A citation-based method for searching scientific literature

Wanding Zhou, Peter W Laird, Hui Shen. Nucleic Acids Res 2017
Times Cited: 190







List of co-cited articles
537 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
30

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
25

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
395
24

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
732
19

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
183
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
370
17


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
15

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
981
13

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
809
12

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
211
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
11


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
329
10

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

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
331
10

DNA methylation-based classification of central nervous system tumours.
David Capper, David T W Jones, Martin Sill, Volker Hovestadt, Daniel Schrimpf, Dominik Sturm, Christian Koelsche, Felix Sahm, Lukas Chavez, David E Reuss,[...]. Nature 2018
752
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

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
625
10

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
203
9

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
491
9

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
159
8

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
56
14


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
305
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


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
344
7

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
7

A DNA methylation biomarker of alcohol consumption.
C Liu, R E Marioni, Å K Hedman, L Pfeiffer, P-C Tsai, L M Reynolds, A C Just, Q Duan, C G Boer, T Tanaka,[...]. Mol Psychiatry 2018
130
7

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
200
7

SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
Wanding Zhou, Timothy J Triche, Peter W Laird, Hui Shen. Nucleic Acids Res 2018
47
14


Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.
Katherine A Hoadley, Christina Yau, Toshinori Hinoue, Denise M Wolf, Alexander J Lazar, Esther Drill, Ronglai Shen, Alison M Taylor, Andrew D Cherniack, Vésteinn Thorsson,[...]. Cell 2018
617
6

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
387
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
255
6

GREAT improves functional interpretation of cis-regulatory regions.
Cory Y McLean, Dave Bristor, Michael Hiller, Shoa L Clarke, Bruce T Schaar, Craig B Lowe, Aaron M Wenger, Gill Bejerano. Nat Biotechnol 2010
6

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

Genetic and environmental influences interact with age and sex in shaping the human methylome.
Jenny van Dongen, Michel G Nivard, Gonneke Willemsen, Jouke-Jan Hottenga, Quinta Helmer, Conor V Dolan, Erik A Ehli, Gareth E Davies, Maarten van Iterson, Charles E Breeze,[...]. Nat Commun 2016
137
6

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.
Philip L De Jager, Gyan Srivastava, Katie Lunnon, Jeremy Burgess, Leonard C Schalkwyk, Lei Yu, Matthew L Eaton, Brendan T Keenan, Jason Ernst, Cristin McCabe,[...]. Nat Neurosci 2014
460
5

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
215
5

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex.
Andrew E Jaffe, Yuan Gao, Amy Deep-Soboslay, Ran Tao, Thomas M Hyde, Daniel R Weinberger, Joel E Kleinman. Nat Neurosci 2016
236
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
652
5


TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
Antonio Colaprico, Tiago C Silva, Catharina Olsen, Luciano Garofano, Claudia Cava, Davide Garolini, Thais S Sabedot, Tathiane M Malta, Stefano M Pagnotta, Isabella Castiglioni,[...]. Nucleic Acids Res 2016
782
5

Oncogenic Signaling Pathways in The Cancer Genome Atlas.
Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K Chatila, Augustin Luna, Konnor C La, Sofia Dimitriadoy, David L Liu, Havish S Kantheti, Sadegh Saghafinia,[...]. Cell 2018
761
5

Meffil: efficient normalization and analysis of very large DNA methylation datasets.
J L Min, G Hemani, G Davey Smith, C Relton, M Suderman. Bioinformatics 2018
46
10

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
338
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.