A citation-based method for searching scientific literature

Shengquan Chen, Guanao Yan, Wenyu Zhang, Jinzhao Li, Rui Jiang, Zhixiang Lin. Nat Commun 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Assessment of computational methods for the analysis of single-cell ATAC-seq data.
Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E Vinyard, Sara P Garcia, Kendell Clement, Miguel A Andrade-Navarro, Jason D Buenrostro, Luca Pinello. Genome Biol 2019
64
100

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
100

An atlas of dynamic chromatin landscapes in mouse fetal development.
David U Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, Andre Wildberg, Bo Ding,[...]. Nature 2020
50
50

Predicting enhancers with deep convolutional neural networks.
Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang. BMC Bioinformatics 2017
30
50

DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers.
Shengquan Chen, Mingxin Gan, Hairong Lv, Rui Jiang. Genomics Proteomics Bioinformatics 2021
2
50

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.
Anshul Kundaje, Sofia Kyriazopoulou-Panagiotopoulou, Max Libbrecht, Cheryl L Smith, Debasish Raha, Elliott E Winters, Steven M Johnson, Michael Snyder, Serafim Batzoglou, Arend Sidow. Genome Res 2012
118
50

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.
Jeremy Schwartzentruber, Andrey Korshunov, Xiao-Yang Liu, David T W Jones, Elke Pfaff, Karine Jacob, Dominik Sturm, Adam M Fontebasso, Dong-Anh Khuong Quang, Martje Tönjes,[...]. Nature 2012
50

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.
Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing,[...]. Nucleic Acids Res 2017
210
50

High-resolution mapping and characterization of open chromatin across the genome.
Alan P Boyle, Sean Davis, Hennady P Shulha, Paul Meltzer, Elliott H Margulies, Zhiping Weng, Terrence S Furey, Gregory E Crawford. Cell 2008
837
50

A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper, Jay Shendure. Nat Genet 2014
50


Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A Cusanovich, Riza Daza, Andrew Adey, Hannah A Pliner, Lena Christiansen, Kevin L Gunderson, Frank J Steemers, Cole Trapnell, Jay Shendure. Science 2015
486
50

A method for scoring the cell type-specific impacts of noncoding variants in personal genomes.
Wenran Li, Zhana Duren, Rui Jiang, Wing Hung Wong. Proc Natl Acad Sci U S A 2020
6
50

Chd1 regulates open chromatin and pluripotency of embryonic stem cells.
Alexandre Gaspar-Maia, Adi Alajem, Fanny Polesso, Rupa Sridharan, Mike J Mason, Amy Heidersbach, João Ramalho-Santos, Michael T McManus, Kathrin Plath, Eran Meshorer,[...]. Nature 2009
358
50

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.
Sam John, Peter J Sabo, Robert E Thurman, Myong-Hee Sung, Simon C Biddie, Thomas A Johnson, Gordon L Hager, John A Stamatoyannopoulos. Nat Genet 2011
622
50

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.
Aslıhan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf, Uwe Ohler. Genome Biol 2019
29
50

SilencerDB: a comprehensive database of silencers.
Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang. Nucleic Acids Res 2021
4
50

The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
50

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
Jeremy M Simon, Paul G Giresi, Ian J Davis, Jason D Lieb. Nat Protoc 2012
193
50

CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean-Pierre Kocher, Liguo Wang. Bioinformatics 2014
211
50


Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.
Jason D Buenrostro, M Ryan Corces, Caleb A Lareau, Beijing Wu, Alicia N Schep, Martin J Aryee, Ravindra Majeti, Howard Y Chang, William J Greenleaf. Cell 2018
206
50

Ensembl 2021.
Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai,[...]. Nucleic Acids Res 2021
135
50

Gene co-opening network deciphers gene functional relationships.
Wenran Li, Meng Wang, Jinghao Sun, Yong Wang, Rui Jiang. Mol Biosyst 2017
9
50

The cis-regulatory dynamics of embryonic development at single-cell resolution.
Darren A Cusanovich, James P Reddington, David A Garfield, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers,[...]. Nature 2018
132
50

Comprehensive analysis of single cell ATAC-seq data with SnapATAC.
Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K Shiau, Xinzhu Zhou, Fangming Xie,[...]. Nat Commun 2021
33
50

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms.
Diana C Hargreaves, Gerald R Crabtree. Cell Res 2011
511
50

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning.
Wenran Li, Wing Hung Wong, Rui Jiang. Nucleic Acids Res 2019
31
50

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.
Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts. Nat Methods 2019
84
50

DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets.
Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer. Nucleic Acids Res 2016
28
50

Chromatin accessibility and the regulatory epigenome.
Sandy L Klemm, Zohar Shipony, William J Greenleaf. Nat Rev Genet 2019
320
50

Single-cell ATAC-seq signal extraction and enhancement with SCATE.
Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji. Genome Biol 2020
7
50

ATACdb: a comprehensive human chromatin accessibility database.
Fan Wang, Xuefeng Bai, Yuezhu Wang, Yong Jiang, Bo Ai, Yong Zhang, Yuejuan Liu, Mingcong Xu, Qiuyu Wang, Xiaole Han,[...]. Nucleic Acids Res 2021
3
50

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
50

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013
50

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
50

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.
Rongbin Zheng, Changxin Wan, Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Chen-Hao Chen, Myles Brown, Xiaoyan Zhang, Clifford A Meyer,[...]. Nucleic Acids Res 2019
161
50

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul,[...]. Nature 2020
234
50

GTRD: a database on gene transcription regulation-2019 update.
Ivan Yevshin, Ruslan Sharipov, Semyon Kolmykov, Yury Kondrakhin, Fedor Kolpakov. Nucleic Acids Res 2019
79
50

The Encyclopedia of DNA elements (ENCODE): data portal update.
Carrie A Davis, Benjamin C Hitz, Cricket A Sloan, Esther T Chan, Jean M Davidson, Idan Gabdank, Jason A Hilton, Kriti Jain, Ulugbek K Baymuradov, Aditi K Narayanan,[...]. Nucleic Acids Res 2018
557
50


A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.
Darren A Cusanovich, Andrew J Hill, Delasa Aghamirzaie, Riza M Daza, Hannah A Pliner, Joel B Berletch, Galina N Filippova, Xingfan Huang, Lena Christiansen, William S DeWitt,[...]. Cell 2018
222
50

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.
Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, Xiaowei Zhuang. Proc Natl Acad Sci U S A 2019
125
50

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
50

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
242
50


Shared and distinct transcriptomic cell types across neocortical areas.
Bosiljka Tasic, Zizhen Yao, Lucas T Graybuck, Kimberly A Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N Economo, Sarada Viswanathan,[...]. Nature 2018
440
50


Molecular Architecture of the Mouse Nervous System.
Amit Zeisel, Hannah Hochgerner, Peter Lönnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Häring, Emelie Braun, Lars E Borm, Gioele La Manno,[...]. Cell 2018
755
50

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
50


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.