Current PubMed bibliography.


Cusick, K. D., Iturbide, A., Gautam, P., Price, A., Polson, S., Erill, I. “Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings”, PLoS ONE, (accepted). (2021).

Sánchez-Osuna, M., Cortés, P., Llagostera, M., Barbe, J., Erill, I. “Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes”, Nucleic Acids Research, (accepted). (2021).

Hobbs, E.T., Goralski, S.M., Mitchell, A., Simpson, A., Leka, D., Kotey, E., Sekira, M., Munro, J.B., Nadendla, S., Jackson, R., Gonzalez-Agirre, A., Krallinger, M., Giglio, M., Erill, I. “ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts”, Frontiers in Research Metrics and Analytics, 6:674205. doi:10.3389/frma.2021.674205 (2021). PMID: 34327299

Adhikari, S., Erill, I., Curtis, P.D. “Transcriptional re-wiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria”, PLOS Genetics, 17(3): e1009433, 33. doi: 10.1371/journal.pgen.1009433. (2021). PMID: 33705385


Koert, K., López, J., Mattson, C., Caruso, S.M., Erill, I. “Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages”, PCI Genomics. doi: 10.1101/842583v5. (2020).

Kılıç, S., Sánchez-Osuna, M., Collado-Padilla, M. Barbe, J., Erill, I. “Flexible comparative genomics of prokaryotic transcriptional regulatory networks”, BMC Genomics, 21:466. doi: 10.1186/s12864-020-06838-x. (2020). PMID: 33327941

Sánchez-Osuna, M., Cortés, P., Llagostera, M., Barbe, J., Erill, I. “Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim”, Microbial Genomics, 6(11). doi: 1099/mgen.0.000440. (2020). PMID: 32969787

Goulet, T.L., Erill, I., Ascunce, M.S., Finley, S.J., Javan, G. “Conceptualization of the holobiont paradigm as it pertains to corals”, Frontiers in Physiology – Aquatic Physiology, 11:566968. PMID: 33071821. doi: 10.3389/fphys.2020.566968. (2020)

Baron, S., Crossman, A., Malik, S., Sidhu, P., Nehra, K., Jamdagni, P., Erill, I. Temple, L. “Complete Genome Sequence of the Streptomyces­Specific Bacteriophage BRock”, Microbiology Resource Announcements, 9(35): e00624-20. PMID: 32855246. doi:10.1128/MRA.00624-20. (2020)

Chen, Q., Britto, R., Erill, I., Jeffery, C., Arthur Liberzon, A., Magrane, M., Onami, J., Robinson-Rechavi, M. Sponarova, J., Yamashita, R., Zobel, J., Verspoor, K. “Quality Matters: Biocuration experts on the impact of duplication and other data quality issues in biological databases”, Genomics, Proteomics & Bioinformatics, 18(2):91-103. doi:10.1016/j.gpb.2018.11.006. (2020). PMID: 32652120


Caruso, S.M., deCarvalho, T.N., Huynh, A., Morcos, G., Kuo, N., Parsa, S., Erill I. “A Novel Genus of Actinobacterial Tectiviridae”, Viruses, 11(12), E1134. doi:10.3390/v11121134. (2019). PMID: 31817897

Sánchez-Osuna, M., Cortés, P. Barbe, J., Erill, I. “Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates”, Frontiers in Microbiology, 9, 3332. doi:10.3389/fmicb.2018.03332. (2019). PMID: 30687297

Giglio, M. G., Tauber, R., Nadendla, S., Munro, J., Olley, D., Ball, S., Mitraka, E., Schriml, L., Gaudet, P., Hobbs, E., Erill, I., Siegele, D., Hu, J. C., Mungall, C., Chibucos, M. “ECO, the Evidence and Conclusion Ontology: Community Standard for Evidence Information”, Nucleic Acids Research, 47(D1), D1186–D1194. doi:10.1093/nar/gky1036. (2019). PMID: 30407590


Ammari, M., Aryamontri, A.C., Attrill, H., Bairoch, A., Berardini, T., Blake, J., Chen, Q.Y., Collado, J., Dauga, D., Dudley, J.T., Engel, S., Erill, I., Fey, P., Gibson, R., Hermjakob, H., Holliday, G., Howe, D., Hunter, C., Landsman, D., Lovering, R., Manthravadi, D., Marchler-Bauer, A., Matthews, B., McDonagh, E.M., Meldal, B., Micklem, G., Mietchen, D., Mungall, C.J., Pruitt, K., Rajamanickam, V.S., Reecy, J.M., Rey, A., Shameer, K., Shipitsyna, A., Toribio, A.L., Tuli, M.A., Uetz, P., Wittig, U., Wood, V. as International Society for Biocuration, “Biocuration: Distilling data into knowledge”, PloS Biology, 16 (4) e2002846. doi: 10.1371/journal.pbio.2002846. (2018). PMID: 29659566

Blocker, D., Koert, M., Mattson, C., Patel, H., Patel, P., Patel, R., Paudel, H., The 2017 UMBC Phage Hunters, Erill, I., Caruso, S.M. “Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages: HotFries, Moozy, Rainydai, Ravenpuff, Scap1, and SenditCS”, Microbiology Resource Announcements, 7:(12) doi:10.1128/MRA.00993-18. (2018). PMID: 30533665

Lee, M., Puglisi, K.M., UMBC STEM-BUILD Cohort 1, Erill, I., Caruso, S.M. “Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages”, Genome Announcements, 6:(25) doi:10.1128/genomeA.00493-18. (2018). PMID: 29930035

Erill, I., Caruso, S.M., 2016 UMBC Phage Hunters “The Complete Genome Sequence of Streptomyces Bacteriophage Abt2graduatex2”, Genome Announcements, 18;6(3). pii: e01480-17. doi: 10.1128/genomeA.01480-17. (2018). PMID: 29348349


Hanauer, D.I., Graham, M.J., SEA-PHAGES, Betancurc, L., Bobrownickib, A., Cresawn, S. G., Garlenae, R.A. Jacobs-Sera, D., Kaufmanne, N., Pope, W.H., Russell, D.A., Jacobs, W. R., Sivanathan, V., Asai, D.J, Hatfull, G.F. “An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning”, Proceedings of the National Academy of Sciences (USA) pii: 201718188. doi: 10.1073/pnas.1718188115. (2017). PMID: 29208718.

Erill, I., Caruso, S. M. & Hu, J. C. “Gamifying critical reading through a genome annotation intercollegiate competition”, Tested Studies for Laboratory Teaching, 39. (2017).

Erill, I., Caruso, S.M., 2016 UMBC Phage Hunters “Bacillus cereus Group Bacteriophage Flapjack Genome Sequence”, Genome Announcements. 5(31). pii: e00700-17. doi: 10.1128/genomeA.00700-17. (2017). PMID: 28774974

Erill, I., Caruso S. M., 2016 UMBC Phage Hunters “Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae”, Genome Announcements, 5(29). pii: e00701-17, doi: 10.1128/genomeA.00701-17 (2017). PMID: 28729280

Sánchez-Osuna, M., Barbé, J., Erill, I. “Comparative genomics of the DNA damage-inducible network in the Patescibacteria”, Environmental Microbiology, doi: 1111/1462-2920.13826 (2017). PMID: 28618189

Erill, I., Puigvert, M., Legrand, L., Guarischi-Sousa, R., Vandecasteele, C., Setubal, J.C., Genin, , Guidot, A., Valls, M. “Comparative analysis of Ralstonia solanacearum methylomes”, Frontiers in Plant Science, 8:504, doi: 10.3389/fpls.2017.00504, (2017). PMID: 28450872


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].


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].


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].


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].


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].


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]


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]


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]


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]


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]


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]


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).