A citation-based method for searching scientific literature

Leif S Ludwig, Caleb A Lareau, Jacob C Ulirsch, Elena Christian, Christoph Muus, Lauren H Li, Karin Pelka, Will Ge, Yaara Oren, Alison Brack, Travis Law, Christopher Rodman, Jonathan H Chen, Genevieve M Boland, Nir Hacohen, Orit Rozenblatt-Rosen, Martin J Aryee, Jason D Buenrostro, Aviv Regev, Vijay G Sankaran. Cell 2019
Times Cited: 146







List of co-cited articles
1088 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA.
Jin Xu, Kevin Nuno, Ulrike M Litzenburger, Yanyan Qi, M Ryan Corces, Ravindra Majeti, Howard Y Chang. Elife 2019
55
49

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
860
24

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
23

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
23

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain.
Bushra Raj, Daniel E Wagner, Aaron McKenna, Shristi Pandey, Allon M Klein, Jay Shendure, James A Gagnon, Alexander F Schier. Nat Biotechnol 2018
256
23

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
21

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
49
42

Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars.
Bastiaan Spanjaard, Bo Hu, Nina Mitic, Pedro Olivares-Chauvet, Sharan Janjuha, Nikolay Ninov, Jan Philipp Junker. Nat Biotechnol 2018
216
18

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
18

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
193
18

Whole-organism lineage tracing by combinatorial and cumulative genome editing.
Aaron McKenna, Gregory M Findlay, James A Gagnon, Marshall S Horwitz, Alexander F Schier, Jay Shendure. Science 2016
347
18

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.
Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Yanyan Qi, Francesca Meschi, Geoffrey P McDermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, M Ryan Corces,[...]. Nat Biotechnol 2019
199
18

Synthetic recording and in situ readout of lineage information in single cells.
Kirsten L Frieda, James M Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K Chow, Zakary S Singer, Mark W Budde, Michael B Elowitz, Long Cai. Nature 2017
205
17

Somatic mutation in single human neurons tracks developmental and transcriptional history.
Michael A Lodato, Mollie B Woodworth, Semin Lee, Gilad D Evrony, Bhaven K Mehta, Amir Karger, Soohyun Lee, Thomas W Chittenden, Alissa M D'Gama, Xuyu Cai,[...]. Science 2015
303
17

Lineage tracing meets single-cell omics: opportunities and challenges.
Daniel E Wagner, Allon M Klein. Nat Rev Genet 2020
121
17

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

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
16

Single-Cell Transcriptomics Meets Lineage Tracing.
Lennart Kester, Alexander van Oudenaarden. Cell Stem Cell 2018
173
16

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
292
16

Whole-organism clone tracing using single-cell sequencing.
Anna Alemany, Maria Florescu, Chloé S Baron, Josi Peterson-Maduro, Alexander van Oudenaarden. Nature 2018
206
16

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
378
15

Population dynamics of normal human blood inferred from somatic mutations.
Henry Lee-Six, Nina Friesgaard Øbro, Mairi S Shepherd, Sebastian Grossmann, Kevin Dawson, Miriam Belmonte, Robert J Osborne, Brian J P Huntly, Inigo Martincorena, Elizabeth Anderson,[...]. Nature 2018
213
15

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
405
14

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.
Chee-Huat Linus Eng, Michael Lawson, Qian Zhu, Ruben Dries, Noushin Koulena, Yodai Takei, Jina Yun, Christopher Cronin, Christoph Karp, Guo-Cheng Yuan,[...]. Nature 2019
425
14

Clonal dynamics of native haematopoiesis.
Jianlong Sun, Azucena Ramos, Brad Chapman, Jonathan B Johnnidis, Linda Le, Yu-Jui Ho, Allon Klein, Oliver Hofmann, Fernando D Camargo. Nature 2014
479
14

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
516
14

Clonal analysis of lineage fate in native haematopoiesis.
Alejo E Rodriguez-Fraticelli, Samuel L Wolock, Caleb S Weinreb, Riccardo Panero, Sachin H Patel, Maja Jankovic, Jianlong Sun, Raffaele A Calogero, Allon M Klein, Fernando D Camargo. Nature 2018
234
14

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
886
14

Lineage tracing on transcriptional landscapes links state to fate during differentiation.
Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein. Science 2020
164
14

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
353
13

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
13

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
13

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
13

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
13

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
378
13

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.
Peter van Galen, Volker Hovestadt, Marc H Wadsworth Ii, Travis K Hughes, Gabriel K Griffin, Sofia Battaglia, Julia A Verga, Jason Stephansky, Timothy J Pastika, Jennifer Lombardi Story,[...]. Cell 2019
258
13

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
13

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.
Daniel E Wagner, Caleb Weinreb, Zach M Collins, James A Briggs, Sean G Megason, Allon M Klein. Science 2018
321
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
722
13

Developmental barcoding of whole mouse via homing CRISPR.
Reza Kalhor, Kian Kalhor, Leo Mejia, Kathleen Leeper, Amanda Graveline, Prashant Mali, George M Church. Science 2018
153
13

Building a lineage from single cells: genetic techniques for cell lineage tracking.
Mollie B Woodworth, Kelly M Girskis, Christopher A Walsh. Nat Rev Genet 2017
128
13

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
472
12

Molecular recording of mammalian embryogenesis.
Michelle M Chan, Zachary D Smith, Stefanie Grosswendt, Helene Kretzmer, Thomas M Norman, Britt Adamson, Marco Jost, Jeffrey J Quinn, Dian Yang, Matthew G Jones,[...]. Nature 2019
121
12

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.
Caleb A Lareau, Fabiana M Duarte, Jennifer G Chew, Vinay K Kartha, Zach D Burkett, Andrew S Kohlway, Dmitry Pokholok, Martin J Aryee, Frank J Steemers, Ronald Lebofsky,[...]. Nat Biotechnol 2019
107
12

Somatic mutations and cell identity linked by Genotyping of Transcriptomes.
Anna S Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Justin Taylor, Robert M Myers, Ghaith Abu-Zeinah, Ryan Brand, Nathaniel D Omans,[...]. Nature 2019
89
13

Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
299
11

Single-cell mapping of lineage and identity in direct reprogramming.
Brent A Biddy, Wenjun Kong, Kenji Kamimoto, Chuner Guo, Sarah E Waye, Tao Sun, Samantha A Morris. Nature 2018
110
11

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang. Science 2015
780
10

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
939
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
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.