A citation-based method for searching scientific literature

Wei Gan, Juan Luo, Yi Zhou Li, Jia Li Guo, Min Zhu, Meng Long Li. BMC Genomics 2019
Times Cited: 9







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



Times Cited
  Times     Co-cited
Similarity


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
77

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

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
66

Predicting chromatin organization using histone marks.
Jialiang Huang, Eugenio Marco, Luca Pinello, Guo-Cheng Yuan. Genome Biol 2015
66
44

Identification of hierarchical chromatin domains.
Caleb Weinreb, Benjamin J Raphael. Bioinformatics 2016
85
44




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
422
33

Long-range enhancer-promoter contacts in gene expression control.
Stefan Schoenfelder, Peter Fraser. Nat Rev Genet 2019
350
22

hicGAN infers super resolution Hi-C data with generative adversarial networks.
Qiao Liu, Hairong Lv, Rui Jiang. Bioinformatics 2019
23
22

Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.
Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma. Quant Biol 2019
31
22

Quantitative prediction of enhancer-promoter interactions.
Polina S Belokopytova, Miroslav A Nuriddinov, Evgeniy A Mozheiko, Daniil Fishman, Veniamin Fishman. Genome Res 2020
20
22

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.
Sean Whalen, Rebecca M Truty, Katherine S Pollard. Nat Genet 2016
205
22

Formation of Chromosomal Domains by Loop Extrusion.
Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny. Cell Rep 2016
847
22

Prediction of enhancer-promoter interactions via natural language processing.
Wanwen Zeng, Mengmeng Wu, Rui Jiang. BMC Genomics 2018
30
22


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
141
22

Capturing chromosome conformation.
Job Dekker, Karsten Rippe, Martijn Dekker, Nancy Kleckner. Science 2002
22


Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.
Tsung-Han S Hsieh, Assaf Weiner, Bryan Lajoie, Job Dekker, Nir Friedman, Oliver J Rando. Cell 2015
321
22

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
160
22

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.
Adrian L Sanborn, Suhas S P Rao, Su-Chen Huang, Neva C Durand, Miriam H Huntley, Andrew I Jewett, Ivan D Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li,[...]. Proc Natl Acad Sci U S A 2015
860
22

An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning.
Fang Jing, Shao-Wu Zhang, Zhen Cao, Shihua Zhang. IEEE/ACM Trans Comput Biol Bioinform 2021
11
22

Dense neural networks for predicting chromatin conformation.
Pau Farré, Alexandre Heurteau, Olivier Cuvier, Eldon Emberly. BMC Bioinformatics 2018
6
33

Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features.
Yan Kai, Jaclyn Andricovich, Zhouhao Zeng, Jun Zhu, Alexandros Tzatsos, Weiqun Peng. Nat Commun 2018
23
22

Predicting 3D genome folding from DNA sequence with Akita.
Geoff Fudenberg, David R Kelley, Katherine S Pollard. Nat Methods 2020
47
22


DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.
Wenran Li, Wing Hung Wong, Rui Jiang. Nucleic Acids Res 2019
51
22

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.
Hang Xu, Shijie Zhang, Xianfu Yi, Dariusz Plewczynski, Mulin Jun Li. Comput Struct Biotechnol J 2020
19
22

Histone H3K27ac separates active from poised enhancers and predicts developmental state.
Menno P Creyghton, Albert W Cheng, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp,[...]. Proc Natl Acad Sci U S A 2010
22

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
22

Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Elphège P Nora, Bryan R Lajoie, Edda G Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L van Berkum, Johannes Meisig, John Sedat,[...]. Nature 2012
22

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
22

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries.
Yixiao Gong, Charalampos Lazaris, Theodore Sakellaropoulos, Aurelie Lozano, Prabhanjan Kambadur, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos. Nat Commun 2018
61
22

Breaking TADs: How Alterations of Chromatin Domains Result in Disease.
Darío G Lupiáñez, Malte Spielmann, Stefan Mundlos. Trends Genet 2016
223
22

Evolutionarily Conserved Principles Predict 3D Chromatin Organization.
M Jordan Rowley, Michael H Nichols, Xiaowen Lyu, Masami Ando-Kuri, I Sarahi M Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G Corces. Mol Cell 2017
259
22

High-resolution TADs reveal DNA sequences underlying genome organization in flies.
Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar, Thomas Manke. Nat Commun 2018
280
22


Predicting Genome Architecture: Challenges and Solutions.
Polina Belokopytova, Veniamin Fishman. Front Genet 2021
6
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
755
22

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
25

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
124
22

On the existence and functionality of topologically associating domains.
Jonathan A Beagan, Jennifer E Phillips-Cremins. Nat Genet 2020
109
22

Recent evidence that TADs and chromatin loops are dynamic structures.
Anders S Hansen, Claudia Cattoglio, Xavier Darzacq, Robert Tjian. Nucleus 2018
110
22

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.
Phillippa C Taberlay, Joanna Achinger-Kawecka, Aaron T L Lun, Fabian A Buske, Kenneth Sabir, Cathryn M Gould, Elena Zotenko, Saul A Bert, Katherine A Giles, Denis C Bauer,[...]. Genome Res 2016
162
22

TAD boundary and strength prediction by integrating sequence and epigenetic profile information.
Yunlong Wang, Yaqi Liu, Qian Xu, Yao Xu, Kai Cao, Nan Deng, Ruimin Wang, Xueying Zhang, Ruiqin Zheng, Guoliang Li,[...]. Brief Bioinform 2021
5
40

Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Jennifer E Phillips-Cremins, Michael E G Sauria, Amartya Sanyal, Tatiana I Gerasimova, Bryan R Lajoie, Joshua S K Bell, Chin-Tong Ong, Tracy A Hookway, Changying Guo, Yuhua Sun,[...]. Cell 2013
761
22

Breaking TADs: insights into hierarchical genome organization.
Pedro P Rocha, Ramya Raviram, Richard Bonneau, Jane A Skok. Epigenomics 2015
28
11

Chromatin organization of transcribed genes in chicken polychromatic erythrocytes.
Sanzida Jahan, Tasnim H Beacon, Shihua He, Carolina Gonzalez, Wayne Xu, Geneviève P Delcuve, Shuo Jia, Pingzhao Hu, James R Davie. Gene 2019
7
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.