A citation-based method for searching scientific literature

Tian Tian, Jie Zhang, Xiang Lin, Zhi Wei, Hakon Hakonarson. Nat Commun 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
50

Deconstructing transcriptional heterogeneity in pluripotent stem cells.
Roshan M Kumar, Patrick Cahan, Alex K Shalek, Rahul Satija, AJay DaleyKeyser, Hu Li, Jin Zhang, Keith Pardee, David Gennert, John J Trombetta,[...]. Nature 2014
226
50

Computational approaches for interpreting scRNA-seq data.
Raghd Rostom, Valentine Svensson, Sarah A Teichmann, Gozde Kar. FEBS Lett 2017
49
50

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.
Lan Jiang, Huidong Chen, Luca Pinello, Guo-Cheng Yuan. Genome Biol 2016
105
50

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
50

(Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices.
Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita. IEEE/ACM Trans Comput Biol Bioinform 2020
13
50

PanoView: An iterative clustering method for single-cell RNA sequencing data.
Ming-Wen Hu, Dong Won Kim, Sheng Liu, Donald J Zack, Seth Blackshaw, Jiang Qian. PLoS Comput Biol 2019
5
50

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
346
50

Impact of similarity metrics on single-cell RNA-seq data clustering.
Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang, Pengyi Yang. Brief Bioinform 2019
31
50

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
482
50

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.
F William Townes, Stephanie C Hicks, Martin J Aryee, Rafael A Irizarry. Genome Biol 2019
71
50


Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.
J Gray Camp, Farhath Badsha, Marta Florio, Sabina Kanton, Tobias Gerber, Michaela Wilsch-Bräuninger, Eric Lewitus, Alex Sykes, Wulf Hevers, Madeline Lancaster,[...]. Proc Natl Acad Sci U S A 2015
453
50

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
50

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis.
Geng Chen, Baitang Ning, Tieliu Shi. Front Genet 2019
180
50

Integrated single cell data analysis reveals cell specific networks and novel coactivation markers.
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang. BMC Syst Biol 2016
11
50

A systematic performance evaluation of clustering methods for single-cell RNA-seq data.
Angelo Duò, Mark D Robinson, Charlotte Soneson. F1000Res 2018
93
50

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
605
50


Spectral clustering based on learning similarity matrix.
Seyoung Park, Hongyu Zhao. Bioinformatics 2018
18
50

SPARSim single cell: a count data simulator for scRNA-seq data.
Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo. Bioinformatics 2020
6
50

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.
Bosiljka Tasic, Vilas Menon, Thuc Nghi Nguyen, Tae Kyung Kim, Tim Jarsky, Zizhen Yao, Boaz Levi, Lucas T Gray, Staci A Sorensen, Tim Dolbeare,[...]. Nat Neurosci 2016
740
50

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments.
Ning Leng, Li-Fang Chu, Chris Barry, Yuan Li, Jeea Choi, Xiaomao Li, Peng Jiang, Ron M Stewart, James A Thomson, Christina Kendziorski. Nat Methods 2015
84
50

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
13
50

Single-cell messenger RNA sequencing reveals rare intestinal cell types.
Dominic Grün, Anna Lyubimova, Lennart Kester, Kay Wiebrands, Onur Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden. Nature 2015
592
50

SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning.
Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu, Emma Pierson, Serafim Batzoglou. Proteomics 2018
19
50

Accounting for technical noise in single-cell RNA-seq experiments.
Philip Brennecke, Simon Anders, Jong Kyoung Kim, Aleksandra A Kołodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A Teichmann, John C Marioni,[...]. Nat Methods 2013
509
50

Method for Determining the Optimal Number of Clusters Based on Agglomerative Hierarchical Clustering.
Shibing Zhou, Zhenyuan Xu, Fei Liu. IEEE Trans Neural Netw Learn Syst 2017
7
50

Dimension Reduction and Clustering Models for Single-Cell RNA Sequencing Data: A Comparative Study.
Chao Feng, Shufen Liu, Hao Zhang, Renchu Guan, Dan Li, Fengfeng Zhou, Yanchun Liang, Xiaoyue Feng. Int J Mol Sci 2020
8
50

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells.
Fan Guo, Liying Yan, Hongshan Guo, Lin Li, Boqiang Hu, Yangyu Zhao, Jun Yong, Yuqiong Hu, Xiaoye Wang, Yuan Wei,[...]. Cell 2015
273
50

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
Alex K Shalek, Rahul Satija, Joe Shuga, John J Trombetta, Dave Gennert, Diana Lu, Peilin Chen, Rona S Gertner, Jellert T Gaublomme, Nir Yosef,[...]. Nature 2014
520
50

Differential Expression Analysis of RNA-seq Reads: Overview, Taxonomy, and Tools.
Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita. IEEE/ACM Trans Comput Biol Bioinform 2020
5
50

Semi Supervised Learning with Deep Embedded Clustering for Image Classification and Segmentation.
Joseph Enguehard, Peter O'Halloran, Ali Gholipour. IEEE Access 2019
7
50

DICOM Metadata repository for technical information in digital medical images.
Hans-Erik Källman, Erik Halsius, Magnus Olsson, Mats Stenström. Acta Oncol 2009
12
50

A framework for medical image retrieval using machine learning and statistical similarity matching techniques with relevance feedback.
Md Mahmudur Rahman, Prabir Bhattacharya, Bipin C Desai. IEEE Trans Inf Technol Biomed 2007
41
50

Using DICOM Metadata for Radiological Image Series Categorization: a Feasibility Study on Large Clinical Brain MRI Datasets.
Romane Gauriau, Christopher Bridge, Lina Chen, Felipe Kitamura, Neil A Tenenholtz, John E Kirsch, Katherine P Andriole, Mark H Michalski, Bernardo C Bizzo. J Digit Imaging 2020
4
50

Understanding and using DICOM, the data interchange standard for biomedical imaging.
W D Bidgood, S C Horii, F W Prior, D E Van Syckle. J Am Med Inform Assoc 1997
126
50

A classification-based approach to semi-supervised clustering with pairwise constraints.
Marek Śmieja, Łukasz Struski, Mário A T Figueiredo. Neural Netw 2020
2
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.