A citation-based method for searching scientific literature

Daniel B Burkhardt, Jay S Stanley, Alexander Tong, Ana Luisa Perdigoto, Scott A Gigante, Kevan C Herold, Guy Wolf, Antonio J Giraldez, David van Dijk, Smita Krishnaswamy. Nat Biotechnol 2021
Times Cited: 7







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



Times Cited
  Times     Co-cited
Similarity


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
57

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
346
57

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
42

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
42

Visualizing structure and transitions in high-dimensional biological data.
Kevin R Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B Burkhardt, William S Chen, Kristina Yim, Antonia van den Elzen, Matthew J Hirn, Ronald R Coifman,[...]. Nat Biotechnol 2019
112
42

A benchmark of batch-effect correction methods for single-cell RNA sequencing data.
Hoa Thi Nhu Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen. Genome Biol 2020
149
42

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
28

Testing for differential abundance in mass cytometry data.
Aaron T L Lun, Arianne C Richard, John C Marioni. Nat Methods 2017
52
28

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
28

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
484
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
28

Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies.
Wen Shi Lee, Adam K Wheatley, Stephen J Kent, Brandon J DeKosky. Nat Microbiol 2020
220
28

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis.
Rowena A Bull, Thiruni N Adikari, James M Ferguson, Jillian M Hammond, Igor Stevanovski, Alicia G Beukers, Zin Naing, Malinna Yeang, Andrey Verich, Hasindu Gamaarachchi,[...]. Nat Commun 2020
31
28

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
Andrew Rambaut, Edward C Holmes, Áine O'Toole, Verity Hill, John T McCrone, Christopher Ruis, Louis du Plessis, Oliver G Pybus. Nat Microbiol 2020
726
28


Iroki: automatic customization and visualization of phylogenetic trees.
Ryan M Moore, Amelia O Harrison, Sean M McAllister, Shawn W Polson, K Eric Wommack. PeerJ 2020
22
28

COVID-19 Transmission Within a Family Cluster by Presymptomatic Carriers in China.
Guoqing Qian, Naibin Yang, Ada Hoi Yan Ma, Liping Wang, Guoxiang Li, Xueqin Chen, Xiaomin Chen. Clin Infect Dis 2020
156
28

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
28



Headache during SARS-CoV-2 infection as an early symptom associated with a more benign course of disease: a case-control study.
Alicia Gonzalez-Martinez, Víctor Fanjul, Carmen Ramos, Jorge Serrano Ballesteros, Marta Bustamante, Almudena Villa Martí, Claudia Álvarez, Yaiza García Del Álamo, José Vivancos, Ana Beatriz Gago-Veiga. Eur J Neurol 2021
10
28

Asymptomatic and Presymptomatic SARS-CoV-2 Infections in Residents of a Long-Term Care Skilled Nursing Facility - King County, Washington, March 2020.
Anne Kimball, Kelly M Hatfield, Melissa Arons, Allison James, Joanne Taylor, Kevin Spicer, Ana C Bardossy, Lisa P Oakley, Sukarma Tanwar, Zeshan Chisty,[...]. MMWR Morb Mortal Wkly Rep 2020
603
28

Presymptomatic Transmission of SARS-CoV-2 - Singapore, January 23-March 16, 2020.
Wycliffe E Wei, Zongbin Li, Calvin J Chiew, Sarah E Yong, Matthias P Toh, Vernon J Lee. MMWR Morb Mortal Wkly Rep 2020
494
28

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
28

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
28

Wishbone identifies bifurcating developmental trajectories from single-cell data.
Manu Setty, Michelle D Tadmor, Shlomit Reich-Zeliger, Omer Angel, Tomer Meir Salame, Pooja Kathail, Kristy Choi, Sean Bendall, Nir Friedman, Dana Pe'er. Nat Biotechnol 2016
283
28

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
319
28

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
202
28

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
28

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
28

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
265
28

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
817
28

Orchestrating high-throughput genomic analysis with Bioconductor.
Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke,[...]. Nat Methods 2015
28

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.
Tallulah S Andrews, Vladimir Yu Kiselev, Davis McCarthy, Martin Hemberg. Nat Protoc 2021
15
28

Single-cell transcriptomic profiling of the aging mouse brain.
Methodios Ximerakis, Scott L Lipnick, Brendan T Innes, Sean K Simmons, Xian Adiconis, Danielle Dionne, Brittany A Mayweather, Lan Nguyen, Zachary Niziolek, Ceren Ozek,[...]. Nat Neurosci 2019
100
14

Spectral biclustering of microarray data: coclustering genes and conditions.
Yuval Kluger, Ronen Basri, Joseph T Chang, Mark Gerstein. Genome Res 2003
155
14

Locally instructed CXCR4hi neutrophils trigger environment-driven allergic asthma through the release of neutrophil extracellular traps.
Coraline Radermecker, Catherine Sabatel, Céline Vanwinge, Cecilia Ruscitti, Pauline Maréchal, Fabienne Perin, Joey Schyns, Natacha Rocks, Marie Toussaint, Didier Cataldo,[...]. Nat Immunol 2019
37
14

Cell type prioritization in single-cell data.
Michael A Skinnider, Jordan W Squair, Claudia Kathe, Mark A Anderson, Matthieu Gautier, Kaya J E Matson, Marco Milano, Thomas H Hutson, Quentin Barraud, Aaron A Phillips,[...]. Nat Biotechnol 2021
14
14

Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis.
Khusali Gupta, Jonathan Levinsohn, George Linderman, Demeng Chen, Thomas Yang Sun, Danni Dong, M Mark Taketo, Marcus Bosenberg, Yuval Kluger, Keith Choate,[...]. Dev Cell 2019
19
14

Skin-resident innate lymphoid cells converge on a pathogenic effector state.
Piotr Bielecki, Samantha J Riesenfeld, Jan-Christian Hütter, Elena Torlai Triglia, Monika S Kowalczyk, Roberto R Ricardo-Gonzalez, Mi Lian, Maria C Amezcua Vesely, Lina Kroehling, Hao Xu,[...]. Nature 2021
21
14

Randomized near-neighbor graphs, giant components and applications in data science.
George C Linderman, Gal Mishne, Ariel Jaffe, Yuval Kluger, Stefan Steinerberger. J Appl Probab 2020
1
100

scDC: single cell differential composition analysis.
Yue Cao, Yingxin Lin, John T Ormerod, Pengyi Yang, Jean Y H Yang, Kitty K Lo. BMC Bioinformatics 2019
4
25

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
171
14

SOCS3 negatively regulates IL-6 signaling in vivo.
Ben A Croker, Danielle L Krebs, Jian-Guo Zhang, Sam Wormald, Tracy A Willson, Edouard G Stanley, Lorraine Robb, Christopher J Greenhalgh, Irmgard Förster, Björn E Clausen,[...]. Nat Immunol 2003
623
14

Causal network perturbations for instance-specific analysis of single cell and disease samples.
Kristina L Buschur, Maria Chikina, Panayiotis V Benos. Bioinformatics 2020
4
25

COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis.
Robert Lorenz Chua, Soeren Lukassen, Saskia Trump, Bianca P Hennig, Daniel Wendisch, Fabian Pott, Olivia Debnath, Loreen Thürmann, Florian Kurth, Maria Theresa Völker,[...]. Nat Biotechnol 2020
338
14


Cell Adhesion Molecules and Their Roles and Regulation in the Immune and Tumor Microenvironment.
Heidi Harjunpää, Marc Llort Asens, Carla Guenther, Susanna C Fagerholm. Front Immunol 2019
131
14


Expression of LAG-3 by tumor-infiltrating lymphocytes is coincident with the suppression of latent membrane antigen-specific CD8+ T-cell function in Hodgkin lymphoma patients.
Maher K Gandhi, Eleanore Lambley, Jaikumar Duraiswamy, Ujjwal Dua, Corey Smith, Suzanne Elliott, Devinder Gill, Paula Marlton, John Seymour, Rajiv Khanna. Blood 2006
160
14


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.