references.bib

@article{bannister2011ptm-review,
  title={Regulation of chromatin by histone modifications},
  author={Bannister, Andrew J and Kouzarides, Tony},
  journal={Cell research},
  volume={21},
  number={3},
  pages={381--395},
  year={2011},
  doi={10.1038/cr.2011.22},
},

@article{flaus2011mechanisms,
  title={Mechanisms for {ATP}-dependent chromatin remodelling: the
                  means to the end},
  author={Flaus, Andrew and Owen-Hughes, Tom},
  journal={Febs Journal},
  volume={278},
  number={19},
  pages={3579--3595},
  year={2011},
  doi={10.1111/j.1742-4658.2011.08281.x},
},

@article{TalbertHenikoff2010,
  title = {Histone variants -- ancient wrap artists of the epigenome},
  author = {Talbert, Paul B. and Henikoff, Stephen},
  journal = {Nature Reviews Molecular Cell Biology},
  volume = {11},
  number = {4},
  pages = {264-275},
  year = {2010},
  doi = {10.1038/nrm2861},
  pmid = {20197778},
},

@incollection{mcginty2014histone,
  title={Histone, nucleosome, and chromatin structure},
  author={McGinty, Robert K and Tan, Song},
  booktitle={Fundamentals of Chromatin},
  pages={1--28},
  year={2014},
  doi={10.1021/cr500373h},
},

@article{kuznetsova2016chromatin,
  title={Chromatin fibers: from classical descriptions to modern
                  interpretation},
  author={Kuznetsova, Maria A and Sheval, Eugene V},
  journal={Cell Biology International},
  year={2016},
  doi={10.1002/cbin.10672},
},

@article{andrews2011nucleosome,
  title={Nucleosome structure(s) and stability: variations on a
                  theme},
  author={Andrews, Andrew J and Luger, Karolin},
  journal={Annual review of biophysics},
  volume={40},
  pages={99--117},
  year={2011},
  doi={10.1146/annurev-biophys-042910-155329},
},

@article{flaus2017unlocking,
  title={Unlocking the nucleosome},
  author={Flaus, Andrew and Owen-Hughes, Tom},
  journal={Science},
  volume={355},
  number={6322},
  pages={245--246},
  year={2017},
  doi={10.1126/science.aam5403},
},

@article{mcnally-frap-code,
  title={Evidence for a common mode of transcription factor
                  interaction with chromatin as revealed by improved
                  quantitative fluorescence recovery after
                  photobleaching},
  author={Mueller, Florian and Wach, Paul and McNally, James G},
  journal={Biophysical journal},
  volume={94},
  number={8},
  pages={3323--3339},
  year={2008},
  doi={10.1529/biophysj.107.123182},
},

@article{stackreg,
  title={A pyramid approach to subpixel registration based on
                  intensity},
  author={Th\'evenaz, Philippe and Ruttimann, Urs E and Unser,
                  Michael},
  journal={IEEE Transactions on Image Processing},
  volume={7},
  number={1},
  pages={27--41},
  year={1998},
},

@article{KimuraCook,
  title={Kinetics of core histones in living human cells: little
                  exchange of {H3} and {H4} and some rapid exchange of
                  {H2B}},
  author={Kimura, Hiroshi and Cook, Peter R.},
  journal={The Journal of cell biology},
  volume={153},
  number={7},
  pages={1341--1353},
  year={2001},
  doi={10.1083/jcb.153.7.1341},
},

@article{flaus2004sin,
  title={Sin mutations alter inherent nucleosome mobility},
  author={Flaus, Andrew and Rencurel, Chantal and Ferreira, Helder and
                  Wiechens, Nicola and Owen-Hughes, Tom},
  journal={The {EMBO} journal},
  volume={23},
  number={2},
  pages={343--353},
  year={2004},
  doi={10.1038/sj.emboj.7600047},
},

@article{HeLaCellCycle,
  title={A search for differential polypeptide synthesis throughout
                  the cell cycle of {HeLa} cells},
  author={Bravo, Rodrigo and Celis, Julio E.},
  journal={The Journal of cell biology},
  volume={84},
  number={3},
  pages={795--802},
  year={1980},
},

@article{visualizationG1chromosomes,
  title={Visualization of {G1} chromosomes: a folded, twisted,
                  supercoiled chromonema model of interphase chromatid
                  structure},
  author={Belmont, Andrew S and Bruce, Kathy},
  journal={The Journal of cell biology},
  volume={127},
  number={2},
  pages={287--302},
  year={1994},
},

@article{earlyg1position,
  title={The radial positioning of chromatin is not inherited through
                  mitosis but is established de novo in early {G1}},
  author={Thomson, Inga and Gilchrist, Susan and Bickmore, Wendy A and
                  Chubb, Jonathan R},
  journal={Current biology},
  volume={14},
  number={2},
  pages={166--172},
  year={2004},
},

@article{RelativeChromosomePosition,
  title={Dynamics of relative chromosome position during the cell
                  cycle},
  author={Essers, Jeroen and van Cappellen, Wiggert A and Theil, Arjan
                  F and van Drunen, Ellen and Jaspers, Nicolaas GJ and
                  Hoeijmakers, Jan HJ and Wyman, Claire and Vermeulen,
                  Wim and Kanaar, Roland},
  journal={Molecular biology of the cell},
  volume={16},
  number={2},
  pages={769--775},
  year={2005},
},

@article{PancreaticCells,
  title={A comprehensive characterization of pancreatic ductal
                  carcinoma cell lines: towards the establishment of
                  an in vitro research platform},
  author={Sipos, Bence and M{\"o}ser, Simone and Kalthoff, Holger and
                  T{\"o}r{\"o}k, Virag and L{\"o}hr, Matthias and
                  Kl{\"o}ppel, G{\"u}nter},
  journal={Virchows Archiv},
  volume={442},
  number={5},
  pages={444--452},
  year={2003},
  doi={10.1007/s00428-003-0784-4},
},

@article{SerumStarvation,
  title={Serum starvation: caveat emptor},
  author={Pirkmajer, Sergej and Chibalin, Alexander V},
  journal={American Journal of Physiology-Cell Physiology},
  volume={301},
  number={2},
  pages={C272--C279},
  year={2011},
  doi={10.1152/ajpcell.00091.2011},
},

@article{Kevin-pCA-TAG,
  title={Assembly of {CENP--A} into centromeric chromatin requires a
                  cooperative array of nucleosomal {DNA} contact
                  sites},
  author={Shelby, Richard D. and Vafa, Omid and Sullivan, Kevin F.},
  journal={The Journal of cell biology},
  volume={136},
  number={3},
  pages={501--513},
  year={1997},
},

@article{DNA-replication-timing,
  title={{DNA} replication timing},
  author={Rhind, Nicholas and Gilbert, David M.},
  journal={Cold Spring Harbor perspectives in biology},
  volume={5},
  number={8},
  pages={a010132},
  year={2013},
  doi={10.1101/cshperspect.a010132},
},

@article{excess-histone,
  title={Histone {mRNA} expression: multiple levels of cell cycle
                  regulation and important developmental
                  consequences},
  author={Marzluff, William F. and Duronio, Robert J.},
  journal={Current opinion in cell biology},
  volume={14},
  number={6},
  pages={692--699},
  year={2002},
},

@article{drosophila-excess-histone1,
  title={Drosophila stem loop binding protein coordinates accumulation
                  of mature histone {mRNA} with cell cycle
                  progression},
  author={Sullivan, Eileen and Santiago, Carlos and Parker, Emily
                  D. and Dominski, Zbigniew and Yang, Xiaocui and
                  Lanzotti, David J. and Ingledue, Tom C. and
                  Marzluff, William F. and Duronio, Robert J.},
  journal={Genes \& development},
  volume={15},
  number={2},
  pages={173--187},
  year={2001},
},

@article{drosophila-excess-histone2,
  title={The maternal effect gene, abnormal oocyte (abo), of
                  {D}rosophila melanogaster encodes a specific
                  negative regulator of histones},
  author={Berloco, Maria and Fanti, Laura and Breiling, Achim and
                  Orlando, Valerio and Pimpinelli, Sergio},
  journal={Proceedings of the National Academy of Sciences},
  volume={98},
  number={21},
  pages={12126--12131},
  year={2001},
},

@article{regulated-histone-proteolysis,
  title={The emergence of regulated histone proteolysis},
  author={Gunjan, Akash and Paik, Johanna and Verreault, Alain},
  journal={Current opinion in genetics \& development},
  volume={16},
  number={2},
  pages={112--118},
  year={2006},
},

@article{histone-ubiqui-proteolysis,
  title={Histone levels are regulated by phosphorylation and
                  ubiquitylation-dependent proteolysis},
  author={Singh, Rakesh Kumar and Kabbaj, Marie-Helene Miquel and
                  Paik, Johanna and Gunjan, Akash},
  journal={Nature cell biology},
  volume={11},
  number={8},
  pages={925--933},
  year={2009},
},

@article{histone-control-immobile1,
  title={High mobility of proteins in the mammalian cell nucleus},
  author={Phair, Robert D. and Misteli, Tom},
  journal={Nature},
  volume={404},
  number={6778},
  pages={604--609},
  year={2000},
},

@article{histone-control-immobile2,
  title={Changes in mobility account for camptothecin-induced
                  subnuclear relocation of topoisomerase {I}},
  author={Christensen, Morten O. and Barthelmes, Hans U. and Feineis,
                  Silke and Knudsen, Birgitta R. and Andersen, Anni
                  H. and Boege, Fritz and Mielke, Christian},
  journal={Journal of Biological Chemistry},
  volume={277},
  number={18},
  pages={15661--15665},
  year={2002},
},

@article{H4PAGFP-chromatin-movement,
  title={Chromatin movement visualized with photoactivable
                  {GFP}--labeled histone {H4}},
  author={Wiesmeijer, Karien and Krouwels, Ilke M. and Tanke, Hans
                  J. and Dirks, Roeland W.},
  journal={Differentiation},
  volume={76},
  number={1},
  pages={83--90},
  year={2008},
  doi={10.1111/j.1432-0436.2007.00234.x},
},

@article{luger1997crystal,
  title={Crystal structure of the nucleosome core particle at 2.8
                  {\AA} resolution},
  author={Luger, Karolin and M{\"a}der, Armin W. and Richmond, Robin
                  K. and Sargent, David F. and Richmond, Timothy J.},
  journal={Nature},
  volume={389},
  number={6648},
  pages={251--260},
  year={1997},
},

@article{SNF-mutants-original-discovery,
  title={Mutants of yeast defective in sucrose utilization},
  author={Carlson, Marian and Osmond, Barbara C. and Botstein, David},
  journal={Genetics},
  volume={98},
  number={1},
  pages={25--40},
  year={1981},
},

@article{SNF-mutants2,
  title={Genes affecting the regulation of {SUC2} gene expression by
                  glucose repression in Saccharomyces cerevisiae},
  author={Neigeborn, Lenore and Carlson, Marian},
  journal={Genetics},
  volume={108},
  number={4},
  pages={845--858},
  year={1984},
},

@article{SWI-mutants,
  title={Five {SWI} genes are required for expression of the {HO} gene
                  in yeast},
  author={Stern, Michael and Jensen, Robert and Herskowitz, Ira},
  journal={Journal of molecular biology},
  volume={178},
  number={4},
  pages={853--868},
  year={1984},
},

@manual{octave,
  title = {{GNU Octave} version 4.2.0 manual: a high-level interactive
                  language for numerical computations},
  author = {John W. Eaton and David Bateman and S\oren Hauberg and Rik
                  Wehbring},
  year = {2016},
  url = {http://www.gnu.org/software/octave/doc/interpreter},
},

@article{imagej1,
  title={{NIH} {I}mage to {ImageJ}: 25 years of image analysis},
  author={Schneider, Caroline A and Rasband, Wayne S and Eliceiri,
                  Kevin W},
  journal={Nature methods},
  volume={9},
  number={7},
  pages={671--675},
  year={2012},
  doi={10.1038/nmeth.2089},
},

@article{kruger1995amino,
  title={Amino acid substitutions in the structured domains of
                  histones {H3} and {H4} partially relieve the
                  requirement of the yeast {SWI/SNF} complex for
                  transcription.},
  author={Kruger, Warren and Peterson, Craig L and Sil, Anita and
                  Coburn, Cara and Arents, Gina and Moudrianakis,
                  Evangelos N and Herskowitz, Ira},
  journal={Genes \& Development},
  volume={9},
  number={22},
  pages={2770--2779},
  year={1995},
  doi={10.1101/gad.9.22.2770},
},

@article{muthurajan2004crystal,
  title={Crystal structures of histone Sin mutant nucleosomes reveal
                  altered protein--{DNA} interactions},
  author={Muthurajan, Uma M and Bao, Yunhe and Forsberg, Lawrence J
                  and Edayathumangalam, Rajeswari S and Dyer, Pamela N
                  and White, Cindy L and Luger, Karolin},
  journal={The {EMBO} journal},
  volume={23},
  number={2},
  pages={260--271},
  year={2004},
  doi={10.1038/sj.emboj.7600046},
},

@article{phair2000high,
  title={High mobility of proteins in the mammalian cell nucleus},
  author={Phair, Robert D and Misteli, Tom},
  journal={Nature},
  volume={404},
  number={6778},
  pages={604--609},
  year={2000},
  doi={10.1038/35007077},
},

@article{agresti2005gr,
  title={{GR} and {HMGB1} interact only within chromatin and influence
                  each other's residence time},
  author={Agresti, Alessandra and Scaffidi, Paola and Riva, Alberto
                  and Caiolfa, Valeria R and Bianchi, Marco E},
  journal={Molecular cell},
  volume={18},
  number={1},
  pages={109--121},
  year={2005},
  doi={10.1016/j.molcel.2005.03.005},
},

@article{essers2005nuclear,
  title={Nuclear dynamics of {PCNA} in {DNA} replication and repair},
  author={Essers, Jeroen and Theil, Arjan F and Baldeyron, C{\'e}line
                  and van Cappellen, Wiggert A and Houtsmuller,
                  Adriaan B and Kanaar, Roland and Vermeulen, Wim},
  journal={Molecular and cellular biology},
  volume={25},
  number={21},
  pages={9350--9359},
  year={2005},
  doi={10.1128/MCB.25.21.9350-9359.2005},
},

@article{abney1997chromatin,
  title={Chromatin dynamics in interphase nuclei and its implications
                  for nuclear structure},
  author={Abney, James R and Cutler, Bryan and Fillbach, Misty L and
                  Axelrod, Daniel and Scalettar, Bethe A},
  journal={The Journal of cell biology},
  volume={137},
  number={7},
  pages={1459--1468},
  year={1997},
  doi={10.1083/jcb.137.7.1459},
},

@article{dey2000bromodomain,
  title={A bromodomain protein, {MCAP}, associates with mitotic
                  chromosomes and affects {G}$_2$-to-{M} transition},
  author={Dey, Anup and Ellenberg, Jan and Farina, Andrea and Coleman,
                  Allen E and Maruyama, Tetsuo and Sciortino,
                  Selvaggia and Lippincott-Schwartz, Jennifer and
                  Ozato, Keiko},
  journal={Molecular and cellular biology},
  volume={20},
  number={17},
  pages={6537--6549},
  year={2000},
  doi={10.1128/MCB.20.17.6537-6549.2000},
},

@article{KevinH2BGFP,
  title={Histone--{GFP} fusion protein enables sensitive analysis of
                  chromosome dynamics in living mammalian cells},
  author={Kanda, Teru and Sullivan, Kevin F. and Wahl, Geoffrey M.},
  journal={Current Biology},
  volume={8},
  number={7},
  pages={377--385},
  year={1998},
  doi={10.1016/S0960-9822(98)70156-3},
},

@article{mcnally-frap-2010,
  title={{FRAP} and kinetic modeling in the analysis of nuclear
                  protein dynamics: what do we really know?},
  author={Mueller, Florian and Mazza, Davide and Stasevich, Timothy J
                  and McNally, James G},
  journal={Current opinion in cell biology},
  volume={22},
  number={3},
  pages={403--411},
  year={2010},
  doi={10.1016/j.ceb.2010.03.002},
},

@article{pMH3-plasmid,
  title={Sequences of four mouse histone {H3} genes: implications for
                  evolution of mouse histone genes},
  author={Taylor, J David and Wellman, Susan E and Marzluff, William
                  F},
  journal={Journal of molecular evolution},
  volume={23},
  number={3},
  pages={242--249},
  year={1986},
  doi={10.1007/BF02115580},
},

@article{stephenson1982locomotory,
  title={Locomotory invasion of human cervical epithelium and avian
                  fibroblasts by {H}e{L}a cells in vitro},
  author={Stephenson, EM},
  journal={Journal of cell science},
  volume={57},
  number={1},
  pages={293--314},
  year={1982},
},

@article{abercrombie1970contact,
  title={Contact inhibition in tissue culture},
  author={Abercrombie, M},
  journal={In vitro},
  volume={6},
  number={2},
  pages={128--142},
  year={1970},
  doi={10.1007/BF02616114},
},

@article{kuipers2011highly,
  title={Highly stable loading of {M}cm proteins onto chromatin in
                  living cells requires replication to unload},
  author={Kuipers, Marjorie A and Stasevich, Timothy J and Sasaki,
                  Takayo and Wilson, Korey A and Hazelwood, Kristin L
                  and McNally, James G and Davidson, Michael W and
                  Gilbert, David M},
  journal={The Journal of cell biology},
  volume={192},
  number={1},
  pages={29--41},
  year={2011},
  doi={10.1083/jcb.201007111},
},

@article{jullien2016chromatibody,
  title={Chromatibody, a novel non-invasive molecular tool to explore
                  and manipulate chromatin in living cells},
  author={Jullien, Denis and Vignard, Julien and Fedor, Yoann and
                  B{\'e}ry, Nicolas and Olichon, Aur{\'e}lien and
                  Crozatier, Mich{\`e}le and Erard, Monique and
                  Cassard, Herv{\'e} and Ducommun, Bernard and Salles,
                  Bernard and Mirey, Gladys},
  journal={J Cell Sci},
  volume={129},
  number={13},
  pages={2673--2683},
  year={2016},
  doi={10.1242/jcs.183103},
},

@article{sun2000size,
  title={Size-dependent positioning of human chromosomes in interphase
                  nuclei},
  author={Sun, Hui Bin and Shen, Jin and Yokota, Hiroki},
  journal={Biophysical journal},
  volume={79},
  number={1},
  pages={184--190},
  year={2000},
  doi={10.1016/S0006-3495(00)76282-5},
},

@article{gorisch2005histone,
  title={Histone acetylation increases chromatin accessibility},
  author={G{\"o}risch, Sabine M and Wachsmuth, Malte and T{\'o}th,
                  Katalin Fejes and Lichter, Peter and Rippe, Karsten},
  journal={Journal of cell science},
  volume={118},
  number={24},
  pages={5825--5834},
  year={2005},
  doi={10.1242/jcs.02689},
},