A citation-based method for searching scientific literature

Karren Dai Yang, Anastasiya Belyaeva, Saradha Venkatachalapathy, Karthik Damodaran, Abigail Katcoff, Adityanarayanan Radhakrishnan, G V Shivashankar, Caroline Uhler. Nat Commun 2021
Times Cited: 7







List of co-cited articles
43 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
57

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.
Kieran R Campbell, Adi Steif, Emma Laks, Hans Zahn, Daniel Lai, Andrew McPherson, Hossein Farahani, Farhia Kabeer, Ciara O'Flanagan, Justina Biele,[...]. Genome Biol 2019
26
57

Integrative Methods and Practical Challenges for Single-Cell Multi-omics.
Anjun Ma, Adam McDermaid, Jennifer Xu, Yuzhou Chang, Qin Ma. Trends Biotechnol 2020
29
57

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, Jose L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen,[...]. Science 2018
222
57

Unsupervised topological alignment for single-cell multi-omics integration.
Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan. Bioinformatics 2020
9
42

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
628
42

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
187
42

Single-cell multimodal omics: the power of many.
Chenxu Zhu, Sebastian Preissl, Bing Ren. Nat Methods 2020
60
42

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.
Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle. Mol Syst Biol 2018
174
42


Single-cell multiomics: technologies and data analysis methods.
Jeongwoo Lee, Do Young Hyeon, Daehee Hwang. Exp Mol Med 2020
32
42

BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data.
Xinjun Wang, Zhe Sun, Yanfu Zhang, Zhongli Xu, Hongyi Xin, Heng Huang, Richard H Duerr, Kong Chen, Ying Ding, Wei Chen. Nucleic Acids Res 2020
9
42

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.
Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C Marioni, Oliver Stegle. Genome Biol 2020
39
42

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.
Zhana Duren, Xi Chen, Mahdi Zamanighomi, Wanwen Zeng, Ansuman T Satpathy, Howard Y Chang, Yong Wang, Wing Hung Wong. Proc Natl Acad Sci U S A 2018
47
42


Reducing the dimensionality of data with neural networks.
G E Hinton, R R Salakhutdinov. Science 2006
28

Predicting cell lineages using autoencoders and optimal transport.
Karren Dai Yang, Karthik Damodaran, Saradha Venkatachalapathy, Ali C Soylemezoglu, G V Shivashankar, Caroline Uhler. PLoS Comput Biol 2020
3
66

Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.
Yu Hou, Huahu Guo, Chen Cao, Xianlong Li, Boqiang Hu, Ping Zhu, Xinglong Wu, Lu Wen, Fuchou Tang, Yanyi Huang,[...]. Cell Res 2016
247
28

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
107
28

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.
Iain C Macaulay, Wilfried Haerty, Parveen Kumar, Yang I Li, Tim Xiaoming Hu, Mabel J Teng, Mubeen Goolam, Nathalie Saurat, Paul Coupland, Lesley M Shirley,[...]. Nat Methods 2015
327
28


Bayesian consensus clustering.
Eric F Lock, David B Dunson. Bioinformatics 2013
86
28

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
476
28

MOLI: multi-omics late integration with deep neural networks for drug response prediction.
Hossein Sharifi-Noghabi, Olga Zolotareva, Colin C Collins, Martin Ester. Bioinformatics 2019
39
28

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
426
28

Computational methods for single-cell omics across modalities.
Mirjana Efremova, Sarah A Teichmann. Nat Methods 2020
40
28

JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES.
Eric F Lock, Katherine A Hoadley, J S Marron, Andrew B Nobel. Ann Appl Stat 2013
135
28

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.
Blue B Lake, Song Chen, Brandon C Sos, Jean Fan, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko,[...]. Nat Biotechnol 2018
256
28

Multi-omics integration-a comparison of unsupervised clustering methodologies.
Giulia Tini, Luca Marchetti, Corrado Priami, Marie-Pier Scott-Boyer. Brief Bioinform 2019
43
28

Integrated genome and transcriptome sequencing of the same cell.
Siddharth S Dey, Lennart Kester, Bastiaan Spanjaard, Magda Bienko, Alexander van Oudenaarden. Nat Biotechnol 2015
242
28

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets.
Evelina Gabasova, John Reid, Lorenz Wernisch. PLoS Comput Biol 2017
18
28

Exploring and analysing single cell multi-omics data with VDJView.
Jerome Samir, Simone Rizzetto, Money Gupta, Fabio Luciani. BMC Med Genomics 2020
6
33

Multi-omics approaches to disease.
Yehudit Hasin, Marcus Seldin, Aldons Lusis. Genome Biol 2017
459
28

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
285
28


Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.
Hannah A Pliner, Jonathan S Packer, José L McFaline-Figueroa, Darren A Cusanovich, Riza M Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina,[...]. Mol Cell 2018
118
28

Integrative analyses of single-cell transcriptome and regulome using MAESTRO.
Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie,[...]. Genome Biol 2020
20
28

Surface protein imputation from single cell transcriptomes by deep neural networks.
Zilu Zhou, Chengzhong Ye, Jingshu Wang, Nancy R Zhang. Nat Commun 2020
10
28

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.
Sai Ma, Bing Zhang, Lindsay M LaFave, Andrew S Earl, Zachary Chiang, Yan Hu, Jiarui Ding, Alison Brack, Vinay K Kartha, Tristan Tay,[...]. Cell 2020
41
28


Multiplexed quantification of proteins and transcripts in single cells.
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach. Nat Biotechnol 2017
278
28

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity.
Longqi Liu, Chuanyu Liu, Andrés Quintero, Liang Wu, Yue Yuan, Mingyue Wang, Mengnan Cheng, Lizhi Leng, Liqin Xu, Guoyi Dong,[...]. Nat Commun 2019
50
28

An Immune Atlas of Clear Cell Renal Cell Carcinoma.
Stéphane Chevrier, Jacob Harrison Levine, Vito Riccardo Tomaso Zanotelli, Karina Silina, Daniel Schulz, Marina Bacac, Carola Hermine Ries, Laurie Ailles, Michael Alexander Spencer Jewett, Holger Moch,[...]. Cell 2017
386
14

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
14

BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes.
Tongxin Wang, Travis S Johnson, Wei Shao, Zixiao Lu, Bryan R Helm, Jie Zhang, Kun Huang. Genome Biol 2019
25
14

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.
Stéphane Chevrier, Helena L Crowell, Vito R T Zanotelli, Stefanie Engler, Mark D Robinson, Bernd Bodenmiller. Cell Syst 2018
94
14

Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry.
Karolyn A Oetjen, Katherine E Lindblad, Meghali Goswami, Gege Gui, Pradeep K Dagur, Catherine Lai, Laura W Dillon, J Philip McCoy, Christopher S Hourigan. JCI Insight 2018
24
14

The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support.
Anja Irmisch, Ximena Bonilla, Stéphane Chevrier, Kjong-Van Lehmann, Franziska Singer, Nora C Toussaint, Cinzia Esposito, Julien Mena, Emanuela S Milani, Ruben Casanova,[...]. Cancer Cell 2021
5
20

The Human Cell Atlas: from vision to reality.
Orit Rozenblatt-Rosen, Michael J T Stubbington, Aviv Regev, Sarah A Teichmann. Nature 2017
201
14


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.