Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, Erez, van Berkum, Nynke L., Williams, Louise, Imakaev, Maxim, Ragoczy, Tobias, Telling, Agnes, Amit, Ido, Lajoie, Bryan R. +11 more·2009·Science
Cited by (244)
Items 101–200 of 244
- Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer FormationChandra, Tamir, Kirschner, Kristina, Thuret, Jean-Yves, Pope, Benjamin D., Ryba, Tyrone, Newman, Scott, Ahmed, Kashif, Samarajiwa, Shamith A., Salama, Rafik, Carroll, Thomas et al. · 2012 · Molecular Cell
- Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal InteractionsGrubert, Fabian, Zaugg, Judith B., Kasowski, Maya, Ursu, Oana, Spacek, Damek V., Martin, Alicia R., Greenside, Peyton, Srivas, Rohith, Phanstiel, Doug H., Pekowska, Aleksandra et al. · 2015 · Cell
- The role of DNA methylation in stress-related psychiatric disordersKlengel, Torsten, Pape, Julius, Binder, Elisabeth B., Mehta, Divya · 2014 · Neuropharmacology
- Deletion of
<i>DXZ4</i>
on the human inactive X chromosome alters higher-order genome architectureDarrow, 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 et al. · 2016 · Proceedings of the National Academy of Sciences
- Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and ClassificationDapas, Matthew, Dunaif, Andrea · 2022 · Endocrine Reviews
- YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitmentBeagan, Jonathan A., Duong, Michael T., Titus, Katelyn R., Zhou, Linda, Cao, Zhendong, Ma, Jingjing, Lachanski, Caroline V., Gillis, Daniel R., Phillips-Cremins, Jennifer E. · 2017 · Genome Research
- Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fateLin, Yin C, Benner, Christopher, Mansson, Robert, Heinz, Sven, Miyazaki, Kazuko, Miyazaki, Masaki, Chandra, Vivek, Bossen, Claudia, Glass, Christopher K, Murre, Cornelis · 2012 · Nature Immunology
- Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disordersGaiteri, C., Ding, Y., French, B., Tseng, G. C., Sibille, E. · 2014 · Genes, Brain and Behavior
- Methods for ChIP-seq analysis: A practical workflow and advanced applicationsNakato, Ryuichiro, Sakata, Toyonori · 2021 · Methods
- Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCFHansen, Anders S., Hsieh, Tsung-Han S., Cattoglio, Claudia, Pustova, Iryna, Saldaña-Meyer, Ricardo, Reinberg, Danny, Darzacq, Xavier, Tjian, Robert · 2019 · Molecular Cell
- Chromatin structure dynamics during the mitosis-to-G1 phase transitionZhang, Haoyue, Emerson, Daniel J., Gilgenast, Thomas G., Titus, Katelyn R., Lan, Yemin, Huang, Peng, Zhang, Di, Wang, Hongxin, Keller, Cheryl A., Giardine, Belinda et al. · 2019 · Nature
- Recent evidence that TADs and chromatin loops are dynamic structuresHansen, Anders S., Cattoglio, Claudia, Darzacq, Xavier, Tjian, Robert · 2018 · Nucleus
- Single-Cell Sequencing of Brain Cell Transcriptomes and EpigenomesArmand, Ethan J., Li, Junhao, Xie, Fangming, Luo, Chongyuan, Mukamel, Eran A. · 2021 · Neuron
- Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact OrganismsCardozo Gizzi, Andrés M., Cattoni, Diego I., Fiche, Jean-Bernard, Espinola, Sergio M., Gurgo, Julian, Messina, Olivier, Houbron, Christophe, Ogiyama, Yuki, Papadopoulos, Giorgio L., Cavalli, Giacomo et al. · 2019 · Molecular Cell
- Long-Range Chromatin InteractionsDekker, Job, Misteli, Tom · 2015 · Cold Spring Harbor Perspectives in Biology
- Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organizationChepelev, Iouri, Wei, Gang, Wangsa, Dara, Tang, Qingsong, Zhao, Keji · 2012 · Cell Research
- Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencingHelman, Elena, Lawrence, Michael S., Stewart, Chip, Sougnez, Carrie, Getz, Gad, Meyerson, Matthew · 2014 · Genome Research
- Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cellsBarutcu, A. Rasim, Lajoie, Bryan R., McCord, Rachel P., Tye, Coralee E., Hong, Deli, Messier, Terri L., Browne, Gillian, van Wijnen, Andre J., Lian, Jane B., Stein, Janet L. et al. · 2015 · Genome Biology
- A statistical approach for inferring the 3D structure of the genomeVaroquaux, Nelle, Ay, Ferhat, Noble, William Stafford, Vert, Jean-Philippe · 2014 · Bioinformatics
- Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte DifferentiationSiersbæk, Rasmus, Madsen, Jesper Grud Skat, Javierre, Biola Maria, Nielsen, Ronni, Bagge, Emilie Kristine, Cairns, Jonathan, Wingett, Steven William, Traynor, Sofie, Spivakov, Mikhail, Fraser, Peter et al. · 2017 · Molecular Cell
- Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogrammingKrijger, Peter Hugo Lodewijk, Di Stefano, Bruno, de Wit, Elzo, Limone, Francesco, van Oevelen, Chris, de Laat, Wouter, Graf, Thomas · 2016 · Cell stem cell
- Dissecting super-enhancer hierarchy based on chromatin interactionsHuang, Jialiang, Li, Kailong, Cai, Wenqing, Liu, Xin, Zhang, Yuannyu, Orkin, Stuart H., Xu, Jian, Yuan, Guo-Cheng · 2018 · Nature Communications
- The road to precision psychiatry: translating genetics into disease mechanismsGandal, Michael J, Leppa, Virpi, Won, Hyejung, Parikshak, Neelroop N, Geschwind, Daniel H · 2016 · Nature Neuroscience
- Deeply conserved synteny and the evolution of metazoan chromosomesSimakov, Oleg, Bredeson, Jessen, Berkoff, Kodiak, Marletaz, Ferdinand, Mitros, Therese, Schultz, Darrin T., O’Connell, Brendan L., Dear, Paul, Martinez, Daniel E., Steele, Robert E. et al. · 2022 · Science Advances
- Enhancer and promoter interactions—long distance callsKrivega, Ivan, Dean, Ann · 2012 · Current Opinion in Genetics & Development
- Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2Kaul, Arya, Bhattacharyya, Sourya, Ay, Ferhat · 2020 · Nature Protocols
- Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genomeLu, J. Yuyang, Chang, Lei, Li, Tong, Wang, Ting, Yin, Yafei, Zhan, Ge, Han, Xue, Zhang, Ke, Tao, Yibing, Percharde, Michelle et al. · 2021 · Cell Research
- Neuron-specific signatures in the chromosomal connectome associated with schizophrenia riskRajarajan, Prashanth, Borrman, Tyler, Liao, Will, Schrode, Nadine, Flaherty, Erin, Casiño, Charlize, Powell, Samuel, Yashaswini, Chittampalli, LaMarca, Elizabeth A., Kassim, Bibi et al. · 2018 · Science
- Robust single-cell Hi-C clustering by convolution- and random-walk-based imputationZhou, Jingtian, Ma, Jianzhu, Chen, Yusi, Cheng, Chuankai, Bao, Bokan, Peng, Jian, Sejnowski, Terrence J., Dixon, Jesse R., Ecker, Joseph R. · 2019 · Proceedings of the National Academy of Sciences
- Subtype-specific 3D genome alteration in acute myeloid leukaemiaXu, Jie, Song, Fan, Lyu, Huijue, Kobayashi, Mikoto, Zhang, Baozhen, Zhao, Ziyu, Hou, Ye, Wang, Xiaotao, Luan, Yu, Jia, Bei et al. · 2022 · Nature
- Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesinMiron, Ezequiel, Oldenkamp, Roel, Brown, Jill M., Pinto, David M. S., Xu, C. Shan, Faria, Ana R., Shaban, Haitham A., Rhodes, James D. P., Innocent, Cassandravictoria, de Ornellas, Sara et al. · 2020 · Science Advances
- Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T CellsHu, Gangqing, Cui, Kairong, Fang, Difeng, Hirose, Satoshi, Wang, Xun, Wangsa, Darawalee, Jin, Wenfei, Ried, Thomas, Liu, Pentao, Zhu, Jinfang et al. · 2018 · Immunity
- Epigenetic Regulation at the Interplay Between Gut Microbiota and Host MetabolismMiro-Blanch, Joan, Yanes, Oscar · 2019 · Frontiers in Genetics
- Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domainsOudelaar, A. Marieke, Davies, James O. J., Hanssen, Lars L. P., Telenius, Jelena M., Schwessinger, Ron, Liu, Yu, Brown, Jill M., Downes, Damien J., Chiariello, Andrea M., Bianco, Simona et al. · 2018 · Nature Genetics
- Xist localization and function: new insights from multiple levelsCerase, Andrea, Pintacuda, Greta, Tattermusch, Anna, Avner, Philip · 2015 · Genome biology
- Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem CellsRhodes, James D.P., Feldmann, Angelika, Hernández-Rodríguez, Benjamín, Díaz, Noelia, Brown, Jill M., Fursova, Nadezda A., Blackledge, Neil P., Prathapan, Praveen, Dobrinic, Paula, Huseyin, Miles K. et al. · 2020 · Cell Reports
- Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scaleZhou, Jian · 2022 · Nature Genetics
- Chromatin alternates between A and B compartments at kilobase scale for subgenic organizationHarris, Hannah L., Gu, Huiya, Olshansky, Moshe, Wang, Ailun, Farabella, Irene, Eliaz, Yossi, Kalluchi, Achyuth, Krishna, Akshay, Jacobs, Mozes, Cauer, Gesine et al. · 2023 · Nature Communications
- Reorganization of chromosome architecture in replicative cellular senescenceCriscione, Steven W., De Cecco, Marco, Siranosian, Benjamin, Zhang, Yue, Kreiling, Jill A., Sedivy, John M., Neretti, Nicola · 2016 · Science Advances
- LRP8-Reelin-regulated neuronal enhancer signature underlying learning and memory formationTelese, Francesca, Ma, Qi, Perez, Patricia Montilla, Notani, Dimple, Oh, Soohwan, Li, Wenbo, Comoletti, Davide, Ohgi, Kenneth A., Taylor, Havilah, Rosenfeld, Michael G. · 2015 · Neuron
- How far from the SNP may the causative genes be?Brodie, Aharon, Azaria, Johnathan Roy, Ofran, Yanay · 2016 · Nucleic Acids Research
- 4D Genome Rewiring during Oncogene-Induced and Replicative SenescenceSati, Satish, Bonev, Boyan, Szabo, Quentin, Jost, Daniel, Bensadoun, Paul, Serra, Francois, Loubiere, Vincent, Papadopoulos, Giorgio Lucio, Rivera-Mulia, Juan-Carlos, Fritsch, Lauriane et al. · 2020 · Molecular Cell
- Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibitionHogg, Simon J., Motorna, Olga, Cluse, Leonie A., Johanson, Timothy M., Coughlan, Hannah D., Raviram, Ramya, Myers, Robert M., Costacurta, Matteo, Todorovski, Izabela, Pijpers, Lizzy et al. · 2021 · Molecular Cell
- Comparison of Hi-C results using in-solution versus in-nucleus ligationNagano, Takashi, Várnai, Csilla, Schoenfelder, Stefan, Javierre, Biola-Maria, Wingett, Steven W., Fraser, Peter · 2015 · Genome Biology
- Function and Regulation of AUTS2, a Gene Implicated in Autism and Human EvolutionOksenberg, Nir, Stevison, Laurie, Wall, Jeffrey D., Ahituv, Nadav · 2013 · PLoS Genetics
- A supervised learning framework for chromatin loop detection in genome-wide contact mapsSalameh, Tarik J., Wang, Xiaotao, Song, Fan, Zhang, Bo, Wright, Sage M., Khunsriraksakul, Chachrit, Ruan, Yijun, Yue, Feng · 2020 · Nature Communications
- Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genomeChen, Hebing, Tian, Yao, Shu, Wenjie, Bo, Xiaochen, Wang, Shengqi · 2012 · PLoS ONE
- Long-Read DNA Sequencing: Recent Advances and Remaining ChallengesWarburton, Peter E., Sebra, Robert P. · 2023 · Annual Review of Genomics and Human Genetics
- SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypesKrueger, Felix, Andrews, Simon R. · 2016 · F1000Research
- Epigenetic regulation: A new frontier for biomedical engineersChen, Zhen, Li, Shuai, Subramaniam, Shankar, Shyy, John Y.-J., Chien, Shu · 2017 · Annual Review of Biomedical Engineering
- Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains bordersGómez-Marín, Carlos, Tena, Juan J., Acemel, Rafael D., López-Mayorga, Macarena, Naranjo, Silvia, de la Calle-Mustienes, Elisa, Maeso, Ignacio, Beccari, Leonardo, Aneas, Ivy, Vielmas, Erika et al. · 2015 · Proceedings of the National Academy of Sciences
- Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cellsFreire-Pritchett, Paula, Schoenfelder, Stefan, Várnai, Csilla, Wingett, Steven W, Cairns, Jonathan, Collier, Amanda J, García-Vílchez, Raquel, Furlan-Magaril, Mayra, Osborne, Cameron S, Fraser, Peter et al. · 2017 · eLife
- Hi-C analyses with GENOVA: a case study with cohesin variantsvan der Weide, Robin H, van den Brand, Teun, Haarhuis, Judith H I, Teunissen, Hans, Rowland, Benjamin D, de Wit, Elzo · 2021 · NAR Genomics and Bioinformatics
- Genomic Perspectives of Transcriptional Regulation in Forebrain DevelopmentNord, Alex S., Pattabiraman, Kartik, Visel, Axel, Rubenstein, John L.R. · 2015 · Neuron
- Long-range single-molecule mapping of chromatin accessibility in eukaryotesShipony, Zohar, Marinov, Georgi K., Swaffer, Matthew P., Sinnott-Armstrong, Nicholas A., Skotheim, Jan M., Kundaje, Anshul, Greenleaf, William J. · 2020 · Nature Methods
- Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensembleMarco, Asaf, Meharena, Hiruy S., Dileep, Vishnu, Raju, Ravikiran M., Davila-Velderrain, Jose, Zhang, Amy Letao, Adaikkan, Chinnakkaruppan, Young, Jennie Z., Gao, Fan, Kellis, Manolis et al. · 2020 · Nature Neuroscience
- 3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genesLu, Yiming, Quan, Cheng, Chen, Hebing, Bo, Xiaochen, Zhang, Chenggang · 2017 · Nucleic Acids Research
- Deletions of chromosomal regulatory boundaries are associated with congenital diseaseIbn-Salem, Jonas, Köhler, Sebastian, Love, Michael I, Chung, Ho-Ryun, Huang, Ni, Hurles, Matthew E, Haendel, Melissa, Washington, Nicole L, Smedley, Damian, Mungall, Christopher J et al. · 2014 · Genome Biology
- EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact mapsWang, Xiaotao, Luan, Yu, Yue, Feng · 2022 · Science Advances
- Detecting hierarchical genome folding with network modularityNorton, Heidi K, Emerson, Daniel J, Huang, Harvey, Kim, Jesi, Titus, Katelyn R, Gu, Shi, Bassett, Danielle S, Phillips-Cremins, Jennifer E · 2018 · Nature Methods
- Chromosome organization by one-sided and two-sided loop extrusionBanigan, Edward J, van den Berg, Aafke A, Brandão, Hugo B, Marko, John F, Mirny, Leonid A · 2020 · eLife
- Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism familiesBlumenthal, Ian, Ragavendran, Ashok, Erdin, Serkan, Klei, Lambertus, Sugathan, Aarathi, Guide, Jolene R., Manavalan, Poornima, Zhou, Julian Q., Wheeler, Vanessa C., Levin, Joshua Z. et al. · 2014 · The American Journal of Human Genetics
- Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expressionBeagan, Jonathan A., Pastuzyn, Elissa D., Fernandez, Lindsey R., Guo, Michael H., Feng, Kelly, Titus, Katelyn R., Chandrashekar, Harshini, Shepherd, Jason D., Phillips-Cremins, Jennifer E. · 2020 · Nature Neuroscience
- Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control RegionBunting, Karen L., Soong, T. David, Singh, Rajat, Jiang, Yanwen, Béguelin, Wendy, Poloway, David W., Swed, Brandon L., Hatzi, Katerina, Reisacher, William, Teater, Matt et al. · 2016 · Immunity
- FISH-ing for captured contacts: towards reconciling FISH and 3CFudenberg, Geoffrey, Imakaev, Maxim · 2017 · Nature Methods
- Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory elementHuang, Peng, Keller, Cheryl A., Giardine, Belinda, Grevet, Jeremy D., Davies, James O.J., Hughes, Jim R., Kurita, Ryo, Nakamura, Yukio, Hardison, Ross C., Blobel, Gerd A. · 2017 · Genes & Development
- High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial DevelopmentWilderman, Andrea, VanOudenhove, Jennifer, Kron, Jeffrey, Noonan, James P., Cotney, Justin · 2018 · Cell Reports
- Hierarchical looping of zigzag nucleosome chains in metaphase chromosomesGrigoryev, Sergei A., Bascom, Gavin, Buckwalter, Jenna M., Schubert, Michael B., Woodcock, Christopher L., Schlick, Tamar · 2016 · Proceedings of the National Academy of Sciences
- The Chromatin Landscape of Cellular SenescenceCriscione, Steven W., Teo, Yee Voan, Neretti, Nicola · 2016 · Trends in Genetics
- Cohesin Protects Genes against γH2AX Induced by DNA Double-Strand BreaksCaron, Pierre, Aymard, Francois, Iacovoni, Jason S., Briois, Sébastien, Canitrot, Yvan, Bugler, Beatrix, Massip, Laurent, Losada, Ana, Legube, Gaëlle · 2012 · PLoS Genetics
- Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell ReprogrammingBeagan, Jonathan A., Gilgenast, Thomas G., Kim, Jesi, Plona, Zachary, Norton, Heidi K., Hu, Gui, Hsu, Sarah C., Shields, Emily J., Lyu, Xiaowen, Apostolou, Effie et al. · 2016 · Cell Stem Cell
- Radiation-induced DNA damage and repair effects on 3D genome organizationSanders, Jacob T., Freeman, Trevor F., Xu, Yang, Golloshi, Rosela, Stallard, Mary A., Hill, Ashtyn M., San Martin, Rebeca, Balajee, Adayabalam S., McCord, Rachel Patton · 2020 · Nature Communications
- Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegenerationDileep, Vishnu, Boix, Carles A., Mathys, Hansruedi, Marco, Asaf, Welch, Gwyneth M., Meharena, Hiruy S., Loon, Anjanet, Jeloka, Ritika, Peng, Zhuyu, Bennett, David A. et al. · 2023 · Cell
- Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes2p15 Consortium, Loviglio, M N, 16p11.2 Consortium, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, van der Werf, I, Waszak, S M, Zazhytska, M et al. · 2017 · Molecular Psychiatry
- Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fishPowell, Daniel L., García-Olazábal, Mateo, Keegan, Mackenzie, Reilly, Patrick, Du, Kang, Díaz-Loyo, Alejandra P., Banerjee, Shreya, Blakkan, Danielle, Reich, David, Andolfatto, Peter et al. · 2020 · Science
- Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCFAljahani, Abrar, Hua, Peng, Karpinska, Magdalena A., Quililan, Kimberly, Davies, James O. J., Oudelaar, A. Marieke · 2022 · Nature Communications
- MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experimentsJuric, Ivan, Yu, Miao, Abnousi, Armen, Raviram, Ramya, Fang, Rongxin, Zhao, Yuan, Zhang, Yanxiao, Qiu, Yunjiang, Yang, Yuchen, Li, Yun et al. · 2019 · PLOS Computational Biology
- Dynamics of the 4D Genome during in Vivo Lineage Specification and DifferentiationOudelaar, A. Marieke, Beagrie, Robert A., Gosden, Matthew, de Ornellas, Sara, Georgiades, Emily, Kerry, Jon, Hidalgo, Daniel, Carrelha, Joana, Shivalingam, Arun, El-Sagheer, Afaf H. et al. · 2020 · Nature Communications
- Models that include supercoiling of topological domains reproduce several known features of interphase chromosomesBenedetti, Fabrizio, Dorier, Julien, Burnier, Yannis, Stasiak, Andrzej · 2014 · Nucleic Acids Research
- Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systemsTan, Longzhi, Xing, Dong, Daley, Nicholas, Xie, X. Sunney · 2019 · Nature Structural & Molecular Biology
- The genomic landscape of cohesin-associated chromatin interactionsDeMare, Laura E., Leng, Jing, Cotney, Justin, Reilly, Steven K., Yin, Jun, Sarro, Richard, Noonan, James P. · 2013 · Genome Research
- Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosomeBrückner, David B., Chen, Hongtao, Barinov, Lev, Zoller, Benjamin, Gregor, Thomas · 2023 · Science
- Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular agingLiu, Zunpeng, Ji, Qianzhao, Ren, Jie, Yan, Pengze, Wu, Zeming, Wang, Si, Sun, Liang, Wang, Zehua, Li, Jiaming, Sun, Guoqiang et al. · 2022 · Developmental Cell
- Hold out the genome: a roadmap to solving the cis-regulatory codede Boer, Carl G., Taipale, Jussi · 2024 · Nature
- Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactionsPress, Maximilian O., Wiser, Andrew H., Kronenberg, Zev N., Langford, Kyle W., Shakya, Migun, Lo, Chien-Chi, Mueller, Kathryn A., Sullivan, Shawn T., Chain, Patrick S. G., Liachko, Ivan · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitorsMeharena, Hiruy S., Marco, Asaf, Dileep, Vishnu, Lockshin, Elana R., Akatsu, Grace Y., Mullahoo, James, Watson, L. Ashley, Ko, Tak, Guerin, Lindsey N., Abdurrob, Fatema et al. · 2022 · Cell Stem Cell
- Analytical tools and current challenges in the modern era of neuroepigenomicsMaze, Ian, Shen, Li, Zhang, Bin, Garcia, Benjamin A, Shao, Ningyi, Mitchell, Amanda, Sun, HaoSheng, Akbarian, Schahram, Allis, C David, Nestler, Eric J · 2014 · Nature Neuroscience
- Prediction of enhancer-promoter interactions via natural language processingZeng, Wanwen, Wu, Mengmeng, Jiang, Rui · 2018 · BMC Genomics
- Identification of copy number variations and translocations in cancer cells from Hi-C dataChakraborty, Abhijit, Ay, Ferhat · 2018 · Bioinformatics
- Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanismsAbyzov, Alexej, Li, Shantao, Kim, Daniel Rhee, Mohiyuddin, Marghoob, Stütz, Adrian M., Parrish, Nicholas F., Mu, Xinmeng Jasmine, Clark, Wyatt, Chen, Ken, Hurles, Matthew et al. · 2015 · Nature Communications
- Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brainZhang, Yanxiao, Amaral, Maria Luisa, Zhu, Chenxu, Grieco, Steven Francis, Hou, Xiaomeng, Lin, Lin, Buchanan, Justin, Tong, Liqi, Preissl, Sebastian, Xu, Xiangmin et al. · 2022 · Cell Research
- DNA double strand break repair, aging and the chromatin connectionGorbunova, Vera, Seluanov, Andrei · 2016 · Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis
- Using single‐cell multiple omics approaches to resolve tumor heterogeneityOrtega, Michael A., Poirion, Olivier, Zhu, Xun, Huang, Sijia, Wolfgruber, Thomas K., Sebra, Robert, Garmire, Lana X. · 2017 · Clinical and Translational Medicine
- 3C-based technologies to study the shape of the genomede Laat, Wouter, Dekker, Job · 2012 · Methods
- Determinants of transcription factor regulatory rangeChen, Chen-Hao, Zheng, Rongbin, Tokheim, Collin, Dong, Xin, Fan, Jingyu, Wan, Changxin, Tang, Qin, Brown, Myles, Liu, Jun S., Meyer, Clifford A. et al. · 2020 · Nature Communications
- Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expressionLibbrecht, Maxwell W., Ay, Ferhat, Hoffman, Michael M., Gilbert, David M., Bilmes, Jeffrey A., Noble, William Stafford · 2015 · Genome Research
- Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genomeThévenin, Annelyse, Ein-Dor, Liat, Ozery-Flato, Michal, Shamir, Ron · 2014 · Nucleic Acids Research
- Jpx RNA regulates CTCF anchor site selection and formation of chromosome loopsOh, Hyun Jung, Aguilar, Rodrigo, Kesner, Barry, Lee, Hun-Goo, Kriz, Andrea J., Chu, Hsueh-Ping, Lee, Jeannie T. · 2021 · Cell
- Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic lociSungalee, Stephanie, Liu, Yuanlong, Lambuta, Ruxandra A., Katanayeva, Natalya, Donaldson Collier, Maria, Tavernari, Daniele, Roulland, Sandrine, Ciriello, Giovanni, Oricchio, Elisa · 2021 · Nature Genetics
- Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin loopingKikuchi, Masataka, Hara, Norikazu, Hasegawa, Mai, Miyashita, Akinori, Kuwano, Ryozo, Ikeuchi, Takeshi, Nakaya, Akihiro · 2019 · BMC Medical Genomics