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
Times Cited: 406
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
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
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
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
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
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
24
Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
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
Yi-an Chen, Mathieu Lemire, Sanaa Choufani, Darci T Butcher, Daria Grafodatskaya, Brent W Zanke, Steven Gallinger, Thomas J Hudson, Rosanna Weksberg. Epigenetics 2013
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
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
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
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
18
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
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
Andrew E Teschendorff, Francesco Marabita, Matthias Lechner, Thomas Bartlett, Jesper Tegner, David Gomez-Cabrero, Stephan Beck. Bioinformatics 2013
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
Timothy J Triche, Daniel J Weisenberger, David Van Den Berg, Peter W Laird, Kimberly D Siegmund. Nucleic Acids Res 2013
13
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12
Functions of DNA methylation: islands, start sites, gene bodies and beyond.
Peter A Jones. Nat Rev Genet 2012
Peter A Jones. Nat Rev Genet 2012
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
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
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.
Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack. Genome Biol 2012
Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack. Genome Biol 2012
10
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
Lucas A Salas, Devin C Koestler, Rondi A Butler, Helen M Hansen, John K Wiencke, Karl T Kelsey, Brock C Christensen. Genome Biol 2018
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
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
10
Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes.
Wanding Zhou, Peter W Laird, Hui Shen. Nucleic Acids Res 2017
Wanding Zhou, Peter W Laird, Hui Shen. Nucleic Acids Res 2017
9
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
Brent S Pedersen, David A Schwartz, Ivana V Yang, Katerina J Kechris. Bioinformatics 2012
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
Andrew E Jaffe, Peter Murakami, Hwajin Lee, Jeffrey T Leek, M Daniele Fallin, Andrew P Feinberg, Rafael A Irizarry. Int J Epidemiol 2012
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
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
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
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
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
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
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
Ruth Pidsley, Chloe C Y Wong, Manuela Volta, Katie Lunnon, Jonathan Mill, Leonard C Schalkwyk. BMC Genomics 2013
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
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
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
Georgina Mansell, Tyler J Gorrie-Stone, Yanchun Bao, Meena Kumari, Leonard S Schalkwyk, Jonathan Mill, Eilis Hannon. BMC Genomics 2019
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
Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E Teschendorff. Bioinformatics 2017
7
Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation.
Nizar Touleimat, Jörg Tost. Epigenomics 2012
Nizar Touleimat, Jörg Tost. Epigenomics 2012
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
Tiffany J Morris, Lee M Butcher, Andrew Feber, Andrew E Teschendorff, Ankur R Chakravarthy, Tomasz K Wojdacz, Stephan Beck. Bioinformatics 2014
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
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
6
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.
Liang Niu, Zongli Xu, Jack A Taylor. Bioinformatics 2016
Liang Niu, Zongli Xu, Jack A Taylor. Bioinformatics 2016
10
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
6
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
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
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
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
6
Capturing heterogeneity in gene expression studies by surrogate variable analysis.
Jeffrey T Leek, John D Storey. PLoS Genet 2007
Jeffrey T Leek, John D Storey. PLoS Genet 2007
5
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
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
8
Accounting for cellular heterogeneity is critical in epigenome-wide association studies.
Andrew E Jaffe, Rafael A Irizarry. Genome Biol 2014
Andrew E Jaffe, Rafael A Irizarry. Genome Biol 2014
5
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
Kevin McGregor, Sasha Bernatsky, Ines Colmegna, Marie Hudson, Tomi Pastinen, Aurélie Labbe, Celia M T Greenwood. Genome Biol 2016
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
Elior Rahmani, Liat Shenhav, Regev Schweiger, Paul Yousefi, Karen Huen, Brenda Eskenazi, Celeste Eng, Scott Huntsman, Donglei Hu, Joshua Galanter,[...]. Epigenetics Chromatin 2017
11
Regularization Paths for Generalized Linear Models via Coordinate Descent.
Jerome Friedman, Trevor Hastie, Rob Tibshirani. J Stat Softw 2010
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
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
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
Saurav Mallik, Gabriel J Odom, Zhen Gao, Lissette Gomez, Xi Chen, Lily Wang. Brief Bioinform 2019
18
Comprehensive analysis of DNA methylation data with RnBeads.
Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Nat Methods 2014
Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Nat Methods 2014
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
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5
Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences.
Sebastian Moran, Carles Arribas, Manel Esteller. Epigenomics 2016
Sebastian Moran, Carles Arribas, Manel Esteller. Epigenomics 2016
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
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
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.