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Items: 1 to 50 of 52

1.

Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates.

Sánchez-Osuna M, Cortés P, Barbé J, Erill I.

Front Microbiol. 2019 Jan 10;9:3332. doi: 10.3389/fmicb.2018.03332. eCollection 2018.

2.

Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages, HotFries, Moozy, Rainydai, RavenPuff, Scap1, and SenditCS.

Blocker D, Koert M, Mattson C, Patel H, Patel P, Patel R, Paudel H; 2017 UMBC Phage Hunters, Erill I, Caruso SM.

Microbiol Resour Announc. 2018 Sep 27;7(12). pii: e00993-18. doi: 10.1128/MRA.00993-18. eCollection 2018 Sep.

3.

ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

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.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194. doi: 10.1093/nar/gky1036.

4.

Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages.

Lee M, Puglisi KM; UMBC STEM-BUILD Cohort 1, Erill I, Caruso SM.

Genome Announc. 2018 Jun 21;6(25). pii: e00493-18. doi: 10.1128/genomeA.00493-18.

5.

Complete Genome Sequence of Streptomyces Bacteriophage Abt2graduatex2.

Erill I, Caruso SM.

Genome Announc. 2018 Jan 18;6(3). pii: e01480-17. doi: 10.1128/genomeA.01480-17.

6.

Bacillus cereus Group Bacteriophage Flapjack Genome Sequence.

Erill I, Caruso SM; 2016 UMBC Phage Hunters.

Genome Announc. 2017 Aug 3;5(31). pii: e00700-17. doi: 10.1128/genomeA.00700-17.

7.

Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae.

Erill I, Caruso SM; 2016 UMBC Phage Hunters.

Genome Announc. 2017 Jul 20;5(29). pii: e00701-17. doi: 10.1128/genomeA.00701-17.

8.

Comparative genomics of the DNA damage-inducible network in the Patescibacteria.

Sánchez-Osuna M, Barbé J, Erill I.

Environ Microbiol. 2017 Sep;19(9):3465-3474. doi: 10.1111/1462-2920.13826. Epub 2017 Jul 21.

PMID:
28618189
9.

Comparative Analysis of Ralstonia solanacearum Methylomes.

Erill I, Puigvert M, Legrand L, Guarischi-Sousa R, Vandecasteele C, Setubal JC, Genin S, Guidot A, Valls M.

Front Plant Sci. 2017 Apr 13;8:504. doi: 10.3389/fpls.2017.00504. eCollection 2017.

10.

Complete Genome Sequence of the Streptomyces Phage Nanodon.

Erill I, Caruso SM.

Genome Announc. 2016 Oct 6;4(5). pii: e01019-16. doi: 10.1128/genomeA.01019-16.

11.

Parametric bootstrapping for biological sequence motifs.

O'Neill PK, Erill I.

BMC Bioinformatics. 2016 Oct 6;17(1):406.

12.

Genome Sequence of Bacillus cereus Group Phage SalinJah.

Erill I, Caruso SM; 2015 UMBC Phage Hunters.

Genome Announc. 2016 Sep 29;4(5). pii: e00953-16. doi: 10.1128/genomeA.00953-16.

13.

Assessment of transfer methods for comparative genomics of regulatory networks in bacteria.

Kılıç S, Erill I.

BMC Bioinformatics. 2016 Aug 31;17 Suppl 8:277. doi: 10.1186/s12859-016-1113-7.

14.

The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

Erill I, Campoy S, Kılıç S, Barbé J.

Front Mol Biosci. 2016 Jul 20;3:33. doi: 10.3389/fmolb.2016.00033. eCollection 2016.

15.

A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data.

Hobbs ET, Pereira T, O'Neill PK, Erill I.

Algorithms Mol Biol. 2016 Jul 8;11:19. doi: 10.1186/s13015-016-0082-8. eCollection 2016.

16.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I.

Database (Oxford). 2016 Apr 25;2016. pii: baw055. doi: 10.1093/database/baw055. Print 2016.

17.

Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis.

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.

Virology. 2016 Feb;489:243-51. doi: 10.1016/j.virol.2015.12.012. Epub 2016 Jan 14.

18.

Erratum for Erill and Caruso, Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba.

Erill I, Caruso SM.

Genome Announc. 2015 Nov 19;3(6). pii: e01458-15. doi: 10.1128/genomeA.01458-15. No abstract available.

19.

Genome Sequences of Two Bacillus cereus Group Bacteriophages, Eyuki and AvesoBmore.

Erill I, Caruso SM.

Genome Announc. 2015 Oct 15;3(5). pii: e01199-15. doi: 10.1128/genomeA.01199-15.

20.

Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba.

Erill I, Caruso SM.

Genome Announc. 2015 Oct 15;3(5). pii: e01178-15. doi: 10.1128/genomeA.01178-15. Erratum in: Genome Announc. 2015;3(6). pii: e01458-15. doi: 10.1128/genomeA.01458-15.

21.

Diagnostic yield of targeted next generation sequencing in various cancer types: an information-theoretic approach.

Hagemann IS, O'Neill PK, Erill I, Pfeifer JD.

Cancer Genet. 2015 Sep;208(9):441-7. doi: 10.1016/j.cancergen.2015.05.030. Epub 2015 May 29.

PMID:
26227479
22.

Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal.

Erill I.

J Bacteriol. 2015 Aug 1;197(15):2454-7. doi: 10.1128/JB.00031-15. Epub 2015 May 26.

23.

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria.

Sanchez-Alberola N, Campoy S, Emerson D, Barbé J, Erill I.

J Bacteriol. 2015 Aug;197(16):2622-30. doi: 10.1128/JB.00035-15. Epub 2015 May 18.

24.

Identification and characterization of VpsR and VpsT binding sites in Vibrio cholerae.

Zamorano-Sánchez D, Fong JC, Kilic S, Erill I, Yildiz FH.

J Bacteriol. 2015 Apr;197(7):1221-35. doi: 10.1128/JB.02439-14. Epub 2015 Jan 26.

25.

Informational requirements for transcriptional regulation.

O'Neill PK, Forder R, Erill I.

J Comput Biol. 2014 May;21(5):373-84. doi: 10.1089/cmb.2014.0032. Epub 2014 Apr 1.

26.

Characterization of the SOS meta-regulon in the human gut microbiome.

Cornish JP, Sanchez-Alberola N, O'Neill PK, O'Keefe R, Gheba J, Erill I.

Bioinformatics. 2014 May 1;30(9):1193-7. doi: 10.1093/bioinformatics/btt753. Epub 2014 Jan 8.

27.

Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon.

Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT.

J Bacteriol. 2014 Feb;196(3):660-71. doi: 10.1128/JB.01007-13. Epub 2013 Nov 22.

28.

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.

Kiliç S, White ER, Sagitova DM, Cornish JP, Erill I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D156-60. doi: 10.1093/nar/gkt1123. Epub 2013 Nov 14.

29.

scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes.

O'Neill PK, Or M, Erill I.

PLoS One. 2013 Oct 7;8(10):e76177. doi: 10.1371/journal.pone.0076177. eCollection 2013.

30.

Inference of self-regulated transcriptional networks by comparative genomics.

Cornish JP, Matthews F, Thomas JR, Erill I.

Evol Bioinform Online. 2012;8:449-61. doi: 10.4137/EBO.S9205. Epub 2012 Aug 6.

31.

BioWord: a sequence manipulation suite for Microsoft Word.

Anzaldi LJ, Muñoz-Fernández D, Erill I.

BMC Bioinformatics. 2012 Jun 7;13:124. doi: 10.1186/1471-2105-13-124.

32.

Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes.

Sanchez-Alberola N, Campoy S, Barbé J, Erill I.

BMC Genomics. 2012 Feb 3;13:58. doi: 10.1186/1471-2164-13-58.

33.

Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons.

Cambray G, Sanchez-Alberola N, Campoy S, Guerin É, Da Re S, González-Zorn B, Ploy MC, Barbé J, Mazel D, Erill I.

Mob DNA. 2011 Apr 30;2(1):6. doi: 10.1186/1759-8753-2-6.

34.

xFITOM: a generic GUI tool to search for transcription factor binding sites.

Bhargava N, Erill I.

Bioinformation. 2010 Jul 6;5(2):49-51.

35.

Relative codon adaptation: a generic codon bias index for prediction of gene expression.

Fox JM, Erill I.

DNA Res. 2010 Jun;17(3):185-96. doi: 10.1093/dnares/dsq012. Epub 2010 May 7.

36.

A rapid and reliable means of assessing hepatic steatosis in vivo via electrical bioimpedance.

Hessheimer AJ, Parramón D, Guimerà A, Erill I, Rimola A, García-Valdecasas JC, Villa R, Fondevila C.

Transplantation. 2009 Sep 15;88(5):716-22. doi: 10.1097/TP.0b013e3181b391c0.

PMID:
19741471
37.

The SOS response controls integron recombination.

Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re S, Gonzalez-Zorn B, Barbé J, Ploy MC, Mazel D.

Science. 2009 May 22;324(5930):1034. doi: 10.1126/science.1172914.

38.

A reexamination of information theory-based methods for DNA-binding site identification.

Erill I, O'Neill MC.

BMC Bioinformatics. 2009 Feb 11;10:57. doi: 10.1186/1471-2105-10-57.

39.

Cohabitation of two different lexA regulons in Pseudomonas putida.

Abella M, Campoy S, Erill I, Rojo F, Barbé J.

J Bacteriol. 2007 Dec;189(24):8855-62. Epub 2007 Oct 12.

40.

Aeons of distress: an evolutionary perspective on the bacterial SOS response.

Erill I, Campoy S, Barbé J.

FEMS Microbiol Rev. 2007 Nov;31(6):637-56. Epub 2007 Sep 18. Review.

41.

In vivo detection of liver steatosis in rats based on impedance spectroscopy.

Parramon D, Erill I, Guimerà A, Ivorra A, Muñoz A, Sola A, Fondevila C, García-Valdecasas JC, Villa R.

Physiol Meas. 2007 Aug;28(8):813-28. Epub 2007 Jul 6.

PMID:
17664674
42.

Induction of the SOS response by bacteriophage lytic development in Salmonella enterica.

Campoy S, Hervàs A, Busquets N, Erill I, Teixidó L, Barbé J.

Virology. 2006 Aug 1;351(2):360-7. Epub 2006 May 19.

43.

Identification of the Acidobacterium capsulatum LexA box reveals a lateral acquisition of the Alphaproteobacteria lexA gene.

Mazón G, Campoy S, Erill I, Barbé J.

Microbiology. 2006 Apr;152(Pt 4):1109-18.

PMID:
16549674
44.

A SiC microdevice for the minimally invasive monitoring of ischemia in living tissues.

Gómez R, Ivorra A, Villa R, Godignon P, Millán J, Erill I, Solà A, Hotter G, Palacios L.

Biomed Microdevices. 2006 Mar;8(1):43-9.

PMID:
16491330
45.

Real-time direct measurement of human liver allograft temperature from recovery to transplantation.

Villa R, Fondevila C, Erill I, Guimerà A, Bombuy E, Gómez-Suárez C, Sacristán JC, García-Valdecasas JC.

Transplantation. 2006 Feb 15;81(3):483-6.

PMID:
16477240
46.

Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.

Erill I, Campoy S, Mazon G, Barbé J.

Nucleic Acids Res. 2006 Jan 10;34(1):66-77. Print 2006.

47.

Expression of canonical SOS genes is not under LexA repression in Bdellovibrio bacteriovorus.

Campoy S, Salvador N, Cortés P, Erill I, Barbé J.

J Bacteriol. 2005 Aug;187(15):5367-75.

48.

Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics.

Erill I, Jara M, Salvador N, Escribano M, Campoy S, Barbé J.

Nucleic Acids Res. 2004 Dec 16;32(22):6617-26. Print 2004.

49.

Reconstruction of the evolutionary history of the LexA-binding sequence.

Mazón G, Erill I, Campoy S, Cortés P, Forano E, Barbé J.

Microbiology. 2004 Nov;150(Pt 11):3783-95.

PMID:
15528664
50.

Widespread distribution of a lexA-regulated DNA damage-inducible multiple gene cassette in the Proteobacteria phylum.

Abella M, Erill I, Jara M, Mazón G, Campoy S, Barbé J.

Mol Microbiol. 2004 Oct;54(1):212-22.

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