A citation-based method for searching scientific literature

Qianqian Song, Jing Su, Lance D Miller, Wei Zhang. Genomics Proteomics Bioinformatics 2021
Times Cited: 7







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



Times Cited
  Times     Co-cited
Similarity




Multi-Omics Analysis of Brain Metastasis Outcomes Following Craniotomy.
Jing Su, Qianqian Song, Shadi Qasem, Stacey O'Neill, Jingyun Lee, Cristina M Furdui, Boris Pasche, Linda Metheny-Barlow, Adrianna H Masters, Hui-Wen Lo,[...]. Front Oncol 2021
6
66

Identification and Validation of the N6-Methyladenosine RNA Methylation Regulator YTHDF1 as a Novel Prognostic Marker and Potential Target for Hepatocellular Carcinoma.
Saiyan Bian, Wenkai Ni, Mengqi Zhu, Qianqian Song, Jianping Zhang, Runzhou Ni, Wenjie Zheng. Front Mol Biosci 2020
12
42



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
25
28


Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
392
28

Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq.
Qianqian Song, Gregory A Hawkins, Leonard Wudel, Ping-Chieh Chou, Elizabeth Forbes, Ashok K Pullikuth, Liang Liu, Guangxu Jin, Lou Craddock, Umit Topaloglu,[...]. Cancer Med 2019
38
28

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
625
28

Preparing next-generation scientists for biomedical big data: artificial intelligence approaches.
Jason H Moore, Mary Regina Boland, Pablo G Camara, Hannah Chervitz, Graciela Gonzalez, Blanca E Himes, Dokyoon Kim, Danielle L Mowery, Marylyn D Ritchie, Li Shen,[...]. Per Med 2019
8
28

A Single-Cell Transcriptome Atlas of the Human Pancreas.
Mauro J Muraro, Gitanjali Dharmadhikari, Dominic Grün, Nathalie Groen, Tim Dielen, Erik Jansen, Leon van Gurp, Marten A Engelse, Francoise Carlotti, Eelco J P de Koning,[...]. Cell Syst 2016
397
28

Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction.
Jin Li, Sai Zhang, Tao Liu, Chenxi Ning, Zhuoxuan Zhang, Wei Zhou. Bioinformatics 2020
34
28

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
511
28

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.
Emelie Berglund, Jonas Maaskola, Niklas Schultz, Stefanie Friedrich, Maja Marklund, Joseph Bergenstråhle, Firas Tarish, Anna Tanoglidi, Sanja Vickovic, Ludvig Larsson,[...]. Nat Commun 2018
126
28

Identifying drug-target interactions based on graph convolutional network and deep neural network.
Tianyi Zhao, Yang Hu, Linda R Valsdottir, Tianyi Zang, Jiajie Peng. Brief Bioinform 2021
31
28

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K Lau,[...]. Nat Biotechnol 2020
87
28

Interpretable Artificial Intelligence: Why and When.
Adarsh Ghosh, Devasenathipathy Kandasamy. AJR Am J Roentgenol 2020
8
28

DNA primase subunit 1 deteriorated progression of hepatocellular carcinoma by activating AKT/mTOR signaling and UBE2C-mediated P53 ubiquitination.
Mengqi Zhu, Mengna Wu, Saiyan Bian, Qianqian Song, Mingbing Xiao, Hua Huang, Li You, Jianping Zhang, Jie Zhang, Chun Cheng,[...]. Cell Biosci 2021
9
28

A robust twelve-gene signature for prognosis prediction of hepatocellular carcinoma.
Guoqing Ouyang, Bin Yi, Guangdong Pan, Xiang Chen. Cancer Cell Int 2020
26
28

The Emerging Roles of Exosomes in the Chemoresistance of Hepatocellular Carcinoma.
Jie Zhang, Qianqian Song, Mengna Wu, Wenjie Zheng. Curr Med Chem 2021
7
28

UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses.
Darshan S Chandrashekar, Bhuwan Bashel, Sai Akshaya Hodigere Balasubramanya, Chad J Creighton, Israel Ponce-Rodriguez, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally. Neoplasia 2017
28

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang. Nucleic Acids Res 2017
28

TIMER2.0 for analysis of tumor-infiltrating immune cells.
Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, X Shirley Liu. Nucleic Acids Res 2020
422
28

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Silas Maniatis, Tarmo Äijö, Sanja Vickovic, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää, Gonzalo Saiz-Castro,[...]. Science 2019
108
14


The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
14

Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.
Kim Thrane, Hanna Eriksson, Jonas Maaskola, Johan Hansson, Joakim Lundeberg. Cancer Res 2018
68
14

Canonical correlation analysis: an overview with application to learning methods.
David R Hardoon, Sandor Szedmak, John Shawe-Taylor. Neural Comput 2004
257
14

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
Sean C Bendall, Kara L Davis, El-Ad David Amir, Michelle D Tadmor, Erin F Simonds, Tiffany J Chen, Daniel K Shenfeld, Garry P Nolan, Dana Pe'er. Cell 2014
488
14


Linnorm: improved statistical analysis for single cell RNA-seq expression data.
Shun H Yip, Panwen Wang, Jean-Pierre A Kocher, Pak Chung Sham, Junwen Wang. Nucleic Acids Res 2017
35
14

Highly multiplexed subcellular RNA sequencing in situ.
Je Hyuk Lee, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur S F Jeanty, Chao Li, Ryoji Amamoto,[...]. Science 2014
475
14

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Luyi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, Matthew E Ritchie. PLoS Comput Biol 2018
35
14

Spatially resolved transcriptome profiling in model plant species.
Stefania Giacomello, Fredrik Salmén, Barbara K Terebieniec, Sanja Vickovic, José Fernandez Navarro, Andrey Alexeyenko, Johan Reimegård, Lauren S McKee, Chanaka Mannapperuma, Vincent Bulone,[...]. Nat Plants 2017
46
14

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes.
Yurong Xin, Jinrang Kim, Haruka Okamoto, Min Ni, Yi Wei, Christina Adler, Andrew J Murphy, George D Yancopoulos, Calvin Lin, Jesper Gromada. Cell Metab 2016
224
14

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
433
14


Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.
Arpiar Saunders, Evan Z Macosko, Alec Wysoker, Melissa Goldman, Fenna M Krienen, Heather de Rivera, Elizabeth Bien, Matthew Baum, Laura Bortolin, Shuyu Wang,[...]. Cell 2018
452
14

Transcriptional output, cell-type densities, and normalization in spatial transcriptomics.
Manuel Saiselet, Joël Rodrigues-Vitória, Adrien Tourneur, Ligia Craciun, Alex Spinette, Denis Larsimont, Guy Andry, Joakim Lundeberg, Carine Maenhaut, Vincent Detours. J Mol Cell Biol 2020
9
14

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang. Science 2015
714
14

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
14

Conserved cell types with divergent features in human versus mouse cortex.
Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Nelson Johansen, Osnat Penn,[...]. Nature 2019
383
14

A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation.
Alexandra Grubman, Gabriel Chew, John F Ouyang, Guizhi Sun, Xin Yi Choo, Catriona McLean, Rebecca K Simmons, Sam Buckberry, Dulce B Vargas-Landin, Daniel Poppe,[...]. Nat Neurosci 2019
161
14

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy,[...]. Science 2016
14

Single-cell RNA sequencing to explore immune cell heterogeneity.
Efthymia Papalexi, Rahul Satija. Nat Rev Immunol 2018
397
14

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Michaela Asp, Stefania Giacomello, Ludvig Larsson, Chenglin Wu, Daniel Fürth, Xiaoyan Qian, Eva Wärdell, Joaquin Custodio, Johan Reimegård, Fredrik Salmén,[...]. Cell 2019
112
14

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
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
440
14

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.
Reuben Moncada, Dalia Barkley, Florian Wagner, Marta Chiodin, Joseph C Devlin, Maayan Baron, Cristina H Hajdu, Diane M Simeone, Itai Yanai. Nat Biotechnol 2020
121
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.