A citation-based method for searching scientific literature

Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz, Charlotte Rolny, Gonçalo Castelo-Branco, Jens Hjerling-Leffler, Sten Linnarsson. Science 2015
Times Cited: 1502







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



Times Cited
  Times     Co-cited
Similarity


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
22

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
781
19

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
19

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
506
19

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
841
18

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
16

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
476
15

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
14

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
14

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
14

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.
David van Dijk, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J Carr, Cassandra Burdziak, Kevin R Moon, Christine L Chaffer, Diwakar Pattabiraman,[...]. Cell 2018
431
13

RNA velocity of single cells.
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan,[...]. Nature 2018
883
12

Single-cell RNA-seq denoising using a deep count autoencoder.
Gökcen Eraslan, Lukas M Simon, Maria Mircea, Nikola S Mueller, Fabian J Theis. Nat Commun 2019
222
12

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
527
12

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
271
11

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
305
11

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
11

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
11

Conserved cell types with divergent features in human versus mouse cortex.
Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Nelson Johansen, Osnat Penn,[...]. Nature 2019
441
10

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar, Sylvain W Lapan, Irene E Whitney, Nicholas M Tran, Evan Z Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z Levin, James Nemesh, Melissa Goldman,[...]. Cell 2016
520
10

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
429
10

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
572
10

Reversed graph embedding resolves complex single-cell trajectories.
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell. Nat Methods 2017
940
9

A survey of human brain transcriptome diversity at the single cell level.
Spyros Darmanis, Steven A Sloan, Ye Zhang, Martin Enge, Christine Caneda, Lawrence M Shuer, Melanie G Hayden Gephart, Ben A Barres, Stephen R Quake. Proc Natl Acad Sci U S A 2015
611
9

Single-cell transcriptomic analysis of Alzheimer's disease.
Hansruedi Mathys, Jose Davila-Velderrain, Zhuyu Peng, Fan Gao, Shahin Mohammadi, Jennie Z Young, Madhvi Menon, Liang He, Fatema Abdurrob, Xueqiao Jiang,[...]. Nature 2019
561
9

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.
Blue B Lake, Song Chen, Brandon C Sos, Jean Fan, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko,[...]. Nat Biotechnol 2018
336
9

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
164
9

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
Alex A Pollen, Tomasz J Nowakowski, Joe Shuga, Xiaohui Wang, Anne A Leyrat, Jan H Lui, Nianzhen Li, Lukasz Szpankowski, Brian Fowler, Peilin Chen,[...]. Nat Biotechnol 2014
489
9

SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
844
9

A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.
Hadas Keren-Shaul, Amit Spinrad, Assaf Weiner, Orit Matcovitch-Natan, Raz Dvir-Szternfeld, Tyler K Ulland, Eyal David, Kuti Baruch, David Lara-Astaiso, Beata Toth,[...]. Cell 2017
9

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
613
9

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
612
9

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
490
9

SAVER: gene expression recovery for single-cell RNA sequencing.
Mo Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio, John I Murray, Arjun Raj, Mingyao Li, Nancy R Zhang. Nat Methods 2018
212
9

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
241
9

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle. Nat Biotechnol 2015
590
8

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics.
Kenneth D Harris, Hannah Hochgerner, Nathan G Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson Gonzales, Peter Somogyi, Nicoletta Kessaris, Sten Linnarsson, Jens Hjerling-Leffler. PLoS Biol 2018
112
8

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq.
Cathryn R Cadwell, Athanasia Palasantza, Xiaolong Jiang, Philipp Berens, Qiaolin Deng, Marlene Yilmaz, Jacob Reimer, Shan Shen, Matthias Bethge, Kimberley F Tolias,[...]. Nat Biotechnol 2016
243
8

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes.
János Fuzik, Amit Zeisel, Zoltán Máté, Daniela Calvigioni, Yuchio Yanagawa, Gábor Szabó, Sten Linnarsson, Tibor Harkany. Nat Biotechnol 2016
203
8


The single-cell transcriptional landscape of mammalian organogenesis.
Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers,[...]. Nature 2019
631
8

Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
584
8

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
419
8

Massively parallel single-nucleus RNA-seq with DroNc-seq.
Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie,[...]. Nat Methods 2017
387
8

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
511
8

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
8


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
450
8

The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy,[...]. Elife 2017
787
8

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas T Graybuck, David J Peeler, Sumit Mukherjee, Wei Chen,[...]. Science 2018
425
7


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.