A citation-based method for searching scientific literature

W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
Times Cited: 3551







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



Times Cited
  Times     Co-cited
Similarity


limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
20

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
15

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
15

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13

Harmonization of cortical thickness measurements across scanners and sites.
Jean-Philippe Fortin, Nicholas Cullen, Yvette I Sheline, Warren D Taylor, Irem Aselcioglu, Philip A Cook, Phil Adams, Crystal Cooper, Maurizio Fava, Patrick J McGrath,[...]. Neuroimage 2018
234
11

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
11

Harmonization of multi-site diffusion tensor imaging data.
Jean-Philippe Fortin, Drew Parker, Birkan Tunç, Takanori Watanabe, Mark A Elliott, Kosha Ruparel, David R Roalf, Theodore D Satterthwaite, Ruben C Gur, Raquel E Gur,[...]. Neuroimage 2017
249
10

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
9

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
9

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
8

DNA methylation arrays as surrogate measures of cell mixture distribution.
Eugene Andres Houseman, William P Accomando, Devin C Koestler, Brock C Christensen, Carmen J Marsit, Heather H Nelson, John K Wiencke, Karl T Kelsey. BMC Bioinformatics 2012
8

Tackling the widespread and critical impact of batch effects in high-throughput data.
Jeffrey T Leek, Robert B Scharpf, Héctor Corrada Bravo, David Simcha, Benjamin Langmead, W Evan Johnson, Donald Geman, Keith Baggerly, Rafael A Irizarry. Nat Rev Genet 2010
6

Statistical harmonization corrects site effects in functional connectivity measurements from multi-site fMRI data.
Meichen Yu, Kristin A Linn, Philip A Cook, Mary L Phillips, Melvin McInnis, Maurizio Fava, Madhukar H Trivedi, Myrna M Weissman, Russell T Shinohara, Yvette I Sheline. Hum Brain Mapp 2018
94
6


lumi: a pipeline for processing Illumina microarray.
Pan Du, Warren A Kibbe, Simon M Lin. Bioinformatics 2008
6

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Martin J Aryee, Andrew E Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P Feinberg, Kasper D Hansen, Rafael A Irizarry. Bioinformatics 2014
6

Computational Radiomics System to Decode the Radiographic Phenotype.
Joost J M van Griethuysen, Andriy Fedorov, Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina G H Beets-Tan, Jean-Christophe Fillion-Robin, Steve Pieper, Hugo J W L Aerts. Cancer Res 2017
6


Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
5



Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
262
5

affy--analysis of Affymetrix GeneChip data at the probe level.
Laurent Gautier, Leslie Cope, Benjamin M Bolstad, Rafael A Irizarry. Bioinformatics 2004
5

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Andrew E Teschendorff, Francesco Marabita, Matthias Lechner, Thomas Bartlett, Jesper Tegner, David Gomez-Cabrero, Stephan Beck. Bioinformatics 2013
804
5

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
613
5

Radiomics: extracting more information from medical images using advanced feature analysis.
Philippe Lambin, Emmanuel Rios-Velazquez, Ralph Leijenaar, Sara Carvalho, Ruud G P M van Stiphout, Patrick Granton, Catharina M L Zegers, Robert Gillies, Ronald Boellard, André Dekker,[...]. Eur J Cancer 2012
5

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
5

Harmonization of large MRI datasets for the analysis of brain imaging patterns throughout the lifespan.
Raymond Pomponio, Guray Erus, Mohamad Habes, Jimit Doshi, Dhivya Srinivasan, Elizabeth Mamourian, Vishnu Bashyam, Ilya M Nasrallah, Theodore D Satterthwaite, Yong Fan,[...]. Neuroimage 2020
56
7

A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis.
Sarah E Reese, Kellie J Archer, Terry M Therneau, Elizabeth J Atkinson, Celine M Vachon, Mariza de Andrade, Jean-Pierre A Kocher, Jeanette E Eckel-Passow. Bioinformatics 2013
69
5


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
572
4

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
4

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
4

Performance comparison of modified ComBat for harmonization of radiomic features for multicenter studies.
R Da-Ano, I Masson, F Lucia, M Doré, P Robin, J Alfieri, C Rousseau, A Mervoyer, C Reinhold, J Castelli,[...]. Sci Rep 2020
46
8

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
4


Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
4

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
282
4

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.
Karan Uppal, Quinlyn A Soltow, Frederick H Strobel, W Stephen Pittard, Kim M Gernert, Tianwei Yu, Dean P Jones. BMC Bioinformatics 2013
198
4

Functional normalization of 450k methylation array data improves replication in large cancer studies.
Jean-Philippe Fortin, Aurélie Labbe, Mathieu Lemire, Brent W Zanke, Thomas J Hudson, Elana J Fertig, Celia Mt Greenwood, Kasper D Hansen. Genome Biol 2014
387
4

N4ITK: improved N3 bias correction.
Nicholas J Tustison, Brian B Avants, Philip A Cook, Yuanjie Zheng, Alexander Egan, Paul A Yushkevich, James C Gee. IEEE Trans Med Imaging 2010
4

Genome-wide methylation profiles reveal quantitative views of human aging rates.
Gregory Hannum, Justin Guinney, Ling Zhao, Li Zhang, Guy Hughes, SriniVas Sadda, Brandy Klotzle, Marina Bibikova, Jian-Bing Fan, Yuan Gao,[...]. Mol Cell 2013
4

ChAMP: updated methylation analysis pipeline for Illumina BeadChips.
Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E Teschendorff. Bioinformatics 2017
219
4

De novo identification of differentially methylated regions in the human genome.
Timothy J Peters, Michael J Buckley, Aaron L Statham, Ruth Pidsley, Katherine Samaras, Reginald V Lord, Susan J Clark, Peter L Molloy. Epigenetics Chromatin 2015
406
4

Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
4

Determining cell type abundance and expression from bulk tissues with digital cytometry.
Aaron M Newman, Chloé B Steen, Chih Long Liu, Andrew J Gentles, Aadel A Chaudhuri, Florian Scherer, Michael S Khodadoust, Mohammad S Esfahani, Bogdan A Luca, David Steiner,[...]. Nat Biotechnol 2019
660
4

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.
Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A Kibbe, Lifang Hou, Simon M Lin. BMC Bioinformatics 2010
4

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
305
4

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
4



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.