A citation-based method for searching scientific literature

Lucas A Salas, Devin C Koestler, Rondi A Butler, Helen M Hansen, John K Wiencke, Karl T Kelsey, Brock C Christensen. Genome Biol 2018
Times Cited: 89







List of co-cited articles
459 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
61

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
43

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
449
28


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
64
34

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
650
23

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
21

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.
Belinda Phipson, Jovana Maksimovic, Alicia Oshlack. Bioinformatics 2016
282
20

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
130
20



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
406
16

DNA Methylation-Derived Neutrophil-to-Lymphocyte Ratio: An Epigenetic Tool to Explore Cancer Inflammation and Outcomes.
Devin C Koestler, Joseph Usset, Brock C Christensen, Carmen J Marsit, Margaret R Karagas, Karl T Kelsey, John K Wiencke. Cancer Epidemiol Biomarkers Prev 2017
42
33

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
19

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

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
14

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
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
594
14


ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip.
Zongli Xu, Liang Niu, Leping Li, Jack A Taylor. Nucleic Acids Res 2016
139
13

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
13

Quantitative reconstruction of leukocyte subsets using DNA methylation.
William P Accomando, John K Wiencke, E Andres Houseman, Heather H Nelson, Karl T Kelsey. Genome Biol 2014
93
12

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Jean-Philippe Fortin, Timothy J Triche, Kasper D Hansen. Bioinformatics 2017
262
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
870
11

DNA methylation of cord blood cell types: Applications for mixed cell birth studies.
Kelly M Bakulski, Jason I Feinberg, Shan V Andrews, Jack Yang, Shannon Brown, Stephanie L McKenney, Frank Witter, Jeremy Walston, Andrew P Feinberg, M Daniele Fallin. Epigenetics 2016
174
10

Immunomethylomic approach to explore the blood neutrophil lymphocyte ratio (NLR) in glioma survival.
John K Wiencke, Devin C Koestler, Lucas A Salas, Joseph L Wiemels, Ritu P Roy, Helen M Hansen, Terri Rice, Lucie S McCoy, Paige M Bracci, Annette M Molinaro,[...]. Clin Epigenetics 2017
38
23

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
387
10

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
426
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
804
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
117
10


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
59
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
536
8

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

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
352
8

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
381
8


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
8

Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data.
Kristina Gervin, Lucas A Salas, Kelly M Bakulski, Menno C van Zelm, Devin C Koestler, John K Wiencke, Liesbeth Duijts, Henriëtte A Moll, Karl T Kelsey, Michael S Kobor,[...]. Clin Epigenetics 2019
38
21

Statistical and integrative system-level analysis of DNA methylation data.
Andrew E Teschendorff, Caroline L Relton. Nat Rev Genet 2018
123
7

Reference-free cell mixture adjustments in analysis of DNA methylation data.
Eugene Andres Houseman, John Molitor, Carmen J Marsit. Bioinformatics 2014
271
7

Methylation-derived Neutrophil-to-Lymphocyte Ratio and Lung Cancer Risk in Heavy Smokers.
Laurie Grieshober, Stefan Graw, Matt J Barnett, Mark D Thornquist, Gary E Goodman, Chu Chen, Devin C Koestler, Carmen J Marsit, Jennifer A Doherty. Cancer Prev Res (Phila) 2018
19
36

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
546
7

Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition.
Kristina Gervin, Christian Magnus Page, Hans Christian D Aass, Michelle A Jansen, Heidi Elisabeth Fjeldstad, Bettina Kulle Andreassen, Liesbeth Duijts, Joyce B van Meurs, Menno C van Zelm, Vincent W Jaddoe,[...]. Epigenetics 2016
44
13

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
46
13

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.
Matthias Farlik, Florian Halbritter, Fabian Müller, Fizzah A Choudry, Peter Ebert, Johanna Klughammer, Samantha Farrow, Antonella Santoro, Valerio Ciaurro, Anthony Mathur,[...]. Cell Stem Cell 2016
125
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
64
9


Epigenome-wide association studies for common human diseases.
Vardhman K Rakyan, Thomas A Down, David J Balding, Stephan Beck. Nat Rev Genet 2011
765
6

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
945
6


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.