A citation-based method for searching scientific literature

Brian B Nadel, David Lopez, Dennis J Montoya, Feiyang Ma, Hannah Waddel, Misha M Khan, Serghei Mangul, Matteo Pellegrini. Gigascience 2021
Times Cited: 6







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



Times Cited
  Times     Co-cited
Similarity


Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.
Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf H Fridman, Markus List, Tatsiana Aneichyk. Bioinformatics 2019
140
66

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
720
50

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
50

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression.
Etienne Becht, Nicolas A Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H Fridman,[...]. Genome Biol 2016
555
50

dtangle: accurate and robust cell type deconvolution.
Gregory J Hunt, Saskia Freytag, Melanie Bahlo, Johann A Gagnon-Bartsch. Bioinformatics 2019
23
50

BLUEPRINT: mapping human blood cell epigenomes.
Joost H A Martens, Hendrik G Stunnenberg. Haematologica 2013
94
50

Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients.
William R Swindell, Andrew Johnston, John J Voorhees, James T Elder, Johann E Gudjonsson. BMC Genomics 2013
82
33

Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues.
Heather E Wheeler, Kaanan P Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, Nancy J Cox, Dan L Nicolae, Hae Kyung Im. PLoS Genet 2016
73
33

A gene atlas of the mouse and human protein-encoding transcriptomes.
Andrew I Su, Tim Wiltshire, Serge Batalov, Hilmar Lapp, Keith A Ching, David Block, Jie Zhang, Richard Soden, Mimi Hayakawa, Gabriel Kreiman,[...]. Proc Natl Acad Sci U S A 2004
33

SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles.
David Lopez, Dennis Montoya, Michael Ambrose, Larry Lam, Leah Briscoe, Claire Adams, Robert L Modlin, Matteo Pellegrini. BMC Genomics 2017
19
33

An expression atlas of human primary cells: inference of gene function from coexpression networks.
Neil A Mabbott, J Kenneth Baillie, Helen Brown, Tom C Freeman, David A Hume. BMC Genomics 2013
136
33

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy.
Bo Li, Eric Severson, Jean-Christophe Pignon, Haoquan Zhao, Taiwen Li, Jesse Novak, Peng Jiang, Hui Shen, Jon C Aster, Scott Rodig,[...]. Genome Biol 2016
727
33

Sorting out the FACS: a devil in the details.
William C Hines, Ying Su, Irene Kuhn, Kornelia Polyak, Mina J Bissell. Cell Rep 2014
50
33

The immune contexture in human tumours: impact on clinical outcome.
Wolf Herman Fridman, Franck Pagès, Catherine Sautès-Fridman, Jérôme Galon. Nat Rev Cancer 2012
33

Digital cell quantification identifies global immune cell dynamics during influenza infection.
Zeev Altboum, Yael Steuerman, Eyal David, Zohar Barnett-Itzhaki, Liran Valadarsky, Hadas Keren-Shaul, Tal Meningher, Ella Mendelson, Michal Mandelboim, Irit Gat-Viks,[...]. Mol Syst Biol 2014
52
33

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
33


Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases.
Francesco Vallania, Andrew Tam, Shane Lofgren, Steven Schaffert, Tej D Azad, Erika Bongen, Winston Haynes, Meia Alsup, Michael Alonso, Mark Davis,[...]. Nat Commun 2018
60
33

The prognostic landscape of genes and infiltrating immune cells across human cancers.
Andrew J Gentles, Aaron M Newman, Chih Long Liu, Scott V Bratman, Weiguo Feng, Dongkyoon Kim, Viswam S Nair, Yue Xu, Amanda Khuong, Chuong D Hoang,[...]. Nat Med 2015
33

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
33

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
33

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.
Julien Racle, Kaat de Jonge, Petra Baumgaertner, Daniel E Speiser, David Gfeller. Elife 2017
208
33

Regulation of the expression of the prostate-specific antigen by claudin-7.
J-Y Zheng, D Yu, M Foroohar, E Ko, J Chan, N Kim, R Chiu, S Pang. J Membr Biol 2003
42
16

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse.
Ye Zhang, Steven A Sloan, Laura E Clarke, Christine Caneda, Colton A Plaza, Paul D Blumenthal, Hannes Vogel, Gary K Steinberg, Michael S B Edwards, Gordon Li,[...]. Neuron 2016
856
16

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Michal Slyper, Caroline B M Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smillie, Gabriela Smith-Rosario, Jingyi Wu, Danielle Dionne,[...]. Nat Med 2020
75
16

Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.
Holger Kirsten, Hoor Al-Hasani, Lesca Holdt, Arnd Gross, Frank Beutner, Knut Krohn, Katrin Horn, Peter Ahnert, Ralph Burkhardt, Kristin Reiche,[...]. Hum Mol Genet 2015
61
16

Massively parallel single-nucleus RNA-seq with DroNc-seq.
Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie,[...]. Nat Methods 2017
354
16

Genetic association testing using the GENESIS R/Bioconductor package.
Stephanie M Gogarten, Tamar Sofer, Han Chen, Chaoyu Yu, Jennifer A Brody, Timothy A Thornton, Kenneth M Rice, Matthew P Conomos. Bioinformatics 2019
45
16

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.
Joe R Davis, Laure Fresard, David A Knowles, Mauro Pala, Carlos D Bustamante, Alexis Battle, Stephen B Montgomery. Am J Hum Genet 2016
32
16

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types.
Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger,[...]. Cell Rep 2019
173
16

Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Abhishek K Sarkar, Po-Yuan Tung, John D Blischak, Jonathan E Burnett, Yang I Li, Matthew Stephens, Yoav Gilad. PLoS Genet 2019
21
16

A high-performance computing toolset for relatedness and principal component analysis of SNP data.
Xiuwen Zheng, David Levine, Jess Shen, Stephanie M Gogarten, Cathy Laurie, Bruce S Weir. Bioinformatics 2012
804
16

Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases.
Mariet Allen, Minerva M Carrasquillo, Cory Funk, Benjamin D Heavner, Fanggeng Zou, Curtis S Younkin, Jeremy D Burgess, High-Seng Chai, Julia Crook, James A Eddy,[...]. Sci Data 2016
129
16

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
16


Identification of context-dependent expression quantitative trait loci in whole blood.
Daria V Zhernakova, Patrick Deelen, Martijn Vermaat, Maarten van Iterson, Michiel van Galen, Wibowo Arindrarto, Peter van 't Hof, Hailiang Mei, Freerk van Dijk, Harm-Jan Westra,[...]. Nat Genet 2017
173
16

A vast resource of allelic expression data spanning human tissues.
Stephane E Castel, François Aguet, Pejman Mohammadi, Kristin G Ardlie, Tuuli Lappalainen. Genome Biol 2020
15
16

Cell-Type Heterogeneity in Adipose Tissue Is Associated with Complex Traits and Reveals Disease-Relevant Cell-Specific eQTLs.
Craig A Glastonbury, Alexessander Couto Alves, Julia S El-Sayed Moustafa, Kerrin S Small. Am J Hum Genet 2019
27
16

Heritability of thromboxane A2 and prostaglandin E2 biosynthetic machinery in a Spanish population.
Luis Vila, Angel Martinez-Perez, Mercedes Camacho, Alfonso Buil, Sonia Alcolea, Nuria Pujol-Moix, Marta Soler, Rosa Antón, Juan-Carlos Souto, Jordi Fontcuberta,[...]. Arterioscler Thromb Vasc Biol 2010
7
16

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations.
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier,[...]. Nat Commun 2017
67
16

Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies.
Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-Xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L Feolo, Nataliya R Sharopova, Anne Sturcke,[...]. Genome Biol 2017
90
16

Annotation-free quantification of RNA splicing using LeafCutter.
Yang I Li, David A Knowles, Jack Humphrey, Alvaro N Barbeira, Scott P Dickinson, Hae Kyung Im, Jonathan K Pritchard. Nat Genet 2018
170
16

Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles.
Benjamin P Fairfax, Seiko Makino, Jayachandran Radhakrishnan, Katharine Plant, Stephen Leslie, Alexander Dilthey, Peter Ellis, Cordelia Langford, Fredrik O Vannberg, Julian C Knight. Nat Genet 2012
325
16

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity.
Simon Joost, Amit Zeisel, Tina Jacob, Xiaoyan Sun, Gioele La Manno, Peter Lönnerberg, Sten Linnarsson, Maria Kasper. Cell Syst 2016
155
16



Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.
Igor Mandric, Tommer Schwarz, Arunabha Majumdar, Kangcheng Hou, Leah Briscoe, Richard Perez, Meena Subramaniam, Christoph Hafemeister, Rahul Satija, Chun Jimmie Ye,[...]. Nat Commun 2020
7
16


Scaling computational genomics to millions of individuals with GPUs.
Amaro Taylor-Weiner, François Aguet, Nicholas J Haradhvala, Sager Gosai, Shankara Anand, Jaegil Kim, Kristin Ardlie, Eliezer M Van Allen, Gad Getz. Genome Biol 2019
11
16

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.
Towfique Raj, Katie Rothamel, Sara Mostafavi, Chun Ye, Mark N Lee, Joseph M Replogle, Ting Feng, Michelle Lee, Natasha Asinovski, Irene Frohlich,[...]. Science 2014
295
16


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.