A citation-based method for searching scientific literature

Andrew E Teschendorff, Charles E Breeze, Shijie C Zheng, Stephan Beck. BMC Bioinformatics 2017
Times Cited: 133







List of co-cited articles
676 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
38

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
31



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
655
19

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

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
813
18

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
17

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
118
17

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
66
25

Statistical and integrative system-level analysis of DNA methylation data.
Andrew E Teschendorff, Caroline L Relton. Nat Rev Genet 2018
129
17

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
97
17

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
61
26

Reference-free cell mixture adjustments in analysis of DNA methylation data.
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
274
16

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
16

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

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
14

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
877
14


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
599
14

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
13

Epigenome-wide association studies without the need for cell-type composition.
James Zou, Christoph Lippert, David Heckerman, Martin Aryee, Jennifer Listgarten. Nat Methods 2014
134
12

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
68
16

Associating cellular epigenetic models with human phenotypes.
Tuuli Lappalainen, John M Greally. Nat Rev Genet 2017
145
10


Pan-cancer deconvolution of tumour composition using DNA methylation.
Ankur Chakravarthy, Andrew Furness, Kroopa Joshi, Ehsan Ghorani, Kirsty Ford, Matthew J Ward, Emma V King, Matt Lechner, Teresa Marafioti, Sergio A Quezada,[...]. Nat Commun 2018
98
10

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
291
10

MeDeCom: discovery and quantification of latent components of heterogeneous methylomes.
Pavlo Lutsik, Martin Slawski, Gilles Gasparoni, Nikita Vedeneev, Matthias Hein, Jörn Walter. Genome Biol 2017
40
22

Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL).
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
66
13


Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.
Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R Zhang, Mingyao Li. Nat Commun 2019
204
9

Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease.
Joshua Moss, Judith Magenheim, Daniel Neiman, Hai Zemmour, Netanel Loyfer, Amit Korach, Yaacov Samet, Myriam Maoz, Henrik Druid, Peter Arner,[...]. Nat Commun 2018
250
9


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
365
8


Cell type-specific gene expression differences in complex tissues.
Shai S Shen-Orr, Robert Tibshirani, Purvesh Khatri, Dale L Bodian, Frank Staedtler, Nicholas M Perry, Trevor Hastie, Minnie M Sarwal, Mark M Davis, Atul J Butte. Nat Methods 2010
306
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
8

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
8

CpGassoc: an R function for analysis of DNA methylation microarray data.
Richard T Barfield, Varun Kilaru, Alicia K Smith, Karen N Conneely. Bioinformatics 2012
140
8

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
21
38

Determining cell type abundance and expression from bulk tissues with digital cytometry.
Aaron M Newman, Chloé B Steen, Chih Long Liu, Andrew J Gentles, Aadel A Chaudhuri, Florian Scherer, Michael S Khodadoust, Mohammad S Esfahani, Bogdan A Luca, David Steiner,[...]. Nat Biotechnol 2019
729
8

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
138
8

CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA.
Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang,[...]. Genome Biol 2017
118
7

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
91
7

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.
Shijie C Zheng, Stephan Beck, Andrew E Jaffe, Devin C Koestler, Kasper D Hansen, Andres E Houseman, Rafael A Irizarry, Andrew E Teschendorff. Nat Methods 2017
47
14

Digital sorting of complex tissues for cell type-specific gene expression profiles.
Yi Zhong, Ying-Wooi Wan, Kaifang Pang, Lionel M L Chow, Zhandong Liu. BMC Bioinformatics 2013
108
7

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
412
7

Epigenome-wide association of PTSD from heterogeneous cohorts with a common multi-site analysis pipeline.
Andrew Ratanatharathorn, Marco P Boks, Adam X Maihofer, Allison E Aiello, Ananda B Amstadter, Allison E Ashley-Koch, Dewleen G Baker, Jean C Beckham, Evelyn Bromet, Michelle Dennis,[...]. Am J Med Genet B Neuropsychiatr Genet 2017
49
14

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
231
7


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.