A citation-based method for searching scientific literature

Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie, David A Weitz, Orit Rozenblatt-Rosen, Feng Zhang, Aviv Regev. Nat Methods 2017
Times Cited: 342







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



Times Cited
  Times     Co-cited
Similarity


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
42

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
31

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
30

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
27

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
21

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.
Blue B Lake, Rizi Ai, Gwendolyn E Kaeser, Neeraj S Salathia, Yun C Yung, Rui Liu, Andre Wildberg, Derek Gao, Ho-Lim Fung, Song Chen,[...]. Science 2016
393
20

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
287
20

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Naama Elefant, Franziska Paul, Irina Zaretsky, Alexander Mildner, Nadav Cohen, Steffen Jung, Amos Tanay,[...]. Science 2014
877
18

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.
Naomi Habib, Yinqing Li, Matthias Heidenreich, Lukasz Swiech, Inbal Avraham-Davidi, John J Trombetta, Cynthia Hession, Feng Zhang, Aviv Regev. Science 2016
240
18

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
18

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
451
17

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

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
556
16

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
381
16

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
357
16

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types.
Trygve E Bakken, Rebecca D Hodge, Jeremy A Miller, Zizhen Yao, Thuc Nghi Nguyen, Brian Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee,[...]. PLoS One 2018
123
15

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
15

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
419
14

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
14

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
135
14

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
704
13

Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
709
13

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
596
13

RNA-sequencing from single nuclei.
Rashel V Grindberg, Joyclyn L Yee-Greenbaum, Michael J McConnell, Mark Novotny, Andy L O'Shaughnessy, Georgina M Lambert, Marcos J Araúzo-Bravo, Jun Lee, Max Fishman, Gillian E Robbins,[...]. Proc Natl Acad Sci U S A 2013
148
13

Quantitative single-cell RNA-seq with unique molecular identifiers.
Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson. Nat Methods 2014
598
13

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
12

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
435
12

Comprehensive single-cell transcriptional profiling of a multicellular organism.
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers,[...]. Science 2017
456
12

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.
Daniel Ramsköld, Shujun Luo, Yu-Chieh Wang, Robin Li, Qiaolin Deng, Omid R Faridani, Gregory A Daniels, Irina Khrebtukova, Jeanne F Loring, Louise C Laurent,[...]. Nat Biotechnol 2012
820
12

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy,[...]. Science 2016
11

An anatomically comprehensive atlas of the adult human brain transcriptome.
Michael J Hawrylycz, Ed S Lein, Angela L Guillozet-Bongaarts, Elaine H Shen, Lydia Ng, Jeremy A Miller, Louie N van de Lagemaat, Kimberly A Smith, Amanda Ebbert, Zackery L Riley,[...]. Nature 2012
11

Single-cell genomics identifies cell type-specific molecular changes in autism.
Dmitry Velmeshev, Lucas Schirmer, Diane Jung, Maximilian Haeussler, Yonatan Perez, Simone Mayer, Aparna Bhaduri, Nitasha Goyal, David H Rowitch, Arnold R Kriegstein. Science 2019
155
11

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
11

Comparative Analysis of Single-Cell RNA Sequencing Methods.
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard. Mol Cell 2017
539
11

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.
Damon Polioudakis, Luis de la Torre-Ubieta, Justin Langerman, Andrew G Elkins, Xu Shi, Jason L Stein, Celine K Vuong, Susanne Nichterwitz, Melinda Gevorgian, Carli K Opland,[...]. Neuron 2019
105
10

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.
Mingfeng Li, Gabriel Santpere, Yuka Imamura Kawasawa, Oleg V Evgrafov, Forrest O Gulden, Sirisha Pochareddy, Susan M Sunkin, Zhen Li, Yurae Shin, Ying Zhu,[...]. Science 2018
203
10

Nuclear RNA-seq of single neurons reveals molecular signatures of activation.
Benjamin Lacar, Sara B Linker, Baptiste N Jaeger, Suguna R Krishnaswami, Jerika J Barron, Martijn J E Kelder, Sarah L Parylak, Apuã C M Paquola, Pratap Venepally, Mark Novotny,[...]. Nat Commun 2016
176
10

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
10

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
730
10

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis.
Geng Chen, Baitang Ning, Tieliu Shi. Front Genet 2019
171
10

CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.
Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai. Cell Rep 2012
612
10

Single-cell chromatin accessibility reveals principles of regulatory variation.
Jason D Buenrostro, Beijing Wu, Ulrike M Litzenburger, Dave Ruff, Michael L Gonzales, Michael P Snyder, Howard Y Chang, William J Greenleaf. Nature 2015
800
10

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.
Michael J Gandal, Pan Zhang, Evi Hadjimichael, Rebecca L Walker, Chao Chen, Shuang Liu, Hyejung Won, Harm van Bakel, Merina Varghese, Yongjun Wang,[...]. Science 2018
335
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
467
9

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
326
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
422
9

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.
Todd M Gierahn, Marc H Wadsworth, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love, Alex K Shalek. Nat Methods 2017
335
9

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
330
9


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
307
9


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.