A citation-based method for searching scientific literature


List of co-cited articles
9 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
60

A human cell atlas of fetal gene expression.
Junyue Cao, Diana R O'Day, Hannah A Pliner, Paul D Kingsley, Mei Deng, Riza M Daza, Michael A Zager, Kimberly A Aldinger, Ronnie Blecher-Gonen, Fan Zhang,[...]. Science 2020
100
40

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
197
40

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
282
40

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
40

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
511
40

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
40

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
40

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
613
40

Lineage tracing meets single-cell omics: opportunities and challenges.
Daniel E Wagner, Allon M Klein. Nat Rev Genet 2020
121
20


APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.
Metin Balaban, Shahab Sarmashghi, Siavash Mirarab. Syst Biol 2020
15
20

Visualizing large hierarchical clusters in hyperbolic space.
J Bingham, S Sudarsanam. Bioinformatics 2000
66
20


The evolution of tumour phylogenetics: principles and practice.
Russell Schwartz, Alejandro A Schäffer. Nat Rev Genet 2017
92
20

Distance metrics for ranked evolutionary trees.
Jaehee Kim, Noah A Rosenberg, Julia A Palacios. Proc Natl Acad Sci U S A 2020
2
50

New Approaches for Inferring Phylogenies in the Presence of Paralogs.
Megan L Smith, Matthew W Hahn. Trends Genet 2021
12
20

Visualising very large phylogenetic trees in three dimensional hyperbolic space.
Timothy Hughes, Young Hyun, David A Liberles. BMC Bioinformatics 2004
26
20

Bayesian phylogeography finds its roots.
Philippe Lemey, Andrew Rambaut, Alexei J Drummond, Marc A Suchard. PLoS Comput Biol 2009
971
20

Unifying the epidemiological and evolutionary dynamics of pathogens.
Bryan T Grenfell, Oliver G Pybus, Julia R Gog, James L N Wood, Janet M Daly, Jenny A Mumford, Edward C Holmes. Science 2004
766
20

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.
Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil, Philip Hugenholtz. Nat Biotechnol 2018
20

Molecular phylogenetics: principles and practice.
Ziheng Yang, Bruce Rannala. Nat Rev Genet 2012
270
20

The New Tree of Eukaryotes.
Fabien Burki, Andrew J Roger, Matthew W Brown, Alastair G B Simpson. Trends Ecol Evol 2020
164
20

Poincaré maps for analyzing complex hierarchies in single-cell data.
Anna Klimovskaia, David Lopez-Paz, Léon Bottou, Maximilian Nickel. Nat Commun 2020
9
20

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
Sudhir Kumar, Glen Stecher, Michael Suleski, S Blair Hedges. Mol Biol Evol 2017
929
20

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
Philip R Kensche, Vera van Noort, Bas E Dutilh, Martijn A Huynen. J R Soc Interface 2008
59
20

Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling.
Rebecca J Rockett, Alicia Arnott, Connie Lam, Rosemarie Sadsad, Verlaine Timms, Karen-Ann Gray, John-Sebastian Eden, Sheryl Chang, Mailie Gall, Jenny Draper,[...]. Nat Med 2020
132
20


Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires.
Enkelejda Miho, Alexander Yermanos, Cédric R Weber, Christoph T Berger, Sai T Reddy, Victor Greiff. Front Immunol 2018
73
20

Comparative genomics as a tool to understand evolution and disease.
Jessica Alföldi, Kerstin Lindblad-Toh. Genome Res 2013
74
20

Representation Tradeoffs for Hyperbolic Embeddings.
Christopher De Sa, Albert Gu, Christopher Ré, Frederic Sala. Proc Mach Learn Res 2018
4
25

Evolution. The tree-thinking challenge.
David A Baum, Stacey Dewitt Smith, Samuel S S Donovan. Science 2005
67
20


Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson. Nat Microbiol 2017
585
20

The latent geometry of the human protein interaction network.
Gregorio Alanis-Lobato, Pablo Mier, Miguel Andrade-Navarro. Bioinformatics 2018
9
20

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales.
Joseph F Walker, Ya Yang, Michael J Moore, Jessica Mikenas, Alfonso Timoneda, Samuel F Brockington, Stephen A Smith. Am J Bot 2017
34
20

Hyperbolic geometry of the olfactory space.
Yuansheng Zhou, Brian H Smith, Tatyana O Sharpee. Sci Adv 2018
17
20

A new view of the tree of life.
Laura A Hug, Brett J Baker, Karthik Anantharaman, Christopher T Brown, Alexander J Probst, Cindy J Castelle, Cristina N Butterfield, Alex W Hernsdorf, Yuki Amano, Kotaro Ise,[...]. Nat Microbiol 2016
821
20

Tracing Antibody Repertoire Evolution by Systems Phylogeny.
Alexander Dimitri Yermanos, Andreas Kevin Dounas, Tanja Stadler, Annette Oxenius, Sai T Reddy. Front Immunol 2018
12
20

Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing.
László G Nagy, Zsolt Merényi, Botond Hegedüs, Balázs Bálint. Nucleic Acids Res 2020
12
20

Single-cell analysis of human adipose tissue identifies depot and disease specific cell types.
Jinchu Vijay, Marie-Frédérique Gauthier, Rebecca L Biswell, Daniel A Louiselle, Jeffrey J Johnston, Warren A Cheung, Bradley Belden, Albena Pramatarova, Laurent Biertho, Margaret Gibson,[...]. Nat Metab 2020
86
20

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types.
Trygve E Bakken, Rebecca D Hodge, Jeremy A Miller, Zizhen Yao, Thuc Nghi Nguyen, Brian Aevermann, Eliza Barkan, Darren Bertagnolli, Tamara Casper, Nick Dee,[...]. PLoS One 2018
145
20

Nuclear RNA-seq of single neurons reveals molecular signatures of activation.
Benjamin Lacar, Sara B Linker, Baptiste N Jaeger, Suguna R Krishnaswami, Jerika J Barron, Martijn J E Kelder, Sarah L Parylak, Apuã C M Paquola, Pratap Venepally, Mark Novotny,[...]. Nat Commun 2016
188
20

Metabolic heterogeneity of activated beige/brite adipocytes in inguinal adipose tissue.
Yun-Hee Lee, Sang-Nam Kim, Hyun-Jung Kwon, James G Granneman. Sci Rep 2017
36
20

Comparative analysis of sequencing technologies for single-cell transcriptomics.
Kedar Nath Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Liang Wu,[...]. Genome Biol 2019
44
20


A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Michal Slyper, Caroline B M Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne,[...]. Nat Med 2020
99
20

Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling.
Rayanne B Burl, Vanesa D Ramseyer, Elizabeth A Rondini, Roger Pique-Regi, Yun-Hee Lee, James G Granneman. Cell Metab 2018
131
20

Single cell analysis reveals immune cell-adipocyte crosstalk regulating the transcription of thermogenic adipocytes.
Prashant Rajbhandari, Douglas Arneson, Sydney K Hart, In Sook Ahn, Graciel Diamante, Luis C Santos, Nima Zaghari, An-Chieh Feng, Brandon J Thomas, Laurent Vergnes,[...]. Elife 2019
58
20

Comprehensive single-cell transcriptional profiling of a multicellular organism.
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers,[...]. Science 2017
516
20


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.