A citation-based method for searching scientific literature

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, Alex Khodaverdian, Nir Yosef, Alexander Meissner, Jonathan S Weissman. Nature 2019
Times Cited: 121







List of co-cited articles
1101 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
49

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
45

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
44

Whole-organism clone tracing using single-cell sequencing.
Anna Alemany, Maria Florescu, Chloé S Baron, Josi Peterson-Maduro, Alexander van Oudenaarden. Nature 2018
206
41

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
40

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
33

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
32

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
29

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
26

A single-cell molecular map of mouse gastrulation and early organogenesis.
Blanca Pijuan-Sala, Jonathan A Griffiths, Carolina Guibentif, Tom W Hiscock, Wajid Jawaid, Fernando J Calero-Nieto, Carla Mulas, Ximena Ibarra-Soria, Richard C V Tyser, Debbie Lee Lian Ho,[...]. Nature 2019
239
26

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
24

Lineage tracing meets single-cell omics: opportunities and challenges.
Daniel E Wagner, Allon M Klein. Nat Rev Genet 2020
121
24

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
23

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
21

An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.
Sarah Bowling, Duluxan Sritharan, Fernando G Osorio, Maximilian Nguyen, Priscilla Cheung, Alejo Rodriguez-Fraticelli, Sachin Patel, Wei-Chien Yuan, Yuko Fujiwara, Bin E Li,[...]. Cell 2020
57
36

Single-Cell Transcriptomics Meets Lineage Tracing.
Lennart Kester, Alexander van Oudenaarden. Cell Stem Cell 2018
173
20

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
20

The embryonic cell lineage of the nematode Caenorhabditis elegans.
J E Sulston, E Schierenberg, J G White, J N Thomson. Dev Biol 1983
19

The emergent landscape of the mouse gut endoderm at single-cell resolution.
Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S Simon, Nestor Saiz, Rui Gardner, Stéphane C Boutet,[...]. Nature 2019
100
18

Recording development with single cell dynamic lineage tracing.
Aaron McKenna, James A Gagnon. Development 2019
61
29

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
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

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
17

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.
Leif S Ludwig, Caleb A Lareau, Jacob C Ulirsch, Elena Christian, Christoph Muus, Lauren H Li, Karin Pelka, Will Ge, Yaara Oren, Alison Brack,[...]. Cell 2019
146
17

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
16

Rapidly evolving homing CRISPR barcodes.
Reza Kalhor, Prashant Mali, George M Church. Nat Methods 2017
106
15

Molecular architecture of lineage allocation and tissue organization in early mouse embryo.
Guangdun Peng, Shengbao Suo, Guizhong Cui, Fang Yu, Ran Wang, Jun Chen, Shirui Chen, Zhiwen Liu, Guoyu Chen, Yun Qian,[...]. Nature 2019
61
24

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?
Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J Telford. Elife 2019
27
55

Continuous genetic recording with self-targeting CRISPR-Cas in human cells.
Samuel D Perli, Cheryl H Cui, Timothy K Lu. Science 2016
108
15

Lineage tracing.
Kai Kretzschmar, Fiona M Watt. Cell 2012
392
14

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
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

Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system.
Jean Livet, Tamily A Weissman, Hyuno Kang, Ryan W Draft, Ju Lu, Robyn A Bennis, Joshua R Sanes, Jeff W Lichtman. Nature 2007
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

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level.
Katie McDole, Léo Guignard, Fernando Amat, Andrew Berger, Grégoire Malandain, Loïc A Royer, Srinivas C Turaga, Kristin Branson, Philipp J Keller. Cell 2018
179
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

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
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

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
13

Unravelling cellular relationships during development and regeneration using genetic lineage tracing.
Chloé S Baron, Alexander van Oudenaarden. Nat Rev Mol Cell Biol 2019
57
22

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
12

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
370
12


A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
378
12

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
109
12

Diffusion pseudotime robustly reconstructs lineage branching.
Laleh Haghverdi, Maren Büttner, F Alexander Wolf, Florian Buettner, Fabian J Theis. Nat Methods 2016
409
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
516
12

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
12


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.