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Hobbs ET, Goralski SM, Mitchell A, Simpson A, Leka D, Kotey E, Sekira M, Munro JB, Nadendla S, Jackson R, Gonzalez-Aguirre A, Krallinger M, Giglio M, Erill I. ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. Front Res Metr Anal. 2021;6:674205. doi: 10.3389/frma.2021.674205. eCollection 2021. PubMed PMID: 34327299; PubMed Central PMCID: PMC8313968.
Adhikari S, Erill I, Curtis PD. Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria. PLoS Genet. 2021 Mar;17(3):e1009433. doi: 10.1371/journal.pgen.1009433. eCollection 2021 Mar. PubMed PMID: 33705385; PubMed Central PMCID: PMC7987155.
Kılıç S, Sánchez-Osuna M, Collado-Padilla A, Barbé J, Erill I. Flexible comparative genomics of prokaryotic transcriptional regulatory networks. BMC Genomics. 2020 Dec 16;21(Suppl 5):466. doi: 10.1186/s12864-020-06838-x. PubMed PMID: 33327941; PubMed Central PMCID: PMC7739468.
Sánchez-Osuna M, Cortés P, Llagostera M, Barbé J, Erill I. Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim. Microb Genom. 2020 Nov;6(11). doi: 10.1099/mgen.0.000440. PubMed PMID: 32969787; PubMed Central PMCID: PMC7725336.
Goulet TL, Erill I, Ascunce MS, Finley SJ, Javan GT. Conceptualization of the Holobiont Paradigm as It Pertains to Corals. Front Physiol. 2020;11:566968. doi: 10.3389/fphys.2020.566968. eCollection 2020. Review. PubMed PMID: 33071821; PubMed Central PMCID: PMC7538806.
Baron SF, Crossman AN, Malik S, Sidhu P, Nehra K, Jamdagni P, Erill I, Temple LM. Complete Genome Sequence of the Streptomyces-Specific Bacteriophage BRock. Microbiol Resour Announc. 2020 Aug 27;9(35). doi: 10.1128/MRA.00624-20. PubMed PMID: 32855246; PubMed Central PMCID: PMC7453282.
Chen Q, Britto R, Erill I, Jeffery CJ, Liberzon A, Magrane M, Onami JI, Robinson-Rechavi M, Sponarova J, Zobel J, Verspoor K. Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genomics Proteomics Bioinformatics. 2020 Apr;18(2):91-103. doi: 10.1016/j.gpb.2018.11.006. Epub 2020 Jul 9. PubMed PMID: 32652120; PubMed Central PMCID: PMC7646089.
Caruso SM, deCarvalho TN, Huynh A, Morcos G, Kuo N, Parsa S, Erill I. A Novel Genus of Actinobacterial Tectiviridae. Viruses. 2019 Dec 7;11(12). doi: 10.3390/v11121134. PubMed PMID: 31817897; PubMed Central PMCID: PMC6950372.
Sánchez-Osuna M, Cortés P, Barbé J, Erill I. Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates. Front Microbiol. 2018;9:3332. doi: 10.3389/fmicb.2018.03332. eCollection 2018. PubMed PMID: 30687297; PubMed Central PMCID: PMC6335563.
Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194. doi: 10.1093/nar/gky1036. PubMed PMID: 30407590; PubMed Central PMCID: PMC6323956.
Blocker D, Koert M, Mattson C, Patel H, Patel P, Patel R, Paudel H, Erill I, Caruso SM. Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages, HotFries, Moozy, Rainydai, RavenPuff, Scap1, and SenditCS. Microbiol Resour Announc. 2018 Sep;7(12). doi: 10.1128/MRA.00993-18. eCollection 2018 Sep. PubMed PMID: 30533665; PubMed Central PMCID: PMC6256688.
Lee M, Puglisi KM, Erill I, Caruso SM. Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages. Genome Announc. 2018 Jun 21;6(25). doi: 10.1128/genomeA.00493-18. PubMed PMID: 29930035; PubMed Central PMCID: PMC6013610.
Erill I, Caruso SM. Complete Genome Sequence of Streptomyces Bacteriophage Abt2graduatex2. Genome Announc. 2018 Jan 18;6(3). doi: 10.1128/genomeA.01480-17. PubMed PMID: 29348349; PubMed Central PMCID: PMC5773734.
Hanauer DI, Graham MJ, Betancur L, Bobrownicki A, Cresawn SG, Garlena RA, Jacobs-Sera D, Kaufmann N, Pope WH, Russell DA, Jacobs WR Jr, Sivanathan V, Asai DJ, Hatfull GF. An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning. Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):13531-13536. doi: 10.1073/pnas.1718188115. Epub 2017 Dec 5. PubMed PMID: 29208718; PubMed Central PMCID: PMC5754813.
Sánchez-Osuna M, Barbé J, Erill I. Comparative genomics of the DNA damage-inducible network in the Patescibacteria. Environ Microbiol. 2017 Sep;19(9):3465-3474. doi: 10.1111/1462-2920.13826. Epub 2017 Jul 21. PubMed PMID: 28618189.
Erill I, Caruso SM. Bacillus cereus Group Bacteriophage Flapjack Genome Sequence. Genome Announc. 2017 Aug 3;5(31). doi: 10.1128/genomeA.00700-17. PubMed PMID: 28774974; PubMed Central PMCID: PMC5543636.
Erill I, Caruso SM. Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae. Genome Announc. 2017 Jul 20;5(29). doi: 10.1128/genomeA.00701-17. PubMed PMID: 28729280; PubMed Central PMCID: PMC5522947.
Erill I, Puigvert M, Legrand L, Guarischi-Sousa R, Vandecasteele C, Setubal JC, Genin S, Guidot A, Valls M. Comparative Analysis of Ralstonia solanacearum Methylomes. Front Plant Sci. 2017;8:504. doi: 10.3389/fpls.2017.00504. eCollection 2017. PubMed PMID: 28450872; PubMed Central PMCID: PMC5390034.
O'Neill PK, Erill I. Parametric bootstrapping for biological sequence motifs. BMC Bioinformatics. 2016 Oct 6;17(1):406. doi: 10.1186/s12859-016-1246-8. PubMed PMID: 27716039; PubMed Central PMCID: PMC5052923.
Erill I, Caruso SM. Complete Genome Sequence of the Streptomyces Phage Nanodon. Genome Announc. 2016 Oct 6;4(5). doi: 10.1128/genomeA.01019-16. PubMed PMID: 27795236; PubMed Central PMCID: PMC5054309.
Erill I, Caruso SM. Genome Sequence of Bacillus cereus Group Phage SalinJah. Genome Announc. 2016 Sep 29;4(5). doi: 10.1128/genomeA.00953-16. PubMed PMID: 27688335; PubMed Central PMCID: PMC5043553.
Kılıç S, Erill I. Assessment of transfer methods for comparative genomics of regulatory networks in bacteria. BMC Bioinformatics. 2016 Aug 31;17 Suppl 8:277. doi: 10.1186/s12859-016-1113-7. PubMed PMID: 27586594; PubMed Central PMCID: PMC5009822.
Erill I, Campoy S, Kılıç S, Barbé J. The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. Front Mol Biosci. 2016;3:33. doi: 10.3389/fmolb.2016.00033. eCollection 2016. PubMed PMID: 27489856; PubMed Central PMCID: PMC4951493.
Hobbs ET, Pereira T, O'Neill PK, Erill I. A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. Algorithms Mol Biol. 2016;11:19. doi: 10.1186/s13015-016-0082-8. eCollection 2016. PubMed PMID: 27398089; PubMed Central PMCID: PMC4938975.
Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I. From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. Database (Oxford). 2016;2016. doi: 10.1093/database/baw055. Print 2016. PubMed PMID: 27114493; PubMed Central PMCID: PMC4843526.
Sauder AB, Quinn MR, Brouillette A, Caruso S, Cresawn S, Erill I, Lewis L, Loesser-Casey K, Pate M, Scott C, Stockwell S, Temple L. Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis. Virology. 2016 Feb;489:243-51. doi: 10.1016/j.virol.2015.12.012. Epub 2016 Jan 14. PubMed PMID: 26773385.
Erill I, Caruso SM. Erratum for Erill and Caruso, Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba. Genome Announc. 2015 Nov 19;3(6). doi: 10.1128/genomeA.01458-15. PubMed PMID: 26586903; PubMed Central PMCID: PMC4653805.
Erill I, Caruso SM. Genome Sequences of Two Bacillus cereus Group Bacteriophages, Eyuki and AvesoBmore. Genome Announc. 2015 Oct 15;3(5). doi: 10.1128/genomeA.01199-15. PubMed PMID: 26472840; PubMed Central PMCID: PMC4611692.
Erill I, Caruso SM. Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba. Genome Announc. 2015 Oct 15;3(5). doi: 10.1128/genomeA.01178-15. PubMed PMID: 26472830; PubMed Central PMCID: PMC4611682.
Hagemann IS, O'Neill PK, Erill I, Pfeifer JD. Diagnostic yield of targeted next generation sequencing in various cancer types: an information-theoretic approach. Cancer Genet. 2015 Sep;208(9):441-7. doi: 10.1016/j.cancergen.2015.05.030. Epub 2015 May 29. PubMed PMID: 26227479.
Sanchez-Alberola N, Campoy S, Emerson D, Barbé J, Erill I. An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria. J Bacteriol. 2015 Aug;197(16):2622-30. doi: 10.1128/JB.00035-15. Epub 2015 May 18. PubMed PMID: 25986903; PubMed Central PMCID: PMC4507345.
Erill I. Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. J Bacteriol. 2015 Aug 1;197(15):2454-7. doi: 10.1128/JB.00031-15. Epub 2015 May 26. PubMed PMID: 26013488; PubMed Central PMCID: PMC4518829.
Zamorano-Sánchez D, Fong JC, Kilic S, Erill I, Yildiz FH. Identification and characterization of VpsR and VpsT binding sites in Vibrio cholerae. J Bacteriol. 2015 Apr;197(7):1221-35. doi: 10.1128/JB.02439-14. Epub 2015 Jan 26. PubMed PMID: 25622616; PubMed Central PMCID: PMC4352665.
O'Neill PK, Forder R, Erill I. Informational requirements for transcriptional regulation. J Comput Biol. 2014 May;21(5):373-84. doi: 10.1089/cmb.2014.0032. Epub 2014 Apr 1. PubMed PMID: 24689750; PubMed Central PMCID: PMC4010175.
Cornish JP, Sanchez-Alberola N, O'Neill PK, O'Keefe R, Gheba J, Erill I. Characterization of the SOS meta-regulon in the human gut microbiome. Bioinformatics. 2014 May 1;30(9):1193-7. doi: 10.1093/bioinformatics/btt753. Epub 2014 Jan 8. PubMed PMID: 24407225; PubMed Central PMCID: PMC3998124.
Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT. Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon. J Bacteriol. 2014 Feb;196(3):660-71. doi: 10.1128/JB.01007-13. Epub 2013 Nov 22. PubMed PMID: 24272778; PubMed Central PMCID: PMC3911152.
Kiliç S, White ER, Sagitova DM, Cornish JP, Erill I. CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. Nucleic Acids Res. 2014 Jan;42(Database issue):D156-60. doi: 10.1093/nar/gkt1123. Epub 2013 Nov 14. PubMed PMID: 24234444; PubMed Central PMCID: PMC3965012.
O'Neill PK, Or M, Erill I. scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes. PLoS One. 2013;8(10):e76177. doi: 10.1371/journal.pone.0076177. eCollection 2013. PubMed PMID: 24116094; PubMed Central PMCID: PMC3792112.
Cornish JP, Matthews F, Thomas JR, Erill I. Inference of self-regulated transcriptional networks by comparative genomics. Evol Bioinform Online. 2012;8:449-61. doi: 10.4137/EBO.S9205. Epub 2012 Aug 6. PubMed PMID: 23032607; PubMed Central PMCID: PMC3422134.
Anzaldi LJ, Muñoz-Fernández D, Erill I. BioWord: a sequence manipulation suite for Microsoft Word. BMC Bioinformatics. 2012 Jun 7;13:124. doi: 10.1186/1471-2105-13-124. PubMed PMID: 22676326; PubMed Central PMCID: PMC3546851.
Sanchez-Alberola N, Campoy S, Barbé J, Erill I. Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes. BMC Genomics. 2012 Feb 3;13:58. doi: 10.1186/1471-2164-13-58. PubMed PMID: 22305460; PubMed Central PMCID: PMC3323433.
Cambray G, Sanchez-Alberola N, Campoy S, Guerin É, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I. Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons. Mob DNA. 2011 Apr 30;2(1):6. doi: 10.1186/1759-8753-2-6. PubMed PMID: 21529368; PubMed Central PMCID: PMC3108266.
Bhargava N, Erill I. xFITOM: a generic GUI tool to search for transcription factor binding sites. Bioinformation. 2010 Jul 6;5(2):49-51. doi: 10.6026/97320630005049. PubMed PMID: 21346861; PubMed Central PMCID: PMC3039987.
Fox JM, Erill I. Relative codon adaptation: a generic codon bias index for prediction of gene expression. DNA Res. 2010 Jun;17(3):185-96. doi: 10.1093/dnares/dsq012. Epub 2010 May 7. PubMed PMID: 20453079; PubMed Central PMCID: PMC2885275.
Hessheimer AJ, Parramón D, Guimerà A, Erill I, Rimola A, García-Valdecasas JC, Villa R, Fondevila C. A rapid and reliable means of assessing hepatic steatosis in vivo via electrical bioimpedance. Transplantation. 2009 Sep 15;88(5):716-22. doi: 10.1097/TP.0b013e3181b391c0. PubMed PMID: 19741471.
Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re S, Gonzalez-Zorn B, Barbé J, Ploy MC, Mazel D. The SOS response controls integron recombination. Science. 2009 May 22;324(5930):1034. doi: 10.1126/science.1172914. PubMed PMID: 19460999.
Erill I, O'Neill MC. A reexamination of information theory-based methods for DNA-binding site identification. BMC Bioinformatics. 2009 Feb 11;10:57. doi: 10.1186/1471-2105-10-57. PubMed PMID: 19210776; PubMed Central PMCID: PMC2680408.
Abella M, Campoy S, Erill I, Rojo F, Barbé J. Cohabitation of two different lexA regulons in Pseudomonas putida. J Bacteriol. 2007 Dec;189(24):8855-62. doi: 10.1128/JB.01213-07. Epub 2007 Oct 12. PubMed PMID: 17933893; PubMed Central PMCID: PMC2168638.
Erill I, Campoy S, Barbé J. Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS Microbiol Rev. 2007 Nov;31(6):637-56. doi: 10.1111/j.1574-6976.2007.00082.x. Epub 2007 Sep 18. Review. PubMed PMID: 17883408.
Parramon D, Erill I, Guimerà A, Ivorra A, Muñoz A, Sola A, Fondevila C, García-Valdecasas JC, Villa R. In vivo detection of liver steatosis in rats based on impedance spectroscopy. Physiol Meas. 2007 Aug;28(8):813-28. doi: 10.1088/0967-3334/28/8/005. Epub 2007 Jul 6. PubMed PMID: 17664674.
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