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Kitts G, Rogers A, Teschler JK, Park JH, Trebino MA, Chaudry I, Erill I, Yildiz FH. The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae. PLoS Pathog. 2023 May;19(5):e1011415. doi: 10.1371/journal.ppat.1011415. eCollection 2023 May. PubMed PMID: 37216386; PubMed Central PMCID: PMC10237652.
Gautam P, Erill I, Cusick K. Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria. Microorganisms. 2023 April; 11(4):1012-. doi: 10.3390/microorganisms11041012.
Sánchez-Osuna M, Barbé J, Erill I. Systematic In Silico Assessment of Antimicrobial Resistance Dissemination across the Global Plasmidome. Antibiotics. 2023 February; 12(2):281-. doi: 10.3390/antibiotics12020281.
Ismail A, Saini T, Al Qaffas A, Erill I, Caruso SM, Temple L, Johnson AA. Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity. Viruses. 2023 Jan 18;15(2). doi: 10.3390/v15020276. PubMed PMID: 36851489; PubMed Central PMCID: PMC9965433.
Ismail A, Saini T, Al Qaffas A, Erill I, Caruso S, Temple L, Johnson A. Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity. Viruses. 2023 January; 15(2):276-. doi: 10.3390/v15020276.
Davis F, Kakacek B, Doorandish D, Goldwasser T, Agboha N, Caruso SM, Erill I. Genome Sequences of Streptomyces Bacteriophages Fabian, FlowerPower, Geostin, RetrieverFever, and Vorvolakos. Microbiol Resour Announc. 2022 Dec 15;11(12):e0099822. doi: 10.1128/mra.00998-22. Epub 2022 Nov 3. PubMed PMID: 36326493; PubMed Central PMCID: PMC9753666.
Park YG, McCarthy GF, Mustafa H, Feild GM, Puram S, Younes HA, Imam D, Erill I, Caruso SM. Complete Genome Sequences of Streptomyces Bacteriophages Annihilus, TonyStarch, Thiqqums, CricKo, ClubPenguin, RosaAsantewaa, and PherryCruz. Microbiol Resour Announc. 2022 Nov 17;11(11):e0092222. doi: 10.1128/mra.00922-22. Epub 2022 Oct 26. PubMed PMID: 36286992; PubMed Central PMCID: PMC9671017.
Park Y, McCarthy G, Mustafa H, Feild G, Puram S, Younes H, Imam D, Erill I, Caruso S. Complete Genome Sequences of <i>Streptomyces</i> Bacteriophages Annihilus, TonyStarch, Thiqqums, CricKo, ClubPenguin, RosaAsantewaa, and PherryCruz. Microbiology Resource Announcements. 2022 November; 11(11):-. doi: 10.1128/mra.00922-22.
Ding P, Ming Z, Liu J, Erill I, Zhang Z. Editorial: Microbiome and microbial informatics. Front Microbiol. 2022;13:1054811. doi: 10.3389/fmicb.2022.1054811. eCollection 2022. PubMed PMID: 36338085; PubMed Central PMCID: PMC9627745.
Mascolo E, Adhikari S, Caruso SM, deCarvalho T, Folch Salvador A, Serra-Sagristà J, Young R, Erill I, Curtis PD. The transcriptional regulator CtrA controls gene expression in Alphaproteobacteria phages: Evidence for a lytic deferment pathway. Front Microbiol. 2022;13:918015. doi: 10.3389/fmicb.2022.918015. eCollection 2022. PubMed PMID: 36060776; PubMed Central PMCID: PMC9437464.
Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs ET, Goralski SM, Chibucos M, Mungall CJ, Tosatto SCE, Erill I, Giglio MG. ECO: the Evidence and Conclusion Ontology, an update for 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D1515-D1521. doi: 10.1093/nar/gkab1025. PubMed PMID: 34986598; PubMed Central PMCID: PMC8728134.
Nadendla S, Jackson R, Munro J, Quaglia F, Mészáros B, Olley D, Hobbs E, Goralski S, Chibucos M, Mungall C, Tosatto S, Erill I, Giglio M. ECO: the Evidence and Conclusion Ontology, an update for 2022. Nucleic Acids Research. 2022 January; 50(D1):D1515-D1521. doi: 10.1093/nar/gkab1025.
Koert M, López-Pérez J, Mattson C, Caruso S, Erill I. Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages. Peer Community Journal. 2021 November; 1:-. doi: 10.24072/pcjournal.25.
Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res. 2021 Nov 8;49(19):11050-11066. doi: 10.1093/nar/gkab773. PubMed PMID: 34614190; PubMed Central PMCID: PMC8565304.
Sánchez-Osuna M, Cortés P, Lee M, Smith A, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Research. 2021 November; 49(19):11050-11066. doi: 10.1093/nar/gkab773.
Ramsey J, McIntosh B, Renfro D, Aleksander SA, LaBonte S, Ross C, Zweifel AE, Liles N, Farrar S, Gill JJ, Erill I, Ades S, Berardini TZ, Bennett JA, Brady S, Britton R, Carbon S, Caruso SM, Clements D, Dalia R, Defelice M, Doyle EL, Friedberg I, Gurney SMR, Hughes L, Johnson A, Kowalski JM, Li D, Lovering RC, Mans TL, McCarthy F, Moore SD, Murphy R, Paustian TD, Perdue S, Peterson CN, Prüß BM, Saha MS, Sheehy RR, Tansey JT, Temple L, Thorman AW, Trevino S, Vollmer AC, Walbot V, Willey J, Siegele DA, Hu JC. Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLoS Comput Biol. 2021 Oct;17(10):e1009463. doi: 10.1371/journal.pcbi.1009463. eCollection 2021 Oct. PubMed PMID: 34710081; PubMed Central PMCID: PMC8553046.
Ramsey J, McIntosh B, Renfro D, Aleksander S, LaBonte S, Ross C, Zweifel A, Liles N, Farrar S, Gill J, Erill I, Ades S, Berardini T, Bennett J, Brady S, Britton R, Carbon S, Caruso S, Clements D, Dalia R, Defelice M, Doyle E, Friedberg I, Gurney S, Hughes L, Johnson A, Kowalski J, Li D, Lovering R, Mans T, McCarthy F, Moore S, Murphy R, Paustian T, Perdue S, Peterson C, Prüß B, Saha M, Sheehy R, Tansey J, Temple L, Thorman A, Trevino S, Vollmer A, Walbot V, Willey J, Siegele D, Hu J. Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLOS Computational Biology. 2021 October; 17(10):e1009463-. doi: 10.1371/journal.pcbi.1009463.
Cusick K, Iturbide A, Gautam P, Price A, Polson S, MacDonald M, Erill I. Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings. PLOS ONE. 2021-9-; 16(9):e0257800-. doi: 10.1371/journal.pone.0257800.
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.
Ramsey J, McIntosh B, Renfro D, Aleksander S, LaBonte S, Ross C, Zweifel A, Liles N, Farrar S, Gill J, Erill I, Ades S, Berardini T, Bennett J, Brady S, Britton R, Carbon S, Caruso S, Clements D, Dalia R, Defelice M, Doyle E, Friedberg I, Gurney S, Hughes L, Johnson A, Kowalski J, Li D, Lovering R, Mans T, McCarthy F, Moore S, Murphy R, Paustian T, Perdue S, Peterson C, Prüß B, Saha M, Sheehy R, Tansey J, Temple L, Thorman A, Trevino S, Vollmer A, Walbot V, Willey J, Siegele D, Hu J. Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO). [preprint]. 2021 May. doi: 10.1101/2021.04.30.440339.
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.
Adhikari S, Erill I, Curtis P. Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria. PLOS Genetics. 2021-3-; 17(3):e1009433-. doi: 10.1371/journal.pgen.1009433.
Alvarez-Gonzalez S, Erill I. Design of Machine Learning Models for the Prediction of Transcription Factor Binding Regions in Bacterial DNA. The 4th XoveTIC Conference. XoveTIC Conference; ; Basel Switzerland: MDPI; c2021.
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.
Kılıç S, Sánchez-Osuna M, Collado-Padilla A, Barbé J, Erill I. Flexible comparative genomics of prokaryotic transcriptional regulatory networks. BMC Genomics. 2020 December; 21(S5):-. doi: 10.1186/s12864-020-06838-x.
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.
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. Microbial Genomics. 2020 November; 6(11):-. doi: 10.1099/mgen.0.000440.
Goulet T, Erill I, Ascunce M, Finley S, Javan G. Conceptualization of the Holobiont Paradigm as It Pertains to Corals. Frontiers in Physiology. 2020-9-; 11:-. doi: 10.3389/fphys.2020.566968.
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.
Sánchez-Osuna M, Cortés P, Llagostera M, Barbé J, Erill I. Recurrent mobilization of ancestral and novel variants of the chromosomal di-hydrofolate reductase gene drives the emergence of clinical resistance to trimethoprim. [preprint]. 2020 July. doi: 10.1101/2020.07.31.230557.
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.
Chen Q, Britto R, Erill I, Jeffery C, Liberzon A, Magrane M, Onami J, 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 April; 18(2):91-103. doi: 10.1016/j.gpb.2018.11.006.
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.. Corpora as evolving entities: Embedding corpora in biomedical ontologies. CEUR Workshop Proceedings. CEUR Workshop Proceedings; 2020; c2020.
Schulz C, Fast C, Wernery U, Kinne J, Joseph S, Schlottau K, Jenckel M, Höper D, Patteril N, Syriac G, Hoffmann B, Beer M. Camelids and Cattle Are Dead-End Hosts for Peste-des-Petits-Ruminants Virus. Viruses. 2019 December; 11(12):1133-. doi: 10.3390/v11121133.
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.
Caruso S, deCarvalho T, Huynh A, Morcos G, Kuo N, Parsa S, Erill I. A Novel Genus of Actinobacterial Tectiviridae. Viruses. 2019 December; 11(12):1134-. doi: 10.3390/v11121134.
Koert M, López-Pérez J, Mattson C, Caruso S, Erill I. Evidence for shared ancestry between Actinobacteria and Firmicutes bacteriophages. [preprint]. 2019 November. doi: 10.1101/842583.
Chen Q, Britto R, Erill I, J. Jeffery C, Liberzon A, Magrane M, Onami J, 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. [preprint]. 2019 October. doi: 10.1101/788034.
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.
Sánchez-Osuna M, Cortés P, Barbé J, Erill I. Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates. Frontiers in Microbiology. 2019-1-; 9:-. doi: 10.3389/fmicb.2018.03332.
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.
Sánchez-Osuna M, Cortés P, Barbé J, Erill I. Origin of the mobile di-hydro-pteroate synthase gene determining sulfonamide resistance in clinical isolates. [preprint]. 2018 November. doi: 10.1101/472472.
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.
Biocuration: Distilling data into knowledge. PLoS Biol. 2018 Apr;16(4):e2002846. doi: 10.1371/journal.pbio.2002846. eCollection 2018 Apr. PubMed PMID: 29659566; PubMed Central PMCID: PMC5919672.
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.
Sánchez-Osuna M, Barbé J, Erill I. Comparative genomics of the DNA damage-inducible network in the Patescibacteria. Environmental Microbiology. 2017 September; 19(9):3465-3474. doi: 10.1111/1462-2920.13826.
Erill I, Caruso S. Bacillus cereus Group Bacteriophage Flapjack Genome Sequence. Genome Announcements. 2017 August; 5(31):-. doi: 10.1128/genomeA.00700-17.
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