A citation-based method for searching scientific literature

Andrew E Jaffe, Rafael A Irizarry. Genome Biol 2014
Times Cited: 521







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



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
48

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
29

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
610
22


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
14

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
13

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
92
14

Reference-free cell mixture adjustments in analysis of DNA methylation data.
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
247
12

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
330
12

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
780
11

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
549
11

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
971
11

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
10

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
97
10

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
705
10

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
10

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
145
9

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
941
9


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
99
8

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
40
20

Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.
Simone Wahl, Alexander Drong, Benjamin Lehne, Marie Loh, William R Scott, Sonja Kunze, Pei-Chien Tsai, Janina S Ried, Weihua Zhang, Youwen Yang,[...]. Nature 2017
365
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
141
8

A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix.
Shijie C Zheng, Amy P Webster, Danyue Dong, Andy Feber, David G Graham, Roisin Sullivan, Sarah Jevons, Laurence B Lovat, Stephan Beck, Martin Widschwendter,[...]. Epigenomics 2018
38
21

Tobacco smoking leads to extensive genome-wide changes in DNA methylation.
Sonja Zeilinger, Brigitte Kühnel, Norman Klopp, Hansjörg Baurecht, Anja Kleinschmidt, Christian Gieger, Stephan Weidinger, Eva Lattka, Jerzy Adamski, Annette Peters,[...]. PLoS One 2013
443
7


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
7

Epigenome-wide association studies without the need for cell-type composition.
James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten. Nat Methods 2014
124
7

BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference.
Elior Rahmani, Regev Schweiger, Liat Shenhav, Theodora Wingert, Ira Hofer, Eilon Gabel, Eleazar Eskin, Eran Halperin. Genome Biol 2018
20
35

An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation.
Eilis Hannon, Emma Dempster, Joana Viana, Joe Burrage, Adam R Smith, Ruby Macdonald, David St Clair, Colette Mustard, Gerome Breen, Sebastian Therman,[...]. Genome Biol 2016
136
7

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
85
8

Epigenetic programming by maternal behavior.
Ian C G Weaver, Nadia Cervoni, Frances A Champagne, Ana C D'Alessio, Shakti Sharma, Jonathan R Seckl, Sergiy Dymov, Moshe Szyf, Michael J Meaney. Nat Neurosci 2004
6

DNA methylation age of blood predicts all-cause mortality in later life.
Riccardo E Marioni, Sonia Shah, Allan F McRae, Brian H Chen, Elena Colicino, Sarah E Harris, Jude Gibson, Anjali K Henders, Paul Redmond, Simon R Cox,[...]. Genome Biol 2015
482
6


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
304
6

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
311
6

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
54
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
51
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
5

Reliability of DNA methylation measures from dried blood spots and mononuclear cells using the HumanMethylation450k BeadArray.
Pierre-Antoine Dugué, Dallas R English, Robert J MacInnis, Chol-Hee Jung, Julie K Bassett, Liesel M FitzGerald, Ee Ming Wong, Jihoon E Joo, John L Hopper, Melissa C Southey,[...]. Sci Rep 2016
29
17

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
83
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
314
5

Missing value estimation methods for DNA microarrays.
O Troyanskaya, M Cantor, G Sherlock, P Brown, T Hastie, R Tibshirani, D Botstein, R B Altman. Bioinformatics 2001
5

Age-associated DNA methylation in pediatric populations.
Reid S Alisch, Benjamin G Barwick, Pankaj Chopra, Leila K Myrick, Glen A Satten, Karen N Conneely, Stephen T Warren. Genome Res 2012
226
5

Correspondence of DNA Methylation Between Blood and Brain Tissue and Its Application to Schizophrenia Research.
Esther Walton, Johanna Hass, Jingyu Liu, Joshua L Roffman, Fabio Bernardoni, Veit Roessner, Matthias Kirsch, Gabriele Schackert, Vince Calhoun, Stefan Ehrlich. Schizophr Bull 2016
133
5

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
459
5

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
191
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.