** 2020 **

 

Alkhnbashi OS, Meier T, Mitrofanov A, Backofen R, Voß B. (2020) CRISPR-Cas bioinformatics. Methods. 172:3-11. doi: 10.1016/j.ymeth.2019.07.013.

Alzheimer M, Svensson SL, König F, Schweinlin M, Metzger M, Walles H, Sharma CM. (2020) A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni. PLoS Pathog. 16:e1008304. doi: 10.1371/journal.ppat.1008304. eCollection 2020 Feb.

Baumdicker F, Sester-Huss E, Pfaffelhuber P (2020). Modifiers of mutation rate in selectively fluctuating environments. Stochastic Processes and Their Applications 130, 6843–6862. doi.org/10.1016/j.spa.2020.06.011

Beisel CL. (2020) Methods for characterizing, applying, and teaching CRISPR-Cas systems. Methods. 172:1-2. doi: 10.1016/j.ymeth.2020.01.004.

Behler J, Hess WR. (2020) Approaches to study CRISPR RNA biogenesis and the key players involved. Methods. 172:12-26. doi: 10.1016/j.ymeth.2019.07.015.

Collias D, Leenay RT, Slotkowski RA, Zuo Z, Collins SP, McGirr BA, Liu J, Beisel CL. (2020) A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9. Sci Adv. 6:eabb4054. doi: 10.1126/sciadv.abb4054.

Collins SP, Beisel CL. (2020) Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination. Mol Cell. 79:703-704. doi:0.1016/j.molcel.2020.07.030.

Donati S, Kuntz M, Pahl V, Farke N, Beuter D, Glatter T, Gomes-Filho JV, Randau L, Wang CY, Link H. (2020) Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism. Cell Syst. S2405-4712(20)30418-X. doi: 10.1016/j.cels.2020.10.011.

Jacobsen T, Ttofali F, Liao C, Manchalu S, Gray BN, Beisel CL. (2020) Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs. Nucleic Acids Res. pii: gkaa272. doi: 10.1093/nar/gkaa272.

Maier LK, Marchfelder A, Randau L (2020). Meeting Report: German Genetics Society-Genome Editing with CRISPR. Bioessays. 42:e1900223. doi: 10.1002/bies.201900223.

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. (2020) Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 18:67-83. doi: 10.1038/s41579-019-0299-x.

Marchfelder A. (2020) CRISPR-Cas: In Rekordzeit von der Grundlagenforschung zur Anwendung. Biospektrum (Heidelb). 26:806. German. doi:10.1007/s12268-020-1500-5.

Marshall R, Beisel CL, Noireaux V. (2020) Rapid Testing of CRISPR Nucleases and Guide RNAs in an E. coli Cell-Free Transcription-Translation System. STAR Protoc. 1:100003. doi: 10.1016/j.xpro.2019.100003.

Mitrofanov A, Alkhnbashi OS, Shmakov SA, Makarova KS, Koonin EV, Backofen R. (2020) CRISPRidentify: identification of CRISPR arrays using machine learning approach. Nucleic Acids Res. gkaa1158. doi: 10.1093/nar/gkaa1158.

Müller-Esparza H, Osorio-Valeriano M, Steube N, Thanbichler M, Randau L. (2020) Bio-Layer Interferometry Analysis of the Target Binding Activity of CRISPR-Cas Effector Complexes. Front Mol Biosci. 7:98. doi:10.3389/fmolb.2020.00098.

Padilha VA, Alkhnbashi OS, Tran VD, Shah SA, L F Carvalho ACP, Backofen R. (2020)

Casboundary: Automated definition of integral Cas cassettes. Bioinformatics. btaa984. doi: 10.1093/bioinformatics/btaa984.

Padilha VA, Alkhnbashi OS, Shah SA, de Carvalho ACPLF, Backofen R. (2020) CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems. Gigascience. 9:giaa062. doi:10.1093/gigascience/giaa062.

Pinilla-Redondo R, Mayo-Muñoz D, Russel J, Garrett RA, Randau L, Sørensen SJ, Shah SA. (2020) Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. Nucleic Acids Res.  48:2000-2012. doi: 10.1093/nar/gkz1197.

Reimann V, Ziemann M, Li H, Zhu T, Behler J, Lu X, Hess WR. (2020) Specificities and functional coordination between the two Cas6 maturation endonucleases in Anabaena sp. PCC 7120 assign orphan CRISPR arrays to three groups. RNA Biol. 17:1442-1453. doi: 10.1080/15476286.2020.1774197.

Stachler AE, Schwarz TS, Schreiber S, Marchfelder A. (2020) CRISPRi as an efficient tool for gene repression in archaea. Methods. 172:76-85. doi: 10.1016/j.ymeth.2019.05.023.

Stachler AE, Wörtz J, Alkhnbashi OS, Turgeman-Grott I, Smith R, Allers T, Backofen R, Gophna U, Marchfelder A. (2020) Adaptation induced by self-targeting in a type I-B CRISPR-Cas system. J Biol Chem. 295:13502-13515. doi:10.1074/jbc.RA120.014030.

Turkowyd B, Schreiber S, Wörtz J, Segal ES, Mevarech M, Duggin IG, Marchfelder A, Endesfelder U. (2020) Establishing Live-Cell Single-Molecule Localization Microscopy Imaging and Single-Particle Tracking in the Archaeon Haloferax volcanii. Front Microbiol. 11:583010. doi:10.3389/fmicb.2020.583010.

Ulbricht A, Nickel L, Weidenbach K, Vargas Gebauer H, Kießling C, Förstner KU, Schmitz RA. (2020) The CARF Protein MM_0565 Affects Transcription of the Casposon- Encoded cas1-solo Gene in Methanosarcina mazei Gö1. Biomolecules. 10:1161. doi: 10.3390/biom10081161.

Wandera KG, Collins SP, Wimmer F, Marshall R, Noireaux V, Beisel CL. (2020) An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system. Methods. 172:42-50. doi: 10.1016/j.ymeth.2019.05.014.

Wimmer F, Beisel CL. (2020) CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers. Front Microbiol. 10:3078. doi: 10.3389/fmicb.2019.03078. eCollection 2019.

Ziegler H, Nellen W. (2020) CRISPR-Cas experiments for schools and the public. Methods.  172:86-94. doi: 10.1016/j.ymeth.2019.08.009.