A citation-based method for searching scientific literature

Josip S Herman, Sagar, Dominic Grün. Nat Methods 2018
Times Cited: 115







List of co-cited articles
962 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
431
31

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
233
28

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
21

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
20

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
20

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
18

Diffusion pseudotime robustly reconstructs lineage branching.
Laleh Haghverdi, Maren Büttner, F Alexander Wolf, Florian Buettner, Fabian J Theis. Nat Methods 2016
372
17

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo,[...]. Science 2017
960
17

Validation of noise models for single-cell transcriptomics.
Dominic Grün, Lennart Kester, Alexander van Oudenaarden. Nat Methods 2014
334
17

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
17

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
17

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
792
16

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.
Franziska Paul, Ya'ara Arkin, Amir Giladi, Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Deborah Winter, David Lara-Astiaso, Meital Gury, Assaf Weiner,[...]. Cell 2015
492
16

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
16

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
16

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells.
Patrick Fernandes Rodrigues, Llucia Alberti-Servera, Anna Eremin, Gary E Grajales-Reyes, Robert Ivanek, Roxane Tussiwand. Nat Immunol 2018
119
15


Human haematopoietic stem cell lineage commitment is a continuous process.
Lars Velten, Simon F Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P Hennig, Christoph Hirche, Christoph Lutz, Eike C Buss, Daniel Nowak,[...]. Nat Cell Biol 2017
347
15

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
710
15

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
397
14

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
14

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
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
732
14

Mapping the human DC lineage through the integration of high-dimensional techniques.
Peter See, Charles-Antoine Dutertre, Jinmiao Chen, Patrick Günther, Naomi McGovern, Sergio Erdal Irac, Merry Gunawan, Marc Beyer, Kristian Händler, Kaibo Duan,[...]. Science 2017
282
13

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
13

Fundamental limits on dynamic inference from single-cell snapshots.
Caleb Weinreb, Samuel Wolock, Betsabeh K Tusi, Merav Socolovsky, Allon M Klein. Proc Natl Acad Sci U S A 2018
96
13

Population snapshots predict early haematopoietic and erythroid hierarchies.
Betsabeh Khoramian Tusi, Samuel L Wolock, Caleb Weinreb, Yung Hwang, Daniel Hidalgo, Rapolas Zilionis, Ari Waisman, Jun R Huh, Allon M Klein, Merav Socolovsky. Nature 2018
157
13

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
374
13

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
511
13

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
489
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
739
12

Lineage tracing on transcriptional landscapes links state to fate during differentiation.
Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein. Science 2020
133
12

Diverse and heritable lineage imprinting of early haematopoietic progenitors.
Shalin H Naik, Leïla Perié, Erwin Swart, Carmen Gerlach, Nienke van Rooij, Rob J de Boer, Ton N Schumacher. Nature 2013
243
11


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
11

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
319
11

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
11

Identification of clonogenic common Flt3+M-CSFR+ plasmacytoid and conventional dendritic cell progenitors in mouse bone marrow.
Nobuyuki Onai, Aya Obata-Onai, Michael A Schmid, Toshiaki Ohteki, David Jarrossay, Markus G Manz. Nat Immunol 2007
479
10

A clonogenic progenitor with prominent plasmacytoid dendritic cell developmental potential.
Nobuyuki Onai, Kazutaka Kurabayashi, Mayuka Hosoi-Amaike, Noriko Toyama-Sorimachi, Kouji Matsushima, Kayo Inaba, Toshiaki Ohteki. Immunity 2013
132
10

The External RNA Controls Consortium: a progress report.
Shawn C Baker, Steven R Bauer, Richard P Beyer, James D Brenton, Bud Bromley, John Burrill, Helen Causton, Michael P Conley, Rosalie Elespuru, Michael Fero,[...]. Nat Methods 2005
214
10

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.
Jason D Buenrostro, M Ryan Corces, Caleb A Lareau, Beijing Wu, Alicia N Schep, Martin J Aryee, Ravindra Majeti, Howard Y Chang, William J Greenleaf. Cell 2018
206
10

Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
918
10

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
9

Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo.
Shalin H Naik, Priyanka Sathe, Hae-Young Park, Donald Metcalf, Anna I Proietto, Aleksander Dakic, Sebastian Carotta, Meredith O'Keeffe, Melanie Bahlo, Anthony Papenfuss,[...]. Nat Immunol 2007
548
9

Transcription factor E2-2 is an essential and specific regulator of plasmacytoid dendritic cell development.
Babacar Cisse, Michele L Caton, Manfred Lehner, Takahiro Maeda, Stefanie Scheu, Richard Locksley, Dan Holmberg, Christiane Zweier, Nicolette S den Hollander, Sarina G Kant,[...]. Cell 2008
422
9

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau,[...]. Nature 2017
180
9

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis.
Amir Giladi, Franziska Paul, Yoni Herzog, Yaniv Lubling, Assaf Weiner, Ido Yofe, Diego Jaitin, Nina Cabezas-Wallscheid, Regine Dress, Florent Ginhoux,[...]. Nat Cell Biol 2018
116
9

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
889
9

A clonogenic common myeloid progenitor that gives rise to all myeloid lineages.
K Akashi, D Traver, T Miyamoto, I L Weissman. Nature 2000
9

Single-cell RNA sequencing to explore immune cell heterogeneity.
Efthymia Papalexi, Rahul Satija. Nat Rev Immunol 2018
397
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.