A citation-based method for searching scientific literature

Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak, Albert Cardona. Nat Methods 2012
Times Cited: 18709







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



Times Cited
  Times     Co-cited
Similarity


NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
6

ImageJ2: ImageJ for the next generation of scientific image data.
Curtis T Rueden, Johannes Schindelin, Mark C Hiner, Barry E DeZonia, Alison E Walter, Ellen T Arena, Kevin W Eliceiri. BMC Bioinformatics 2017
5

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
4

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
4

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
4

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
4


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
3

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
3

The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher,[...]. Nucleic Acids Res 2019
3

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Daniel J Klionsky, Kotb Abdelmohsen, Akihisa Abe, Md Joynal Abedin, Hagai Abeliovich, Abraham Acevedo Arozena, Hiroaki Adachi, Christopher M Adams, Peter D Adams, Khosrow Adeli,[...]. Autophagy 2016
2

Atg9A trafficking through the recycling endosomes is required for autophagosome formation.
Kenta Imai, Feike Hao, Naonobu Fujita, Yasuhiro Tsuji, Yukako Oe, Yasuhiro Araki, Maho Hamasaki, Takeshi Noda, Tamotsu Yoshimori. J Cell Sci 2016
67
2

Microfluidic organs-on-chips.
Sangeeta N Bhatia, Donald E Ingber. Nat Biotechnol 2014
2

Unraveling the roles of PLIN5: linking cell biology to physiology.
Rachael R Mason, Matthew J Watt. Trends Endocrinol Metab 2015
46
4



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
2

Single-Cell Transcriptomics Meets Lineage Tracing.
Lennart Kester, Alexander van Oudenaarden. Cell Stem Cell 2018
140
2

Reconstituting organ-level lung functions on a chip.
Dongeun Huh, Benjamin D Matthews, Akiko Mammoto, Martín Montoya-Zavala, Hong Yuan Hsin, Donald E Ingber. Science 2010
2

Induction of pluripotent stem cells from adult human fibroblasts by defined factors.
Kazutoshi Takahashi, Koji Tanabe, Mari Ohnuki, Megumi Narita, Tomoko Ichisaka, Kiichiro Tomoda, Shinya Yamanaka. Cell 2007
2


HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
2


Current methods in medical image segmentation.
D L Pham, C Xu, J L Prince. Annu Rev Biomed Eng 2000
505
2

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
2



Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.
Mamta Tahiliani, Kian Peng Koh, Yinghua Shen, William A Pastor, Hozefa Bandukwala, Yevgeny Brudno, Suneet Agarwal, Lakshminarayan M Iyer, David R Liu, L Aravind,[...]. Science 2009
2

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
2

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.
Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D Thomas. Nucleic Acids Res 2019
832
2

Regulation of lifespan by neural excitation and REST.
Joseph M Zullo, Derek Drake, Liviu Aron, Patrick O'Hern, Sameer C Dhamne, Noah Davidsohn, Chai-An Mao, William H Klein, Alexander Rotenberg, David A Bennett,[...]. Nature 2019
44
4

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
2

Protein homology detection by HMM-HMM comparison.
Johannes Söding. Bioinformatics 2005
2


The Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
2

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
2

Dysfunction in GABA signalling mediates autism-like stereotypies and Rett syndrome phenotypes.
Hsiao-Tuan Chao, Hongmei Chen, Rodney C Samaco, Mingshan Xue, Maria Chahrour, Jong Yoo, Jeffrey L Neul, Shiaoching Gong, Hui-Chen Lu, Nathaniel Heintz,[...]. Nature 2010
733
2



Brain development in rodents and humans: Identifying benchmarks of maturation and vulnerability to injury across species.
Bridgette D Semple, Klas Blomgren, Kayleen Gimlin, Donna M Ferriero, Linda J Noble-Haeusslein. Prog Neurobiol 2013
831
2

TrackMate: An open and extensible platform for single-particle tracking.
Jean-Yves Tinevez, Nick Perry, Johannes Schindelin, Genevieve M Hoopes, Gregory D Reynolds, Emmanuel Laplantine, Sebastian Y Bednarek, Spencer L Shorte, Kevin W Eliceiri. Methods 2017
745
2


A biomarker that identifies senescent human cells in culture and in aging skin in vivo.
G P Dimri, X Lee, G Basile, M Acosta, G Scott, C Roskelley, E E Medrano, M Linskens, I Rubelj, O Pereira-Smith. Proc Natl Acad Sci U S A 1995
2

Matrix elasticity directs stem cell lineage specification.
Adam J Engler, Shamik Sen, H Lee Sweeney, Dennis E Discher. Cell 2006
2


Nanoparticle-liver interactions: Cellular uptake and hepatobiliary elimination.
Yi-Nan Zhang, Wilson Poon, Anthony J Tavares, Ian D McGilvray, Warren C W Chan. J Control Release 2016
341
2

Directing Nanoparticle Biodistribution through Evasion and Exploitation of Stab2-Dependent Nanoparticle Uptake.
Frederick Campbell, Frank L Bos, Sandro Sieber, Gabriela Arias-Alpizar, Bjørn E Koch, Jörg Huwyler, Alexander Kros, Jeroen Bussmann. ACS Nano 2018
78
2

The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs.
Kristen M Kwan, Esther Fujimoto, Clemens Grabher, Benjamin D Mangum, Melissa E Hardy, Douglas S Campbell, John M Parant, H Joseph Yost, John P Kanki, Chi-Bin Chien. Dev Dyn 2007
2

The integrated stress response.
Karolina Pakos-Zebrucka, Izabela Koryga, Katarzyna Mnich, Mila Ljujic, Afshin Samali, Adrienne M Gorman. EMBO Rep 2016
671
2



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.