A citation-based method for searching scientific literature

J B Tenenbaum, V de Silva, J C Langford. Science 2000
Times Cited: 1602







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



Times Cited
  Times     Co-cited
Similarity



Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.
R R Coifman, S Lafon, A B Lee, M Maggioni, B Nadler, F Warner, S W Zucker. Proc Natl Acad Sci U S A 2005
400
11

Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
9

Reducing the dimensionality of data with neural networks.
G E Hinton, R R Salakhutdinov. Science 2006
8

Deep learning.
Yann LeCun, Yoshua Bengio, Geoffrey Hinton. Nature 2015
8


Principal component analysis: a review and recent developments.
Ian T Jolliffe, Jorge Cadima. Philos Trans A Math Phys Eng Sci 2016
6

Visualizing structure and transitions in high-dimensional biological data.
Kevin R Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B Burkhardt, William S Chen, Kristina Yim, Antonia van den Elzen, Matthew J Hirn, Ronald R Coifman,[...]. Nat Biotechnol 2019
196
6

Eigenfaces for recognition.
M Turk, A Pentland. J Cogn Neurosci 1991
843
5

The WU-Minn Human Connectome Project: an overview.
David C Van Essen, Stephen M Smith, Deanna M Barch, Timothy E J Behrens, Essa Yacoub, Kamil Ugurbil. Neuroimage 2013
5

Hessian eigenmaps: locally linear embedding techniques for high-dimensional data.
David L Donoho, Carrie Grimes. Proc Natl Acad Sci U S A 2003
149
5

Unsupervised Learning Methods for Molecular Simulation Data.
Aldo Glielmo, Brooke E Husic, Alex Rodriguez, Cecilia Clementi, Frank Noé, Alessandro Laio. Chem Rev 2021
41
12

FSL.
Mark Jenkinson, Christian F Beckmann, Timothy E J Behrens, Mark W Woolrich, Stephen M Smith. Neuroimage 2012
5

The minimal preprocessing pipelines for the Human Connectome Project.
Matthew F Glasser, Stamatios N Sotiropoulos, J Anthony Wilson, Timothy S Coalson, Bruce Fischl, Jesper L Andersson, Junqian Xu, Saad Jbabdi, Matthew Webster, Jonathan R Polimeni,[...]. Neuroimage 2013
5

The art of using t-SNE for single-cell transcriptomics.
Dmitry Kobak, Philipp Berens. Nat Commun 2019
207
5

Representation learning: a review and new perspectives.
Yoshua Bengio, Aaron Courville, Pascal Vincent. IEEE Trans Pattern Anal Mach Intell 2013
5

Rotational Invariant Dimensionality Reduction Algorithms.
Zhihui Lai, Yong Xu, Jian Yang, Linlin Shen, David Zhang. IEEE Trans Cybern 2017
17
23

Graph Regularized Nonnegative Matrix Factorization for Data Representation.
Deng Cai, Xiaofei He, Jiawei Han, Thomas S Huang. IEEE Trans Pattern Anal Mach Intell 2011
288
4


Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
612
4

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
482
4

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis. Genome Biol 2019
389
4

Essential dynamics of proteins.
A Amadei, A B Linssen, H J Berendsen. Proteins 1993
4

Large-Scale Gradients in Human Cortical Organization.
Julia M Huntenburg, Pierre-Louis Bazin, Daniel S Margulies. Trends Cogn Sci 2018
236
4

BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets.
Reinder Vos de Wael, Oualid Benkarim, Casey Paquola, Sara Lariviere, Jessica Royer, Shahin Tavakol, Ting Xu, Seok-Jun Hong, Georg Langs, Sofie Valk,[...]. Commun Biol 2020
87
4

FreeSurfer.
Bruce Fischl. Neuroimage 2012
4

Situating the default-mode network along a principal gradient of macroscale cortical organization.
Daniel S Margulies, Satrajit S Ghosh, Alexandros Goulas, Marcel Falkiewicz, Julia M Huntenburg, Georg Langs, Gleb Bezgin, Simon B Eickhoff, F Xavier Castellanos, Michael Petrides,[...]. Proc Natl Acad Sci U S A 2016
629
4

The isomap algorithm and topological stability.
Mukund Balasubramanian, Eric L Schwartz. Science 2002
96
4

Long short-term memory.
S Hochreiter, J Schmidhuber. Neural Comput 1997
3

Face recognition using laplacianfaces.
Xiaofei He, Shuicheng Yan, Yuxiao Hu, P Niyogi, Hong-Jiang Zhang. IEEE Trans Pattern Anal Mach Intell 2005
329
3

Approximate Orthogonal Sparse Embedding for Dimensionality Reduction.
Zhihui Lai, Wai Keung Wong, Yong Xu, Jian Yang, David Zhang. IEEE Trans Neural Netw Learn Syst 2016
26
11

Multilinear sparse principal component analysis.
Zhihui Lai, Yong Xu, Qingcai Chen, Jian Yang, David Zhang. IEEE Trans Neural Netw Learn Syst 2014
34
8

Estimating the intrinsic dimension of datasets by a minimal neighborhood information.
Elena Facco, Maria d'Errico, Alex Rodriguez, Alessandro Laio. Sci Rep 2017
39
7

The graph neural network model.
Franco Scarselli, Marco Gori, Ah Chung Tsoi, Markus Hagenbuchner, Gabriele Monfardini. IEEE Trans Neural Netw 2009
309
3

Local Affine Multidimensional Projection.
Paulo Joia, Fernando V Paulovich, Danilo Coimbra, José Alberto Cuminato, Luis Gustavo Nonato. IEEE Trans Vis Comput Graph 2011
29
10

Similarity network fusion for aggregating data types on a genomic scale.
Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg. Nat Methods 2014
706
3

Clustering algorithms: A comparative approach.
Mayra Z Rodriguez, Cesar H Comin, Dalcimar Casanova, Odemir M Bruno, Diego R Amancio, Luciano da F Costa, Francisco A Rodrigues. PLoS One 2019
67
4

Atomic-resolution protein structure determination by cryo-EM.
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark. Nature 2020
202
3

Likelihood-based classification of cryo-EM images using FREALIGN.
Dmitry Lyumkis, Axel F Brilot, Douglas L Theobald, Nikolaus Grigorieff. J Struct Biol 2013
170
3

Single-particle cryo-EM at atomic resolution.
Takanori Nakane, Abhay Kotecha, Andrija Sente, Greg McMullan, Simonas Masiulis, Patricia M G E Brown, Ioana T Grigoras, Lina Malinauskaite, Tomas Malinauskas, Jonas Miehling,[...]. Nature 2020
274
3

New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim Jh Hagen, Erik Lindahl, Sjors Hw Scheres. Elife 2018
3

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
3


Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images.
Pawel A Penczek, Marek Kimmel, Christian M T Spahn. Structure 2011
68
4

Directly reconstructing principal components of heterogeneous particles from cryo-EM images.
Hemant D Tagare, Alp Kucukelbir, Fred J Sigworth, Hongwei Wang, Murali Rao. J Struct Biol 2015
41
7

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.
Jiayi Wu, Yong-Bei Ma, Charles Congdon, Bevin Brett, Shuobing Chen, Yaofang Xu, Qi Ouyang, Youdong Mao. PLoS One 2017
23
13

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.
Ellen D Zhong, Tristan Bepler, Bonnie Berger, Joseph H Davis. Nat Methods 2021
91
3

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M White, Matthew J O'Meara, Veronica V Rezelj, Jeffrey Z Guo, Danielle L Swaney,[...]. Nature 2020
3

Robust recovery of subspace structures by low-rank representation.
Guangcan Liu, Zhouchen Lin, Shuicheng Yan, Ju Sun, Yong Yu, Yi Ma. IEEE Trans Pattern Anal Mach Intell 2013
370
3

The curse(s) of dimensionality.
Naomi Altman, Martin Krzywinski. Nat Methods 2018
64
4


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.