Microbiome Editing Technologies
Genome-wide characterization of diverse bacteriophages enabled by RNA-binding CRISPRi
Adler BA*, Al-Shimary MJ*, Patel JR, Ambruster EG, Colognori D, Charles EJ, Miller KV, Lahiri A, Trinidad M, Boger R, Nomburg J, Beurnier S, Cui ML, Barrangou R, Mutalik VK, Schoeniger JS, Pogliano JA, Savage DF, Doudna JAǂ, Cress BFǂ
bioRxiv (2023)
Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection
Armbruster EG, Lee J, Hutchings J, VanderWal A, Enustun E, Adler BA, Aindow A, Deep A, Rodriguez Z, Morgan C, Ghassemian M, Charles EJ, Cress BF, Savage DF, Doudna JA, Pogliano K, Corbett KD, Villa E, Pogliano JA
bioRxiv (2023)
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection
Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Gu Y, Deep A, Naritomi JT, Liang Q, Aigner S, Adler BA, Cress BF, Doudna JA, Chaikeeratisak V, Cleveland DW, Ghassemian M, Yeo GW, Pogliano JA, Corbett KD
bioRxiv (2023)
Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages λ and P1
Piya D, Nolan N, Moore ML, Ramirez Hernandez LA, Cress BF, Young R, Arkin AP, & Mutalik VK
bioRxiv (2023)
Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors
Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, & Doudna JA
Cell 185, 4574–4586.e16 (2022)
Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing
Adler BA, Hessler T, Cress BF, Lahiri A, Mutalik VK, Barrangou R, Banfield JF, & Doudna JA
Nat Microbiol 7, 1967–1979 (2022)
Otoupal PB, Cress BF, Doudna JA, & Schoeniger JS
Nucleic Acids Res 50, 8986–8998 (2022).
Species- and site-specific genome editing in complex bacterial communities
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, Deutschbauer AM, Banfield JF, & Doudna JA
Nat Microbiol 7, 34–47 (2022)
A CRISPR-Cas9–integrase complex generates precise DNA fragments for genome integration
Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, & Doudna JA
Nucleic Acids Res 49, 3546–3556 (2021)
Controlling and enhancing CRISPR systems
Shivram H, Cress BF, Knott GJ, & Doudna JA
Nat Chem Biol 17, 10–19 (2021)
CRISPR-CasΦ from huge phages is a hypercompact genome editor
Pausch P, Al-Shayeb B, Bisom-Rapp E, Tsuchida CA, Li Z, Cress BF, Knott GJ, Jacobsen SE, Banfield JF, & Doudna JA
Science 369, 333–337 (2020)
Mikael PE, Udangawa R, Sorci M, Cress BF, Shtein Z, Belfort G, Shoseyov O, Dordick JS, & Linhardt RJ
Regenerative Engineering and Translational Medicine 5, 362–372 (2019)
Design and Characterization of Biosensors for the Screening of Modular Assembled Naringenin Biosynthetic Library in Saccharomyces cerevisiae
Wang R, Cress BF, Yang Z, Hordines JC, 3rd, Zhao S, Jung GY, Wang Z, & Koffas MAG
ACS Synth Biol 8, 2121–2130 (2019)
Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a
Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, & Doudna JA
Elife 8, (2019)
Heavy heparin: a stable isotope‐enriched, chemoenzymatically‐synthesized, poly‐component drug
Cress BF*, Bhaskar U*, Vaidyanathan D, Williams A, Cai C, Liu X, Fu L, M-Chari V, Zhang F, Mousa SA, Dordick JS, Koffas MAG, & Linhardt RJ
Angew Chem 131, 6023–6027 (2019)
Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli
Tokuyama K, Toya Y, Matsuda F, Cress BF, Koffas MAG, & Shimizu H
Metab Eng 52, 215–223 (2019)
Sarnaik A, Abernathy MH, Han X, Ouyang Y, Xia K, Chen Y, Cress BF, Zhang F, Lali A, Pandit R, Linhardt RJ, Tang YJ, & Koffas MAG
Algal Research 37, 57–63 (2019)
RNA aptamers with specificity for heparosan and chondroitin glycosaminoglycans
Kizer M, Li P, Cress BF, Lin L, Jing TT, Zhang X, Xia K, Linhardt RJ, & Wang X
ACS Omega 3, 13667–13675 (2018)
CRISPRi-mediated metabolic engineering of E. coli for O-methylated anthocyanin production
Cress BF, Leitz QD, Kim DC, Amore TD, Suzuki JY, Linhardt RJ, & Koffas MAG
Microb Cell Fact 16, 10 (2017)
Williams A, He W, Cress BF, Liu X, Alexandria J, Yoshizawa H, Nishimura K, Toida T, Koffas M, & Linhardt RJ
Biotechnol J 12, (2017)
Complete Biosynthesis of Anthocyanins Using E. coli Polycultures
Jones JA, Vernacchio VR, Collins SM, Shirke AN, Xiu Y, Englaender JA, Cress BF, McCutcheon CC, Linhardt RJ, Gross RA, & Koffas MAG
MBio 8, (2017)
Ito T, Murai M, Ninokura S, Kitazumi Y, Mezic KG, Cress BF, Koffas MAG, Morgan JE, Barquera B, & Miyoshi H
J Biol Chem 292, 7727–7742 (2017)
Englaender JA, Jones JA, Cress BF, Kuhlman TE, Linhardt RJ, & Koffas MAG
ACS Synth Biol 6, 710–720 (2017)
Tailor-made exopolysaccharides—CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa
Rütering M, Cress BF, Schilling M, Rühmann B, Koffas MAG, Sieber V, & Schmid J
Synth Biol 2, ysx007 (2017)
Ibrahim MHA, Cress BF, Linhardt RJ, Koffas MAG, & Gross RA
Genome Announc 4, (2016)
Heparin's solution structure determined by small‐angle neutron scattering
Rubinson KA, Chen Y, Cress BF, Zhang F, & Linhardt RJ
Biopolymers 105, 905–913 (2016)
Synthesis and biological evaluation of 5, 7-dihydroxyflavanone derivatives as antimicrobial agents
Zhang X, Khalidi O, Kim SY, Wang R, Schultz V, Cress BF, Gross RA, Koffas MAG, & Linhardt RJ
Bioorg Med Chem Lett 26, 3089–3092 (2016)
Cress BF, Jones JA, Kim DC, Leitz QD, Englaender JA, Collins SM, Linhardt RJ, & Koffas MAG
Nucleic Acids Res 44, 4472–4485 (2016)
Sensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways
Cress BF, Trantas EA, Ververidis F, Linhardt RJ, & Koffas MAG
Curr Opin Biotechnol 36, 205–214 (2015)
Cress BF, Toparlak ÖD, Guleria S, Lebovich M, Stieglitz JT, Englaender JA, Jones JA, Linhardt RJ, & Koffas MAG
ACS Synth Biol 4, 987–1000 (2015)
Bhan N, Cress BF, Linhardt RJ, & Koffas MAG
Biochimie 115, 136–143 (2015)
ePathOptimize: a combinatorial approach for transcriptional balancing of metabolic pathways
Jones JA, Vernacchio VR, Lachance DM, Lebovich M, Fu L, Shirke AN, Schultz VL, Cress BF, Linhardt RJ, & Koffas MAG
Sci Rep 5, 11301 (2015)
Masquerading microbial pathogens: capsular polysaccharides mimic host-tissue molecules
Cress BF, Englaender JA, He W, Kasper D, Linhardt RJ, & Koffas MAG
FEMS Microbiol Rev 38, 660–697 (2014)
Using Recombinant Microorganisms for the Synthesis and Modification of Flavonoids and Stilbenes
Joo EJ, Cress BF, & Koffas MAG
Polyphenols in Human Health and Disease 483–488 (2014).
Draft genome sequence of Escherichia coli strain Nissle 1917 (serovar O6: K5: H1)
Cress BF, Linhardt RJ, & Koffas MAG
Genome Announc 1, e0004713 (2013)
Draft genome sequence of Escherichia coli strain ATCC 23502 (Serovar O5: K4: H4)
Cress BF, Greene ZR, Linhardt RJ, & Koffas MAG
Genome Announc 1, e0004613 (2013)
Draft genome sequence of Pseudoalteromonas luteoviolacea strain B (ATCC 29581)
Cress BF, Erkert KA, Barquera B, & Koffas MAG
Genome Announc 1, e0004813 (2013)
Draft Genome Sequence of Escherichia coli Strain ATCC 23506 (Serovar O10:K5:H4)
Cress BF, Greene ZR, Linhardt RJ, & Koffas MAG
Genome Announc 1, e0004913 (2013)
Isoflavonoid Production by Genetically Engineered Microorganisms
Cress BF, Linhardt RJ & Koffas MAG
Natural Products: Phytochemistry, Botany and Metabolism of Alkaloids, Phenolics and Terpenes 1647–1681 (2013)