A citation-based method for searching scientific literature

Yun Liu, Martin J Aryee, Leonid Padyukov, M Daniele Fallin, Espen Hesselberg, Arni Runarsson, Lovisa Reinius, Nathalie Acevedo, Margaret Taub, Marcus Ronninger, Klementy Shchetynsky, Annika Scheynius, Juha Kere, Lars Alfredsson, Lars Klareskog, Tomas J Ekström, Andrew P Feinberg. Nat Biotechnol 2013
Times Cited: 555







List of co-cited articles
650 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
26

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
20



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
15

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
615
13

Epigenome-wide association studies for common human diseases.
Vardhman K Rakyan, Thomas A Down, David J Balding, Stephan Beck. Nat Rev Genet 2011
734
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
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
801
11

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
10

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
355
9

Epigenome-wide association studies without the need for cell-type composition.
James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten. Nat Methods 2014
128
8

Reference-free cell mixture adjustments in analysis of DNA methylation data.
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
250
8


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
967
8

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
983
8

DNA methylome signature in rheumatoid arthritis.
Kazuhisa Nakano, John W Whitaker, David L Boyle, Wei Wang, Gary S Firestein. Ann Rheum Dis 2013
207
8

Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, Robert H Dowen, R David Hawkins, Gary Hon, Julian Tonti-Filippini, Joseph R Nery, Leonard Lee, Zhen Ye, Que-Minh Ngo,[...]. Nature 2009
8

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
96
8

Epigenome-wide association study of rheumatoid arthritis identifies differentially methylated loci in B cells.
Antonio Julià, Devin Absher, María López-Lasanta, Nuria Palau, Andrea Pluma, Lindsay Waite Jones, John R Glossop, William E Farrell, Richard M Myers, Sara Marsal. Hum Mol Genet 2017
26
30

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
8

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
142
7

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
452
7

Genetics and epigenetics of rheumatoid arthritis.
Sebastien Viatte, Darren Plant, Soumya Raychaudhuri. Nat Rev Rheumatol 2013
222
7

Review of processing and analysis methods for DNA methylation array data.
C S Wilhelm-Benartzi, D C Koestler, M R Karagas, J M Flanagan, B C Christensen, K T Kelsey, C J Marsit, E A Houseman, R Brown. Br J Cancer 2013
94
7

Disentangling molecular relationships with a causal inference test.
Joshua Millstein, Bin Zhang, Jun Zhu, Eric E Schadt. BMC Genet 2009
136
7

Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation.
Loukia G Tsaprouni, Tsun-Po Yang, Jordana Bell, Katherine J Dick, Stavroula Kanoni, James Nisbet, Ana Viñuela, Elin Grundberg, Christopher P Nelson, Eshwar Meduri,[...]. Epigenetics 2014
181
6

Genome-wide DNA methylation analysis in multiple tissues in primary Sjögren's syndrome reveals regulatory effects at interferon-induced genes.
Juliana Imgenberg-Kreuz, Johanna K Sandling, Jonas Carlsson Almlöf, Jessica Nordlund, Linnea Signér, Katrine Braekke Norheim, Roald Omdal, Lars Rönnblom, Maija-Leena Eloranta, Ann-Christine Syvänen,[...]. Ann Rheum Dis 2016
78
7

Statistical and integrative system-level analysis of DNA methylation data.
Andrew E Teschendorff, Caroline L Relton. Nat Rev Genet 2018
99
6

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
565
6

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
42
14

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer.
Andrew E Teschendorff, Usha Menon, Aleksandra Gentry-Maharaj, Susan J Ramus, Daniel J Weisenberger, Hui Shen, Mihaela Campan, Houtan Noushmehr, Christopher G Bell, A Peter Maxwell,[...]. Genome Res 2010
516
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
249
6

DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis.
Lara Kular, Yun Liu, Sabrina Ruhrmann, Galina Zheleznyakova, Francesco Marabita, David Gomez-Cabrero, Tojo James, Ewoud Ewing, Magdalena Lindén, Bartosz Górnikiewicz,[...]. Nat Commun 2018
54
11

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
332
6


2010 Rheumatoid arthritis classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative.
Daniel Aletaha, Tuhina Neogi, Alan J Silman, Julia Funovits, David T Felson, Clifton O Bingham, Neal S Birnbaum, Gerd R Burmester, Vivian P Bykerk, Marc D Cohen,[...]. Arthritis Rheum 2010
6

Genetics of rheumatoid arthritis contributes to biology and drug discovery.
Yukinori Okada, Di Wu, Gosia Trynka, Towfique Raj, Chikashi Terao, Katsunori Ikari, Yuta Kochi, Koichiro Ohmura, Akari Suzuki, Shinji Yoshida,[...]. Nature 2014
6

Associating cellular epigenetic models with human phenotypes.
Tuuli Lappalainen, John M Greally. Nat Rev Genet 2017
122
6

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
55
10

DNA methylation mediates genotype and smoking interaction in the development of anti-citrullinated peptide antibody-positive rheumatoid arthritis.
Weida Meng, Zaihua Zhu, Xia Jiang, Chun Lai Too, Steffen Uebe, Maja Jagodic, Ingrid Kockum, Shahnaz Murad, Luigi Ferrucci, Lars Alfredsson,[...]. Arthritis Res Ther 2017
25
24

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
6


Regulation of DNA methylation in rheumatoid arthritis synoviocytes.
Kazuhisa Nakano, David L Boyle, Gary S Firestein. J Immunol 2013
77
6


Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Danny Leung, Nisha Rajagopal, Joseph R Nery, Mark A Urich, Huaming Chen,[...]. Nature 2015
326
5

Transcription factors as readers and effectors of DNA methylation.
Heng Zhu, Guohua Wang, Jiang Qian. Nat Rev Genet 2016
213
5


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
341
5

Persistent epigenetic differences associated with prenatal exposure to famine in humans.
Bastiaan T Heijmans, Elmar W Tobi, Aryeh D Stein, Hein Putter, Gerard J Blauw, Ezra S Susser, P Eline Slagboom, L H Lumey. Proc Natl Acad Sci U S A 2008
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.