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Items: 24

1.

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T.

Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87. doi: 10.1093/nar/gkz310.

2.

Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH.

Villebro R, Shaw S, Blin K, Weber T.

J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):469-475. doi: 10.1007/s10295-018-02131-9. Epub 2019 Jan 4.

PMID:
30610412
3.

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters.

Blin K, Pascal Andreu V, de Los Santos ELC, Del Carratore F, Lee SY, Medema MH, Weber T.

Nucleic Acids Res. 2019 Jan 8;47(D1):D625-D630. doi: 10.1093/nar/gky1060.

4.

Patscanui: an intuitive web interface for searching patterns in DNA and protein data.

Blin K, Wohlleben W, Weber T.

Nucleic Acids Res. 2018 Jul 2;46(W1):W205-W208. doi: 10.1093/nar/gky321.

5.

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing.

Tong Y, Robertsen HL, Blin K, Weber T, Lee SY.

Methods Mol Biol. 2018;1671:163-184. doi: 10.1007/978-1-4939-7295-1_11.

PMID:
29170959
6.

Recent development of computational resources for new antibiotics discovery.

Kim HU, Blin K, Lee SY, Weber T.

Curr Opin Microbiol. 2017 Oct;39:113-120. doi: 10.1016/j.mib.2017.10.027. Epub 2017 Nov 16. Review.

PMID:
29156309
7.

Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.

Blin K, Kim HU, Medema MH, Weber T.

Brief Bioinform. 2017 Nov 3. doi: 10.1093/bib/bbx146. [Epub ahead of print]

PMID:
29112695
8.

Dissemination of antibiotic resistance genes from antibiotic producers to pathogens.

Jiang X, Ellabaan MMH, Charusanti P, Munck C, Blin K, Tong Y, Weber T, Sommer MOA, Lee SY.

Nat Commun. 2017 Jun 7;8:15784. doi: 10.1038/ncomms15784.

9.

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery.

Alanjary M, Kronmiller B, Adamek M, Blin K, Weber T, Huson D, Philmus B, Ziemert N.

Nucleic Acids Res. 2017 Jul 3;45(W1):W42-W48. doi: 10.1093/nar/gkx360.

10.

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH.

Nucleic Acids Res. 2017 Jul 3;45(W1):W36-W41. doi: 10.1093/nar/gkx319.

11.

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters.

Kautsar SA, Suarez Duran HG, Blin K, Osbourn A, Medema MH.

Nucleic Acids Res. 2017 Jul 3;45(W1):W55-W63. doi: 10.1093/nar/gkx305.

12.

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters.

Blin K, Medema MH, Kottmann R, Lee SY, Weber T.

Nucleic Acids Res. 2017 Jan 4;45(D1):D555-D559. doi: 10.1093/nar/gkw960. Epub 2016 Oct 24.

13.

Ten Simple Rules for Taking Advantage of Git and GitHub.

Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.

PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi: 10.1371/journal.pcbi.1004947. eCollection 2016 Jul. No abstract available. Erratum in: PLoS Comput Biol. 2019 Jun 14;15(6):e1007142.

14.

CRISPy-web: An online resource to design sgRNAs for CRISPR applications.

Blin K, Pedersen LE, Weber T, Lee SY.

Synth Syst Biotechnol. 2016 Feb 12;1(2):118-121. doi: 10.1016/j.synbio.2016.01.003. eCollection 2016 Jun.

15.

Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.

16.

antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH.

Nucleic Acids Res. 2015 Jul 1;43(W1):W237-43. doi: 10.1093/nar/gkv437. Epub 2015 May 6.

17.

DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.

Blin K, Dieterich C, Wurmus R, Rajewsky N, Landthaler M, Akalin A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D160-7. doi: 10.1093/nar/gku1180. Epub 2014 Nov 21.

18.

Improved lanthipeptide detection and prediction for antiSMASH.

Blin K, Kazempour D, Wohlleben W, Weber T.

PLoS One. 2014 Feb 20;9(2):e89420. doi: 10.1371/journal.pone.0089420. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e103665.

19.

Proteomic approach to reveal the regulatory function of aconitase AcnA in oxidative stress response in the antibiotic producer Streptomyces viridochromogenes Tü494.

Michta E, Ding W, Zhu S, Blin K, Ruan H, Wang R, Wohlleben W, Mast Y.

PLoS One. 2014 Feb 3;9(2):e87905. doi: 10.1371/journal.pone.0087905. eCollection 2014.

20.

Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids.

Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Iftime D, Musiol EM, Blin K, Wohlleben W, Pühler A, Kalinowski J, Weber T.

J Biotechnol. 2013 Dec;168(4):739-40. doi: 10.1016/j.jbiotec.2013.10.004. Epub 2013 Oct 16.

PMID:
24140291
21.

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.

Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W204-12. doi: 10.1093/nar/gkt449. Epub 2013 Jun 3.

22.

The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494.

Michta E, Schad K, Blin K, Ort-Winklbauer R, Röttig M, Kohlbacher O, Wohlleben W, Schinko E, Mast Y.

Environ Microbiol. 2012 Dec;14(12):3203-19. doi: 10.1111/1462-2920.12006. Epub 2012 Nov 1.

PMID:
23116164
23.

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W339-46. doi: 10.1093/nar/gkr466. Epub 2011 Jun 14.

24.

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity.

Röttig M, Medema MH, Blin K, Weber T, Rausch C, Kohlbacher O.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W362-7. doi: 10.1093/nar/gkr323. Epub 2011 May 9.

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