A citation-based method for searching scientific literature

Joanna Kalucka, Laura P M H de Rooij, Jermaine Goveia, Katerina Rohlenova, Sébastien J Dumas, Elda Meta, Nadine V Conchinha, Federico Taverna, Laure-Anne Teuwen, Koen Veys, Melissa García-Caballero, Shawez Khan, Vincent Geldhof, Liliana Sokol, Rongyuan Chen, Lucas Treps, Mila Borri, Pauline de Zeeuw, Charlotte Dubois, Tobias K Karakach, Kim D Falkenberg, Magdalena Parys, Xiangke Yin, Stefan Vinckier, Yuxiang Du, Robert A Fenton, Luc Schoonjans, Mieke Dewerchin, Guy Eelen, Bernard Thienpont, Lin Lin, Lars Bolund, Xuri Li, Yonglun Luo, Peter Carmeliet. Cell 2020
Times Cited: 294







List of co-cited articles
860 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
24

A molecular atlas of cell types and zonation in the brain vasculature.
Michael Vanlandewijck, Liqun He, Maarja Andaloussi Mäe, Johanna Andrae, Koji Ando, Francesca Del Gaudio, Khayrun Nahar, Thibaud Lebouvier, Bàrbara Laviña, Leonor Gouveia,[...]. Nature 2018
698
21


Single-Cell RNA Sequencing Unveils Unique Transcriptomic Signatures of Organ-Specific Endothelial Cells.
David T Paik, Lei Tian, Ian M Williams, Siyeon Rhee, Hao Zhang, Chun Liu, Ridhima Mishra, Sean M Wu, Kristy Red-Horse, Joseph C Wu. Circulation 2020
54
24



CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.
Mirjana Efremova, Miquel Vento-Tormo, Sarah A Teichmann, Roser Vento-Tormo. Nat Protoc 2020
536
12

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
12

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
998
11

Basic and therapeutic aspects of angiogenesis.
Michael Potente, Holger Gerhardt, Peter Carmeliet. Cell 2011
11

Inference and analysis of cell-cell communication using CellChat.
Suoqin Jin, Christian F Guerrero-Juarez, Lihua Zhang, Ivan Chang, Raul Ramos, Chen-Hsiang Kuan, Peggy Myung, Maksim V Plikus, Qing Nie. Nat Commun 2021
251
10

Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration.
Daniel J Nolan, Michael Ginsberg, Edo Israely, Brisa Palikuqi, Michael G Poulos, Daylon James, Bi-Sen Ding, William Schachterle, Ying Liu, Zev Rosenwaks,[...]. Dev Cell 2013
380
9

Endothelial cell heterogeneity.
William C Aird. Cold Spring Harb Perspect Med 2012
422
9

Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis.
Katerina Rohlenova, Jermaine Goveia, Melissa García-Caballero, Abhishek Subramanian, Joanna Kalucka, Lucas Treps, Kim D Falkenberg, Laura P M H de Rooij, Yingfeng Zheng, Lin Lin,[...]. Cell Metab 2020
72
11

A molecular cell atlas of the human lung from single-cell RNA sequencing.
Kyle J Travaglini, Ahmad N Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V Sit, Stephen Chang, Stephanie D Conley, Yasuo Mori, Jun Seita,[...]. Nature 2020
303
8

VEGF guides angiogenic sprouting utilizing endothelial tip cell filopodia.
Holger Gerhardt, Matthew Golding, Marcus Fruttiger, Christiana Ruhrberg, Andrea Lundkvist, Alexandra Abramsson, Michael Jeltsch, Christopher Mitchell, Kari Alitalo, David Shima,[...]. J Cell Biol 2003
8

Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations.
Aditya S Kalluri, Shamsudheen K Vellarikkal, Elazer R Edelman, Lan Nguyen, Ayshwarya Subramanian, Patrick T Ellinor, Aviv Regev, Sekar Kathiresan, Rajat M Gupta. Circulation 2019
104
8


Angiocrine functions of organ-specific endothelial cells.
Shahin Rafii, Jason M Butler, Bi-Sen Ding. Nature 2016
439
8

Shear-induced Notch-Cx37-p27 axis arrests endothelial cell cycle to enable arterial specification.
Jennifer S Fang, Brian G Coon, Noelle Gillis, Zehua Chen, Jingyao Qiu, Thomas W Chittenden, Janis M Burt, Martin A Schwartz, Karen K Hirschi. Nat Commun 2017
111
8

Role of PFKFB3-driven glycolysis in vessel sprouting.
Katrien De Bock, Maria Georgiadou, Sandra Schoors, Anna Kuchnio, Brian W Wong, Anna Rita Cantelmo, Annelies Quaegebeur, Bart Ghesquière, Sandra Cauwenberghs, Guy Eelen,[...]. Cell 2013
750
8

Cells of the adult human heart.
Monika Litviňuková, Carlos Talavera-López, Henrike Maatz, Daniel Reichart, Catherine L Worth, Eric L Lindberg, Masatoshi Kanda, Krzysztof Polanski, Matthias Heinig, Michael Lee,[...]. Nature 2020
274
8

Pericytes regulate the blood-brain barrier.
Annika Armulik, Guillem Genové, Maarja Mäe, Maya H Nisancioglu, Elisabet Wallgard, Colin Niaudet, Liqun He, Jenny Norlin, Per Lindblom, Karin Strittmatter,[...]. Nature 2010
8

Single-Cell RNA Sequencing Reveals Renal Endothelium Heterogeneity and Metabolic Adaptation to Water Deprivation.
Sébastien J Dumas, Elda Meta, Mila Borri, Jermaine Goveia, Katerina Rohlenova, Nadine V Conchinha, Kim Falkenberg, Laure-Anne Teuwen, Laura de Rooij, Joanna Kalucka,[...]. J Am Soc Nephrol 2020
51
13

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
846
7

Pericytes are required for blood-brain barrier integrity during embryogenesis.
Richard Daneman, Lu Zhou, Amanuel A Kebede, Ben A Barres. Nature 2010
7

A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver.
Donato Inverso, Jingjing Shi, Ki Hong Lee, Moritz Jakab, Shani Ben-Moshe, Shubhada R Kulkarni, Martin Schneider, Guanxiong Wang, Marziyeh Komeili, Paula Argos Vélez,[...]. Dev Cell 2021
15
46

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
7

Construction of a human cell landscape at single-cell level.
Xiaoping Han, Ziming Zhou, Lijiang Fei, Huiyu Sun, Renying Wang, Yao Chen, Haide Chen, Jingjing Wang, Huanna Tang, Wenhao Ge,[...]. Nature 2020
271
7

Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
575
7

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis.
Robert C Wirka, Dhananjay Wagh, David T Paik, Milos Pjanic, Trieu Nguyen, Clint L Miller, Ramen Kundu, Manabu Nagao, John Coller, Tiffany K Koyano,[...]. Nat Med 2019
190
7

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors.
Christopher S McGinnis, Lyndsay M Murrow, Zev J Gartner. Cell Syst 2019
371
7

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
845
6

NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys. Nat Methods 2020
235
6

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
6

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
6

Suppression of Notch signalling by the COUP-TFII transcription factor regulates vein identity.
Li-Ru You, Fu-Jung Lin, Christopher T Lee, Francesco J DeMayo, Ming-Jer Tsai, Sophia Y Tsai. Nature 2005
430
6

Profiling the mouse brain endothelial transcriptome in health and disease models reveals a core blood-brain barrier dysfunction module.
Roeben Nocon Munji, Allison Luen Soung, Geoffrey Aaron Weiner, Fabien Sohet, Bridgette Deanne Semple, Alpa Trivedi, Kayleen Gimlin, Masakazu Kotoda, Masaaki Korai, Sidar Aydin,[...]. Nat Neurosci 2019
111
6

Capillary cell-type specialization in the alveolus.
Astrid Gillich, Fan Zhang, Colleen G Farmer, Kyle J Travaglini, Serena Y Tan, Mingxia Gu, Bin Zhou, Jeffrey A Feinstein, Mark A Krasnow, Ross J Metzger. Nature 2020
56
10

Mfsd2a is critical for the formation and function of the blood-brain barrier.
Ayal Ben-Zvi, Baptiste Lacoste, Esther Kur, Benjamin J Andreone, Yoav Mayshar, Han Yan, Chenghua Gu. Nature 2014
502
6

Single-cell analysis of early progenitor cells that build coronary arteries.
Tianying Su, Geoff Stanley, Rahul Sinha, Gaetano D'Amato, Soumya Das, Siyeon Rhee, Andrew H Chang, Aruna Poduri, Brian Raftrey, Thanh Theresa Dinh,[...]. Nature 2018
101
6

EndoDB: a database of endothelial cell transcriptomics data.
Shawez Khan, Federico Taverna, Katerina Rohlenova, Lucas Treps, Vincent Geldhof, Laura de Rooij, Liliana Sokol, Andreas Pircher, Lena-Christin Conradi, Joanna Kalucka,[...]. Nucleic Acids Res 2019
39
15

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
6

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
6

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells.
Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Amir Rattner, Loyal A Goff, Joseph R Ecker, Jeremy Nathans. Elife 2018
106
6

An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates.
Jermaine Goveia, Katerina Rohlenova, Federico Taverna, Lucas Treps, Lena-Christin Conradi, Andreas Pircher, Vincent Geldhof, Laura P M H de Rooij, Joanna Kalucka, Liliana Sokol,[...]. Cancer Cell 2020
104
6

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
935
5

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
5

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
455
5

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
5


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.