Publications

245. Gilfillan D, Vilander AC, Pan M, Goh YJ, O’Flaherty S, Feng N, Fox BE, Lang C, Greenberg HB, Abdo Z, Barrangou R, Dean GA. (2023) Lactobacillus acidophilus Expressing Murine Rotavirus VP8 and Mucosal Adjuvants Induce Virus-Specific Immune Responses. Vaccines 11:1774. doi: 10.3390/vaccines11121774.

244. Barrangou R. (2024) First Drug Approval Rises the CRISPR Tide. CRISPR J 6:487. doi: 10.1089/crispr.2023.29168.editorial

243. Pyhtila B, Kasowitz S, Leeson R, Barrangou R. (2023) The Expanding Dissemination and Distribution Patterns of Diverse CRISPR Plasmids by Addgene. CRISPR J 6:493-501. doi: 10.1089/crispr.2023.0059

242. Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon PH, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert RS, Knott GJ, Lapinaite A, Pausch P, Cofsky JC, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. (2023) CasPEDIA Database: a functional classification system for class 2 CRISPR Cas enzymes. Nucleic Acids Res 52:D590-D596. doi: 10.1093/nar/gkad890.

241. Barrangou R. (2023) The CRISPR Toolbox: The End of the Beginning. CRISPR J 6:403. doi: 10.1089/crispr.2023.29167.editorial.

240. Barrangou R. (2023) CRISPR Milestones for Sustainable Agriculture and Forestry. CRISPR J 6:303-304. doi: 10.1089/crispr.2023.29163.editorial.

239. Page CA, Pérez-Díaz IM, Pan M, Barrangou R. (2023) Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry. Foods 2:2455. doi: 10.3390/foods12132455.

238. Sulis DB, Jiang X, Yang C, Marques BM, Matthews ML, Miller Z, Lan K, Cofre-Vega C, Liu B, Sun R, Sederoff H, Bing RG, Sun X, Williams CM, Jameel H, Phillips R, Chang HM, Peszlen I, Huang YY, Li W, Kelly RM, Sederoff RR, Chiang VL, Barrangou R, Wang JP. (2023) Multiplex CRISPR editing of wood for sustainable fiber production. Science. 381(6654):216-221. doi: 10.1126/science.add4514.

237. Page CA, Pérez-Díaz IM, Pan M, Barrangou R. (2023) Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry. Foods. 12(13):2455. doi: 10.3390/foods12132455.

236. Barrangou R. (2023) CRISPR Conventions in a Polarized Era. CRISPR J. 6:183-184. doi: 10.1089/crispr.2023.29160.editorial.

235. Cress B, Barrangou R. (2023) Special Issue: Manipulating the Microbiome with CRISPR. CRISPR J. 6:86. doi: 10.1089/crispr.2023.0005.cfp.

234. Barrangou R. (2023) Amplifying CRISPR: Next-Generation Diagnostics. CRISPR J 6:85. doi: 10.1089/crispr.2023.0004.editorial.

233. Foley MH, Walker ME, Stewart AK, O’Flaherty S, Gentry EC, Patel S, Beaty VV, Allen G, Pan M, Simpson JB, Perkins C, Vanhoy ME, Dougherty MK, McGill SK, Gulati AS, Dorrestein PC, Baker ES, Redinbo MR, Barrangou R, Theriot CM. (2023) Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. Nat Microbiol. doi: 10.1038/s41564-023-01337-7

232. Barrangou R. (2023) CRISPR Crops and Sustainable Agriculture. CRISPR J. 6:1. doi: 10.1089/crispr.2023.0002.editorial.

231. O’Flaherty S, Cobian N, Barrangou R. (2023) Impact of Pomegranate on Probiotic Growth, Viability, Transcriptome and Metabolism. Microorganisms 11, 404

230. Roberts A, Nethery MA, Barrangou R. (2022) Functional characterization of diverse type I-F CRISPR-associated transposons. Nucleic Acids Res. doi: 10.1093/nar/gkac985.

229. Barrangou R. (2022) Better guidance for CRISPR. CRISPR J.

228. Nethery MA, Hidalgo-Cantabrana C, Roberts A, Barrangou R. (2022) CRISPR-based engineering of phages for in situ bacterial base editing. Proc Natl Acad Sci U S A. 119(46):e2206744119. doi: 10.1073/pnas.2206744119.

227. Adler BA, Hessler T, Cress BF, Lahiri A, Mutalik VK, Barrangou R, Banfield J, Doudna JA. (2022) Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. Nat Microbiol. doi: 10.1038/s41564-022-01258-x.

226. Barrangou R. (2022) Extreme Genome Editing. CRISPR J. 5:629-630. doi: 10.1089/crispr.2022.29155.editorial.

225. Barrangou R. (2022) Navigating Viral Space with CRISPR Technologies. CRISPR J. 5:487. doi: 10.1089/crispr.2022.29153.editorial.

224. Theriot C, Thanissery R, O’Flaherty S, Barrangou R. (2022) Probiotic coloniatoin dynamics after oral consumption of VSL#3 by antibiotic-treated mice. Microbiome Res Rep 1:21. doi: 10.20517/mrr.2022.07.

223. Pan M, Morovic W, Hidalgo-Cantabrana C, Roberts A, Walden KKO, Goh YJ, Barrangou R. (2022) Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2205068119. doi: 10.1073/pnas.2205068119.

222. Barrangou R. (2022) Celebrating a Decade of CRISPR-Fueled Genome Editing.

CRISPR J. 5:354-355. doi: 10.1089/crispr.2022.29150.rba

221. Monte DFM, Nethery MA, Berman H, Keelara S, Lincopan, N, Fedorka-Vary PJ, Barrangou R, Landgraf M. (2022) Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil. Front Microbiol. doi: 10.3389/fmicb.2022.867278.

220. Chamberlain M, O’Flaherty S, Cobián N, Barrangou R. (2022) Metabolomic Analysis of Lactobacillus acidophilus, L. gasseri, L. crispatus, and Lacticaseibacillus rhamnosus Strains in the Presence of Pomegranate Extract. Front Microbiol. May 18;13:863228. doi: 10.3389/fmicb.2022.863228. eCollection 2022.

219. Sanozky-Dawes R, Barrangou R. (2022) Lactobacillus, glycans and drivers of health in the vaginal microbiome. Microbiome Res Rep 1:18. doi: 10.20517/mrr.2022.03

218. Barrangou R. (2022) CRISPR à la carte. CRISPR J 5:170. doi: 10.1089/crispr.2022.29147.rba.

217. Barrangou R. (2022) CRISPR Rewrites the Future of Medicine. CRISPR J 5:1. doi: 10.1089/crispr.2022.29144.rba.

216. Barrangou R, Marraffini LA. (2022) Turning CRISPR on with antibiotics. Cell Host Microbe30:12-14. doi: 10.1016/j.chom.2021.12.013

215. Barrangou R. (2021) CRISPR Milestones and Anticipating What Is Next for the Journal. CRISPR J  4:771-772. doi: 10.1089/crispr.2021.29139.rba.

214. Ventura M, van Sinderen D, Turroni F, Milani C, Munoz J, Haller D, Ross P, Collado MC, Allen-Vercoe E, Del Rio D, Altermann E, Katayama T, Zoetendal EG, Belzer C, Mena P, Im SH, Gueimonde M, Margolles A, Ruiz L, Lacroix C, Stanton C, Barbara G, Saminen S, Scott KP, Barrangou R, Bottacini F, Marco ML. (2021) Editors’ Prelude to Microbiome Research Reports. Microbiome Res Rep Rep 1:1doi: 10.20517/mrr.2021.01

213. Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbaur AM, Banfield JF, Doudna JA. (2021).Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol. doi: 10.1038/s41564-021-01014-7.

212. Cobian N, Garlet A, Hidalgo-Cantabrana C, Barrangou R. (2021). Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications. Front Microbiol. doi: 10.3389/fmicb.2021.758749.

211. Yu H, Xue L, Barrangou R, Chen S, Huang Y. (2021) Toward inclusive global governance of human genome editing. Proc Natl Acad Sci U S A 18:e2118540118. doi: 10.1073/pnas.2118540118

210. Huang Y, Zhang Y, Wu M, Porter A, Barrangou R. (2021) Determination of Factors Driving the Genome Editing Field in the CRISPR Era Using Bibliometrics. CRISPR J 4:728-738. doi: 10.1089/crispr.2021.0001.

209. Barrangou R. (2021) As CRISPR Technologies Ripen, What Should We Prioritize? CRISPR J 4:627. doi: 10.1089/crispr.2021.29138.rba.

208. Nethery MA, Korvink M, Makarova KS, Wolf YI, Koonin EV, Barrangou R. (2021) CRISPRclassify: Repeat-Based Classification of CRISPR Loci. CRISPR J4:558-574. doi: 10.1089/crispr.2021.0021.

207. Barrangou R.(2021) Clinical Milestone for CRISPR Medicines. CRISPR J 4:459. doi: 10.1089/crispr.2021.29135.rba.

206. Barrangou R, Hill C. (2021) Todd R. Klaenhammer, an inspirational food microbiologist who leaves a lasting legacy. Proc Natl Acad Sci U S A. 118:e2107754118. doi: 10.1073/pnas.2107754118

205. Barrangou R. (2021) The CRISPR chronicles and the power of storytelling. CRISPR J 4:158-159

204. Saha K, Sontheimer EJ and the SCGE. (2021) The NIH Somatic Cell Genome Editing program. Nature592: 195-204

203. Barrangou R. (2021) Political Support Sets the Tone for CRISPR Enthusiasts. CRISPR J4:1-2

202. Kuiken T, Barrangou R, Grieger K. (2021). (Broken) Promises of Sustainable Food and Agriculture through New Biotechnologies: The CRISPR Case. CRISPR J. doi: 10.1089/crispr.2020.0098.

201. Foley MH, O’Flaherty S, Allen G, Rivera AJ, Stewart AK, Barrangou R, Theriot CM. (2021). Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization.  Proc Natl Acad Sci U S A. doi: 10.1073/pnas.2017709118.

200. Goh YJ, Barrangou R, Klaenhammer TR. (2021) In Vivo Transcriptome of Lactobacillus acidophilus and Colonization Impact on Murine Host Intestinal Gene Expression. mBio 12(1):e03399-20. doi: 10.1128/mBio.03399-20.

199. Goh YJ, Barrangou R. (2021) A portable CRISPR-Cas9N system for flexible genome engineering in Lactobacillus acidophilus, Lactobacillus gasseri and Lactobacillus paracasei. Appl Environ Microbiol. doi: 10.1128/AEM.02669-20.

198. McClements DJ, Barrangou R, Hill C, Kokini JL, Ann Lila M, Meyer AS, Yu L. (2020) Building a Resilient, Sustainable, and Healthier Food Supply through Innovation and Technology. Annu Rev Food Sci Technol. doi: 10.1146/annurev-food-092220-030824.

197. Barrangou R. (2020) Sharpening the CRISPR Toolbox. CRISPR J. 3:421. doi: 10.1089/crispr.2020.29114.rba.

196. Brandt K, Barrangou R. (2020) Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid. BMC Microbiol. 20:339. doi: 10.1186/s12866-020-02027-8.

195. Angrist M, Barrangou R, Baylis F, Brokowski C, Burgio G, Caplan A, Chapman CR, Church GM, Cook-Deegan R, Cwik B, Doudna JA, Evans JH, Greely HT, Hercher L, Hurlbut JB, Hynes RO, Ishii T, Kiani S, Lee LH, Levrier G, Liu DR, Lunshof JE, Macintosh KL, Mathews DJH, Meslin EM, Mills PHR, Montoliu L, Musunuru K, Nicol D, O’Neill H, Qiu R, Ranisch R, Sherkow JS, Soni S, Terry S, Topol E, Williamson R, Zhang F, Davies K. (2020) Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing. CRISPR J. 3:332-349. doi: 10.1089/crispr.2020.29106.man.

194. Barrangou R. (2020) Nobel Dreams Come True for Doudna and Charpentier. CRISPR J. 3:317-318. doi: 10.1089/crispr.2020.29109.rba.

193. Barrangou R. (2020) Commissions, Consensus, and CRISPR. CRISPR J. 2020 3:316-317. doi: 10.1089/crispr.2020.29107.rba.

192. O’Flaherty S, Foley MH, Rivera AJ, Theriot CM, Barrangou R. (2020)  Complete Genome Sequence of Lactobacillus johnsonii NCK2677, Isolated from Mice. Microbiol Resour Announc 9:e00918-20. doi:10.1128/MRA.00918-20

191. Monte DFM, Nethery MA, Barrangou R, Landgraf M, Fedorka-Cray PJ. (2020) Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources. Food Microbiol 93:103601. Doi: 10.1016.j.fm.2020.103601

190. LaManna CM, Pythila B, Barrangou R. (2020) Sharing the CRISPR Toolbox with an Expanding Community. CRISPR J 3:248-252. doi: 10.1089/crispr.2020.0075

189. Barrangou R. (2020) In times like these, we all need a moment of science. CRISPR J 3:223 doi: 10.1089/crispr.2020.29102.rba

188. Klotz C, Goh YJ, O’Flaherty S, Barrangou R. (2020) S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM. BMC Microbiol 20:248. doi: 10.1186/s12866-020-01908-2.

187. Barrangou R, Sontheimer EJ. (2020) Shutting down RNA-targeting CRISPR. Science 369:31-32. doi: 10.1126/science.abc8243

186. Barrangou R. (2020) Finding SECURE Ground: USDA Edits the Biotechnology Regulatory Framework. CRISPR J 3:136–137 doi: 10.1089/crispr.2020.29096.rba

185. Roberts A, Barrangou R. (2020) Applications of CRISPR-Cas systems in Lactic Acid Bacteria. FEMS Microbiol Rev doi: 10.1093/femsre/fuaa016

184. Pan M, Nethery MA, Hidalgo-Cantabrana C, Barrangou R. (2020) Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium. Microorganisms doi: 10.3390/microorganisms8050720

183. Brandt K, Nethery MA, O’Flaherty S, Barrangou R. (2020) Genomic characterization of Lactobacillus fermentum DSM 20052. BMC Genomics21(1):328. doi: 10.1186/s12864-020-6740-8

182. Davies K, Barrangou R. (2020) COVID-19 and the CRISPR Community Response. CRISPR J 3:66. doi: 10.1089/crispr.2020.29092.rba

181. Reed AD, Nethery MA, Stewart A, Barrangou R, Theriot CM. (2020) Strain-dependent inhibition of Clostridioides difficile by commensal Clostridia encoding the bile acid inducible (bai) operon. J Bacteriol pii: JB.00039-20. doi: 10.1128/JB.00039-20

180. Klotz C, Goh YJ, O’Flaherty S, Johnson B, Barrangou R. (2020) Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface. Front Microbiol 11:345. doi: 10.3389/fmicb.2020.00345

179. Selle K, Fletcher JR, Tuson H, Schmitt DS, McMillan L, Vridhambal GS, Rivera AJ, Montgomery SA, Fortier L-C, Barrangou R, Theriot CM, Ousterout DG. (2020) In vivo targeting of Clostridioides difficile using phage delivered CRISPR-Cas3 antimicrobials. mBio 11:e00019-20. doi: 10.1128/mBio.00019-20.

178. Barrangou R, Sontheimer EJ. (2020) CRISPR Shields: Fending Off Diverse Cas Nucleases with Nucleus-like Structures. Mol Cell 77:934-936. doi: 10.1016/j.molcel.2020.02.015.

177. Barrangou R. (2020) Ushering in the next CRISPR decade. CRISPR J 3:2 DOI: 10.1089/crispr.2020.29085.rba

176. Pan M, Barrangou R. (2020) Combining omics technologies with CRISPR-based genome editing to study food microbes. Curr Opin Biotechnol 61:198-208. doi:10.1016/j.copbio.2019.12.027

175. M Pan, C Hidalgo-Cantabrana, R Barrangou. (2020) Host and body site-specific adaptation of Lactobacillus crispatus genomes. NAR Genomics & Bioinformatics 2, lqaa001

174. Pan M, Hidalgo-Cantabrana C, Goh YJ, Sanozky-Dawes R, Barrangou R. (2020) Comparative Analysis of Lactobacillus gasseri and Lactobacillus crispatus Isolated From Human Urogenital and Gastrointestinal Tracts. Front Microbiol doi: 10.3389/fmicb.2019.03146

173. Hidalgo-Cantabrana C, Barrangou R. (2020)  Characterization and applications of Type I CRISPR-Cas systems. Biochem Soc Trans doi: 10.1042/BST20190119

172. 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. (2019) Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol doi:10.1038/s41579-019-0299-x.

171. Barrangou R. (2019) Partnering with bioRxiv. CRISPR J 2:342 doi:10.1089/crispr.2019.29076.rba

170. Barrangou R. (2019) Foresight is 2020: ten bold predictions for the new CRISPR year. CRISPR J 2:341-342 DOI: 10.1089/crispr.2019.29075.rba

169. Nethery MA, Henriksen ED, Daughtry KV, Johanningsmeier SD, Barrangou R. (2019) Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage. BMC Genomics 20:902. doi: 10.1186/s12864-019-6274-0.

168. Young JK, Gasior SL, Jones S, Wang L, Navarro P, Vickroy B, Barrangou R. (2019) The repurposing of type I-E CRISPR-Cascade for gene activation in plants. Comm Biol doi: 10.1038/s42003-019-0637-6

167. Huang Y, Porter A, Zhang Y, Barrangou R. (2019) Collaborative networks in gene editing. Nat Biotechnol. 37:1107-1109. doi: 10.1038/s41587-019-0275-z

166. Barrangou R. (2019) Thinking about CRISPR: the ethics of human genome editing. CRISPR J 2:247-248 doi: 10.1089/crispr.2019.29072.rba

165. Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, Reddy TE, Beisel CL, Barrangou R, Gersbach CA. (2019) Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. Nat Biotechnol. doi: 10.1038/s41587-019-0235-7

164. Barrangou R.(2019) Bringing CRISPR to the cinema. CRISPR J 2:187 doi: 10.1089/crispr.2019.29070.rba.

163. Davis TH. (2019) Profile of Rodolphe Barrangou. Proc Natl Acad Sci U S A 116:15754-15756. doi: 10.1073/pnas.1911079116.

162. Hidalgo-Cantabrana C, Goh YJ, Pan M, Sanozky-Dawes R, Barrangou R.(2019) Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus. Proc Natl Acad Sci U S A 116:15774-15783. doi: 10.1073/pnas.1905421116.

161. Selle K, Andersen JM, Barrangou R.(2019) Short communication: Transcriptional response to a large genomic island deletion in the dairy starter culture Streptococcus thermophilus. J Dairy Sci. 102:7800-7806. doi: 10.3168/jds.2019-16397

160. Barrangou R. (2019) Taking CRISPR to New Heights. CRISPR J 2:133 doi: 10.1089/crispr.2019.29064.rba.

159. Cañez C, Selle K, Goh YJ, Barrangou R. (2019) Outcomes and characterization of Chromosomal Self-Targeting by Native CRISPR-Cas Systems in Streptococcus thermophilus. FEMS Microbiol Lett. doi: 10.1093/femsle/fnz105

158. Barrangou R, Notebaart RA. (2019) CRISPR-Directed Microbiome Manipulation across the Food Supply Chain. Trends Microbiol S0966-842X(19)30070-8. doi: 10.1016/j.tim.2019.03.006

157. Barrangou R. (2019) Time To Let CRISPR B.E.? CRISPR J 2: 67. doi: 10.1089/crispr.2019.29055.rdb

156. Brandt K, Barrangou R. (2019) Applications of CRISPR Technologies Across the Food Supply Chain. Annu Rev Food Sci Technol 25:10:133-150. doi: 10.1146/annurev-food-032818-121204

155. Varble A, Meaden S, Barrangou R, Westra ER, Marraffini LA. (2019) Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci. Nat Microbiol doi: 10.1038/s41564-019-0400-2

154. Foley MH, O’Flaherty S, Barrangou R, Theriot CM. (2019) Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract. PLoS Pathogens doi: 10.1371/journal.ppat.1007581

153. Barrangou R. (2019) CRISPR on the move in 2019. CRISPR J 2:1-2. doi: 10.1089/CRISPR.2019.29043.rba

152. Nethery MA, Barrangou R. (2019) Predicting and visualizing features of CRISPR–Cas systems. Methods in Enzymology 616:1-25. doi: 10.1016/bs.mie.2018.10.016

151. Goh YJ, Barrangou R. (2019) Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli. Curr Op Biotechnol 56, 163-171

150. Barrangou R. (2018) CRISPR crossroad for genome editing. CRISPR J 1:349-350. Doi: 10.1089/crispr.2018.29040.rba

149. Barrangou R. (2018) Expanding the CRISPR Landscape on a cas by cas Basis. CRISPR J 1:303-303. doi: 10.1089/crispr.2018.29035.rba

148. Morovic W, Roos P, Zabel B, Hidalgo-Cantabrana C, Kiefer A, Barrangou R. (2018) Transcriptional and functional analysis of Bifidobacterium animalis subsp. lactis exposure to tetracycline. Appl Environ Microbiol. pii: AEM.01999-18. doi: 10.1128/AEM.01999-18.

147. Hidalgo-Cantabrana C, Goh YJ, Barrangou R. (2018) Characterization and Repurposing of Type I and Type II CRISPR-Cas Systems in Bacteria. J Mol Biol. S0022-2836(18)31107-0. doi: 10.1016/j.jmb.2018.09.013

146. Klotz C, Barrangou R. (2018) Engineering components of the Lactobacillus S-layer for biotherapeutic applications. Frontiers Microbiol  doi: 10.3389/fmicb.2018.02264

145. Bikard D, Barrangou R. (2018) CRISPR-Cas systems as weapons against pathogenic bacteria. Biol Auj 211:265-270. doi: 10.1051/jbio/2018004

144. Hidalgo-Cantabrana C, Sanozky-Dawes R, Barrangou R. (2018) Insights into the human virome using CRISPR spacers from microbiomes. Viruses 10:479. doi: 10.3390/v10090479

143. Nethery MA, Barrangou R. (2018) CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline. RNA Biol. doi: 10.1080/15476286.2018.1493332.

142. Faure G, Shmakov SA, Makarova KS, Wolf YI, Crawley AB, Barrangou R, Koonin EV. (2018) Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems. RNA Biol. doi: 10.1080/15476286.2018.1493331.

141. Curchoe CL, Barrangou R. (2018) Pomp and circumstance: making the case for CRISPR. CRISPR J 1:252-253. doi: 10.1089/crispr/2018.2930.oxf

140. Barrangou R. (2018) CRISPR craziness: a response to the EU court ruling. CRISPR J 1:250-251. doi: 10.1089/crispr.2018.29025.edi

139. Crawley AB, Barrangou R. (2018) Conserved genome organization and core transcriptome of the Lactobacillus acidophilus complex. Frontiers Microbiol. 9:1834. doi: 10.3389/fmicb.2018.01834

138. Crawley AB, Henriksen ED, Stout E, Brandt K, Barrangou R. (2018) Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli. Sci Rep. 8:11544. doi: 10.1038/s41598-018-29746-3.

137. Stout EA, Sanozky-Dawes R, Goh YJ, Crawley AB, Klaenhammer TR, Barrangou R. (2018) Deletion-based escape of CRISPR-Cas9 targeting in Lactobacillus gasseri. Microbiology. doi: 10.1099/mic.0.000689

136. Davies K, Barrangou R. (2018) MasterChef at Work. CRISPR J 1:219-222. doi: 10.1089/crispr.2018.29015.int

124. Weissman JL, Holmes R, Barrangou R, Moineau S, Fagan WF, Levin BR, Johnson PLF (2018). Immune Loss as a Driver of Coexistence During Host-Phage Coevolution. ISME J 12:585-597. doi: 10.1038/ismej.2017.194.

123. Klotz C, O’Flaherty A, Goh YJ, Barrangou R (2017) Investigating the effect of growth phase on the surface-layer associated proteome of Lactobacillus acidophilus using quantitative proteomics. Frontiers in Microbiology 8:2174. doi: 10.3389/fmicb.2017.02174.

122. Theilmann MC, Goh YJ, Nielsen KF, Klaenhammer TR, Barrangou R, Abou Hachem M. (2017). Lactobacillus acidophilus metabolizes dietary plant glucosides and externalizes their bio-active phytochemicals. mBio 8.pii: e01421-17. doi: 10.1128/mBio.01421-17.

121. Barrangou R, Bikard D. (2017). CRISPR-Cas systems: at the cutting edge of microbiology. Curr Opin Microbiol 37:vii-viii. doi: 10.1016/j.mib.2017.09.015.

120. Hidalgo Cantabrana H, Crawley AB, Sanchez B, Barrangou R (2017) Characterization and exploitation of CRISPR loci in Bifidobacterium longum. Frontiers Microbiol 8:1851. doi: 10.3389/fmicb.2017.01851. eCollection 2017

119. Toms A, Barrangou R. (2017). On the global CRISPR array behavior in Class I systems. Biol Direct. 12:20 doi: 10.1186/s13062-017-0193-2

118. Donohue PD, Barrangou R, May AP. (2017) Advances in industrial biotechnology using CRISPR-Cas systems. Trends Biotechnol S0167-7799(17)30187-7. doi: 10.1016/j.tibtech.2017.07.007

117. Bikard D, Barrangou R. (2017) Using CRISPR-Cas systems as antimicrobials. Curr Opin Microbiol 37:155-160. doi: 10.1016/j.mib.2017.08.005

116. van Pijkeren JP, Barrangou R. (2017). Genome editing of food-grade lactobacilli to develop therapeutic probiotics. Microbiol Spectr 5:5. doi:10.1128/microbiolspec.BAD-0013-2016

115. QnAs with Rodolphe Barrangou. (2017). Proc Natl Acad Sci USA114:7183-7184. doi: 10.1073/pnas.1710348114

114. Hidalgo-Cantabrana C, O’Flaherty S, Barrangou R. (2017) CRISPR-based engineering of next-generation lactic acid bacteria. Curr Opin Microbiol. 37:79-87. doi: 10.1016/j.mib.2017.05.015

113. Johnson BR, O’Flaherty SJ, Goh YJ, Carroll I, Barrangou R, Klaenhammer TR. (2017) The S-layer associated serine protease homolog PrtX impacts cell surface-mediated microbe-host interactions of Lactobacillus acidophilus NCFM. Front. Microbiol. doi:10.3389/fmicb.2017.01185

112. Barrangou R, Horvath P. (2017) A decade of discovery: CRISPR functions and applications. Nat Microbiol. 2:17092. doi: 10.1038/nmicrobiol.2017.92

111. Barrangou R, Ousterout DG. (2017) Repurposing CRISPR-Cas systems as DNA-based smart antimicrobials. Cell & Gene Therapy Insights. 3:63-72 doi:10.18609/cg .2017.008

110. Selle K, Goh YJ, Johnson BR, O’Flaherty S, Andersen JM, Barrangou R, Klaenhammer TR. (2017) Deletion of Lipoteichoic Acid Synthase Impacts Expression of Genes Encoding Cell Surface Proteins in Lactobacillus acidophilus. Front Microbiol. 8:553. doi: 10.3389/fmicb.2017.00553.

109. Barrangou R, Gersbach CA. (2017) Expanding the CRISPR Toolbox: Targeting RNA with Cas13b. Mol Cell. 65:582-584. doi: 10.1016/j.molcel.2017.02.002

108. Stout E, Klaenhammer T, Barrangou R. (2017) CRISPR-Cas Technologies and Applications in Food Bacteria. Annu Rev Food Sci Technol. 8:413-437. doi: 10.1146/annurev-food-072816-024723.

107. Morovic W, Hibberd AA, Zabel B, Barrangou R, Stahl B. (2016) Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases. Front. Microbiol. 7:1747 dx.doi.org/10.3389/fmicb.2016.01747

106. Barrangou R, Doudna JA. (2016) Applications of CRISPR technologies in research and beyond. Nature Biotechnology 34:933-941 doi:10.1038/nbt.3659

105. Andersen JM, Shoup M, Robinson C, Britton R, Olsen KEP, Barrangou R. (2016) CRISPR diversity and microevolution in Clostridium difficile. Genome Biology and Evolution. doi: 10.1093/gbe/evw203

104. Briner AE, Barrangou R. (2016) Guide RNAs: A Glimpse at the Sequences that Drive CRISPR–Cas Systems. CRISPR-Cas a laboratory manual. Cold Spring Harb Protoc. (7):pdb.top090902. doi: 10.1101/pdb.top090902

103. Briner AE, Henriksen ED, Barrangou R. (2016) Prediction and validation of native and engineered Cas9 guide sequences. CRISPR-Cas a laboratory manual. Cold Spring Harb Protoc. (7):pdb.prot086785. doi: 10.1101/pdb.prot086785

102. Brandt K, Barrangou R. (2016) Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences. Front Microbiol. 7:657. doi: 10.3389/fmicb.2016.00657.

101. Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL. (2016) Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems. Mol Cell. 62:137-47. doi: 10.1016/j.molcel.2016.02.031

100. Briner AE, Barrangou R. (2016) Deciphering and shaping bacterial diversity through CRISPR. Current Op Microbiol. 31:101-108. doi: 10.1016/j.mib.2016.03.006

99. Hymes J, Johnson B, Barrangou R, Klaenhammer TR. (2016) Functional analysis of an S-layer associated fibronectin binding protein in Lactobacillus acidophilus. App Environ Microbiol pii: AEM.00024-16

98. Barrangou R, Dudley EG. (2016) CRISPR-based typing and next-generation tracking technologies. Ann Rev Food Sci Technol 7:395-411. doi: 10.1146/annurev-food-022814-015729

97. Barrangou R, van Pijkeren JP. (2015) Exploiting CRISPR-Cas immune systems for genome editing in bacteria. Curr Op Biotechnol 37:61-68. doi: 10.1016/j.copbio.2015.10.003

96. Barrangou R. (2015) Diversity of CRISPR-Cas immune systems and molecular machines. Genome Biol 16:247. doi: 10.1186/s13059-015-0816-9

95. Johnson BR, Hymes J, Sanozky-Dawes R, Henriksen ED, Barrangou R, Klaenhammer TR. (2015) Exoproteome analysis of S-layer forming lactobacilli reveals conserved S-layer associated proteins (SLAPs). App Environ Microbiol 82:134-45. doi: 10.1128/AEM.01968-15

94. Selle KM, Barrangou R. (2015) CRISPR-based technologies and the future of food science. J Food Sci 80:R2367-72. doi: 10.1111/1750-3841.13094

93. Sun Z, Harris HMB, McCann A, Yang X, Argimon S, Zhang W, Guo C, Jeffery IB, Cooney JC, Kagawa TF, Liu W, Song Y, Salvetti E, Wrobel A, Rasinkangas P, Parkhill J, Rea MC, O’Sullivan O, Ritari J, Douillard FP, Ross RP, Yang R, Briner AE, Felis G, de Vos WM, Barrangou R, Klaenhammer TR, Caufield PW, Cui Y, Zhang H, O’Toole PW. (2015) Expanding the biotechnology potential of lactobacilli through comparative genomics. Nature Comm 6:8322. doi: 10.1038/ncomms9322.

92. Makarova KS, Wolf YI, Alkhnbashi O, Costa F, Shah S, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJM, Terns RM, Terns MA, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. (2015) An updated evolutionary classification scheme for CRISPR-Cas systems. Nature Rev Microbiol 13:722-36. doi:10.1038/nrmicro3569

91. Sun CL, Thomas BC, Barrangou R, Banfield JF. (2015) Metagenomic reconstructions of bacterial CRISPR loci constrain population histories. ISME J 10:858–870. doi: 10.1038/ismej.2015.162

90. Sanozky-Dawes R, Selle K, O’Flaherty SO, Klaenhammer TR, Barrangou R. (2015) Occurrence and activity of a type II CRISPR-Cas system in Lactobacillus gasseri. Microbiology. 161:1752-61 doi: 10.1099/mic.0.000129

89. Briner AE, Lugli GA, Milani C, Duranti S, Turroni F, Gueimonde M, Margolles A, van Sinderen D, Ventura M, Barrangou R (2015) Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium. PLoS One 10:e0133661

88. Sontheimer EJ, Barrangou R (2015) The Bacterial Origins of the CRISPR Genome-Editing Revolution. Hum Gene Ther 26:413-24

87. Selle K, Klaenhammer TR, Barrangou R (2015) CRISPR-based screening of genomic island excision events in bacteria. Proc Natl Acad Sci USA 112:8076-81

86. Dupuis MÈ, Barrangou R, Moineau S (2015) Procedures for Generating CRISPR Mutants with Novel Spacers Acquired from Viruses or Plasmids. Methods Mol Biol. 1311:195-222

85. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF (2015) CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. MBio. 6:e00262-15

84. Kyung KH, Medina Pradas E, Kim SG, Lee YJ, Kim KH, Choi JJ, Cho JH, Chung CH, Barrangou R, Breidt F (2015) Microbial ecology of watery kimchi. J Food Sci. 80:M1031-8

83. Barrangou R, Birmingham A, Wiemann S, Beijersbergen RL, Hornung V, Smith A (2015) Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference. Nucleic Acids Res. 43:3407-19

82. Selle K, Barrangou R (2015) Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol. 23:225-32

81. Barrangou R (2015) The roles of CRISPR-Cas systems in adaptive immunity and beyond. Curr Opin Immunol. 32:36-41

80. Barrangou R, van der Oost J. (2015) Bacteriophage exclusion, a new defense system. EMBO J. 34:134-135

79. Barrangou R, May AP (2015) Unraveling the potential of CRISPR-Cas9 for gene therapy. Expert Opin Biol Ther 15:311-4

78. Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley E. (2015) Characterization and Evolution of Salmonella CRISPR-Cas Systems. Microbiology 161:374-386.

77. Barrangou R, Horvath P. (2014) Functions and applications of RNA-guided CRISPR-Cas immune systems. Enc Mol Cell Biol Mol Med DOI: 10.1002/3527600906.mcb.20130001

76. Beisel CL, Gomaa AA, Barrangou R. (2014) A CRISPR design for next-generation antimicrobials. Genome Biol 15:516

75. Briner AE, Donohoue PD, Gomaa AA, Selle K, Slorach EM, Nye CH, Haurwitz RE, Beisel CL, May AP, Barrangou R. (2014) Guide RNA functional modules direct Cas9 activity and orthogonality. Mol Cell 56:333-9

74. Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, Sanchez B, Viappiani A, Mancabelli L, Taminiau B, Delcenserie V, Barrangou R, Margolles A, van Sinderen D, Ventura M. (2014) Genomic encyclopedia of type strains of the genus Bifidobacterium. Appl Environ Microbiol 80:6290-302

73. Wehnes CA, Rehberger TG, Barrangou R, Smith AH. (2014) Determination of Salmonella clustered regularly interspaced short palindromic repeats (CRISPR) diversity on dairy farms in Wisconsin and Minnesota. J Dairy Sci 97:6370-7

72. Barrangou R, Klaenhammer TR. (2014) Bacteria get vaccinated. Nature 513:175-6

71. Barrangou R. (2014) Cas9 targeting and the CRISPR revolution. Science 344:707-8

70. Carte J, Christopher RT, Smith JT, Olson S, Barrangou R, Moineau S, Glover CV 3rd, Graveley BR, Terns RM, Terns MP. (2014) The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. Mol Microbiol 93:98-112

69. Barrangou R, Marraffini LA. (2014) CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell 54:234-44

68. Pettengill JB, Timme RE, Barrangou R, Toro M, Allard MW, Strain E, Musser SM, Brown EW. (2014) The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica. PeerJ 2:e340

67. Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL. (2014) Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. MBio 5:e00928-13

66. Toro M, Cao G, Ju W, Allard M, Barrangou R, Zhao S, Brown E, Meng J. (2014) Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli. Appl Environ Microbiol 80:1411-20

65. Briner AE, Barrangou R. (2014) Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity. Appl Environ Microbiol. 80:994-1001

64. Abou Hachem M, Møller MS, Andersen JM, Fredslund A, Majumder A, Nakai H, Lo Leggio L, Goh YJ, Barrangou R, Klaenhammer TR, Svensson B. (2013) A snapshot into the metabolism of isomalto-oligosaccharides in probiotic bacteria. J Appl Glycosci 60:95-100

63. Abou Hachem M, Andersen JM, Barrangou R, Møller MS, Fredslund F, Majumder A, Ejby M, Lahtinen SJ, Jacobsen S, Lo Leggio L, Goh YJ, Klaenhammer TR, Svensson B. (2013) Recent insight into oligosaccharide uptake and metabolism in probiotic bacteria. Biocat Biotransform 31:226-235

62. Barrangou R, Coûté-Monvoisin AC, Stahl B, Chavichvily I, Damange F, Romero DA, Boyaval P, Fremaux C, Horvath P. (2013) Genomic impact of CRISPR immunization against bacteriophages. Biochem Soc Trans 41:1383-91.

61. Shariat N, Sandt CH, DiMarzio MJ, Barrangou R, Dudley E.G. (2013) CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates. BMC Microbiol 13:254.

60. Timme RE, Pettengill JB, Allard MW, Strain E, Barrangou R, Wehnes C, Van Kessel JS, Karns JS, Musser SM, Brown EW. (2013) Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters. Genome Biol Evol 5:2109-23.

59. Loquasto JR, Barrangou R, Dudley EG, Stahl B, Chen C, Roberts RF. (2013) Bifidobacterium animalis subsp. lactis ATCC 27673 is a genomically unique strain within this conserved subspecies. Appl Environ Microbiol 79:6903-10

58. Yin S, Jensen MA, Bai J, Debroy C, Barrangou R, Dudley EG. (2013) The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition. Appl Environ Microbiol 79:5710-20

57. Dimarzio M, Shariat N, Kariyawasam S, Barrangou R, Dudley EG. (2013) Antibiotic Resistance in Salmonella enterica Serovar Typhimurium Associates with CRISPR Sequence Type. Antimicrob Agents Chemother 9:4282-9

56. Shariat N, Kirchner MK, Sandt CH, Trees E, Barrangou R, Dudley EG. (2013) Subtyping of Salmonella enterica serovar Newport outbreak isolates by CRISPR-MVLST and determination of the relationship between CRISPR-MVLST and PFGE results. J Clin Microbiol 51:2328-36

55. Stahl B, Barrangou R. (2013) Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14. Genome Announc 1:e00376-13

54. Andersen JM, Barrangou R, Abou Hachem M, Lahtinen SJ, Goh YJ, Svensson B, Klaenhammer TR. (2013) Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04. BMC Genomics 14:312

53. Karvelis T, Gasiunas G, Miksys A, Barrangou R, Horvath P, Siksnys V. (2013) crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol 10:841-51

52. Horvath P, Barrangou R. (2013) RNA-guided genome editing à la carte. Cell Res 23:733-4.

51. Barrangou R. (2013) CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 4:267-78

50. Shariat N, DiMarzio MJ, Yin S, Dettinger L, Sandt CH, Lute JR, Barrangou R, Dudley EG. (2013) The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis. Food Microbiol 34:164-73

49. Levin BR, Moineau S, Bushman M, Barrangou R (2013) The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR-Mediated Immunity. PLoS Genet 9:e1003312

48. Paez-Espino D, Morovic W, Sun CL, Thomas BC, Ueda K, Stahl B, Barrangou R, Banfield JF. (2013) Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun 4:1430

47. Sinkunas T, Gasiunas G, Waghmare SP, Dickman MJ, Barrangou R, Horvath P, Siksnys V. (2013) In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. EMBO J 32:385-94

46. Sun CL, Barrangou R, Thomas BC, Horvath P, Fremaux C, Banfield JF. (2013) Phage mutations in response to CRISPR diversification in a bacterial population. Env Microbiol 15:463-70

45. Gasiunas G, Barrangou R, Horvath P, Siksnys V. (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA 109:E2579-86

44. Barrangou R, Horvath P. (2012) CRISPR: New Horizons in Phage Resistance and Strain Identification. Annu Rev Food Sci Technol 3:143-62

43. Weinberger AD, Sun CL, Pluciński MM, Denef VJ, Thomas BC, Horvath P, Barrangou R, Gilmore MS, Getz WM, Banfield JF. (2012) Persisting Viral Sequences Shape Microbial CRISPR-based Immunity. PLoS Comput Biol 8:e1002475.

42. Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, Verberkmoes NC. (2012) Phage-Induced Expression of CRISPR-Associated Proteins Is Revealed by Shotgun Proteomics in Streptococcus thermophilus. PLoS One 7:e38077

41. Barrangou R. (2012) RNA-mediated programmable DNA cleavage. Nat Biotechnol 30:836-8.

40. Stahl B, Barrangou R. (2012) Complete genome sequences of probiotic strains Bifidobacterium animalis subsp. lactis B420 and Bi-07. J Bacteriol 194:4131-2

39. Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL. (2012) Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 5:533.

38. Andersen JM, Barrangou R, Hachem MA, Lahtinen SJ, Goh YJ, Svensson B, Klaenhammer TR. (2012) Transcriptional analysis of prebiotic uptake and catabolism by Lactobacillus acidophilus NCFM. PLoS One 7:e44409.

37. Abou Hachem M, Fredslund F, Andersen JM, Jonsgaard Larsen R, Majumder A, Ejby M, Van Zanten G, Lahtinen SJ, Barrangou R, Klaenhammer TR, Jacobsen S, Coutinho PM, Lo Leggio L, Svensson B. (2012) Raffinose family oligosaccharide utilisation by probiotic bacteria: insight into substrate recognition, molecular architecture and diversity of GH36 alpha-galactosidases. Biocat Biotransform 30: 316-325

36. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV. (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467-77.

35. Bhaya D, Davison M, Barrangou R. (2011) CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45:273-97.

34. Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39:9275-82

33. Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. (2011) Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J 30:1335-42

32. Liu F, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG. (2011) Novel virulence gene and clustered regularly interspaced short palindromic repeat (CRISPR) multilocus sequence typing scheme for subtyping of the major serovars of Salmonella enterica subsp. enterica. Appl Environ Microbiol 77:1946-56

31. Liu F, Kariyawasam S, Jayarao BM, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG. (2011) Subtyping Salmonella serovar Enteritidis isolates from different sources using sequence typing based on virulence genes and CRISPRs. Appl Environ Microbiol 77:4520-6

30. Duong T, Miller MJ, Barrangou R, Azcarate-Peril MA, Klaenhammer TR. (2011) Construction of vectors for inducible and constitutive gene expression in Lactobacillus. Microb Biotechnol 4:357-67

29. Andersen JM, Barrangou R, Abou Hachem M, Lahtinen S, Goh YJ, Svensson B, Klaenhammer TR. (2011) Transcriptional and functional analysis of galactooligosaccharide uptake by lacS in Lactobacillus acidophilus. Proc Natl Acad Sci USA 108:17785-90

28. Loquasto JR, Barrangou R, Dudley EG, Roberts RF. (2011) The complete genome sequence of Bifidobacterium animalis subspecies animalis ATCC 25527(T) and comparative analysis of growth in milk with B. animalis subspecies lactis DSM 10140(T). J Dairy Sci 94:5864-70.

27. Horvath P, Barrangou R. (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167-170

26. Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S. (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67-71

25. Putaala H, Barrangou R, Leyer GJ, Ouwehand AC, Hansen EB, Romero DA, Rautonen N. (2010) Analysis of the human intestinal epithelial cell transcriptional response to Lactobacillus acidophilus, Lactobacillus salivarius, Bifidobacterium lactis and Escherichia coli. Beneficial Microbes 1:283-295

24. Horvath P, Coûté-Monvoisin AC, Romero DA, Boyaval P, Fremaux C, Barrangou R. (2009) Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int J Food Microbiol 131:62-70

23. Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, Coûté-Monvoisin AC, Leyer G, Rendulic S, Steele JL, Broadbent JR, Oberg T, Dudley EG, Schuster S, Romero DA, Roberts RF. (2009) Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol 191:4144-4151

22. Briczinski EP, Loquasto JR, Barrangou R, Dudley EG, Roberts AM, Roberts RF. (2009) Strain-specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions. Appl Environ Microbiol 75:7501-7508

21. Ventura M, Turroni F, Lima-Mendez G, Foroni E, Zomer A, Duranti S, Giubellini V, Bottacini F, Horvath P, Barrangou R, Sela DA, Mills DA, van Sinderen D. (2009) Comparative analyses of prophage-like elements present in bifidobacterial genomes. Appl Environ Microbiol 75:6929-6936

20. Barrangou R, Horvath P. (2009) The CRISPR system protects microbes against phages, plasmids. Microbe 4:224-230

19. Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, Romero DA, Horvath P, Moineau S. (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190:1390-1400

18. Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R. (2008) Diversity, activity and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190:1401-1412

17. Azcarate-Peril MA, Altermann E, Goh YJ, Tallon R, Sanozky-Dawes RB, Pfeiler EA, O’Flaherty S, Buck BL, Dobson A, Duong T, Miller MJ, Barrangou R, Klaenhammer TR. (2008) Analysis of the genome sequence of Lactobacillus gasseri ATCC33323 reveals the molecular basis of an autochthonous intestinal organism. App Environ Microbiol 74:4610-4625

16. Klaenhammer TR, Altermann E, Pfeiler E, Buck BL, Goh YJ, O’Flaherty S, Barrangou R, Duong T. (2008) Functional genomics of probiotic lactobacilli. J Clin Gastroenterol 42:S160-162.

15. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-12

14. Klaenhammer TR, Azcarate-Peril MA, Altermann E, Barrangou R. (2007) Influence of the dairy environment on gene expression and substrate utilization in lactic acid bacteria. J Nutr 137:748S-50S

13. Yoon SS, Barrangou R, Breidt Jr F, Fleming HP. (2007) Detection and characterization of a lytic Pediococcus bacteriophage from fermenting cucumber brine. J Microbiol Biotechnol 17:262-270

12. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O’Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer TR, Richardson P, Kozyavkin S, Weimer B, Mills D. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103:15611-15616

11. Barrangou R, Azcarate-Peril MA, Duong T, Conners SB, Kelly RM, Klaenhammer TR. (2006) Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proc Natl Acad Sci USA 103:3816-3821

10. Ventura M, Canchaya C, Bernini V, Altermann E, Barrangou R, McGrath S, Claesson MJ, Li Y, Leahy S, Walker CD, Zink R, Neviani E, Steele J, Broadbent J, Klaenhammer TR, Fitzgerald GF, O’toole PW, van Sinderen D. (2006) Compartive genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius and Lactobacillus casei. Appl Environ Microbiol 72:3130-3146

9. Duong T, Barrangou R, Russell WM, Klaenhammer TR. (2006) Characterization of the tre locus and analysis of trehalose cryoprotection in Lactobacillus acidophilus NCFM. Appl Environ Microbiol 72:1218-1225

8. Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M, Lick S, Hamrick A, Cano R, Klaenhammer TR. (2005) Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA 102:3887-4216

7. Klaenhammer TR, Barrangou R, Buck BL, Azcarate-Peril MA, Altermann E. (2005) Genomic features of lactic acid bacteria effecting bioprocessing and health. FEMS Microbiol Rev 29:393-409

6. Klaenhammer TR, Azcarate-Peril MA, Barrangou R, Duong T, Altermann E. (2005) Genomic perspectives on probiotic lactic acid bacteria. Biosc Microflora 24:31-33

5. Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, Barrangou R, Mollet B, Mercenier A, Klaenhammer TR, Arigoni F, Schell MA. (2004) The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC533. Proc Natl Acad Sci USA 101:2512-2517

4. Barrangou R, Altermann E, Hutkins R, Cano R, Klaenhammer TR. (2003) Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus. Proc Natl Acad Sci USA 100:8957-8962

3. Barrangou R, Yoon SS, Breidt Jr F Jr, Fleming HP, Klaenhammer TR. (2002) Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation. Appl Environ Microbiol 68:5452-5458

2. Barrangou R, Yoon SS, Breidt F Jr, Fleming HP, Klaenhammer TR. (2002) Identification and characterization of Leuconostoc fallax strains isolated from an industrial sauerkraut fermentation. Appl Environ Microbiol 2877-2884

1. Yoon SS, Barrangou R, Breidt Jr F, Klaenhammer TR, Fleming HP. (2002) Isolation and characterization of bacteriophages from fermenting sauerkraut. Appl Environ Microbiol 68:973-976

Books and Book Chapters

7. Briner AE, Barrangou R. (2016) Guide RNAs: A Glimpse at the Sequences that Drive CRISPR–Cas Systems. CRISPR-Cas a laboratory manual. CSHL Protocols. 17-23

6. Briner AE, Henriksen ED, Barrangou R. (2016) Prediction and validation of native and engineered Cas9 guide sequences. CRISPR-Cas a laboratory manual. CSHL Protocols. 24-30

5. Barrangou R, van der Oost J. eds. (2012) CRISPR-Cas systems: RNA-mediated adaptive immunity in bacteria and archaea. Springer Science & Business Media

4. Horvath P, Gasiunas G, Siksnys V, Barrangou R. (2012) Applications of the versatile CRISPR-Cas systems. CRISPR-Cas systems: RNA-mediated adaptive immunity in bacteria and archaea. Springer Science & Business Media 267-286

3. Barrangou R, Lahtinen SJ, Ibrahim F, Ouwehand AC. (2012) Genus lactobacillus. Lactic acid bacteria. Microbiological and functional aspects, 73

2. Barrangou R, Horvath P. (2011) Lactic Acid Bacteria Defenses Against Phages. Stress Responses of Lactic Acid Bacteria. Springer US, 459-478

1. Barrangou R, Horvath P. (2010) Protection against foreign DNA. Bacterial stress responses. American Society for Microbiology Press, 333-348