ChIP sequencing (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "ChIP sequencing" in English language version.

refsWebsite

Global rank English rank

48nih.gov

4^th place

29doi.org

2^nd place

9worldcat.org

5^th place

5semanticscholar.org

11^th place

8^th place

4harvard.edu

18^th place

17^th place

1caltech.edu

887^th place

714^th place

1illumina.com

low place

1abcam.com

low place

1biocompare.com

low place

abcam.com

"ChIP guide: epigenetics applications | Abcam". www.abcam.com. Retrieved 2 March 2020.

biocompare.com

"HeLa S3 from ATCC | Biocompare.com". www.biocompare.com. Retrieved 21 March 2020.

caltech.edu

authors.library.caltech.edu

Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). Science. 316 (5830): 1497–502. Bibcode:2007Sci...316.1497J. doi:10.1126/science.1141319. PMID 17540862. S2CID 519841.

doi.org

Muhammad, Isiaka Ibrahim; Kong, Sze Ling; Akmar Abdullah, Siti Nor; Munusamy, Umaiyal (25 December 2019). "RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism". International Journal of Molecular Sciences. 21 (1): 167. doi:10.3390/ijms21010167. ISSN 1422-0067. PMC 6981605. PMID 31881735.
Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). Science. 316 (5830): 1497–502. Bibcode:2007Sci...316.1497J. doi:10.1126/science.1141319. PMID 17540862. S2CID 519841.
Song, Lingyun; Crawford, Gregory E. (February 2010). "DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells". Cold Spring Harbor Protocols. 2010 (2): pdb.prot5384. doi:10.1101/pdb.prot5384. ISSN 1559-6095. PMC 3627383. PMID 20150147.
Giresi, Paul G.; Kim, Jonghwan; McDaniell, Ryan M.; Iyer, Vishwanath R.; Lieb, Jason D. (June 2007). "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin". Genome Research. 17 (6): 877–885. doi:10.1101/gr.5533506. ISSN 1088-9051. PMC 1891346. PMID 17179217.
Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data". Nature Biotechnology. 31 (7): 615–622. doi:10.1038/nbt.2596. ISSN 1087-0156. PMID 23770639. S2CID 32510475.
Kim TH, Dekker J (April 2018). "Formaldehyde Cross-Linking". Cold Spring Harbor Protocols. 2018 (4): pdb.prot082594. doi:10.1101/pdb.prot082594. PMID 29610357.
Kim TH, Dekker J (April 2018). "Preparation of Cross-Linked Chromatin for ChIP". Cold Spring Harbor Protocols. 2018 (4): pdb.prot082602. doi:10.1101/pdb.prot082602. PMID 29610358.
Park, Peter J. (October 2009). "ChIP-seq: advantages and challenges of a maturing technology". Nature Reviews. Genetics. 10 (10): 669–680. doi:10.1038/nrg2641. ISSN 1471-0064. PMC 3191340. PMID 19736561.
Chen, Yiwen; Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Liu, Tao; Zhang, Yong; Kim, Tae-Kyung; He, Housheng Hansen; Zieba, Jennifer; Ruan, Yijun (June 2012). "Systematic evaluation of factors influencing ChIP-seq fidelity". Nature Methods. 9 (6): 609–614. doi:10.1038/nmeth.1985. ISSN 1548-7105. PMC 3477507. PMID 22522655.
Jung, Youngsook L.; Luquette, Lovelace J.; Ho, Joshua W. K.; Ferrari, Francesco; Tolstorukov, Michael; Minoda, Aki; Issner, Robbyn; Epstein, Charles B.; Karpen, Gary H.; Kuroda, Mitzi I.; Park, Peter J. (May 2014). "Impact of sequencing depth in ChIP-seq experiments". Nucleic Acids Research. 42 (9): e74. doi:10.1093/nar/gku178. ISSN 1362-4962. PMC 4027199. PMID 24598259.
Ho, Joshua W. K.; Bishop, Eric; Karchenko, Peter V.; Nègre, Nicolas; White, Kevin P.; Park, Peter J. (28 February 2011). "ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis". BMC Genomics. 12: 134. doi:10.1186/1471-2164-12-134. ISSN 1471-2164. PMC 3053263. PMID 21356108.
Jothi, et al. (2008). "Genome-wide identification of in vivo protein–DNA binding sites from ChIP-seq data". Nucleic Acids Res. 36 (16): 5221–5231. doi:10.1093/nar/gkn488. PMC 2532738. PMID 18684996.
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, et al. (January 2005). "Genomic maps and comparative analysis of histone modifications in human and mouse". Cell. 120 (2): 169–81. doi:10.1016/j.cell.2005.01.001. PMID 15680324. S2CID 7193829.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al. (August 2007). "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing". Nature Methods. 4 (8): 651–7. doi:10.1038/nmeth1068. PMID 17558387. S2CID 28531263.
Schmid CD, Bucher P (November 2007). "ChIP-Seq data reveal nucleosome architecture of human promoters". Cell. 131 (5): 831–2, author reply 832–3. doi:10.1016/j.cell.2007.11.017. PMID 18045524. S2CID 29234049.
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. (September 2010). "ChIP-Seq identification of weakly conserved heart enhancers". Nature Genetics. 42 (9): 806–10. doi:10.1038/ng.650. PMC 3138496. PMID 20729851.
Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, et al. (February 2011). "Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans". Genome Research. 21 (2): 245–54. doi:10.1101/gr.114587.110. PMC 3032928. PMID 21177963.
Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data". Nature Biotechnology. 31 (7): 615–22. doi:10.1038/nbt.2596. PMID 23770639.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. (2008). "Model-based analysis of ChIP-Seq (MACS)". Genome Biology. 9 (9): R137. doi:10.1186/gb-2008-9-9-r137. PMC 2592715. PMID 18798982.
Xing H, Mo Y, Liao W, Zhang MQ (2012). "Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data". PLOS Comput Biol. 8 (7): e1002613. Bibcode:2012PLSCB...8E2613X. doi:10.1371/journal.pcbi.1002613. PMC 5429005. PMID 22844240.
Thomas R, Thomas S, Holloway AK, Pollard KS (2017). "Features that define the best ChIP-seq peak calling algorithms". Brief Bioinform. 18 (3): 441–450. doi:10.1093/bib/bbw035. PMC 5429005. PMID 27169896.
Xu H, Wei CL, Lin F, Sung WK (October 2008). "An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data". Bioinformatics. 24 (20): 2344–9. doi:10.1093/bioinformatics/btn402. PMID 18667444.
Allhoff M, Seré K, Chauvistré H, Lin Q, Zenke M, Costa IG (December 2014). "Detecting differential peaks in ChIP-seq signals with ODIN". Bioinformatics. 30 (24): 3467–75. doi:10.1093/bioinformatics/btu722. PMID 25371479.
Xu, Jinrui; Kudron, Michelle M; Victorsen, Alec; Gao, Jiahao; Ammouri, Haneen N; Navarro, Fabio C P; Gevirtzman, Louis; Waterston, Robert H; White, Kevin P; Reinke, Valerie; Gerstein, Mark (21 December 2020). "To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq". Nucleic Acids Research. 49 (3): gkaa1155. doi:10.1093/nar/gkaa1155. ISSN 0305-1048. PMC 7897498. PMID 33347581.
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, et al. (November 2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–9. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Darnell RB (2010). "HITS-CLIP: panoramic views of protein-RNA regulation in living cells". Wiley Interdisciplinary Reviews. RNA. 1 (2): 266–286. doi:10.1002/wrna.31. PMC 3222227. PMID 21935890.
Wang H, Mayhew D, Chen X, Johnston M, Mitra RD (May 2011). "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins". Genome Research. 21 (5): 748–55. doi:10.1101/gr.114850.110. PMC 3083092. PMID 21471402.
Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B (January 2018). "ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments". Nucleic Acids Research. 46 (D1): D267 – D275. doi:10.1093/nar/gkx1092. PMC 5753247. PMID 29126285.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, et al. (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

harvard.edu

ui.adsabs.harvard.edu

Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). Science. 316 (5830): 1497–502. Bibcode:2007Sci...316.1497J. doi:10.1126/science.1141319. PMID 17540862. S2CID 519841.
Xing H, Mo Y, Liao W, Zhang MQ (2012). "Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data". PLOS Comput Biol. 8 (7): e1002613. Bibcode:2012PLSCB...8E2613X. doi:10.1371/journal.pcbi.1002613. PMC 5429005. PMID 22844240.
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, et al. (November 2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–9. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, et al. (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

illumina.com

"Whole-Genome Chromatin IP Sequencing (ChIP-Seq)" (PDF). Illumina, Inc. 26 November 2007.

nih.gov

pubmed.ncbi.nlm.nih.gov

Muhammad, Isiaka Ibrahim; Kong, Sze Ling; Akmar Abdullah, Siti Nor; Munusamy, Umaiyal (25 December 2019). "RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism". International Journal of Molecular Sciences. 21 (1): 167. doi:10.3390/ijms21010167. ISSN 1422-0067. PMC 6981605. PMID 31881735.
Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). Science. 316 (5830): 1497–502. Bibcode:2007Sci...316.1497J. doi:10.1126/science.1141319. PMID 17540862. S2CID 519841.
Song, Lingyun; Crawford, Gregory E. (February 2010). "DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells". Cold Spring Harbor Protocols. 2010 (2): pdb.prot5384. doi:10.1101/pdb.prot5384. ISSN 1559-6095. PMC 3627383. PMID 20150147.
Giresi, Paul G.; Kim, Jonghwan; McDaniell, Ryan M.; Iyer, Vishwanath R.; Lieb, Jason D. (June 2007). "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin". Genome Research. 17 (6): 877–885. doi:10.1101/gr.5533506. ISSN 1088-9051. PMC 1891346. PMID 17179217.
Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data". Nature Biotechnology. 31 (7): 615–622. doi:10.1038/nbt.2596. ISSN 1087-0156. PMID 23770639. S2CID 32510475.
Kim TH, Dekker J (April 2018). "Formaldehyde Cross-Linking". Cold Spring Harbor Protocols. 2018 (4): pdb.prot082594. doi:10.1101/pdb.prot082594. PMID 29610357.
Kim TH, Dekker J (April 2018). "Preparation of Cross-Linked Chromatin for ChIP". Cold Spring Harbor Protocols. 2018 (4): pdb.prot082602. doi:10.1101/pdb.prot082602. PMID 29610358.
Park, Peter J. (October 2009). "ChIP-seq: advantages and challenges of a maturing technology". Nature Reviews. Genetics. 10 (10): 669–680. doi:10.1038/nrg2641. ISSN 1471-0064. PMC 3191340. PMID 19736561.
Chen, Yiwen; Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Liu, Tao; Zhang, Yong; Kim, Tae-Kyung; He, Housheng Hansen; Zieba, Jennifer; Ruan, Yijun (June 2012). "Systematic evaluation of factors influencing ChIP-seq fidelity". Nature Methods. 9 (6): 609–614. doi:10.1038/nmeth.1985. ISSN 1548-7105. PMC 3477507. PMID 22522655.
Jung, Youngsook L.; Luquette, Lovelace J.; Ho, Joshua W. K.; Ferrari, Francesco; Tolstorukov, Michael; Minoda, Aki; Issner, Robbyn; Epstein, Charles B.; Karpen, Gary H.; Kuroda, Mitzi I.; Park, Peter J. (May 2014). "Impact of sequencing depth in ChIP-seq experiments". Nucleic Acids Research. 42 (9): e74. doi:10.1093/nar/gku178. ISSN 1362-4962. PMC 4027199. PMID 24598259.
Ho, Joshua W. K.; Bishop, Eric; Karchenko, Peter V.; Nègre, Nicolas; White, Kevin P.; Park, Peter J. (28 February 2011). "ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis". BMC Genomics. 12: 134. doi:10.1186/1471-2164-12-134. ISSN 1471-2164. PMC 3053263. PMID 21356108.
Jothi, et al. (2008). "Genome-wide identification of in vivo protein–DNA binding sites from ChIP-seq data". Nucleic Acids Res. 36 (16): 5221–5231. doi:10.1093/nar/gkn488. PMC 2532738. PMID 18684996.
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, et al. (January 2005). "Genomic maps and comparative analysis of histone modifications in human and mouse". Cell. 120 (2): 169–81. doi:10.1016/j.cell.2005.01.001. PMID 15680324. S2CID 7193829.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al. (August 2007). "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing". Nature Methods. 4 (8): 651–7. doi:10.1038/nmeth1068. PMID 17558387. S2CID 28531263.
Schmid CD, Bucher P (November 2007). "ChIP-Seq data reveal nucleosome architecture of human promoters". Cell. 131 (5): 831–2, author reply 832–3. doi:10.1016/j.cell.2007.11.017. PMID 18045524. S2CID 29234049.
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. (September 2010). "ChIP-Seq identification of weakly conserved heart enhancers". Nature Genetics. 42 (9): 806–10. doi:10.1038/ng.650. PMC 3138496. PMID 20729851.
Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, et al. (February 2011). "Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans". Genome Research. 21 (2): 245–54. doi:10.1101/gr.114587.110. PMC 3032928. PMID 21177963.
Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data". Nature Biotechnology. 31 (7): 615–22. doi:10.1038/nbt.2596. PMID 23770639.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. (2008). "Model-based analysis of ChIP-Seq (MACS)". Genome Biology. 9 (9): R137. doi:10.1186/gb-2008-9-9-r137. PMC 2592715. PMID 18798982.
Xing H, Mo Y, Liao W, Zhang MQ (2012). "Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data". PLOS Comput Biol. 8 (7): e1002613. Bibcode:2012PLSCB...8E2613X. doi:10.1371/journal.pcbi.1002613. PMC 5429005. PMID 22844240.
Thomas R, Thomas S, Holloway AK, Pollard KS (2017). "Features that define the best ChIP-seq peak calling algorithms". Brief Bioinform. 18 (3): 441–450. doi:10.1093/bib/bbw035. PMC 5429005. PMID 27169896.
Xu H, Wei CL, Lin F, Sung WK (October 2008). "An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data". Bioinformatics. 24 (20): 2344–9. doi:10.1093/bioinformatics/btn402. PMID 18667444.
Allhoff M, Seré K, Chauvistré H, Lin Q, Zenke M, Costa IG (December 2014). "Detecting differential peaks in ChIP-seq signals with ODIN". Bioinformatics. 30 (24): 3467–75. doi:10.1093/bioinformatics/btu722. PMID 25371479.
Xu, Jinrui; Kudron, Michelle M; Victorsen, Alec; Gao, Jiahao; Ammouri, Haneen N; Navarro, Fabio C P; Gevirtzman, Louis; Waterston, Robert H; White, Kevin P; Reinke, Valerie; Gerstein, Mark (21 December 2020). "To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq". Nucleic Acids Research. 49 (3): gkaa1155. doi:10.1093/nar/gkaa1155. ISSN 0305-1048. PMC 7897498. PMID 33347581.
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, et al. (November 2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–9. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Darnell RB (2010). "HITS-CLIP: panoramic views of protein-RNA regulation in living cells". Wiley Interdisciplinary Reviews. RNA. 1 (2): 266–286. doi:10.1002/wrna.31. PMC 3222227. PMID 21935890.
Wang H, Mayhew D, Chen X, Johnston M, Mitra RD (May 2011). "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins". Genome Research. 21 (5): 748–55. doi:10.1101/gr.114850.110. PMC 3083092. PMID 21471402.
Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B (January 2018). "ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments". Nucleic Acids Research. 46 (D1): D267 – D275. doi:10.1093/nar/gkx1092. PMC 5753247. PMID 29126285.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, et al. (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

ncbi.nlm.nih.gov

Muhammad, Isiaka Ibrahim; Kong, Sze Ling; Akmar Abdullah, Siti Nor; Munusamy, Umaiyal (25 December 2019). "RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism". International Journal of Molecular Sciences. 21 (1): 167. doi:10.3390/ijms21010167. ISSN 1422-0067. PMC 6981605. PMID 31881735.
Song, Lingyun; Crawford, Gregory E. (February 2010). "DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells". Cold Spring Harbor Protocols. 2010 (2): pdb.prot5384. doi:10.1101/pdb.prot5384. ISSN 1559-6095. PMC 3627383. PMID 20150147.
Giresi, Paul G.; Kim, Jonghwan; McDaniell, Ryan M.; Iyer, Vishwanath R.; Lieb, Jason D. (June 2007). "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin". Genome Research. 17 (6): 877–885. doi:10.1101/gr.5533506. ISSN 1088-9051. PMC 1891346. PMID 17179217.
Park, Peter J. (October 2009). "ChIP-seq: advantages and challenges of a maturing technology". Nature Reviews. Genetics. 10 (10): 669–680. doi:10.1038/nrg2641. ISSN 1471-0064. PMC 3191340. PMID 19736561.
Chen, Yiwen; Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Liu, Tao; Zhang, Yong; Kim, Tae-Kyung; He, Housheng Hansen; Zieba, Jennifer; Ruan, Yijun (June 2012). "Systematic evaluation of factors influencing ChIP-seq fidelity". Nature Methods. 9 (6): 609–614. doi:10.1038/nmeth.1985. ISSN 1548-7105. PMC 3477507. PMID 22522655.
Jung, Youngsook L.; Luquette, Lovelace J.; Ho, Joshua W. K.; Ferrari, Francesco; Tolstorukov, Michael; Minoda, Aki; Issner, Robbyn; Epstein, Charles B.; Karpen, Gary H.; Kuroda, Mitzi I.; Park, Peter J. (May 2014). "Impact of sequencing depth in ChIP-seq experiments". Nucleic Acids Research. 42 (9): e74. doi:10.1093/nar/gku178. ISSN 1362-4962. PMC 4027199. PMID 24598259.
Ho, Joshua W. K.; Bishop, Eric; Karchenko, Peter V.; Nègre, Nicolas; White, Kevin P.; Park, Peter J. (28 February 2011). "ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis". BMC Genomics. 12: 134. doi:10.1186/1471-2164-12-134. ISSN 1471-2164. PMC 3053263. PMID 21356108.
Jothi, et al. (2008). "Genome-wide identification of in vivo protein–DNA binding sites from ChIP-seq data". Nucleic Acids Res. 36 (16): 5221–5231. doi:10.1093/nar/gkn488. PMC 2532738. PMID 18684996.
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. (September 2010). "ChIP-Seq identification of weakly conserved heart enhancers". Nature Genetics. 42 (9): 806–10. doi:10.1038/ng.650. PMC 3138496. PMID 20729851.
Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, et al. (February 2011). "Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans". Genome Research. 21 (2): 245–54. doi:10.1101/gr.114587.110. PMC 3032928. PMID 21177963.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. (2008). "Model-based analysis of ChIP-Seq (MACS)". Genome Biology. 9 (9): R137. doi:10.1186/gb-2008-9-9-r137. PMC 2592715. PMID 18798982.
Xing H, Mo Y, Liao W, Zhang MQ (2012). "Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data". PLOS Comput Biol. 8 (7): e1002613. Bibcode:2012PLSCB...8E2613X. doi:10.1371/journal.pcbi.1002613. PMC 5429005. PMID 22844240.
Thomas R, Thomas S, Holloway AK, Pollard KS (2017). "Features that define the best ChIP-seq peak calling algorithms". Brief Bioinform. 18 (3): 441–450. doi:10.1093/bib/bbw035. PMC 5429005. PMID 27169896.
Xu, Jinrui; Kudron, Michelle M; Victorsen, Alec; Gao, Jiahao; Ammouri, Haneen N; Navarro, Fabio C P; Gevirtzman, Louis; Waterston, Robert H; White, Kevin P; Reinke, Valerie; Gerstein, Mark (21 December 2020). "To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq". Nucleic Acids Research. 49 (3): gkaa1155. doi:10.1093/nar/gkaa1155. ISSN 0305-1048. PMC 7897498. PMID 33347581.
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, et al. (November 2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–9. Bibcode:2008Natur.456..464L. doi:10.1038/nature07488. PMC 2597294. PMID 18978773.
Darnell RB (2010). "HITS-CLIP: panoramic views of protein-RNA regulation in living cells". Wiley Interdisciplinary Reviews. RNA. 1 (2): 266–286. doi:10.1002/wrna.31. PMC 3222227. PMID 21935890.
Wang H, Mayhew D, Chen X, Johnston M, Mitra RD (May 2011). "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins". Genome Research. 21 (5): 748–55. doi:10.1101/gr.114850.110. PMC 3083092. PMID 21471402.
Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B (January 2018). "ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments". Nucleic Acids Research. 46 (D1): D267 – D275. doi:10.1093/nar/gkx1092. PMC 5753247. PMID 29126285.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, et al. (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

semanticscholar.org

api.semanticscholar.org

Johnson DS, Mortazavi A, Myers RM, Wold B (June 2007). "Genome-wide mapping of in vivo protein-DNA interactions" (PDF). Science. 316 (5830): 1497–502. Bibcode:2007Sci...316.1497J. doi:10.1126/science.1141319. PMID 17540862. S2CID 519841.
Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data". Nature Biotechnology. 31 (7): 615–622. doi:10.1038/nbt.2596. ISSN 1087-0156. PMID 23770639. S2CID 32510475.
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, et al. (January 2005). "Genomic maps and comparative analysis of histone modifications in human and mouse". Cell. 120 (2): 169–81. doi:10.1016/j.cell.2005.01.001. PMID 15680324. S2CID 7193829.
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al. (August 2007). "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing". Nature Methods. 4 (8): 651–7. doi:10.1038/nmeth1068. PMID 17558387. S2CID 28531263.
Schmid CD, Bucher P (November 2007). "ChIP-Seq data reveal nucleosome architecture of human promoters". Cell. 131 (5): 831–2, author reply 832–3. doi:10.1016/j.cell.2007.11.017. PMID 18045524. S2CID 29234049.

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Muhammad, Isiaka Ibrahim; Kong, Sze Ling; Akmar Abdullah, Siti Nor; Munusamy, Umaiyal (25 December 2019). "RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism". International Journal of Molecular Sciences. 21 (1): 167. doi:10.3390/ijms21010167. ISSN 1422-0067. PMC 6981605. PMID 31881735.
Song, Lingyun; Crawford, Gregory E. (February 2010). "DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells". Cold Spring Harbor Protocols. 2010 (2): pdb.prot5384. doi:10.1101/pdb.prot5384. ISSN 1559-6095. PMC 3627383. PMID 20150147.
Giresi, Paul G.; Kim, Jonghwan; McDaniell, Ryan M.; Iyer, Vishwanath R.; Lieb, Jason D. (June 2007). "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin". Genome Research. 17 (6): 877–885. doi:10.1101/gr.5533506. ISSN 1088-9051. PMC 1891346. PMID 17179217.
Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam (July 2013). "Uniform, optimal signal processing of mapped deep-sequencing data". Nature Biotechnology. 31 (7): 615–622. doi:10.1038/nbt.2596. ISSN 1087-0156. PMID 23770639. S2CID 32510475.
Park, Peter J. (October 2009). "ChIP-seq: advantages and challenges of a maturing technology". Nature Reviews. Genetics. 10 (10): 669–680. doi:10.1038/nrg2641. ISSN 1471-0064. PMC 3191340. PMID 19736561.
Chen, Yiwen; Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Liu, Tao; Zhang, Yong; Kim, Tae-Kyung; He, Housheng Hansen; Zieba, Jennifer; Ruan, Yijun (June 2012). "Systematic evaluation of factors influencing ChIP-seq fidelity". Nature Methods. 9 (6): 609–614. doi:10.1038/nmeth.1985. ISSN 1548-7105. PMC 3477507. PMID 22522655.
Jung, Youngsook L.; Luquette, Lovelace J.; Ho, Joshua W. K.; Ferrari, Francesco; Tolstorukov, Michael; Minoda, Aki; Issner, Robbyn; Epstein, Charles B.; Karpen, Gary H.; Kuroda, Mitzi I.; Park, Peter J. (May 2014). "Impact of sequencing depth in ChIP-seq experiments". Nucleic Acids Research. 42 (9): e74. doi:10.1093/nar/gku178. ISSN 1362-4962. PMC 4027199. PMID 24598259.
Ho, Joshua W. K.; Bishop, Eric; Karchenko, Peter V.; Nègre, Nicolas; White, Kevin P.; Park, Peter J. (28 February 2011). "ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis". BMC Genomics. 12: 134. doi:10.1186/1471-2164-12-134. ISSN 1471-2164. PMC 3053263. PMID 21356108.
Xu, Jinrui; Kudron, Michelle M; Victorsen, Alec; Gao, Jiahao; Ammouri, Haneen N; Navarro, Fabio C P; Gevirtzman, Louis; Waterston, Robert H; White, Kevin P; Reinke, Valerie; Gerstein, Mark (21 December 2020). "To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq". Nucleic Acids Research. 49 (3): gkaa1155. doi:10.1093/nar/gkaa1155. ISSN 0305-1048. PMC 7897498. PMID 33347581.