Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A Kibbe, Lifang Hou, Simon M Lin. BMC Bioinformatics 2010
Times Cited: 953
Times Cited: 953
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
41
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
34
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
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
24
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
20
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
19
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
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
15
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
14
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
13
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
12
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
11
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
11
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
11
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
10
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
9
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
9
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
9
Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes.
Eilis Hannon, Katie Lunnon, Leonard Schalkwyk, Jonathan Mill. Epigenetics 2015
Eilis Hannon, Katie Lunnon, Leonard Schalkwyk, Jonathan Mill. Epigenetics 2015
7
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
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
14
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
7
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
6
A cross-package Bioconductor workflow for analysing methylation array data.
Jovana Maksimovic, Belinda Phipson, Alicia Oshlack. F1000Res 2016
Jovana Maksimovic, Belinda Phipson, Alicia Oshlack. F1000Res 2016
12
Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood.
Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R Alan Harris, Aleksandar Milosavljevic, Claire Troakes,[...]. Genome Biol 2012
Matthew N Davies, Manuela Volta, Ruth Pidsley, Katie Lunnon, Abhishek Dixit, Simon Lovestone, Cristian Coarfa, R Alan Harris, Aleksandar Milosavljevic, Claire Troakes,[...]. Genome Biol 2012
6
Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.
Lovisa E Reinius, Nathalie Acevedo, Maaike Joerink, Göran Pershagen, Sven-Erik Dahlén, Dario Greco, Cilla Söderhäll, Annika Scheynius, Juha Kere. PLoS One 2012
Lovisa E Reinius, Nathalie Acevedo, Maaike Joerink, Göran Pershagen, Sven-Erik Dahlén, Dario Greco, Cilla Söderhäll, Annika Scheynius, Juha Kere. PLoS One 2012
6
methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.
Xu Ren, Pei Fen Kuan. Bioinformatics 2019
Xu Ren, Pei Fen Kuan. Bioinformatics 2019
18
Systematic identification of genetic influences on methylation across the human life course.
Tom R Gaunt, Hashem A Shihab, Gibran Hemani, Josine L Min, Geoff Woodward, Oliver Lyttleton, Jie Zheng, Aparna Duggirala, Wendy L McArdle, Karen Ho,[...]. Genome Biol 2016
Tom R Gaunt, Hashem A Shihab, Gibran Hemani, Josine L Min, Geoff Woodward, Oliver Lyttleton, Jie Zheng, Aparna Duggirala, Wendy L McArdle, Karen Ho,[...]. Genome Biol 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
14
ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip.
Zongli Xu, Liang Niu, Leping Li, Jack A Taylor. Nucleic Acids Res 2016
Zongli Xu, Liang Niu, Leping Li, Jack A Taylor. Nucleic Acids Res 2016
6
Genome-wide DNA methylation comparison between live human brain and peripheral tissues within individuals.
Patricia R Braun, Shizhong Han, Benjamin Hing, Yasunori Nagahama, Lindsey N Gaul, Jonathan T Heinzman, Andrew J Grossbach, Liesl Close, Brian J Dlouhy, Matthew A Howard,[...]. Transl Psychiatry 2019
Patricia R Braun, Shizhong Han, Benjamin Hing, Yasunori Nagahama, Lindsey N Gaul, Jonathan T Heinzman, Andrew J Grossbach, Liesl Close, Brian J Dlouhy, Matthew A Howard,[...]. Transl Psychiatry 2019
6
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
6
RnBeads 2.0: comprehensive analysis of DNA methylation data.
Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Genome Biol 2019
Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Genome Biol 2019
12
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
5
Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies.
Andrew E Teschendorff, Joanna Zhuang, Martin Widschwendter. Bioinformatics 2011
Andrew E Teschendorff, Joanna Zhuang, Martin Widschwendter. Bioinformatics 2011
5
Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome.
Juan Sandoval, Holger Heyn, Sebastian Moran, Jordi Serra-Musach, Miguel A Pujana, Marina Bibikova, Manel Esteller. Epigenetics 2011
Juan Sandoval, Holger Heyn, Sebastian Moran, Jordi Serra-Musach, Miguel A Pujana, Marina Bibikova, Manel Esteller. Epigenetics 2011
5
High density DNA methylation array with single CpG site resolution.
Marina Bibikova, Bret Barnes, Chan Tsan, Vincent Ho, Brandy Klotzle, Jennie M Le, David Delano, Lu Zhang, Gary P Schroth, Kevin L Gunderson,[...]. Genomics 2011
Marina Bibikova, Bret Barnes, Chan Tsan, Vincent Ho, Brandy Klotzle, Jennie M Le, David Delano, Lu Zhang, Gary P Schroth, Kevin L Gunderson,[...]. Genomics 2011
5
Allele-specific FKBP5 DNA demethylation mediates gene-childhood trauma interactions.
Torsten Klengel, Divya Mehta, Christoph Anacker, Monika Rex-Haffner, Jens C Pruessner, Carmine M Pariante, Thaddeus W W Pace, Kristina B Mercer, Helen S Mayberg, Bekh Bradley,[...]. Nat Neurosci 2013
Torsten Klengel, Divya Mehta, Christoph Anacker, Monika Rex-Haffner, Jens C Pruessner, Carmine M Pariante, Thaddeus W W Pace, Kristina B Mercer, Helen S Mayberg, Bekh Bradley,[...]. Nat Neurosci 2013
5
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
5
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
9
REVIGO summarizes and visualizes long lists of gene ontology terms.
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc. PLoS One 2011
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc. PLoS One 2011
5
Environmental Influences on the Epigenome: Exposure- Associated DNA Methylation in Human Populations.
Elizabeth M Martin, Rebecca C Fry. Annu Rev Public Health 2018
Elizabeth M Martin, Rebecca C Fry. Annu Rev Public Health 2018
5
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
DNA methylation and body-mass index: a genome-wide analysis.
Katherine J Dick, Christopher P Nelson, Loukia Tsaprouni, Johanna K Sandling, Dylan Aïssi, Simone Wahl, Eshwar Meduri, Pierre-Emmanuel Morange, France Gagnon, Harald Grallert,[...]. Lancet 2014
Katherine J Dick, Christopher P Nelson, Loukia Tsaprouni, Johanna K Sandling, Dylan Aïssi, Simone Wahl, Eshwar Meduri, Pierre-Emmanuel Morange, France Gagnon, Harald Grallert,[...]. Lancet 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
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
5
Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals.
Rudolf Jaenisch, Adrian Bird. Nat Genet 2003
Rudolf Jaenisch, Adrian Bird. Nat Genet 2003
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
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.
Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard. Genome Biol 2011
Jordana T Bell, Athma A Pai, Joseph K Pickrell, Daniel J Gaffney, Roger Pique-Regi, Jacob F Degner, Yoav Gilad, Jonathan K Pritchard. Genome Biol 2011
4
DNA methylation and its basic function.
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
Lisa D Moore, Thuc Le, Guoping Fan. Neuropsychopharmacology 2013
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.