A citation-based method for searching scientific literature

Gunsagar S Gulati, Shaheen S Sikandar, Daniel J Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J Berger, Francisco Ilagan, Angera H Kuo, Robert W Hsieh, Shang Cai, Maider Zabala, Ferenc A Scheeren, Neethan A Lobo, Dalong Qian, Feiqiao B Yu, Frederick M Dirbas, Michael F Clarke, Aaron M Newman. Science 2020
Times Cited: 58







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



Times Cited
  Times     Co-cited
Similarity


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
36

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
36

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
31

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
29

Generalizing RNA velocity to transient cell states through dynamical modeling.
Volker Bergen, Marius Lange, Stefan Peidli, F Alexander Wolf, Fabian J Theis. Nat Biotechnol 2020
171
27

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
444
25

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
22

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
821
20

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
744
18

SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
631
18

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
720
17

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
292
17

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark, Avi Ma'ayan. BMC Bioinformatics 2013
15

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
13

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
13

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis. Genome Biol 2019
199
13

Lineage tracing on transcriptional landscapes links state to fate during differentiation.
Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein. Science 2020
114
12


CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.
Mirjana Efremova, Miquel Vento-Tormo, Sarah A Teichmann, Roser Vento-Tormo. Nat Protoc 2020
253
12

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
337
12

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
12

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
10

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
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

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
270
8

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
227
8

Whole-organism clone tracing using single-cell sequencing.
Anna Alemany, Maria Florescu, Chloé S Baron, Josi Peterson-Maduro, Alexander van Oudenaarden. Nature 2018
180
8

Skin fibrosis. Identification and isolation of a dermal lineage with intrinsic fibrogenic potential.
Yuval Rinkevich, Graham G Walmsley, Michael S Hu, Zeshaan N Maan, Aaron M Newman, Micha Drukker, Michael Januszyk, Geoffrey W Krampitz, Geoffrey C Gurtner, H Peter Lorenz,[...]. Science 2015
297
8

Focal adhesion kinase links mechanical force to skin fibrosis via inflammatory signaling.
Victor W Wong, Kristine C Rustad, Satoshi Akaishi, Michael Sorkin, Jason P Glotzbach, Michael Januszyk, Emily R Nelson, Kemal Levi, Josemaria Paterno, Ivan N Vial,[...]. Nat Med 2011
254
8

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
222
8

Diffusion pseudotime robustly reconstructs lineage branching.
Laleh Haghverdi, Maren Büttner, F Alexander Wolf, Florian Buettner, Fabian J Theis. Nat Methods 2016
355
8

Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells.
Kook Hui Ryu, Ling Huang, Hyun Min Kang, John Schiefelbein. Plant Physiol 2019
109
8

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types.
Christine N Shulse, Benjamin J Cole, Doina Ciobanu, Junyan Lin, Yuko Yoshinaga, Mona Gouran, Gina M Turco, Yiwen Zhu, Ronan C O'Malley, Siobhan M Brady,[...]. Cell Rep 2019
94
8

Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds.
Christian F Guerrero-Juarez, Priya H Dedhia, Suoqin Jin, Rolando Ruiz-Vega, Dennis Ma, Yuchen Liu, Kosuke Yamaga, Olga Shestova, Denise L Gay, Zaixin Yang,[...]. Nat Commun 2019
120
8


Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.
Itay Tirosh, Andrew S Venteicher, Christine Hebert, Leah E Escalante, Anoop P Patel, Keren Yizhak, Jonathan M Fisher, Christopher Rodman, Christopher Mount, Mariella G Filbin,[...]. Nature 2016
401
8

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
312
6

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
99
6

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
188
6

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
186
6

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
115
6

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
6

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
6

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.
Dvir Aran, Agnieszka P Looney, Leqian Liu, Esther Wu, Valerie Fong, Austin Hsu, Suzanna Chak, Ram P Naikawadi, Paul J Wolters, Adam R Abate,[...]. Nat Immunol 2019
397
6

Single-cell reconstruction of the early maternal-fetal interface in humans.
Roser Vento-Tormo, Mirjana Efremova, Rachel A Botting, Margherita Y Turco, Miquel Vento-Tormo, Kerstin B Meyer, Jong-Eun Park, Emily Stephenson, Krzysztof Polański, Angela Goncalves,[...]. Nature 2018
513
6

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
149
6

Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana.
Ken Jean-Baptiste, José L McFaline-Figueroa, Cristina M Alexandre, Michael W Dorrity, Lauren Saunders, Kerry L Bubb, Cole Trapnell, Stanley Fields, Christine Queitsch, Josh T Cuperus. Plant Cell 2019
74
6

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing.
Tom Denyer, Xiaoli Ma, Simon Klesen, Emanuele Scacchi, Kay Nieselt, Marja C P Timmermans. Dev Cell 2019
104
6

A high-resolution root spatiotemporal map reveals dominant expression patterns.
Siobhan M Brady, David A Orlando, Ji-Young Lee, Jean Y Wang, Jeremy Koch, José R Dinneny, Daniel Mace, Uwe Ohler, Philip N Benfey. Science 2007
738
6

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors.
Christopher S McGinnis, Lyndsay M Murrow, Zev J Gartner. Cell Syst 2019
204
6


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.