A citation-based method for searching scientific literature

Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
Times Cited: 179



Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
Times Cited: 474




List of shared articles



Times cited

Computational methods for the integrative analysis of single-cell data.
Mattia Forcato, Oriana Romano, Silvio Bicciato. Brief Bioinform 2021
12

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test.
Yun Zhang, Brian D Aevermann, Trygve E Bakken, Jeremy A Miller, Rebecca D Hodge, Ed S Lein, Richard H Scheuermann. Brief Bioinform 2021
1

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.
Tallulah S Andrews, Vladimir Yu Kiselev, Davis McCarthy, Martin Hemberg. Nat Protoc 2021
10


Supervised Adversarial Alignment of Single-Cell RNA-seq Data.
Songwei Ge, Haohan Wang, Amir Alavi, Eric Xing, Ziv Bar-Joseph. J Comput Biol 2021
1


Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef. Mol Syst Biol 2021
10

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.
Ruben Chazarra-Gil, Stijn van Dongen, Vladimir Yu Kiselev, Martin Hemberg. Nucleic Acids Res 2021
6



Integration and transfer learning of single-cell transcriptomes via cFIT.
Minshi Peng, Yue Li, Brie Wamsley, Yuting Wei, Kathryn Roeder. Proc Natl Acad Sci U S A 2021
3

Critical downstream analysis steps for single-cell RNA sequencing data.
Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, Quan Zou. Brief Bioinform 2021
0

Single-Cell RNA Sequencing in Parkinson's Disease.
Shi-Xun Ma, Su Bin Lim. Biomedicines 2021
1

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID.
Akira Cortal, Loredana Martignetti, Emmanuelle Six, Antonio Rausell. Nat Biotechnol 2021
1

Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalities.
Rohit Singh, Brian L Hie, Ashwin Narayan, Bonnie Berger. Genome Biol 2021
1

Computational principles and challenges in single-cell data integration.
Ricard Argelaguet, Anna S E Cuomo, Oliver Stegle, John C Marioni. Nat Biotechnol 2021
6

Cell-level metadata are indispensable for documenting single-cell sequencing datasets.
Sidhant Puntambekar, Jay R Hesselberth, Kent A Riemondy, Rui Fu. PLoS Biol 2021
0


SSBER: removing batch effect for single-cell RNA sequencing data.
Yin Zhang, Fei Wang. BMC Bioinformatics 2021
0

Interpretation of T cell states from single-cell transcriptomics data using reference atlases.
Massimo Andreatta, Jesus Corria-Osorio, Sören Müller, Rafael Cubas, George Coukos, Santiago J Carmona. Nat Commun 2021
4

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods.
Zoe A Clarke, Tallulah S Andrews, Jawairia Atif, Delaram Pouyabahar, Brendan T Innes, Sonya A MacParland, Gary D Bader. Nat Protoc 2021
0

Integrating multiple references for single-cell assignment.
Bin Duan, Shaoqi Chen, Xiaohan Chen, Chenyu Zhu, Chen Tang, Shuguang Wang, Yicheng Gao, Shaliu Fu, Qi Liu. Nucleic Acids Res 2021
0

Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
45


Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor.
Stephan Fischer, Megan Crow, Benjamin D Harris, Jesse Gillis. Nat Protoc 2021
0

RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.
Florian Schmidt, Bobby Ranjan, Quy Xiao Xuan Lin, Vaidehi Krishnan, Ignasius Joanito, Mohammad Amin Honardoost, Zahid Nawaz, Prasanna Nori Venkatesh, Joanna Tan, Nirmala Arul Rayan,[...]. Nucleic Acids Res 2021
0


Leveraging the Cell Ontology to classify unseen cell types.
Sheng Wang, Angela Oliveira Pisco, Aaron McGeever, Maria Brbic, Marinka Zitnik, Spyros Darmanis, Jure Leskovec, Jim Karkanias, Russ B Altman. Nat Commun 2021
0



Efficient and precise single-cell reference atlas mapping with Symphony.
Joyce B Kang, Aparna Nathan, Kathryn Weinand, Fan Zhang, Nghia Millard, Laurie Rumker, D Branch Moody, Ilya Korsunsky, Soumya Raychaudhuri. Nat Commun 2021
0

BBKNN: fast batch alignment of single cell transcriptomes.
Krzysztof Polański, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann, Jong-Eun Park. Bioinformatics 2020
107

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data.
Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei. Bioinformatics 2020
14

Evaluation of single-cell classifiers for single-cell RNA sequencing data sets.
Xinlei Zhao, Shuang Wu, Nan Fang, Xiao Sun, Jue Fan. Brief Bioinform 2020
13

Orchestrating single-cell analysis with Bioconductor.
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson,[...]. Nat Methods 2020
71


An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates.
Jermaine Goveia, Katerina Rohlenova, Federico Taverna, Lucas Treps, Lena-Christin Conradi, Andreas Pircher, Vincent Geldhof, Laura P M H de Rooij, Joanna Kalucka, Liliana Sokol,[...]. Cancer Cell 2020
66

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
142




Advances and challenges in epigenomic single-cell sequencing applications.
Martin Philpott, Adam P Cribbs, Tom Brown, Tom Brown, Udo Oppermann. Curr Opin Chem Biol 2020
8

Single Cell RNA Sequencing in Atherosclerosis Research.
Jesse W Williams, Holger Winkels, Christopher P Durant, Konstantin Zaitsev, Yanal Ghosheh, Klaus Ley. Circ Res 2020
24

BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization.
Federico Taverna, Jermaine Goveia, Tobias K Karakach, Shawez Khan, Katerina Rohlenova, Lucas Treps, Abhishek Subramanian, Luc Schoonjans, Mieke Dewerchin, Guy Eelen,[...]. Nucleic Acids Res 2020
12