A citation-based method for searching scientific literature

Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
Times Cited: 463







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



Times Cited
  Times     Co-cited
Similarity



CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.
Tamar Hashimshony, Naftalie Senderovich, Gal Avital, Agnes Klochendler, Yaron de Leeuw, Leon Anavy, Dave Gennert, Shuqiang Li, Kenneth J Livak, Orit Rozenblatt-Rosen,[...]. Genome Biol 2016
484
4

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
644
4

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
536
4

Decontamination of ambient RNA in single-cell RNA-seq with DecontX.
Shiyi Yang, Sean E Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima, Joshua D Campbell. Genome Biol 2020
39
10


Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
4

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
4

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
4

SCnorm: robust normalization of single-cell RNA-seq data.
Rhonda Bacher, Li-Fang Chu, Ning Leng, Audrey P Gasch, James A Thomson, Ron M Stewart, Michael Newton, Christina Kendziorski. Nat Methods 2017
139
3

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.
Keegan D Korthauer, Li-Fang Chu, Michael A Newton, Yuan Li, James Thomson, Ron Stewart, Christina Kendziorski. Genome Biol 2016
100
3

BBKNN: fast batch alignment of single cell transcriptomes.
Krzysztof Polański, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann, Jong-Eun Park. Bioinformatics 2020
151
3

DEsingle for detecting three types of differential expression in single-cell RNA-seq data.
Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2018
70
4

Single-cell transcriptomics unveils gene regulatory network plasticity.
Giovanni Iacono, Ramon Massoni-Badosa, Holger Heyn. Genome Biol 2019
68
4

Web-based analysis and publication of flow cytometry experiments.
Nikesh Kotecha, Peter O Krutzik, Jonathan M Irish. Curr Protoc Cytom 2010
308
3

Metabolic landscape of the tumor microenvironment at single cell resolution.
Zhengtao Xiao, Ziwei Dai, Jason W Locasale. Nat Commun 2019
138
3

Single-cell RNA sequencing to explore immune cell heterogeneity.
Efthymia Papalexi, Rahul Satija. Nat Rev Immunol 2018
452
3

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.
Sofie Van Gassen, Britt Callebaut, Mary J Van Helden, Bart N Lambrecht, Piet Demeester, Tom Dhaene, Yvan Saeys. Cytometry A 2015
581
3

Computational approaches for interpreting scRNA-seq data.
Raghd Rostom, Valentine Svensson, Sarah A Teichmann, Gozde Kar. FEBS Lett 2017
54
5

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.
Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Salto, Amit Zeisel, Lars E Borm, Simon R W Stott, Enrique M Toledo, J Carlos Villaescusa,[...]. Cell 2016
355
3

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
79
3

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
Luke Zappia, Belinda Phipson, Alicia Oshlack. PLoS Comput Biol 2018
110
3

Single-Cell Transcriptome Atlas of Murine Endothelial Cells.
Joanna Kalucka, Laura P M H de Rooij, Jermaine Goveia, Katerina Rohlenova, Sébastien J Dumas, Elda Meta, Nadine V Conchinha, Federico Taverna, Laure-Anne Teuwen, Koen Veys,[...]. Cell 2020
257
3


Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
576
3

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease.
Jihwan Park, Rojesh Shrestha, Chengxiang Qiu, Ayano Kondo, Shizheng Huang, Max Werth, Mingyao Li, Jonathan Barasch, Katalin Suszták. Science 2018
439
3

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, Jose L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen,[...]. Science 2018
299
3

Resolving the fibrotic niche of human liver cirrhosis at single-cell level.
P Ramachandran, R Dobie, J R Wilson-Kanamori, E F Dora, B E P Henderson, N T Luu, J R Portman, K P Matchett, M Brice, J A Marwick,[...]. Nature 2019
366
3

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
3

The Human Transcription Factors.
Samuel A Lambert, Arttu Jolma, Laura F Campitelli, Pratyush K Das, Yimeng Yin, Mihai Albu, Xiaoting Chen, Jussi Taipale, Timothy R Hughes, Matthew T Weirauch. Cell 2018
697
3

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer.
Lei Zhang, Xin Yu, Liangtao Zheng, Yuanyuan Zhang, Yansen Li, Qiao Fang, Ranran Gao, Boxi Kang, Qiming Zhang, Julie Y Huang,[...]. Nature 2018
312
3

Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang,[...]. Cell 2017
806
3

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
3

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
3

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
3

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma.
Ankur Sharma, Justine Jia Wen Seow, Charles-Antoine Dutertre, Rhea Pai, Camille Blériot, Archita Mishra, Regina Men Men Wong, Gurmit Singh Naranjan Singh, Samydurai Sudhagar, Shabnam Khalilnezhad,[...]. Cell 2020
79
3

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.
Susanne C van den Brink, Fanny Sage, Ábel Vértesy, Bastiaan Spanjaard, Josi Peterson-Maduro, Chloé S Baron, Catherine Robin, Alexander van Oudenaarden. Nat Methods 2017
359
3

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.
Åsa Segerstolpe, Athanasia Palasantza, Pernilla Eliasson, Eva-Marie Andersson, Anne-Christine Andréasson, Xiaoyan Sun, Simone Picelli, Alan Sabirsh, Maryam Clausen, Magnus K Bjursell,[...]. Cell Metab 2016
617
3

A Single-Cell Transcriptome Atlas of the Human Pancreas.
Mauro J Muraro, Gitanjali Dharmadhikari, Dominic Grün, Nathalie Groen, Tim Dielen, Erik Jansen, Leon van Gurp, Marten A Engelse, Francoise Carlotti, Eelco J P de Koning,[...]. Cell Syst 2016
454
3

Demystifying "drop-outs" in single-cell UMI data.
Tae Hyun Kim, Xiang Zhou, Mengjie Chen. Genome Biol 2020
22
13


A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Maayan Baron, Adrian Veres, Samuel L Wolock, Aubrey L Faust, Renaud Gaujoux, Amedeo Vetere, Jennifer Hyoje Ryu, Bridget K Wagner, Shai S Shen-Orr, Allon M Klein,[...]. Cell Syst 2016
482
3

Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.
Li Li, Ji Dong, Liying Yan, Jun Yong, Xixi Liu, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Hongshan Guo, Xiaoye Wang,[...]. Cell Stem Cell 2017
169
3

A test metric for assessing single-cell RNA-seq batch correction.
Maren Büttner, Zhichao Miao, F Alexander Wolf, Sarah A Teichmann, Fabian J Theis. Nat Methods 2019
111
3

A human cell atlas of fetal gene expression.
Junyue Cao, Diana R O'Day, Hannah A Pliner, Paul D Kingsley, Mei Deng, Riza M Daza, Michael A Zager, Kimberly A Aldinger, Ronnie Blecher-Gonen, Fan Zhang,[...]. Science 2020
105
3

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data.
Qianhui Huang, Yu Liu, Yuheng Du, Lana X Garmire. Genomics Proteomics Bioinformatics 2021
17
17

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.
Caleb A Lareau, Leif S Ludwig, Christoph Muus, Satyen H Gohil, Tongtong Zhao, Zachary Chiang, Karin Pelka, Jeffrey M Verboon, Wendy Luo, Elena Christian,[...]. Nat Biotechnol 2021
53
5

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.
Saiful Islam, Una Kjällquist, Annalena Moliner, Pawel Zajac, Jian-Bing Fan, Peter Lönnerberg, Sten Linnarsson. Nat Protoc 2012
168
3

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.
Jean Fan, Neeraj Salathia, Rui Liu, Gwendolyn E Kaeser, Yun C Yung, Joseph L Herman, Fiona Kaper, Jian-Bing Fan, Kun Zhang, Jerold Chun,[...]. Nat Methods 2016
197
3



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.