45","article-title":"PMCMRplus: calculate pairwise multiple comparisons of mean rank sums extended","author":"Pohlert","year":"2024"},{"key":"2025030817161764200_B46","doi-asserted-by":"crossref","first-page":"248","DOI":"10.32614\/RJ-2016-017","article-title":"scmamp: statistical comparison of multiple algorithms in multiple problems","volume":"8","author":"Calvo","year":"2016","journal-title":"The R Journal"},{"key":"2025030817161764200_B47","doi-asserted-by":"publisher","first-page":"4955","DOI":"10.1128\/JB.181.16.4955-4960.1999","article-title":"Transcript cleavage, attenuation, and an internal promoter in the Rhodobacter capsulatus puc operon","volume":"181","author":"LeBlanc","year":"1999","journal-title":"J Bacteriol"},{"key":"2025030817161764200_B48","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1080\/15476286.2017.1306175","article-title":"Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA","volume":"14","author":"Gr\u00fcll","year":"2017","journal-title":"RNA Biol"},{"key":"2025030817161764200_B49","doi-asserted-by":"publisher","first-page":"16194","DOI":"10.1038\/s41598-021-95435-3","article-title":"Clusters of hairpins induce intrinsic transcription termination in bacteria","volume":"11","author":"Gupta","year":"2021","journal-title":"Sci Rep"},{"key":"2025030817161764200_B50","doi-asserted-by":"publisher","first-page":"e0228479","DOI":"10.1371\/journal.pone.0228479","article-title":"iterb-PPse: identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC","volume":"15","author":"Fan","year":"2020","journal-title":"PloS One"},{"key":"2025030817161764200_B51","doi-asserted-by":"publisher","first-page":"8245","DOI":"10.1093\/nar\/gky563","article-title":"A multivariate prediction model for Rho-dependent termination of transcription","volume":"46","author":"Nadiras","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B52","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1093\/nar\/gkw749","article-title":"Computational prediction of regulatory, premature transcription termination in bacteria","volume":"45","author":"Millman","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B53","doi-asserted-by":"publisher","first-page":"5845","DOI":"10.1093\/nar\/gkr168","article-title":"RNIE: genome-wide prediction of bacterial intrinsic terminators","volume":"39","author":"Gardner","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B54","doi-asserted-by":"publisher","first-page":"16143","DOI":"10.1038\/nmicrobiol.2016.143","article-title":"Widespread formation of alternative 3\u2032 UTR isoforms via transcription termination in archaea","volume":"1","author":"Dar","year":"2016","journal-title":"Nat Microbiol"},{"key":"2025030817161764200_B55","doi-asserted-by":"crossref","first-page":"6174","DOI":"10.1093\/nar\/gkac497","article-title":"Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp","volume":"50","author":"Takada","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B56","doi-asserted-by":"crossref","first-page":"e61880","DOI":"10.7554\/eLife.61880","article-title":"NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA","volume":"10","author":"Mandell","year":"2021","journal-title":"eLife"},{"key":"2025030817161764200_B57","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.cell.2018.03.007","article-title":"Evolutionary convergence of pathway-specific enzyme expression stoichiometry","volume":"173","author":"Lalanne","year":"2018","journal-title":"Cell"},{"key":"2025030817161764200_B58","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41586-020-2638-5","article-title":"Functionally uncoupled transcription-translation in Bacillus subtilis","volume":"585","author":"Johnson","year":"2020","journal-title":"Nature"},{"key":"2025030817161764200_B59","doi-asserted-by":"publisher","first-page":"e25","DOI":"10.1371\/JOURNAL.PCBI.0010025","article-title":"Prediction of transcriptional terminators in Bacillus subtilis and related species","volume":"1","author":"Hoon","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"2025030817161764200_B60","doi-asserted-by":"crossref","first-page":"e2103579118","DOI":"10.1073\/pnas.2103579118","article-title":"An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium","volume":"118","author":"Fuchs","year":"2021","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025030817161764200_B61","doi-asserted-by":"crossref","first-page":"e0052422","DOI":"10.1128\/mbio.00524-22","article-title":"Mapping the complex transcriptional landscape of the phytopathogenic bacterium Dickeya dadantii","volume":"13","author":"Forquet","year":"2022","journal-title":"mBio"},{"key":"2025030817161764200_B62","doi-asserted-by":"crossref","first-page":"6797","DOI":"10.1093\/nar\/gky274","article-title":"High-resolution RNA 3\u2019-ends mapping of bacterial Rho-dependent transcripts","volume":"46","author":"Dar","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B63","doi-asserted-by":"crossref","first-page":"D212","DOI":"10.1093\/nar\/gky1077","article-title":"RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12","volume":"47","author":"Santos-Zavaleta","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B64","doi-asserted-by":"crossref","first-page":"4171","DOI":"10.1093\/nar\/gkac206","article-title":"Synthetic 3\u2032-UTR valves for optimal metabolic flux control in Escherichia coli","volume":"50","author":"Choe","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B65","doi-asserted-by":"crossref","first-page":"e02253-19","DOI":"10.1128\/mBio.02253-19","article-title":"A rhlI 5\u2032 UTR-derived sRNA regulates RhlR-dependent quorum sensing in Pseudomonas aeruginosa","volume":"10","author":"Thomason","year":"2019","journal-title":"mBio"},{"key":"2025030817161764200_B66","doi-asserted-by":"crossref","first-page":"3558","DOI":"10.1038\/s41467-022-31177-8","article-title":"RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3\u2032UTR required for intermediate vancomycin resistance","volume":"13","author":"Mediati","year":"2022","journal-title":"Nat Commun"},{"key":"2025030817161764200_B67","doi-asserted-by":"crossref","first-page":"576","DOI":"10.3390\/ijms23010576","article-title":"Regulation of heterogenous lexA expression in Staphylococcus aureus by an antisense RNA originating from transcriptional read-through upon natural mispairings in the sbrB intrinsic terminator","volume":"23","author":"Bastet","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025030817161764200_B68","first-page":"9971","article-title":"Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39","volume":"46","author":"Slager","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2025030817161764200_B69","doi-asserted-by":"crossref","first-page":"e1007461","DOI":"10.1371\/journal.ppat.1007461","article-title":"The transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence","volume":"14","author":"Warrier","year":"2018","journal-title":"PLoS Pathog"},{"key":"2025030817161764200_B70","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1186\/s12864-022-08314-0","article-title":"Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information","volume":"23","author":"Lee","year":"2022","journal-title":"BMC Genomics"},{"key":"2025030817161764200_B71","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/s41597-020-00775-w","article-title":"Genome-scale determination of 5\u2032 and 3\u2032 boundaries of RNA transcripts in Streptomyces genomes","volume":"7","author":"Lee","year":"2020","journal-title":"Sci Data"},{"key":"2025030817161764200_B72","doi-asserted-by":"crossref","first-page":"844200","DOI":"10.3389\/fbioe.2022.844200","article-title":"System-level analysis of transcriptional and translational regulatory elements in Streptomyces griseus","volume":"10","author":"Hwang","year":"2022","journal-title":"Front Bioeng Biotechnol"},{"key":"2025030817161764200_B73","doi-asserted-by":"publisher","first-page":"2074","DOI":"10.3389\/FMICB.2019.02074\/FULL","article-title":"The transcription unit architecture of Streptomyces lividans TK24","volume":"10","author":"Lee","year":"2019","journal-title":"Front Microbiol"},{"key":"2025030817161764200_B74","doi-asserted-by":"crossref","first-page":"e0099621","DOI":"10.1128\/mSystems.00996-21","article-title":"Direct RNA sequencing unfolds the complex transcriptome of Vibrio parahaemolyticus","volume":"6","author":"kadi","year":"2021","journal-title":"mSystems"},{"key":"2025030817161764200_B75","doi-asserted-by":"crossref","first-page":"e00250-20","DOI":"10.1128\/mSystems.00250-20","article-title":"Genome-scale transcription-translation mapping reveals features of Zymomonas mobilis transcription units and promoters","volume":"5","author":"Vera","year":"2020","journal-title":"mSystems"},{"key":"2025030817161764200_B76","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1186\/s12864-015-1583-4","article-title":"Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae","volume":"16","author":"Rosinski-Chupin","year":"2015","journal-title":"BMC Genomics"},{"key":"2025030817161764200_B77","doi-asserted-by":"crossref","first-page":"e0094321","DOI":"10.1128\/mSystems.00943-21","article-title":"Different regulatory modes of Synechocystis sp. PCC 6803 in response to photosynthesis inhibitory conditions","volume":"6","author":"Cho","year":"2021","journal-title":"mSystems"},{"key":"2025030817161764200_B78","doi-asserted-by":"crossref","first-page":"667450","DOI":"10.3389\/fmicb.2021.667450","article-title":"Multi-omic analyses reveal habitat adaptation of marine cyanobacterium Synechocystis sp. PCC 7338","volume":"12","author":"Jeong","year":"2021","journal-title":"Front Microbiol"},{"key":"2025030817161764200_B79","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1080\/15476286.2020.1723328","article-title":"Identification of RNA 3\u2032 ends and termination sites in Haloferax volcanii","volume":"17","author":"Berkemer","year":"2020","journal-title":"RNA Biol"},{"key":"2025030817161764200_B80","doi-asserted-by":"publisher","first-page":"e70464","DOI":"10.7554\/ELIFE.70464","article-title":"aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy","volume":"10","author":"Li","year":"2021","journal-title":"eLife"},{"key":"2025030817161764200_B81","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1186\/s13059-023-02956-3","article-title":"Correcting gradient-based interpretations of deep neural networks for genomics","volume":"24","author":"Majdandzic","year":"2023","journal-title":"Genome Biol"},{"key":"2025030817161764200_B82","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat Biotechnol"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/7\/1\/lqaf016\/62341979\/lqaf016.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/7\/1\/lqaf016\/62341979\/lqaf016.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,8]],"date-time":"2025-03-08T12:16:50Z","timestamp":1741436210000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqaf016\/8063809"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,7]]},"references-count":82,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqaf016","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.07.05.602086","asserted-by":"object"}]},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2025,1,7]]},"article-number":"lqaf016"}}