Devin C Koestler, Meaghan J Jones, Joseph Usset, Brock C Christensen, Rondi A Butler, Michael S Kobor, John K Wiencke, Karl T Kelsey. BMC Bioinformatics 2016
Times Cited: 66
Times Cited: 66
Times Cited
Times Co-cited
Similarity
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
81
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
48
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
42
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
34
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
33
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.
Yun Liu, Martin J Aryee, Leonid Padyukov, M Daniele Fallin, Espen Hesselberg, Arni Runarsson, Lovisa Reinius, Nathalie Acevedo, Margaret Taub, Marcus Ronninger,[...]. Nat Biotechnol 2013
Yun Liu, Martin J Aryee, Leonid Padyukov, M Daniele Fallin, Espen Hesselberg, Arni Runarsson, Lovisa Reinius, Nathalie Acevedo, Margaret Taub, Marcus Ronninger,[...]. Nat Biotechnol 2013
31
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
25
Quantitative reconstruction of leukocyte subsets using DNA methylation.
William P Accomando, John K Wiencke, E Andres Houseman, Heather H Nelson, Karl T Kelsey. Genome Biol 2014
William P Accomando, John K Wiencke, E Andres Houseman, Heather H Nelson, Karl T Kelsey. Genome Biol 2014
24
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.
Andrew E Teschendorff, Charles E Breeze, Shijie C Zheng, Stephan Beck. BMC Bioinformatics 2017
Andrew E Teschendorff, Charles E Breeze, Shijie C Zheng, Stephan Beck. BMC Bioinformatics 2017
24
Reference-free cell mixture adjustments in analysis of DNA methylation data.
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
19
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
19
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.
Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban G Burchard, Eleazar Eskin, James Zou,[...]. Nat Methods 2016
Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban G Burchard, Eleazar Eskin, James Zou,[...]. Nat Methods 2016
19
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
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
18
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.
E Andres Houseman, Molly L Kile, David C Christiani, Tan A Ince, Karl T Kelsey, Carmen J Marsit. BMC Bioinformatics 2016
E Andres Houseman, Molly L Kile, David C Christiani, Tan A Ince, Karl T Kelsey, Carmen J Marsit. BMC Bioinformatics 2016
18
Cell-type deconvolution in epigenome-wide association studies: a review and recommendations.
Andrew E Teschendorff, Shijie C Zheng. Epigenomics 2017
Andrew E Teschendorff, Shijie C Zheng. Epigenomics 2017
18
Cell-type deconvolution from DNA methylation: a review of recent applications.
Alexander J Titus, Rachel M Gallimore, Lucas A Salas, Brock C Christensen. Hum Mol Genet 2017
Alexander J Titus, Rachel M Gallimore, Lucas A Salas, Brock C Christensen. Hum Mol Genet 2017
18
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
16
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
16
DNA Methylation-Derived Neutrophil-to-Lymphocyte Ratio: An Epigenetic Tool to Explore Cancer Inflammation and Outcomes.
Devin C Koestler, Joseph Usset, Brock C Christensen, Carmen J Marsit, Margaret R Karagas, Karl T Kelsey, John K Wiencke. Cancer Epidemiol Biomarkers Prev 2017
Devin C Koestler, Joseph Usset, Brock C Christensen, Carmen J Marsit, Margaret R Karagas, Karl T Kelsey, John K Wiencke. Cancer Epidemiol Biomarkers Prev 2017
26
Epigenome-wide association studies without the need for cell-type composition.
James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten. Nat Methods 2014
James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten. Nat Methods 2014
16
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
15
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
Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition.
Kristina Gervin, Christian Magnus Page, Hans Christian D Aass, Michelle A Jansen, Heidi Elisabeth Fjeldstad, Bettina Kulle Andreassen, Liesbeth Duijts, Joyce B van Meurs, Menno C van Zelm, Vincent W Jaddoe,[...]. Epigenetics 2016
Kristina Gervin, Christian Magnus Page, Hans Christian D Aass, Michelle A Jansen, Heidi Elisabeth Fjeldstad, Bettina Kulle Andreassen, Liesbeth Duijts, Joyce B van Meurs, Menno C van Zelm, Vincent W Jaddoe,[...]. Epigenetics 2016
22
Immunomethylomic approach to explore the blood neutrophil lymphocyte ratio (NLR) in glioma survival.
John K Wiencke, Devin C Koestler, Lucas A Salas, Joseph L Wiemels, Ritu P Roy, Helen M Hansen, Terri Rice, Lucie S McCoy, Paige M Bracci, Annette M Molinaro,[...]. Clin Epigenetics 2017
John K Wiencke, Devin C Koestler, Lucas A Salas, Joseph L Wiemels, Ritu P Roy, Helen M Hansen, Terri Rice, Lucie S McCoy, Paige M Bracci, Annette M Molinaro,[...]. Clin Epigenetics 2017
26
Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
13
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
13
Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis.
Devin C Koestler, Brock Christensen, Margaret R Karagas, Carmen J Marsit, Scott M Langevin, Karl T Kelsey, John K Wiencke, E Andres Houseman. Epigenetics 2013
Devin C Koestler, Brock Christensen, Margaret R Karagas, Carmen J Marsit, Scott M Langevin, Karl T Kelsey, John K Wiencke, E Andres Houseman. Epigenetics 2013
13
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
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
12
DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer.
Andrew E Teschendorff, Yang Gao, Allison Jones, Matthias Ruebner, Matthias W Beckmann, David L Wachter, Peter A Fasching, Martin Widschwendter. Nat Commun 2016
Andrew E Teschendorff, Yang Gao, Allison Jones, Matthias Ruebner, Matthias W Beckmann, David L Wachter, Peter A Fasching, Martin Widschwendter. Nat Commun 2016
12
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
12
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
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
12
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
10
Epigenome-wide association studies for common human diseases.
Vardhman K Rakyan, Thomas A Down, David J Balding, Stephan Beck. Nat Rev Genet 2011
Vardhman K Rakyan, Thomas A Down, David J Balding, Stephan Beck. Nat Rev Genet 2011
10
Correlation of an epigenetic mitotic clock with cancer risk.
Zhen Yang, Andrew Wong, Diana Kuh, Dirk S Paul, Vardhman K Rakyan, R David Leslie, Shijie C Zheng, Martin Widschwendter, Stephan Beck, Andrew E Teschendorff. Genome Biol 2016
Zhen Yang, Andrew Wong, Diana Kuh, Dirk S Paul, Vardhman K Rakyan, R David Leslie, Shijie C Zheng, Martin Widschwendter, Stephan Beck, Andrew E Teschendorff. Genome Biol 2016
10
Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective.
E Andres Houseman, Karl T Kelsey, John K Wiencke, Carmen J Marsit. BMC Bioinformatics 2015
E Andres Houseman, Karl T Kelsey, John K Wiencke, Carmen J Marsit. BMC Bioinformatics 2015
12
Using control genes to correct for unwanted variation in microarray data.
Johann A Gagnon-Bartsch, Terence P Speed. Biostatistics 2012
Johann A Gagnon-Bartsch, Terence P Speed. Biostatistics 2012
10
Associating cellular epigenetic models with human phenotypes.
Tuuli Lappalainen, John M Greally. Nat Rev Genet 2017
Tuuli Lappalainen, John M Greally. Nat Rev Genet 2017
10
Identification of differentially methylated cell types in epigenome-wide association studies.
Shijie C Zheng, Charles E Breeze, Stephan Beck, Andrew E Teschendorff. Nat Methods 2018
Shijie C Zheng, Charles E Breeze, Stephan Beck, Andrew E Teschendorff. Nat Methods 2018
10
Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data.
Kristina Gervin, Lucas A Salas, Kelly M Bakulski, Menno C van Zelm, Devin C Koestler, John K Wiencke, Liesbeth Duijts, Henriëtte A Moll, Karl T Kelsey, Michael S Kobor,[...]. Clin Epigenetics 2019
Kristina Gervin, Lucas A Salas, Kelly M Bakulski, Menno C van Zelm, Devin C Koestler, John K Wiencke, Liesbeth Duijts, Henriëtte A Moll, Karl T Kelsey, Michael S Kobor,[...]. Clin Epigenetics 2019
17
Estimation of blood cellular heterogeneity in newborns and children for epigenome-wide association studies.
Paul Yousefi, Karen Huen, Hong Quach, Girish Motwani, Alan Hubbard, Brenda Eskenazi, Nina Holland. Environ Mol Mutagen 2015
Paul Yousefi, Karen Huen, Hong Quach, Girish Motwani, Alan Hubbard, Brenda Eskenazi, Nina Holland. Environ Mol Mutagen 2015
17
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
9
DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies.
Xu Gao, Min Jia, Yan Zhang, Lutz Philipp Breitling, Hermann Brenner. Clin Epigenetics 2015
Xu Gao, Min Jia, Yan Zhang, Lutz Philipp Breitling, Hermann Brenner. Clin Epigenetics 2015
9
DNA Methylation in Whole Blood: Uses and Challenges.
E Andres Houseman, Stephanie Kim, Karl T Kelsey, John K Wiencke. Curr Environ Health Rep 2015
E Andres Houseman, Stephanie Kim, Karl T Kelsey, John K Wiencke. Curr Environ Health Rep 2015
9
Prognostic role of neutrophil-to-lymphocyte ratio in solid tumors: a systematic review and meta-analysis.
Arnoud J Templeton, Mairéad G McNamara, Boštjan Šeruga, Francisco E Vera-Badillo, Priya Aneja, Alberto Ocaña, Raya Leibowitz-Amit, Guru Sonpavde, Jennifer J Knox, Ben Tran,[...]. J Natl Cancer Inst 2014
Arnoud J Templeton, Mairéad G McNamara, Boštjan Šeruga, Francisco E Vera-Badillo, Priya Aneja, Alberto Ocaña, Raya Leibowitz-Amit, Guru Sonpavde, Jennifer J Knox, Ben Tran,[...]. J Natl Cancer Inst 2014
9
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
9
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
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.