A citation-based method for searching scientific literature

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
Times Cited: 406







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



Times Cited
  Times     Co-cited
Similarity


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
54

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
45

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
32

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
30

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
282
24

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
19


Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray.
Yi-an Chen, Mathieu Lemire, Sanaa Choufani, Darci T Butcher, Daria Grafodatskaya, Brent W Zanke, Steven Gallinger, Thomas J Hudson, Rosanna Weksberg. Epigenetics 2013
870
18

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
18

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.
Ruth Pidsley, Elena Zotenko, Timothy J Peters, Mitchell G Lawrence, Gail P Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J Clark. Genome Biol 2016
449
18

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
262
16

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
13

Low-level processing of Illumina Infinium DNA Methylation BeadArrays.
Timothy J Triche, Daniel J Weisenberger, David Van Den Berg, Peter W Laird, Kimberly D Siegmund. Nucleic Acids Res 2013
352
13

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12


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
11


An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray.
Lucas A Salas, Devin C Koestler, Rondi A Butler, Helen M Hansen, John K Wiencke, Karl T Kelsey, Brock C Christensen. Genome Biol 2018
89
11

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
10


Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
Brent S Pedersen, David A Schwartz, Ivana V Yang, Katerina J Kechris. Bioinformatics 2012
199
9

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.
Andrew E Jaffe, Peter Murakami, Hwajin Lee, Jeffrey T Leek, M Daniele Fallin, Andrew P Feinberg, Rafael A Irizarry. Int J Epidemiol 2012
376
9

DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis.
Bonnie R Joubert, Janine F Felix, Paul Yousefi, Kelly M Bakulski, Allan C Just, Carrie Breton, Sarah E Reese, Christina A Markunas, Rebecca C Richmond, Cheng-Jian Xu,[...]. Am J Hum Genet 2016
423
8

An epigenetic biomarker of aging for lifespan and healthspan.
Morgan E Levine, Ake T Lu, Austin Quach, Brian H Chen, Themistocles L Assimes, Stefania Bandinelli, Lifang Hou, Andrea A Baccarelli, James D Stewart, Yun Li,[...]. Aging (Albany NY) 2018
546
8

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies.
Benjamin Lehne, Alexander W Drong, Marie Loh, Weihua Zhang, William R Scott, Sian-Tsung Tan, Uzma Afzal, James Scott, Marjo-Riitta Jarvelin, Paul Elliott,[...]. Genome Biol 2015
169
7

A data-driven approach to preprocessing Illumina 450K methylation array data.
Ruth Pidsley, Chloe C Y Wong, Manuela Volta, Katie Lunnon, Jonathan Mill, Leonard C Schalkwyk. BMC Genomics 2013
536
7

DNA methylation-based measures of biological age: meta-analysis predicting time to death.
Brian H Chen, Riccardo E Marioni, Elena Colicino, Marjolein J Peters, Cavin K Ward-Caviness, Pei-Chien Tsai, Nicholas S Roetker, Allan C Just, Ellen W Demerath, Weihua Guan,[...]. Aging (Albany NY) 2016
456
7

Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array.
Georgina Mansell, Tyler J Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard S Schalkwyk, Jonathan Mill, Eilis Hannon. BMC Genomics 2019
80
8

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
7


ChAMP: 450k Chip Analysis Methylation Pipeline.
Tiffany J Morris, Lee M Butcher, Andrew Feber, Andrew E Teschendorff, Ankur R Chakravarthy, Tomasz K Wojdacz, Stephan Beck. Bioinformatics 2014
441
6

Epigenetic Signatures of Cigarette Smoking.
Roby Joehanes, Allan C Just, Riccardo E Marioni, Luke C Pilling, Lindsay M Reynolds, Pooja R Mandaviya, Weihua Guan, Tao Xu, Cathy E Elks, Stella Aslibekyan,[...]. Circ Cardiovasc Genet 2016
381
6

RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.
Liang Niu, Zongli Xu, Jack A Taylor. Bioinformatics 2016
57
10


Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease.
Steve Horvath, Michael Gurven, Morgan E Levine, Benjamin C Trumble, Hillard Kaplan, Hooman Allayee, Beate R Ritz, Brian Chen, Ake T Lu, Tammy M Rickabaugh,[...]. Genome Biol 2016
313
6

DNA methylation of cord blood cell types: Applications for mixed cell birth studies.
Kelly M Bakulski, Jason I Feinberg, Shan V Andrews, Jack Yang, Shannon Brown, Stephanie L McKenney, Frank Witter, Jeremy Walston, Andrew P Feinberg, M Daniele Fallin. Epigenetics 2016
174
6


Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder.
B P F Rutten, E Vermetten, C H Vinkers, G Ursini, N P Daskalakis, E Pishva, L de Nijs, L C Houtepen, L Eijssen, A E Jaffe,[...]. Mol Psychiatry 2018
57
8


An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies.
Kevin McGregor, Sasha Bernatsky, Ines Colmegna, Marie Hudson, Tomi Pastinen, Aurélie Labbe, Celia M T Greenwood. Genome Biol 2016
88
5

Genome-wide methylation data mirror ancestry information.
Elior Rahmani, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng, Scott Huntsman, Donglei Hu, Joshua Galanter,[...]. Epigenetics Chromatin 2017
42
11

Regularization Paths for Generalized Linear Models via Coordinate Descent.
Jerome Friedman, Trevor Hastie, Rob Tibshirani. J Stat Softw 2010
5

Disease variants alter transcription factor levels and methylation of their binding sites.
Marc Jan Bonder, René Luijk, Daria V Zhernakova, Matthijs Moed, Patrick Deelen, Martijn Vermaat, Maarten van Iterson, Freerk van Dijk, Michiel van Galen, Jan Bot,[...]. Nat Genet 2017
224
5

An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays.
Saurav Mallik, Gabriel J Odom, Zhen Gao, Lissette Gomez, Xi Chen, Lily Wang. Brief Bioinform 2019
27
18

Comprehensive analysis of DNA methylation data with RnBeads.
Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Nat Methods 2014
384
5

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5


Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
5

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
5


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.