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@article{weblogo,
title = {{WebLogo}: a sequence logo generator},
author = {Crooks, G.E. and Hon, G. and Chandonia, J.M. and Brenner, S.E.},
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number = {6},
pages = {1188--1190},
year = {2004},
doi = {10.1101/gr.849004},
pmid = {15173120},
pmcid = {PMC419797},
},
@article{seqlogo,
author = {T. D. Schneider and R. M. Stephens},
title = {Sequence logos: a new way to display consensus sequences},
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pmcid = {PMC332411},
},
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publisher = {Elsevier},
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},
@inproceedings{nomenclature,
title = {Foreword: Histone Nomenclature},
booktitle = {The structure and function of chromatin},
series = {Ciba foundation symposium},
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organization = {Ciba foundation},
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isbn = {9021940310},
},
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author = {Alfred Zweidler},
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year = {1977},
doi = {10.1016/S0091-679X(08)61145-0},
pmid = {703614},
},
@article{reproducible-research-law,
author = {{\relax Yale Law School Roundtable on Data {and} Code Sharing}},
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year = {2010},
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doi = {10.1109/MCSE.2010.113},
address = {Los Alamitos, CA, USA},
},
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pmid = {16646837},
},
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title = {Chromatin compaction in terminally differentiated avian blood cells: the role of linker histone {H5} and non-histone protein {MENT}},
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pmcid = {PMC3139888},
},
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title = {A transcription map of the major histocompatibility complex ({MHC}) class {I} region},
author = {Gruen, JR and Nalabolu, SR and Chu, TW and Bowlus, C and Fan, WF and Goei, VL and Wei, H and Sivakamasundari, R and Liu, Y-C and Xu, HX and others},
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doi = {10.1006/geno.1996.0427},
pmid = {8812418},
},
%% See poster in supplementary data. That's where the data we reference
%% really is.
@article{MHC-complete-sequencing-1999,
title = {Complete sequence and gene map of a human major histocompatibility complex},
volume = {401},
number = {6756},
journal = {Nature},
author = {{\relax The MHC sequencing consortium}},
month = {Oct},
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pmid = {10553908},
},
@article{MHC-III-analysis,
title = {Analysis of the gene-dense major histocompatibility complex class {III} region and its comparison to mouse},
author = {Xie, Tao and Rowen, Lee and Aguado, Bego{\~n}a and Ahearn, Mary Ellen and Madan, Anup and Qin, Shizhen and Campbell, R Duncan and Hood, Leroy},
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pages = {2621--2636},
year = {2003},
doi = {10.1101/gr.1736803},
pmid = {14656967},
pmcid = {PMC403804},
},
%% There is no DOI for this article, even at the publisher site
@article{MHC-repressed-by-HIST,
title = {Evolving views of the major histocompatibility complex},
author = {Gruen, Jeffrey R and Weissman, Sherman M},
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},
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title = {Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome},
author = {Andrew J. Sharp and Sierra Hansen and Rebecca R. Selzer and Ze Cheng and Regina Regan and Jane A. Hurst and Helen Stewart and Sue M. Price and Edward Blair and Raoul C. Hennekam and Carrie A. Fitzpatrick and Rick Segraves and Todd A. Richmond and Cheryl Guiver and Donna G. Albertson and Daniel Pinkel and Peggy S. Eis and Stuart Schwartz and Samantha J. L. Knight and Evan E. Eichler},
journal = {Nature Genetics},
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pmid = {16906162},
},
@article{HISTTwo-prone-deletion-focus,
title = {Recurrent reciprocal 1q21. 1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities},
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volume = {40},
number = {12},
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year = {2008},
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pmid = {19029900},
pmcid = {PMC2680128},
},
@article{close-regulators,
title = {The regulation of histone synthesis in the cell cycle},
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pmid = {1883210},
},
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journal = {Science},
volume = {339},
number = {6117},
pages = {318-321},
year = {2013},
doi = {10.1126/science.1228705},
pmid = {23329046},
pmcid = {PMC3552377},
},
@article{SLBP-regulation,
title = {Stem-loop binding protein, the protein that binds the 3' end of histone {mRNA} is cell cycle regulated by both translational and posttranslational mechanisms},
author = {Whitfield, Michael L. and Zheng, Lian-Xing and Baldwin, Amy and Ohta, Tomohiko and Hurt, Myra M. and Marzluff, William F.},
journal = {Molecular and Cellular Biology},
volume = {20},
number = {12},
pages = {4188--4198},
year = {2000},
doi = {10.1128/MCB.20.12.4188-4198.2000},
pmid = {10825184},
pmcid = {PMC85788},
},
%% There is no DOI for this article, even at the publisher site
@article{HDE-sequence,
title = {The conserved {CAAGAAAGA} spacer sequence is an essential element for the formation of 3'termini of the sea urchin {H3} histone {mRNA} by {RNA} processing},
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pmcid = {PMC554211},
},
@article{HTwoAX-transcripts,
title = {{H2A.X}. a histone isoprotein with a conserved {C}-terminal sequence, is encoded by a novel {mRNA} with both {DNA} replication type and {polyA} 3' processing signals},
author = {Cecilia Mannironi and William M. Bonner and Christopher L. Hatch},
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year = {1989},
doi = {10.1093/nar/17.22.9113},
pmid = {2587254},
pmcid = {PMC335118},
},
@incollection{mutnomenclature2003,
title = {Mutation nomenclature},
author = {den Dunnen, J.T. and Antonarakis, S.E.},
booktitle = {Current Protocols in Human Genetics},
publisher = {Springer-Verlag},
chapter = {37},
pages = {7.13.1-7.13.8},
year = {2003},
doi = {10.1002/0471142905.hg0713s37},
pmid = {18428344},
isbn = {9780471142904},
},
%% Advance online so page numbers not yet given
@article{mutnomenclature2016,
title = {HGVS Recommendations for the Description of Sequence Variants: 2016 Update},
author = {Johan T. den Dunnen and Raymond Dalgleish and Donna R. Maglott and Reece K. Hart and Marc S. Greenblatt and Jean McGowan-Jordan and Anne-Francoise Roux and Timothy Smith and Stylianos E. Antonarakis and and Peter E.M. Taschner1},
journal = {Human Mutation},
volume = {37},
number = {5},
pages = {00000},
year = {2016},
doi = {10.1002/humu.22981},
pmid = {18428344},
},
@article{bioperl,
title = {The {Bioperl} toolkit: {Perl} modules for the life sciences},
author = {Jason E. Stajich and David Block and Kris Boulez and Steven E. Brenner and Stephen A. Chervitz and Chris Dagdigian and Georg Fuellen and James G. R. Gilbert and Ian Korf and Hilmar Lapp and Heikki Lehv{\"a}slaiho and Chad Matsalla and Chris J. Mungall and Brian I. Osborne and Matthew R. Pocock and Peter Schattner and Martin Senger and Lincoln D. Stein and Elia Stupka and Mark D. Wilkinson and Ewan Birney},
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volume = {12},
number = {10},
pages = {1611--1618},
year = {2002},
doi = {10.1101/gr.361602},
pmid = {12368254},
pmcid = {PMC187536},
},
@article{tcoffee2000,
title = {{T-Coffee}: a novel method for fast and accurate multiple sequence alignment},
author = {Notredame, C. and Higgins, D.G. and Heringa, J. and others},
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number = {1},
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pmid = {10964570},
},
@article{andrew-snf2-catalogue,
title = {Identification of multiple distinct {Snf2} subfamilies with conserved structural motifs},
author = {Flaus, Andrew and Martin, David M.A. and Barton, Geoffrey J. and Owen--Hughes, Tom},
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year = {2006},
doi = {10.1093/nar/gkl295},
pmid = {16738128},
pmcid = {PMC1474054},
},
@article{SCons2005,
title = {Building software with {SCons}},
author = {Knight, Steven},
journal = {Computing in Science and Engineering},
volume = {7},
number = {1},
pages = {79--88},
year = {2005},
doi = {10.1109/MCSE.2005.11(410)},
},
@incollection{our-H2AX-review,
author = {David Miguel Susano Pinto and Andrew Flaus},
title = {Structure and function of histone {H2AX}},
booktitle = {Genome Stability and Human Diseases},
year = {2010},
pages = {55--78},
editor = {Heinz--Peter Nasheuer},
publisher = {Springer Netherlands},
doi = {10.1007/978-90-481-3471-7\_4},
pmid = {20012577},
isbn = {978-90-481-3471-7},
},
@article{Luger1997structure,
title = {Crystal structure of the nucleosome core particle at 2.8{{\r A}} resolution},
author = {Luger, K. and Mader, A.W. and Richmond, R.K. and Sargent, D.F. and Richmond, T.J.},
journal = {Nature},
volume = {389},
number = {6648},
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doi = {10.1038/38444},
pmid = {9305837},
},
@article{HarshmanFreitas2013,
title = {{H1} histones: current perspectives and challenges},
author = {Harshman, S.W. and Young, N.L. and Parthun, M.R. and Freitas, M.A.},
journal = {Nucleic Acids Research},
volume = {41},
number = {21},
pages = {9593-609},
year = {2013},
doi = {10.1093/nar/gkt700},
pmid = {23945933},
pmcid = {PMC3834806},
},
@article{Kornberg1974,
title = {Chromatin structure: a repeating unit of histones and DNA},
author = {Kornberg, R.D.},
journal = {Science},
volume = {184},
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pages = {868–871},
year = {1974},
doi = {10.1126/science.184.4139.868},
pmid = {4825889},
},
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title = {Making scientific computations reproducible},
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number = {6},
pages = {61-67},
year = {2000},
doi = {10.1109/5992.881708},
},
@article{AlbigDoenecke1998,
title = {The haemochromatosis candidate gene {HFE} ({HLA-H}) of man and mouse is located in syntenic regions within the histone gene cluster},
author = {Albig, W. and Drabent, B. and Burmester, N. and Bode, C. and Doenecke, D.},
journal = {Journal of Cellular Biochemistry},
volume = {69},
number = {2},
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doi = {10.1002/(SICI)1097-4644(19980501)69:23.0.CO;2-V},
pmid = {9548560},
},
@incollection{Eirinlopez2009,
author = {Eirin-Lopez, J.M. and Gonz{\'a}lez-Romero, R. and Dryhurst, D. and M{\'e}ndez, J. and and Ausi{\'o}, J.},
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