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Publications

 

See here for a complete & updated PubMed bibliography.

2016

2015 UMBC Phage Hunters, Erill, I., Caruso, S.M. “The Complete Genome Sequence of Streptomyces phage Nanodon”, Genome Announcements, 4(5). pii: e01019-16. doi: 10.1128/genomeA.01019-16, (2016). [PubMed]

2015 UMBC Phage Hunters, Erill, I., Caruso, S.M. “The Sequenced Genome of Bacillus cereus group phage SalinJah”, Genome Announcements, 4(5):e00953-16. doi:10.1128/genomeA.00953-16, (2016). PMID: 26472830
O’Neill, P.K., Erill, I. “Parametric Bootstrapping for Biological Sequence Motifs”, BMC Bioinformatics, 17(1):406, (2016). [PubMed]

Erill, I., Campoy, S., Kılıç, S., Barbé, J. “The Verrucomicrobia LexA-binding Motif: Insights into the Evolutionary Dynamics of the SOS Response”, Frontiers in Molecular Biosciences, 3:33, doi: 10.3389/fmolb.2016.00033, (2016). [PubMed]

Hobbs, E. T., Pereira, T., O’Neill, P. K., Erill, I. “A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data”, Algorithms for Molecular Biology, 11:19. doi: 10.1186/s13015-016-0082-8, (2016).  [PubMed]

Kılıç, S., Erill, I. Assessment of transfer methods for comparative genomics of regulatory networks in Bacteria, BMC Bioinformatics, 17 Suppl. 8:277. doi: 10.1186/s12859-016-1113-7, (2016). [PubMed]

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. 489:243-51, (2016) [PubMed].

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, doi: 10.1093/database/baw055 (2016) [PubMed].

2015

Erill I, Caruso SM. “Genome Sequences of Two Bacillus cereus Group Bacteriophages, Eyuki and AvesoBmoreGenome announcements, 3(5), (2015) [PubMed].

Erill I, Caruso SM. “Complete Genome Sequence of Bacillus cereus Group Phage TsarBombaGenome announcements, 3(5), (2015) [PubMed].

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 genetics, 208(9):441-7, (2015) [PubMed].

Erill I. “Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal”, Journal of bacteriology, 197(15):2454-7, (2015) [PubMed].

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”, Journal of bacteriology, 197(16):2622-30, (2015) [PubMed].

Zamorano-Sánchez D, Fong JC, Kilic S, Erill I, Yildiz FH. “Identification and characterization of VpsR and VpsT binding sites in Vibrio cholerae”, Journal of bacteriology, 197(7):1221-35, (2015) [PubMed].

2014

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. 30(9):1193-7 (2014) [PubMed].

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, 196(3):660-71, (2014) [PubMed].

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, D156-60, (2014) [PubMed].

O’Neill PK, Forder R, Erill I. “Informational requirements for transcriptional regulation” Journal of computational biology, 21(5):373-84, (2014) [PubMed].

2013

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 Oct 7;8(10):e76177 [PubMed].

2012

Anzaldi LJ, Muñoz-Fernández D, Erill I. “BioWord: a sequence manipulation suite for Microsoft Word” BMC Bioinformatics, 7;13(1):124 (2012) [PubMed].

Erill, I. “Information theory and biological sequences: insights from an evolutionary perspective” in Information Theory: New Research, Deloumeaux, P. & Gorzalka, J. D. (ed), Nova Science Publishers, Hauppauge NY, (2012).

Sanchez-Alberola N, Campoy S, Barbé J, Erill I. “Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes” BMC Genomics, 13:58 (2012) [PubMed].

Cornish JP, Matthews F, Thomas JR, Erill I. “Inference of self-regulated transcriptional networks by comparative genomics” Evolutionary bioinformatics, 8:449-61 (2012) [PubMed].

2011

Cambray, G; Sanchez-Alberola, N; Campoy, S; Guerin, E; Da Re, S; Gonzalez-Zorn, B; Ploy, M. C; Barbe, J; Mazel, D; Erill, I. “Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons”, Mobile DNA. 2(1):6, (2011). [PubMed]

2010

Fox, J. M; Erill, I. “Relative Codon Adaptation: A Generic Codon Bias Index for Prediction of Gene Expression”, DNA Research, 17 (3), 185-196, (2010). [PubMed]

Bhargava, N; Erill, I. “xFITOM: a generic GUI tool to search for transcription factor binding sites”, Bioinformation, 5, 49-50, (2010). [PubMed]

2009

Hessheimer, A.J; Parramón, D; Guimerà, A; Erill, I; Rimola, A; García-Valdecasas, J.C; Villa, R; Fondevila, C. “A rapid and reliable means of assessing hepatic steatosis in vivo via electrical bioimpedance”, Transplantation, 2009, 88(5):716-722. [PubMed]

Guerin, E.; Cambray, G.; Sanchez-Alberola, N.; Campoy, S.; Erill, I.; Da Re, S.; Gonzalez-Zorn, B.; Barbe, J.; Ploy, M.-C.; Mazel, D. “The SOS Response Controls Integron Recombination” (2009) Science, 324, 1034. [PubMed]

Erill, I; O’Neill, M.C. “A reexamination of information theory-based methods for DNA-binding site identification” BMC Bioinformatics. 2009 Feb 11;10(1):57 [PubMed]

2007

Erill, I; Campoy, S; Barbé, J. “Aeons of distress: an evolutionary perspective on the bacterial SOS response”, FEMS Microbiology Reviews, 31, 637-656, (2007). [PubMed]

Abella, M; Campoy, S; Erill, I; Rojo, F; Barbé, J. “Cohabitation of two different lexA regulons in Pseudomonas putida”, Journal of Bacteriology, 189, 8855-8862, 2007, published online ahead of print on 12 October 2007 (doi:10.1128/JB.01213-07). [PubMed]

2006

Mazon, G; Campoy, S; Erill, I; Barbe, J; Identification of the Acidobacterium capsulatum LexA box reveals a lateral acquisition of the Alphaproteobacteria lexA gene. Microbiology, 152, 1109-1118, (2006). [PubMed]

Erill, I; Campoy, S; Mazon, G; Barbe, J; “Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain”, Nucleic Acids Research, 10, 66-77, (2006). [PubMed]

2004

Erill, I; Jara, M; Salvador, N; Escribano, M; Campoy, S; Barbe, J; “Differences in LexA regulon structure among Proteobacteria through in-vivo assisted comparative genomics”, Nucleic Acids Research, 32, 6617-6626, (2004). [PubMed]

Mazon, G; Erill, I; Campoy, S; Cortes, P; Forano, E; Barbe, J. “Reconstruction of the evolutionary history of the LexA-binding sequence”, Microbiology, 150, 3783-3795, (2004). [PubMed]

2003

Erill, I; Escribano, M; Campoy, S; Barbé, J; “In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon”, Bioinformatics, 19, 2225- 2236, (2003).