Encode Ccres Database

references/citation.bib

@ARTICLE{Dunham2012,
  ABSTRACT = {The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80{\%} of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.},
  AUTHOR = {Dunham, Ian and Kundaje, Anshul and Aldred, Shelley F. and Collins, Patrick J. and Davis, Carrie A. and Doyle, Francis and Epstein, Charles B. and Frietze, Seth and Harrow, Jennifer and Kaul, Rajinder and Khatun, Jainab and Lajoie, Bryan R. and Landt, Stephen G. and Lee, Bum-Kyu and Pauli, Florencia and Rosenbloom, Kate R. and Sabo, Peter and Safi, Alexias and Sanyal, Amartya and Shoresh, Noam and Simon, Jeremy M. and Song, Lingyun and Trinklein, Nathan D. and Altshuler, Robert C. and Birney, Ewan and Brown, James B. and Cheng, Chao and Djebali, Sarah and Dong, Xianjun and Ernst, Jason and Furey, Terrence S. and Gerstein, Mark and Giardine, Belinda and Greven, Melissa and Hardison, Ross C. and Harris, Robert S. and Herrero, Javier and Hoffman, Michael M. and Iyer, Sowmya and Kellis, Manolis and Kheradpour, Pouya and Lassmann, Timo and Li, Qunhua and Lin, Xinying and Marinov, Georgi K. and Merkel, Angelika and Mortazavi, Ali and Parker, Stephen C. J. and Reddy, Timothy E. and Rozowsky, Joel and Schlesinger, Felix and Thurman, Robert E. and Wang, Jie and Ward, Lucas D. and Whitfield, Troy W. and Wilder, Steven P. and Wu, Weisheng and Xi, Hualin S. and Yip, Kevin Y. and Zhuang, Jiali and Bernstein, Bradley E. and Green, Eric D. and Gunter, Chris and Snyder, Michael and Pazin, Michael J. and Lowdon, Rebecca F. and Dillon, Laura A. L. and Adams, Leslie B. and Kelly, Caroline J. and Zhang, Julia and Wexler, Judith R. and Good, Peter J. and Feingold, Elise A. and Crawford, Gregory E. and Dekker, Job and Elnitski, Laura and Farnham, Peggy J. and Giddings, Morgan C. and Gingeras, Thomas R. and Guigó, Roderic and Hubbard, Timothy J. and Kent, W. James and Lieb, Jason D. and Margulies, Elliott H. and Myers, Richard M. and Stamatoyannopoulos, John A. and Tenenbaum, Scott A. and Weng, Zhiping and White, Kevin P. and Wold, Barbara and Yu, Yanbao and Wrobel, John and Risk, Brian A. and Gunawardena, Harsha P. and Kuiper, Heather C. and Maier, Christopher W. and Xie, Ling and Chen, Xian and Mikkelsen, Tarjei S. and Gillespie, Shawn and Goren, Alon and Ram, Oren and Zhang, Xiaolan and Wang, Li and Issner, Robbyn and Coyne, Michael J. and Durham, Timothy and Ku, Manching and Truong, Thanh and Eaton, Matthew L. and Dobin, Alex and Tanzer, Andrea and Lagarde, Julien and Lin, Wei and Xue, Chenghai and Williams, Brian A. and Zaleski, Chris and Röder, Maik and Kokocinski, Felix and Abdelhamid, Rehab F. and Alioto, Tyler and Antoshechkin, Igor and Baer, Michael T. and Batut, Philippe and Bell, Ian and Bell, Kimberly and Chakrabortty, Sudipto and Chrast, Jacqueline and Curado, Joao and Derrien, Thomas and Drenkow, Jorg and Dumais, Erica and Dumais, Jackie and Duttagupta, Radha and Fastuca, Megan and Fejes-Toth, Kata and Ferreira, Pedro and Foissac, Sylvain and Fullwood, Melissa J. and Gao, Hui and Gonzalez, David and Gordon, Assaf and Howald, Cédric and Jha, Sonali and Johnson, Rory and Kapranov, Philipp and King, Brandon and Kingswood, Colin and Li, Guoliang and Luo, Oscar J. and Park, Eddie and Preall, Jonathan B. and Presaud, Kimberly and Ribeca, Paolo and Robyr, Daniel and Ruan, Xiaoan and Sammeth, Michael and Sandhu, Kuljeet Singh and Schaeffer, Lorain and See, Lei-Hoon and Shahab, Atif and Skancke, Jorgen and Suzuki, Ana Maria and Takahashi, Hazuki and Tilgner, Hagen and Trout, Diane and Walters, Nathalie and Wang, Huaien and Hayashizaki, Yoshihide and Reymond, Alexandre and Antonarakis, Stylianos E. and Hannon, Gregory J. and Ruan, Yijun and Carninci, Piero and Sloan, Cricket A. and Learned, Katrina and Malladi, Venkat S. and Wong, Matthew C. and Barber, Galt P. and Cline, Melissa S. and Dreszer, Timothy R. and Heitner, Steven G. and Karolchik, Donna and Kirkup, Vanessa M. and Meyer, Laurence R. and Long, Jeffrey C. and Maddren, Morgan and Raney, Brian J. and Grasfeder, Linda L. and Giresi, Paul G. and Battenhouse, Anna and Sheffield, Nathan C. and Showers, Kimberly A. and London, Darin and Bhinge, Akshay A. and Shestak, Christopher and Schaner, Matthew R. and Ki Kim, Seul and Zhang, Zhuzhu Z. and Mieczkowski, Piotr A. and Mieczkowska, Joanna O. and Liu, Zheng and McDaniell, Ryan M. and Ni, Yunyun and Rashid, Naim U. and Kim, Min Jae and Adar, Sheera and Zhang, Zhancheng and Wang, Tianyuan and Winter, Deborah and Keefe, Damian and Iyer, Vishwanath R. and Zheng, Meizhen and Wang, Ping and Gertz, Jason and Vielmetter, Jost and Partridge, E. and Varley, Katherine E. and Gasper, Clarke and Consortium, The ENCODE Project},
  URL = {https://doi.org/10.1038/nature11247},
  DATE = {2012-09-01},
  DOI = {10.1038/nature11247},
  ISSN = {1476-4687},
  JOURNALTITLE = {Nature},
  NUMBER = {7414},
  PAGES = {57--74},
  TITLE = {An integrated encyclopedia of DNA elements in the human genome},
  VOLUME = {489},
}

@ARTICLE{Consortium2020,
  AUTHOR = {{ENCODE Project Consortium}},
  DATE = {2020},
  DOI = {10.1038/s41586-020-2493-4},
  JOURNALTITLE = {Nature},
  NUMBER = {7818},
  PAGES = {699--710},
  TITLE = {Expanded encyclopaedias of DNA elements in the human and mouse genomes},
  VOLUME = {583},
}

@ARTICLE{Luo2020,
  ABSTRACT = {The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation.},
  AUTHOR = {Luo, Yunhai and Hitz, Benjamin C and Gabdank, Idan and Hilton, Jason A and Kagda, Meenakshi S and Lam, Bonita and Myers, Zachary and Sud, Paul and Jou, Jennifer and Lin, Khine and Baymuradov, Ulugbek K and Graham, Keenan and Litton, Casey and Miyasato, Stuart R and Strattan, J Seth and Jolanki, Otto and Lee, Jin-Wook and Tanaka, Forrest Y and Adenekan, Philip and O’Neill, Emma and Cherry, J Michael},
  URL = {https://doi.org/10.1093/nar/gkz1062},
  DATE = {2020-01},
  DOI = {10.1093/nar/gkz1062},
  EPRINT = {https://academic.oup.com/nar/article-pdf/48/D1/D882/32874907/gkz1062.pdf},
  ISSN = {0305-1048},
  JOURNALTITLE = {Nucleic Acids Research},
  NUMBER = {D1},
  PAGES = {D882--D889},
  TITLE = {New developments on the Encyclopedia of DNA Elements (ENCODE) data portal},
  VOLUME = {48},
}