Mark Bathe, Ph.D. - Related publications

2009- Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Zhang T. DNA origami-based microtubule analogue. Nanotechnology. 31: 50LT01. PMID 33034304 DOI: 10.1088/1361-6528/abb395   
2020 Zhang T, Cui W, Tian T, Shi S, Lin Y. Progress in Biomedical Applications of Tetrahedral Framework Nucleic Acid-Based Functional Systems. Acs Applied Materials & Interfaces. PMID 32975109 DOI: 10.1021/acsami.0c13806   
2020 Zhang T, Cui W, Tian T, Shi S, Lin Y. Progress in Biomedical Applications of Tetrahedral Framework Nucleic Acid-Based Functional Systems. Acs Applied Materials & Interfaces. PMID 32975109 DOI: 10.1021/acsami.0c13806   
2020 Lämmle CA, Varady A, Müller TG, Sturtzel C, Riepl M, Mathes B, Eichhorst J, Sporbert A, Lehmann M, Kräusslich HG, Distel M, Broichhagen J. Photocaged Hoechst enables subnuclear visualization and cell selective staining of DNA in vivo. Chembiochem : a European Journal of Chemical Biology. PMID 32974998 DOI: 10.1002/cbic.202000465   
2020 Velasco-Berrelleza V, Burman M, Shepherd JW, Leake MC, Golestanian R, Noy A. SerraNA: a program to determine nucleic acids elasticity from simulation data. Physical Chemistry Chemical Physics : Pccp. 22: 19254-19266. PMID 32902529 DOI: 10.1039/d0cp02713h   
2020 Joyeux M, Junier I. Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome. Biophysical Journal. 119: 1215-1225. PMID 32822585 DOI: 10.1016/j.bpj.2020.08.004   
2020 Rodriguez J, Mosquera J, Learte-Aymamı S, Vázquez ME, Mascareñas JL. Stimuli-Responsive DNA Binding by Synthetic Systems. Accounts of Chemical Research. PMID 32997936 DOI: 10.1021/acs.accounts.0c00415   
2020 Murugan R. A lattice model on the rate of in vivo site-specific DNA-protein interactions. Physical Biology. PMID 33022664 DOI: 10.1088/1478-3975/abbe9a   
2020 Yim SS, Johns NI, Noireaux V, Wang HH. Protecting linear DNA templates in cell-free expression systems from diverse bacteria. Acs Synthetic Biology. PMID 32926785 DOI: 10.1021/acssynbio.0c00277   
2020 Storch M, Haines MC, Baldwin GS. DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology. Synthetic Biology (Oxford, England). 5: ysaa010. PMID 32995552 DOI: 10.1093/synbio/ysaa010   
2020 De Riso G, Fiorillo DFG, Fierro A, Cuomo M, Chiariotti L, Miele G, Cocozza S. Modeling DNA Methylation Profiles through a Dynamic Equilibrium between Methylation and Demethylation. Biomolecules. 10. PMID 32899254 DOI: 10.3390/biom10091271   
2020 Pryor JM, Potapov V, Kucera RB, Bilotti K, Cantor EJ, Lohman GJS. Enabling one-pot Golden Gate assemblies of unprecedented complexity using data-optimized assembly design. Plos One. 15: e0238592. PMID 32877448 DOI: 10.1371/journal.pone.0238592   
2020 Liu Y, Cheng J, Fan S, Ge H, Luo T, Tang L, Ji B, Zhang C, Cui D, Ke Y, Song J. Modular Reconfigurable DNA Origami: from 2D to 3D. Angewandte Chemie (International Ed. in English). PMID 32894584 DOI: 10.1002/anie.202010433   
2020 Sharma R, Kk S, Holmstrom ED, Westerlund F. Real-time compaction of nanoconfined DNA by an intrinsically disordered macromolecular counterion. Biochemical and Biophysical Research Communications. PMID 32951838 DOI: 10.1016/j.bbrc.2020.06.051   
2020 Liu Z, Sun J, Zhao G, Xiong S, Ma Y, Zheng M. Transient Stem-Loop Structure of Nucleic Acid Template May Interfere with Polymerase Chain Reaction through Endonuclease Activity of Taq DNA Polymerase. Gene. 145095. PMID 32866587 DOI: 10.1016/j.gene.2020.145095   
2020 Reinking HK, Kang HS, Götz MJ, Li HY, Kieser A, Zhao S, Acampora AC, Weickert P, Fessler E, Jae LT, Sattler M, Stingele J. DNA Structure-Specific Cleavage of DNA-Protein Crosslinks by the SPRTN Protease. Molecular Cell. PMID 32853547 DOI: 10.1016/j.molcel.2020.08.003   
2020 Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA. Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Progress in Biophysics and Molecular Biology. PMID 32966823 DOI: 10.1016/j.pbiomolbio.2020.09.003   
2020 Das S, Roy S, Bhattacharyya D. DNA base sequence specificity through partial intercalation: DFT-D based energy analysis of molecular dynamics snapshots. Journal of Molecular Graphics & Modelling. 101: 107722. PMID 32882634 DOI: 10.1016/j.jmgm.2020.107722   
2020 Cook AW, Toseland CP. The roles of nuclear myosin in the DNA damage response. Journal of Biochemistry. PMID 33035317 DOI: 10.1093/jb/mvaa113   
2020 Schibany S, Hinrichs R, Hernández-Tamayo R, Graumann PL. The Major Chromosome Condensation Factors Smc, HBsu, and Gyrase in Bacillus subtilis Operate via Strikingly Different Patterns of Motion. Msphere. 5. PMID 32907955 DOI: 10.1128/mSphere.00817-20   
2020 Sherlin L, Farmer A, Martin P, Rotsinger J, Laliberte J, Chakrabarty S, Abe K, Ashworth R, Chittur S. ThruPLEX HV: a simplified system for preparation of molecular-tagged NGS libraries. Journal of Biomolecular Techniques : Jbt. 31: S12. PMID 32831696   
2020 El Hamoui O, Yadav I, Radiom M, Wien F, Berret JF, van der Maarel JRC, Arluison V. Interactions between DNA and the Hfq Amyloid-like Region Trigger a Viscoelastic Response. Biomacromolecules. PMID 32786728 DOI: 10.1021/acs.biomac.0c00747   
2020 Lattuada E, Leo M, Caprara D, Salvatori L, Stoppacciaro A, Sciortino F, Filetici P. DNA-GEL, Novel Nanomaterial for Biomedical Applications and Delivery of Bioactive Molecules. Frontiers in Pharmacology. 11: 01345. PMID 33013376 DOI: 10.3389/fphar.2020.01345   
2020 Fero MJ, Craft JK, Vu T, Hillson NJ. Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5. Methods in Molecular Biology (Clifton, N.J.). 2205: 19-47. PMID 32809191 DOI: 10.1007/978-1-0716-0908-8_2   
2020 Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nature Communications. 11: 5250. PMID 33067435 DOI: 10.1038/s41467-020-19047-7   
2020 Heijo H, Shimogama S, Nakano S, Miyata A, Iwao Y, Hara Y. DNA Content Contributes to Nuclear Size Control in . Molecular Biology of the Cell. mbcE20020113. PMID 32997613 DOI: 10.1091/mbc.E20-02-0113   
2020 Tibbs J, Tabei SMA, Kidd TE, Peters JP. Effects of Intercalating Molecules on the Polymer Properties of DNA. The Journal of Physical Chemistry. B. PMID 32941733 DOI: 10.1021/acs.jpcb.0c06867   
2020 Pan Y, Zhou S, Guan J. Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach. Bmc Bioinformatics. 21: 384. PMID 32938375 DOI: 10.1186/s12859-020-03675-3   
2020 Yao G, Zhang F, Wang F, Peng T, Liu H, Poppleton E, Šulc P, Jiang S, Liu L, Gong C, Jing X, Liu X, Wang L, Liu Y, Fan C, et al. Meta-DNA structures. Nature Chemistry. PMID 32895523 DOI: 10.1038/s41557-020-0539-8   
2020 Song J, Freeman ADJ, Knebel A, Gartner A, Lilley DMJ. Human ANKLE1 is a nuclease specific for branched DNA. Journal of Molecular Biology. PMID 32866453 DOI: 10.1016/j.jmb.2020.08.022   
2020 Mizi A, Zhang S, Papantonis A. Genome folding and refolding in differentiation and cellular senescence. Current Opinion in Cell Biology. 67: 56-63. PMID 32911122 DOI: 10.1016/   
2020 Wang H, Luo D, Wang H, Wang F, Liu X. Construction of smart stimuli-responsive DNA nanostructures for biomedical applications. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 32830363 DOI: 10.1002/chem.202003145   
2020 Sahoo S, Bera S, Dhara D. Histidine-based Reduction Sensitive Star-Polymer Inclusion Complex as Potential DNA Carrier: Biophysical Studies Using Time-Resolved Fluorescence as an Important Tool. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 32865419 DOI: 10.1021/acs.langmuir.0c01636   
2020 Unnikrishnan A, Amero C, Yadav DK, Stachowski K, Potter D, Foster MP. DNA binding induces a -to- switch in Cre recombinase to enable intasome assembly. Proceedings of the National Academy of Sciences of the United States of America. PMID 32968014 DOI: 10.1073/pnas.2011448117   
2020 Gu Q, Cao HH, Zhang Y, Wang H, Petrek Z, Shi F, Josephs EA, Ye T. Toward a Quantitative Relationship between Nanoscale Spatial Organization and Hybridization Kinetics of Surface Immobilized Hairpin DNA Probes. Acs Sensors. PMID 32945167 DOI: 10.1021/acssensors.0c01278   
2020 Dai L, Yu J. Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA. Biochemical and Biophysical Research Communications. PMID 32933752 DOI: 10.1016/j.bbrc.2020.08.004   
2020 Xia X, Hu H, Ciamarra MP, Ni R. Linker-mediated self-assembly of mobile DNA-coated colloids. Science Advances. 6. PMID 32937313 DOI: 10.1126/sciadv.aaz6921   
2020 Desai PR, Brahmachari S, Marko JF, Das S, Neuman KC. Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. Nucleic Acids Research. PMID 33045724 DOI: 10.1093/nar/gkaa836   
2020 Chen X, Xun D, Zheng R, Zhao L, Lu Y, Huang J, Wang R, Wang Y. Deep-Learning-Assisted Assessment of DNA Damage Based on Foci Images and Its Application in High-Content Screening of Lead Compounds. Analytical Chemistry. PMID 32986405 DOI: 10.1021/acs.analchem.0c03741   
2020 Kamagata K, Ouchi K, Tan C, Mano E, Mandali S, Wu Y, Takada S, Takahashi S, Johnson RC. The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA. Nucleic Acids Research. PMID 32997109 DOI: 10.1093/nar/gkaa799   
2020 Fossépré M, Tuvi-Arad I, Beljonne D, Richeter S, Clément S, Surin M. Binding mode multiplicity and multiscale chirality in the supramolecular assembly of DNA and a π-conjugated polymer. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 32910539 DOI: 10.1002/cphc.202000630   
2020 Geng H, Yin Z, Zhou C, Guo C. Construction of a Simple and Intelligent DNA-based Computing System for Multiplexing Logic Operations. Acta Biomaterialia. PMID 33035692 DOI: 10.1016/j.actbio.2020.09.054   
2020 Li Y, Huang Q, Yao G, Wang X, Zhang F, Wang T, Shao C, Zheng X, Jing X, Zhou H. Remodeling Chromatin Induces Z-DNA Conformation Detected through Fourier Transform Infrared Spectroscopy. Analytical Chemistry. PMID 33085464 DOI: 10.1021/acs.analchem.0c02432   
2020 Wang D, Yu L, Ji B, Chang S, Song J, Ke Y. Programming the Curvatures in Reconfigurable DNA Domino Origami by Using Asymmetric Units. Nano Letters. PMID 33095024 DOI: 10.1021/acs.nanolett.0c03348   
2020 Akerman I, Kasaai B, Bazarova A, Sang PB, Peiffer I, Artufel M, Derelle R, Smith G, Rodriguez-Martinez M, Romano M, Kinet S, Tino P, Theillet C, Taylor N, Ballester B, et al. A predictable conserved DNA base composition signature defines human core DNA replication origins. Nature Communications. 11: 4826. PMID 32958757 DOI: 10.1038/s41467-020-18527-0   
2020 Halliwell JA, Gravells P, Bryant HE. DNA Fiber Assay for the Analysis of DNA Replication Progression in Human Pluripotent Stem Cells. Current Protocols in Stem Cell Biology. 54: e115. PMID 32584505 DOI: 10.1002/cpsc.115   
2020 Wang Y, Wang D, Jia F, Miller A, Tan X, Chen P, Zhang L, Lu H, Fang Y, Kang X, Cai J, Ren M, Zhang K. Self-Assembled DNA-PEG Bottlebrushes Enhance Antisense Activity and Pharmacokinetics of Oligonucleotides. Acs Applied Materials & Interfaces. PMID 32936615 DOI: 10.1021/acsami.0c13995   
2020 Bhatia DD, Wunder C, Johannes L. Self-assembled, programmable DNA nanodevices for biological and biomedical applications. Chembiochem : a European Journal of Chemical Biology. PMID 32961015 DOI: 10.1002/cbic.202000372   
2020 Lee H, Wiegand DJ, Griswold K, Punthambaker S, Chun H, Kohman RE, Church GM. Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage. Nature Communications. 11: 5246. PMID 33067441 DOI: 10.1038/s41467-020-18681-5   
2020 Samanta A, Sabatino V, Ward TR, Walther A. Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes. Nature Nanotechnology. PMID 32895521 DOI: 10.1038/s41565-020-0761-y