A citation-based method for searching scientific literature

Silvia Galan, Nick Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, Juan M Vaquerizas. Nat Genet 2020
Times Cited: 7







List of co-cited articles
41 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
Suhas S P Rao, Miriam H Huntley, Neva C Durand, Elena K Stamenova, Ivan D Bochkov, James T Robinson, Adrian L Sanborn, Ido Machol, Arina D Omer, Eric S Lander,[...]. Cell 2014
100

Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S Liu, Bing Ren. Nature 2012
85

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
71

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
Neva C Durand, Muhammad S Shamim, Ido Machol, Suhas S P Rao, Miriam H Huntley, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
942
57

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Nicolas Servant, Nelle Varoquaux, Bryan R Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot. Genome Biol 2015
876
42


HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Maxwell R Mumbach, Adam J Rubin, Ryan A Flynn, Chao Dai, Paul A Khavari, William J Greenleaf, Howard Y Chang. Nat Methods 2016
515
42

Visualizing DNA folding and RNA in embryos at single-cell resolution.
Leslie J Mateo, Sedona E Murphy, Antonina Hafner, Isaac S Cinquini, Carly A Walker, Alistair N Boettiger. Nature 2019
183
42

3D structures of individual mammalian genomes studied by single-cell Hi-C.
Tim J Stevens, David Lando, Srinjan Basu, Liam P Atkinson, Yang Cao, Steven F Lee, Martin Leeb, Kai J Wohlfahrt, Wayne Boucher, Aoife O'Shaughnessy-Kirwan,[...]. Nature 2017
437
42

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.
Mohamed Nadhir Djekidel, Yang Chen, Michael Q Zhang. Genome Res 2018
28
28

Organization and function of the 3D genome.
Boyan Bonev, Giacomo Cavalli. Nat Rev Genet 2016
453
28

Cooler: scalable storage for Hi-C data and other genomically labeled arrays.
Nezar Abdennur, Leonid A Mirny. Bioinformatics 2020
157
28

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets.
John C Stansfield, Kellen G Cresswell, Vladimir I Vladimirov, Mikhail G Dozmorov. BMC Bioinformatics 2018
49
28

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.
Anthony D Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L Barr,[...]. Cell Rep 2016
413
28

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
897
28

An oestrogen-receptor-alpha-bound human chromatin interactome.
Melissa J Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei,[...]. Nature 2009
28

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
28

Cell-cycle dynamics of chromosomal organization at single-cell resolution.
Takashi Nagano, Yaniv Lubling, Csilla Várnai, Carmel Dudley, Wing Leung, Yael Baran, Netta Mendelson Cohen, Steven Wingett, Peter Fraser, Amos Tanay. Nature 2017
377
28

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome.
Tsung-Han S Hsieh, Geoffrey Fudenberg, Anton Goloborodko, Oliver J Rando. Nat Methods 2016
86
28

YY1 Is a Structural Regulator of Enhancer-Promoter Loops.
Abraham S Weintraub, Charles H Li, Alicia V Zamudio, Alla A Sigova, Nancy M Hannett, Daniel S Day, Brian J Abraham, Malkiel A Cohen, Behnam Nabet, Dennis L Buckley,[...]. Cell 2017
434
28

Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.
Darío G Lupiáñez, Katerina Kraft, Verena Heinrich, Peter Krawitz, Francesco Brancati, Eva Klopocki, Denise Horn, Hülya Kayserili, John M Opitz, Renata Laxova,[...]. Cell 2015
28

Condensin-driven remodelling of X chromosome topology during dosage compensation.
Emily Crane, Qian Bian, Rachel Patton McCord, Bryan R Lajoie, Bayly S Wheeler, Edward J Ralston, Satoru Uzawa, Job Dekker, Barbara J Meyer. Nature 2015
440
28

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.
Diego I Cattoni, Andrés M Cardozo Gizzi, Mariya Georgieva, Marco Di Stefano, Alessandro Valeri, Delphine Chamousset, Christophe Houbron, Stephanie Déjardin, Jean-Bernard Fiche, Inma González,[...]. Nat Commun 2017
89
28

Structural variation in the 3D genome.
Malte Spielmann, Darío G Lupiáñez, Stefan Mundlos. Nat Rev Genet 2018
264
28

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
28

Ultrastructural Details of Mammalian Chromosome Architecture.
Nils Krietenstein, Sameer Abraham, Sergey V Venev, Nezar Abdennur, Johan Gibcus, Tsung-Han S Hsieh, Krishna Mohan Parsi, Liyan Yang, René Maehr, Leonid A Mirny,[...]. Mol Cell 2020
163
28

Insulator dysfunction and oncogene activation in IDH mutant gliomas.
William A Flavahan, Yotam Drier, Brian B Liau, Shawn M Gillespie, Andrew S Venteicher, Anat O Stemmer-Rachamimov, Mario L Suvà, Bradley E Bernstein. Nature 2016
708
28

Cohesin Loss Eliminates All Loop Domains.
Suhas S P Rao, Su-Chen Huang, Brian Glenn St Hilaire, Jesse M Engreitz, Elizabeth M Perez, Kyong-Rim Kieffer-Kwon, Adrian L Sanborn, Sarah E Johnstone, Gavin D Bascom, Ivan D Bochkov,[...]. Cell 2017
842
28

Coactivator condensation at super-enhancers links phase separation and gene control.
Benjamin R Sabari, Alessandra Dall'Agnese, Ann Boija, Isaac A Klein, Eliot L Coffey, Krishna Shrinivas, Brian J Abraham, Nancy M Hannett, Alicia V Zamudio, John C Manteiga,[...]. Science 2018
28

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.
Tsung-Han S Hsieh, Claudia Cattoglio, Elena Slobodyanyuk, Anders S Hansen, Oliver J Rando, Robert Tjian, Xavier Darzacq. Mol Cell 2020
167
28

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin.
Jun-Han Su, Pu Zheng, Seon S Kinrot, Bogdan Bintu, Xiaowei Zhuang. Cell 2020
140
28

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.
Ferhat Ay, Evelien M Bunnik, Nelle Varoquaux, Sebastiaan M Bol, Jacques Prudhomme, Jean-Philippe Vert, William Stafford Noble, Karine G Le Roch. Genome Res 2014
137
28

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution.
Qiancheng You, Anthony Youzhi Cheng, Xi Gu, Bryan T Harada, Miao Yu, Tong Wu, Bing Ren, Zhengqing Ouyang, Chuan He. Nat Biotechnol 2021
20
28

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.
Tao Yang, Feipeng Zhang, Galip Gürkan Yardımcı, Fan Song, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. Genome Res 2017
173
28

A three-dimensional model of the yeast genome.
Zhijun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung Kim, Choli Lee, Jay Shendure, Stanley Fields, C Anthony Blau, William S Noble. Nature 2010
645
28

Spatial organization of chromatin domains and compartments in single chromosomes.
Siyuan Wang, Jun-Han Su, Brian J Beliveau, Bogdan Bintu, Jeffrey R Moffitt, Chao-ting Wu, Xiaowei Zhuang. Science 2016
314
28

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
28

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.
Judith H I Haarhuis, Robin H van der Weide, Vincent A Blomen, J Omar Yáñez-Cuna, Mario Amendola, Marjon S van Ruiten, Peter H L Krijger, Hans Teunissen, René H Medema, Bas van Steensel,[...]. Cell 2017
390
28

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
28

Systematic evaluation of chromosome conformation capture assays.
Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, Sergey V Venev, Nils Krietenstein, Krishna Mohan Parsi, Hakan Ozadam, Marlies E Oomen, Ankita Nand, Hui Mao,[...]. Nat Methods 2021
26
28

Multiscale and integrative single-cell Hi-C analysis with Higashi.
Ruochi Zhang, Tianming Zhou, Jian Ma. Nat Biotechnol 2022
21
28

Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway.
Natasha Jansz, Tatyana Nesterova, Andrew Keniry, Megan Iminitoff, Peter F Hickey, Greta Pintacuda, Osamu Masui, Simon Kobelke, Niall Geoghegan, Kelsey A Breslin,[...]. Cell Rep 2018
36
14

The cohesin complex and its roles in chromosome biology.
Jan-Michael Peters, Antonio Tedeschi, Julia Schmitz. Genes Dev 2008
346
14

HiCNorm: removing biases in Hi-C data via Poisson regression.
Ming Hu, Ke Deng, Siddarth Selvaraj, Zhaohui Qin, Bing Ren, Jun S Liu. Bioinformatics 2012
145
14

The 3D genome in transcriptional regulation and pluripotency.
David U Gorkin, Danny Leung, Bing Ren. Cell Stem Cell 2014
239
14

Chromatin loops as allosteric modulators of enhancer-promoter interactions.
Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, Leonid A Mirny. PLoS Comput Biol 2014
71
14

The Three-Dimensional Organization of Mammalian Genomes.
Miao Yu, Bing Ren. Annu Rev Cell Dev Biol 2017
182
14

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming.
Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François Le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero,[...]. Nat Genet 2018
183
14

Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast.
Kyoung-Dong Kim, Hideki Tanizawa, Osamu Iwasaki, Ken-Ichi Noma. Nat Genet 2016
49
14

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles.
Zhenjia Wang, Mete Civelek, Clint L Miller, Nathan C Sheffield, Michael J Guertin, Chongzhi Zang. Bioinformatics 2018
47
14


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.