{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,9]],"date-time":"2026-08-09T23:40:40Z","timestamp":1786318840241,"version":"build-2736575974"},"reference-count":96,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2020,8,1]],"date-time":"2020-08-01T00:00:00Z","timestamp":1596240000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,8,1]],"date-time":"2020-08-01T00:00:00Z","timestamp":1596240000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,8,1]],"date-time":"2021-08-01T00:00:00Z","timestamp":1627776000000},"content-version":"vor","delay-in-days":365,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/501100001230","name":"Macquarie University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001230","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Virology"],"published-print":{"date-parts":[[2020,8]]},"DOI":"10.1016\/j.virol.2020.05.008","type":"journal-article","created":{"date-parts":[[2020,5,24]],"date-time":"2020-05-24T07:59:37Z","timestamp":1590307177000},"page":"47-56","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":26,"special_numbering":"C","title":["A high-resolution map of bacteriophage \u03d5X174 transcription"],"prefix":"10.1016","volume":"547","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7721-8321","authenticated-orcid":false,"given":"Dominic Y.","family":"Logel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2359-1301","authenticated-orcid":false,"given":"Paul R.","family":"Jaschke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.virol.2020.05.008_bib1","doi-asserted-by":"crossref","first-page":"W690","DOI":"10.1093\/nar\/gki445","article-title":"RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements","volume":"33","author":"Abreu-Goodger","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.virol.2020.05.008_bib2","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/0092-8674(86)90370-3","article-title":"Synthesis of bacteriophage phi X174 in vitro: mechanism of switch from DNA replication to DNA packaging","volume":"47","author":"Aoyama","year":"1986","journal-title":"Cell"},{"key":"10.1016\/j.virol.2020.05.008_bib3","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/S0022-2836(76)80115-5","article-title":"Transcription of bacteriophage phi-X174 in vitro: selective initiation with oligonucleotides","volume":"108","author":"Axelrod","year":"1976","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib4","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/S0022-2836(76)80116-7","article-title":"Transcription of bacteriophage phiX174 in vitro: analysis with restriction enzymes","volume":"108","author":"Axelrod","year":"1976","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib5","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1101\/gad.1.1.57","article-title":"Induction of the heat shock response of E. coli through stabilization of sigma 32 by the phage lambda cIII protein","volume":"1","author":"Bahl","year":"1987","journal-title":"Genes Dev."},{"key":"10.1016\/j.virol.2020.05.008_bib6","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/264034a0","article-title":"Overlapping genes in bacteriophage phiX174","volume":"264","author":"Barrell","year":"1976","journal-title":"Nature"},{"key":"10.1016\/j.virol.2020.05.008_bib7","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/0022-2836(87)90371-8","article-title":"Sense and antisense transcription of bacteriophage T4 gene 32: processing and stability of the mRNAs","volume":"194","author":"Belin","year":"1987","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib8","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1128\/jvi.7.5.549-558.1971","article-title":"Genetic map of bacteriophage phiX174","volume":"7","author":"Benbow","year":"1971","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib9","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1128\/jvi.10.1.99-114.1972","article-title":"Direction of translation and size of bacteriophage phiX174 cistrons","volume":"10","author":"Benbow","year":"1972","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib10","doi-asserted-by":"crossref","first-page":"5617","DOI":"10.1128\/jb.172.10.5617-5623.1990","article-title":"Translational efficiency of phi X174 lysis gene E is unaffected by upstream translation of the overlapping gene D reading frame","volume":"172","author":"Bl\u00e4si","year":"1990","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.virol.2020.05.008_bib11","doi-asserted-by":"crossref","first-page":"4362","DOI":"10.1128\/jvi.62.11.4362-4364.1988","article-title":"Evaluation of the interaction of phi X174 gene products E and K in E-mediated lysis of Escherichia coli","volume":"62","author":"Bl\u00e4si","year":"1988","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib12","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1126\/science.1232758","article-title":"Amplifying genetic logic gates","volume":"340","author":"Bonnet","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.virol.2020.05.008_bib13","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1128\/jvi.53.1.340-342.1985","article-title":"Mapping of transcription terminators of bacteriophages phi X174 and G4 by sequence analysis","volume":"53","author":"Brendel","year":"1985","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib14","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1006\/viro.1996.0264","article-title":"Analysis of the nucleotide sequence of the treehopper-transmitted geminivirus, tomato pseudo-curly top virus, suggests a recombinant origin","volume":"219","author":"Briddon","year":"1996","journal-title":"Virology"},{"key":"10.1016\/j.virol.2020.05.008_bib15","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1186\/1471-2148-10-378","article-title":"Positive selection at high temperature reduces gene transcription in the bacteriophage \u03c6X174","volume":"10","author":"Brown","year":"2010","journal-title":"BMC Evol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib16","series-title":"BBMap","author":"Bushnell","year":"2019"},{"key":"10.1016\/j.virol.2020.05.008_bib17","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1016\/j.molcel.2004.05.010","article-title":"Transcriptional interference between convergent promoters caused by elongation over the promoter","volume":"14","author":"Callen","year":"2004","journal-title":"Mol. Cell"},{"key":"10.1016\/j.virol.2020.05.008_bib18","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nature11184","article-title":"Proto-genes and de novo gene birth","volume":"487","author":"Carvunis","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.virol.2020.05.008_bib19","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/j.virol.2016.05.022","article-title":"Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages","volume":"496","author":"Casjens","year":"2016","journal-title":"Virology"},{"key":"10.1016\/j.virol.2020.05.008_bib20","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/newbio243233a0","article-title":"Isolation and genetic localization of three \u03c6X174 promoter regions","volume":"243","author":"Chen","year":"1973","journal-title":"Nat. New Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib21","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1038\/nmeth.2515","article-title":"Characterization of 582 natural and synthetic terminators and quantification of their design constraints","volume":"10","author":"Chen","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.virol.2020.05.008_bib22","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1128\/jvi.53.3.807-813.1985","article-title":"Expression of the cloned bacteriophage phi X174 A* gene in Escherichia coli inhibits DNA replication and cell division","volume":"53","author":"Colasanti","year":"1985","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib23","doi-asserted-by":"crossref","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 Salvo","year":"2019","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.virol.2020.05.008_bib24","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1046\/j.1365-2958.2002.03038.x","article-title":"Action at a distance in CI repressor regulation of the bacteriophage 186 genetic switch","volume":"45","author":"Dodd","year":"2002","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.virol.2020.05.008_bib25","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1093\/molbev\/msu089","article-title":"The evolution of genes within genes and the control of DNA replication in microviruses","volume":"31","author":"Doore","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.virol.2020.05.008_bib26","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.virol.2016.01.020","article-title":"The microviridae: diversity, assembly, and experimental evolution","volume":"491","author":"Doore","year":"2016","journal-title":"Virology"},{"key":"10.1016\/j.virol.2020.05.008_bib27","series-title":"The Bacteriophages","first-page":"129","article-title":"PhiX174 et al., the Microviridae","author":"Fane","year":"2006"},{"key":"10.1016\/j.virol.2020.05.008_bib28","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1093\/genetics\/128.4.663","article-title":"Second-site suppressors of a cold-sensitive prohead accessory protein of bacteriophage phi X174","volume":"128","author":"Fane","year":"1991","journal-title":"Genetics"},{"key":"10.1016\/j.virol.2020.05.008_bib29","doi-asserted-by":"crossref","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":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.virol.2020.05.008_bib30","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1094\/Phyto-81-980","article-title":"Cloning of the complete DNA genomes of four bean-infecting geminiviruses and determining their infectivity by electric discharge particle acceleration","volume":"81","author":"Gilbertson","year":"1991","journal-title":"Phytopathology"},{"key":"10.1016\/j.virol.2020.05.008_bib31","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/276236a0","article-title":"Nucleotide sequence of bacteriophage G4 DNA","volume":"276","author":"Godson","year":"1978","journal-title":"Nature"},{"key":"10.1016\/j.virol.2020.05.008_bib32","doi-asserted-by":"crossref","first-page":"952","DOI":"10.15252\/msb.20167461","article-title":"Genetic circuit characterization and debugging using RNA-seq","volume":"13","author":"Gorochowski","year":"2017","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib33","doi-asserted-by":"crossref","first-page":"10263","DOI":"10.1093\/nar\/gks824","article-title":"UVA-induced DNA double-strand breaks result from the repair of clustered oxidative DNA damages","volume":"40","author":"Greinert","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.virol.2020.05.008_bib34","series-title":"The Bacteriophages","first-page":"1","article-title":"Biology of the bacteriophage \u03d5X174","author":"Hayashi","year":"1988"},{"key":"10.1016\/j.virol.2020.05.008_bib35","doi-asserted-by":"crossref","first-page":"3519","DOI":"10.1073\/pnas.73.10.3519","article-title":"Mapping of in vivo messenger RNAs for bacteriophage phiX-174","volume":"73","author":"Hayashi","year":"1976","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.virol.2020.05.008_bib36","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1073\/pnas.50.4.664","article-title":"Restriction of in vivo genetic transcription to one of the complementary strands of DNA","volume":"50","author":"Hayashi","year":"1963","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.virol.2020.05.008_bib37","doi-asserted-by":"crossref","first-page":"5937","DOI":"10.1093\/nar\/13.16.5937","article-title":"Cloned DNA sequences that determine mRNA stability of bacteriophage phi X174 in vivo are functional","volume":"13","author":"Hayashi","year":"1985","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.virol.2020.05.008_bib38","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1128\/jvi.38.1.198-207.1981","article-title":"Bacteriophage phi X174-specific mRNA synthesis in cells deficient in termination factor rho activity","volume":"38","author":"Hayashi","year":"1981","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib39","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1007\/BF00334377","article-title":"mRNA stabilizing signals encoded in the genome of the bacteriophage phi x174","volume":"216","author":"Hayashi","year":"1989","journal-title":"Mol. Gen. Genet."},{"key":"10.1016\/j.virol.2020.05.008_bib40","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1038\/s42003-018-0220-6","article-title":"A minimum information standard for reproducing bench-scale bacterial cell growth and productivity","volume":"1","author":"Hecht","year":"2018","journal-title":"Commun. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib41","doi-asserted-by":"crossref","first-page":"3615","DOI":"10.1093\/nar\/gkx070","article-title":"Measurements of translation initiation from all 64 codons in E. coli","volume":"45","author":"Hecht","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.virol.2020.05.008_bib42","series-title":"Bacteriophage PhiX174: Viral Genes and Functions","author":"Hutchison","year":"1969"},{"key":"10.1016\/j.virol.2020.05.008_bib43","doi-asserted-by":"crossref","first-page":"24206","DOI":"10.1073\/pnas.1905990116","article-title":"Definitive demonstration by synthesis of genome annotation completeness","volume":"116","author":"Jaschke","year":"2019","journal-title":"Proc. Natl. Acad. Sci. Unit. States Am."},{"key":"10.1016\/j.virol.2020.05.008_bib44","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.virol.2012.09.020","article-title":"A fully decompressed synthetic bacteriophage PhiX174 genome assembled and archived in yeast","volume":"434","author":"Jaschke","year":"2012","journal-title":"Virology"},{"key":"10.1016\/j.virol.2020.05.008_bib45","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/0378-1119(94)00835-G","article-title":"The periplasmic endonuclease I of escherichia coli has amino-acid sequence homology to the extracellular DNases of Vibrio cholerae and Aeromonas hydrophila","volume":"154","author":"Jekel","year":"1995","journal-title":"Gene"},{"key":"10.1016\/j.virol.2020.05.008_bib46","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/0022-2836(70)90262-7","article-title":"The eight genes of bacteriophages phi X174 and S13 and comparison of the phage-specified proteins","volume":"49","author":"Jeng","year":"1970","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib47","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/0014-5793(79)80167-2","article-title":"Effect of Escherichia coli rho factor and RNase III on the formation of phi X174 RNA in vitro","volume":"98","author":"Kapitza","year":"1979","journal-title":"FEBS Lett."},{"key":"10.1016\/j.virol.2020.05.008_bib48","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/0167-4781(92)90440-B","article-title":"Nucleotide sequence of the genome of the bacteriophage alpha 3: interrelationship of the genome structure and the gene products with those of the phages, phi X174, G4 and phi K","volume":"1130","author":"Kodaira","year":"1992","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.virol.2020.05.008_bib49","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0196905","article-title":"High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding","volume":"13","author":"Komura","year":"2018","journal-title":"PloS One"},{"key":"10.1016\/j.virol.2020.05.008_bib50","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1016\/j.jmb.2012.07.027","article-title":"Binding and translocation of termination factor rho studied at the single-molecule level","volume":"423","author":"Koslover","year":"2012","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib51","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1111\/j.1365-2958.1991.tb01900.x","article-title":"The role of the OOP antisense RNA in coliphage lambda development","volume":"5","author":"Krinke","year":"1991","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.virol.2020.05.008_bib52","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/0378-1119(85)90050-2","article-title":"Nucleotide sequence and genome organization of bacteriophage S13 DNA","volume":"40","author":"Lau","year":"1985","journal-title":"Gene"},{"key":"10.1016\/j.virol.2020.05.008_bib53","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02041-16","article-title":"Transcription profiling of Bacillus subtilis cells infected with AR9, a giant phage encoding two multisubunit RNA polymerases","volume":"8","author":"Lavysh","year":"2017","journal-title":"mBio"},{"key":"10.1016\/j.virol.2020.05.008_bib54","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1093\/nar\/16.1.229","article-title":"Infectivity and complete nucleotide-sequence of the genome of a south-african isolate of maize streak virus","volume":"16","author":"Lazarowitz","year":"1988","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.virol.2020.05.008_bib55","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1016\/0378-1119(86)90067-3","article-title":"The organization of the araBAD operon of Escherichia coli","volume":"47","author":"Lee","year":"1986","journal-title":"Gene"},{"key":"10.1016\/j.virol.2020.05.008_bib56","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1101\/gad.1.2.197","article-title":"Control of gene expression in bacteriophage P22 by a small antisense RNA. I. Characterization in vitro of the Psar promoter and the sar RNA transcript","volume":"1","author":"Liao","year":"1987","journal-title":"Genes Dev."},{"key":"10.1016\/j.virol.2020.05.008_bib57","first-page":"39","article-title":"Deletion and fusion analysis of the phage phi X174 lysis gene","volume":"40","author":"Maratea","year":"1985","journal-title":"E. Gene"},{"key":"10.1016\/j.virol.2020.05.008_bib58","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1128\/jvi.6.3.310-319.1970","article-title":"Process of infection with bacteriophage phiX174. XXXVI. Measurement of virus-specific proteins during a normal cycle of infection","volume":"6","author":"Mayol","year":"1970","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib59","doi-asserted-by":"crossref","first-page":"7310","DOI":"10.1128\/AEM.02721-09","article-title":"Bacteriophage PhiX174's ecological niche and the flexibility of its Escherichia coli lipopolysaccharide receptor","volume":"76","author":"Michel","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.virol.2020.05.008_bib60","doi-asserted-by":"crossref","first-page":"9293","DOI":"10.1128\/JVI.01245-16","article-title":"Global transcriptional analysis of virus-host interactions between phage \u03c629 and Bacillus subtilis","volume":"90","author":"Mojard\u00edn","year":"2016","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib61","doi-asserted-by":"crossref","first-page":"4877","DOI":"10.1073\/pnas.76.10.4877","article-title":"Isolation and identification of bacteriophage phi X174 prohead","volume":"76","author":"Mukai","year":"1979","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.virol.2020.05.008_bib62","doi-asserted-by":"crossref","first-page":"1723","DOI":"10.1007\/s007050050412","article-title":"Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses","volume":"143","author":"Niagro","year":"1998","journal-title":"Arch. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib63","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1471-2180-7-82","article-title":"Global analysis of host response to induction of a latent bacteriophage","volume":"7","author":"Osterhout","year":"2007","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.virol.2020.05.008_bib64","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/0022-5193(82)90374-5","article-title":"Characteristic base sequence patterns of promoter and terminator sites in \u03d5X174 and fd phage DNAs","volume":"97","author":"Otsuka","year":"1982","journal-title":"J. Theor. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib65","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1074\/mcp.O112.020131","article-title":"Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics","volume":"11","author":"Peterson","year":"2012","journal-title":"Mol. Cell. Proteomics : MCP"},{"key":"10.1016\/j.virol.2020.05.008_bib66","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/274034a0","article-title":"Potential for variability through multiple gene products of bacteriophage \u03a6X174","volume":"274","author":"Pollock","year":"1978","journal-title":"Nature"},{"key":"10.1016\/j.virol.2020.05.008_bib67","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1002\/j.1460-2075.1995.tb07085.x","article-title":"The rpoE gene encoding the sigma E (sigma 24) heat shock sigma factor of Escherichia coli","volume":"14","author":"Raina","year":"1995","journal-title":"EMBO J."},{"key":"10.1016\/j.virol.2020.05.008_bib68","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1128\/jvi.27.3.677-687.1978","article-title":"Localization of Escherichia coli RNA polymerase binding sites on bacteriophage S13 and \u00f8X174 DNA: alignment with restriction enzyme maps","volume":"27","author":"Rassart","year":"1978","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib69","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1128\/jvi.29.1.179-184.1979","article-title":"Localization of Escherichia coli RNA polymerase binding sites on bacteriophage S13 and \u00f8X174 DNAs by electron microscopy","volume":"29","author":"Rassart","year":"1979","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib70","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":"10.1016\/j.virol.2020.05.008_bib71","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/nrmicro2853","article-title":"Going viral: next-generation sequencing applied to phage populations in the human gut","volume":"10","author":"Reyes","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.virol.2020.05.008_bib72","article-title":"Conserved and variable functions of the sigmaE stress response in related genomes","volume":"4","author":"Rhodius","year":"2006","journal-title":"PLoS Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib73","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/0167-4781(94)90185-6","article-title":"Mapping the initiation sites of in vitro transcripts of bacteriophage S13","volume":"1218","author":"Ringuette","year":"1994","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.virol.2020.05.008_bib74","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1007\/s00239-009-9267-9","article-title":"The genetics of adaptation for eight microvirid bacteriophages","volume":"69","author":"Rokyta","year":"2009","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.virol.2020.05.008_bib75","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01593-19","article-title":"Finally, a role befitting astar: strongly conserved, unessential microvirus A* proteins ensure the product fidelity of packaging reactions","volume":"94","author":"Roznowski","year":"2020","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib76","series-title":"Automatic Annotation of Microbial Genomes and Metagenomic Sequences. Metagenomics and its Applications in Agriculture","first-page":"61","author":"Salamov","year":"2011"},{"key":"10.1016\/j.virol.2020.05.008_bib77","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1038\/265687a0","article-title":"Nucleotide sequence of bacteriophage phi X174 DNA","volume":"265","author":"Sanger","year":"1977","journal-title":"Nature"},{"key":"10.1016\/j.virol.2020.05.008_bib78","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1186\/s12864-017-3827-y","article-title":"A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples","volume":"18","author":"Schuierer","year":"2017","journal-title":"BMC Genom."},{"key":"10.1016\/j.virol.2020.05.008_bib79","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/bioinformatics\/btw629","article-title":"bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli","volume":"33","author":"Shahmuradov","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.virol.2020.05.008_bib80","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.tig.2005.04.009","article-title":"Transcriptional interference--a crash course","volume":"21","author":"Shearwin","year":"2005","journal-title":"Trends Genet."},{"key":"10.1016\/j.virol.2020.05.008_bib81","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1101\/SQB.1968.033.01.051","article-title":"Stages in the replication of bacteriophage phi X174 DNA in vivo","volume":"33","author":"Sinsheimer","year":"1968","journal-title":"Cold Spring Harbor Symp. Quant. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib82","doi-asserted-by":"crossref","first-page":"15440","DOI":"10.1073\/pnas.2237126100","article-title":"Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides","volume":"100","author":"Smith","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.virol.2020.05.008_bib83","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1016\/0022-2836(76)90203-5","article-title":"The in vitro transcription units of bacteriophage phiX174. I. Characterization of synthetic parameters and measurement of transcript molecular weights","volume":"103","author":"Smith","year":"1976","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib84","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1016\/0022-2836(76)90204-7","article-title":"The in vitro transcription units of bacteriophage phiX174. II. In vitro initiation sites of phiX174 transcription","volume":"103","author":"Smith","year":"1976","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib85","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/0022-2836(76)90205-9","article-title":"The in vitro transcription units of bacteriophage phiX174. III. Initiation with specific 5' end oligonucleotides of in vitro phiX174 RNA","volume":"103","author":"Smith","year":"1976","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib86","first-page":"625","article-title":"Identification of the in vivo promoters of bacteriophages S13 and phi X174 and measurement of their relative activities","volume":"76","author":"Sorensen","year":"1998","journal-title":"Biochem. Cell. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib87","doi-asserted-by":"crossref","first-page":"1761","DOI":"10.1002\/j.1460-2075.1986.tb04424.x","article-title":"The nucleotide sequence of an infectious clone of the geminivirus beet curly top virus","volume":"5","author":"Stanley","year":"1986","journal-title":"EMBO J."},{"key":"10.1016\/j.virol.2020.05.008_bib88","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/nature12816","article-title":"Icosahedral bacteriophage PhiX174 forms a tail for DNA transport during infection","volume":"505","author":"Sun","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.virol.2020.05.008_bib89","doi-asserted-by":"crossref","first-page":"13708","DOI":"10.1073\/pnas.1716614114","article-title":"Structural changes of tailless bacteriophage PhiX174 during penetration of bacterial cell walls","volume":"114","author":"Sun","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.virol.2020.05.008_bib90","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1128\/jvi.33.1.557-560.1980","article-title":"Gene K of bacteriophage phi X 174 codes for a nonessential protein","volume":"33","author":"Tessman","year":"1980","journal-title":"J. Virol."},{"key":"10.1016\/j.virol.2020.05.008_bib91","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.51971","article-title":"Discovery of several thousand highly diverse circular DNA viruses","volume":"9","author":"Tisza","year":"2020","journal-title":"Elife"},{"key":"10.1016\/j.virol.2020.05.008_bib92","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1021\/acssynbio.9b00021","article-title":"Measuring amber initiator tRNA orthogonality in a genomically recoded organism","volume":"8","author":"Vincent","year":"2019","journal-title":"ACS Synth. Biol."},{"key":"10.1016\/j.virol.2020.05.008_bib93","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s12064-012-0162-3","article-title":"Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples","volume":"131","author":"Wagner","year":"2012","journal-title":"Theor. Biosci."},{"key":"10.1016\/j.virol.2020.05.008_bib94","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1038\/s41467-018-04026-w","article-title":"Random sequences rapidly evolve into de novo promoters","volume":"9","author":"Yona","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.virol.2020.05.008_bib95","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1002\/jcc.21596","article-title":"NUPACK: analysis and design of nucleic acid systems","volume":"32","author":"Zadeh","year":"2011","journal-title":"J. Comput. Chem."},{"key":"10.1016\/j.virol.2020.05.008_bib96","article-title":"Differential transcription of bacteriophage phiX174 genes at 37 degrees C and 42 degrees C","volume":"7","author":"Zhao","year":"2012","journal-title":"PloS One"}],"container-title":["Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0042682220300957?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0042682220300957?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,23]],"date-time":"2025-09-23T00:52:41Z","timestamp":1758588761000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0042682220300957"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8]]},"references-count":96,"alternative-id":["S0042682220300957"],"URL":"https:\/\/doi.org\/10.1016\/j.virol.2020.05.008","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.03.05.979765","asserted-by":"object"}]},"ISSN":["0042-6822"],"issn-type":[{"value":"0042-6822","type":"print"}],"subject":[],"published":{"date-parts":[[2020,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A high-resolution map of bacteriophage \u03d5X174 transcription","name":"articletitle","label":"Article Title"},{"value":"Virology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.virol.2020.05.008","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}