A citation-based method for searching scientific literature

El-ad David Amir, Kara L Davis, Michelle D Tadmor, Erin F Simonds, Jacob H Levine, Sean C Bendall, Daniel K Shenfeld, Smita Krishnaswamy, Garry P Nolan, Dana Pe'er. Nat Biotechnol 2013
Times Cited: 922







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



Times Cited
  Times     Co-cited
Similarity


FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.
Sofie Van Gassen, Britt Callebaut, Mary J Van Helden, Bart N Lambrecht, Piet Demeester, Tom Dhaene, Yvan Saeys. Cytometry A 2015
446
24

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder,[...]. Cell 2015
678
19

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.
Peng Qiu, Erin F Simonds, Sean C Bendall, Kenneth D Gibbs, Robert V Bruggner, Michael D Linderman, Karen Sachs, Garry P Nolan, Sylvia K Plevritis. Nat Biotechnol 2011
581
18

Mass Cytometry: Single Cells, Many Features.
Matthew H Spitzer, Garry P Nolan. Cell 2016
500
12

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.
Sean C Bendall, Erin F Simonds, Peng Qiu, El-ad D Amir, Peter O Krutzik, Rachel Finck, Robert V Bruggner, Rachel Melamed, Angelica Trejo, Olga I Ornatsky,[...]. Science 2011
11

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
11

Web-based analysis and publication of flow cytometry experiments.
Nikesh Kotecha, Peter O Krutzik, Jonathan M Irish. Curr Protoc Cytom 2010
273
10

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry.
Charlotte Giesen, Hao A O Wang, Denis Schapiro, Nevena Zivanovic, Andrea Jacobs, Bodo Hattendorf, Peter J Schüffler, Daniel Grolimund, Joachim M Buhmann, Simone Brandt,[...]. Nat Methods 2014
666
9

Automated identification of stratifying signatures in cellular subpopulations.
Robert V Bruggner, Bernd Bodenmiller, David L Dill, Robert J Tibshirani, Garry P Nolan. Proc Natl Acad Sci U S A 2014
237
9


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

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
8

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
8

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
8

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
8

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.
Eli R Zunder, Rachel Finck, Gregory K Behbehani, El-Ad D Amir, Smita Krishnaswamy, Veronica D Gonzalez, Cynthia G Lorang, Zach Bjornson, Matthew H Spitzer, Bernd Bodenmiller,[...]. Nat Protoc 2015
245
7

Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry.
Dmitry R Bandura, Vladimir I Baranov, Olga I Ornatsky, Alexei Antonov, Robert Kinach, Xudong Lou, Serguei Pavlov, Sergey Vorobiev, John E Dick, Scott D Tanner. Anal Chem 2009
645
7

Normalization of mass cytometry data with bead standards.
Rachel Finck, Erin F Simonds, Astraea Jager, Smita Krishnaswamy, Karen Sachs, Wendy Fantl, Dana Pe'er, Garry P Nolan, Sean C Bendall. Cytometry A 2013
352
7

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
6

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
6

Computational flow cytometry: helping to make sense of high-dimensional immunology data.
Yvan Saeys, Sofie Van Gassen, Bart N Lambrecht. Nat Rev Immunol 2016
206
6

The end of gating? An introduction to automated analysis of high dimensional cytometry data.
Florian Mair, Felix J Hartmann, Dunja Mrdjen, Vinko Tosevski, Carsten Krieg, Burkhard Becher. Eur J Immunol 2016
121
6

A Beginner's Guide to Analyzing and Visualizing Mass Cytometry Data.
Abigail K Kimball, Lauren M Oko, Bonnie L Bullock, Raphael A Nemenoff, Linda F van Dyk, Eric T Clambey. J Immunol 2018
58
10

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5

A deep profiler's guide to cytometry.
Sean C Bendall, Garry P Nolan, Mario Roederer, Pratip K Chattopadhyay. Trends Immunol 2012
403
5

CellProfiler: image analysis software for identifying and quantifying cell phenotypes.
Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A Guertin, Joo Han Chang, Robert A Lindquist, Jason Moffat,[...]. Genome Biol 2006
5

Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE).
Karthik Shekhar, Petter Brodin, Mark M Davis, Arup K Chakraborty. Proc Natl Acad Sci U S A 2014
149
5

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.
Stéphane Chevrier, Helena L Crowell, Vito R T Zanotelli, Stefanie Engler, Mark D Robinson, Bernd Bodenmiller. Cell Syst 2018
97
5

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
Sean C Bendall, Kara L Davis, El-Ad David Amir, Michelle D Tadmor, Erin F Simonds, Tiffany J Chen, Daniel K Shenfeld, Garry P Nolan, Dana Pe'er. Cell 2014
482
5

Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications.
Divij Mathew, Josephine R Giles, Amy E Baxter, Derek A Oldridge, Allison R Greenplate, Jennifer E Wu, Cécile Alanio, Leticia Kuri-Cervantes, M Betina Pampena, Kurt D'Andrea,[...]. Science 2020
523
5

Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19.
Takuya Sekine, André Perez-Potti, Olga Rivera-Ballesteros, Kristoffer Strålin, Jean-Baptiste Gorin, Annika Olsson, Sian Llewellyn-Lacey, Habiba Kamal, Gordana Bogdanovic, Sandra Muschiol,[...]. Cell 2020
604
5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
613
4

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills. Bioinformatics 2017
397
4

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
4

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline.
Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W Newell, Michael Poidinger, Jinmiao Chen. PLoS Comput Biol 2016
149
4

Multiplexed ion beam imaging of human breast tumors.
Michael Angelo, Sean C Bendall, Rachel Finck, Matthew B Hale, Chuck Hitzman, Alexander D Borowsky, Richard M Levenson, John B Lowe, Scot D Liu, Shuchun Zhao,[...]. Nat Med 2014
436
4

Detection of minimal residual disease in B lymphoblastic leukemia using viSNE.
Joseph A DiGiuseppe, Michelle D Tadmor, Dana Pe'er. Cytometry B Clin Cytom 2015
25
16

Interpreting flow cytometry data: a guide for the perplexed.
Leonore A Herzenberg, James Tung, Wayne A Moore, Leonard A Herzenberg, David R Parks. Nat Immunol 2006
286
4

flowCore: a Bioconductor package for high throughput flow cytometry.
Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman. BMC Bioinformatics 2009
233
4

flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.
Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, João Pedro de Magalhães, Anis Larbi. Bioinformatics 2016
60
6

Minimizing Batch Effects in Mass Cytometry Data.
Ronald P Schuyler, Conner Jackson, Josselyn E Garcia-Perez, Ryan M Baxter, Sidney Ogolla, Rosemary Rochford, Debashis Ghosh, Pratyaydipta Rudra, Elena W Y Hsieh. Front Immunol 2019
25
16


Convergent antibody responses to SARS-CoV-2 in convalescent individuals.
Davide F Robbiani, Christian Gaebler, Frauke Muecksch, Julio C C Lorenzi, Zijun Wang, Alice Cho, Marianna Agudelo, Christopher O Barnes, Anna Gazumyan, Shlomo Finkin,[...]. Nature 2020
768
4

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
4

Factors associated with COVID-19-related death using OpenSAFELY.
Elizabeth J Williamson, Alex J Walker, Krishnan Bhaskaran, Seb Bacon, Chris Bates, Caroline E Morton, Helen J Curtis, Amir Mehrkar, David Evans, Peter Inglesby,[...]. Nature 2020
4

Immunological and inflammatory profiles in mild and severe cases of COVID-19.
Jin-Wen Song, Chao Zhang, Xing Fan, Fan-Ping Meng, Zhe Xu, Peng Xia, Wen-Jing Cao, Tao Yang, Xiao-Peng Dai, Si-Yu Wang,[...]. Nat Commun 2020
109
4

Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection.
Jennifer M Dan, Jose Mateus, Yu Kato, Kathryn M Hastie, Esther Dawen Yu, Caterina E Faliti, Alba Grifoni, Sydney I Ramirez, Sonya Haupt, April Frazier,[...]. Science 2021
568
4

Divergent SARS-CoV-2-specific T- and B-cell responses in severe but not mild COVID-19 patients.
Anna E Oja, Anno Saris, Cherien A Ghandour, Natasja A M Kragten, Boris M Hogema, Esther J Nossent, Leo M A Heunks, Susan Cuvalay, Ed Slot, Federica Linty,[...]. Eur J Immunol 2020
41
9

Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity.
Carolyn Rydyznski Moderbacher, Sydney I Ramirez, Jennifer M Dan, Alba Grifoni, Kathryn M Hastie, Daniela Weiskopf, Simon Belanger, Robert K Abbott, Christina Kim, Jinyong Choi,[...]. Cell 2020
378
4

Acute SARS-CoV-2 Infection Impairs Dendritic Cell and T Cell Responses.
Runhong Zhou, Kelvin Kai-Wang To, Yik-Chun Wong, Li Liu, Biao Zhou, Xin Li, Haode Huang, Yufei Mo, Tsz-Yat Luk, Thomas Tsz-Kan Lau,[...]. Immunity 2020
157
4


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.