Publications


Publications

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 In press. 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 U S A 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 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 U S A 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

 

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