cached image

John F. Marko - Publications

Affiliations: 
Physics & Astronomy Northwestern University, Evanston, IL 
Area:
Applications of statistical mechanics and polymer physics to biophysical problems.
Website:
http://www.physics.northwestern.edu/people/personalpages/jmarko.html

177 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
2022 Nomidis SK, Carlon E, Gruber S, Marko JF. DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. Nucleic Acids Research. 50: 4974-4987. PMID 35474142 DOI: 10.1093/nar/gkac268  0.444
2021 Guo MS, Kawamura R, Littlehale ML, Marko JF, Laub MT. High-resolution, genome-wide mapping of positive supercoiling in chromosomes. Elife. 10. PMID 34279217 DOI: 10.7554/eLife.67236  0.631
2021 Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, et al. HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. Elife. 10. PMID 34106828 DOI: 10.7554/eLife.63972  0.329
2021 Zaichuk T, Marko JF. Single-molecule micromanipulation studies of methylated DNA. Biophysical Journal. PMID 33838135 DOI: 10.1016/j.bpj.2021.03.039  0.307
2020 Serrano D, Cordero G, Kawamura R, Sverzhinsky A, Sarker M, Roy S, Malo C, Pascal JM, Marko JF, D'Amours D. The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Molecular Cell. PMID 33301731 DOI: 10.1016/j.molcel.2020.11.011  0.621
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  0.391
2020 Biggs RJ, Liu N, Peng Y, Marko JF, Qiao H. Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization. Communications Biology. 3: 542. PMID 32999386 DOI: 10.1038/s42003-020-01265-w  0.343
2020 Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA. Chromosome organization by one-sided and two-sided loop extrusion. Elife. 9. PMID 32250245 DOI: 10.7554/Elife.53558  0.465
2020 Mirny LA, Musacchio A, Marko JF. Decision letter: Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner Elife. DOI: 10.7554/Elife.53885.Sa1  0.41
2020 Banigan EJ, Berg AAvd, Brandão HB, Marko JF, Mirny LA. Author response: Chromosome organization by one-sided and two-sided loop extrusion Elife. DOI: 10.7554/Elife.53558.Sa2  0.367
2019 Marko JF. Physics and Biology (of Chromosomes). Journal of Molecular Biology. PMID 31866291 DOI: 10.1016/J.Jmb.2019.11.022  0.343
2019 Brahmachari S, Marko JF. Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 31757850 DOI: 10.1073/Pnas.1906355116  0.471
2019 Erbaş A, Marko JF. How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. Current Opinion in Chemical Biology. 53: 118-124. PMID 31586479 DOI: 10.1016/J.Cbpa.2019.08.007  0.463
2019 Renn JP, Bhattacharyya S, Bai H, He C, Li H, Oberhauser AF, Marko JF, Makarov DE, Matouschek A. Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force. Scientific Reports. 9: 11101. PMID 31366931 DOI: 10.1038/S41598-019-46525-W  0.303
2019 Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF. Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. Molecular Biology of the Cell. 30: 2320-2330. PMID 31365328 DOI: 10.1091/Mbc.E19-05-0286  0.374
2019 Marko JF, De Los Rios P, Barducci A, Gruber S. DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes. Nucleic Acids Research. PMID 31175837 DOI: 10.1093/Nar/Gkz497  0.566
2019 Nomidis SK, Skoruppa E, Carlon E, Marko JF. Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. Physical Review. E. 99: 032414. PMID 30999490 DOI: 10.1103/Physreve.99.032414  0.447
2019 Stephens AD, Banigan EJ, Marko JF. Chromatin's physical properties shape the nucleus and its functions. Current Opinion in Cell Biology. 58: 76-84. PMID 30889417 DOI: 10.1016/J.Ceb.2019.02.006  0.321
2019 Biggs R, Liu P, Stephens AD, Marko JF. Effects of altering histone post-translational modifications on mitotic chromosome structure and mechanics. Molecular Biology of the Cell. mbcE18090592. PMID 30625026 DOI: 10.1091/Mbc.E18-09-0592  0.442
2018 Brahmachari S, Marko JF. DNA Mechanics and Topology. Advances in Experimental Medicine and Biology. 1092: 11-39. PMID 30368746 DOI: 10.1007/978-3-319-95294-9_2  0.541
2018 Skoruppa E, Nomidis SK, Marko JF, Carlon E. Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. Physical Review Letters. 121: 088101. PMID 30192578 DOI: 10.1103/Physrevlett.121.088101  0.503
2018 Sun M, Biggs R, Hornick J, Marko JF. Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. PMID 30143891 DOI: 10.1007/S10577-018-9584-1  0.74
2018 Brahmachari S, Dittmore A, Takagi Y, Neuman KC, Marko JF. Defect-facilitated buckling in supercoiled double-helix DNA. Physical Review. E. 97: 022416. PMID 29548184 DOI: 10.1103/Physreve.97.022416  0.465
2018 Gunn KH, Marko JF, Mondragón A. Single-Molecule Magnetic Tweezer Analysis of Topoisomerases. Methods in Molecular Biology (Clifton, N.J.). 1703: 139-152. PMID 29177739 DOI: 10.1007/978-1-4939-7459-7_10  0.505
2017 Stephens AD, Banigan EJ, Marko JF. Separate roles for chromatin and lamins in nuclear mechanics. Nucleus (Austin, Tex.). 1-6. PMID 29227210 DOI: 10.1080/19491034.2017.1414118  0.329
2017 Brahmachari S, Gunn KH, Giuntoli RD, Mondragón A, Marko JF. Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. Physical Review Letters. 119: 188103. PMID 29219598 DOI: 10.1103/Physrevlett.119.188103  0.504
2017 Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF. Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Molecular Biology of the Cell. PMID 29142071 DOI: 10.1091/Mbc.E17-06-0410  0.302
2017 Keenholtz RA, Dhanaraman T, Palou R, Yu J, D'Amours D, Marko JF. Oligomerization and ATP stimulate condensin-mediated DNA compaction. Scientific Reports. 7: 14279. PMID 29079757 DOI: 10.1038/S41598-017-14701-5  0.543
2017 Dittmore A, Brahmachari S, Takagi Y, Marko JF, Neuman KC. Supercoiling DNA Locates Mismatches. Physical Review Letters. 119: 147801. PMID 29053317 DOI: 10.1103/Physrevlett.119.147801  0.474
2017 Brahmachari S, Marko JF. Torque and buckling in stretched intertwined double-helix DNAs. Physical Review. E. 95: 052401. PMID 28618488 DOI: 10.1103/Physreve.95.052401  0.495
2017 Martin RL, Maiorano J, Beitel GJ, Marko JF, McVicker G, Fondufe-Mittendorf YN. A comparison of nucleosome organization in Drosophila cell lines. Plos One. 12: e0178590. PMID 28570602 DOI: 10.1371/Journal.Pone.0178590  0.358
2017 Gunn KH, Marko JF, Mondragón A. An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Nature Structural & Molecular Biology. PMID 28414321 DOI: 10.1038/Nsmb.3401  0.508
2017 Kamar RI, Banigan EJ, Erbas A, Giuntoli RD, Olvera de la Cruz M, Johnson RC, Marko JF. Facilitated dissociation of transcription factors from single DNA binding sites. Proceedings of the National Academy of Sciences of the United States of America. PMID 28364020 DOI: 10.1073/Pnas.1701884114  0.407
2017 Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF. Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Molecular Biology of the Cell. PMID 28057760 DOI: 10.1091/Mbc.E16-09-0653  0.329
2017 Goloborodko A, Imakaev M, Marko JF, Mirny L. Compaction and Segregation of Sister Chromatids by Loop-Extruding Enzymes Biophysical Journal. 112: 373a. DOI: 10.1016/J.Bpj.2016.11.2024  0.47
2016 Keenholtz RA, Grindley ND, Hatfull GF, Marko JF. Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase. Nucleic Acids Research. PMID 27550179 DOI: 10.1093/Nar/Gkw724  0.425
2016 Brangwynne CP, Marko JF. Cell division: A sticky problem for chromosomes. Nature. PMID 27362225 DOI: 10.1038/Nature18904  0.432
2016 Goloborodko A, Marko JF, Mirny LA. Chromosome Compaction by Active Loop Extrusion. Biophysical Journal. 110: 2162-2168. PMID 27224481 DOI: 10.1016/J.Bpj.2016.02.041  0.434
2016 Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. Elife. 5. PMID 27192037 DOI: 10.7554/Elife.14864  0.447
2016 Banigan EJ, Marko JF. Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. Physical Review. E. 93: 049904. PMID 27182590 DOI: 10.1103/Physreve.93.049904  0.394
2016 Eastland A, Hornick J, Kawamura R, Nanavati D, Marko JF. Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. PMID 27145786 DOI: 10.1007/S10577-016-9528-6  0.767
2016 Hadizadeh N, Johnson RC, Marko JF. Facilitated dissociation of a nucleoid protein from the bacterial chromosome. Journal of Bacteriology. PMID 27044624 DOI: 10.1128/Jb.00225-16  0.566
2016 Xiao B, McLean MM, Lei X, Marko JF, Johnson RC. Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase. Scientific Reports. 6: 23697. PMID 27032966 DOI: 10.1038/Srep23697  0.682
2016 Kharerin H, Bhat PJ, Marko JF, Padinhateeri R. Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression. Scientific Reports. 6: 20319. PMID 26843321 DOI: 10.1038/Srep20319  0.359
2016 Marko JF. Micromechanical Study of Mammalian Metaphase Chromosomes and Nuclei Biophysical Journal. 110: 522a. DOI: 10.1016/J.Bpj.2015.11.2794  0.517
2015 Giuntoli RD, Linzer NB, Banigan EJ, Sing CE, de la Cruz MO, Graham JS, Johnson RC, Marko JF. DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response. Journal of Molecular Biology. 427: 3123-36. PMID 26220077 DOI: 10.1016/J.Jmb.2015.07.015  0.514
2015 Hornick JE, Duncan FE, Sun M, Kawamura R, Marko JF, Woodruff TK. Age-associated alterations in the micromechanical properties of chromosomes in the mammalian egg. Journal of Assisted Reproduction and Genetics. 32: 765-9. PMID 25758987 DOI: 10.1007/S10815-015-0453-Y  0.742
2015 Marko JF. Biophysics of protein-DNA interactions and chromosome organization. Physica A. 418: 126-153. PMID 25419039 DOI: 10.1016/J.Physa.2014.07.045  0.587
2015 Kamar RI, Marko JF. Facilitated Dissociation of Protein from a Single DNA Binding Site Biophysical Journal. 108: 205a. DOI: 10.1016/J.Bpj.2014.11.1133  0.493
2014 Terekhova K, Marko JF, Mondragón A. Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases I and III. Nucleic Acids Research. 42: 11657-67. PMID 25232096 DOI: 10.1093/Nar/Gku785  0.524
2014 Banigan EJ, Marko JF. Torque correlation length and stochastic twist dynamics of DNA. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 062706. PMID 25019813 DOI: 10.1103/Physreve.89.062706  0.393
2014 Cocco S, Marko JF, Monasson R. Stochastic ratchet mechanisms for replacement of proteins bound to DNA Physical Review Letters. 112. PMID 24972228 DOI: 10.1103/Physrevlett.112.238101  0.445
2014 Sing CE, Olvera de la Cruz M, Marko JF. Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. Nucleic Acids Research. 42: 3783-91. PMID 24393773 DOI: 10.1093/Nar/Gkt1327  0.438
2014 Parmar JJ, Marko JF, Padinhateeri R. Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence. Nucleic Acids Research. 42: 128-36. PMID 24068556 DOI: 10.1093/Nar/Gkt854  0.413
2014 Hadizadeh N, Guet CC, Johnson RC, Marko JF. Structure and Mechanical Properties of the Bacterial Chromosome in E.Coli Biophysical Journal. 106: 79a. DOI: 10.1016/J.Bpj.2013.11.510  0.461
2014 Banigan EJ, Marko JF. Elastic Twist Dynamics of DNA Biophysical Journal. 106: 279a-280a. DOI: 10.1016/J.Bpj.2013.11.1636  0.465
2013 Marko JF, Neukirch S. Global force-torque phase diagram for the DNA double helix: structural transitions, triple points, and collapsed plectonemes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 062722. PMID 24483501 DOI: 10.1103/Physreve.88.062722  0.497
2013 Parsaeian A, de la Cruz MO, Marko JF. Binding-rebinding dynamics of proteins interacting nonspecifically with a long DNA molecule. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 040703. PMID 24229102 DOI: 10.1103/Physreve.88.040703  0.42
2013 Sun M, Nishino T, Marko JF. The SMC1-SMC3 cohesin heterodimer structures DNA through supercoiling-dependent loop formation. Nucleic Acids Research. 41: 6149-60. PMID 23620281 DOI: 10.1093/Nar/Gkt303  0.783
2013 Terekhova K, Marko JF, Mondragón A. Studies of bacterial topoisomerases I and III at the single-molecule level. Biochemical Society Transactions. 41: 571-5. PMID 23514156 DOI: 10.1042/Bst20120297  0.488
2013 Gunn KH, Soczek KM, Marko JF, Mondragon A. Studies of DNA Gyrase at the Single Molecule Level Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.477  0.521
2013 Gunn KH, Soczek KM, Critchelow CJ, Marko JF, Mondragon A. Studies of DNA Gyrase at the Single Molecule Level Biophysical Journal. 104: 73a. DOI: 10.1016/j.bpj.2012.11.441  0.332
2013 Xiao B, Johnson RC, Marko JF. Observation of Synapse Rotation of Engineered Recombinase HIN-H107Y Biophysical Journal. 104: 368a. DOI: 10.1016/J.Bpj.2012.11.2047  0.692
2012 Zhang H, Marko JF. Range of interaction between DNA-bending proteins is controlled by the second-longest correlation length for bending fluctuations. Physical Review Letters. 109: 248301. PMID 23368394 DOI: 10.1103/Physrevlett.109.248301  0.675
2012 Xiao B, Freedman BS, Miller KE, Heald R, Marko JF. Histone H1 compacts DNA under force and during chromatin assembly. Molecular Biology of the Cell. 23: 4864-71. PMID 23097493 DOI: 10.1091/Mbc.E12-07-0518  0.666
2012 Hadizadeh Yazdi N, Guet CC, Johnson RC, Marko JF. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 86: 1318-33. PMID 23078205 DOI: 10.1111/Mmi.12071  0.762
2012 Alipour E, Marko JF. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Research. 40: 11202-12. PMID 23074191 DOI: 10.1093/Nar/Gks925  0.477
2012 Bai H, Kath JE, Zörgiebel FM, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proceedings of the National Academy of Sciences of the United States of America. 109: 16546-51. PMID 23011800 DOI: 10.1073/Pnas.1203118109  0.754
2012 Terekhova K, Gunn KH, Marko JF, Mondragón A. Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Nucleic Acids Research. 40: 10432-40. PMID 22923519 DOI: 10.1093/Nar/Gks780  0.511
2012 Marko JF, Neukirch S. Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 011908. PMID 22400592 DOI: 10.1103/Physreve.85.011908  0.483
2012 Zhang H, Marko JF. The Longitudinal Correlation Length Controls the Range of Interactions Between DNA-Bending Proteins Biophysical Journal. 102: 74a. DOI: 10.1016/J.Bpj.2011.11.430  0.708
2012 Bai H, Kath J, Zorgebiel F, Grindley ND, Marko JF. Remote Control of DNA-Acting Enzymes by Molecular Boundary Conditions Biophysical Journal. 102: 70a. DOI: 10.1016/J.Bpj.2011.11.412  0.419
2012 Terekhova K, Marko JF, Mondragón A. Studying the Differences in Relaxation Activity by Topoisomerase I and III at the Single Molecule Level Biophysical Journal. 102: 51a. DOI: 10.1016/J.Bpj.2011.11.308  0.52
2012 Graham JS, Johnson RC, Marko JF. Visualizing Higher-Order Conformations in Single DNA Molecules Biophysical Journal. 102: 276a. DOI: 10.1016/J.Bpj.2011.11.1523  0.447
2011 Graham JS, Johnson RC, Marko JF. Counting proteins bound to a single DNA molecule. Biochemical and Biophysical Research Communications. 415: 131-4. PMID 22020072 DOI: 10.1016/J.Bbrc.2011.10.029  0.486
2011 Sheinin MY, Forth S, Marko JF, Wang MD. Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors. Physical Review Letters. 107: 108102. PMID 21981534 DOI: 10.1103/Physrevlett.107.108102  0.518
2011 Marko JF. Scaling of Linking and Writhing Numbers for Spherically Confined and Topologically Equilibrated Flexible Polymers. Journal of Statistical Physics. 142: 1353-1370. PMID 21686050 DOI: 10.1007/S10955-011-0172-4  0.313
2011 Neukirch S, Marko JF. Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA. Physical Review Letters. 106: 138104. PMID 21517425 DOI: 10.1103/Physrevlett.106.138104  0.484
2011 Bai H, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proceedings of the National Academy of Sciences of the United States of America. 108: 7419-24. PMID 21502527 DOI: 10.1073/Pnas.1018436108  0.772
2011 Xiao B, Zhang H, Johnson RC, Marko JF. Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation. Nucleic Acids Research. 39: 5568-77. PMID 21427084 DOI: 10.1093/Nar/Gkr141  0.796
2011 Sun M, Kawamura R, Marko JF. Micromechanics of human mitotic chromosomes. Physical Biology. 8: 015003. PMID 21301072 DOI: 10.1088/1478-3975/8/1/015003  0.79
2011 Fu H, Chen H, Zhang X, Qu Y, Marko JF, Yan J. Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching. Nucleic Acids Research. 39: 3473-81. PMID 21177651 DOI: 10.1093/Nar/Gkq1278  0.572
2011 Graham JS, Johnson RC, Marko JF. Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Research. 39: 2249-59. PMID 21097894 DOI: 10.1093/Nar/Gkq1140  0.466
2011 Hadizadeh N, Guet C, Johnson RC, Marko JF. Structure and Dynamics of the Bacterial Chromosome in E. coli Biophysical Journal. 100: 78a. DOI: 10.1016/J.Bpj.2010.12.634  0.459
2011 Graham JS, Johnson RC, Marko JF. Sequence Dependence of Binding and Exchange of Nonspecific Dna-Binding Proteins Biophysical Journal. 100: 70a. DOI: 10.1016/J.Bpj.2010.12.584  0.433
2011 Xiao B, Zhang H, Johnson RC, Marko JF. Measurements of Force-Driven Changes in Bound Protein Numbers on a Single DNA Biophysical Journal. 100: 70a. DOI: 10.1016/J.Bpj.2010.12.583  0.803
2010 Zhang H, Marko JF. Intrinsic and force-generated cooperativity in a theory of DNA-bending proteins. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 82: 051906. PMID 21230499 DOI: 10.1103/Physreve.82.051906  0.711
2010 Marko JF. Linking topology of large DNA molecules. Physica A. 389: 2997-3001. PMID 20606760 DOI: 10.1016/J.Physa.2010.01.003  0.511
2010 Xiao B, Johnson RC, Marko JF. Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Research. 38: 6176-85. PMID 20497998 DOI: 10.1093/Nar/Gkq435  0.688
2010 Fu H, Chen H, Marko JF, Yan J. Two distinct overstretched DNA states. Nucleic Acids Research. 38: 5594-600. PMID 20435680 DOI: 10.1093/Nar/Gkq309  0.592
2010 Kawamura R, Pope LH, Christensen MO, Sun M, Terekhova K, Boege F, Mielke C, Andersen AH, Marko JF. Mitotic chromosomes are constrained by topoisomerase II-sensitive DNA entanglements. The Journal of Cell Biology. 188: 653-63. PMID 20194637 DOI: 10.1083/Jcb.200910085  0.798
2010 Hadizadeh N, Marko JF. Structure and Dynamics of the Bacterial Chromosome in E. Coli Monitored by Gfp-Fis Biophysical Journal. 98: 658a. DOI: 10.1016/J.Bpj.2009.12.3612  0.458
2010 Marko JF, Neukirch S. Theory for the DNA Supercoiling Transition in Extension-Rotation Experiments Biophysical Journal. 98: 469a. DOI: 10.1016/J.Bpj.2009.12.2554  0.342
2010 Alipour-Assiabi E, Marko JF. Self Organization in DNA-Loop-Extruding Enzymes Biophysical Journal. 98: 469a. DOI: 10.1016/J.Bpj.2009.12.2552  0.427
2010 Sun M, Nishino T, Marko JF. Single-DNA Detection of Stepwise DNA Compaction by Cohesin SMC Protein Complexes Biophysical Journal. 98: 438a. DOI: 10.1016/J.Bpj.2009.12.2376  0.799
2010 Xiao B, Johnson RC, Marko JF. Salt Concentration and Force Affect HU-DNA Interaction Biophysical Journal. 98: 267a. DOI: 10.1016/J.Bpj.2009.12.1453  0.632
2010 Johnson RC, Stella S, Dhar G, McLean MM, Heiss JK, Marko JF. DNA Shape Recognition by the Nucleoid Protein Fis and Its Role in Chromosome Compaction and DNA Recombination Biophysical Journal. 98: 206a. DOI: 10.1016/J.Bpj.2009.12.1099  0.543
2010 Graham JS, Johnson RC, Marko JF. Direct Visualization of Fis-DNA Interactions Biophysical Journal. 98: 206a. DOI: 10.1016/J.Bpj.2009.12.1098  0.512
2009 Skoko D, Li M, Huang Y, Mizuuchi M, Cai M, Bradley CM, Pease PJ, Xiao B, Marko JF, Craigie R, Mizuuchi K. Barrier-to-autointegration factor (BAF) condenses DNA by looping. Proceedings of the National Academy of Sciences of the United States of America. 106: 16610-5. PMID 19805345 DOI: 10.1073/Pnas.0909077106  0.827
2009 Marko JF. Linking topology of tethered polymer rings with applications to chromosome segregation and estimation of the knotting length. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 051905. PMID 19518478 DOI: 10.1103/Physreve.79.051905  0.336
2009 Baum-Snow EA, Marko JF. Modeling The Behavior Of DNA-Loop-Extruding Enzymes Biophysical Journal. 96: 418a. DOI: 10.1016/J.Bpj.2008.12.2138  0.479
2009 Graham JS, Johnson RC, Marko JF. Visualization of Force-Mediated Looping Dynamics of a Single DNA Molecule by the E. coli protein FIS Biophysical Journal. 96: 418a. DOI: 10.1016/J.Bpj.2008.12.2134  0.501
2009 Sun M, Bai H, Grindley ND, Marko JF. Single-molecule Study of Site-specific DNA Recombination by γδ Resolvase Biophysical Journal. 96: 59a. DOI: 10.1016/J.Bpj.2008.12.204  0.775
2009 Hadizadeh N, Marko JF. Structure and Dynamics of the Bacterial Chromosome Biophysical Journal. 96: 20a. DOI: 10.1016/J.Bpj.2008.12.1007  0.453
2008 Zhang H, Marko JF. Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 031916. PMID 18517431 DOI: 10.1103/Physreve.77.031916  0.723
2008 Marko JF. Micromechanical studies of mitotic chromosomes. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 16: 469-97. PMID 18461485 DOI: 10.1007/S10577-008-1233-7  0.49
2007 Marko JF. Torque and dynamics of linking number relaxation in stretched supercoiled DNA. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 021926. PMID 17930084 DOI: 10.1016/J.Bpj.2012.11.022  0.501
2007 Taneja B, Schnurr B, Slesarev A, Marko JF, Mondragón A. Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism. Proceedings of the National Academy of Sciences of the United States of America. 104: 14670-5. PMID 17804808 DOI: 10.1073/Pnas.0701989104  0.436
2007 Ranjith P, Yan J, Marko JF. Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts. Proceedings of the National Academy of Sciences of the United States of America. 104: 13649-54. PMID 17698962 DOI: 10.1073/Pnas.0701459104  0.504
2007 Adams CD, Schnurr B, Marko JF, Reznikoff WS. Pulling apart catalytically active Tn5 synaptic complexes using magnetic tweezers. Journal of Molecular Biology. 367: 319-27. PMID 17257617 DOI: 10.1016/J.Jmb.2006.12.064  0.477
2007 Yan J, Maresca TJ, Skoko D, Adams CD, Xiao B, Christensen MO, Heald R, Marko JF. Micromanipulation studies of chromatin fibers in Xenopus egg extracts reveal ATP-dependent chromatin assembly dynamics. Molecular Biology of the Cell. 18: 464-74. PMID 17108322 DOI: 10.1091/Mbc.E06-09-0800  0.803
2006 Ranjith P, Marko JF. Filling of the one-dimensional lattice by k-mers proceeds via fast power-law-like kinetics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 74: 041602. PMID 17155065 DOI: 10.1103/Physreve.74.041602  0.317
2006 Adams CD, Schnurr B, Skoko D, Marko JF, Reznikoff WS. Tn5 transposase loops DNA in the absence of Tn5 transposon end sequences. Molecular Microbiology. 62: 1558-68. PMID 17074070 DOI: 10.1111/J.1365-2958.2006.05471.X  0.812
2006 Skoko D, Yoo D, Bai H, Schnurr B, Yan J, McLeod SM, Marko JF, Johnson RC. Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis. Journal of Molecular Biology. 364: 777-98. PMID 17045294 DOI: 10.1016/J.Jmb.2006.09.043  0.841
2006 Steiniger M, Adams CD, Marko JF, Reznikoff WS. Defining characteristics of Tn5 Transposase non-specific DNA binding. Nucleic Acids Research. 34: 2820-32. PMID 16717287 DOI: 10.1093/Nar/Gkl179  0.5
2006 Pope LH, Xiong C, Marko JF. Proteolysis of mitotic chromosomes induces gradual and anisotropic decondensation correlated with a reduction of elastic modulus and structural sensitivity to rarely cutting restriction enzymes. Molecular Biology of the Cell. 17: 104-13. PMID 16221892 DOI: 10.1091/Mbc.E05-04-0321  0.441
2005 Skoko D, Yan J, Johnson RC, Marko JF. Low-force DNA condensation and discontinuous high-force decondensation reveal a loop-stabilizing function of the protein Fis. Physical Review Letters. 95: 208101. PMID 16384101 DOI: 10.1103/Physrevlett.95.208101  0.847
2005 Sankararaman S, Marko JF. Entropic compression of interacting DNA loops. Physical Review Letters. 95: 078104. PMID 16196828 DOI: 10.1103/Physrevlett.95.078104  0.494
2005 Yan J, Kawamura R, Marko JF. Statistics of loop formation along double helix DNAs. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 061905. PMID 16089763 DOI: 10.1103/Physreve.71.061905  0.663
2005 Sankararaman S, Marko JF. Formation of loops in DNA under tension. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 71: 021911. PMID 15783356 DOI: 10.1103/Physreve.71.021911  0.514
2005 Ben-Yehuda S, Fujita M, Liu XS, Gorbatyuk B, Skoko D, Yan J, Marko JF, Liu JS, Eichenberger P, Rudner DZ, Losick R. Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA. Molecular Cell. 17: 773-82. PMID 15780934 DOI: 10.1016/J.Molcel.2005.02.023  0.846
2005 Pope LH, Bennink ML, Van Leijenhorst-Groener KA, Nikova D, Greve J, Marko JF. Single chromatin fiber stretching reveals physically distinct populations of disassembly events Biophysical Journal. 88: 3572-3583. PMID 15695630 DOI: 10.1529/Biophysj.104.053074  0.418
2005 Yan J, Kawamura R, Marko JF. Erratum: Statistics of loop formation along double helix DNAs [Phys. Rev. E71, 061905 (2005)] Physical Review E. 72. DOI: 10.1103/Physreve.72.059901  0.68
2005 Marko JF. Course 7 Introduction to single-DNA micromechanics Les Houches Summer School Proceedings. 82: 211-270. DOI: 10.1016/S0924-8099(05)80034-4  0.383
2004 Skoko D, Wong B, Johnson RC, Marko JF. Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes. Biochemistry. 43: 13867-74. PMID 15504049 DOI: 10.1021/Bi048428O  0.835
2004 Yan J, Marko JF. Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Physical Review Letters. 93: 108108. PMID 15447460 DOI: 10.1103/Physrevlett.93.108108  0.585
2004 Cocco S, Yan J, Léger JF, Chatenay D, Marko JF. Overstretching and force-driven strand separation of double-helix DNA. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 011910. PMID 15324091 DOI: 10.1103/Physreve.70.011910  0.605
2004 Yan J, Skoko D, Marko JF. Near-field-magnetic-tweezer manipulation of single DNA molecules. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 011905. PMID 15324086 DOI: 10.1103/Physreve.70.011905  0.8
2004 Halford SE, Marko JF. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Research. 32: 3040-52. PMID 15178741 DOI: 10.1093/Nar/Gkh624  0.485
2003 Cocco S, Marko JF, Monasson R. Slow nucleic acid unzipping kinetics from sequence-defined barriers European Physical Journal E. 10: 153-161. PMID 15011069 DOI: 10.1140/Epje/E2003-00019-8  0.393
2003 Poirier MG, Marko JF. Micromechanical studies of mitotic chromosomes. Current Topics in Developmental Biology. 55: 75-141. PMID 12959194 DOI: 10.1016/S0070-2153(03)01002-0  0.713
2003 Yan J, Marko JF. Effects of DNA-distorting proteins on DNA elastic response. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 68: 011905. PMID 12935174 DOI: 10.1103/Physreve.68.011905  0.611
2003 Marko JF, Poirier MG. Micromechanics of chromatin and chromosomes. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 81: 209-20. PMID 12897855 DOI: 10.1139/O03-047  0.716
2003 Cocco S, Marko JF, Monasson R, Sarkar A, Yan J. Force-extension behavior of folding polymers European Physical Journal E. 10: 249-263. DOI: 10.1140/Epje/I2002-10113-2  0.611
2003 Yan J, Marko JF. Publisher’s Note: Effects of DNA-distorting proteins on DNA elastic response [Phys. Rev. E68, 011905 (2003)] Physical Review E. 68. DOI: 10.1103/Physreve.68.039901  0.578
2003 Marko JF, Cocco S. The micromechanics of DNA Physics World. 16: 37-41. DOI: 10.1088/2058-7058/16/3/40  0.483
2002 Cocco S, Monasson R, Marko JF. Unzipping dynamics of long DNAs. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 66: 051914. PMID 12513530 DOI: 10.1103/Physreve.66.051914  0.473
2002 Poirier MG, Marko JF. Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold. Proceedings of the National Academy of Sciences of the United States of America. 99: 15393-7. PMID 12438695 DOI: 10.1073/Pnas.232442599  0.716
2002 Sarkar A, Eroglu S, Poirier MG, Gupta P, Nemani A, Marko JF. Dynamics of chromosome compaction during mitosis. Experimental Cell Research. 277: 48-56. PMID 12061816 DOI: 10.1006/Excr.2002.5507  0.735
2002 Poirier MG, Marko JF. Effect of internal friction on biofilament dynamics. Physical Review Letters. 88: 228103. PMID 12059455 DOI: 10.1103/Physrevlett.88.228103  0.634
2002 Poirier MG, Eroglu S, Marko JF. The bending rigidity of mitotic chromosomes. Molecular Biology of the Cell. 13: 2170-9. PMID 12058078 DOI: 10.1091/Mbc.01-08-0401  0.671
2002 Cocco S, Monasson R, Marko JF. Force and kinetic barriers to initiation of DNA unzipping. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 041907. PMID 12005873 DOI: 10.1103/Physreve.65.041907  0.485
2002 Poirier MG, Monhait T, Marko JF. Reversible hypercondensation and decondensation of mitotic chromosomes studied using combined chemical-micromechanical techniques. Journal of Cellular Biochemistry. 85: 422-34. PMID 11948697 DOI: 10.1002/Jcb.10132  0.688
2002 Cocco S, Marko JF, Monasson R. Theoretical models for single-molecule DNA and RNA experiments: From elasticity to unzipping Comptes Rendus Physique. 3: 569-584. DOI: 10.1016/S1631-0705(02)01345-2  0.428
2001 Sarkar A, Marko JF. Removal of DNA-bound proteins by DNA twisting Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 64: 061909/1-061909/10. PMID 11736212 DOI: 10.1103/Physreve.64.061909  0.672
2001 Cocco S, Monasson R, Marko JF. Force and kinetic barriers to unzipping of the DNA double helix Proceedings of the National Academy of Sciences of the United States of America. 98: 8608-8613. PMID 11447279 DOI: 10.1073/Pnas.151257598  0.488
2001 Sarkar A, Léger JF, Chatenay D, Marko JF. Structural transitions in DNA driven by external force and torque. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 051903. PMID 11414929 DOI: 10.1103/Physreve.63.051903  0.647
2001 Marshall WF, Marko JF, Agard DA, Sedat JW. Chromosome elasticity and mitotic polar ejection force measured in living Drosophila embryos by four-dimensional microscopy-based motion analysis. Current Biology : Cb. 11: 569-78. PMID 11369201 DOI: 10.1016/S0960-9822(01)00180-4  0.424
2001 Yan J, Magnasco MO, Marko JF. Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 031909. PMID 11308680 DOI: 10.1103/Physreve.63.031909  0.584
2001 Poirier MG, Nemani A, Gupta P, Eroglu S, Marko JF. Probing chromosome structure with dynamic force relaxation Physical Review Letters. 86: 360-363. DOI: 10.1103/Physrevlett.86.360  0.68
2000 Stanford NP, Szczelkun MD, Marko JF, Halford SE. One- and three-dimensional pathways for proteins to reach specific DNA sites Embo Journal. 19: 6546-6557. PMID 11101527 DOI: 10.1093/Emboj/19.23.6546  0.441
2000 Poirier M, Eroglu S, Chatenay D, Marko JF. Reversible and irreversible unfolding of mitotic newt chromosomes by applied force. Molecular Biology of the Cell. 11: 269-76. PMID 10637307 DOI: 10.1091/Mbc.11.1.269  0.689
1999 Yan J, Magnasco MO, Marko JF. A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases. Nature. 401: 932-5. PMID 10553912 DOI: 10.1038/44872  0.595
1999 Léger JF, Romano G, Sarkar A, Robert J, Bourdieu L, Chatenay D, Marko JF. Structural transitions of a twisted and stretched DNA molecule Physical Review Letters. 83: 1066-1069. DOI: 10.1103/Physrevlett.83.1066  0.653
1999 Marko JF. Coupling of intramolecular and intermolecular linkage complexity of two DNAs Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 900-912. DOI: 10.1103/Physreve.59.900  0.429
1998 Leger JF, Robert J, Bourdieu L, Chatenay D, Marko JF. RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations. Proceedings of the National Academy of Sciences of the United States of America. 95: 12295-9. PMID 9770480 DOI: 10.1073/Pnas.95.21.12295  0.53
1998 Marko JF. DNA under high tension: Overstretching, undertwisting, and relaxation dynamics Physical Review E. 57: 2134-2149. DOI: 10.1103/Physreve.57.2134  0.45
1997 Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chromosomes undergo constrained diffusional motion in living cells. Current Biology : Cb. 7: 930-9. PMID 9382846 DOI: 10.1016/S0960-9822(06)00412-X  0.416
1997 Marko JF, Siggia ED. Polymer models of meiotic and mitotic chromosomes Molecular Biology of the Cell. 8: 2217-2231. PMID 9362064 DOI: 10.1091/Mbc.8.11.2217  0.436
1997 Marko JF. Twist and shout (and pull): Molecular chiropractors undo DNA Proceedings of the National Academy of Sciences of the United States of America. 94: 11770-11772. PMID 9342311 DOI: 10.1073/Pnas.94.22.11770  0.504
1997 Marko JF, Siggia ED. Driving proteins off DNA using applied tension Biophysical Journal. 73: 2173-2178. PMID 9336213 DOI: 10.1016/S0006-3495(97)78248-1  0.476
1997 Houchmandzadeh B, Marko JF, Chatenay D, Libchaber A. Elasticity and structure of eukaryote chromosomes studied by micromanipulation and micropipette aspiration. The Journal of Cell Biology. 139: 1-12. PMID 9314524 DOI: 10.1083/Jcb.139.1.1  0.452
1997 Oram M, Marko JF, Halford SE. Communications between distant sites on supercoiled DNA from non-exponential kinetics for DNA synapsis by resolvase. Journal of Molecular Biology. 270: 396-412. PMID 9237906 DOI: 10.1006/Jmbi.1997.1109  0.515
1997 Vologodskii AV, Marko JF. Extension of torsionally stressed DNA by external force Biophysical Journal. 73: 123-132. PMID 9199777 DOI: 10.1016/S0006-3495(97)78053-6  0.431
1997 Marko JF. Stretching must twist DNA Europhysics Letters. 38: 183-188. DOI: 10.1209/Epl/I1997-00223-5  0.498
1997 Marko JF. Supercoiled and braided DNA under tension Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 55: 1758-1772. DOI: 10.1103/Physreve.55.1758  0.494
1997 Marko JF. The internal ‘slithering’ dynamics of supercoiled DNA Physica a-Statistical Mechanics and Its Applications. 244: 263-277. DOI: 10.1016/S0378-4371(97)00295-1  0.493
1997 Marko JF. The internal 'slithering' dynamics of supercoiled DNA Physica a: Statistical Mechanics and Its Applications. 244: 263-277.  0.393
1996 Marko JF. Stretched, Twisted, Supercoiled and Braided DNA Mrs Proceedings. 463. DOI: 10.1557/Proc-463-31  0.512
1996 Barkema GT, Caron C, Marko JF. Scaling properties of gel electrophoresis of DNA Biopolymers. 38: 665-667. DOI: 10.1002/(Sici)1097-0282(199605)38:5<665::Aid-Bip10>3.0.Co;2-7  0.409
1995 Marko JF, Siggia ED. Statistical mechanics of supercoiled DNA Physical Review E. 52: 2912-2938. DOI: 10.1103/Physreve.52.2912  0.5
1995 Marko JF, Siggia ED. Stretching DNA Macromolecules. 28: 8759-8770.  0.369
1994 Bustamante C, Marko JF, Siggia ED, Smith S. Entropic elasticity of λ-phage DNA Science. 265: 1599-1600. PMID 8079175 DOI: 10.1126/Science.8079175  0.49
1994 Marko JF, Siggia ED. Fluctuations and supercoiling of DNA Science. 265: 506-508. PMID 8036491 DOI: 10.1126/Science.8036491  0.513
1994 Marko JF, Siggia ED. Bending and twisting elasticity of DNA Macromolecules. 27: 981-988. DOI: 10.1021/Ma00082A015  0.385
1989 Raja VN, Ratna BR, Shashidhar R, Heppke G, Bahr C, Marko JF, Indekeu JO, Berker AN. Pressure studies on phase transitions in 4-alkoxyphenyl-4'-nitrobenzoyloxybenzoates. Physical Review. A. 39: 4341-4344. PMID 9901780 DOI: 10.1103/Physreva.39.4341  0.439
1989 Marko JF, Indekeu JO, Berker AN. Mixtures in the frustrated spin-gas theory of reentrant polar liquid crystals. Physical Review. A. 39: 4201-4206. PMID 9901750 DOI: 10.1103/PhysRevA.39.4201  0.44
Show low-probability matches.