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Elio A. Abbondanzieri, Ph.D. - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
biophysics, single molecules, motor proteins, transcription
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Shahu S, Vtyurina N, Das M, Meyer AS, Ganji M, Abbondanzieri EA. Bridging DNA contacts allow Dps from E. coli to condense DNA. Nucleic Acids Research. PMID 38572752 DOI: 10.1093/nar/gkae223  0.309
2024 Shahu S, Vtyurina N, Das M, Meyer AS, Ganji M, Abbondanzieri EA. Bridging DNA contacts allow Dps from to condense DNA. Biorxiv : the Preprint Server For Biology. PMID 38328146 DOI: 10.1101/2024.01.22.576774  0.306
2018 Kim SH, Ganji M, Kim E, van der Torre J, Abbondanzieri E, Dekker C. DNA sequence encodes the position of DNA supercoils. Elife. 7. PMID 30523779 DOI: 10.7554/Elife.36557  0.399
2018 Janissen R, Arens MMA, Vtyurina NN, Rivai Z, Sunday ND, Eslami-Mossallam B, Gritsenko AA, Laan L, de Ridder D, Artsimovitch I, Dekker NH, Abbondanzieri EA, Meyer AS. Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription. Cell. PMID 30057118 DOI: 10.1016/J.Cell.2018.06.049  0.466
2018 Kim SH, Ganji M, Kim E, Torre Jvd, Abbondanzieri E, Dekker C. Author response: DNA sequence encodes the position of DNA supercoils Elife. DOI: 10.7554/Elife.36557.055  0.374
2017 Hyun Kim S, Ganji M, van der Torre J, Abbondanzieri E, Dekker C. DNA Sequence can Pin the Position of DNA Supercoils Biophysical Journal. 112: 214a. DOI: 10.1016/J.Bpj.2016.11.1182  0.419
2016 Ganji M, Docter M, Le Grice SF, Abbondanzieri EA. DNA binding proteins explore multiple local configurations during docking via rapid rebinding. Nucleic Acids Research. PMID 27471033 DOI: 10.1093/Nar/Gkw666  0.389
2016 Ganji M, Kim SH, van der Torre J, Abbondanzieri E, Dekker C. Intercalation-based single-molecule fluorescence assay to study DNA supercoil dynamics. Nano Letters. PMID 27356180 DOI: 10.1021/Acs.Nanolett.6B02213  0.455
2016 Vtyurina NN, Dulin D, Docter MW, Meyer AS, Dekker NH, Abbondanzieri EA. Hysteresis in DNA compaction by Dps is described by an Ising model. Proceedings of the National Academy of Sciences of the United States of America. PMID 27091987 DOI: 10.1073/Pnas.1521241113  0.42
2016 Hyun Kim S, Ganji M, van J, Torre d, Abbondanzieri E, Dekker C. The Occurrence of Plectonemes in Supercoiled DNA Depends on DNA Sequence Biophysical Journal. 110: 563a. DOI: 10.1016/J.Bpj.2015.11.3013  0.432
2016 Ganji M, Docter M, Le Grice SF, Abbondanzieri E. Flipping by DNA Bound Proteins Occurs through Rapid Rebinding Biophysical Journal. 110: 515a. DOI: 10.1016/J.Bpj.2015.11.2752  0.468
2016 Vtyurina NN, Dulin D, Docter MW, Meyer AS, Dekker NH, Abbondanzieri EA. An Ising Model Describes Hysteresis in a Novel form of Cooperative Binding Biophysical Journal. 110: 239a. DOI: 10.1016/J.Bpj.2015.11.1317  0.31
2015 Abbondanzieri EA. Mechanism of Nucleoid Collapse in E. coli Biophysical Journal. 108: 541a. DOI: 10.1016/J.Bpj.2014.11.2968  0.444
2015 Vtyurina N, Dulin D, Docter M, Dekker N, Meyer A, Abbondanzieri E. Chromosome Reorganization by the Highly Cooperative Dps Protein Biophysical Journal. 108: 15a. DOI: 10.1016/J.Bpj.2014.11.107  0.415
2014 Abbondanzieri EA, Le Grice SF. Unraveling the gymnastics of reverse transcription through single molecule spectroscopy. Aids Research and Human Retroviruses. 30: 209-10. PMID 24588577 DOI: 10.1089/aid.2014.0023  0.307
2014 Abbondanzieri EA, Vtyurina N, Meyer A. Nucleoid Reorganization by the Stress Response Protein Dps Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.511  0.443
2008 Liu S, Abbondanzieri EA, Rausch JW, Le Grice SF, Zhuang X. Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science (New York, N.Y.). 322: 1092-7. PMID 19008444 DOI: 10.1126/Science.1163108  0.465
2008 Abbondanzieri EA, Bokinsky G, Rausch JW, Zhang JX, Le Grice SF, Zhuang X. Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature. 453: 184-9. PMID 18464735 DOI: 10.1038/Nature06941  0.499
2007 Greenleaf WJ, Frieda KL, Abbondanzieri EA, Woodside MT, Block SM. High-resolution, single-molecule optical trapping measurements of transcription with basepair accuracy: Instrumentation and methods Proceedings of Spie - the International Society For Optical Engineering. 6644. DOI: 10.1117/12.739631  0.692
2005 Greenleaf WJ, Woodside MT, Abbondanzieri EA, Block SM. Passive all-optical force clamp for high-resolution laser trapping. Physical Review Letters. 95: 208102. PMID 16384102 DOI: 10.1103/Physrevlett.95.208102  0.685
2005 Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM. Direct observation of base-pair stepping by RNA polymerase. Nature. 438: 460-5. PMID 16284617 DOI: 10.1038/Nature04268  0.728
2005 Abbondanzieri EA, Shaevitz JW, Block SM. Picocalorimetry of transcription by RNA polymerase. Biophysical Journal. 89: L61-3. PMID 16239336 DOI: 10.1529/Biophysj.105.074195  0.697
2005 Neuman KC, Abbondanzieri EA, Block SM. Measurement of the effective focal shift in an optical trap. Optics Letters. 30: 1318-20. PMID 15981519 DOI: 10.1364/Ol.30.001318  0.653
2003 Shaevitz JW, Abbondanzieri EA, Landick R, Block SM. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature. 426: 684-7. PMID 14634670 DOI: 10.1038/Nature02191  0.715
2003 Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell. 115: 437-47. PMID 14622598 DOI: 10.1016/S0092-8674(03)00845-6  0.738
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