A citation-based method for searching scientific literature

Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro, Joshua Gould, Gabriel K Griffin, Åke Borg, Mostafa Ronaghi, Jonas Frisén, Joakim Lundeberg, Aviv Regev, Patrik L Ståhl. Nat Methods 2019
Times Cited: 177



Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
Times Cited: 402




List of shared articles



Times cited

Uncovering an Organ's Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics.
Jie Liao, Xiaoyan Lu, Xin Shao, Ling Zhu, Xiaohui Fan. Trends Biotechnol 2021
25

The Power of Single-Cell Analysis for the Study of Liver Pathobiology.
Angela L Chu, Joel D Schilling, Kevin R King, Ariel E Feldstein. Hepatology 2021
2

Spatial molecular profiling: platforms, applications and analysis tools.
Minzhe Zhang, Thomas Sheffield, Xiaowei Zhan, Qiwei Li, Donghan M Yang, Yunguan Wang, Shidan Wang, Yang Xie, Tao Wang, Guanghua Xiao. Brief Bioinform 2021
3


Deciphering cell-cell interactions and communication from gene expression.
Erick Armingol, Adam Officer, Olivier Harismendy, Nathan E Lewis. Nat Rev Genet 2021
48

Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy.
Satyen H Gohil, J Bryan Iorgulescu, David A Braun, Derin B Keskin, Kenneth J Livak. Nat Rev Clin Oncol 2021
20

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Robert R Stickels, Evan Murray, Pawan Kumar, Jilong Li, Jamie L Marshall, Daniela J Di Bella, Paola Arlotta, Evan Z Macosko, Fei Chen. Nat Biotechnol 2021
33

Spatially resolved transcriptomics adds a new dimension to genomics.
Ludvig Larsson, Jonas Frisén, Joakim Lundeberg. Nat Methods 2021
20

Spatially resolved transcriptomics and its applications in cancer.
Silas Maniatis, Joana Petrescu, Hemali Phatnani. Curr Opin Genet Dev 2021
8

A High-Dimensional Window into the Micro-Environment of Triple Negative Breast Cancer.
Iris Nederlof, Hugo M Horlings, Christina Curtis, Marleen Kok. Cancers (Basel) 2021
2

mbkmeans: Fast clustering for single cell data using mini-batch k-means.
Stephanie C Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso. PLoS Comput Biol 2021
3

Elucidating the cellular dynamics of the brain with single-cell RNA sequencing.
Aida Cardona-Alberich, Manon Tourbez, Sarah F Pearce, Christopher R Sibley. RNA Biol 2021
3

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.
Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett,[...]. Science 2021
27

Space: the final frontier - achieving single-cell, spatially resolved transcriptomics in plants.
Sai Guna Ranjan Gurazada, Kevin L Cox, Kirk J Czymmek, Blake C Meyers. Emerg Top Life Sci 2021
3

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.
Marc Elosua-Bayes, Paula Nieto, Elisabetta Mereu, Ivo Gut, Holger Heyn. Nucleic Acids Res 2021
21

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex.
Kristen R Maynard, Leonardo Collado-Torres, Lukas M Weber, Cedric Uytingco, Brianna K Barry, Stephen R Williams, Joseph L Catallini, Matthew N Tran, Zachary Besich, Madhavi Tippani,[...]. Nat Neurosci 2021
16

Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond.
Florian M Pauler, Quanah J Hudson, Susanne Laukoter, Simon Hippenmeyer. Neurochem Int 2021
1

Robust decomposition of cell type mixtures in spatial transcriptomics.
Dylan M Cable, Evan Murray, Luli S Zou, Aleksandrina Goeva, Evan Z Macosko, Fei Chen, Rafael A Irizarry. Nat Biotechnol 2021
18

Single-cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs.
Ulrich Pfisterer, Julia Bräunig, Per Brattås, Markus Heidenblad, Göran Karlsson, Thoas Fioretos. Genes Chromosomes Cancer 2021
0

Spatially mapped single-cell chromatin accessibility.
Casey A Thornton, Ryan M Mulqueen, Kristof A Torkenczy, Andrew Nishida, Eve G Lowenstein, Andrew J Fields, Frank J Steemers, Wenri Zhang, Heather L McConnell, Randy L Woltjer,[...]. Nat Commun 2021
6

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.
Songlei Liu, Sukanya Punthambaker, Eswar P R Iyer, Thomas Ferrante, Daniel Goodwin, Daniel Fürth, Andrew C Pawlowski, Kunal Jindal, Jenny M Tam, Lauren Mifflin,[...]. Nucleic Acids Res 2021
1

Graph of graphs analysis for multiplexed data with application to imaging mass cytometry.
Ya-Wei Eileen Lin, Tal Shnitzer, Ronen Talmon, Franz Villarroel-Espindola, Shruti Desai, Kurt Schalper, Yuval Kluger. PLoS Comput Biol 2021
0

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion.
Zhuliu Li, Tianci Song, Jeongsik Yong, Rui Kuang. PLoS Comput Biol 2021
0

Applicability of spatial transcriptional profiling to cancer research.
Rania Bassiouni, Lee D Gibbs, David W Craig, John D Carpten, Troy A McEachron. Mol Cell 2021
1

Spatial transcriptomics for respiratory research and medicine.
Sandra Curras-Alonso, Juliette Soulier, Thomas Walter, Florian Mueller, Arturo Londoño-Vallejo, Charles Fouillade. Eur Respir J 2021
0

Mapping Spatial Genetic Landscapes in Tissue Sections through Microscale Integration of Sampling Methodology into Genomic Workflows.
Lena Voith von Voithenberg, Aditya Kashyap, Lennart Opitz, Catharine Aquino, Timothy Sykes, Maike Nieser, Lorenzo F T Petrini, Nadia Enrriquez Casimiro, Xander F van Kooten, Saskia Biskup,[...]. Small 2021
0

Spatial tissue profiling by imaging-free molecular tomography.
Halima Hannah Schede, Christian G Schneider, Johanna Stergiadou, Lars E Borm, Anurag Ranjak, Tracy M Yamawaki, Fabrice P A David, Peter Lönnerberg, Maria Antonietta Tosches, Simone Codeluppi,[...]. Nat Biotechnol 2021
0

XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
Youjin Lee, Derek Bogdanoff, Yutong Wang, George C Hartoularos, Jonathan M Woo, Cody T Mowery, Hunter M Nisonoff, David S Lee, Yang Sun, James Lee,[...]. Sci Adv 2021
0

Spatial Transcriptomics: Molecular Maps of the Mammalian Brain.
Cantin Ortiz, Marie Carlén, Konstantinos Meletis. Annu Rev Neurosci 2021
3

A new era for plant science: spatial single-cell transcriptomics.
Stefania Giacomello. Curr Opin Plant Biol 2021
2

Current and Prospective Methods for Assessing Anti-Tumor Immunity in Colorectal Cancer.
Yulia I Nussbaum, Yariswamy Manjunath, Kanve N Suvilesh, Wesley C Warren, Chi-Ren Shyu, Jussuf T Kaifi, Matthew A Ciorba, Jonathan B Mitchem. Int J Mol Sci 2021
1

Mechanisms of breast cancer metastasis.
S David Nathanson, Michael Detmar, Timothy P Padera, Lucy R Yates, Danny R Welch, Thomas C Beadnell, Adam D Scheid, Emma D Wrenn, Kevin Cheung. Clin Exp Metastasis 2021
0


Review of multi-omics data resources and integrative analysis for human brain disorders.
Xianjun Dong, Chunyu Liu, Mikhail Dozmorov. Brief Funct Genomics 2021
2

Advances in Tumor Sampling and Sequencing in Breast Cancer and their Application in Precision Diagnostics and Therapeutics.
Amos Chungwon Lee, Han-Byoel Lee, Huiran Yeom, Seo Woo Song, Su Deok Kim, Ahyoun Choi, Sumin Lee, Yongju Lee, Wonshik Han, Sunghoon Kwon. Adv Exp Med Biol 2021
0

Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury.
Ricardo Melo Ferreira, Angela R Sabo, Seth Winfree, Kimberly S Collins, Danielle Janosevic, Connor J Gulbronson, Ying-Hua Cheng, Lauren Casbon, Daria Barwinska, Michael J Ferkowicz,[...]. JCI Insight 2021
0

Bridging scales: From cell biology to physiology using in situ single-cell technologies.
Maeve P Nagle, Gabriela S Tam, Evan Maltz, Zachary Hemminger, Roy Wollman. Cell Syst 2021
1

Clump sequencing exposes the spatial expression programs of intestinal secretory cells.
Rita Manco, Inna Averbukh, Ziv Porat, Keren Bahar Halpern, Ido Amit, Shalev Itzkovitz. Nat Commun 2021
2

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

Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects.
Lu Huo, Jiao Jiao Li, Ling Chen, Zuguo Yu, Gyorgy Hutvagner, Jinyan Li. Brief Bioinform 2021
0

Microscopic examination of spatial transcriptome using Seq-Scope.
Chun-Seok Cho, Jingyue Xi, Yichen Si, Sung-Rye Park, Jer-En Hsu, Myungjin Kim, Goo Jun, Hyun Min Kang, Jun Hee Lee. Cell 2021
3


Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment.
Nan Wang, Xia Li, Rongshui Wang, Zhiyong Ding. Biotechnol J 2021
1

A convolutional neural network for common coordinate registration of high-resolution histology images.
Aidan C Daly, Krzysztof J Geras, Richard A Bonneau. Bioinformatics 2021
0

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics.
Sophia K Longo, Margaret G Guo, Andrew L Ji, Paul A Khavari. Nat Rev Genet 2021
10

Recent advances in tools to map the microbiome.
Hao Shi, Benjamin Grodner, Iwijn De Vlaminck. Curr Opin Biomed Eng 2021
0


Plasticity and heterogeneity of thermogenic adipose tissue.
Wenfei Sun, Salvatore Modica, Hua Dong, Christian Wolfrum. Nat Metab 2021
1

Applications of Single-Cell Omics in Tumor Immunology.
Junwei Liu, Saisi Qu, Tongtong Zhang, Yufei Gao, Hongyu Shi, Kaichen Song, Wei Chen, Weiwei Yin. Front Immunol 2021
2

Generating and Using Transcriptomically Based Retinal Cell Atlases.
Karthik Shekhar, Joshua R Sanes. Annu Rev Vis Sci 2021
0