A citation-based method for searching scientific literature

Ming-Wen Hu, Dong Won Kim, Sheng Liu, Donald J Zack, Seth Blackshaw, Jiang Qian. PLoS Comput Biol 2019
Times Cited: 3







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



Times Cited
  Times     Co-cited
Similarity


Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis.
Xiaoying Fan, Ji Dong, Suijuan Zhong, Yuan Wei, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao,[...]. Cell Res 2018
68
66

scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
170
66

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
670
66

SAIC: an iterative clustering approach for analysis of single cell RNA-seq data.
Lu Yang, Jiancheng Liu, Qiang Lu, Arthur D Riggs, Xiwei Wu. BMC Genomics 2017
11
66

SC3: consensus clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green,[...]. Nat Methods 2017
447
66

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.
Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti, Serafim Batzoglou. Nat Methods 2017
192
66

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
66

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods.
Monika Krzak, Yordan Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini. Front Genet 2019
7
66

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
66

Discovery of rare cells from voluminous single cell expression data.
Aashi Jindal, Prashant Gupta, Jayadeva, Debarka Sengupta. Nat Commun 2018
24
66

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
209
66

Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development.
Meelad M Dawlaty, Achim Breiling, Thuc Le, Günter Raddatz, M Inmaculada Barrasa, Albert W Cheng, Qing Gao, Benjamin E Powell, Zhe Li, Mingjiang Xu,[...]. Dev Cell 2013
279
33

Reprogramming mammalian somatic cells.
N Rodriguez-Osorio, R Urrego, J B Cibelli, K Eilertsen, E Memili. Theriogenology 2012
65
33

Cloning of Macaque Monkeys by Somatic Cell Nuclear Transfer.
Zhen Liu, Yijun Cai, Yan Wang, Yanhong Nie, Chenchen Zhang, Yuting Xu, Xiaotong Zhang, Yong Lu, Zhanyang Wang, Muming Poo,[...]. Cell 2018
24
33

Gadd45a promotes DNA demethylation through TDG.
Zheng Li, Tian-Peng Gu, Alain R Weber, Jia-Zhen Shen, Bin-Zhong Li, Zhi-Guo Xie, Ruichuan Yin, Fan Guo, Xiaomeng Liu, Fuchou Tang,[...]. Nucleic Acids Res 2015
51
33

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
287
33

Inhibition of Aberrant DNA Re-methylation Improves Post-implantation Development of Somatic Cell Nuclear Transfer Embryos.
Rui Gao, Chenfei Wang, Yawei Gao, Wenchao Xiu, Jiayu Chen, Xiaochen Kou, Yanhong Zhao, Yuhan Liao, Dandan Bai, Zhibin Qiao,[...]. Cell Stem Cell 2018
31
33


Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq.
Dylan Kotliar, Adrian Veres, M Aurel Nagy, Shervin Tabrizi, Eran Hodis, Douglas A Melton, Pardis C Sabeti. Elife 2019
36
33

Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming.
Francesca Aguilo, Fan Zhang, Ana Sancho, Miguel Fidalgo, Serena Di Cecilia, Ajay Vashisht, Dung-Fang Lee, Chih-Hung Chen, Madhumitha Rengasamy, Blanca Andino,[...]. Cell Stem Cell 2015
149
33

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
33


Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals.
Hui Zheng, Bo Huang, Bingjie Zhang, Yunlong Xiang, Zhenhai Du, Qianhua Xu, Yuanyuan Li, Qiujun Wang, Jing Ma, Xu Peng,[...]. Mol Cell 2016
149
33

Producing primate embryonic stem cells by somatic cell nuclear transfer.
J A Byrne, D A Pedersen, L L Clepper, M Nelson, W G Sanger, S Gokhale, D P Wolf, S M Mitalipov. Nature 2007
335
33

Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing.
Suying Cao, Jianyong Han, Jun Wu, Qiuyan Li, Shichao Liu, Wei Zhang, Yangli Pei, Xiaoan Ruan, Zhonghua Liu, Xumin Wang,[...]. BMC Genomics 2014
81
33

iRNAD: a computational tool for identifying D modification sites in RNA sequence.
Zhao-Chun Xu, Peng-Mian Feng, Hui Yang, Wang-Ren Qiu, Wei Chen, Hao Lin. Bioinformatics 2019
40
33

Exploring timing activation of functional pathway based on differential co-expression analysis in preimplantation embryogenesis.
Yongchun Zuo, Guanghua Su, Shanshan Wang, Lei Yang, Mingzhi Liao, Zhuying Wei, Chunling Bai, Guangpeng Li. Oncotarget 2016
18
33

Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation.
Shogo Matoba, Yuting Liu, Falong Lu, Kumiko A Iwabuchi, Li Shen, Azusa Inoue, Yi Zhang. Cell 2014
213
33

Transcription factor POU6F1 is important for proliferation of clear cell adenocarcinoma of the ovary and is a potential new molecular target.
Nao Suzuki, Norihito Yoshioka, Atsushi Uekawa, Noriomi Matsumura, Akiko Tozawa, Jyunki Koike, Ikuo Konishi, Kazushige Kiguchi, Bunpei Ishizuka. Int J Gynecol Cancer 2010
9
33

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.
Ashraful Haque, Jessica Engel, Sarah A Teichmann, Tapio Lönnberg. Genome Med 2017
204
33

Id proteins in development, cell cycle and cancer.
Marianna B Ruzinova, Robert Benezra. Trends Cell Biol 2003
453
33

EmExplorer: a database for exploring time activation of gene expression in mammalian embryos.
Bosu Hu, Lei Zheng, Chunshen Long, Mingmin Song, Tao Li, Lei Yang, Yongchun Zuo. Open Biol 2019
19
33

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing.
Andrew Keniry, Linden J Gearing, Natasha Jansz, Joy Liu, Aliaksei Z Holik, Peter F Hickey, Sarah A Kinkel, Darcy L Moore, Kelsey Breslin, Kelan Chen,[...]. Epigenetics Chromatin 2016
39
33

RNAi-mediated knockdown of Xist can rescue the impaired postimplantation development of cloned mouse embryos.
Shogo Matoba, Kimiko Inoue, Takashi Kohda, Michihiko Sugimoto, Eiji Mizutani, Narumi Ogonuki, Toshinobu Nakamura, Kuniya Abe, Toru Nakano, Fumitoshi Ishino,[...]. Proc Natl Acad Sci U S A 2011
89
33

Essential roles of HDAC1 and 2 in lineage development and genome-wide DNA methylation during mouse preimplantation development.
Panpan Zhao, Huanan Wang, Han Wang, Yanna Dang, Lei Luo, Shuang Li, Yan Shi, Lefeng Wang, Shaohua Wang, Jesse Mager,[...]. Epigenetics 2020
8
33

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing.
Wenqiang Liu, Xiaoyu Liu, Chenfei Wang, Yawei Gao, Rui Gao, Xiaochen Kou, Yanhong Zhao, Jingyi Li, You Wu, Wenchao Xiu,[...]. Cell Discov 2016
91
33

Recent advances in dynamic m6A RNA modification.
Guangchao Cao, Hua-Bing Li, Zhinan Yin, Richard A Flavell. Open Biol 2016
119
33


The co-regulatory networks of tumor suppressor genes, oncogenes, and miRNAs in colorectal cancer.
Martha L Slattery, Jennifer S Herrick, Lila E Mullany, Wade S Samowitz, John R Sevens, Lori Sakoda, Roger K Wolff. Genes Chromosomes Cancer 2017
45
33

iRNA-m7G: Identifying N7-methylguanosine Sites by Fusing Multiple Features.
Wei Chen, Pengmian Feng, Xiaoming Song, Hao Lv, Hao Lin. Mol Ther Nucleic Acids 2019
39
33

Tough beginnings: alterations in the transcriptome of cloned embryos during the first two cell cycles.
Rita Vassena, Zhiming Han, Shaorong Gao, Donald A Baldwin, Richard M Schultz, Keith E Latham. Dev Biol 2007
54
33

Recent Advances in Machine Learning Methods for Predicting Heat Shock Proteins.
Wei Chen, Pengmian Feng, Tao Liu, Dianchuan Jin. Curr Drug Metab 2019
46
33

Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells.
Geppino Falco, Sung-Lim Lee, Ilaria Stanghellini, Uwem C Bassey, Toshio Hamatani, Minoru S H Ko. Dev Biol 2007
151
33

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg. Nat Protoc 2016
33

A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data.
Sanghamitra Bandyopadhyay, Saurav Mallik, Anirban Mukhopadhyay. IEEE/ACM Trans Comput Biol Bioinform 2014
41
33


Viable offspring derived from fetal and adult mammalian cells.
I Wilmut, A E Schnieke, J McWhir, A J Kind, K H Campbell. Nature 1997
33

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
Anoop P Patel, Itay Tirosh, John J Trombetta, Alex K Shalek, Shawn M Gillespie, Hiroaki Wakimoto, Daniel P Cahill, Brian V Nahed, William T Curry, Robert L Martuza,[...]. Science 2014
33

KDM6A and KDM6B play contrasting roles in nuclear transfer embryos revealed by MERVL reporter system.
Lei Yang, Lishuang Song, Xuefei Liu, Lige Bai, Guangpeng Li. EMBO Rep 2018
21
33

Recent advancements in cloning by somatic cell nuclear transfer.
Atsuo Ogura, Kimiko Inoue, Teruhiko Wakayama. Philos Trans R Soc Lond B Biol Sci 2013
112
33


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.