A citation-based method for searching scientific literature


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



Times Cited
  Times     Co-cited
Similarity


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
280
64


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
64

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.
Jaehoon Shin, Daniel A Berg, Yunhua Zhu, Joseph Y Shin, Juan Song, Michael A Bonaguidi, Grigori Enikolopov, David W Nauen, Kimberly M Christian, Guo-li Ming,[...]. Cell Stem Cell 2015
386
57

Diffusion pseudotime robustly reconstructs lineage branching.
Laleh Haghverdi, Maren Büttner, F Alexander Wolf, Florian Buettner, Fabian J Theis. Nat Methods 2016
355
57

Pseudotime estimation: deconfounding single cell time series.
John E Reid, Lorenz Wernisch. Bioinformatics 2016
56
50

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
50

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto,[...]. Sci Immunol 2017
137
42


Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
543
35

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
35


Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle. Nat Biotechnol 2015
561
35

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.
Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti, Serafim Batzoglou. Nat Methods 2017
199
35

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.
Joshua D Welch, Alexander J Hartemink, Jan F Prins. Genome Biol 2016
80
35

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
35

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
35

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
35

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
184
35

Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
533
35

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
35

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
35

pcaReduce: hierarchical clustering of single cell transcriptional profiles.
Justina Žurauskienė, Christopher Yau. BMC Bioinformatics 2016
102
28

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
28

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
28

Revealing the vectors of cellular identity with single-cell genomics.
Allon Wagner, Aviv Regev, Nir Yosef. Nat Biotechnol 2016
247
28

Single-cell messenger RNA sequencing reveals rare intestinal cell types.
Dominic Grün, Anna Lyubimova, Lennart Kester, Kay Wiebrands, Onur Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden. Nature 2015
575
28

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
28


SC3: consensus clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green,[...]. Nat Methods 2017
462
28

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape.
Eugenio Marco, Robert L Karp, Guoji Guo, Paul Robson, Adam H Hart, Lorenzo Trippa, Guo-Cheng Yuan. Proc Natl Acad Sci U S A 2014
148
28


SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
720
28

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.
Lan Jiang, Huidong Chen, Luca Pinello, Guo-Cheng Yuan. Genome Biol 2016
99
21

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development.
Jinmiao Chen, Andreas Schlitzer, Svetoslav Chakarov, Florent Ginhoux, Michael Poidinger. Nat Commun 2016
41
21

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
21

Robust lineage reconstruction from high-dimensional single-cell data.
Gregory Giecold, Eugenio Marco, Sara P Garcia, Lorenzo Trippa, Guo-Cheng Yuan. Nucleic Acids Res 2016
16
21

Computational methods for trajectory inference from single-cell transcriptomics.
Robrecht Cannoodt, Wouter Saelens, Yvan Saeys. Eur J Immunol 2016
69
21

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
155
21

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Laleh Haghverdi, Florian Buettner, Fabian J Theis. Bioinformatics 2015
247
21

Single-cell mRNA quantification and differential analysis with Census.
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell. Nat Methods 2017
398
21

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.
Andrea Ocone, Laleh Haghverdi, Nikola S Mueller, Fabian J Theis. Bioinformatics 2015
68
21

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
21

Classification of low quality cells from single-cell RNA-seq data.
Tomislav Ilicic, Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Frederik Otzen Bagger, Davis James McCarthy, John C Marioni, Sarah A Teichmann. Genome Biol 2016
223
21

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm.
Li-Fang Chu, Ning Leng, Jue Zhang, Zhonggang Hou, Daniel Mamott, David T Vereide, Jeea Choi, Christina Kendziorski, Ron Stewart, James A Thomson. Genome Biol 2016
125
21

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.
David A duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani, Koji Tsuda. BMC Bioinformatics 2016
32
21

A general and flexible method for signal extraction from single-cell RNA-seq data.
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert. Nat Commun 2018
180
21


Human haematopoietic stem cell lineage commitment is a continuous process.
Lars Velten, Simon F Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P Hennig, Christoph Hirche, Christoph Lutz, Eike C Buss, Daniel Nowak,[...]. Nat Cell Biol 2017
327
21

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Naama Elefant, Franziska Paul, Irina Zaretsky, Alexander Mildner, Nadav Cohen, Steffen Jung, Amos Tanay,[...]. Science 2014
869
21


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.