Bibliography for DNA Option Course 2018 - 2019 BETA

@article{Abe_Dror_Yang_Slattery_Zhou_Bussemaker_Rohs_Mann_2015, title={Deconvolving the Recognition of DNA Shape from Sequence}, volume={161}, DOI={10.1016/j.cell.2015.02.008}, number={2}, journal={Cell}, author={Abe, Namiko and Dror, Iris and Yang, Lin and Slattery, Matthew and Zhou, Tianyin and Bussemaker, Harmen J. and Rohs, Remo and Mann, Richard S.}, year={2015}, month={Apr}, pages={307–318} }

@article{Adli_2018, title={The CRISPR tool kit for genome editing and beyond}, volume={9}, DOI={10.1038/s41467-018-04252-2}, number={1}, journal={Nature Communications}, author={Adli, Mazhar}, year={2018}, month={Dec} }

@book{Alberts_2015, address={New York, NY}, edition={Sixth edition}, title={Molecular biology of the cell}, publisher={Garland Science, Taylor and Francis Group}, author={Alberts, Bruce}, year={2015} }

@article{Bogdanove_Bohm_Miller_Morgan_Stoddard_2018, title={Engineering altered protein–DNA recognition specificity}, volume={46}, DOI={10.1093/nar/gky289}, number={10}, journal={Nucleic Acids Research}, author={Bogdanove, Adam J and Bohm, Andrew and Miller, Jeffrey C and Morgan, Richard D and Stoddard, Barry L}, year={2018}, month={Jun}, pages={4845–4871} }

@book{Calladine_2004, address={San Diego, Calif}, edition={3rd ed}, title={1. Understanding DNA: the molecule & how it works}, publisher={Academic}, author={Calladine, C. R.}, year={2004} }

@article{Cejka_2017, title={Biochemistry: Complex assistance for DNA invasion}, DOI={10.1038/nature24149}, journal={Nature}, author={Cejka, Petr}, year={2017}, month={Oct} }

@article{Chandrasekaran_Anderson_Kizer_Halvorsen_Wang_2016, title={5. Beyond the Fold: Emerging Biological Applications of DNA Origami}, volume={17}, DOI={10.1002/cbic.201600038}, number={12}, journal={ChemBioChem}, author={Chandrasekaran, Arun Richard and Anderson, Nate and Kizer, Megan and Halvorsen, Ken and Wang, Xing}, year={2016}, month={Jun}, pages={1081–1089} }

@article{Chen_Chan_Hsieh_2013, title={New Mechanistic and Functional Insights into DNA Topoisomerases}, volume={82}, DOI={10.1146/annurev-biochem-061809-100002}, number={1}, journal={Annual Review of Biochemistry}, author={Chen, Stefanie Hartman and Chan, Nei-Li and Hsieh, Tao-shih}, year={2013}, month={Jun}, pages={139–170} }

@article{Clapier_Iwasa_Cairns_Peterson_2017, title={16. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes}, volume={18}, DOI={10.1038/nrm.2017.26}, number={7}, journal={Nature Reviews Molecular Cell Biology}, author={Clapier, Cedric R. and Iwasa, Janet and Cairns, Bradley R. and Peterson, Craig L.}, year={2017}, month={May}, pages={407–422} }

@article{Deindl_Hwang_Hota_Blosser_Prasad_Bartholomew_Zhuang_2013, title={ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps and Single-Base-Pair Exit Steps}, volume={152}, DOI={10.1016/j.cell.2012.12.040}, number={3}, journal={Cell}, author={Deindl, Sebastian and Hwang, William L. and Hota, Swetansu K. and Blosser, Timothy R. and Prasad, Punit and Bartholomew, Blaine and Zhuang, Xiaowei}, year={2013}, month={Jan}, pages={442–452} }

@article{Doublié_Zahn_2014, title={Structural insights into eukaryotic DNA replication}, volume={5}, DOI={10.3389/fmicb.2014.00444}, journal={Frontiers in Microbiology}, author={Doublié, Sylvie and Zahn, Karl E.}, year={2014}, month={Aug} }

@article{Gilbert_Allan_2014, title={Supercoiling in DNA and chromatin}, volume={25}, DOI={10.1016/j.gde.2013.10.013}, journal={Current Opinion in Genetics & Development}, author={Gilbert, Nick and Allan, James}, year={2014}, month={Apr}, pages={15–21} }

@article{Goodarzi_Jeggo_2013, title={25. The Repair and Signaling Responses to DNA Double-Strand Breaks}, volume={82}, url={http://ezproxy.lib.gla.ac.uk/login?url=http://linkinghub.elsevier.com/retrieve/pii/B9780124076761000019}, DOI={10.1016/B978-0-12-407676-1.00001-9}, journal={Adv Genet}, publisher={Elsevier}, author={Goodarzi, Aaron A. and Jeggo, Penelope A.}, year={2013}, pages={1–45} }

@article{Graham_Marians_Kowalczykowski_2017, title={Independent and Stochastic Action of DNA Polymerases in the Replisome}, volume={169}, DOI={10.1016/j.cell.2017.05.041}, number={7}, journal={Cell}, author={Graham, James E. and Marians, Kenneth J. and Kowalczykowski, Stephen C.}, year={2017}, month={Jun}, pages={1201-1213.e17} }

@article{Hänsel-Hertsch_Di Antonio_Balasubramanian_2017, title={4. DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential}, volume={18}, DOI={10.1038/nrm.2017.3}, number={5}, journal={Nature Reviews Molecular Cell Biology}, author={Hänsel-Hertsch, Robert and Di Antonio, Marco and Balasubramanian, Shankar}, year={2017}, month={Feb}, pages={279–284} }

@article{Hille_Richter_Wong_Bratovič_Ressel_Charpentier_2018, title={The Biology of CRISPR-Cas: Backward and Forward}, volume={172}, DOI={10.1016/j.cell.2017.11.032}, number={6}, journal={Cell}, author={Hille, Frank and Richter, Hagen and Wong, Shi Pey and Bratovič, Majda and Ressel, Sarah and Charpentier, Emmanuelle}, year={2018}, month={Mar}, pages={1239–1259} }

@article{Jia_Chai_Zhang_Fan_2017, title={Novel insights into chromosomal conformations in cancer}, volume={16}, DOI={10.1186/s12943-017-0741-5}, number={1}, journal={Molecular Cancer}, author={Jia, Ruobing and Chai, Peiwei and Zhang, He and Fan, Xianqun}, year={2017}, month={Dec} }

@article{Kaniecki_De Tullio_Greene_2017, title={A change of view: homologous recombination at single-molecule resolution}, volume={19}, DOI={10.1038/nrg.2017.92}, number={4}, journal={Nature Reviews Genetics}, author={Kaniecki, Kyle and De Tullio, Luisina and Greene, Eric C.}, year={2017}, month={Dec}, pages={191–207} }

@book{Krebs_Goldstein_Kilpatrick_2018, address={Burlington, Mass}, edition={12th ed}, title={Lewin’s genes XII}, publisher={Jones & Bartlett Learning}, author={Krebs, Jocelyn E. and Goldstein, Elliott S. and Kilpatrick, Stephen T.}, year={2018} }

@article{Ledford_2017, title={Five big mysteries about CRISPR’s origins}, volume={541}, DOI={10.1038/541280a}, number={7637}, journal={Nature}, author={Ledford, Heidi}, year={2017}, month={Jan}, pages={280–282} }

@article{Lelli_Slattery_Mann_2012, title={14. Disentangling the Many Layers of Eukaryotic Transcriptional Regulation}, volume={46}, DOI={10.1146/annurev-genet-110711-155437}, number={1}, journal={Annual Review of Genetics}, author={Lelli, Katherine M. and Slattery, Matthew and Mann, Richard S.}, year={2012}, month={Dec}, pages={43–68} }

@article{Lesbats_Engelman_Cherepanov_2016, title={23. Retroviral DNA Integration}, volume={116}, DOI={10.1021/acs.chemrev.6b00125}, number={20}, journal={Chemical Reviews}, author={Lesbats, Paul and Engelman, Alan N. and Cherepanov, Peter}, year={2016}, month={Oct}, pages={12730–12757} }

@article{Liu_Keijzers_Rasmussen_2017, title={24. DNA mismatch repair and its many roles in eukaryotic cells}, volume={773}, DOI={10.1016/j.mrrev.2017.07.001}, journal={Mutation Research/Reviews in Mutation Research}, author={Liu, Dekang and Keijzers, Guido and Rasmussen, Lene Juel}, year={2017}, month={Jul}, pages={174–187} }

@book{Lodish_2013, address={New York}, edition={7th ed., international ed}, title={Molecular cell biology}, publisher={W.H. Freeman and Company}, author={Lodish, Harvey F.}, year={2013} }

@article{2018a, title={Understanding the origins of human cancer}, url={http://science.sciencemag.org/content/350/6265/1175.1.long}, journal={Science}, author={Ludmil B Alexandrov}, year={2018} }

@article{2016, title={Mutational signatures associated with tobacco smoking in human cancer}, url={http://ezproxy.lib.gla.ac.uk/login?url=http://science.sciencemag.org/content/354/6312/618.long}, journal={Mutational signatures associated with tobacco smoking in human cancer}, author={Ludmil B Alexandrov et al.}, year={2016} }

@article{2018b, title={The chromatin accessibility landscape of primary human cancers}, url={http://science.sciencemag.org/content/362/6413/eaav1898.long}, journal={Science}, author={M Ryan Corces et al.}, year={2018} }

@article{Marteijn_Lans_Vermeulen_Hoeijmakers_2014, title={26. Understanding nucleotide excision repair and its roles in cancer and ageing}, volume={15}, DOI={10.1038/nrm3822}, number={7}, journal={Nature Reviews Molecular Cell Biology}, author={Marteijn, Jurgen A. and Lans, Hannes and Vermeulen, Wim and Hoeijmakers, Jan H. J.}, year={2014}, month={Jun}, pages={465–481} }

@article{Modrich_2016, title={Mechanisms in                              and Human Mismatch Repair (Nobel Lecture)}, volume={55}, DOI={10.1002/anie.201601412}, number={30}, journal={Angewandte Chemie International Edition}, author={Modrich, Paul}, year={2016}, month={Jul}, pages={8490–8501} }

@article{Montaño_Rice_2011, title={Moving DNA around: DNA transposition and retroviral integration}, volume={21}, DOI={10.1016/j.sbi.2011.03.004}, number={3}, journal={Current Opinion in Structural Biology}, author={Montaño, Sherwin P and Rice, Phoebe A}, year={2011}, month={Jun}, pages={370–378} }

@article{Nelson_Finch_Luisi_Klug_1987, title={3. The structure of an oligo(dA)-oligo(dT) tract and its biological implications}, volume={330}, url={http://ezproxy.lib.gla.ac.uk/login?url=https://www.nature.com/nature/journal/v330/n6145/abs/330221a0.html}, number={6145}, journal={Nature}, author={Nelson, Hillary C. M. and Finch, John T. and Luisi, Bonaventura F. and Klug, Aaron}, year={1987}, month={Nov}, pages={221–226} }

@article{Nogales_Louder_He_2017, title={12. Structural Insights into the Eukaryotic Transcription Initiation Machinery}, volume={46}, DOI={10.1146/annurev-biophys-070816-033751}, number={1}, journal={Annual Review of Biophysics}, author={Nogales, Eva and Louder, Robert K. and He, Yuan}, year={2017}, month={May}, pages={59–83} }

@article{Nudler_2009, title={13. RNA Polymerase Active Center: The Molecular Engine of Transcription}, volume={78}, DOI={10.1146/annurev.biochem.76.052705.164655}, number={1}, journal={Annual Review of Biochemistry}, author={Nudler, Evgeny}, year={2009}, month={Jun}, pages={335–361} }

@article{Pennisi_2003, title={DNA’s Cast of Thousands}, volume={300}, DOI={10.1126/science.300.5617.282}, number={5617}, journal={Science}, author={Pennisi, E.}, year={2003}, month={Apr}, pages={282–285} }

@article{Pomerantz_O’Donnell_2007, title={18. Replisome mechanics: insights into a twin DNA polymerase machine}, volume={15}, DOI={10.1016/j.tim.2007.02.007}, number={4}, journal={Trends in Microbiology}, author={Pomerantz, Richard T. and O’Donnell, Mike}, year={2007}, month={Apr}, pages={156–164} }

@article{Renkawitz_Lademann_Jentsch_2014, title={19. Mechanisms and principles of homology search during recombination}, volume={15}, DOI={10.1038/nrm3805}, number={6}, journal={Nature Reviews Molecular Cell Biology}, author={Renkawitz, Jörg and Lademann, Claudio A. and Jentsch, Stefan}, year={2014}, month={May}, pages={369–383} }

@article{Rice_Yang_Mizuuchi_Nash_1996, title={7. Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn}, volume={87}, DOI={10.1016/S0092-8674(00)81824-3}, number={7}, journal={Cell}, author={Rice, Phoebe A and Yang, Shu-wei and Mizuuchi, Kiyoshi and Nash, Howard A}, year={1996}, month={Dec}, pages={1295–1306} }

@article{Rohs_Jin_West_Joshi_Honig_Mann_2010, title={6. Origins of Specificity in Protein-DNA Recognition}, volume={79}, DOI={10.1146/annurev-biochem-060408-091030}, number={1}, journal={Annual Review of Biochemistry}, author={Rohs, Remo and Jin, Xiangshu and West, Sean M. and Joshi, Rohit and Honig, Barry and Mann, Richard S.}, year={2010}, month={Jun}, pages={233–269} }

@article{Rowley_Corces_2018, title={Organizational principles of 3D genome architecture}, volume={19}, DOI={10.1038/s41576-018-0060-8}, number={12}, journal={Nature Reviews Genetics}, author={Rowley, M. Jordan and Corces, Victor G.}, year={2018}, month={Dec}, pages={789–800} }

@article{Schoeffler_Berger_2008, title={11. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology}, volume={41}, DOI={10.1017/S003358350800468X}, number={01}, journal={Quarterly Reviews of Biophysics}, author={Schoeffler, Allyn J. and Berger, James M.}, year={2008}, month={Feb} }

@article{Swinger_Rice_2004, title={IHF and HU: flexible architects of bent DNA}, volume={14}, DOI={10.1016/j.sbi.2003.12.003}, number={1}, journal={Current Opinion in Structural Biology}, author={Swinger, Kerren K and Rice, Phoebe A}, year={2004}, month={Feb}, pages={28–35} }

@article{Terakawa_Bisht_Eeftens_Dekker_Haering_Greene_2017, title={The condensin complex is a mechanochemical motor that translocates along DNA}, volume={358}, DOI={10.1126/science.aan6516}, number={6363}, journal={Science}, author={Terakawa, Tsuyoshi and Bisht, Shveta and Eeftens, Jorine M. and Dekker, Cees and Haering, Christian H. and Greene, Eric C.}, year={2017}, month={Nov}, pages={672–676} }

@article{Tessarz_Kouzarides_2014, title={Histone core modifications regulating nucleosome structure and dynamics}, volume={15}, DOI={10.1038/nrm3890}, number={11}, journal={Nature Reviews Molecular Cell Biology}, author={Tessarz, Peter and Kouzarides, Tony}, year={2014}, month={Oct}, pages={703–708} }

@article{Uhlmann_2016, title={17. SMC complexes: from DNA to chromosomes}, volume={17}, DOI={10.1038/nrm.2016.30}, number={7}, journal={Nature Reviews Molecular Cell Biology}, author={Uhlmann, Frank}, year={2016}, month={Apr}, pages={399–412} }

@article{Watson_Crick_1953, title={2. A Structure for Deoxyribose Nucleic Acid}, url={https://ezproxy.lib.gla.ac.uk/login?url=https://www.nature.com/articles/171737a0.pdf}, author={Watson, J.D. and Crick, F.H.C.}, year={1953} }

@article{West_2009, title={The search for a human Holliday junction resolvase}, volume={37}, DOI={10.1042/BST0370519}, number={3}, journal={Biochemical Society Transactions}, author={West, Stephen C.}, year={2009}, month={Jun}, pages={519–526} }

@article{Wigley_2012, title={21. Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB}, volume={11}, DOI={10.1038/nrmicro2917}, number={1}, journal={Nature Reviews Microbiology}, author={Wigley, Dale B.}, year={2012}, month={Dec}, pages={9–13} }

@article{Wright_Liu_Knott_Doxzen_Nogales_Doudna_2017, title={Structures of the CRISPR genome integration complex}, volume={357}, DOI={10.1126/science.aao0679}, number={6356}, journal={Science}, author={Wright, Addison V. and Liu, Jun-Jie and Knott, Gavin J. and Doxzen, Kevin W. and Nogales, Eva and Doudna, Jennifer A.}, year={2017}, month={Sep}, pages={1113–1118} }

@article{Zhao_Steinfeld_Liang_Chen_Maranon_Jian Ma_Kwon_Rao_Wang_Sheng_et al._2017, title={BRCA1–BARD1 promotes RAD51-mediated homologous DNA pairing}, volume={550}, DOI={10.1038/nature24060}, number={7676}, journal={Nature}, author={Zhao, Weixing and Steinfeld, Justin B. and Liang, Fengshan and Chen, Xiaoyong and Maranon, David G. and Jian Ma, Chu and Kwon, Youngho and Rao, Timsi and Wang, Weibin and Sheng, Chen and Song, Xuemei and Deng, Yanhong and Jimenez-Sainz, Judit and Lu, Lucy and Jensen, Ryan B. and Xiong, Yong and Kupfer, Gary M. and Wiese, Claudia and Greene, Eric C. and Sung, Patrick}, year={2017}, month={Oct}, pages={360–365} }