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: 17375







List of co-cited articles
58 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
7

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
6

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

A pyramid approach to subpixel registration based on intensity.
P Thévenaz, U E Ruttimann, M Unser. IEEE Trans Image Process 1998
3

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
3

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
3

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

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
3

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
3

Matrix elasticity directs stem cell lineage specification.
Adam J Engler, Shamik Sen, H Lee Sweeney, Dennis E Discher. Cell 2006
3

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
672
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

A molecular perspective of mammalian autophagosome biogenesis.
Thomas J Mercer, Andrea Gubas, Sharon A Tooze. J Biol Chem 2018
114
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


Globally optimal stitching of tiled 3D microscopic image acquisitions.
Stephan Preibisch, Stephan Saalfeld, Pavel Tomancak. Bioinformatics 2009
902
2


Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).
Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Dustin Ebert, Caitlin Mills, Xinyu Guo, Paul D Thomas. Nat Protoc 2019
262
2

CellProfiler: image analysis software for identifying and quantifying cell phenotypes.
Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A Guertin, Joo Han Chang, Robert A Lindquist, Jason Moffat,[...]. Genome Biol 2006
2

Analyzing real-time PCR data by the comparative C(T) method.
Thomas D Schmittgen, Kenneth J Livak. Nat Protoc 2008
2


Birefringence imaging of posterior eye by multi-functional Jones matrix optical coherence tomography.
Satoshi Sugiyama, Young-Joo Hong, Deepa Kasaragod, Shuichi Makita, Sato Uematsu, Yasushi Ikuno, Masahiro Miura, Yoshiaki Yasuno. Biomed Opt Express 2015
28
7

Depth-resolved model-based reconstruction of attenuation coefficients in optical coherence tomography.
K A Vermeer, J Mo, J J A Weda, H G Lemij, J F de Boer. Biomed Opt Express 2013
118
2

Polarization sensitive optical coherence tomography - a review [Invited].
Johannes F de Boer, Christoph K Hitzenberger, Yoshiaki Yasuno. Biomed Opt Express 2017
91
2

Noise-immune complex correlation for optical coherence angiography based on standard and Jones matrix optical coherence tomography.
Shuichi Makita, Kazuhiro Kurokawa, Young-Joo Hong, Masahiro Miura, Yoshiaki Yasuno. Biomed Opt Express 2016
32
6

Retinal pigment epithelium segmentation by polarization sensitive optical coherence tomography.
Erich Götzinger, Michael Pircher, Wolfgang Geitzenauer, Christian Ahlers, Bernhard Baumann, Stephan Michels, Ursula Schmidt-Erfurth, Christoph K Hitzenberger. Opt Express 2008
148
2

Polarization sensitive optical coherence tomography of melanin provides intrinsic contrast based on depolarization.
Bernhard Baumann, Stefan O Baumann, Thomas Konegger, Michael Pircher, Erich Götzinger, Ferdinand Schlanitz, Christopher Schütze, Harald Sattmann, Marco Litschauer, Ursula Schmidt-Erfurth,[...]. Biomed Opt Express 2012
74
2

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.
Daniel E Wagner, Caleb Weinreb, Zach M Collins, James A Briggs, Sean G Megason, Allon M Klein. Science 2018
225
2

Single-Cell Transcriptomics Meets Lineage Tracing.
Lennart Kester, Alexander van Oudenaarden. Cell Stem Cell 2018
128
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

Characterization of the Circumlimbal Suture Model of Chronic IOP Elevation in Mice and Assessment of Changes in Gene Expression of Stretch Sensitive Channels.
Da Zhao, Christine T O Nguyen, Vickie H Y Wong, Jeremiah K H Lim, Zheng He, Andrew I Jobling, Erica L Fletcher, Holly R Chinnery, Algis J Vingrys, Bang V Bui. Front Neurosci 2017
19
10


Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
2


Current methods in medical image segmentation.
D L Pham, C Xu, J L Prince. Annu Rev Biomed Eng 2000
460
2

The ImageJ ecosystem: An open platform for biomedical image analysis.
Johannes Schindelin, Curtis T Rueden, Mark C Hiner, Kevin W Eliceiri. Mol Reprod Dev 2015
924
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

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
2


The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Y Hein, Tamar Geiger, Matthias Mann, Jürgen Cox. Nat Methods 2016
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

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

An expanded palette of genetically encoded Ca²⁺ indicators.
Yongxin Zhao, Satoko Araki, Jiahui Wu, Takayuki Teramoto, Yu-Fen Chang, Masahiro Nakano, Ahmed S Abdelfattah, Manabi Fujiwara, Takeshi Ishihara, Takeharu Nagai,[...]. Science 2011
708
2

Calcium signaling.
David E Clapham. Cell 2007
2

Optogenetic control of cellular forces and mechanotransduction.
Léo Valon, Ariadna Marín-Llauradó, Thomas Wyatt, Guillaume Charras, Xavier Trepat. Nat Commun 2017
73
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.