A citation-based method for searching scientific literature

Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury, Britt Adamson, Thomas M Norman, Eric S Lander, Jonathan S Weissman, Nir Friedman, Aviv Regev. Cell 2016
Times Cited: 444







List of co-cited articles
1068 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Pooled CRISPR screening with single-cell transcriptome readout.
Paul Datlinger, André F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock. Nat Methods 2017
285
49

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.
Diego Adhemar Jaitin, Assaf Weiner, Ido Yofe, David Lara-Astiaso, Hadas Keren-Shaul, Eyal David, Tomer Meir Salame, Amos Tanay, Alexander van Oudenaarden, Ido Amit. Cell 2016
293
42

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.
Britt Adamson, Thomas M Norman, Marco Jost, Min Y Cho, James K Nuñez, Yuwen Chen, Jacqueline E Villalta, Luke A Gilbert, Max A Horlbeck, Marco Y Hein,[...]. Cell 2016
351
38

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
673
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
21

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
19

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks.
Adam J Rubin, Kevin R Parker, Ansuman T Satpathy, Yanyan Qi, Beijing Wu, Alvin J Ong, Maxwell R Mumbach, Andrew L Ji, Daniel S Kim, Seung Woo Cho,[...]. Cell 2019
76
21

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
Joseph M Replogle, Thomas M Norman, Albert Xu, Jeffrey A Hussmann, Jin Chen, J Zachery Cogan, Elliott J Meer, Jessica M Terry, Daniel P Riordan, Niranjan Srinivas,[...]. Nat Biotechnol 2020
41
36

Genome-scale CRISPR-Cas9 knockout screening in human cells.
Ophir Shalem, Neville E Sanjana, Ella Hartenian, Xi Shi, David A Scott, Tarjei Mikkelson, Dirk Heckl, Benjamin L Ebert, David E Root, John G Doench,[...]. Science 2014
15

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
777
14

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.
Eleni P Mimitou, Anthony Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto Herrera, Efthymia Papalexi, Zhengqing Ouyang,[...]. Nat Methods 2019
109
14

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.
Luke A Gilbert, Max A Horlbeck, Britt Adamson, Jacqueline E Villalta, Yuwen Chen, Evan H Whitehead, Carla Guimaraes, Barbara Panning, Hidde L Ploegh, Michael C Bassik,[...]. Cell 2014
14

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

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
676
13

Genetic screens in human cells using the CRISPR-Cas9 system.
Tim Wang, Jenny J Wei, David M Sabatini, Eric S Lander. Science 2014
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

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija. Genome Biol 2018
188
12

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
12

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
12

Search-and-replace genome editing without double-strand breaks or donor DNA.
Andrew V Anzalone, Peyton B Randolph, Jessie R Davis, Alexander A Sousa, Luke W Koblan, Jonathan M Levy, Peter J Chen, Christopher Wilson, Gregory A Newby, Aditya Raguram,[...]. Nature 2019
753
12

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
Lei S Qi, Matthew H Larson, Luke A Gilbert, Jennifer A Doudna, Jonathan S Weissman, Adam P Arkin, Wendell A Lim. Cell 2013
11

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
445
11

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.
Shiqi Xie, Jialei Duan, Boxun Li, Pei Zhou, Gary C Hon. Mol Cell 2017
113
11

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
402
10


Targeted Perturb-seq enables genome-scale genetic screens in single cells.
Daniel Schraivogel, Andreas R Gschwind, Jennifer H Milbank, Daniel R Leonce, Petra Jakob, Lukas Mathur, Jan O Korbel, Christoph A Merten, Lars Velten, Lars M Steinmetz. Nat Methods 2020
18
55

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex.
Silvana Konermann, Mark D Brigham, Alexandro E Trevino, Julia Joung, Omar O Abudayyeh, Clea Barcena, Patrick D Hsu, Naomi Habib, Jonathan S Gootenberg, Hiroshi Nishimasu,[...]. Nature 2015
10

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
245
10

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
10

Multiplex genome engineering using CRISPR/Cas systems.
Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu, Wenyan Jiang, Luciano A Marraffini,[...]. Science 2013
10

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
668
10

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
315
9

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons.
Ruilin Tian, Mariam A Gachechiladze, Connor H Ludwig, Matthew T Laurie, Jason Y Hong, Diane Nathaniel, Anika V Prabhu, Michael S Fernandopulle, Rajan Patel, Mehrnoosh Abshari,[...]. Neuron 2019
83
10

Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.
Charles P Fulco, Joseph Nasser, Thouis R Jones, Glen Munson, Drew T Bergman, Vidya Subramanian, Sharon R Grossman, Rockwell Anyoha, Benjamin R Doughty, Tejal A Patwardhan,[...]. Nat Genet 2019
118
9

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.
Molly Gasperini, Andrew J Hill, José L McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D Zhang, Dana Jackson, Anh Leith, Jacob Schreiber, William S Noble,[...]. Cell 2019
120
9

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
576
9


CUT&Tag for efficient epigenomic profiling of small samples and single cells.
Hatice S Kaya-Okur, Steven J Wu, Christine A Codomo, Erica S Pledger, Terri D Bryson, Jorja G Henikoff, Kami Ahmad, Steven Henikoff. Nat Commun 2019
221
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
400
9

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
9

Highly efficient Cas9-mediated transcriptional programming.
Alejandro Chavez, Jonathan Scheiman, Suhani Vora, Benjamin W Pruitt, Marcelle Tuttle, Eswar P R Iyer, Shuailiang Lin, Samira Kiani, Christopher D Guzman, Daniel J Wiegand,[...]. Nat Methods 2015
659
9

CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
Luke A Gilbert, Matthew H Larson, Leonardo Morsut, Zairan Liu, Gloria A Brar, Sandra E Torres, Noam Stern-Ginossar, Onn Brandman, Evan H Whitehead, Jennifer A Doudna,[...]. Cell 2013
9

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
Oren Parnas, Marko Jovanovic, Thomas M Eisenhaure, Rebecca H Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski, Randall J Platt, Itay Tirosh, Neville E Sanjana,[...]. Cell 2015
238
9

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
9

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.
Thomas M Norman, Max A Horlbeck, Joseph M Replogle, Alex Y Ge, Albert Xu, Marco Jost, Luke A Gilbert, Jonathan S Weissman. Science 2019
42
19

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.
Christopher S McGinnis, David M Patterson, Juliane Winkler, Daniel N Conrad, Marco Y Hein, Vasudha Srivastava, Jennifer L Hu, Lyndsay M Murrow, Jonathan S Weissman, Zena Werb,[...]. Nat Methods 2019
94
8

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
227
8

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A Cusanovich, Riza Daza, Andrew Adey, Hannah A Pliner, Lena Christiansen, Kevin L Gunderson, Frank J Steemers, Cole Trapnell, Jay Shendure. Science 2015
463
8

Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens.
Aleksandra Wroblewska, Maxime Dhainaut, Benjamin Ben-Zvi, Samuel A Rose, Eun Sook Park, El-Ad David Amir, Anela Bektesevic, Alessia Baccarini, Miriam Merad, Adeeb H Rahman,[...]. Cell 2018
36
22

Optical Pooled Screens in Human Cells.
David Feldman, Avtar Singh, Jonathan L Schmid-Burgk, Rebecca J Carlson, Anja Mezger, Anthony J Garrity, Feng Zhang, Paul C Blainey. Cell 2019
45
17


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.