Browse by Journal

Belokopytova, Polina and Viesná, Emil and Chiliński, Mateusz and Qi, Yifeng and Salari, Hossein and Di Stefano, Marco and Esposito, Andrea and Conte, Mattia and Chiariello, Andrea M and Teif, Vladimir B and Plewczynski, Dariusz and Zhang, Bin and Jost, Daniel and Fishman, Veniamin (2022) 3DGenBench: a web-server to benchmark computational models for 3D Genomics. Nucleic Acids Research, 50 (W1). W4-W12. DOI https://doi.org/10.1093/nar/gkac396

Clarkson, Christopher T and Deeks, Emma A and Samarista, Ralph and Mamayusupova, Hulkar and Zhurkin, Victor B and Teif, Vladimir B (2019) CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Research, 47 (21). pp. 11181-11196. DOI https://doi.org/10.1093/nar/gkz908

Catoni, M and Tsang, JMF and Greco, AP and Zabet, NR (2018) DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Research, 46 (19). e114-. DOI https://doi.org/10.1093/nar/gky602

Zabet, Nicolae Radu and Catoni, Marco and Prischi, Filippo and Paszkowski, Jerzy (2017) Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Research, 45 (7). gkw1330-gkw1330. DOI https://doi.org/10.1093/nar/gkw1330

Zabet, Nicolae Radu and Adryan, Boris (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Research, 43 (1). pp. 84-94. DOI https://doi.org/10.1093/nar/gku1269

Pradeepa, Madapura M and Grimes, Graeme R and Taylor, Gillian CA and Sutherland, Heidi G and Bickmore, Wendy A (2014) Psip1/Ledgf p75 restrains<i>Hox</i>gene expression by recruiting both trithorax and polycomb group proteins. Nucleic Acids Research, 42 (14). pp. 9021-9032. DOI https://doi.org/10.1093/nar/gku647

Ezer, Daphne and Zabet, Nicolae Radu and Adryan, Boris (2014) Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Research, 42 (7). pp. 4196-4207. DOI https://doi.org/10.1093/nar/gku078

Chen, Dijun and Fu, Liang-Yu and Zhang, Zhao and Li, Guoliang and Zhang, Hang and Jiang, Li and Harrison, Andrew P and Shanahan, Hugh P and Klukas, Christian and Zhang, Hong-Yu and Ruan, Yijun and Chen, Ling-Ling and Chen, Ming (2014) Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Research, 42 (5). pp. 3028-3043. DOI https://doi.org/10.1093/nar/gkt1294

Tan, BG and Vijgenboom, E and Worrall, JAR (2014) Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans. Nucleic Acids Research, 42 (2). pp. 1326-1340. DOI https://doi.org/10.1093/nar/gkt902

Marco, Antonio and Ninova, Maria and Ronshaugen, Matthew and Griffiths-Jones, Sam (2013) Clusters of microRNAs emerge by new hairpins in existing transcripts. Nucleic Acids Research, 41 (16). pp. 7745-7752. DOI https://doi.org/10.1093/nar/gkt534

Hughes, Craig D and Wang, Hong and Ghodke, Harshad and Simons, Michelle and Towheed, Atif and Peng, Ye and Van Houten, Bennett and Kad, Neil M (2013) Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes. Nucleic Acids Research, 41 (9). pp. 4901-4912. DOI https://doi.org/10.1093/nar/gkt177

Harrison, A and Binder, H and Buhot, A and Burden, CJ and Carlon, E and Gibas, C and Gamble, LJ and Halperin, A and Hooyberghs, J and Kreil, DP and Levicky, R and Noble, PA and Ott, A and Pettitt, BM and Tautz, D and Pozhitkov, AE (2013) Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research, 41 (5). pp. 2779-2796. DOI https://doi.org/10.1093/nar/gks1358

Hui, Jerome HL and Marco, Antonio and Hunt, Suzanne and Melling, Janet and Griffiths-Jones, Sam and Ronshaugen, Matthew (2013) Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods. Nucleic Acids Research, 41 (5). pp. 3352-3361. DOI https://doi.org/10.1093/nar/gks1445

Upton, Graham JG and Harrison, Andrew P (2012) Motif effects in Affymetrix GeneChips seriously affect probe intensities. Nucleic Acids Research, 40 (19). pp. 9705-9716. DOI https://doi.org/10.1093/nar/gks717

Shanahan, Hugh P and Memon, Farhat N and Upton, Graham JG and Harrison, Andrew P (2012) Normalized Affymetrix expression data are biased by G-quadruplex formation. Nucleic Acids Research, 40 (8). pp. 3307-3315. DOI https://doi.org/10.1093/nar/gkr1230

Dunn, Andrew R and Kad, Neil M and Nelson, Shane R and Warshaw, David M and Wallace, Susan S (2011) Single Qdot-labeled glycosylase molecules use a wedge amino acid to probe for lesions while scanning along DNA. Nucleic Acids Research, 39 (17). pp. 7487-7498. DOI https://doi.org/10.1093/nar/gkr459

Simpson, CL and Knight, J and Butcher, LM and Hansen, VK and Meaburn, EL and Schalkwyk, LC and Craig, IW and Powell, JF and Sham, PC and Al-Chalabi, A (2005) A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Research, 33 (3). e25-e25. DOI https://doi.org/10.1093/nar/gni028

Priestley, A (1998) Molecular and biochemical characterisation of DNA-dependent protein kinase-defective rodent mutant irs-20. Nucleic Acids Research, 26 (8). pp. 1965-1973. DOI https://doi.org/10.1093/nar/26.8.1965

Hofman, Jason D and Schalkwyk, Leonard C and Doolittle, W Ford (1986) ISH51: a large, degenerate family of insertion sequence-like elements in the genome of the archaehacterium,<i>Halobacterium volcanii</i>. Nucleic Acids Research, 14 (17). pp. 6983-7000. DOI https://doi.org/10.1093/nar/14.17.6983