A citation-based method for searching scientific literature

Alex A Pollen, Tomasz J Nowakowski, Joe Shuga, Xiaohui Wang, Anne A Leyrat, Jan H Lui, Nianzhen Li, Lukasz Szpankowski, Brian Fowler, Peilin Chen, Naveen Ramalingam, Gang Sun, Myo Thu, Michael Norris, Ronald Lebofsky, Dominique Toppani, Darnell W Kemp, Michael Wong, Barry Clerkson, Brittnee N Jones, Shiquan Wu, Lawrence Knutsson, Beatriz Alvarado, Jing Wang, Lesley S Weaver, Andrew P May, Robert C Jones, Marc A Unger, Arnold R Kriegstein, Jay A A West. Nat Biotechnol 2014
Times Cited: 464







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



Times Cited
  Times     Co-cited
Similarity


Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.
Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda. Genome Biol 2013
226
5

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder,[...]. Cell 2015
678
5

Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development.
Katarína Tiklová, Åsa K Björklund, Laura Lahti, Alessandro Fiorenzano, Sara Nolbrant, Linda Gillberg, Nikolaos Volakakis, Chika Yokota, Markus M Hilscher, Thomas Hauling,[...]. Nat Commun 2019
61
8

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
155
5

Single-cell dissection of transcriptional heterogeneity in human colon tumors.
Piero Dalerba, Tomer Kalisky, Debashis Sahoo, Pradeep S Rajendran, Michael E Rothenberg, Anne A Leyrat, Sopheak Sim, Jennifer Okamoto, Darius M Johnston, Dalong Qian,[...]. Nat Biotechnol 2011
464
5

Highly multiplexed subcellular RNA sequencing in situ.
Je Hyuk Lee, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur S F Jeanty, Chao Li, Ryoji Amamoto,[...]. Science 2014
459
5

High-definition spatial transcriptomics for in situ tissue profiling.
Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro,[...]. Nat Methods 2019
177
5


Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal.
Simone A Fietz, Robert Lachmann, Holger Brandl, Martin Kircher, Nikolay Samusik, Roland Schröder, Naharajan Lakshmanaperumal, Ian Henry, Johannes Vogt, Axel Riehn,[...]. Proc Natl Acad Sci U S A 2012
180
5

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.
Xiannian Zhang, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, Jianbin Wang. Mol Cell 2019
100
5

Spatio-temporal transcriptome of the human brain.
Hyo Jung Kang, Yuka Imamura Kawasawa, Feng Cheng, Ying Zhu, Xuming Xu, Mingfeng Li, André M M Sousa, Mihovil Pletikos, Kyle A Meyer, Goran Sedmak,[...]. Nature 2011
5

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain.
Kristofer Davie, Jasper Janssens, Duygu Koldere, Maxime De Waegeneer, Uli Pech, Łukasz Kreft, Sara Aibar, Samira Makhzami, Valerie Christiaens, Carmen Bravo González-Blas,[...]. Cell 2018
216
5

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.
Sueli Marques, Amit Zeisel, Simone Codeluppi, David van Bruggen, Ana Mendanha Falcão, Lin Xiao, Huiliang Li, Martin Häring, Hannah Hochgerner, Roman A Romanov,[...]. Science 2016
378
5

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
337
5

Single-cell RNA-seq: advances and future challenges.
Antoine-Emmanuel Saliba, Alexander J Westermann, Stanislaw A Gorski, Jörg Vogel. Nucleic Acids Res 2014
343
5


Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.
Arpiar Saunders, Evan Z Macosko, Alec Wysoker, Melissa Goldman, Fenna M Krienen, Heather de Rivera, Elizabeth Bien, Matthew Baum, Laura Bortolin, Shuyu Wang,[...]. Cell 2018
418
5

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, Marc H Wadsworth, Tyler Burks, Lan T Nguyen,[...]. Nat Biotechnol 2020
123
5

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Yong Wang, Jill Waters, Marco L Leung, Anna Unruh, Whijae Roh, Xiuqing Shi, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang,[...]. Nature 2014
587
4

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.
Georgi K Marinov, Brian A Williams, Ken McCue, Gary P Schroth, Jason Gertz, Richard M Myers, Barbara J Wold. Genome Res 2014
286
4

Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm.
Jianbin Wang, H Christina Fan, Barry Behr, Stephen R Quake. Cell 2012
304
4

Imaging individual mRNA molecules using multiple singly labeled probes.
Arjun Raj, Patrick van den Bogaard, Scott A Rifkin, Alexander van Oudenaarden, Sanjay Tyagi. Nat Methods 2008
4

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
4

Identifying cell populations with scRNASeq.
Tallulah S Andrews, Martin Hemberg. Mol Aspects Med 2018
91
4

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.
Xiao Wang, William E Allen, Matthew A Wright, Emily L Sylwestrak, Nikolay Samusik, Sam Vesuna, Kathryn Evans, Cindy Liu, Charu Ramakrishnan, Jia Liu,[...]. Science 2018
303
4

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
182
4

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
4

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
613
4

Multiplexed quantification of proteins and transcripts in single cells.
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach. Nat Biotechnol 2017
293
4

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.
Dominic Grün, Mauro J Muraro, Jean-Charles Boisset, Kay Wiebrands, Anna Lyubimova, Gitanjali Dharmadhikari, Maaike van den Born, Johan van Es, Erik Jansen, Hans Clevers,[...]. Cell Stem Cell 2016
222
4

Phenotype molding of stromal cells in the lung tumor microenvironment.
Diether Lambrechts, Els Wauters, Bram Boeckx, Sara Aibar, David Nittner, Oliver Burton, Ayse Bassez, Herbert Decaluwé, Andreas Pircher, Kathleen Van den Eynde,[...]. Nat Med 2018
413
4

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
Sean C Bendall, Kara L Davis, El-Ad David Amir, Michelle D Tadmor, Erin F Simonds, Tiffany J Chen, Daniel K Shenfeld, Garry P Nolan, Dana Pe'er. Cell 2014
482
4

Decoding human fetal liver haematopoiesis.
Dorin-Mirel Popescu, Rachel A Botting, Emily Stephenson, Kile Green, Simone Webb, Laura Jardine, Emily F Calderbank, Krzysztof Polanski, Issac Goh, Mirjana Efremova,[...]. Nature 2019
127
4

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq.
Johannes W Bagnoli, Christoph Ziegenhain, Aleksandar Janjic, Lucas E Wange, Beate Vieth, Swati Parekh, Johanna Geuder, Ines Hellmann, Wolfgang Enard. Nat Commun 2018
61
6

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
123
4

Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.
Fuchou Tang, Catalin Barbacioru, Siqin Bao, Caroline Lee, Ellen Nordman, Xiaohui Wang, Kaiqin Lao, M Azim Surani. Cell Stem Cell 2010
360
4

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
James A Briggs, Caleb Weinreb, Daniel E Wagner, Sean Megason, Leonid Peshkin, Marc W Kirschner, Allon M Klein. Science 2018
195
4

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
4

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion.
Marta Florio, Mareike Albert, Elena Taverna, Takashi Namba, Holger Brandl, Eric Lewitus, Christiane Haffner, Alex Sykes, Fong Kuan Wong, Jula Peters,[...]. Science 2015
275
4

Single-cell epigenomics: techniques and emerging applications.
Omer Schwartzman, Amos Tanay. Nat Rev Genet 2015
139
4

Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics.
Feng Guo, Sixing Li, Mehmet Umut Caglar, Zhangming Mao, Wu Liu, Andrew Woodman, Jamie J Arnold, Claus O Wilke, Tony Jun Huang, Craig E Cameron. Cell Rep 2017
31
12

Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units.
Marine Combe, Raquel Garijo, Ron Geller, José M Cuevas, Rafael Sanjuán. Cell Host Microbe 2015
47
8

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.
Kyu-Tae Kim, Hye Won Lee, Hae-Ock Lee, Sang Cheol Kim, Yun Jee Seo, Woosung Chung, Hye Hyeon Eum, Do-Hyun Nam, Junhyong Kim, Kyeung Min Joo,[...]. Genome Biol 2015
160
4

Microfluidic single-cell whole-transcriptome sequencing.
Aaron M Streets, Xiannian Zhang, Chen Cao, Yuhong Pang, Xinglong Wu, Liang Xiong, Lu Yang, Yusi Fu, Liang Zhao, Fuchou Tang,[...]. Proc Natl Acad Sci U S A 2014
166
4


How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives.
Alessandra Dal Molin, Barbara Di Camillo. Brief Bioinform 2019
25
16


The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
4

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
4

AutoImpute: Autoencoder based imputation of single-cell RNA-seq data.
Divyanshu Talwar, Aanchal Mongia, Debarka Sengupta, Angshul Majumdar. Sci Rep 2018
37
10


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.