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: 22181







List of co-cited articles
48 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
8

CellProfiler 3.0: Next-generation image processing for biology.
Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A Cimini, Kyle W Karhohs, Minh Doan, Liya Ding, Susanne M Rafelski, Derek Thirstrup,[...]. PLoS Biol 2018
607
5

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
4

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
952
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

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
4

Democratising deep learning for microscopy with ZeroCostDL4Mic.
Lucas von Chamier, Romain F Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K Mattila, Eleni Karinou,[...]. Nat Commun 2021
44
6

Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification.
Ignacio Arganda-Carreras, Verena Kaynig, Curtis Rueden, Kevin W Eliceiri, Johannes Schindelin, Albert Cardona, H Sebastian Seung. Bioinformatics 2017
422
3

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
3

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
3

deepTools2: a next generation web server for deep-sequencing data analysis.
Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke. Nucleic Acids Res 2016
3

Content-aware image restoration: pushing the limits of fluorescence microscopy.
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley,[...]. Nat Methods 2018
221
2

ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging.
Daisuke Kurihara, Yoko Mizuta, Yoshikatsu Sato, Tetsuya Higashiyama. Development 2015
224
2

A protocol for combining fluorescent proteins with histological stains for diverse cell wall components.
Robertas Ursache, Tonni Grube Andersen, Peter Marhavý, Niko Geldner. Plant J 2018
131
2


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

GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death.
Lorenzo Sborgi, Sebastian Rühl, Estefania Mulvihill, Joka Pipercevic, Rosalie Heilig, Henning Stahlberg, Christopher J Farady, Daniel J Müller, Petr Broz, Sebastian Hiller. EMBO J 2016
481
2

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

Inhibition of Endosteal Vascular Niche Remodeling Rescues Hematopoietic Stem Cell Loss in AML.
Delfim Duarte, Edwin D Hawkins, Olufolake Akinduro, Heather Ang, Katia De Filippo, Isabella Y Kong, Myriam Haltalli, Nicola Ruivo, Lenny Straszkowski, Stephin J Vervoort,[...]. Cell Stem Cell 2018
143
2


Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set.
Niko Geldner, Valérie Dénervaud-Tendon, Derek L Hyman, Ulrike Mayer, York-Dieter Stierhof, Joanne Chory. Plant J 2009
394
2


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
2

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
2


Measurement of co-localization of objects in dual-colour confocal images.
E M M Manders, F J Verbeek, J A Aten. J Microsc 1993
643
2

Dissection of Drosophila melanogaster Flight Muscles for Omics Approaches.
Shao-Yen Kao, Elena Nikonova, Keshika Ravichandran, Maria L Spletter. J Vis Exp 2019
8
25

ilastik: interactive machine learning for (bio)image analysis.
Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N Straehle, Bernhard X Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy,[...]. Nat Methods 2019
428
2

Computer visualization of three-dimensional image data using IMOD.
J R Kremer, D N Mastronarde, J R McIntosh. J Struct Biol 1996
2

The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
2

Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations.
Nils Gustafsson, Siân Culley, George Ashdown, Dylan M Owen, Pedro Matos Pereira, Ricardo Henriques. Nat Commun 2016
217
2

Quantitative mapping and minimization of super-resolution optical imaging artifacts.
Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques. Nat Methods 2018
102
2

SRRF: Universal live-cell super-resolution microscopy.
Siân Culley, Kalina L Tosheva, Pedro Matos Pereira, Ricardo Henriques. Int J Biochem Cell Biol 2018
52
3


Niche regulation of muscle satellite cell self-renewal and differentiation.
Shihuan Kuang, Mark A Gillespie, Michael A Rudnicki. Cell Stem Cell 2008
312
2

Self-organizing optic-cup morphogenesis in three-dimensional culture.
Mototsugu Eiraku, Nozomu Takata, Hiroki Ishibashi, Masako Kawada, Eriko Sakakura, Satoru Okuda, Kiyotoshi Sekiguchi, Taiji Adachi, Yoshiki Sasai. Nature 2011
2


V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.
Hanchuan Peng, Zongcai Ruan, Fuhui Long, Julie H Simpson, Eugene W Myers. Nat Biotechnol 2010
372
2

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.
Javier Tapial, Kevin C H Ha, Timothy Sterne-Weiler, André Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez,[...]. Genome Res 2017
131
2

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
2

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
2

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
2


Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes.
Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman. Genome Biol 2002
2

Parkinson's disease.
Lorraine V Kalia, Anthony E Lang. Lancet 2015
2

Transmission of α-synuclein seeds in neurodegenerative disease: recent developments.
Richard J Karpowicz, John Q Trojanowski, Virginia M-Y Lee. Lab Invest 2019
47
4

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
2


Fine processes of Nestin-GFP-positive radial glia-like stem cells in the adult dentate gyrus ensheathe local synapses and vasculature.
Jonathan Moss, Elias Gebara, Eric A Bushong, Irene Sánchez-Pascual, Ruadhan O'Laoi, Imane El M'Ghari, Jacqueline Kocher-Braissant, Mark H Ellisman, Nicolas Toni. Proc Natl Acad Sci U S A 2016
63
1


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.