Craig J. Benham - Related publications

Affiliations: 
Applied Mathematics University of California, Davis, Davis, CA 
Area:
Bioinformatics Biology, General Biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Dantas Machado AC, Cooper BH, Lei X, Di Felice R, Chen L, Rohs R. Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout. Nucleic Acids Research. PMID 32738045 DOI: 10.1093/nar/gkaa642   
2020 Delibaş E, Arslan A. DNA sequence similarity analysis using image texture analysis based on first-order statistics. Journal of Molecular Graphics & Modelling. 99: 107603. PMID 32442904 DOI: 10.1016/j.jmgm.2020.107603   
2020 Malig M, Chedin F. Characterization of R-Loop Structures Using Single-Molecule R-Loop Footprinting and Sequencing. Methods in Molecular Biology (Clifton, N.J.). 2161: 209-228. PMID 32681515 DOI: 10.1007/978-1-0716-0680-3_15   
2020 Chakraborty P. New insight into the biology of R-loops. Mutation Research. 821: 111711. PMID 32516653 DOI: 10.1016/j.mrfmmm.2020.111711   
2020 Kuzmenko A, Oguienko A, Esyunina D, Yudin D, Petrova M, Kudinova A, Maslova O, Ninova M, Ryazansky S, Leach D, Aravin AA, Kulbachinskiy A. DNA targeting and interference by a bacterial Argonaute nuclease. Nature. PMID 32731256 DOI: 10.1038/s41586-020-2605-1   
2020 Jang HK, Song B, Hwang GH, Bae S. Current trends in gene recovery mediated by the CRISPR-Cas system. Experimental & Molecular Medicine. PMID 32651459 DOI: 10.1038/s12276-020-0466-1   
2020 Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D. MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors. Bioinformatics (Oxford, England). 36: 3322-3326. PMID 32129840 DOI: 10.1093/bioinformatics/btaa140   
2020 Yu H, Li J, Liu G, Zhao G, Wang Y, Hu W, Deng Z, Wu G, Gan J, Zhao YL, He X. DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses. Nucleic Acids Research. PMID 32621606 DOI: 10.1093/nar/gkaa574   
2020 Völker J, Plum GE, Breslauer KJ. Heat Capacity Changes (ΔCp) for Interconversions Between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches. The Journal of Physical Chemistry. B. PMID 32531155 DOI: 10.1021/acs.jpcb.0c04065   
2020 Krieg E, Gupta K, Dahl A, Lesche M, Boye S, Lederer A, Shih WM. A smart polymer for sequence-selective binding, pulldown, and release of DNA targets. Communications Biology. 3: 369. PMID 32651444 DOI: 10.1038/s42003-020-1082-2   
2020 Fleming AM, Zhu J, Jara-Espejo M, Burrows CJ. Cruciform DNA Sequences in Gene Promoters Can Impact Transcription upon Oxidative Modification of 2'-Deoxyguanosine. Biochemistry. PMID 32567845 DOI: 10.1021/acs.biochem.0c00387   
2020 Ren H, Xi Y, Li Z, Zhang D, Huang F, Fang X, Zhao X, Zhang X, Chen A, Chen T, Yuan J. Novel target capture DNA library preparation method using CircLigase-mediated hook ligation. New Biotechnology. PMID 32688061 DOI: 10.1016/j.nbt.2020.06.007   
2020 Yang D, Liu W, Deng X, Xie W, Chen H, Zhong Z, Ma J. GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes. Biophysical Journal. PMID 32738216 DOI: 10.1016/j.bpj.2020.06.034   
2020 Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E, Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA. DNA capture by a CRISPR-Cas9-guided adenine base editor. Science (New York, N.Y.). 369: 566-571. PMID 32732424 DOI: 10.1126/science.abb1390   
2020 Chen H, Yang H, Zhu X, Yadav T, Ouyang J, Truesdell SS, Tan J, Wang Y, Duan M, Wei L, Zou L, Levine AS, Vasudevan S, Lan L. mC modification of mRNA serves a DNA damage code to promote homologous recombination. Nature Communications. 11: 2834. PMID 32503981 DOI: 10.1038/s41467-020-16722-7   
2020 Yellman CM. Precise Replacement of Proteasome Genes with Human Orthologs by an Integrative Targeting Method. G3 (Bethesda, Md.). PMID 32680853 DOI: 10.1534/g3.120.401526   
2020 Georgieva D, Liu Q, Wang K, Egli D. Detection of base analogs incorporated during DNA replication by nanopore sequencing. Nucleic Acids Research. PMID 32710620 DOI: 10.1093/nar/gkaa517   
2020 Zhang Z, Zhan Z, Wang B, Chen Y, Chen X, Wan C, Fu Y, Huang L. Archaeal Chromatin Proteins Cren7 and Sul7d Compact DNA by Bending and Bridging. Mbio. 11. PMID 32518188 DOI: 10.1128/mBio.00804-20   
2020 Cofsky JC, Karandur D, Huang CJ, Witte IP, Kuriyan J, Doudna JA. CRISPR-Cas12a exploits R-loop asymmetry to form double-strand breaks. Elife. 9. PMID 32519675 DOI: 10.7554/eLife.55143   
2020 Subramanian H, Gatenby RA. Evolutionary advantage of anti-parallel strand orientation of duplex DNA. Scientific Reports. 10: 9883. PMID 32555277 DOI: 10.1038/s41598-020-66705-3   
2020 Zhang J, Fan JS, Li S, Yang Y, Sun P, Zhu Q, Wang J, Jiang B, Yang D, Liu M. Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation. Nucleic Acids Research. PMID 32710623 DOI: 10.1093/nar/gkaa619   
2020 Lourenço RF, Saurabh S, Herrmann J, Wakatsuki S, Shapiro L. The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA. Mbio. 11. PMID 32518183 DOI: 10.1128/mBio.00448-20   
2020 Maezawa T, Ohtsuki S, Hidaka K, Sugiyama H, Endo M, Takahashi Y, Takakura Y, Nishikawa M. DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells. Nanoscale. 12: 14818-14824. PMID 32633313 DOI: 10.1039/d0nr02361b   
2020 Zabolotnaya E, Mela I, Williamson MJ, Bray SM, Yau SK, Papatziamou D, Edwardson JM, Robinson NP, Henderson RM. Modes of action of the archaeal Mre11/Rad50 DNA-repair complex revealed by fast-scan atomic force microscopy. Proceedings of the National Academy of Sciences of the United States of America. PMID 32541055 DOI: 10.1073/pnas.1915598117   
2020 Bao HL, Masuzawa T, Oyoshi T, Xu Y. Oligonucleotides DNA containing 8-trifluoromethyl-2'-deoxyguanosine for observing Z-DNA structure. Nucleic Acids Research. 48: 7041-7051. PMID 32678885 DOI: 10.1093/nar/gkaa505   
2020 Matkarimov BT, Zharkov DO, Saparbaev MK. Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage. Mutagenesis. 35: 107-118. PMID 31782485 DOI: 10.1093/mutage/gez045   
2020 Kekic T, Barisic I. modelling of DNA nanostructures. Computational and Structural Biotechnology Journal. 18: 1191-1201. PMID 32528637 DOI: 10.1016/j.csbj.2020.05.016   
2020 Gopi S, Naganathan AN. Non-specific DNA-driven quinary interactions promote structural transitions in proteins. Physical Chemistry Chemical Physics : Pccp. 22: 12671-12677. PMID 32458879 DOI: 10.1039/d0cp01758b   
2020 Thompson A, Barrett S, Weiden A, Venkatesh A, Seto M, Gottlieb S, Leconte AM. Accurate and efficient one-pot reverse transcription and amplification of 2' fluoro-modified nucleic acids by commercial DNA polymerases. Biochemistry. PMID 32659079 DOI: 10.1021/acs.biochem.0c00494   
2020 Kawai H, Sato K, Shirahama W, Suzuki T, Kamiya H. Single-stranded DNA versus tailed duplex in sequence conversion of DNA. Nucleosides, Nucleotides & Nucleic Acids. 1-6. PMID 32727258 DOI: 10.1080/15257770.2020.1790596   
2020 Faltejsková K, Jakubec D, Vondrášek J. Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation. International Journal of Molecular Sciences. 21. PMID 32498246 DOI: 10.3390/ijms21113986   
2020 Zacheja T, Toth A, Harami GM, Yang Q, Schwindt E, Kovács M, Paeschke K, Burkovics P. Mgs1 protein supports genome stability via recognition of G-quadruplex DNA structures. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 32748509 DOI: 10.1096/fj.202000886R   
2020 Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chemical Reviews. PMID 32672036 DOI: 10.1021/acs.chemrev.0c00294   
2020 Choi Y, Bae HJ, Lee AC, Choi H, Lee D, Ryu T, Hyun J, Kim S, Kim H, Song SH, Kim K, Park W, Kwon S. DNA Micro-Disks for the Management of DNA-Based Data Storage with Index and Write-Once-Read-Many (WORM) Memory Features. Advanced Materials (Deerfield Beach, Fla.). e2001249. PMID 32725925 DOI: 10.1002/adma.202001249   
2020 Bradford KC, Wilkins H, Hao P, Li ZM, Wang B, Burke D, Wu D, Smith AE, Spaller L, Du C, Gauer JW, Chan E, Hsieh P, Weninger KR, Erie DA. Dynamic human MutSα-MutLα complexes compact mismatched DNA. Proceedings of the National Academy of Sciences of the United States of America. PMID 32586954 DOI: 10.1073/pnas.1918519117   
2020 Zhang B, Zhao S, Wan H, Liu Y, Zhang F, Guo X, Zeng W, Zhang H, Zeng L, Qu J, Wu BQ, Wan X, Cantor CR, Ge D. High-resolution DNA size enrichment using a magnetic nano-platform and application in non-invasive prenatal testing. The Analyst. PMID 32748914 DOI: 10.1039/d0an00813c   
2020 Sandoval-Pérez A, Berger RML, Garaizar A, Farr SE, Brehm MA, König G, Schneider SW, Collepardo-Guevara R, Huck V, Rädler JO, Aponte-Santamaría C. DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions. Nucleic Acids Research. PMID 32496552 DOI: 10.1093/nar/gkaa466   
2020 Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal PK, Van Houten B, Freudenthal BD. AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop. Nucleic Acids Research. PMID 32542366 DOI: 10.1093/nar/gkaa496   
2020 Howard MJ, Horton JK, Zhao ML, Wilson SH. Lysines in the lyase active site of DNA polymerase β destabilize non-specific DNA binding, facilitating searching and DNA gap recognition. The Journal of Biological Chemistry. PMID 32647014 DOI: 10.1074/jbc.RA120.013547   
2020 Tisi R, Vertemara J, Zampella G, Longhese MP. Functional and structural insights into the MRX/MRN complex, a key player in recognition and repair of DNA double-strand breaks. Computational and Structural Biotechnology Journal. 18: 1137-1152. PMID 32489527 DOI: 10.1016/j.csbj.2020.05.013   
2020 Ronato DA, Mersaoui SY, Busatto FF, Affar EB, Richard S, Masson JY. Limiting the DNA Double-Strand Break Resectosome for Genome Protection. Trends in Biochemical Sciences. PMID 32513599 DOI: 10.1016/j.tibs.2020.05.003   
2020 Suzuki H, Fujiyoshi K, Kaji N, Tokeshi M, Baba Y. Observation of Ethanol-Induced Condensation and Decondensation Processes at a Single-DNA Molecular Level in Microfluidic Devices Equipped with a Rapid Solution Exchange System. Analytical Chemistry. PMID 32483963 DOI: 10.1021/acs.analchem.0c01417   
2020 Jiang Z, Wu J, Jiang M, Xie Y, Bu W, Liu C, Zhang G, Luo M. A Novel Technique for Constructing Infectious Cloning of Type 3 Porcine Circovirus. Frontiers in Microbiology. 11: 1067. PMID 32582064 DOI: 10.3389/fmicb.2020.01067   
2020 Pradhan M, Govindaraju A, Jagdish A, Christensen SM. The linker region of LINEs modulates DNA cleavage and DNA polymerization. Analytical Biochemistry. 113809. PMID 32511965 DOI: 10.1016/j.ab.2020.113809   
2020 Vecellio M, Wu H, Lu Q, Selmi C. The multifaceted functional role of DNA methylation in immune-mediated rheumatic diseases. Clinical Rheumatology. PMID 32613397 DOI: 10.1007/s10067-020-05255-5   
2020 Ito K, Murayama Y, Kurokawa Y, Kanamaru S, Kokabu Y, Maki T, Mikawa T, Argunhan B, Tsubouchi H, Ikeguchi M, Takahashi M, Iwasaki H. Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51. Nature Communications. 11: 2950. PMID 32528002 DOI: 10.1038/s41467-020-16750-3   
2020 Wang XS, Lee BJ, Zha S. The recent advances in non-homologous end-joining through the lens of lymphocyte development. Dna Repair. 94: 102874. PMID 32623318 DOI: 10.1016/j.dnarep.2020.102874   
2020 Gilat N, Torchinsky D, Margalit S, Michaeli Y, Avraham S, Sharim H, Elkoshi N, Levy C, Zirkin S, Ebenstein Y. Rapid Quantification of Oxidation and UV Induced DNA Damage by Repair Assisted Damage Detection-(Rapid RADD). Analytical Chemistry. PMID 32578422 DOI: 10.1021/acs.analchem.0c01393   
2020 Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S, Mann M, Russmann C, Wierer M. Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nature Communications. 11: 3019. PMID 32541649 DOI: 10.1038/s41467-020-16837-x   
2020 Myka KK, Marians KJ. Two components of DNA replication-dependent LexA cleavage. The Journal of Biological Chemistry. PMID 32513870 DOI: 10.1074/jbc.RA120.014224