Статті в журналах з теми "3D genome structure"
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Zhou, Tianming, Ruochi Zhang, and Jian Ma. "The 3D Genome Structure of Single Cells." Annual Review of Biomedical Data Science 4, no. 1 (July 20, 2021): 21–41. http://dx.doi.org/10.1146/annurev-biodatasci-020121-084709.
Повний текст джерелаMohanta, Tapan Kumar, Awdhesh Kumar Mishra, and Ahmed Al-Harrasi. "The 3D Genome: From Structure to Function." International Journal of Molecular Sciences 22, no. 21 (October 27, 2021): 11585. http://dx.doi.org/10.3390/ijms222111585.
Повний текст джерелаHuang, Kai, Yue Li, Anne R. Shim, Ranya K. A. Virk, Vasundhara Agrawal, Adam Eshein, Rikkert J. Nap, Luay M. Almassalha, Vadim Backman, and Igal Szleifer. "Physical and data structure of 3D genome." Science Advances 6, no. 2 (January 2020): eaay4055. http://dx.doi.org/10.1126/sciadv.aay4055.
Повний текст джерелаHeinz, Sven, Lorane Texari, Michael G. B. Hayes, Matthew Urbanowski, Max W. Chang, Ninvita Givarkes, Alexander Rialdi, et al. "Transcription Elongation Can Affect Genome 3D Structure." Cell 174, no. 6 (September 2018): 1522–36. http://dx.doi.org/10.1016/j.cell.2018.07.047.
Повний текст джерелаWlasnowolski, Michal, Michal Sadowski, Tymon Czarnota, Karolina Jodkowska, Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan, and Dariusz Plewczynski. "3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome." Nucleic Acids Research 48, W1 (May 22, 2020): W170—W176. http://dx.doi.org/10.1093/nar/gkaa388.
Повний текст джерелаShepherd, Jeremiah J., Lingxi Zhou, William Arndt, Yan Zhang, W. Jim Zheng, and Jijun Tang. "Exploring genomes with a game engine." Faraday Discuss. 169 (2014): 443–53. http://dx.doi.org/10.1039/c3fd00152k.
Повний текст джерелаPoblete, Simón, and Horacio V. Guzman. "Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models." Viruses 13, no. 8 (August 6, 2021): 1555. http://dx.doi.org/10.3390/v13081555.
Повний текст джерелаTrieu, Tuan, and Jianlin Cheng. "3D genome structure modeling by Lorentzian objective function." Nucleic Acids Research 45, no. 3 (November 28, 2016): 1049–58. http://dx.doi.org/10.1093/nar/gkw1155.
Повний текст джерелаLi, Chao, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, and Yixue Li. "The 3DGD: a database of genome 3D structure." Bioinformatics 30, no. 11 (February 12, 2014): 1640–42. http://dx.doi.org/10.1093/bioinformatics/btu081.
Повний текст джерелаTjong, Harianto, Wenyuan Li, Reza Kalhor, Chao Dai, Shengli Hao, Ke Gong, Yonggang Zhou, et al. "Population-based 3D genome structure analysis reveals driving forces in spatial genome organization." Proceedings of the National Academy of Sciences 113, no. 12 (March 7, 2016): E1663—E1672. http://dx.doi.org/10.1073/pnas.1512577113.
Повний текст джерелаKim, Kyukwang, Insu Jang, Mooyoung Kim, Jinhyuk Choi, Min-Seo Kim, Byungwook Lee, and Inkyung Jung. "3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome." Nucleic Acids Research 49, no. D1 (November 27, 2020): D38—D46. http://dx.doi.org/10.1093/nar/gkaa1078.
Повний текст джерелаOhno, Masae, Tadashi Ando, David G. Priest, and Yuichi Taniguchi. "Hi-CO: 3D genome structure analysis with nucleosome resolution." Nature Protocols 16, no. 7 (May 28, 2021): 3439–69. http://dx.doi.org/10.1038/s41596-021-00543-z.
Повний текст джерелаTANIGUCHI, Yuichi, and Masae OHNO. "Resolving 3D Higher-order Molecular Structure of the Genome." Seibutsu Butsuri 59, no. 6 (2019): 305–9. http://dx.doi.org/10.2142/biophys.59.305.
Повний текст джерелаDi Stefano, Marco, and Giacomo Cavalli. "Integrative studies of 3D genome organization and chromatin structure." Current Opinion in Structural Biology 77 (December 2022): 102493. http://dx.doi.org/10.1016/j.sbi.2022.102493.
Повний текст джерелаKozubek, Stanislav, Emilie Lukásová, Pavla Jirsová, Irena Koutná, Michal Kozubek, Alena Ganová, Eva Bártová, Martin Falk, and Renata Paseková. "3D Structure of the human genome: order in randomness." Chromosoma 111, no. 5 (December 2002): 321–31. http://dx.doi.org/10.1007/s00412-002-0210-8.
Повний текст джерелаZhegalova, Irina V., Petr A. Vasiluev, Ilya M. Flyamer, Anastasia S. Shtompel, Eugene Glazyrina, Nadezda Shilova, Marina Minzhenkova, et al. "Trisomies Reorganize Human 3D Genome." International Journal of Molecular Sciences 24, no. 22 (November 7, 2023): 16044. http://dx.doi.org/10.3390/ijms242216044.
Повний текст джерелаDias, João Diogo, Nazim Sarica, Axel Cournac, Romain Koszul, and Christine Neuveut. "Crosstalk between Hepatitis B Virus and the 3D Genome Structure." Viruses 14, no. 2 (February 21, 2022): 445. http://dx.doi.org/10.3390/v14020445.
Повний текст джерелаShao, Dan, Yu Yang, Shourong Shi, and Haibing Tong. "Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments." Genes 13, no. 12 (December 9, 2022): 2317. http://dx.doi.org/10.3390/genes13122317.
Повний текст джерелаLi, An, and Zhang. "The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development." Cells 8, no. 8 (July 29, 2019): 788. http://dx.doi.org/10.3390/cells8080788.
Повний текст джерелаDethoff, Elizabeth A., Mark A. Boerneke, Nandan S. Gokhale, Brejnev M. Muhire, Darren P. Martin, Matthew T. Sacco, Michael J. McFadden, et al. "Pervasive tertiary structure in the dengue virus RNA genome." Proceedings of the National Academy of Sciences 115, no. 45 (October 19, 2018): 11513–18. http://dx.doi.org/10.1073/pnas.1716689115.
Повний текст джерелаZhang, Yan, Yijun Ruan, and Guoliang Li. "The 5th International 3D Genomics Workshop 2018: conference report." Epigenomics 11, no. 12 (September 2019): 1353–57. http://dx.doi.org/10.2217/epi-2019-0185.
Повний текст джерелаMacKay, Kimberly, and Anthony Kusalik. "Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data." Briefings in Functional Genomics 19, no. 4 (April 29, 2020): 292–308. http://dx.doi.org/10.1093/bfgp/elaa004.
Повний текст джерелаKim, Yoori, and Hongtao Yu. "Shaping of the 3D genome by the ATPase machine cohesin." Experimental & Molecular Medicine 52, no. 12 (December 2020): 1891–97. http://dx.doi.org/10.1038/s12276-020-00526-2.
Повний текст джерелаWang, Maojun, Jianying Li, Pengcheng Wang, Fang Liu, Zhenping Liu, Guannan Zhao, Zhongping Xu, et al. "Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton." Molecular Biology and Evolution 38, no. 9 (May 11, 2021): 3621–36. http://dx.doi.org/10.1093/molbev/msab128.
Повний текст джерелаSun, Xiaoyue, Jing Zhang, and Chunwei Cao. "CTCF and Its Partners: Shaper of 3D Genome during Development." Genes 13, no. 8 (August 2, 2022): 1383. http://dx.doi.org/10.3390/genes13081383.
Повний текст джерелаWang, Juan, Tina Yi-Ting Huang, Ye Hou, Elizabeth Bartom, Xinyan Lu, Ali Shilatifard, Feng Yue, and Amanda Saratsis. "Epigenomic landscape and 3D genome structure in pediatric high-grade glioma." Science Advances 7, no. 23 (June 2021): eabg4126. http://dx.doi.org/10.1126/sciadv.abg4126.
Повний текст джерелаTheis, Corinna, Craig L. Zirbel, Christian Höner zu Siederdissen, Christian Anthon, Ivo L. Hofacker, Henrik Nielsen, and Jan Gorodkin. "RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure." PLOS ONE 10, no. 10 (October 28, 2015): e0139900. http://dx.doi.org/10.1371/journal.pone.0139900.
Повний текст джерелаVaroquaux, N., F. Ay, W. S. Noble, and J. P. Vert. "A statistical approach for inferring the 3D structure of the genome." Bioinformatics 30, no. 12 (June 15, 2014): i26—i33. http://dx.doi.org/10.1093/bioinformatics/btu268.
Повний текст джерелаFilion, Guillaume J., and Miguel Beato. "3D genome structure. Organization of the nucleus in space and time." FEBS Letters 589, no. 20PartA (September 9, 2015): 2867–68. http://dx.doi.org/10.1016/j.febslet.2015.09.003.
Повний текст джерелаPombo, Ana. "Specialization of 3D genome structure in different cell types and states." Biophysical Journal 123, no. 3 (February 2024): 441a. http://dx.doi.org/10.1016/j.bpj.2023.11.2688.
Повний текст джерелаCollins, Brandon, Oluwatosin Oluwadare, and Philip Brown. "ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction." Genes 12, no. 11 (November 3, 2021): 1757. http://dx.doi.org/10.3390/genes12111757.
Повний текст джерелаTorosin, Nicole S., Aparna Anand, Tirupathi Rao Golla, Weihuan Cao, and Christopher E. Ellison. "3D genome evolution and reorganization in the Drosophila melanogaster species group." PLOS Genetics 16, no. 12 (December 7, 2020): e1009229. http://dx.doi.org/10.1371/journal.pgen.1009229.
Повний текст джерелаChen, Haiming, Jie Chen, Lindsey A. Muir, Scott Ronquist, Walter Meixner, Mats Ljungman, Thomas Ried, Stephen Smale, and Indika Rajapakse. "Functional organization of the human 4D Nucleome." Proceedings of the National Academy of Sciences 112, no. 26 (June 15, 2015): 8002–7. http://dx.doi.org/10.1073/pnas.1505822112.
Повний текст джерелаVadnais, David, and Oluwatosin Oluwadare. "ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction." Current Issues in Molecular Biology 45, no. 3 (March 17, 2023): 2549–60. http://dx.doi.org/10.3390/cimb45030167.
Повний текст джерелаIkhsan, Fajri, Ahmad Shulhany, and Syarif Abdullah. "Metallothionein Protein Modeling from Pseudomonas aeruginosa PAO1 as A Metal Biosorber Candidate." Jurnal Biodjati 8, no. 2 (November 28, 2023): 248–61. http://dx.doi.org/10.15575/biodjati.v8i2.29170.
Повний текст джерелаYamaguchi, A. "Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species." Nucleic Acids Research 31, no. 1 (January 1, 2003): 463–68. http://dx.doi.org/10.1093/nar/gkg117.
Повний текст джерелаTrieu, Tuan, Oluwatosin Oluwadare, Julia Wopata, and Jianlin Cheng. "GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure." Bioinformatics 35, no. 8 (September 12, 2018): 1416–18. http://dx.doi.org/10.1093/bioinformatics/bty802.
Повний текст джерелаKrijger, Peter Hugo Lodewijk, Bruno Di Stefano, Elzo de Wit, Francesco Limone, Chris van Oevelen, Wouter de Laat, and Thomas Graf. "Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming." Cell Stem Cell 18, no. 5 (May 2016): 597–610. http://dx.doi.org/10.1016/j.stem.2016.01.007.
Повний текст джерелаGong, Ke, Harianto Tjong, Xianghong Jasmine Zhou, and Frank Alber. "Comparative 3D Genome Structure Analysis of the Fission and the Budding Yeast." PLOS ONE 10, no. 3 (March 23, 2015): e0119672. http://dx.doi.org/10.1371/journal.pone.0119672.
Повний текст джерелаHuang, Tina, Juan Wang, Ye Hu, Andrea Piunti, Elizabeth Bartom, Feng Yue, and Amanda Saratsis. "EPCO-17. 3D GENOME STRUCTURE REGULATES TRANSCRIPTION IN PEDIATRIC HIGH-GRADE GLIOMA." Neuro-Oncology 25, Supplement_5 (November 1, 2023): v127. http://dx.doi.org/10.1093/neuonc/noad179.0480.
Повний текст джерелаOrozco, Gisela. "Fine mapping with epigenetic information and 3D structure." Seminars in Immunopathology 44, no. 1 (January 2022): 115–25. http://dx.doi.org/10.1007/s00281-021-00906-4.
Повний текст джерелаZhou, Jingtian, Jianzhu Ma, Yusi Chen, Chuankai Cheng, Bokan Bao, Jian Peng, Terrence J. Sejnowski, Jesse R. Dixon, and Joseph R. Ecker. "Robust single-cell Hi-C clustering by convolution- and random-walk–based imputation." Proceedings of the National Academy of Sciences 116, no. 28 (June 24, 2019): 14011–18. http://dx.doi.org/10.1073/pnas.1901423116.
Повний текст джерелаBelyaeva, Anastasiya, Saradha Venkatachalapathy, Mallika Nagarajan, G. V. Shivashankar, and Caroline Uhler. "Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription." Proceedings of the National Academy of Sciences 114, no. 52 (December 11, 2017): 13714–19. http://dx.doi.org/10.1073/pnas.1708028115.
Повний текст джерелаIershov, Anton, Konstantin Odynets, Alexander Kornelyuk, and Vadim Kavsan. "Homology modeling of 3D structure of human chitinase-like protein CHI3L2." Open Life Sciences 5, no. 4 (August 1, 2010): 407–20. http://dx.doi.org/10.2478/s11535-010-0039-8.
Повний текст джерелаChen, Yu, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, and Andrew S. Belmont. "Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler." Journal of Cell Biology 217, no. 11 (August 28, 2018): 4025–48. http://dx.doi.org/10.1083/jcb.201807108.
Повний текст джерелаMakai, Diána, András Cseh, Adél Sepsi, and Szabolcs Makai. "A Multigraph-Based Representation of Hi-C Data." Genes 13, no. 12 (November 23, 2022): 2189. http://dx.doi.org/10.3390/genes13122189.
Повний текст джерелаStilianoudakis, Spiro C., Maggie A. Marshall, and Mikhail G. Dozmorov. "preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution." Bioinformatics 38, no. 3 (November 6, 2021): 621–30. http://dx.doi.org/10.1093/bioinformatics/btab743.
Повний текст джерелаBoninsegna, Lorenzo, Asli Yildirim, Guido Polles, Yuxiang Zhan, Sofia A. Quinodoz, Elizabeth H. Finn, Mitchell Guttman, Xianghong Jasmine Zhou, and Frank Alber. "Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations." Nature Methods, July 11, 2022. http://dx.doi.org/10.1038/s41592-022-01527-x.
Повний текст джерелаWang, Ruiting, Fengling Chen, Qian Chen, Xin Wan, Minglei Shi, Antony K. Chen, Zhao Ma, et al. "MyoD is a 3D genome structure organizer for muscle cell identity." Nature Communications 13, no. 1 (January 11, 2022). http://dx.doi.org/10.1038/s41467-021-27865-6.
Повний текст джерелаVadnais, David, Michael Middleton, and Oluwatosin Oluwadare. "ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data." BioData Mining 15, no. 1 (September 21, 2022). http://dx.doi.org/10.1186/s13040-022-00305-x.
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