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)

​

CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors 

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)

 

Production and characterization of recombinant collagen-binding resilin nanocomposite for regenerative medicine applications 

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)

 

Metabolic engineering of cyanobacteria for photoautotrophic production of heparosan, a pharmaceutical precursor of heparin 

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)

 

Cloning and Expression of Recombinant Chondroitinase ACII and Its Comparison to the Arthrobacter aurescens Enzyme 

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)

 

Identification of the binding sites for ubiquinone and inhibitors in the Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae by photoaffinity labeling 

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)

 

Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli 

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)

 

Draft genome sequence of Bacillus subtilis Ia1a, a new strain for poly-γ-glutamic acid and exopolysaccharide production 

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)

​

Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli 

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)

​

CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli 

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)

​

Expanding the chemical space of polyketides through structure-guided mutagenesis of Vitis vinifera stilbene synthase 

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)