Negro G, Semeraro M, Cook P, Marenduzzo D
iScience. 2024; 27(12):111218.
PMID: 39618494
PMC: 11607604.
DOI: 10.1016/j.isci.2024.111218.
Kalsan M, Jabeen A, Ahmad S
Methods Mol Biol. 2024; 2812:317-343.
PMID: 39068371
DOI: 10.1007/978-1-0716-3886-6_18.
van der Valk R, van Erp B, Qin L, Moolenaar G, Dame R
Methods Mol Biol. 2024; 2819:443-454.
PMID: 39028518
DOI: 10.1007/978-1-0716-3930-6_20.
Sun Y, Xu X, Lin L, Xu K, Zheng Y, Ren C
Genome Biol. 2023; 24(1):90.
PMID: 37095580
PMC: 10124043.
DOI: 10.1186/s13059-023-02916-x.
Fitzgerald D, Stringer A, Smith C, Lapierre P, Wade J
mBio. 2023; 14(3):e0253522.
PMID: 37067422
PMC: 10294691.
DOI: 10.1128/mbio.02535-22.
FadB is a dehydrogenase that mediates cholate resistance and survival under human colonic conditions.
Alsultan A, Walton G, Andrews S, Clarke S
Microbiology (Reading). 2023; 169(3).
PMID: 36947574
PMC: 10191381.
DOI: 10.1099/mic.0.001314.
Genome-wide mapping of the PhoB regulon reveals many transcriptionally inert, intragenic binding sites.
Fitzgerald D, Stringer A, Smith C, Lapierre P, Wade J
bioRxiv. 2023; .
PMID: 36798257
PMC: 9934606.
DOI: 10.1101/2023.02.07.527549.
Histone-like nucleoid structuring (H-NS) protein silences the beta-glucoside () utilization operon in by forming a DNA loop.
Lam K, Zhang Z, Saier M
Comput Struct Biotechnol J. 2022; 20:6287-6301.
PMID: 36420159
PMC: 9678765.
DOI: 10.1016/j.csbj.2022.11.027.
Developmental timing of programmed DNA elimination in recapitulates germline transposon evolutionary dynamics.
Zangarelli C, Arnaiz O, Bourge M, Gorrichon K, Jaszczyszyn Y, Mathy N
Genome Res. 2022; 32(11-12):2028-2042.
PMID: 36418061
PMC: 9808624.
DOI: 10.1101/gr.277027.122.
Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.
Starr C, Bryant Z, Spakowitz A
Biophys J. 2022; 121(10):1949-1962.
PMID: 35421389
PMC: 9199097.
DOI: 10.1016/j.bpj.2022.04.009.
The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis.
Rekvig O
Front Immunol. 2022; 12:808008.
PMID: 35087528
PMC: 8786728.
DOI: 10.3389/fimmu.2021.808008.
Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.
Qian J, Xu W, Dunlap D, Finzi L
Transcription. 2021; 12(4):219-231.
PMID: 34719335
PMC: 8632135.
DOI: 10.1080/21541264.2021.1997315.
Distribution and phasing of sequence motifs that facilitate CRISPR adaptation.
Santiago-Frangos A, Buyukyoruk M, Wiegand T, Krishna P, Wiedenheft B
Curr Biol. 2021; 31(16):3515-3524.e6.
PMID: 34174210
PMC: 8552246.
DOI: 10.1016/j.cub.2021.05.068.
Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.
Chen Y, Yang H, Chu J
Chem Sci. 2021; 11(19):4969-4979.
PMID: 34122953
PMC: 8159235.
DOI: 10.1039/d0sc00480d.
Anticipating response function in gene regulatory networks.
Gautam P, Sinha S
J R Soc Interface. 2021; 18(179):20210206.
PMID: 34062105
PMC: 8169214.
DOI: 10.1098/rsif.2021.0206.
DNA looping by protamine follows a nonuniform spatial distribution.
McMillan R, Kuntz V, Devenica L, Bediako H, Carter A
Biophys J. 2021; 120(12):2521-2531.
PMID: 34023297
PMC: 8390855.
DOI: 10.1016/j.bpj.2021.04.022.
Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles.
Clauvelin N, Olson W
J Phys Chem B. 2021; 125(9):2277-2287.
PMID: 33635080
PMC: 9434916.
DOI: 10.1021/acs.jpcb.0c11612.
The loopometer: a quantitative in vivo assay for DNA-looping proteins.
Hao N, Sullivan A, Shearwin K, Dodd I
Nucleic Acids Res. 2021; 49(7):e39.
PMID: 33511418
PMC: 8053113.
DOI: 10.1093/nar/gkaa1284.
Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins.
Becker N, Peters J, Schwab T, Phillips W, Wallace J, Clark K
Biophys J. 2020; 119(10):2045-2054.
PMID: 33091377
PMC: 7732741.
DOI: 10.1016/j.bpj.2020.10.007.
Expanding the toolbox for sp. PCC 6803: validation of replicative vectors and characterization of a novel set of promoters.
Ferreira E, Pacheco C, Pinto F, Pereira J, Lamosa P, Oliveira P
Synth Biol (Oxf). 2020; 3(1):ysy014.
PMID: 32995522
PMC: 7445879.
DOI: 10.1093/synbio/ysy014.