4DN pre-prints

See the 4DN bioRxiv channel.


Pre-print publications funded by NIH 4DN program
Pre-print Publication Posted date
Co-opted transposons help perpetuate conserved higher-order chromosomal structures, Mayank NK Choudhary, Ryan Z Friedman, Julia T Wang, Hyo Sik Jang, Xiaoyu Zhuo, Ting Wang, doi: https://doi.org/10.1101/485342 December 5, 2018
Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs, Yan, Z., Huang, N., Wu, W., Chen, W., Jiang, Y., Chen, J., Huang, X., Wen, X., Xu, J., Jin, Q., Zhang, K., Chen, Z., Chien, S., Zhong, S., doi: https://doi.org/10.1101/472019 November 20, 2018
Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population Scale, Sadowski, M., Kraft, A., Szalaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., Plewczynski, D., doi: https://doi.org/10.1101/266981 September 14, 2018
Photon count estimation in single-molecule localization microscopy, Rieger, B., Stallinga, S., Hulleman, C. N., Thorsen, R. O., Grunwald, D., Hammer, M., doi: https://doi.org/10.1101/396424 August 20, 2018
A combination of transcription factors mediates inducible interchromosomal pairing, Kim, S., Dunham, M., Shendure, J., doi: https://doi.org/10.1101/385047 August 5, 2018
Nuclear speckle fusion via long-range directional motion regulates the number and size of speckles, Jiah Kim, Kyu Young Han, Nimish Khanna, Taekjip Ha, Andrew S. Belmont, doi: https://doi.org/10.1101/347955 June 15, 2018
RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome, Weizhong Chen, Zhangming Yan, Simin Li, Norman Huang, Xuerui Huang, Jin Zhang, Sheng Zhong, doi: https://doi.org/10.1101/300483 April 12, 2018
Identification of cis elements for spatio-temporal control of DNA replication, Jiao Sima, Abhijit Chakraborty, Vishnu Dileep, Marco Michalski, Juan Carlos Rivera-Mulia, Claudia Trevilla-Garcia, Kyle N Klein, Daniel Bartlett, Brian K Washburn, Michelle T Paulsen, Daniel Vera, Elphège P Nora, Katerina Kraft, Stefan Mundlos, Benoit G Bruneau, Mats Ljungman, Peter Fraser, Ferhat Ay, David M Gilbert, doi: https://doi.org/10.1101/285650 March 21, 2018
Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks, Singh, S., Yang, Y., Poczos, B., Ma, J., doi: https://doi.org/10.1101/085241 February 5, 2018
GITAR: An open source tool for analysis and visualization of Hi-C data, Calandrelli, R., Wu, Q., Guan, J., Zhong, S., doi: https://https://doi.org/10.1101/259515 February 4, 2018
C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2, Gao, X. D., Tu, L.-C., Mir, A., Rodriguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S. A., Zhu, L. J., Wolfe, S. A., Sontheimer, E. J., doi: https://doi.org/10.1101/171819 January 31, 2018
Correlative live and super-resolution imaging reveals the dynamic structure of replication domains, Xiang, W., Roberti, M. J., Heriche, J.-K., Huet, S., Alexander, S., Ellenberg, J., doi: https://doi.org/10.1101/189373 January 24, 2018
Building a genome browser with GIVE, Cao, X., Yan, Z., Wu, Q., Zheng, A., Zhong, S., doi: https://doi.org/10.1101/177832 January 13, 2018
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome, Bonora, G., Deng, X., Fang, H., Ramani, V., Qui, R., Berletch, J., Filippova, G. N., Duan, Z., Schendure, J., Noble, W. S., Disteche, C. M., doi: https://doi.org/10.1101/165340 December 15, 2017
Allele-specific control of replication timing and genome organization during development, Juan Carlos Rivera-Mulia, Andrew Dimond, Daniel Vera, Claudia Trevilla-Garcia, Takayo Sasaki, Jared Zimmerman, Catherine Dupont, Joost Gribnau, Peter Fraser, David M Gilbert, doi: https://doi.org/10.1101/221762 November 21, 2017
Single-molecule fluorescent amplification of RNA using clampFISH probes, Sara H Rouhanifard, Margaret Dunagin, Ian A Mellis, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj, doi: https://doi.org/10.1101/222794 November 21, 2017
Dynamic reorganization of nuclear architecture during human cardiogenesis, Paul A Fields, Vijay Ramani, Giancarlo Bonora, Galip Gurkan Yardimci, Alessandro Bertero, Hans Reinecke, Lil Pabon, William S Noble, Jay Shendure, Charles Murry, doi: https://doi.org/10.1101/222877 November 21, 2017
Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus, Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason Lai, Alexander Shishkin, Prashant Bhat, Vickie Trinh, Erik Aznauryan, Pamela Russell, Christine Cheng, Marko Jovanovic, Amy Chow, Patrick McDonel, Manuel Garber, Mitchell Guttman, doi: https://doi.org/10.1101/219683 November 18, 2017
Quantitative imaging of chromatin decompaction in living cells, Elisa Dultz, Roberta Mancini, Guido Polles, Pascal Vallotton, Frank Alber, Karsten Weis, doi: https://doi.org/10.1101/219253 November 15, 2017
CHRAC/ACF Contribute to the Repressive Ground State of Chromatin, Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker, doi: https://doi.org/10.1101/218768 November 13, 2017
A Cell Type-Specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs, Mira Jeong, Xingfan Huang, Xiaotian Zhang, Jianzhong Su, Muhammad Shamim, Ivan Bochkov, Jaime Reyes, Haiyoung Jung, Emily Heikamp, Aviva Presser Aiden, Wei Li, Erez Aiden, Margaret A. Goodell, doi: https://doi.org/10.1101/212928 November 9, 2017
Removing unwanted variation between samples in Hi-C experiments, Kipper Fletez-Brant, Yunjiang Qiu, David U Gorkin, Ming Hu, Kasper D Hansen, doi: https://doi.org/10.1101/214361 November 6, 2017
HiGlass: Web-based Visual Comparison And Exploration Of Genome Interaction Maps, Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M Luber, Scott B Ouellette, Alaleh Ahzir, Nikhil Kumar, Jeewon Hwang, Burak H Alver, Hanspeter Pfister, Leonid A Mirny, Peter J Park, Nils Gehlenborg, bioRxiv, doi: https://doi.org/10.1101/121889 October 30, 2017
Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies, Amin Allahyar, Carlo Vermeulen, Britta Bouwman, Peter Krijger, Marjon Verstegen, Geert Geeven, Melissa van Kranenburg, Mark Pieterse, Roy Straver, Judith Haarhuis, Hans Teunissen, Ivo Renkens, Wigard Kloosterman, Benjamin Rowland, Elzo de Wit, Jeroen de Ridder, Wouter de Laat, doi: https://doi.org/10.1101/206094 October 20, 2017
Juicebox.js provides a cloud-based visualization system for Hi-C data, James Robinson, Douglass Turner, Neva C. Durand, Helga Thorvaldsdottir, Jill P. Mesirov, Erez Lieberman Aiden, doi: https://doi.org/10.1101/205740 October 19, 2017
Fluorescence polarization control for on-off switching of single molecules at cryogenic temperatures, Christiaan Hulleman, Maximiliaan Huisman, Robert Moerland, David Grunwald, Sjoerd Stallinga, Bernd Rieger, doi: https://doi.org/10.1101/204776 October 17, 2017
Genomic binding dynamics of PBAF are regulated via select chromatin states, Charles A Kenworthy, Vincent Wong, Patrycja Dziuba, Luke D Lavis, Wei-Li Liu, Robert H Singer, Robert A Coleman, doi: https://doi.org/10.1101/111674 October 4, 2017
Chromatin Organization by an Interplay of Loop Extrusion and Compartmental Segregation, Johannes Nuebler, Geoffrey Fudenberg, Maxim Imakaev, Nezar Abdennur, Leonid Mirny, doi: https://doi.org/10.1101/196261 October 3, 2017
ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution Microscopy, Sandro Morganella, Oeyvind Oedegaard, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney, bioRxiv, doi: https://doi.org/10.1101/115436 September 28, 2017
CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics, Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Yu-Chieh Chung, David Grunwald, Shaojie Zhang, Thoru Pederson, doi: https://doi.org/10.1101/195966 September 29, 2017
Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries, James Sun, Linda Zhou, Daniel J Emerson, Thomas G. Gilgenast, Katelyn Titus, Jonathan A. Beagan, Jennifer E. Phillips-Cremins, doi: https://doi.org/10.1101/191213 September 20, 2017
Correlative live and super-resolution imaging reveals the dynamic structure of replication domains, Wanqing Xiang, M. Julia Roberti, Jean-Karim Heriche, Sebastian Huet, Stephanie Alexander, Jan Ellenberg, doi: https://doi.org/10.1101/189373 September 17, 2017
Measuring the reproducibility and quality of Hi-C data, Galip Yardimci, Hakan Ozadam, Michael E.G. Sauria, Oana Ursu, Koon-Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng Yue, Job Dekker, William S Noble, doi: https://doi.org/10.1101/188755 September 14, 2017
SHAMAN: bin-free randomization, normalization and screening of Hi-C matrices, Netta Mendelson Cohen, Pedro Olivares-Chauvet, Yaniv Lubling, Yael Baran, Aviezer Lifshitz, Michael Hoichman, Amos Tanay, doi: https://doi.org/10.1101/187203 September 12, 2017
Fast, robust and precise 3D localization for arbitrary point spread functions, Yiming Li, Markus Mund, Philipp Hoess, Ulf Matti, Bianca Nijmeijer, Vilma Jimenez Sabinina, Jan Ellenberg, Ingmar Schoen, Jonas Ries, doi: https://doi.org/10.1101/172643 August 10, 2017
Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays, Johan H. Gibcus, Kumiko Samejima, Anton Goloborodko, Itaru Samejima, Natalia Naumova, Masato Kanemaki, Linfeng Xie, James R. Paulson, William C. Earnshaw, Leonid A. Mirny, Job Dekker, doi: https://doi.org/10.1101/174649 August 10, 2017
Heterogeneity and Intrinsic Variation in Spatial Genome Organization, Elizabeth Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, Tom Misteli, doi: https://doi.org/10.1101/171801 August 3, 2017
C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2, Xin D. Gao, Li-Chun Tu, Aamir Mir, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer, bioRxiv, doi: https://doi.org/10.1101/171819 August 2, 2017
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome, Giancarlo Bonora, Xinxian Deng, He Fang, Vijay Ramani, Ruolan Qui, Joel Berletch, Gala N Filippova, Zhijun Duan, Jay Schendure, William S Noble, Christine M Disteche, bioRxiv, doi: https://doi.org/10.1101/165340 July 19, 2017
Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells, Charles G. Danko, Lauren A. Choate, Brooke A. Marks, Edward J. Rice, Zhong Wang, Tinyi Chu, Andre L. Martins, Noah Dukler, Scott A. Coonrod, Elia D. Tait Wojno, John T. Lis, W. Lee Kraus, Adam Siepel, bioRxiv, doi: https://doi.org/10.1101/083212 July 16, 2017
Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program, Vishnu Dileep, David M. Gilbert, bioRxiv, doi: https://doi.org/10.1101/158352 July 14, 2017
CRISPR/Cas9-mediated Knock-in of an Optimized TetO Repeat for Live Cell Imaging of Endogenous Loci, Ipek Tasan, Gabriela Sustackova, Liguo Zhang, Jiah Kim, Mayandi Sivaguru, Mohammad HamediRad, Yuchuan Wang, Justin Genova, Jian Ma, Andrew S. Belmont, Huimin Zhao, bioRxiv, doi: https://doi.org/10.1101/162156 July 12, 2017
HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples, Fritz Lekschas, Benjamin Bach, Peter Kerpedjiev, Nils Gehlenborg, Hanspeter Pfister, bioRxiv, doi: https://doi.org/10.1101/123588 July 9, 2017
A Fluorogenic Array Tag for Temporally Unlimited Single Molecule Tracking, Rajarshi P Ghosh, Matthew J Franklin, Will E Draper, Quanming Shi, Jan T Liphardt, bioRxiv, doi: https://doi.org/10.1101/159004 July 3, 2017
Chromatin accessibility dynamics of myogenesis at single cell resolution, Hannah Pliner, Jonathan Packer, Jose McFaline-Figueroa, Darren Cusanovich, Riza Daza, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina, Andrew Adey, Frank Steemers, Jay Shendure, Cole Trapnell, doi: https://doi.org/10.1101/155473 June 26, 2017
Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPs, Akiko Noma, Carlas S. Smith, Maximillian Huisman, Robert M. Martin, Melissa J. Moore, David Grunwald, doi: https://doi.org/10.1101/156091 June 26, 2017
qSR: A software for quantitative analysis of single molecule and super-resolution data, J. Owen Andrews, Arjun Narayanan, Jan-Hendrik Spille, Won-Ki Cho, Jesse D. Thaler, Ibrahim I. Cisse, bioRxiv, doi: https://doi.org/10.1101/146241 June 5, 2017
Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images — How Reliable Is It?, Li-Chun Tu, Maximiliaan Huisman, Yu-Chieh Chung, Carlas Smith, David Grunwald, bioRxiv, doi: https://doi.org/10.1101/145110 June 2, 2017
Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture, Haochen Li, Reza Kalhor, Bing Li, Trent Su, Arnold Berk, Siavash Kurdistani, Frank Alber, Lin Chen, bioRxiv, doi: https://doi.org/10.1101/142604 May 26, 2017
A Comparison Between Single Cell RNA Sequencing And Single Molecule RNA FISH For Rare Cell Analysis, Eduardo A. Torre, Hannah Dueck, Sydney Shaffer, Janko Gospocic, Rohit Gupte, Roberto Bonasio, Junhyong Kim, John Murray, Arjun Raj, bioRxiv, doi: https://doi.org/10.1101/138289 May 18, 2017
Gene Expression Recovery For Single Cell RNA Sequencing, o Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio, John Murray, Arjun Raj, Mingyao Li, Nancy R. Zhang, bioRxiv, doi: https://doi.org/10.1101/138677 May 17, 2017
An Integrative Framework For Detecting Structural Variations In Cancer Genomes, Jesse Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T. Le, Galip Gurkan Yardimci, Abhijit Chakraborty, Darrin V. Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera Mulia, Hakan Ozadam, Bryan R. Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T. Odom, John A. Stamatoyannopoulos, James R. Broach, Ross Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M Gilbert, Feng Yue, bioRxiv, doi: https://doi.org/10.1101/119651 March 28, 2017
Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells, Naoki Kubo, Haruhiko Ishii, David Gorkin, Franz Meitinger, Xiong Xiong, Rongxin Fang, Tristin Liu, Zhen Ye, Bin Li, Jesse Dixon, Arshad Desai, Huimin Zhao, Bing Ren, bioRxiv, doi: https://doi.org/10.1101/118737 March 20, 2017
Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genome, Wayne Dawson, Dariusz Plewczynski, bioRxiv, doi: https://doi.org/10.1101/105676 March 8, 2017
HiCPlus: Resolution Enhancement of Hi-C interaction heatmap, Yan Zhang, Lin An, Ming Hu, Jijun Tang, Feng Yue, bioRxiv, doi: https://doi.org/10.1101/112631 March 1, 2017
Repli-seq: genome-wide analysis of replication timing by next-generation sequencing, Claire Marchal, Takayo Sasaki, Daniel Vera, Korey Wilson, Jiao Sima, Juan-Carlos Rivera-Mulia, Claudia Trevilla Garcia, Coralin Nogues, Ebtesam Nafie, David M Gilbert, bioRxiv, doi: https://doi.org/10.1101/104653 March 1, 2017
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions, Yanli Wang, Bo Zhang, Lijun Zhang, Lin An, Jie Xu, Daofeng Li, Mayank NK Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue, bioRxiv, doi: https://doi.org/10.1101/112268 February 27, 2017
A fluorogenic nanobody array tag for prolonged single molecule imaging in live cells, Rajarshi Ghosh, Will Draper, J. Matthew Franklin, Quanming Shi, Jan Liphardt, bioRxiv, doi: https://doi.org/10.1101/111690 February 27, 2017
Real-time chromatin dynamics at the single gene level during transcription activation, Thomas Germier, Silvia Kocanova, Nike Walther, Aurelien Bancaud, Haitham Ahmed Shaban, Hafida Sellou, Antonio Politi, Jan Ellenberg, Franck Gallardo, Kerstin Bystricky, bioRxiv, doi: https://doi.org/10.1101/111179 February 23, 2017
Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers, Jian Yan, Shi-An A. Chen, Andrea Local, Tristin Liu, Yunjiang Qiu, Ah-Young Lee, Inkyung Jung, Sebastian Preissl, Chloe M Rivera, Chaocheng Wang, Haruhiko Ishii, Rongxin Fang, Zhen Ye, Kai Ge, Ming Hu, Bing Ren, bioRxiv, doi: https://doi.org/10.1101/110239 February 21, 2017
Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing, Junyue Cao, Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N. Furlan, Frank J. Steemers, Andrew Adey, Robert H. Waterston, Cole Trapnell, Jay Shendure, bioRxiv, doi: https://doi.org/10.1101/104844 February 2, 2017
Direct visualization of transcriptional activation by physical enhancer-promoter proximity, Hongtao Chen and Thomas Gregor, bioRxiv, doi: https://doi.org/10.1101/099523 January 31, 2017
Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture, Jacob Schreiber, Maxwell Libbrecht, Jeffrey Bilmes, William Noble, bioRxiv, doi: https://doi.org/10.1101/103614 January 30, 2017
PGS: a dynamic and automated population-based genome structure software, Nan Hua, ..., Frank Alber, bioRxiv, doi: https://doi.org/10.1101/103358 January 26, 2017
Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISH, Yodai Takei, Sheel Shah, Sho Harvey, Lei S Qi, Long Cai, bioRxiv, doi: https://doi.org/10.1101/101477 January 18, 2017
The 3D genome organization of Drosophila melanogaster through data integration, Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo, Frank Alber, bioRxiv, doi: https://doi.org/10.1101/099911 January 15, 2017
Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map, Kyle P. Eagen, Erez Lieberman Aiden, Roger D. Kornberg, bioRxiv, doi: https://doi.org/10.1101/099804 January 12, 2017
Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization, Elphege P Nora, Anton Goloborodko, Anne-Laure Valton, Johan Harmen Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid Mirny, Benoit Bruneau, bioRxiv, doi: https://doi.org/10.1101/095802 January 9, 2017
Cohesin dependent compaction of mitotic chromosomes, Stephanie A Schalbetter, ..., Jon Baxter, bioRxiv, doi: https://doi.org/10.1101/094946 December 17, 2016
Cell cycle dynamics of chromosomal organisation at single-cell resolution, Peter Fraser and Amos Tanay, bioRxiv, doi: https://doi.org/10.1101/094466 December 15, 2016
Detecting hierarchical 3-D genome domain reconfiguration with network modularity, Heidi K Norton, Harvey Huang, Daniel J Emerson, Jesi Kim, Shi Gu, Danielle S Bassett, Jennifer E Phillips-Cremins, bioRxiv, doi: https://doi.org/10.1101/089011 November 22, 2016
Calibrating photon counts from a single image, Bernd Rieger, arXiv: 1611.05654 November 17, 2016
Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks, Shashank Singh, Yang Yang, Barnabas Poczos, Jian Ma, doi: https://doi.org/10.1101/085241 November 2, 2016
Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome, Tsung-Han Hsieh, Geoffrey Fudenberg, Anton Goloborodko, Oliver Rando, doi: https://doi.org/10.1101/071357 August 24, 2016