A citation-based method for searching scientific literature

Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W Newell, Michael Poidinger, Jinmiao Chen. PLoS Comput Biol 2016
Times Cited: 149







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



Times Cited
  Times     Co-cited
Similarity


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
36

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
20

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.
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
922
18

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
17


High-dimensional analysis of the murine myeloid cell system.
Burkhard Becher, Andreas Schlitzer, Jinmiao Chen, Florian Mair, Hermi R Sumatoh, Karen Wei Weng Teng, Donovan Low, Christiane Ruedl, Paola Riccardi-Castagnoli, Michael Poidinger,[...]. Nat Immunol 2014
235
14

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
14

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
13

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
13

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
12

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.
Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W Newell, John Ramey, Mark M Davis, Spyros A Kalams, Stephen C De Rosa, Raphael Gottardo. PLoS Comput Biol 2014
97
11

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

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
9

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets.
Malgorzata Nowicka, Carsten Krieg, Helena L Crowell, Lukas M Weber, Felix J Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P Levesque, Mark D Robinson. F1000Res 2017
109
9

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

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
8

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
8

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
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
8

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
13

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
8

Mapping the Diversity of Follicular Helper T Cells in Human Blood and Tonsils Using High-Dimensional Mass Cytometry Analysis.
Michael T Wong, Jinmiao Chen, Sriram Narayanan, Wenyu Lin, Rosslyn Anicete, Henry Tan Kun Kiaang, Maria Alicia Curotto De Lafaille, Michael Poidinger, Evan W Newell. Cell Rep 2015
84
9

Automated mapping of phenotype space with single-cell data.
Nikolay Samusik, Zinaida Good, Matthew H Spitzer, Kara L Davis, Garry P Nolan. Nat Methods 2016
139
7

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
7

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
7


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
7

Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets.
Anna C Belkina, Christopher O Ciccolella, Rina Anno, Richard Halpert, Josef Spidlen, Jennifer E Snyder-Cappione. Nat Commun 2019
56
12

Mass Cytometry: Single Cells, Many Features.
Matthew H Spitzer, Garry P Nolan. Cell 2016
500
6

The who's who of T-cell differentiation: human memory T-cell subsets.
Yolanda D Mahnke, Tess M Brodie, Federica Sallusto, Mario Roederer, Enrico Lugli. Eur J Immunol 2013
406
6

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
6

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
10

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

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types.
Vincent van Unen, Thomas Höllt, Nicola Pezzotti, Na Li, Marcel J T Reinders, Elmar Eisemann, Frits Koning, Anna Vilanova, Boudewijn P F Lelieveldt. Nat Commun 2017
84
7

Highly multiparametric analysis by mass cytometry.
Olga Ornatsky, Dmitry Bandura, Vladimir Baranov, Mark Nitz, Mitchell A Winnik, Scott Tanner. J Immunol Methods 2010
226
6

destiny: diffusion maps for large-scale single-cell data in R.
Philipp Angerer, Laleh Haghverdi, Maren Büttner, Fabian J Theis, Carsten Marr, Florian Buettner. Bioinformatics 2016
205
6

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering.
Lukas M Weber, Malgorzata Nowicka, Charlotte Soneson, Mark D Robinson. Commun Biol 2019
42
14

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
6

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
6

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

Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry.
Henrik E Mei, Michael D Leipold, Axel Ronald Schulz, Cariad Chester, Holden T Maecker. J Immunol 2015
94
5

Testing for differential abundance in mass cytometry data.
Aaron T L Lun, Arianne C Richard, John C Marioni. Nat Methods 2017
50
10

Distinct Cellular Mechanisms Underlie Anti-CTLA-4 and Anti-PD-1 Checkpoint Blockade.
Spencer C Wei, Jacob H Levine, Alexandria P Cogdill, Yang Zhao, Nana-Ama A S Anang, Miles C Andrews, Padmanee Sharma, Jing Wang, Jennifer A Wargo, Dana Pe'er,[...]. Cell 2017
541
5

A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF).
Liyun Lai, Raymond Ong, Juntao Li, Salvatore Albani. Cytometry A 2015
54
9

Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab.
Nadeem Riaz, Jonathan J Havel, Vladimir Makarov, Alexis Desrichard, Walter J Urba, Jennifer S Sims, F Stephen Hodi, Salvador Martín-Algarra, Rajarsi Mandal, William H Sharfman,[...]. Cell 2017
634
5

IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade.
Mark Ayers, Jared Lunceford, Michael Nebozhyn, Erin Murphy, Andrey Loboda, David R Kaufman, Andrew Albright, Jonathan D Cheng, S Peter Kang, Veena Shankaran,[...]. J Clin Invest 2017
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

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Laleh Haghverdi, Florian Buettner, Fabian J Theis. Bioinformatics 2015
247
5

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.
Mehrnoush Malek, Mohammad Jafar Taghiyar, Lauren Chong, Greg Finak, Raphael Gottardo, Ryan R Brinkman. Bioinformatics 2015
59
8


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.