ENCODE (English Wikipedia)
Analysis of information sources in references of the Wikipedia article "ENCODE" in English language version.
Last modified:
Ref.Un. Ref.Website
Global rank
English rank
14th place
9th place
8,866th place
low place
1st place
1st place
low place
low place
15th place
8th place
4th place
4th place
1,007th place
665th place
low place
low place
207th place
347th place
4,656th place
3,908th place
low place
low place
1,143rd place
973rd place
low place
low place
low place
low place
7th place
7th place
low place
low place
low place
low place
low place
low place
low place
low place
low place
low place
adsabs.harvard.edu (Global: 14th place; English: 9th place)
ui.adsabs.harvard.edu
- The ENCODE Project Consortium (2004). "The ENCODE (ENCyclopedia Of DNA Elements) Project". Science. 306 (5696): 636–640. Bibcode:2004Sci...306..636E. doi:10.1126/science.1105136. PMID 15499007. S2CID 22837649.
- ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
- Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E (September 2012). "Genomics: ENCODE explained". Nature. 489 (7414): 52–5. Bibcode:2012Natur.489...52E. doi:10.1038/489052a. PMID 22955614. S2CID 5366257.
- Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 (7414): 57–74. Bibcode:2012Natur.489...57T. doi:10.1038/nature11247. PMC 3439153. PMID 22955616.
- Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, et al. (September 2012). "The accessible chromatin landscape of the human genome". Nature. 489 (7414): 75–82. Bibcode:2012Natur.489...75T. doi:10.1038/nature11232. PMC 3721348. PMID 22955617.
- Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, et al. (September 2012). "An expansive human regulatory lexicon encoded in transcription factor footprints". Nature. 489 (7414): 83–90. Bibcode:2012Natur.489...83N. doi:10.1038/nature11212. PMC 3736582. PMID 22955618.
- Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, et al. (September 2012). "Architecture of the human regulatory network derived from ENCODE data". Nature. 489 (7414): 91–100. Bibcode:2012Natur.489...91G. doi:10.1038/nature11245. PMC 4154057. PMID 22955619.
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
- Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, et al. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science. 330 (6012): 1775–1787. Bibcode:2010Sci...330.1775G. doi:10.1126/science.1196914. PMC 3142569. PMID 21177976.
- modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science. 330 (6012): 1787–1797. Bibcode:2010Sci...330.1787R. doi:10.1126/science.1198374. PMC 3192495. PMID 21177974.
- Celniker S (2009-06-11). "Unlocking the secrets of the genome". Nature. 459 (7249): 927–930. Bibcode:2009Natur.459..927C. doi:10.1038/459927a. PMC 2843545. PMID 19536255.
- Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; et al. (2015). "Integrative analysis of 111 reference human epigenomes". Nature. 518 (7539): 317–330. Bibcode:2015Natur.518..317.. doi:10.1038/nature14248. PMC 4530010. PMID 25693563.
- White MA, Myers CA, Corbo JC, Cohen BA (July 2013). "Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks". Proc. Natl. Acad. Sci. U.S.A. 110 (29): 11952–7. Bibcode:2013PNAS..11011952W. doi:10.1073/pnas.1307449110. PMC 3718143. PMID 23818646.
- Mike White (17 July 2013). "Finding function in the genome with a null hypothesis". The Finch & Pea.
- Kellis M, et al. (2014). "Defining functional DNA elements in the human genome". Proc. Natl. Acad. Sci. U.S.A. 111 (17): 6131–8. Bibcode:2014PNAS..111.6131K. doi:10.1073/pnas.1318948111. PMC 4035993. PMID 24753594.
- Abascal F, Acosta R, Addleman NJ, Adrian J, et al. (30 July 2020). "Expanded Encyclopaedias of DNA elements in the Human and Mouse Genomes". Nature. 583 (7818): 699–710. Bibcode:2020Natur.583..699E. doi:10.1038/s41586-020-2493-4. PMC 7410828. PMID 32728249.
The ENCODE Project aims to delineate precisely and comprehensively the segments of the human and mouse genomes that encode functional elements.
archives-ouvertes.fr (Global: 1,143rd place; English: 973rd place)
hal.archives-ouvertes.fr
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
doi.org (Global: 2nd place; English: 2nd place)
- Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM (January 2016). "Principles of metadata organization at the ENCODE data coordination center. (2016 update)". Database. 2016 baw001. doi:10.1093/database/baw001. PMC 4792520. PMID 26980513.
- Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ (January 2011). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Res. 39 (Database issue): D871–5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257.
- The ENCODE Project Consortium (2004). "The ENCODE (ENCyclopedia Of DNA Elements) Project". Science. 306 (5696): 636–640. Bibcode:2004Sci...306..636E. doi:10.1126/science.1105136. PMID 15499007. S2CID 22837649.
- ENCODE Project Consortium (2011). Becker PB (ed.). "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLOS Biology. 9 (4) e1001046. doi:10.1371/journal.pbio.1001046. PMC 3079585. PMID 21526222.
- ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
- Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG (2006). "EGASP: The human ENCODE Genome Annotation Assessment Project". Genome Biology. 7 (Suppl 1): S2.1–31. doi:10.1186/gb-2006-7-s1-s2. PMC 1810551. PMID 16925836.
- Davis, Carrie A.; Hitz, Benjamin C.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Hilton, Jason A.; Jain, Kriti; Baymuradov, Ulugbek K.; Narayanan, Aditi K.; Onate, Kathrina C. (2018-01-04). "The Encyclopedia of DNA elements (ENCODE): data portal update". Nucleic Acids Research. 46 (D1): D794–D801. doi:10.1093/nar/gkx1081. ISSN 1362-4962. PMC 5753278. PMID 29126249.
- Weinstock GM (2007). "ENCODE: More genomic empowerment". Genome Research. 17 (6): 667–668. doi:10.1101/gr.6534207. PMID 17567987.
- Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E (September 2012). "Genomics: ENCODE explained". Nature. 489 (7414): 52–5. Bibcode:2012Natur.489...52E. doi:10.1038/489052a. PMID 22955614. S2CID 5366257.
- Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 (7414): 57–74. Bibcode:2012Natur.489...57T. doi:10.1038/nature11247. PMC 3439153. PMID 22955616.
- Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, et al. (September 2012). "The accessible chromatin landscape of the human genome". Nature. 489 (7414): 75–82. Bibcode:2012Natur.489...75T. doi:10.1038/nature11232. PMC 3721348. PMID 22955617.
- Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, et al. (September 2012). "An expansive human regulatory lexicon encoded in transcription factor footprints". Nature. 489 (7414): 83–90. Bibcode:2012Natur.489...83N. doi:10.1038/nature11212. PMC 3736582. PMID 22955618.
- Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, et al. (September 2012). "Architecture of the human regulatory network derived from ENCODE data". Nature. 489 (7414): 91–100. Bibcode:2012Natur.489...91G. doi:10.1038/nature11245. PMC 4154057. PMID 22955619.
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
- Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL (2015). "Ontology application and use at the ENCODE DCC". Database (Oxford). 2015. doi:10.1093/database/bav010. PMC 4360730. PMID 25776021.
- Brian J. Raney; et al. (2010-10-30). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Res. 39 (Database issue). Nucleic Acids Research: D871–5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257.
- Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, et al. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science. 330 (6012): 1775–1787. Bibcode:2010Sci...330.1775G. doi:10.1126/science.1196914. PMC 3142569. PMID 21177976.
- modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science. 330 (6012): 1787–1797. Bibcode:2010Sci...330.1787R. doi:10.1126/science.1198374. PMC 3192495. PMID 21177974.
- Celniker S (2009-06-11). "Unlocking the secrets of the genome". Nature. 459 (7249): 927–930. Bibcode:2009Natur.459..927C. doi:10.1038/459927a. PMC 2843545. PMID 19536255.
- Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; et al. (2015). "Integrative analysis of 111 reference human epigenomes". Nature. 518 (7539): 317–330. Bibcode:2015Natur.518..317.. doi:10.1038/nature14248. PMC 4530010. PMID 25693563.
- Cho, Young-Dan; Kim, Woo-Jin; Ryoo, Hyun-Mo; Kim, Hong-Gee; Kim, Kyoung-Hwa; Ku, Young; Seol, Yang-Jo (2021-04-26). "Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives". Clinical Epigenetics. 13 (1): 92. doi:10.1186/s13148-021-01074-w. ISSN 1868-7083. PMC 8077755. PMID 33902683. S2CID 233402899.
- Graur D; Zheng Y; Price N; Azevedo RB; Zufall RA; Elhaik E (2013). "On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE". Genome Biol Evol. 5 (3): 578–90. doi:10.1093/gbe/evt028. PMC 3622293. PMID 23431001.
- White MA, Myers CA, Corbo JC, Cohen BA (July 2013). "Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks". Proc. Natl. Acad. Sci. U.S.A. 110 (29): 11952–7. Bibcode:2013PNAS..11011952W. doi:10.1073/pnas.1307449110. PMC 3718143. PMID 23818646.
- Mike White (17 July 2013). "Finding function in the genome with a null hypothesis". The Finch & Pea.
- Mattick JS, Dinger ME (2013). "The extent of functionality in the human genome". The HUGO Journal. 7 (1) 2. doi:10.1186/1877-6566-7-2. PMC 4685169.
- Kellis M, et al. (2014). "Defining functional DNA elements in the human genome". Proc. Natl. Acad. Sci. U.S.A. 111 (17): 6131–8. Bibcode:2014PNAS..111.6131K. doi:10.1073/pnas.1318948111. PMC 4035993. PMID 24753594.
- Germain, Pierre-Luc; Ratti, Emanuele; Boem, Federico (November 2014). "Junk or Functional DNA? ENCODE and the Function Controversy". Biology & Philosophy. 29 (6): 807–831. doi:10.1007/s10539-014-9441-3. S2CID 84480632.
- Abascal F, Acosta R, Addleman NJ, Adrian J, et al. (30 July 2020). "Expanded Encyclopaedias of DNA elements in the Human and Mouse Genomes". Nature. 583 (7818): 699–710. Bibcode:2020Natur.583..699E. doi:10.1038/s41586-020-2493-4. PMC 7410828. PMID 32728249.
The ENCODE Project aims to delineate precisely and comprehensively the segments of the human and mouse genomes that encode functional elements.
- Maher B (September 2012). "ENCODE: The human encyclopaedia". Nature. 489 (7414): 46–8. doi:10.1038/489046a. PMID 22962707.
- Wang J (2012-11-29). "Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium". Nucleic Acids Research. 41 (Database issue): D171-6. doi:10.1093/nar/gks1221. PMC 3531197. PMID 23203885.
encodeproject.org (Global: low place; English: low place)
- "The ENCODE Project: Project Overview". www.endodeproject.org. Retrieved 2023-02-23.
- "Data Use, Software, and Analysis Release Policies – ENCODE". www.encodeproject.org. Retrieved 2021-12-18.
- "The ENCODE Project: Project Overview". www.endodeproject.org. Retrieved 2023-02-23.
- "Search – ENCODE".
- "Search – ENCODE".
evolverzone.com (Global: low place; English: low place)
genomicron.evolverzone.com
- Gregory TR (2012-09-06). "The ENCODE media hype machine". Genomicron. Archived from the original on 2015-04-06. Retrieved 2013-08-17.
- Gregory TR (2013-04-11). "Critiques of ENCODE in peer-reviewed journals. « Genomicron". Genomicron. Archived from the original on 21 April 2013.
factorbook.org (Global: low place; English: low place)
genome.gov (Global: 8,866th place; English: low place)
- "The ENCODE Project: ENCyclopedia Of DNA Elements". www.genome.gov. Retrieved 2016-05-13.
- "ENCODE Project". www.genome.gov. Archived from the original on 2016-05-17. Retrieved 2016-05-16.
- ENCODE Program Staff (2012-10-18). "ENCODE: Pilot Project: overview". National Human Genome Research Institute.
- ENCODE Program Staff (2012-02-19). "ENCODE: Pilot Project: Target Selection". National Human Genome Research Institute.
- "Genome.gov | ENCODE and modENCODE Projects". The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. Retrieved 2011-08-05.
- "Genome.gov | ENCODE Participants and Projects". The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01. Retrieved 2011-08-05.
- "The modENCODE Project: Model Organism ENCyclopedia Of DNA Elements (modENCODE)". NHGRI website. Retrieved 2008-11-13.
- "modENCODE Participants and Projects". NHGRI website. Retrieved 2008-11-13.
- "2015 Release: NIH grants aim to decipher the language of gene regulation". www.genome.gov. Archived from the original on 2016-04-06.
genomeinformatician.blogspot.com (Global: low place; English: low place)
- Birney, Ewan (September 5, 2012). "ENCODE: My own thoughts". Ewan's Blog: Bioinformatician at large.
ihec-epigenomes.org (Global: low place; English: low place)
- GmbH, Eurice. "United States of America · IHEC". ihec-epigenomes.org. Retrieved 2017-07-18.
lbl.gov (Global: 3,154th place; English: 3,216th place)
- "Berkeley Lab Life Sciences Awarded NIH Grants for Fruit Fly, Nematode Studies". Lawrence Berkeley National Laboratory website. 2007-05-14. Archived from the original on 2008-09-21. Retrieved 2008-11-13.
mendelspod.com (Global: low place; English: low place)
- Timpson T (2013-03-05). "Debating ENCODE: Dan Graur, Michael Eisen". Mendelspod. Archived from the original on 2015-04-11. Retrieved 2013-08-15.
modencode.org (Global: low place; English: low place)
- "modENCODE". The National Human Genome Research Institute.
nature.com (Global: 207th place; English: 347th place)
nature.com
- "Fig. 3: Publications using ENCODE data. | Nature". Natureevents Directory. ISSN 1476-4687.
blogs.nature.com
- Maher B (2012-09-06). "Fighting about ENCODE and junk". News Blog. Nature Publishing Group. Archived from the original on 2013-08-06. Retrieved 2013-08-17.
nih.gov (Global: 5th place; English: 5th place)
pubmed.ncbi.nlm.nih.gov
- Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM (January 2016). "Principles of metadata organization at the ENCODE data coordination center. (2016 update)". Database. 2016 baw001. doi:10.1093/database/baw001. PMC 4792520. PMID 26980513.
- Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ (January 2011). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Res. 39 (Database issue): D871–5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257.
- The ENCODE Project Consortium (2004). "The ENCODE (ENCyclopedia Of DNA Elements) Project". Science. 306 (5696): 636–640. Bibcode:2004Sci...306..636E. doi:10.1126/science.1105136. PMID 15499007. S2CID 22837649.
- ENCODE Project Consortium (2011). Becker PB (ed.). "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLOS Biology. 9 (4) e1001046. doi:10.1371/journal.pbio.1001046. PMC 3079585. PMID 21526222.
- ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
- Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG (2006). "EGASP: The human ENCODE Genome Annotation Assessment Project". Genome Biology. 7 (Suppl 1): S2.1–31. doi:10.1186/gb-2006-7-s1-s2. PMC 1810551. PMID 16925836.
- Davis, Carrie A.; Hitz, Benjamin C.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Hilton, Jason A.; Jain, Kriti; Baymuradov, Ulugbek K.; Narayanan, Aditi K.; Onate, Kathrina C. (2018-01-04). "The Encyclopedia of DNA elements (ENCODE): data portal update". Nucleic Acids Research. 46 (D1): D794–D801. doi:10.1093/nar/gkx1081. ISSN 1362-4962. PMC 5753278. PMID 29126249.
- Weinstock GM (2007). "ENCODE: More genomic empowerment". Genome Research. 17 (6): 667–668. doi:10.1101/gr.6534207. PMID 17567987.
- Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E (September 2012). "Genomics: ENCODE explained". Nature. 489 (7414): 52–5. Bibcode:2012Natur.489...52E. doi:10.1038/489052a. PMID 22955614. S2CID 5366257.
- Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 (7414): 57–74. Bibcode:2012Natur.489...57T. doi:10.1038/nature11247. PMC 3439153. PMID 22955616.
- Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, et al. (September 2012). "The accessible chromatin landscape of the human genome". Nature. 489 (7414): 75–82. Bibcode:2012Natur.489...75T. doi:10.1038/nature11232. PMC 3721348. PMID 22955617.
- Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, et al. (September 2012). "An expansive human regulatory lexicon encoded in transcription factor footprints". Nature. 489 (7414): 83–90. Bibcode:2012Natur.489...83N. doi:10.1038/nature11212. PMC 3736582. PMID 22955618.
- Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, et al. (September 2012). "Architecture of the human regulatory network derived from ENCODE data". Nature. 489 (7414): 91–100. Bibcode:2012Natur.489...91G. doi:10.1038/nature11245. PMC 4154057. PMID 22955619.
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
- Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL (2015). "Ontology application and use at the ENCODE DCC". Database (Oxford). 2015. doi:10.1093/database/bav010. PMC 4360730. PMID 25776021.
- Brian J. Raney; et al. (2010-10-30). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Res. 39 (Database issue). Nucleic Acids Research: D871–5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257.
- Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, et al. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science. 330 (6012): 1775–1787. Bibcode:2010Sci...330.1775G. doi:10.1126/science.1196914. PMC 3142569. PMID 21177976.
- modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science. 330 (6012): 1787–1797. Bibcode:2010Sci...330.1787R. doi:10.1126/science.1198374. PMC 3192495. PMID 21177974.
- Celniker S (2009-06-11). "Unlocking the secrets of the genome". Nature. 459 (7249): 927–930. Bibcode:2009Natur.459..927C. doi:10.1038/459927a. PMC 2843545. PMID 19536255.
- Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; et al. (2015). "Integrative analysis of 111 reference human epigenomes". Nature. 518 (7539): 317–330. Bibcode:2015Natur.518..317.. doi:10.1038/nature14248. PMC 4530010. PMID 25693563.
- Cho, Young-Dan; Kim, Woo-Jin; Ryoo, Hyun-Mo; Kim, Hong-Gee; Kim, Kyoung-Hwa; Ku, Young; Seol, Yang-Jo (2021-04-26). "Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives". Clinical Epigenetics. 13 (1): 92. doi:10.1186/s13148-021-01074-w. ISSN 1868-7083. PMC 8077755. PMID 33902683. S2CID 233402899.
- Graur D; Zheng Y; Price N; Azevedo RB; Zufall RA; Elhaik E (2013). "On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE". Genome Biol Evol. 5 (3): 578–90. doi:10.1093/gbe/evt028. PMC 3622293. PMID 23431001.
- White MA, Myers CA, Corbo JC, Cohen BA (July 2013). "Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks". Proc. Natl. Acad. Sci. U.S.A. 110 (29): 11952–7. Bibcode:2013PNAS..11011952W. doi:10.1073/pnas.1307449110. PMC 3718143. PMID 23818646.
- Mike White (17 July 2013). "Finding function in the genome with a null hypothesis". The Finch & Pea.
- Kellis M, et al. (2014). "Defining functional DNA elements in the human genome". Proc. Natl. Acad. Sci. U.S.A. 111 (17): 6131–8. Bibcode:2014PNAS..111.6131K. doi:10.1073/pnas.1318948111. PMC 4035993. PMID 24753594.
- Abascal F, Acosta R, Addleman NJ, Adrian J, et al. (30 July 2020). "Expanded Encyclopaedias of DNA elements in the Human and Mouse Genomes". Nature. 583 (7818): 699–710. Bibcode:2020Natur.583..699E. doi:10.1038/s41586-020-2493-4. PMC 7410828. PMID 32728249.
The ENCODE Project aims to delineate precisely and comprehensively the segments of the human and mouse genomes that encode functional elements.
- Maher B (September 2012). "ENCODE: The human encyclopaedia". Nature. 489 (7414): 46–8. doi:10.1038/489046a. PMID 22962707.
- Wang J (2012-11-29). "Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium". Nucleic Acids Research. 41 (Database issue): D171-6. doi:10.1093/nar/gks1221. PMC 3531197. PMID 23203885.
ncbi.nlm.nih.gov
- Hong EL, Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe GR, Podduturi NR, Tanaka F, Hilton JA, Cherry JM (January 2016). "Principles of metadata organization at the ENCODE data coordination center. (2016 update)". Database. 2016 baw001. doi:10.1093/database/baw001. PMC 4792520. PMID 26980513.
- Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ (January 2011). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Res. 39 (Database issue): D871–5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257.
- ENCODE Project Consortium (2011). Becker PB (ed.). "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLOS Biology. 9 (4) e1001046. doi:10.1371/journal.pbio.1001046. PMC 3079585. PMID 21526222.
- ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
- Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG (2006). "EGASP: The human ENCODE Genome Annotation Assessment Project". Genome Biology. 7 (Suppl 1): S2.1–31. doi:10.1186/gb-2006-7-s1-s2. PMC 1810551. PMID 16925836.
- Davis, Carrie A.; Hitz, Benjamin C.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Hilton, Jason A.; Jain, Kriti; Baymuradov, Ulugbek K.; Narayanan, Aditi K.; Onate, Kathrina C. (2018-01-04). "The Encyclopedia of DNA elements (ENCODE): data portal update". Nucleic Acids Research. 46 (D1): D794–D801. doi:10.1093/nar/gkx1081. ISSN 1362-4962. PMC 5753278. PMID 29126249.
- Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 (7414): 57–74. Bibcode:2012Natur.489...57T. doi:10.1038/nature11247. PMC 3439153. PMID 22955616.
- Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, et al. (September 2012). "The accessible chromatin landscape of the human genome". Nature. 489 (7414): 75–82. Bibcode:2012Natur.489...75T. doi:10.1038/nature11232. PMC 3721348. PMID 22955617.
- Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, et al. (September 2012). "An expansive human regulatory lexicon encoded in transcription factor footprints". Nature. 489 (7414): 83–90. Bibcode:2012Natur.489...83N. doi:10.1038/nature11212. PMC 3736582. PMID 22955618.
- Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, et al. (September 2012). "Architecture of the human regulatory network derived from ENCODE data". Nature. 489 (7414): 91–100. Bibcode:2012Natur.489...91G. doi:10.1038/nature11245. PMC 4154057. PMID 22955619.
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
- Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL (2015). "Ontology application and use at the ENCODE DCC". Database (Oxford). 2015. doi:10.1093/database/bav010. PMC 4360730. PMID 25776021.
- Brian J. Raney; et al. (2010-10-30). "ENCODE whole-genome data in the UCSC genome browser (2011 update)". Nucleic Acids Res. 39 (Database issue). Nucleic Acids Research: D871–5. doi:10.1093/nar/gkq1017. PMC 3013645. PMID 21037257.
- Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, et al. (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science. 330 (6012): 1775–1787. Bibcode:2010Sci...330.1775G. doi:10.1126/science.1196914. PMC 3142569. PMID 21177976.
- modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science. 330 (6012): 1787–1797. Bibcode:2010Sci...330.1787R. doi:10.1126/science.1198374. PMC 3192495. PMID 21177974.
- Celniker S (2009-06-11). "Unlocking the secrets of the genome". Nature. 459 (7249): 927–930. Bibcode:2009Natur.459..927C. doi:10.1038/459927a. PMC 2843545. PMID 19536255.
- Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J.; Amin, Viren; Whitaker, John W.; Schultz, Matthew D.; Ward, Lucas D.; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S.; Eaton, Matthew L.; Wu, Yi-Chieh; Pfenning, Andreas R.; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R. Alan; Shoresh, Noam; Epstein, Charles B.; Gjoneska, Elizabeta; Leung, Danny; et al. (2015). "Integrative analysis of 111 reference human epigenomes". Nature. 518 (7539): 317–330. Bibcode:2015Natur.518..317.. doi:10.1038/nature14248. PMC 4530010. PMID 25693563.
- Cho, Young-Dan; Kim, Woo-Jin; Ryoo, Hyun-Mo; Kim, Hong-Gee; Kim, Kyoung-Hwa; Ku, Young; Seol, Yang-Jo (2021-04-26). "Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives". Clinical Epigenetics. 13 (1): 92. doi:10.1186/s13148-021-01074-w. ISSN 1868-7083. PMC 8077755. PMID 33902683. S2CID 233402899.
- Graur D; Zheng Y; Price N; Azevedo RB; Zufall RA; Elhaik E (2013). "On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE". Genome Biol Evol. 5 (3): 578–90. doi:10.1093/gbe/evt028. PMC 3622293. PMID 23431001.
- White MA, Myers CA, Corbo JC, Cohen BA (July 2013). "Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks". Proc. Natl. Acad. Sci. U.S.A. 110 (29): 11952–7. Bibcode:2013PNAS..11011952W. doi:10.1073/pnas.1307449110. PMC 3718143. PMID 23818646.
- Mike White (17 July 2013). "Finding function in the genome with a null hypothesis". The Finch & Pea.
- Mattick JS, Dinger ME (2013). "The extent of functionality in the human genome". The HUGO Journal. 7 (1) 2. doi:10.1186/1877-6566-7-2. PMC 4685169.
- Kellis M, et al. (2014). "Defining functional DNA elements in the human genome". Proc. Natl. Acad. Sci. U.S.A. 111 (17): 6131–8. Bibcode:2014PNAS..111.6131K. doi:10.1073/pnas.1318948111. PMC 4035993. PMID 24753594.
- Abascal F, Acosta R, Addleman NJ, Adrian J, et al. (30 July 2020). "Expanded Encyclopaedias of DNA elements in the Human and Mouse Genomes". Nature. 583 (7818): 699–710. Bibcode:2020Natur.583..699E. doi:10.1038/s41586-020-2493-4. PMC 7410828. PMID 32728249.
The ENCODE Project aims to delineate precisely and comprehensively the segments of the human and mouse genomes that encode functional elements.
- Wang J (2012-11-29). "Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium". Nucleic Acids Research. 41 (Database issue): D171-6. doi:10.1093/nar/gks1221. PMC 3531197. PMID 23203885.
nih.gov
- "National Human Genome Research Institute - Organization". The NIH Almanac. United States National Institutes of Health. Retrieved 2011-08-05.
reporter.nih.gov
nytimes.com (Global: 7th place; English: 7th place)
- Kolata G (2012-09-05). "Far From 'Junk,' DNA Dark Matter Proves Crucial to Health". The New York Times.
roadmapepigenomics.org (Global: low place; English: low place)
- "Roadmap Epigenomics Project - Home". Archived from the original on 2021-04-08. Retrieved 2014-01-10.
sandwalk.blogspot.com (Global: low place; English: low place)
- Moran LA (2013-03-15). "Sandwalk: On the Meaning of the Word "Function"". Sandwalk.
science.org (Global: 1,007th place; English: 665th place)
- The ENCODE Project Consortium (2004). "The ENCODE (ENCyclopedia Of DNA Elements) Project". Science. 306 (5696): 636–640. Bibcode:2004Sci...306..636E. doi:10.1126/science.1105136. PMID 15499007. S2CID 22837649.
sciencenews.org (Global: 4,656th place; English: 3,908th place)
- Saey, Tina Hesman (6 October 2012). "Team releases sequel to the human genome". Society for Science & the Public. Archived from the original on 23 October 2012. Retrieved 18 October 2012.
semanticscholar.org (Global: 15th place; English: 8th place)
api.semanticscholar.org
- The ENCODE Project Consortium (2004). "The ENCODE (ENCyclopedia Of DNA Elements) Project". Science. 306 (5696): 636–640. Bibcode:2004Sci...306..636E. doi:10.1126/science.1105136. PMID 15499007. S2CID 22837649.
- Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E (September 2012). "Genomics: ENCODE explained". Nature. 489 (7414): 52–5. Bibcode:2012Natur.489...52E. doi:10.1038/489052a. PMID 22955614. S2CID 5366257.
- Cho, Young-Dan; Kim, Woo-Jin; Ryoo, Hyun-Mo; Kim, Hong-Gee; Kim, Kyoung-Hwa; Ku, Young; Seol, Yang-Jo (2021-04-26). "Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives". Clinical Epigenetics. 13 (1): 92. doi:10.1186/s13148-021-01074-w. ISSN 1868-7083. PMC 8077755. PMID 33902683. S2CID 233402899.
- Germain, Pierre-Luc; Ratti, Emanuele; Boem, Federico (November 2014). "Junk or Functional DNA? ENCODE and the Function Controversy". Biology & Philosophy. 29 (6): 807–831. doi:10.1007/s10539-014-9441-3. S2CID 84480632.
thefinchandpea.com (Global: low place; English: low place)
- White MA, Myers CA, Corbo JC, Cohen BA (July 2013). "Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks". Proc. Natl. Acad. Sci. U.S.A. 110 (29): 11952–7. Bibcode:2013PNAS..11011952W. doi:10.1073/pnas.1307449110. PMC 3718143. PMID 23818646.
- Mike White (17 July 2013). "Finding function in the genome with a null hypothesis". The Finch & Pea.
web.archive.org (Global: 1st place; English: 1st place)
- Saey, Tina Hesman (6 October 2012). "Team releases sequel to the human genome". Society for Science & the Public. Archived from the original on 23 October 2012. Retrieved 18 October 2012.
- "ENCODE Project". www.genome.gov. Archived from the original on 2016-05-17. Retrieved 2016-05-16.
- "Berkeley Lab Life Sciences Awarded NIH Grants for Fruit Fly, Nematode Studies". Lawrence Berkeley National Laboratory website. 2007-05-14. Archived from the original on 2008-09-21. Retrieved 2008-11-13.
- "2015 Release: NIH grants aim to decipher the language of gene regulation". www.genome.gov. Archived from the original on 2016-04-06.
- "Roadmap Epigenomics Project - Home". Archived from the original on 2021-04-08. Retrieved 2014-01-10.
- Maher B (2012-09-06). "Fighting about ENCODE and junk". News Blog. Nature Publishing Group. Archived from the original on 2013-08-06. Retrieved 2013-08-17.
- Gregory TR (2012-09-06). "The ENCODE media hype machine". Genomicron. Archived from the original on 2015-04-06. Retrieved 2013-08-17.
- Gregory TR (2013-04-11). "Critiques of ENCODE in peer-reviewed journals. « Genomicron". Genomicron. Archived from the original on 21 April 2013.
- Timpson T (2013-03-05). "Debating ENCODE: Dan Graur, Michael Eisen". Mendelspod. Archived from the original on 2015-04-11. Retrieved 2013-08-15.
worldcat.org (Global: 4th place; English: 4th place)
search.worldcat.org
- Davis, Carrie A.; Hitz, Benjamin C.; Sloan, Cricket A.; Chan, Esther T.; Davidson, Jean M.; Gabdank, Idan; Hilton, Jason A.; Jain, Kriti; Baymuradov, Ulugbek K.; Narayanan, Aditi K.; Onate, Kathrina C. (2018-01-04). "The Encyclopedia of DNA elements (ENCODE): data portal update". Nucleic Acids Research. 46 (D1): D794–D801. doi:10.1093/nar/gkx1081. ISSN 1362-4962. PMC 5753278. PMID 29126249.
- "Fig. 3: Publications using ENCODE data. | Nature". Natureevents Directory. ISSN 1476-4687.
- Cho, Young-Dan; Kim, Woo-Jin; Ryoo, Hyun-Mo; Kim, Hong-Gee; Kim, Kyoung-Hwa; Ku, Young; Seol, Yang-Jo (2021-04-26). "Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives". Clinical Epigenetics. 13 (1): 92. doi:10.1186/s13148-021-01074-w. ISSN 1868-7083. PMC 8077755. PMID 33902683. S2CID 233402899.