A citation-based method for searching scientific literature

Andrew E Teschendorff, Francesco Marabita, Matthias Lechner, Thomas Bartlett, Jesper Tegner, David Gomez-Cabrero, Stephan Beck. Bioinformatics 2013
Times Cited: 739







List of co-cited articles
517 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
37

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
27

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
27


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
405
20

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
310
20

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
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
821
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
378
18

Comprehensive analysis of DNA methylation data with RnBeads.
Yassen Assenov, Fabian Müller, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock. Nat Methods 2014
365
17

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
338
16

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
997
15

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
15

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
498
13

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
12

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
163
12


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
339
11

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
218
10

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
10

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
423
9




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
8

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
8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

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
59
11

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
61
11

An epigenetic signature in peripheral blood predicts active ovarian cancer.
Andrew E Teschendorff, Usha Menon, Aleksandra Gentry-Maharaj, Susan J Ramus, Simon A Gayther, Sophia Apostolidou, Allison Jones, Matthias Lechner, Stephan Beck, Ian J Jacobs,[...]. PLoS One 2009
216
7

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia.
Jessica Nordlund, Christofer L Bäcklin, Per Wahlberg, Stephan Busche, Eva C Berglund, Maija-Leena Eloranta, Trond Flaegstad, Erik Forestier, Britt-Marie Frost, Arja Harila-Saari,[...]. Genome Biol 2013
184
7


Epigenetic age acceleration predicts cancer, cardiovascular, and all-cause mortality in a German case cohort.
Laura Perna, Yan Zhang, Ute Mons, Bernd Holleczek, Kai-Uwe Saum, Hermann Brenner. Clin Epigenetics 2016
230
6

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
6

ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip.
Zongli Xu, Liang Niu, Leping Li, Jack A Taylor. Nucleic Acids Res 2016
119
6

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences.
Adam E Field, Neil A Robertson, Tina Wang, Aaron Havas, Trey Ideker, Peter D Adams. Mol Cell 2018
149
6

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
213
6

Reference-free cell mixture adjustments in analysis of DNA methylation data.
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
256
6

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
258
6

The epigenomics of cancer.
Peter A Jones, Stephen B Baylin. Cell 2007
6


clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
6

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
6

The correlation of methylation levels measured using Illumina 450K and EPIC BeadChips in blood samples.
Mark W Logue, Alicia K Smith, Erika J Wolf, Hannah Maniates, Annjanette Stone, Steven A Schichman, Regina E McGlinchey, William Milberg, Mark W Miller. Epigenomics 2017
52
9

Epigenome-wide association studies for common human diseases.
Vardhman K Rakyan, Thomas A Down, David J Balding, Stephan Beck. Nat Rev Genet 2011
741
5

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

Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation.
Benjamin T Mayne, Shalem Y Leemaqz, Alicia K Smith, James Breen, Claire T Roberts, Tina Bianco-Miotto. Epigenomics 2017
36
13

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
269
5

An epigenetic clock for gestational age at birth based on blood methylation data.
Anna K Knight, Jeffrey M Craig, Christiane Theda, Marie Bækvad-Hansen, Jonas Bybjerg-Grauholm, Christine S Hansen, Mads V Hollegaard, David M Hougaard, Preben B Mortensen, Shantel M Weinsheimer,[...]. Genome Biol 2016
91
5

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
631
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.