A citation-based method for searching scientific literature

Polina Belokopytova, Veniamin Fishman. Front Genet 2021
Times Cited: 6







List of co-cited articles
26 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
66

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
50


Quantitative prediction of enhancer-promoter interactions.
Polina S Belokopytova, Miroslav A Nuriddinov, Evgeniy A Mozheiko, Daniil Fishman, Veniamin Fishman. Genome Res 2020
19
50

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
33

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
33

Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing.
Li Li, Xiaowen Lyu, Chunhui Hou, Naomi Takenaka, Huy Q Nguyen, Chin-Tong Ong, Caelin Cubeñas-Potts, Ming Hu, Elissa P Lei, Giovanni Bosco,[...]. Mol Cell 2015
186
33

Identification of hierarchical chromatin domains.
Caleb Weinreb, Benjamin J Raphael. Bioinformatics 2016
82
33

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
411
33

A high-resolution map of the three-dimensional chromatin interactome in human cells.
Fulai Jin, Yan Li, Jesse R Dixon, Siddarth Selvaraj, Zhen Ye, Ah Young Lee, Chia-An Yen, Anthony D Schmitt, Celso A Espinoza, Bing Ren. Nature 2013
748
33


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
33

On the existence and functionality of topologically associating domains.
Jonathan A Beagan, Jennifer E Phillips-Cremins. Nat Genet 2020
100
33

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J Filion, Marc A Marti-Renom. PLoS Comput Biol 2017
124
33


Recent evidence that TADs and chromatin loops are dynamic structures.
Anders S Hansen, Claudia Cattoglio, Xavier Darzacq, Robert Tjian. Nucleus 2018
104
33

Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries.
James H Sun, Linda Zhou, Daniel J Emerson, Sai A Phyo, Katelyn R Titus, Wanfeng Gong, Thomas G Gilgenast, Jonathan A Beagan, Beverly L Davidson, Flora Tassone,[...]. Cell 2018
88
33

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.
Zhonghui Tang, Oscar Junhong Luo, Xingwang Li, Meizhen Zheng, Jacqueline Jufen Zhu, Przemyslaw Szalaj, Pawel Trzaskoma, Adriana Magalska, Jakub Wlodarczyk, Blazej Ruszczycki,[...]. Cell 2015
529
33

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
Neva C Durand, James T Robinson, Muhammad S Shamim, Ido Machol, Jill P Mesirov, Eric S Lander, Erez Lieberman Aiden. Cell Syst 2016
484
33

Three-dimensional folding and functional organization principles of the Drosophila genome.
Tom Sexton, Eitan Yaffe, Ephraim Kenigsberg, Frédéric Bantignies, Benjamin Leblanc, Michael Hoichman, Hugues Parrinello, Amos Tanay, Giacomo Cavalli. Cell 2012
33

Two major mechanisms of chromosome organization.
Leonid A Mirny, Maxim Imakaev, Nezar Abdennur. Curr Opin Cell Biol 2019
77
33

Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.
Huan Tao, Hao Li, Kang Xu, Hao Hong, Shuai Jiang, Guifang Du, Junting Wang, Yu Sun, Xin Huang, Yang Ding,[...]. Brief Bioinform 2021
5
40

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
129
33

Formation of new chromatin domains determines pathogenicity of genomic duplications.
Martin Franke, Daniel M Ibrahim, Guillaume Andrey, Wibke Schwarzer, Verena Heinrich, Robert Schöpflin, Katerina Kraft, Rieke Kempfer, Ivana Jerković, Wing-Lee Chan,[...]. Nature 2016
343
33

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
782
33

Multiscale 3D Genome Rewiring during Mouse Neural Development.
Boyan Bonev, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L Papadopoulos, Yaniv Lubling, Xiaole Xu, Xiaodan Lv, Jean-Philippe Hugnot, Amos Tanay,[...]. Cell 2017
545
33

Quantitative modeling of transcription factor binding specificities using DNA shape.
Tianyin Zhou, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard S Mann, Harmen J Bussemaker, Raluca Gordân, Remo Rohs. Proc Natl Acad Sci U S A 2015
131
16

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
Morgane Thomas-Chollier, Andrew Hufton, Matthias Heinig, Sean O'Keeffe, Nassim El Masri, Helge G Roider, Thomas Manke, Martin Vingron. Nat Protoc 2011
138
16


A critical assessment of topologically associating domain prediction tools.
Rola Dali, Mathieu Blanchette. Nucleic Acids Res 2017
65
16

Organization and function of the 3D genome.
Boyan Bonev, Giacomo Cavalli. Nat Rev Genet 2016
426
16

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.
Elissavet Kentepozidou, Sarah J Aitken, Christine Feig, Klara Stefflova, Ximena Ibarra-Soria, Duncan T Odom, Maša Roller, Paul Flicek. Genome Biol 2020
38
16

Understanding the 3D genome: Emerging impacts on human disease.
Anton Krumm, Zhijun Duan. Semin Cell Dev Biol 2019
28
16

Analysis of the relationship between coexpression domains and chromatin 3D organization.
María E Soler-Oliva, José A Guerrero-Martínez, Valentina Bachetti, José C Reyes. PLoS Comput Biol 2017
23
16

Gene Positioning Effects on Expression in Eukaryotes.
Huy Q Nguyen, Giovanni Bosco. Annu Rev Genet 2015
26
16

Cancer Is Associated with Alterations in the Three-Dimensional Organization of the Genome.
Lifei Li, Nicolai K H Barth, Christian Pilarsky, Leila Taher. Cancers (Basel) 2019
8
16

TopDom: an efficient and deterministic method for identifying topological domains in genomes.
Hanjun Shin, Yi Shi, Chao Dai, Harianto Tjong, Ke Gong, Frank Alber, Xianghong Jasmine Zhou. Nucleic Acids Res 2016
119
16

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
Michael P Schnetz, Lusy Handoko, Batool Akhtar-Zaidi, Cynthia F Bartels, C Filipe Pereira, Amanda G Fisher, David J Adams, Paul Flicek, Gregory E Crawford, Thomas Laframboise,[...]. PLoS Genet 2010
180
16

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.
Kadir C Akdemir, Victoria T Le, Sahaana Chandran, Yilong Li, Roel G Verhaak, Rameen Beroukhim, Peter J Campbell, Lynda Chin, Jesse R Dixon, P Andrew Futreal. Nat Genet 2020
87
16

The macro and micro of chromosome conformation capture.
Viraat Y Goel, Anders S Hansen. Wiley Interdiscip Rev Dev Biol 2021
11
16



Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.
Matthew Halvorsen, Ruth Huh, Nikolay Oskolkov, Jia Wen, Sergiu Netotea, Paola Giusti-Rodriguez, Robert Karlsson, Julien Bryois, Björn Nystedt, Adam Ameur,[...]. Nat Commun 2020
22
16

TADs as modular and dynamic units for gene regulation by hormones.
François Le Dily, Miguel Beato. FEBS Lett 2015
13
16

Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors.
MuhChyi Chai, Tsukasa Sanosaka, Hironobu Okuno, Zhi Zhou, Ikuko Koya, Satoe Banno, Tomoko Andoh-Noda, Yoshikuni Tabata, Rieko Shimamura, Tetsutaro Hayashi,[...]. Genes Dev 2018
19
16

Comparison of computational methods for Hi-C data analysis.
Mattia Forcato, Chiara Nicoletti, Koustav Pal, Carmen Maria Livi, Francesco Ferrari, Silvio Bicciato. Nat Methods 2017
156
16

TADBD: a sensitive and fast method for detection of typologically associated domain boundaries.
Hongqiang Lyu, Lin Li, Zhifang Wu, Tian Wang, Jiguang Zheng, Hongda Wang. Biotechniques 2020
3
33


Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.
Regina Z Cer, Duncan E Donohue, Uma S Mudunuri, Nuri A Temiz, Michael A Loss, Nathan J Starner, Goran N Halusa, Natalia Volfovsky, Ming Yi, Brian T Luke,[...]. Nucleic Acids Res 2013
79
16

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture.
Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal, Keji Yan, Yingying Lei, Liang Li, Yijun Ruan, Zhen F Fu,[...]. Nat Genet 2018
42
16


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.