المؤلفون: Hu, Yan, Horlbeck, Max A., Zhang, Ruochi, Ma, Sai, Shrestha, Rojesh, Kartha, Vinay K., Duarte, Fabiana M., Hock, Conrad, Savage, Rachel E., Labade, Ajay, Kletzien, Heidi, Meliki, Alia, Castillo, Andrew, Durand, Neva C., Mattei, Eugenio, Anderson, Lauren J., Tay, Tristan, Earl, Andrew S., Shoresh, Noam, Epstein, Charles B., Wagers, Amy J., Buenrostro, Jason D.

المصدر: Nature ; ISSN 0028-0836 1476-4687

الاتاحة: https://doi.org/10.1038/s41586-024-08443-4
https://www.nature.com/articles/s41586-024-08443-4.pdf
https://www.nature.com/articles/s41586-024-08443-4

المؤلفون: Sandoval-Velasco, Marcela, Dudchenko, Olga, Rodríguez, Juan Antonio, Estrada, Cynthia Pérez, Dehasque, Marianne, Fontsere, Claudia, Mak, Sarah S. T., Khan, Ruqayya, Contessoto, Vinícius G., Oliveira Junior, Antonio B., Kalluchi, Achyuth, Herrera, Bernardo J. Zubillaga, Jeong, Jiyun, Roy, Renata P., Christopher, Ishawnia, Weisz, David, Omer, Arina D., Batra, Sanjit S., Shamim, Muhammad S., Durand, Neva C., O'Connell, Brendan, Roca, Alfred L., Plikus, Maksim V., Kusliy, Mariya A., Romanenko, Svetlana A., Lemskaya, Natalya A., Serdyukova, Natalya A., Modina, Svetlana A., Perelman, Polina L., Kizilova, Elena A., Baiborodin, Sergei I., Rubtsov, Nikolai B., Machol, Gur, Rath, Krisha, Mahajan, Ragini, Kaur, Parwinder, Gnirke, Andreas, Garcia-Treviño, Isabel, Coke, Rob, Flanagan, Joseph P., Pletch, Kelcie, Ruiz-Herrera, Aurora, Plotnikov, Valerii, Pavlov, Innokentiy S., Pavlova, Naryya I., Protopopov, Albert V., Di Pierro, Michele, Graphodatsky, Alexander S., Lander, Eric S., Rowley, M. Jordan, Wolynes, Peter G., Onuchic, José N., Dalén, Love, Marti-Renom, Marc A., Gilbert, M. Thomas P., Aiden, Erez Lieberman

المصدر: Sandoval-Velasco , M , Dudchenko , O , Rodríguez , J A , Estrada , C P , Dehasque , M , Fontsere , C , Mak , S S T , Khan , R , Contessoto , V G , Oliveira Junior , A B , Kalluchi , A , Herrera , B J Z , Jeong , J , Roy , R P , Christopher , I , Weisz , D , Omer , A D , Batra , S S , Shamim , M S , Durand , N C , O'Connell , B , Roca ....

مصطلحات موضوعية: ancient DNA, chromatin loops, fossil, genome architecture, genome assembly, glass transition, Hi-C, vitrification, woolly mammoth, X inactivation

وصف الملف: application/pdf

الاتاحة: https://researchprofiles.ku.dk/da/publications/threedimensional-genome-architecture-persists-in-a-52000yearold-woolly-mammoth-skin-sample(19d1a798-e0d8-4d16-bc9d-c32e7c8ffa75).html
https://doi.org/10.1016/j.cell.2024.06.002
https://curis.ku.dk/ws/files/412530191/1_s2.0_S0092867424006421_main.pdf

المؤلفون: Gate, Rachel E, Cheng, Christine S, Aiden, Aviva P, Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M Grace, Subramaniam, Meena, Shamim, Muhammad, Hougen, Kendrick L, Wortman, Ivo, Huang, Su-Chen, Durand, Neva C, Feng, Ting, De Jager, Philip L, Chang, Howard Y, Aiden, Erez Lieberman, Benoist, Christophe, Beer, Michael A, Ye, Chun J, Regev, Aviv

المصدر: Nature Genetics. 50(8)

مصطلحات موضوعية: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Stem Cell Research, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Adult, Autoimmune Diseases, CD4-Positive T-Lymphocytes, Chromatin, Female, Gene Expression Regulation, Genotype, Humans, Male, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/8762v2z6

المؤلفون: Adastra, Per A., Durand, Neva C., Mitra, Namita, Pulido, Saul Godinez, Mahajan, Ragini, Blackburn, Alyssa, Colaric, Zane L., Theisen, Joshua W. M., Weisz, David, Dudchenko, Olga, Gnirke, Andreas, Rao, Suhas S. P., Kaur, Parwinder, Aiden, Erez Lieberman, Aiden, Aviva Presser

المساهمون: Giri, Basant, Howard Hughes Medical Institute, Thrasher Research Fund, United States - Israel Binational Science Foundation, Directorate for Mathematical and Physical Sciences

المصدر: PLOS ONE ; volume 18, issue 11, page e0294283 ; ISSN 1932-6203

الاتاحة: http://dx.doi.org/10.1371/journal.pone.0294283
https://dx.plos.org/10.1371/journal.pone.0294283

المؤلفون: Gschwind, Andreas R, Mualim, Kristy S, Karbalayghareh, Alireza, Sheth, Maya U, Dey, Kushal K, Jagoda, Evelyn, Nurtdinov, Ramil N, Xi, Wang, Tan, Anthony S, Jones, Hank, Ma, X Rosa, Yao, David, Nasser, Joseph, Avsec, Žiga, James, Benjamin T, Shamim, Muhammad S, Durand, Neva C, Rao, Suhas S P, Mahajan, Ragini, Doughty, Benjamin R, Andreeva, Kalina, Ulirsch, Jacob C, Fan, Kaili, Perez, Elizabeth M, Nguyen, Tri C, Kelley, David R, Finucane, Hilary K, Moore, Jill E, Weng, Zhiping, Kellis, Manolis, Bassik, Michael C, Price, Alkes L, Beer, Michael A, Guigó, Roderic, Stamatoyannopoulos, John A, Lieberman Aiden, Erez, Greenleaf, William J, Leslie, Christina S, Steinmetz, Lars M, Kundaje, Anshul, Engreitz, Jesse M

المساهمون: Program in Bioinformatics and Integrative Biology

المصدر: bioRxiv : the preprint server for biology ; United States

مصطلحات موضوعية: Genomics, gene regulation

Relation: bioRxiv; https://doi.org/10.1101/2023.11.09.563812; Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM. An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv [Preprint]. 2023 Nov 13:2023.11.09.563812. doi:10.1101/2023.11.09.563812. PMID: 38014075; PMCID: PMC10680627.; http://hdl.handle.net/20.500.14038/52868; bioRxiv : the preprint server for biology

الاتاحة: https://doi.org/10.1101/2023.11.09.563812
https://hdl.handle.net/20.500.14038/52868

المؤلفون: Hitz, Benjamin C., Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi S., Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J. Seth, Sloan, Cricket A., Dreszer, Timothy, Rowe, Laurence D., Podduturi, Nikhil R., Malladi, Venkat S., Chan, Esther T., Davidson, Jean M., Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L., Lee, Brian T., Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S., Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C., Dudchenko, Olga, Weisz, David, Rao, Suhas S. P., Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, James Kent, W., Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J. Michael

Relation: https://www.encodeproject.org/; https://doi.org/10.1101/2023.04.04.535623

الاتاحة: https://doi.org/10.1101/2023.04.04.535623

المؤلفون: Garg, Vanika, Dudchenko, Olga, Wang, Jinpeng, Khan, Aamir W., Gupta, Saurabh, Kaur, Parwinder, Han, Kai, Saxena, Rachit K., Kale, Sandip M., Pham, Melanie, Yu, Jigao, Chitikineni, Annapurna, Zhang, Zhikang, Fan, Guangyi, Lui, Christopher, Valluri, Vinodkumar, Meng, Fanbo, Bhandari, Aditi, Liu, Xiaochuan, Yang, Tao, Chen, Hua, Valliyodan, Babu, Roorkiwal, Manish, Shi, Chengcheng, Yang, Hong Bin, Durand, Neva C., Pandey, Manish K., Li, Guowei, Barmukh, Rutwik, Wang, Xingjun, Chen, Xiaoping, Lam, Hon-Ming, Jiang, Huifang, Zong, Xuxiao, Liang, Xuanqiang, Liu, Xin, Liao, Boshou, Guo, Baozhu, Jackson, Scott, Nguyen, Henry T., Zhuang, Weijian, Shubo, Wan, Wang, Xiyin, Aiden, Erez Lieberman, Bennetzen, Jeffrey L., Varshney, Rajeev K.

المساهمون: Bill & Melinda Gates Foundation

المصدر: Journal of Advanced Research ; volume 42, page 315-329 ; ISSN 2090-1232

الاتاحة: http://dx.doi.org/10.1016/j.jare.2021.10.009
https://api.elsevier.com/content/article/PII:S2090123221002058?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S2090123221002058?httpAccept=text/plain

المؤلفون: Wike, Candice L., Guo, Yixuan, Tan, Mengyao, Nakamura, Ryohei, Shaw, Dana Klatt, Díaz, Noelia, Whittaker-Tademy, Aneasha F., Durand, Neva C., Aiden, Erez Lieberman, Vaquerizas, Juan M., Grunwald, David, Takeda, Hiroyuki, Cairns, Bradley R.

المساهمون: Center for Theoretical Biological Physics

وصف الملف: application/pdf

Relation: Wike, Candice L., Guo, Yixuan, Tan, Mengyao, et al. "Chromatin architecture transitions from zebrafish sperm through early embryogenesis." Genome Research, 31, no. 6 (2021) Cold Spring Harbor Laboratory Press: 981-994. https://doi.org/10.1101/gr.269860.120.; https://hdl.handle.net/1911/110835; GenomeRes-2021-Wike-981-94; https://doi.org/10.1101/gr.269860.120

الاتاحة: https://hdl.handle.net/1911/110835
https://doi.org/10.1101/gr.269860.120

المؤلفون: Nakamura, Ryohei, Motai, Yuichi, Kumagai, Masahiko, Wike, Candice L., Nishiyama, Haruyo, Nakatani, Yoichiro, Durand, Neva C., Kondo, Kaori, Kondo, Takashi, Tsukahara, Tatsuya, Shimada, Atsuko, Cairns, Bradley R., Aiden, Erez Lieberman, Morishita, Shinichi, Takeda, Hiroyuki

المساهمون: Center for Theoretical Biological Physics

وصف الملف: application/pdf

Relation: Nakamura, Ryohei, Motai, Yuichi, Kumagai, Masahiko, et al. "CTCF looping is established during gastrulation in medaka embryos." Genome Research, 31, (2021) Cold Spring Harbor Laboratory Press: 968-980. https://doi.org/10.1101/gr.269951.120.; https://hdl.handle.net/1911/111930; GenomeRes-2021-Nakamura-968-80; https://doi.org/10.1101/gr.269951.120

الاتاحة: https://hdl.handle.net/1911/111930
https://doi.org/10.1101/gr.269951.120

المؤلفون: Dudchenko, Olga, Batra, Sanjit S., Omer, Arina D., Nyquist, Sarah K., Hoeger, Marie, Durand, Neva C., Shamim, Muhammad S., Machol, Ido, Lander, Eric S., Aiden, Aviva Presser, Aiden, Erez Lieberman

المصدر: Science, 2017 Apr 01. 356(6333), 92-95.

URL الوصول: https://www.jstor.org/stable/24918168

المؤلفون: Darrow, Emily M., Huntley, Miriam H., Dudchenko, Olga, Stamenova, Elena K., Durand, Neva C., Sun, Zhuo, Huang, Su-Chen, Sanborn, Adrian L., Machol, Ido, Shamim, Muhammad, Seberg, Andrew P., Lander, Eric S., Chadwick, Brian P., Aiden, Erez Lieberman

المصدر: Proceedings of the National Academy of Sciences of the United States of America, 2016 Aug 01. 113(31), E4504-E4512.

URL الوصول: https://www.jstor.org/stable/26471068

المؤلفون: Sanborn, Adrian L., Rao, Suhas S. P., Huang, Su-Chen, Durand, Neva C., Huntley, Miriam H., Jewett, Andrew I., Bochkov, Ivan D., Chinnappan, Dharmaraj, Cutkosky, Ashok, Li, Jian, Geeting, Kristopher P., Gnirke, Andreas, Melnikov, Alexandre, McKenna, Doug, Stamenova, Elena K., Lander, Eric S., Aiden, Erez Lieberman

المصدر: Proceedings of the National Academy of Sciences of the United States of America, 2015 Nov . 112(47), E6456-E6465.

URL الوصول: https://www.jstor.org/stable/26465897

المؤلفون: Nir, Guy, Farabella, Irene, Pérez Estrada, Cynthia, Ebeling, Carl G., Beliveau, Brian J., Sasaki, Hiroshi M., Lee, S. Dean, Nguyen, Son C., McCole, Ruth B., Chattoraj, Shyamtanu, Erceg, Jelena, AlHaj Abed, Jumana, Martins, Nuno M. C., Nguyen, Huy Q., Hannan, Mohammed A., Russell, Sheikh, Durand, Neva C., Rao, Suhas S. P., Kishi, Jocelyn Y., Soler-Vila, Paula, Di Pierro, Michele, Onuchic, José N., Callahan, Steven P., Schreiner, John M., Stuckey, Jeff A., Yin, Peng, Aiden, Erez Lieberman, Marti-Renom, Marc A., Wu, C.-ting

المساهمون: Copenhaver, Gregory P.

المصدر: PLOS Genetics ; volume 14, issue 12, page e1007872 ; ISSN 1553-7404

الاتاحة: http://dx.doi.org/10.1371/journal.pgen.1007872
http://dx.plos.org/10.1371/journal.pgen.1007872

المؤلفون: Robinson, James T., Turner, Douglass, Durand, Neva C., Thorvaldsdóttir, Helga, Mesirov, Jill P., Aiden, Erez Lieberman

المساهمون: NIH, NSF Physics Frontiers Center, Welch Foundation, NVIDIA Research Center, IBM University Challenge, Google Research, Cancer Prevention Research Institute of Texas Scholar, McNair Medical Institute Scholar, NIH 4D Nucleome, NIH Encyclopedia of DNA Elements (ENCODE) Mapping Center, President's Early Career, NIH National Cancer Institute, NIH NCI Informatics Technology for Cancer Research

المصدر: Cell Systems ; volume 6, issue 2, page 256-258.e1 ; ISSN 2405-4712

الاتاحة: http://dx.doi.org/10.1016/j.cels.2018.01.001
https://api.elsevier.com/content/article/PII:S2405471218300012?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S2405471218300012?httpAccept=text/plain

المؤلفون: Vian, Laura, Pękowska, Aleksandra, Rao, Suhas S.P., Kieffer-Kwon, Kyong-Rim, Jung, Seolkyoung, Baranello, Laura, Huang, Su-Chen, El Khattabi, Laila, Dose, Marei, Pruett, Nathanael, Sanborn, Adrian L., Canela, Andres, Maman, Yaakov, Oksanen, Anna, Resch, Wolfgang, Li, Xingwang, Lee, Byoungkoo, Kovalchuk, Alexander L., Tang, Zhonghui, Nelson, Steevenson, Di Pierro, Michele, Cheng, Ryan R., Machol, Ido, St Hilaire, Brian Glenn, Durand, Neva C., Shamim, Muhammad S., Stamenova, Elena K., Onuchic, José N., Ruan, Yijun, Nussenzweig, Andre, Levens, David, Aiden, Erez Lieberman, Casellas, Rafael

المساهمون: NIAMS, NCI, NIAID, NIH Helix Systems, Paul and Daisy Soros Fellowship, Fannie and John Hertz Foundation Fellowship, Cornelia de Lange Syndrome Foundation, NIH New Innovator Award, NSF Physics Frontiers Center Award, NHGRI Center for Excellence for Genomic Sciences, Welch Foundation, NVIDIA Research Center Award, IBM University Challenge Award, Google Research Award, Cancer Prevention Research Institute of Texas Scholar Award, USDA Agriculture and Food Research Initiative Grant, McNair Medical Institute Scholar Award, NIH Encyclopedia of DNA Elements Mapping Center Award, President’s Early Career Award in Science and Engineering, NSF

المصدر: Cell ; volume 173, issue 5, page 1165-1178.e20 ; ISSN 0092-8674

الاتاحة: http://dx.doi.org/10.1016/j.cell.2018.03.072
https://api.elsevier.com/content/article/PII:S0092867418304045?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0092867418304045?httpAccept=text/plain

المؤلفون: Durand, Neva C., Shamim, Muhammad S., Machol, Ido, Rao, Suhas S.P., Huntley, Miriam H., Aiden, Erez Lieberman, Lander, Eric Steven

المساهمون: Massachusetts Institute of Technology. Department of Biology, Lander, Eric Steven

المصدر: Elsevier

وصف الملف: application/pdf

Relation: http://dx.doi.org/10.1016/j.cels.2016.07.002; Cell Systems; http://hdl.handle.net/1721.1/106809; Durand, Neva C. et al. “Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.” Cell Systems 3.1 (2016): 95–98.

الاتاحة: http://hdl.handle.net/1721.1/106809

المؤلفون: Durand, Neva C., Robinson, James T., Shamim, Muhammad S., Machol, Ido, Mesirov, Jill P., Lander, Eric S., Aiden, Erez Lieberman

المصدر: Cell Systems ; volume 3, issue 1, page 99-101 ; ISSN 2405-4712

الاتاحة: http://dx.doi.org/10.1016/j.cels.2015.07.012
https://api.elsevier.com/content/article/PII:S240547121500054X?httpAccept=text/plain
https://api.elsevier.com/content/article/PII:S240547121500054X?httpAccept=text/xml

المؤلفون: Durand, Neva C., Robinson, James T., Shamim, Muhammad S., Machol, Ido, Aiden, Erez Lieberman, Lander, Eric Steven, Mesirov, Jill P.

المساهمون: Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Mesirov, Jill P, Lander, Eric Steven

المصدر: Elsevier

وصف الملف: application/pdf

Relation: http://dx.doi.org/10.1016/j.cels.2015.07.012; Cell Systems; http://hdl.handle.net/1721.1/105759; Durand, Neva C., James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. “Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.” Cell Systems 3, no. 1 (July 2016): 99-101.

الاتاحة: http://hdl.handle.net/1721.1/105759

المؤلفون: Rao, Suhas S.P., Huntley, Miriam H., Durand, Neva C., Stamenova, Elena K., Bochkov, Ivan D., Robinson, James T., Sanborn, Adrian L., Machol, Ido, Omer, Arina D., Lander, Eric S., Aiden, Erez Lieberman

المصدر: Cell ; volume 162, issue 3, page 687-688 ; ISSN 0092-8674

الاتاحة: https://doi.org/10.1016/j.cell.2015.07.024
https://api.elsevier.com/content/article/PII:S0092867415009010?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0092867415009010?httpAccept=text/plain

المؤلفون: Rao, Suhas S.P., Huntley, Miriam H., Durand, Neva C., Stamenova, Elena K., Bochkov, Ivan D., Robinson, James T., Sanborn, Adrian L., Machol, Ido, Omer, Arina D., Lander, Eric S., Aiden, Erez Lieberman

المصدر: Cell ; volume 159, issue 7, page 1665-1680 ; ISSN 0092-8674

الاتاحة: http://dx.doi.org/10.1016/j.cell.2014.11.021
https://api.elsevier.com/content/article/PII:S0092867414014974?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0092867414014974?httpAccept=text/plain