4DN pre-prints

See the 4DN bioRxiv channel.


Pre-print publications funded by NIH 4DN program
Title Authors DOI Date
Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T. 10.1101/2020.11.24.3967132020-11-24
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation Bonora, G., Ramani, V., Singh, R., Fang, H., Jackson, D., Srivatsan, S., Qiu, R., Lee, C., Trapnell, C., Shendure, J., Duan, Z., Deng, X., Noble, W. S., Disteche, C. M. 10.1101/2020.11.20.3907652020-11-20
Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors Ypsilanti, A. R., Pattabiraman, K., Catta-Preta, R., Golonzhka, O., Lindtner, S., Tang, K., Jones, I., Abnousi, A., Juric, I., Hu, M., Shen, Y., Dickel, D. E., Visel, A., Pennachio, L. A., Hawrylycz, M., Thompson, C., Zeng, H., Barozzi, I., Nord, A. S., Rubenstein, J. L. R. 10.1101/2020.11.03.3669142020-11-04
HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test Lagler, T. M., Yang, Y., Abnousi, A., Hu, M., Li, Y. 10.1101/2020.10.28.3598692020-10-29
HiCRep.py: Fast comparison of Hi-C contact matrices in Python Lin, D., Sanders, J., Noble, W. S. 10.1101/2020.10.27.3577562020-10-28
DNA-loop extruding SMC complexes can traverse one another in vivo Brandão, H. B., Ren, Z., Karaboja, X., Mirny, L. A., Wang, X. 10.1101/2020.10.26.3563292020-10-27
Deep learning enables fast and dense single-molecule localization with high accuracy Speiser, A., Müller, L.-R., Matti, U., Obara, C. J., Legant, W. R., Kreshuk, A., Macke, J. H., Ries, J., Turaga, S. C. 10.1101/2020.10.26.3551642020-10-26
MCM complexes are barriers that restrict cohesin-mediated loop extrusion Dequeker, B. J. H., Brandao, H. B., Scherr, M. J., Gassler, J., Powell, S., Gaspar, I., Flyamer, I. M., Tang, W., Stocsits, R., Davidson, I. F., Peters, J.-M., Duderstadt, K. E., Mirny, L. A., Tachibana, K. 10.1101/2020.10.15.3403562020-10-15
HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics Strom, A. R., Biggs, R. J., Banigan, E. J., Wang, X., Chiu, K., Herman, C., Collado, J., Yue, F., Ritland Politz, J. C., Tait, L. J., Scalzo, D., Telling, A., Groudine, M., Brangwynne, C. P., Marko, J., Stephens, A. D. 10.1101/2020.10.09.3319002020-10-09
Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia Janssens, D., Meers, M. P., Wu, S. J., Babaeva, E., Meshinchi, S., Sarthy, J. F., Ahmad, K., Henikoff, S. 10.1101/2020.10.06.3289482020-10-08
Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches Desai, P. R., Brahmachari, S., Marko, J. F., Das, S., Neuman, K. C. 10.1101/2019.12.20.8855332020-10-04
PYMEVisualize: an open-source tool for exploring 3D super-resolution data Marin, Z., Graff, M., Barentine, A. E. S., Soeller, C., Chung, K. K. H., Fuentes, L. A., Baddeley, D. 10.1101/2020.09.29.3156712020-09-30
Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization Marko, J. F., Qiao, H., Liu, N., Biggs, R. J., Peng, Y. 10.1101/2020.08.31.2764022020-09-01
Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization Bashkirova, E., Monahan, K., Campbell, C. E., Osinski, J. M., Tan, L., Schieren, I., Barnea, G., Xie, S., Gronostajski, R. M., Lomvardas, S. 10.1101/2020.08.30.2740352020-08-30
A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates Geusz, R. J., Wang, A., Lam, D. K., Vinckier, N. K., Alysandratos, K.-D., Roberts, D. A., Wang, J., Kefalopoulou, S., Qiu, Y., Chiou, J., Gaulton, K. J., Ren, B., Kotton, D. N., Sander, M. 10.1101/2020.08.28.2630202020-08-29
RNA promotes the formation of spatial compartments in the nucleus Quinodoz, S. A., Bhat, P., Ollikainen, N., Jachowicz, J. W., Banerjee, A. K., Chovanec, P., Blanco, M. R., Chow, A., Markaki, Y., Plath, K., Guttman, M. 10.1101/2020.08.25.2674352020-08-25
Epigenetic memory as a time integral over prior history of Polycomb phase separation Eeftens, J. M., Kapoor, M., Brangwynne, C. P. 10.1101/2020.08.19.2547062020-08-19
A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells Arrastia, M. V., Jachowicz, J. W., Ollikainen, N., Curtis, M. S., Lai, C., Quinodoz, S., Selck, D. A., Guttman, M., Ismagilov, R. F. 10.1101/2020.08.11.2420812020-08-12
Transcript assembly improves expression quantification of transposable elements in single cell RNA-seq data Shao, W., Wang, T. 10.1101/2020.07.31.2310272020-07-31
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C Beagrie, R. A., Thieme, C. J., Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kramer, D. C., Chiariello, A. M., Bianco, S., Kukalev, A., Li, Y., Kempfer, R., Scialdone, A., Welch, L. A., Nicodemi, M., Pombo, A. 10.1101/2020.07.31.2302842020-07-31
Single-Molecule Micromanipulation Studies Of Methylated DNA Zaichuk, T., Marko, J. 10.1101/2020.07.29.2271992020-07-30
PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for DummiesBokota, G., Sroka, J., Basu, S., Das, N., Trzaskoma, P., Yushkevich, Y., Grabowska, A., Magalska, A., Plewczynski, D. 10.1101/2020.07.16.2067892020-07-17
Simultaneous Epigenetic Perturbation and Genome Imaging Reveal Distinct Roles of H3K9me3 in Chromatin Architecture and TranscriptionFeng, Y., Wang, Y., Wang, X., He, X., Yang, C., Naseri, A., Pederson, T., Zheng, J., Zhang, S., Xiao, X., Xie, W., Ma, H. 10.1101/2020.07.15.2047192020-07-16
CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin DomainsHuang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A., Yu, M., Hu, R., Juric, I., Hu, M., Nicodemi, M., Zhuang, X., Ren, B. 10.1101/2020.07.07.1925262020-07-08
Unsupervised manifold alignment for single-cell multi-omics dataSingh, R., Demetci, P., Bonora, G., Ramani, V., Lee, C., Fang, H., Duan, Z., Deng, X., Shendure, J., Disteche, C., Noble, W. S. 10.1101/2020.06.13.1491952020-06-15
Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identityMellis, I. A., Edelstein, H. I., Truitt, R., Beck, L. E., Symmons, O., Goyal, Y., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Yang, W., Jain, R., Raj, A. 10.1101/2020.06.11.1472072020-06-12
Chromatin Mechanics Dictates Subdiffusion and Coarsening Dynamics of Embedded CondensatesLee, D. S. W., Wingreen, N. S., Brangwynne, C. P. 10.1101/2020.06.03.1285612020-06-04
Gene regulation gravitates towards either addition or multiplication when combining the effects of two signalsSanford, E. M., Emert, B. L., Cote, A., Raj, A. 10.1101/2020.05.26.1169622020-05-27
Chromatin folding variability across single-cells results from state degeneracy in phase-separationConte, M., Fiorillo, L., Bianco, S., Chiariello, A. M., Esposito, A., Nicodemi, M. 10.1101/2020.05.16.0992752020-05-16
Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balanceSchep, R., Brinkman, E. K., Leemans, C., Vergara, X., Morris, B., van Schaik, T., Manzo, S. G., Peric Hupkes, D., van den Berg, J., Beijersbergen, R., Medema, R. H., van Steensel, B. 10.1101/2020.05.05.0784362020-05-05
Gromov-Wasserstein optimal transport to align single-cell multi-omics dataDemetci, P., Santorella, R., Sandstede, B., Noble, W. S., Singh, R. 10.1101/2020.04.28.0667872020-04-29
The qBED track: a novel genome browser visualization for point processesMoudgil, A., Li, D., Hsu, S., Purushotham, D., Wang, T., Mitra, R. D. 10.1101/2020.04.27.0600612020-04-29
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C dataJain, D., Chu, C., Alver, B. H., Lee, S., Lee, E. A., Park, P. J. 10.1101/2020.04.27.0601452020-04-28
Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatinFiorillo, L., Musella, F., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Conte, M., Prisco, A., Pombo, A., Nicodemi, M. 10.1101/2020.04.24.0599152020-04-25
Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experimentsChen, Z., Shaw, A., Wilson, H., Woringer, M., Darzacq, X., Marqusee, S., Wang, Q., Bustamante, C. 10.1101/2020.04.10.0364422020-04-11
The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genesCote, A. J., Cote, C. J., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Boyden, E. S., Berger, S., Churchman, L. S., Raj, A. 10.1101/2020.04.06.0280922020-04-07
Cell-type specialization in the brain is encoded by specific long-range chromatin topologiesWinick-Ng, W., Kukalev, A., Harabula, I., Zea Redondo, L., Meijer, M., Serebreni, L., Bianco, S., Szabo, D., Chiariello, A. M., Irastorza Azcarate, I., Fiorillo, L., Musella, F., Thieme, C., Irani, E., Torlai Triglia, E., Kolodziejczyk, A. A., Abentung, A., Apostolova, G., Paul, E. J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S., Dechant, G., Ungless, M. A., Nicodemi, M., Castelo-Branco, G., Pombo, A. 10.1101/2020.04.02.0209902020-04-02
CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian CellsKubo N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H., Ren, B. 10.1101/2020.03.21.0016932020-03-23
Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell LinesCheng, R. R., Contessoto, V., Aiden, E. L., Wolynes, P. G., Di Pierro, M., Onuchic, J. N. 10.1101/2020.03.21.0019172020-03-22
Accurate 4Pi single-molecule localization using an experimental PSF modelLi, Y., Buglakova, E., Zhang, Y., Thevathasan, J. V., Bewersdorf, J., Ries, J. 10.1101/2020.03.18.9971632020-03-19
EMU: reconfigurable graphical user interfaces for Micro-ManagerDeschamps, J., Ries, J. 10.1101/2020.03.18.9974942020-03-19
Retrospective identification of rare cell populations underlying drug resistance connects molecular variability with cell fateEmert, B., Cote, C., Torre, E. A., Dardani, I. P., Jiang, C., Jain, N., Shaffer, S. M., Raj, A.10.1101/2020.03.18.9966602020-03-19
Detecting chromatin interactions along and between sister chromatids with SisterCOomen, M. E., Hedger, A. K., Watts, J. K., Dekker, J.10.1101/2020.03.10.9862082020-03-11
SPIN reveals genome-wide landscape of nuclear compartmentalizationWang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Hupkes, D. P., Chen, Y., Gilbert, D. M., van Steensel, B., Belmont, A. S., Ma, J.10.1101/2020.03.09.9829672020-03-10
Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid LeukemiaRuan, Y.10.1101/2020.03.05.9790702020-03-06
Regulation of gene expression by repression condensates during developmentTreen, N., Shimobayashi, S. F., Eeftens, J., Brangwynne, C. P., Levine, M.10.1101/2020.03.03.9756802020-03-04
An Improved 4’-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNAWielenberg, K., Wang, M., Yang, M., Ozer, A., Lis, J. T., Lin, H.10.1101/2020.02.29.9713172020-02-29
Subtype-specific epigenomic landscape and 3D genome structure in bladder cancerIyyanki, T. S., Zhang, B., Jin, Q., Yang, H., Liu, T., Wang, X., Song, F., Luan, Y., Yamashita, H., Wang, L., Warrick, J., Raman, J., Meeks, J., DeGraff, D. J., Yue, F.10.1101/2020.02.26.9666972020-02-29
Fluorophore-labelled RNA aptamers to common protein tags as super-resolution imaging reagents.Wang, J., Singh, A., Ozer, A., Zipfel, W. R.10.1101/2020.02.27.9685782020-02-28
Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemiaYang, H., Zhang, H., Luan, Y., Liu, T., Roberts, K. G., Qian, M., Zhang, B., Yang, W., Perez-Andreu, V., Xu, J., Iyyanki, S., Kuang, D., Reshmi, S. C., Gastier-Foster, J., Smith, C., Pui, C., Evans, W. E., Hunger, S. P., Platanias, L. C., Relling, M. V., Mullighan, C. G., Loh, M. L., Yue, F., Yang, J. J.10.1101/2020.02.23.9616722020-02-25
CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome ReorganizationFeng, Y., Wang, Y., Yang, C., Naseri, A., Pederson, T., Zheng, J., Xiao, X., Zhang, S., Xie, W., Ma, H.10.1101/2020.02.18.9546102020-02-19
Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture MappingWelch, L. R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W. F., Welch, J. D., Pombo, A.10.1101/2020.02.10.9410472020-02-13
Exploring the coronavirus epidemic using the new WashU Virus Genome BrowserFlynn, J., Purushotham, D., Choudhary, M. N., Zhuo, X., Fan, C., Matt, G., Li, D., Wang, T.10.1101/2020.02.07.9391242020-02-11
Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)Trzaskoma, P., Ruszczycki, B., Lee, B., Pels, K. K., Krawczyk, K., Bokota, G., Szczepankiewicz, A. A., Aaron, J., Walczak, A., Sliwinska, M., Magalska, A., Kadloff, M., Wolny, A., Parteka, Z., Arabasz, S., Kiss- Arabasz, M., Plewczynski, D., Ruan, Y., Wilczynski, G. M.10.1101/2020.02.05.9351062020-02-06
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping dataMarkowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Pombo, A., Schwarz, R. F.10.1101/2020.01.30.9270612020-01-31
Probing multi-way chromatin interaction with hypergraph representation learningZhang, R., Ma, J.10.1101/2020.01.22.9161712020-01-23
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleusMa, J., Do, M., Le Gros, M. A., Peskin, C. S., Larabell, C. A., Mori, Y., Isaacson, S. A.10.1101/2020.01.16.9093332020-01-17
Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviorsShaffer, S. M., Emert, B. L., Reyes-Hueros, R., Cote, C., Harmange, G., Sizemore, A. E., Gupte, R., Torre, E., Singh, A., Bassett, D. S., Raj, A.10.1101/3790162019-12-21
Cell cycle dynamics of lamina associated DNAvan Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B.10.1101/2019.12.19.8819792019-12-19
Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation LearningLekschas, F., Peterson, B., Haehn, D., Ma, E., Gehlenborg, N., Pfister, H.10.1101/5975182019-12-12
Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wildHumble, E., Dobrynin, P., Senn, H., Chuven, J., Scott, A. F., Mohr, D. W., Dudchenko, O., Omer, A. D., Colaric, Z., Lieberman Aiden, E., Wildt, D., Oliagi, S., Tamazian, G., Pukazhenthi, B., Ogden, R., Koepfli, K.-P.10.1101/8673412019-12-08
Efficient Homology-directed Repair with Circular ssDNA DonorsIyer, S., Mir, A., Ibraheim, R., Lee, J., VegaBadillo, J., Roscoe, B., Zhu, L. J., Liu, P., Luk, K., Mintzer, E., de Brito, J. S., Zamore, P., Sontheimer, E. J., Wolfe, S.10.1101/8641992019-12-05
High-Resolution 3D Fluorescent Imaging of Intact TissuesEl-Nachef, D., Martinson, A. M., Yang, X., Murry, C. E., MacLellan, W. R.10.1101/8552542019-11-26
Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C dataKim, H.-J., Yardimici, G. G., Bonora, G., Ramani, V., Liu, J., Qiu, R., Lee, C., Hesson, J., Ware, C. B., Shendure, J., Duan, Z., Noble, W. S.10.1101/5348002019-11-18
Genetic screening for single-cell variability modulators driving therapy resistanceTorre, E. A., Arai, E., Bayatpour, S., Beck, L. E., Emert, B. L., Shaffer, S. M., Mellis, I. A., Fane, M., Alicea, G., Budinich, K. A., Weeraratna, A., Shi, J., Raj, A.10.1101/6388092019-11-10
Hyper-SAGNN: a self-attention based graph neural network for hypergraphsZhang, R., Zou, Y., Ma, J.-2019-11-06
MS2-TRIBE evaluates protein-RNA interactions and nuclear organization of transcription by RNA editingBiswas, J., Rahman, R., Gupta, V., Rosbash, M., Singer, R.10.1101/8296062019-11-04
TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear specklesZhang, L., Zhang, Y., Chen, Y., Gholamalamdari, O., Ma, J., Belmont, A. S.10.1101/8244332019-10-30
Chromosome disentanglement driven via optimal compaction of loop-extruded brush structuresBrahmachari, S., Marko, J. F.10.1101/6161022019-10-25
Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image dataHuisman, M., Hammer, M., Rigano, A., Farzam, F., Gopinathan, R., Smith, C., Grunwald, D., Strambio-De-Castillia, C.-2019-10-24
Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architectureCremer, M., Brandstetter, K., Maiser, A., Rao, S. S., Schmid, V., Mitra, N., Mamberti, S., Klein, K. N., Gilbert, D. M., Leonhardt, H., Cardoso, M. C., Lieberman Aiden, E., Harz, H., Cremer, T.10.1101/8166112019-10-24
Chromosome organization by one-sided and two-sided loop extrusionBanigan, E. J., van den Berg, A. A., Brandao, H. B., Marko, J. F., Mirny, L. A.10.1101/8153402019-10-22
Composition dependent phase separation underlies directional flux through the nucleolusRiback, J. A., Zhu, L., Ferrolino, M. C., Tolbert, M., Mitrea, D. M., Sanders, D. W., Wei, M.-T., Kriwacki, R. W., Brangwynne, C. P.10.1101/8092102019-10-22
A cost-efficient open source laser engine for microscopySchroeder, D., Deschamps, J., Dasgupta, A., Matti, U., Ries, J.10.1101/7964822019-10-15
Co-opted transposons help perpetuate conserved higher-order chromosomal structuresChoudhary, M. N., Friedman, R. Z., Wang, J. T., Jang, H. S., Zhuo, X., Wang, T.10.1101/4853422019-10-14
Architectural RNA is required for heterochromatin organizationThakur, J., Fang, H., Llagas, T., Disteche, C. M., Henikoff, S.10.1101/7848352019-09-27
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPLWutz, G., St. Hilaire, B. T. G., Ladurner, R., Stocsits, R., Nagasaka, K., Pignard, B., Sanborn, A., Tang, W., Varnai, C., Ivanov, M., Schoenfelder, S., van der Lelij, P., Huang, X., Duernberger, G., Roitinger, E., Mechtler, K., Davidson, I. F., Fraser, P., Aiden, E. L., Peters, J. M.10.1101/7790582019-09-23
Direct, sensitive and specific detection of individual single- or double-strand DNA breaks by fluorescence microscopyKordon, M., Zarebski, M., Solarczyk, K., Ma, H., Pederson, T., Dobrucki, J. W.10.1101/7722692019-09-18
Chromatin is frequently unknotted at the megabase scaleGoundaroulis, D., Aiden, E. L., Stasiak, A.10.1101/7628722019-09-09
High Resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cellsZhao, P.A., Sasaki, T., Gilbert, D. M.10.1101/7556292019-09-05
NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded CellsYang, L., Ghosh, R. P., Franklin, J. M., You, C., Liphardt, J.10.1101/7497542019-08-28
PBAF regulates compartmentalization of actively transcribing chromatin hubsKenworthy, C. A., Liou, S.-H., Chandris, P., Wong, V., Dziuba, P., Lavis, L. D., Liu, W.-L., Singer, R. H., Coleman, R. A.10.1101/1116742019-08-22
Nucleated transcriptional condensates amplify gene expressionWei, M.-T., Chang, Y.-C., Shimobayashi, S. F., Shin, Y., Brangwynne, C. P.10.1101/7373872019-08-21
A supervised learning framework for chromatin loop detection in genome-wide contact mapsSalameh, T. J., Wang, X., Song, F., Zhang, B., Wright, S. M., Khunsriraksakul, C., Yue, F.10.1101/7396982019-08-20
Distinct features of nucleolus-associated domains in mouse embryonic stem cellsBizhanova, A., Yan, A., Yu, J., Zhu, L. J., Kaufman, P. D.10.1101/7404802019-08-20
Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living CellsWang, H., Nakamura, M., Zhao, D., Nguyen, C. M., Yu, C., Lo, A., Daley, T., La Russa, M., Liu, Y., Qi, L. S.10.1101/7344832019-08-14
Measuring significant changes in chromatin conformation with ACCOSTCook, K. B., Le Roch, K. G., Vert, J.-P., Noble, W.10.1101/7277682019-08-06
Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable InsetsLekschas, F., Behrisch, M., Bach, B., Kerpedjiev, P., Gehlenborg, N., Pfister, H.10.1101/3010362019-07-25
Dynamic changes in RNA-chromatin interactome promote endothelial dysfunctionCalandrelli, R., Xu, L., Luo, Y., Wu, W., Fan, X., Nguyen, T., Chen, C., Sriram, K., Natarajan, R., Chen, Z., Zhong, S.10.1101/7129502019-07-24
Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGICZhao, B., Chaturvedi, P., Zimmerman, D. L., Belmont, A. S.10.1101/7080242019-07-23
pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracksZhang, H. B., Kim, M., Chuang, J. H., Ruan, Y.10.1101/7096832019-07-20
Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancerSchuh, L., Saint-Antoine, M., Sanford, E., Emert, B., Singh, A., Marr, C., Goyal, Y., Raj, A.10.1101/7042472019-07-18
Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-CBelaghzal, H., Borrman, T., Stephens, A. D., Lafontaine, D. L., Venev, S. V., Marko, J. F., Weng, Z., Dekker, J.10.1101/7049572019-07-16
Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosomeFANG, H., Bonora, G., Lewandowski, J., Thakur, J., Filippova, G. N., Henikoff, S., Shendure, J., Duan, Z., Rinn, J., Deng, X., Noble, W. S., Disteche, C. M.10.1101/6872362019-06-30
Chemogenetic control of nanobodiesFarrants, H., Tarnawski, M., Müller, T. G., Otsuka, S., Hiblot, J., Koch, B., Kueblbeck, M., Kräusslich, H.-G., Ellenberg, J., Johnsson, K.10.1101/6835572019-06-27
Local rewiring of genome - nuclear lamina interactions by transcription.Brueckner, L., Zhao, P. A., van Schaik, T., Leemans, C., Sima, J., Peric-Hupkes, D., Gilbert, D. M., van Steensel, B.10.1101/6852552019-06-27
A chromosome folding intermediate at the condensin-to-cohesin transition during telophaseAbramo, K., Valton, A.-L., Venev, S. V., Ozadam, H., Fox, A. N., Dekker, J.10.1101/6784742019-06-21
Multiplex chromatin interaction analysis by signal processing and statistical algorithmsKim, M., Zheng, M., Tian, S. Z., Capurso, D., Lee, B., Chuang, J. H., Ruan, Y.10.1101/6652322019-06-10
HiNT: a computational method for detecting copy number variations and translocations from Hi-C dataWang, S., Lee, S., Chu, C., Jain, D., Nelson, G., Walsh, J. M., Alver, B. H., Park, P. J.10.1101/6570802019-06-03
DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexesMarko, J. F., De Los Rios, P., Barducci, A., Gruber, S.10.1101/3253732019-05-23
Inferring diploid 3D chromatin structures from Hi-C dataCauer, A., Yardimci, G. G., Vert, J.-P., Varoquaux, N., Noble, W.10.1101/6442942019-05-21
Jointly embedding multiple single-cell omics measurementsLiu, J., Huang, Y., Singh, R., Vert, J.-P., Noble, W.10.1101/6443102019-05-21
Spring Model - chromatin modeling tool based on OpenMMKadlof, M., Rozycka, J., Plewczynski, D.10.1101/6423222019-05-20
Ultrastructural details of mammalian chromosome architectureKrietenstein, N., Abraham, S., Venev, S., Abdennur, N., Gibcus, J., Hsieh, T.-H., Parsi, K. M., Yang, L., Maehr, R., Mirny, L., Dekker, J., Rando, O.10.1101/6399222019-05-17
Resolving the 3D landscape of transcription-linked mammalian chromatin foldingHsieh, T.-H. S., Slobodyanyuk, E., Hansen, A. S., Cattoglio, C., Rando, O. J., Tjian, R., Darzacq, X.10.1101/6387752019-05-17
Improved CUT&RUN chromatin profiling and analysis toolsMeers, M. P., Bryson, T. D., Henikoff, S.10.1101/5691292019-05-16
Concerted localization resets precede YAP-dependent transcriptionFranklin, J. M., Ghosh, R. P., Shi, Q., Liphardt, J. T.10.1101/5390492019-05-06
Spatial genome re-organization between fetal and adult hematopoietic stem cellsChen, C., Yu, W., Tober, J., Gao, P., He, B., Lee, K., Trieu, T., Blobel, G., Speck, N., Tan, K.10.1101/6282142019-05-05
Photoactivation of silicon rhodamines via a light-induced protonationFrei, M. S., Hoess, P., Lampe, M., Nijmeijer, B., Kueblbeck, M., Ellenberg, J., Ries, J., Pitsch, S., Reymond, L., Johnsson, K.10.1101/6268532019-05-04
Tibanna: software for scalable execution of portable pipelines on the cloudLee, S., Johnson, J., Vitzthum, C., Kırlı, K., Alver, B. H., Park, P. J.10.1101/4409742019-04-29
Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cellsRuan, Y., Plewczynski, D., Zhu, J. J., Parteka, Z., Lee, B., Szalaj, P., Wang, P., Jodkowska, K., Arron, J., Chew, T. L.10.1101/6219202019-04-29
FIREcaller: an R package for detecting frequently interacting regions from Hi-C dataCrowley, C., Yang, Y., Qiu, Y., Hu, B., Won, H., Ren, B., Hu, M., Li, Y.10.1101/6192882019-04-29
Mapping RNA-chromatin interactions by sequencing with iMARGI V.2Wu, W., Yan, Z., Nguyen, T. C., Chen, Z., Chien, S., Zhong, S.-2019-04-18
ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactionsTian, S. Z., Capurso, D., Kim, M., Lee, B., Zheng, M., Ruan, Y.10.1101/6130342019-04-18
Multi-scale deep tensor factorization learns a latent representation of the human epigenomeSchreiber, J., Durham, T. J., Bilmes, J., Noble, W. S.10.1101/3649762019-04-11
Re-configuration of Chromatin Structure During the Mitosis-G1 Phase TransitionZhang, H., Emerson, D., Gilgenast, T., Titus, K., Lan, Y., Huang, P., Zhang, D., Wang, H., Keller, C., Giardine, B., Hardison, R., Phillips-Cremins, J., Blobel, G.10.1101/6043552019-04-11
RNA polymerases as moving barriers to condensin loop extrusionBrandao, H. B., Wang, X., Paul, P., van den Berg, A., Rudner, D. Z., Mirny, L. A.10.1101/6042802019-04-10
Transcription amplification by nuclear speckle associationKim, J., Khanna, N., Belmont, A. S.10.1101/6042982019-04-09
Common DNA sequence variation influences 3-dimensional conformation of the human genomeGorkin, D., Qiu, Y., Hu, M., Fletez-Brant, K., Liu, T., Schmitt, A., Noor, A., Chiou, J., Gaulton, K., Sebat, J., Li, Y., Hansen, K., Ren, B.10.1101/5927412019-03-30
Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINTSchlichthaerle, T., Strauss, M. T., Schueder, F., Auer, A., Nijmeijer, B., Kueblbeck, M., Jimenez Sabinina, V., Thevatasan, J. V., Ries, J., Ellenberg, J., Jungmann, R.10.1101/5799612019-03-23
Nuclear pores as versatile reference standards for quantitative superresolution microscopyThevathasan, J. V., Kahnwald, M., Cieslinski, K., Hoess, P., Peneti, S. K., Reitberger, M., Heid, D., Kasuba, K. C., Hoerner, S. J., Li, Y., Wu, Y.-L., Mund, M., Matti, U., Pereira, P. M., Henriques, R., Nijmeijer-Winter, B., Kueblbeck, M., Jimenez Sabinina, V., Ellenberg, J., Ries, J.10.1101/5826682019-03-20
Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cellsRamani, V., Deng, X., Qiu, R., Lee, C., Disteche, C. M., Noble, W. S., Duan, Z., Shendure, J.10.1101/5795732019-03-15
CUT&Tag for efficient epigenomic profiling of small samples and single cellsKaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., Henikoff, S.10.1101/5689152019-03-06
Absolute quantification of cohesin, CTCF and their regulators in human cellsHolzmann, J., Politi, A. Z., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., Dürnberger, G., Tang, W., Ladurner, R., Stocsits, R. R., Busslinger, G. A., Novak, B., Mechtler, K., Davidson, I. F., Ellenberg, J., Peters, J.-M.10.1101/5604252019-02-27
EpiAlignment: alignment with both DNA sequence and epigenomic dataLu, J., Cao, X., Zhong, S.10.1101/5621992019-02-27
Supervised classification enables rapid annotation of cell atlasesPliner, H. A., Shendure, J., Trapnell, C.10.1101/5386522019-02-25
Determining cellular CTCF and cohesin abundances to constrain 3D genome modelsCattoglio, C., Pustova, I., Walther, N., Ho, J. J., Hantsche-Grininger, M., Inouye, C. J., Hossain, M. J., Dailey, G. M., Ellenberg, J., Darzacq, X., Tjian, R., Hansen, A. S.10.1101/3706502019-02-24
Cooler: scalable storage for Hi-C data andother genomically-labeled arraysAbdennur, N., Mirny, L.10.1101/5576602019-02-22
Localization microscopy at doubled precision with patterned illuminationCnossen, J., Hinsdale, T., Thorsen, R., Schueder, F., Jungmann, R., Smith, C. S., Rieger, B., Stallinga, S.10.1101/5543372019-02-20
Comparing 3D genome organization in multiple species using Phylo-HMRFYang, Y., Zhang, Y., Ren, B., Dixon, J., Ma, J.10.1101/5525052019-02-19
Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathyBertero, A., Fields, P. A., Smith, A. S., Leonard, A., Beussman, K., Sniadecki, N. J., Kim, D.-H., Tse, H.-F., Pabon, L., Shendure, J., Noble, W. S., Murry, C. E.10.1101/5552502019-02-19
Dynamics of gene expression in single root cells of A. thalianaJean-Baptiste, K., McFaline-Figueroa, J. L., Alexandre, C. M., Dorrity, M. W., Saunders, L., Bubb, K. L., Trapnell, C., Fields, S., Queitsch, C., Cuperus, J. T.10.1101/4485142019-02-11
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleomeTian, D., Zhang, R., Zhang, Y., Zhu, X., Ma, J.10.1101/5420922019-02-07
Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traitsGiusti-Rodriguez, P. M., Sullivan, P. F.10.1101/4063302019-01-30
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamplesSchreiber, J., Bilmes, J., Noble, W.10.1101/5332732019-01-29
Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb DevelopmentPaliou, C., Guckelberger, P., Schöpflin, R., Heinrich, V., Esposito, A., Chiariello, A. M. M., Bianco, S., Annunziatella, C., Helmuth, J., Haas, S., Jerkovic, I., Brieske, N., Wittler, L., Timmermann, B., Nicodemi, M., Vingron, M., Mundlos, S., Andrey, G.10.1101/5288772019-01-23
Effects of altering histone post-translational modifications on mitotic chromosome structure and mechanicsBiggs, R., Stephens, A. D., Liu, P., Marko, J. F.10.1101/4235412019-01-04
ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualizationCapurso, D., Wang, J., Tian, S. Z., Cai, L., Namburi, S., Lee, B., Tjong, H., Tang, Z., Wang, P., Wei, C.-L., Ruan, Y., Li, S.10.1101/5066832018-12-27
Revealing Hi-C subcompartments by imputing high-resolution inter-chromosomal chromatin interactionsXiong, K., Ma, J.10.1101/5055032018-12-23
An RNA-binding region regulates CTCF clustering and chromatin loopingHansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Darzacq, X., Tjian, R.10.1101/4954322018-12-16
Guided nuclear exploration increases CTCF target search efficiencyHansen, A. S., Amitai, A., Cattoglio, C., Tjian, R., Darzacq, X.10.1101/4954572018-12-13
Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cellsCheng, L.-C., Baboo, S., Lindsay, C., Brusman, L. E., Martinez-Bartolome, S., Tapia, O., Zhang, X., Yates, J. R., Gerace, L.10.1101/4864152018-12-03
Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast HeterochromatinVertii, A., Ou, J., Yu, J., Yan, A., Pages, H., Liu, H., Zhu, L. J., Kaufman, P. D.10.1101/4845682018-12-03
Limits of chromosome compaction by loop-extruding motorsBanigan, E. J., Mirny, L. A.10.1101/4764242018-11-21
Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairsYan, 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.10.1101/4720192018-11-20
Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneumDudchenko, O., Pham, M., Lui, C., Batra, S. S., Hoeger, M., Nyquist, S. K., Durand, N. C., Shamim, M. S., Machol, I., Erskine, W., Aiden, E. L., Kaur, P.10.1101/4735532018-11-20
Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cellsLi, G., Liu, Y., Zhang, Y., Fang, R., Kellis, M., Ren, B.10.1101/4709632018-11-15
Promoter-intrinsic and local chromatin features determine gene repression in lamina-associated domainsLeemans, C., van der Zwalm, M., Brueckner, L., Comoglio, F., van Schaik, T., Pagie, L., van Arensbergen, J., van Steensel, B.10.1101/4640812018-11-06
Satb1 integrates DNA sequence, shape, motif density and torsional stress to differentially bind targets in nucleosome-dense regions.GHOSH, R. P., SHI, Q., YANG, L., REDDICK, M. P., NIKITINA, T., ZHURKIN, V. B., FORDYCE, P., STASEVICH, T. J., CHANG, H. Y., GREENLEAF, W. J., LIPHARDT, J. T.10.1101/4502622018-10-26
Highly Structured Homolog Pairing Reflects Functional Organization of the Drosophila GenomeAlHaj Abed, J., Erceg, J., Goloborodko, A., Nguyen, S. C., McCole, R. B., Saylor, W., Fudenberg, G., Lajoie, B. R., Dekker, J., Mirny, L. A., Wu, T.10.1101/4438872018-10-17
The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryosErceg, J., AlHaj Abed, J., Goloborodko, A., Lajoie, B. R., Fudenberg, G., Abdennur, N., Imakaev, M., McCole, R. B., Nguyen, S. C., Saylor, W., Joyce, E. F., Senaratne, T. N., Hannan, M. A., Nir, G., Dekker, J., Mirny, L. A., Wu, C.-t.10.1101/4430282018-10-17
Antigen receptor locus dynamics is orchestrated near the sol-gel phase transition to enforce stepwise VDJ gene rearrangementKhanna, N., Zhang, J., Dudko, O., Murre, C.10.1101/4414442018-10-12
Condensin II inactivation in interphase does not affect chromatin folding or gene expressionAbdennur, N., Schwarzer, W., Pekowska, A., Shaltiel, I. A., Huber, W., Haering, C. H., Mirny, L., Spitz, F.10.1101/4374592018-10-07
Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formationStephens, A. D., Liu, P. Z., Kandula, V., Chen, H., Almassalha, L. M., Backman, V., O'Halloran, T., Adam, S. A., Goldman, R. D., Banigan, E. J., Marko, J. F.10.1101/4234422018-09-21
Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyondNomidis, S. K., Skoruppa, E., Carlon, E., Marko, J. F.10.1101/4226832018-09-20
Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population ScaleSadowski, M., Kraft, A., Szalaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., Plewczynski, D.10.1101/2669812018-09-14
MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experimentsJuric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Yang, Y., Li, Y., Ren, B., Hu, M.10.1101/4118352018-09-08
The accessible chromatin landscape of the hippocampus at single-cell resolutionSinnamon, J. R., Torkenczy, K. A., Linhoff, M. W., Vitak, S. A., Pliner, H. A., Trapnell, C., Steemers, F. J., Mandel, G., Adey, A. C.10.1101/4076682018-09-04
EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and functionLawlor, N., Marquez, E. J., Orchard, P., Narisu, N., Shamim, M. S., Thibodeau, A., Varshney, A., Kursawe, R., Erdos, M. R., Kanke, M., Gu, H., Pak, E., Dutra, A., Russell, S., Li, X., Piecuch, E., Luo, O., Chines, P. S., Fuchbserger, C., Sethupathy, P., Aiden, A. P., Ruan, Y., Aiden, E. L., Collins, F. S., Ucar, D., Parker, S. C. J., Stitzel, M. L.10.1101/3991392018-08-23
Photon count estimation in single-molecule localization microscopyRieger, B., Stallinga, S., Hulleman, C. N., Thorsen, R. O., Grunwald, D., Hammer, M.10.1101/3964242018-08-20
BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studiesSun, Z., Chen, L., Xin, H., Huang, Q., Cillo, A., Tabib, T., Ding, Y., Kolls, J., Bruno, T., Lafyatis, R., Vignali, D., Chen, K., Hu, M., Chen, W.10.1101/3926622018-08-16
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional burstingSymmons, O., Chang, M., Mellis, I., Kalish, J. M., Bartolomei, M. S., Raj, A.10.1101/3863592018-08-07
A combination of transcription factors mediates inducible interchromosomal pairingKim, S., Dunham, M., Shendure, J.10.1101/3850472018-08-05
Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffoldMarko, J., Biggs, R., Sun, M., Hornick, J.10.1101/3849822018-08-04
Transient DNA Binding Induces RNA Polymerase II Compartmentalization During Herpesviral Infection Distinct From Phase SeparationMcSwiggen, D. T., Hansen, A. S., Marie-Nelly, H., Teves, S., Heckert, A., Dugast-Darzacq, C., Hao, Y., Umemoto, K. K., Tjian, R., Darzacq, X.10.1101/3750712018-07-30
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modelingNir, G., Farabella, I., Perez Estrada, C., Ebeling, C. G., Beliveau, B. J., Sasaki, H. M., Lee, S. H., Nguyen, S. C., McCole, R. B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N. M. C., Nguyen, H. Q., Hannan, M. A., Russell, S., Durand, N. C., Rao, S. S. P., Kishi, J. Y., Soler-Vila, P., Di Pierro, M., Onuchic, J. N., Callahan, S., Schreiner, J., Stuckey, J., Yin, P., Lieberman Aiden, E., Marti-Renom, M. A., Wu, C.- t.10.1101/3740582018-07-28
Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryosMir, M., Stadler, M. R., Ortiz, S. A., Harrison, M. M., Darzacq, X., Eisen, M. B.10.1101/3778122018-07-26
Receptor-ligand rebinding kinetics in confinementErbas, A., Olvera de la Cruz, M., Marko, J.10.1101/3703952018-07-16
Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architectureSchreiber, J., Libbrecht, M., Bilmes, J., Noble, W.10.1101/1036142018-07-15
CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioningOomen, M. E., Hansen, A., Liu, Y., Darzacq, X., Dekker, J.10.1101/3658662018-07-11
LADL: Light-activated dynamic looping for endogenous gene expression controlRege, M., Kim, J. H., Valeri, J., Dunagin, M., Metzger, A., Gong, W., Beagan, J., Raj, A., Phillips-Cremins, J. E.10.1101/3493402018-06-18
Feasibility of constructing multi-dimensional genomic maps of juvenile idiopathic arthritisJarvis, J. N., Zhu, L., Jiang, K., Wong, L., Buck, M. J., Chen, Y., Moncrief, H., Macintosh, L. A., Liu, T., Sing, X., Li, D., Wang, T., O'Neil, K. M.10.1101/3498112018-06-18
Nuclear speckle fusion via long-range directional motion regulates the number and size of specklesKim, J., Han, K. Y., Khanna, N., Ha, T., Belmont, A. S.10.1101/3479552018-06-15
RNA polymerase II clustering through CTD phase separationBoehning, M., Dugast-Darzacq, C., Rankovic, M., Hansen, A. S., Yu, T.-K., Marie-Nelly, H., McSwiggen, D. T., Kokic, G., Dailey, G. M., Cramer, P., Darzacq, X., Zweckstetter, M.10.1101/3163722018-06-15
High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid miceYin, Y., Jiang, Y., Berletch, J. B., Disteche, C. M., Noble, W. S., Steemers, F. J., Adey, A. C., Shendure, J. A.10.1101/3380532018-06-12
HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction MapsKerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S. B., Azhir, A., Kumar, N., Hwang, J., Lee, S., Alver, B. H., Pfister, H., Mirny, L. A., Park, P. J., Gehlenborg, N.10.1101/1218892018-06-04
Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organizationKim, J.-S., He, X., Liu, J., Duan, Z., Kim, T., Gerard, J., Kim, B., Lane, W. S., Noble, W. S., Budnik, B., Waldman, T.10.1101/3252092018-05-17
Dynamic and Selective Low-Complexity Domain Interactions Revealed by Live-Cell Single-Molecule ImagingChong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G., Cattoglio, C., Banala, S., Lavis, L., Darzacq, X., Tjian, R.10.1101/2087102018-05-16
GITAR: an Open Source Tool for Analysis and Visualization of Hi-C DataCalandrelli, R., Wu, Q., Guan, J., Zhong, S.10.1101/2595152018-05-08
Exponential fluorescent amplification of individual RNAs using clampFISH probesRouhanifard, S. H., Mellis, I. A., Dunagin, M., Bayatpour, S., Symmons, O., Cote, A., Raj, A.10.1101/2227942018-05-07
TSA-Seq Mapping of Nuclear Genome OrganizationChen, Y., Zhang, Y., Wang, Y., Zhang, L., Brinkman, E. K., Adam, S. A., Goldman, R., van Steensel, B., Ma, J., Belmont, A. S.10.1101/3078922018-04-25
Complementary chromosome folding by transcription factors and cohesinPereira, M. C. F., Brackley, C. A., Michieletto, D., Annunziatella, C., Bianco, S., Chiariello, A. M., Nicodemi, M., Marenduzzo, D.10.1101/3053592018-04-23
Quantitative imaging of chromatin decompaction in living cellsDultz, E., Mancini, R., Polles, G., Vallotton, P., Alber, F., Weis, K.10.1101/2192532018-04-22
Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arraysGibcus, J. H., Samejima, K., Goloborodko, A., Samejima, I., Naumova, N., Kanemaki, M., Xie, L., Paulson, J. R., Earnshaw, W. C., Mirny, L. A., Dekker, J.10.1101/1746492018-04-20
RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genomeChen, W., Yan, Z., Li, S., Huang, N., Huang, X., Zhang, J., Zhong, S.10.1101/3004832018-04-12
An inter-chromosomal transcription hub activates the unfolded protein response in plasma cellsBortnick, A., He, Z., Aubrey, M., Chandra, V., Denholtz, M., Chen, K., Lin, Y. C., Murre, C.10.1101/2959152018-04-07
A quantitative map of human Condensins provides new insights into mitotic chromosome architectureWalther, N., Hossain, M. J., Politi, A. Z., Koch, B., Kueblbeck, M., Oedegaard-Fougner, O., Lampe, M., Ellenberg, J.10.1101/2378342018-03-22
Identification of cis elements for spatio-temporal control of DNA replicationSima, J., Chakraborty, A., Dileep, V., Michalski, M., Rivera-Mulia, J. C., Trevilla-Garcia, C., Klein, K. N., Bartlett, D., Washburn, B. K., Paulsen, M. T., Vera, D., Nora, E. P., Kraft, K., Mundlos, S., Bruneau, B. G., Ljungman, M., Fraser, P., Ay, F., Gilbert, D. M.10.1101/2856502018-03-21
Mapping local and global liquid-liquid phase behavior in living cells using light-activated multivalent seedsBracha, D., Walls, M. T., Wei, M.-T., Zhu, L., Kurian, M., Toettcher, J. E., Brangwynne, C. P.10.1101/2836552018-03-16
Continuous-trait probabilistic model for comparing multi-species functional genomic dataYang, Y., Gu, Q., Zhang, Y., Sasaki, T., Crivello, J., O'Neill, R. J., Gilbert, D. M., Ma, J.10.1101/2830932018-03-16
GIVE: toward portable genome browsers for personal websitesCao, X., Yan, Z., Wu, Q., Zheng, A., Zhong, S.10.1101/1778322018-03-15
SAVER: Gene expression recovery for UMI-based single cell RNA sequencingHuang, M., Wang, J., Torre, E., Dueck, H., Shaffer, S., Bonasio, R., Murray, J., Raj, A., Li, M., Zhang, N. R.10.1101/1386772018-03-08
Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulationBartman, C. R., Keller, C. A., Giardine, B., Hardison, R. C., Blobel, G. A., Raj, A.10.1101/2753542018-03-02
ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution MicroscopyBarton, C., Morganella, S., Oedegaard, O., Alexander, S., Ries, J., Fitzgerald, T., Ellenberg, J., Birney, E.10.1101/1154362018-02-22
Emerging Evidence of Chromosome Folding by Loop ExtrusionFudenberg, G., Abdennur, N., Imakaev, M., Goloborodko, A., Mirny, L.10.1101/2646482018-02-16
Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural NetworksSingh, S., Yang, Y., Poczos, B., Ma, J.10.1101/0852412018-02-05
Measuring the reproducibility and quality of Hi-C dataYardımcı, G. G., Ozadam, H., Sauria, M. E. G., Ursu, O., Yan, K.-K., Yang, T., Chakraborty, A., Kaul, A., Lajoie, B. R., Song, F., Zhan, Y., Ay, F., Gerstein, M., Kundaje, A., Li, Q., Taylor, J., Yue, F., Dekker, J., Noble, W. S.10.1101/1887552018-02-05
Defect-Facilitated Buckling in Supercoiled Double-Helix DNABrahmachari, S., Dittmore, A., Takagi, Y., Neuman, K. C., Marko, J. F.10.1101/2596892018-02-04
Predicting CTCF-mediated chromatin loops using CTCF-MPZhang, R., Wang, Y., Yang, Y., Zhang, Y., Ma, J.10.1101/2594162018-02-02
C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2Gao, 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.10.1101/1718192018-01-31
Bend-Induced Twist Waves and the Structure of Nucleosomal DNASkoruppa, E., Nomidis, S. K., Marko, J. F., Carlon, E.10.1101/2568182018-01-30
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000Dudchenko, O., Shamim, M. S., Batra, S., Durand, N. C., Musial, N. T., Mostofa, R., Pham, M., Glenn St Hilaire, B., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S. K., Korchina, V., Pletch, K., Flanagan, J. P., Tomaszewicz, A., McAloose, D., Perez Estrada, C., Novak, B. J., Omer, A. D., Aiden, E. L.10.1101/2547972018-01-28
Multiplex Chromatin Interaction Analysis with Single-Molecule PrecisionZheng, M., Tian, S. Z., Maurya, R., Lee, B., Kim, M., Capurso, D., Piecuch, E., Gong, L., Zhu, J. J., Wong, C. H., Ngan, C. Y., Wang, P., Ruan, X., Wei, C.-L., Ruan, Y.10.1101/2520492018-01-25
Correlative live and super-resolution imaging reveals the dynamic structure of replication domainsXiang, W., Roberti, M. J., Heriche, J.-K., Huet, S., Alexander, S., Ellenberg, J.10.1101/1893732018-01-24
Heterochromatin drives organization of conventional and inverted nucleiFalk, M., Feodorova, Y., Naumova, N., Imakaev, M., Lajoie, B. R., Leonhardt, H., Joffe, B., Dekker, J., Fudenberg, G., Solovei, I., Mirny, L.10.1101/2440382018-01-09
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector controlMatthews, B. J., Dudchenko, O., Kingan, S., Koren, S., Antoshechkin, I., Crawford, J. E., Glassford, W. J., Herre, M., Redmond, S. N., Rose, N. H., Weedall, G. D., Wu, Y., Batra, S. S., Brito-Sierra, C. A., Buckingham, S. D., Campbell, C. L., Chan, S., Cox, E., Evans, B. R., Fansiri, T., Filipovic, I., Fontaine, A., Gloria-Soria, A., Hall, R., Joardar, V. S., Jones, A. K., Kay, R. G. G., Kodali, V., Lee, J., Lycett, G. J., Mitchell, S. N., Muehling, J., Murphy, M. R., Omer, A., Partridge, F. A., Peluso, P., Aiden, A. P., Ramasamy, V., Rasic, G., Roy, S., Saavedra-Rodriguez, K., Sharan, S., Sha10.1101/2407472017-12-29
Chromatin interaction data visualization in the WashU Epigenome BrowserLi, D., Hsu, S., Purushotham, D., Wang, T.10.1101/2393682017-12-24
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosomeBonora, G., Deng, X., Fang, H., Ramani, V., Qui, R., Berletch, J., Filippova, G. N., Duan, Z., Schendure, J., Noble, W. S., Disteche, C. M.10.1101/1653402017-12-15
Allele-specific control of replication timing and genome organization during developmentRivera-Mulia, J. C., Dimond, A., Vera, D., Trevilla-Garcia, C., Sasaki, T., Zimmerman, J., Dupont, C., Gribnau, J., Fraser, P., Gilbert, D. M.10.1101/2217622017-11-21
Dynamic reorganization of nuclear architecture during human cardiogenesisFields, P. A., Ramani, V., Bonora, G., Yardimci, G. G., Bertero, A., Reinecke, H., Pabon, L., Noble, W. S., Shendure, J., Murry, C.10.1101/2228772017-11-21
Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleusQuinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M., Shishkin, A., Bhat, P., Trinh, V., Aznauryan, E., Russell, P., Cheng, C., Jovanovic, M., Chow, A., McDonel, P., Garber, M., Guttman, M.10.1101/2196832017-11-18
CHRAC/ACF Contribute to the Repressive Ground State of ChromatinScacchetti, A., Brueckner, L., Jain, D., Schauer, T., Zhang, X., Schnorrer, F., van Steensel, B., Straub, T., Becker, P. B.10.1101/2187682017-11-13
A Cell Type-Specific Class of Chromatin Loops Anchored at Large DNA Methylation NadirsJeong, M., Huang, X., Zhang, X., Su, J., Shamim, M., Bochkov, I., Reyes, J., Jung, H., Heikamp, E., Presser Aiden, A., Li, W., Aiden, E., Goodell, M. A.10.1101/2129282017-11-09
Removing unwanted variation between samples in Hi-C experimentsFletez-Brant, K., Qiu, Y., Gorkin, D. U., Hu, M., Hansen, K. D.10.1101/2143612017-11-06
Chromatin histone modifications and rigidity affect nuclear morphology independent of laminsStephens, A. D., Liu, P. Z., Banigan, E. J., Almassalha, L. M., Backman, V., Adam, S. A., Goldman, R., Marko, J.10.1101/2063672017-10-29
Spot-On: robust model-based analysis of single-particle tracking experimentsHansen, A. S., Woringer, M., Grimm, J. B., Lavis, L. D., Tjian, R., Darzacq, X.10.1101/1719832017-10-26
Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA TopologiesAllahyar, A., Vermeulen, C., Bouwman, B., Krijger, P., Verstegen, M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J., Teunissen, H., Renkens, I., Kloosterman, W., Rowland, B., de Wit, E., de Ridder, J., de Laat, W.10.1101/2060942017-10-20
Juicebox.js provides a cloud-based visualization system for Hi-C dataRobinson, J., Turner, D., Durand, N. C., Thorvaldsdottir, H., Mesirov, J. P., Aiden, E. L.10.1101/2057402017-10-19
Fluorescence polarization control for on-off switching of single molecules at cryogenic temperaturesHulleman, C., Huisman, M., Moerland, R., Grunwald, D., Stallinga, S., Rieger, B.10.1101/2047762017-10-17
Chromatin Organization by an Interplay of Loop Extrusion and Compartmental SegregationNuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N., Mirny, L.10.1101/1962612017-10-03
Mechanics and buckling of biopolymeric shells and cell nucleiBanigan, E. J., Stephens, A. D., Marko, J. F.10.1101/1975662017-10-02
Nucleation of multiple buckled structures in intertwined DNA double helicesBrahmachari, S., Gunn, K. H., Giuntoli, R. D., Mondragon, A., Marko, J. F.10.1101/1963452017-09-30
CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome DynamicsMa, H., Tu, L.-C., Naseri, A., Chung, Y.-C., Grunwald, D., Zhang, S., Pederson, T.10.1101/1959662017-09-29
Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundariesSun, J., Zhou, L., Emerson, D. J., Gilgenast, T. G., Titus, K., Beagan, J. A., Phillips-Cremins, J. E.10.1101/1912132017-09-20
High-throughput identification of RNA nuclear enrichment sequencesShukla, C. J., McCorkindale, A. L., Gerhardinger, C., Korthauer, K. D., Cabili, M. N., Shechner, D. M., Irizarry, R. A., Maass, P. G., Rinn, J. L.10.1101/1896542017-09-15
SHAMAN: bin-free randomization, normalization and screening of Hi-C matricesCohen, N. M., Olivares-Chauvet, P., Lubling, Y., Baran, Y., Lifshitz, A., Hoichman, M., Tanay, A.10.1101/1872032017-09-12
Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolutionMa, W., Ay, F., Lee, C., Gulsoy, G., Deng, X., Cook, S., Hesson, J., Cavanaugh, C., Ware, C. B., Krumm, A., Shendure, J., Blau, C. A., Disteche, C. M., Noble, W. S., Duan, Z.10.1101/1848462017-09-05
A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome ArchitectureGassler, J., Brandao, H. B., Imakaev, M., Flyamer, I. M., Ladstatter, S., Bickmore, W. A., Peters, J.-M., Mirny, L. A., Tachibana-Konwalski, K.10.1101/1777662017-08-17
3D Single-Molecule Super-Resolution Microscopy With A Tilted Light SheetGustavsson, A.-K., Petrov, P. N., Lee, M. Y., Shechtman, Y., Moerner, W. E.10.1101/1356992017-08-14
Fast, robust and precise 3D localization for arbitrary point spread functionsLi, Y., Mund, M., Hoess, P., Matti, U., Nijmeijer, B., Jimenez Sabinina, V., Ellenberg, J., Schoen, I., Ries, J.10.1101/1726432017-08-10
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficientYang, T., Zhang, F., Yardimci, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F., Li, Q.10.1101/1013862017-08-04
Heterogeneity and Intrinsic Variation in Spatial Genome OrganizationFinn, E., Pegoraro, G., Brandao, H. B., Valton, A.-L., Oomen, M. E., Dekker, J., Mirny, L., Misteli, T.10.1101/1718012017-08-03
Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cellsDanko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L., Siepel, A.10.1101/0832122017-07-16
Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program.Dileep, V., Gilbert, D. M.10.1101/1583522017-07-14
CRISPR/Cas9-mediated Knock-in of an Optimized TetO Repeat for Live Cell Imaging of Endogenous LociTasan, I., Sustackova, G., Zhang, L., Kim, J., Sivaguru, M., HamediRad, M., Wang, Y., Genova, J., Ma, J., Belmont, A. S., Zhao, H.10.1101/1621562017-07-12
HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small MultiplesLekschas, F., Bach, B., Kerpedjiev, P., Gehlenborg, N., Pfister, H.10.1101/1235882017-07-09
A Fluorogenic Array Tag for Temporally Unlimited Single Molecule TrackingGhosh, R. P., Franklin, M. J., Draper, W. E., Shi, Q., Liphardt, J. T.10.1101/1590042017-07-03
Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPsNoma, A., Smith, C. S., Huisman, M., Martin, R. M., Moore, M. J., Grunwald, D.10.1101/1560912017-06-26
Chromatin accessibility dynamics of myogenesis at single cell resolutionPliner, H., Packer, J., McFaline-Figueroa, J., Cusanovich, D., Daza, R., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., Steemers, F., Shendure, J., Trapnell, C.10.1101/1554732017-06-26
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinkingKaewsapsak, P., Shechner, D. M., Mallard, W., Rinn, J. L., Ting, A. Y.10.1101/1530982017-06-21
Dense Bicoid Hubs Accentuate Binding along the Morphogen GradientMir, M., Reimer, A., Haines, J. E., Li, X.-Y., Stadler, M., Garcia, H., Eisen, M. B., Darzacq, X.10.1101/1331242017-06-08
qSR: A software for quantitative analysis of single molecule and super-resolution dataAndrews, J. O., Narayanan, A., Spille, J.-H., Cho, W.-K., Thaler, J. D., Cisse, I. I.10.1101/1462412017-06-05
Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images -- How Reliable Is It?Tu, L.-C., Huisman, M., Chung, Y.-C., Smith, C., Grunwald, D.10.1101/1451102017-06-02
Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation CaptureLi, H., Kalhor, R., Li, B., Su, T., Berk, A., Kurdistani, S., Alber, F., Chen, L.10.1101/1426042017-05-26
Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage DevelopmentPhanstiel, D. H., Van Bortle, K., Spacek, D. V., Hess, G. T., Saad Shamim, M., Machol, I., Love, M. I., Lieberman Aiden, E., Bassik, M. C., Snyder, M. P.10.1101/1420262017-05-25
A Comparison Between Single Cell RNA Sequencing And Single Molecule RNA FISH For Rare Cell AnalysisTorre, E. A., Dueck, H., Shaffer, S., Gospocic, J., Gupte, R., Bonasio, R., Kim, J., Murray, J., Raj, A.10.1101/1382892017-05-18
Cohesin Loss Eliminates All Loop Domains, Leading To Links Among Superenhancers And Downregulation Of Nearby GenesRao, S., Huang, S.-C., Glenn St. Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bochkov, I. D., Huang, X., Shamim, M. S., Omer, A. D., Bernstein, B. E., Casellas, R., Lander, E. S., Lieberman Aiden, E.10.1101/1397822017-05-18
Torque and buckling in stretched intertwined double-helix DNAsMarko, J., Brahmachari, S.10.1101/1359052017-05-09
Facilitated Dissociation Of Transcription Factors From Single DNA Binding SitesKamar, R. I., Banigan, E. J., Erbas, A., Giuntoli, R. D., Olvera de la Cruz, M., Johnson, R. C., Marko, J. F.10.1101/1359472017-05-09
Ki-67 Contributes To Normal Cell Cycle Progression And Inactive X Heterochromatin In p21 Checkpoint-Proficient Human CellsSun, X., Bizhanova, A., Matheson, T. D., Yu, J., Zhu, L. J., Kaufman, P. D.10.1101/1347672017-05-08
Supercoiling DNA locates mismatchesDittmore, A., Brahmachari, S., Takagi, Y., Marko, J. F., Neuman, K. C.10.1101/1305672017-04-25
Nuclear Microenvironments Modulate Transcription From Low-Affinity EnhancersCrocker, J., Tsai, A., Muthusamy, A. K., Lavis, L. D., Singer, R. H., Stern, D. L.10.1101/1282802017-04-18
A Versatile Compressed Sensing Scheme For Faster And Less Phototoxic 3D Fluorescence MicroscopyWoringer, M., Darzacq, X., Zimmer, C., Mir, M.10.1101/1258152017-04-10
An Integrative Framework For Detecting Structural Variations In Cancer GenomesDixon, J., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardimci, G. G., Chakraborty, A., Bann, D. V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Mulia, J. C. R., Ozadam, H., Lajoie, B. R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D. T., Stamatoyannopoulos, J. A., Broach, J. R., Hardison, R., Ay, F., Noble, W. S., Dekker, J., Gilbert, D. M., Yue, F.10.1101/1196512017-03-28
Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem CellsKubo, N., Ishii, H., Gorkin, D., Meitinger, F., Xiong, X., Fang, R., Liu, T., Ye, Z., Li, B., Dixon, J., Desai, A., Zhao, H., Ren, B.10.1101/1187372017-03-20
HUGIn: Hi-C Unifying Genomic InterrogatorMartin, J. S., Xu, Z., Reiner, A. P., Mohlke, K. L., Sullivan, P., Ren, B., Hu, M., Li, Y.10.1101/1175312017-03-16
Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genomeDawson, W., Plewczynski, D.10.1101/1056762017-03-08
Repli-seq: genome-wide analysis of replication timing by next-generation sequencingMarchal, C., Sasaki, T., Vera, D., Wilson, K., Sima, J., Rivera-Mulia, J.-C., Trevilla Garcia, C., Nogues, C., Nafie, E., Gilbert, D. M.10.1101/1046532017-03-01
HiCPlus: Resolution Enhancement of Hi-C interaction heatmapZhang, Y., An, L., Hu, M., Tang, J., Yue, F.10.1101/1126312017-03-01
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactionsWang, Y., Zhang, B., Zhang, L., An, L., Xu, J., Li, D., Choudhary, M. N., Li, Y., Hu, M., Hardison, R., Wang, T., Yue, F.10.1101/1122682017-02-27
A fluorogenic nanobody array tag for prolonged single molecule imaging in live cellsGhosh, R., Draper, W., Franklin, J. M., Shi, Q., Liphardt, J.10.1101/1116902017-02-27
p53 dynamically directs TFIID assembly on target gene promotersColeman, R. A., Qiao, Z., Singh, S. K., Peng, C. S., Cianfrocco, M., Zhang, Z., Piasecka, A., Aldeborgh, H., Basishvili, G., Liu, W.-L.10.1101/0830142017-02-24
Real-time chromatin dynamics at the single gene levelduring transcription activationGermier, T., Kocanova, S., Walther, N., Bancaud, A., Shaban, H. A., Sellou, H., Politi, A., Ellenberg, J., Gallardo, F., Bystricky, K.10.1101/1111792017-02-23
Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at EnhancersYan, J., Chen, S.-A. A., Local, A., Liu, T., Qiu, Y., Lee, A.-Y., Jung, I., Preissl, S., Rivera, C. M., Wang, C., Ishii, H., Fang, R., Ye, Z., Ge, K., Hu, M., Ren, B.10.1101/1102392017-02-21
Reversed graph embedding resolves complex single-cell developmental trajectoriesQiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H., Trapnell, C.10.1101/1106682017-02-21
Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexingCao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., Adey, A., Waterston, R. H., Trapnell, C., Shendure, J.10.1101/1048442017-02-02
Direct visualization of transcriptional activation by physical enhancer-promoter proximityChen, H., Fujioka, M., Jaynes, J. B., Gregor, T.10.1101/0995232017-01-31
The 4D Nucleome ProjectDekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O'Shea, C. C., Park, P. J., Ren, B., Ritland, J. C., Shendure, J., Zhong, S., The 4D Nucleome Network10.1101/1034992017-01-26
PGS: a dynamic and automated population-based genome structure softwareHua, N., Tjong, H., Shin, H., Gong, K., Zhou, X. J., Alber, F.10.1101/1033582017-01-26
Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISHTakei, Y., Shah, S., Harvey, S., Qi, L. S., Cai, L.10.1101/1014772017-01-18
The 3D genome organization of Drosophila melanogaster through data integrationLi, Q., Tjong, H., Li, X., Gong, K., Zhou, X. J., Chiolo, I., Alber, F.10.1101/0999112017-01-15
Comprehensive characterization of neutrophil genome topologyZhu, Y., Gong, K., Denholtz, M., Chandra, V., Kamps, M. P., Alber, F., Murre, C.10.1101/1001982017-01-15
Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction MapEagen, K. P., Lieberman Aiden, E., Kornberg, R. D.10.1101/0998042017-01-12
Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalizationNora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L., Bruneau, B.10.1101/0958022017-01-09
Cohesin dependent compaction of mitotic chromosomesSchalbetter, S. A., Goloborodko, A., Fudenberg, G., Belton, J. M., Miles, C., Yu, M., Dekker, J., Mirny, L., Baxter, J.10.1101/0949462016-12-17
Two independent modes of chromosome organization are revealed by cohesin removalSchwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C., Mirny, L., Spitz, F.10.1101/0941852016-12-15
Cell cycle dynamics of chromosomal organisation at single-cell resolutionNagano, T., Lubling, Y., Varnai, C., Dudley, C., Leung, W., Baran, Y., Mandelson Cohen, N., Wingett, S., Fraser, P., Tanay, A.10.1101/0944662016-12-15
CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct DynamicsHansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., Darzacq, X.10.1101/0934762016-12-13
The dynamic three-dimensional organization of the diploid yeast genomeKim, S., Liachko, I., Brickner, D. G., Cook, K., Noble, W. S., Brickner, J. H., Shendure, J., Dunham, M.10.1101/0918272016-12-05
HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATIONBelaghzal, H., Dekker, J., Gibcus, J. H.10.1101/0900012016-11-27
Detecting hierarchical 3-D genome domain reconfiguration with network modularityNorton, H. K., Huang, H., Emerson, D. J., Kim, J., Gu, S., Bassett, D. S., Phillips-Cremins, J. E.10.1101/0890112016-11-22
Calibrating photon counts from a single imageHeintzmann, R., Relich, P. K., Nieuwenhuizen, R. P. J., Lidke, K. A., Rieger, B.-2016-11-17
Visualizing adenosine to inosine RNA editing in single mammalian cellsMellis, I. A., Gupte, R. K., Raj, A., Rouhanifard, S. H.10.1101/0881462016-11-16
Software tools for visualizing Hi-C dataYardimci, G. G., Noble, W. S.10.1101/0860172016-11-07
The p150N domain of Chromatin Assembly Factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layerMatheson, T., Kaufman, P.10.1101/0823392016-10-21
FISH-ing for captured contacts: towards reconciling FISH and 3CFudenberg, G., Imakaev, M.10.1101/0814482016-10-17
Comparative analysis of 2D and 3D distance measurements to study spatial genome organizationElizabeth Finn, Gianluca Pegoraro, Sigal Shachar, Tom Misteli10.1101/0768932016-09-23
MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQRongxin Fang, Miao Yu, Guoqiang Li, Sora Chee, Tristin Liu, Anthony Schmitt, Bing Ren10.1101/0742942016-09-09
Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genomeTsung-Han Hsieh, Geoffrey Fudenberg, Anton Goloborodko, Oliver Rando10.1101/0713572016-08-24
A Dynamic Mode of Mitotic Bookmarking by Transcription FactorsSheila S Teves, Luye An, Anders S Hansen, Liangqi Xie, Xavier Darzacq, Robert Tjian10.1101/0664642016-08-01
Massively multiplex single-cell Hi-CVijay Ramani, Xinxian Deng, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure10.1101/0650522016-07-23
Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolutionAmit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar10.1101/0540312016-05-18
Formation of Chromosomal Domains by Loop ExtrusionGeoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny10.1101/0246202016-03-15
Compaction and segregation of sister chromatids via active loop extrusionAnton Goloborodko, Maxim V. Imakaev, John F. Marko, Leonid A. Mirny10.1101/0382812016-01-30
RTFBSDB: an integrated framework for transcription factor binding site analysisZhong Wang, Andre L Martins, Charles G Danko10.1101/0360532016-01-06