bioconductor: RnBeads | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02388-x

Gene set enrichment analysis for genome-wide DNA methylation data
Cited by: 61
Author(s): Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
Software Mentions: 16
Published: over 3 years ago

Bigmelon: tools for analysing large DNA methylation datasets
Cited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: over 6 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago

10.15252/emmm.201809443

<scp>PDX</scp> models recapitulate the genetic and epigenetic landscape of pediatric T‐cell leukemia
Cited by: 35
Author(s): Paulina Richter-Pechańska, Joachim Kunz, Beat Bornhäuser, Caroline Von Knebel Doeberitz, Tobias Rausch, Büşra Erarslan-Uysal, Yassen Assenov, Viktoras Frismantas, Blerim Marovca, Sebastian M. Waszak, Martin Zimmermann, Julia Seemann, Margit Happich, Martin Stanulla, Martin Schrappe, Gunnar Cario, Gabriele Escherich, Kseniya Bakharevich, Renate Kirschner-Schwabe, Cornelia Eckert, Martina U. Muckenthaler, Jan O. Korbel, Jean‐Pierre Bourquin, Andreas E. Kulozik
Software Mentions: 12
Published: about 6 years ago

10.1038/s41598-019-44765-4

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Cited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: over 5 years ago

10.1186/s13059-021-02329-8

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
Cited by: 13
Author(s): Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos
Software Mentions: 11
Published: over 3 years ago

10.3390/ijms22031190

Genome-Wide DNA Methylation Analysis of a Cohort of 41 Patients Affected by Oculo-Auriculo-Vertebral Spectrum (OAVS)
Cited by: 12
Author(s): Valentina Guida, Luciano Calzari, Maria Teresa Fadda, Francesca Piceci‐Sparascio, María Cristina Digilio, Laura Bernardini, Francesco Brancati, Teresa Mattina, Daniela Melis, Francesca Forzano, Silvana Briuglia, Tommaso Mazza, Sebastiano Bianca, Enza Maria Valente, Leila Bagherjad Salehi, Paolo Prontera, Mario Pagnoni, Romano Tenconi, Bruno Dallapiccola, Giorgio Iannetti, Luigi Corsaro, Alessandro De Luca, Davide Gentilini
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13059-021-02484-y

Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications
Cited by: 5
Author(s): Benjamin Planterose Jiménez, Manfred Kayser, Athina Vidaki
Software Mentions: 10
Published: over 3 years ago

10.1186/s13073-020-00786-7

A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
Cited by: 11
Author(s): Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo, Teresa Manzo, Luigi Nezi, Ugo Cavallaro, Davide Cacchiarelli, Jörn Walter, Giuseppe Testa
Software Mentions: 9
Published: about 4 years ago

10.3390/ijms21145044

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth
Cited by: 10
Author(s): Elena Spada, Luciano Calzari, Luigi Corsaro, Teresa Fazia, Monica Mencarelli, Anna Maria Di Blasio, Luisa Bernardinelli, G. Zangheri, Michele Vignali, Davide Gentilini
Software Mentions: 9
Published: over 4 years ago

10.1172/jci.insight.140443

Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung
Cited by: 6
Author(s): Maria Llamazares Prada, Elisa Espinet, Vedrana Mijošek, Uwe Schwartz, Pavlo Lutsik, Raluca Tamas, Mandy Richter, Annika Behrendt, Stephanie Pohl, Naja P. Benz, Thomas Muley, Arne Warth, Claus Peter Heusel, Hauke Winter, Jonathan Landry, Felix J.F. Herth, Tinne Mertens, Harry Karmouty‐Quintana, Ina Koch, Vladimı́r Beneš, Jan O. Korbel, Sebastian M. Waszak, Andreas Trumpp, David Wyatt, Heiko Stahl, Christoph Plass, Renata Z. Jurkowska
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-018-29378-7

Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer
Cited by: 7
Author(s): Beatríz González, Ferran Fece de la Cruz, Johanna Samuelsson, Andreu Alibés, Sergio Alonso
Software Mentions: 8
Published: over 6 years ago

10.1186/s13058-018-1022-y

Clonal relatedness in tumour pairs of breast cancer patients
Cited by: 14
Author(s): Jana Biermann, Toshima Z. Parris, Szilárd Nemes, Anna Danielsson, Hanna Engqvist, Elisabeth Werner Rönnerman, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 8
Published: over 6 years ago

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: about 6 years ago

10.1186/s13059-019-1664-9

RnBeads 2.0: comprehensive analysis of DNA methylation data
Cited by: 188
Author(s): Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer, Christoph Bock
Software Mentions: 8
Published: almost 6 years ago

10.1186/s13148-018-0510-3

Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception
Cited by: 25
Author(s): Davide Gentilini, Edgardo Somigliana, Luca Pagliardini, Elisa Rabellotti, Paolo Garagnani, Luisa Bernardinelli, Enrico Papaleo, Massimo Candiani, Anna Maria Di Blasio, Paola Viganò
Software Mentions: 7
Published: over 6 years ago

10.1186/s13072-021-00415-6

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Cited by: 1
Author(s): Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana I. Shashkova, Marion Arnoux, Édouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul Lyons, Michel Georges, Jörn Walter
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-55453-8

MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
Cited by: 2
Author(s): Andigoni Malousi, Sofia Kouidou, Maria Tsagiopoulou, Nikos Papakonstantinou, Emmanouil Bouras, Elisavet Georgiou, Georgios Tzimagiorgis, Kostas Stamatopoulos
Software Mentions: 7
Published: about 5 years ago

10.1186/s12859-020-03734-9

MADA: a web service for analysing DNA methylation array data
Cited by: 1
Author(s): Xinyu Hu, Li Tang, Linconghua Wang, Fang‐Xiang Wu, Min Li
Software Mentions: 7
Published: about 4 years ago

10.1186/s12859-015-0568-2

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns
Cited by: 95
Author(s): Tiphaine Martin, İdil Yet, Pei-Chien Tsai, Jordana T. Bell
Software Mentions: 7
Published: over 9 years ago

10.3389/fimmu.2020.609891

Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype
Cited by: 26
Author(s): Christopher Kressler, Gilles Gasparoni, Karl Nordström, Dania Hamo, Abdulrahman Salhab, Christoforos Dimitropoulos, Sascha Tierling, Petra Reinke, Hans‐Dieter Volk, Jörn Walter, Alf Hamann, Julia K. Polansky
Software Mentions: 7
Published: almost 4 years ago

10.3389/fgene.2019.00774

A Hybrid Ensemble Approach for Identifying Robust Differentially Methylated Loci in Pan-Cancers
Cited by: 3
Author(s): Qi Tian, Jianxiao Zou, Yuan Fang, Zhongli Yu, Jie Tang, Ying Song, Shicai Fan
Software Mentions: 7
Published: over 5 years ago

10.1089/cmb.2020.0081

GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis
Cited by: 5
Author(s): Xiao Wang, Dan Hao, Haja N. Kadarmideen
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12918-015-0211-x

Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential
Cited by: 41
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 6
Published: over 9 years ago

10.1038/s42003-020-01479-y

Epigenetic landscape of pancreatic neuroendocrine tumours reveals distinct cells of origin and means of tumour progression
Cited by: 48
Author(s): Annunziata Di Domenico, Christodoulos P. Pipinikas, Renaud Maire, Konstantin Bräutigam, Cédric Simillion, Matthias S. Dettmer, Erik Vassella, Chrissie Thirlwell, Aurel Perren, Ilaria Marinoni
Software Mentions: 6
Published: about 4 years ago

10.1016/j.celrep.2015.11.024

Differential DNA Methylation Analysis without a Reference Genome
Cited by: 35
Author(s): Johanna Klughammer, Paul Datlinger, Dieter Printz, Nathan C. Sheffield, Matthias Farlik, Johanna Hadler, Gerhard Fritsch, Christoph Bock
Software Mentions: 6
Published: about 9 years ago

10.15252/embj.2018100882

Life‐long impairment of glucose homeostasis upon prenatal exposure to psychostimulants
Cited by: 11
Author(s): Solomiia Korchynska, Maria Krassnitzer, Katarzyna Maleńczyk, Rashmi B. Prasad, Evgenii Tretiakov, Sabah Rehman, Valentina Cinquina, Victoria Gernedl, Matthias Farlik, Julian Petersen, S Hannes, Julia Schachenhofer, Sonali N. Reisinger, Alice Zambon, Olof Asplund, Isabella Artner, Erik Keimpema, Gert Lübec, Jan Mulder, Christoph Bock, Daniela D. Pollak, Roman A. Romanov, Christian Pifl, Leif Groop, Tomas Hökfelt, Tibor Harkany
Software Mentions: 6
Published: about 5 years ago

10.1186/s13072-017-0144-2

Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function
Cited by: 19
Author(s): Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein‐Hitpass, Anupam Sinha, Karl‐Heinz Jöckel, Markus M. Nöthen, Per Hoffmann, Markus M. Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
Software Mentions: 6
Published: over 7 years ago

10.1186/s12859-021-03982-3

Nonlinear ridge regression improves cell-type-specific differential expression analysis
Cited by: 4
Author(s): Fumihiko Takeuchi, Norihiro Kato
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-020-02175-0

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity
Cited by: 32
Author(s): Won‐Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrão, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng, Wei Lü, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J. Jack Lee, Erik P. Sulman, Ganesh Rao, Stephen G. Swisher, Lixia Diao, Jing Wang, John V. Heymach, Jason T. Huse, Paul Scheet, Ignacio I. Wistuba, Don L. Gibbons, P. Andrew Futreal, Jianhua Zhang, Daniel R. Gomez, Jianjun Zhang
Software Mentions: 5
Published: about 4 years ago

10.1172/jci.insight.146196

Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis
Cited by: 9
Author(s): Carolin Czauderna, Alicia Poplawski, Colm J. O’Rourke, Darko Castven, Benjamín Pérez-Aguilar, Diana Becker, Markus M. Nöthen, Margarete Odenthal, W Amer, M Schmiel, Uta Drebber, Harald Binder, Dirk A. Ridder, Mario Schindeldecker, Beate K. Straub, Peter R. Galle, Jesper B. Andersen, Snorri S. Thorgeirsson, Young Nyun Park, Jens U. Marquardt
Software Mentions: 5
Published: over 3 years ago

10.1186/s13072-015-0045-1

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay
Cited by: 11
Author(s): Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
Software Mentions: 5
Published: about 9 years ago

10.1093/gigascience/giaa066

CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes
Cited by: 5
Author(s): Sara-Jayne Thursby, Darin K Lobo, Kristina Pentieva, Shudong Zhang, Rachelle E Irwin, Colum P. Walsh
Software Mentions: 5
Published: over 4 years ago

10.1093/gigascience/giaa049

Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy
Cited by: 11
Author(s): Katarzyna Murat, Björn Grüning, Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J. Tobin, Krzysztof Poterlowicz
Software Mentions: 5
Published: over 4 years ago

10.18632/oncotarget.17462

Epigenome-wide association study in hepatocellular carcinoma: Identification of stochastic epigenetic mutations through an innovative statistical approach
Cited by: 43
Author(s): Davide Gentilini, Stefania Scala, Germano Gaudenzi, Paolo Garagnani, Miriam Capri, Matteo Cescon, Gian Luca Grazi, Maria Giulia Bacalini, Serena Pisoni, Alessandra Dicitore, Luisa Circelli, Sara Santagata, Francesco Izzo, Anna Maria Di Blasio, Luca Persani, Claudio Franceschi, Giovanna Mantovani
Software Mentions: 5
Published: over 7 years ago

10.3389/fmolb.2021.716544

GeneTrail: A Framework for the Analysis of High-Throughput Profiles
Cited by: 1
Author(s): Nico Gerstner, Tim Kehl, Kerstin Lenhof, Lea Eckhart, Lara Schneider, Daniel Stöckel, Christina Backes, Eckart Meese, Andreas Keller, Hans‐Peter Lenhof
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms21186853

DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa
Cited by: 7
Author(s): Nina Milutin Gašperov, Ivan Sabol, Ksenija Božinović, Emil Dediol, Marinka Mravak‐Stipetić, Danilo Licastro, Simeone Dal Monego, Magdalena Grce
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2019.00770

Maternal Smoking During Pregnancy Induces Persistent Epigenetic Changes Into Adolescence, Independent of Postnatal Smoke Exposure and Is Associated With Cardiometabolic Risk
Cited by: 65
Author(s): Sebastian Rauschert, Phillip E. Melton, Graham C. Burdge, Jeffrey M. Craig, Keith M. Godfrey, Joanna D. Holbrook, Karen A. Lillycrop, Trevor A. Mori, Lawrence J. Beilin, Wendy H. Oddy, Craig E. Pennell, Rae‐Chi Huang
Software Mentions: 5
Published: over 5 years ago

10.1186/s13148-020-00877-7

Methylome profiling of young adults with depression supports a link with immune response and psoriasis
Cited by: 10
Author(s): Coral Lapsley, Rachelle E Irwin, Margaret McLafferty, Sara Jayne Thursby, Siobhan O’Neill, Anthony J. Bjourson, Colum P. Walsh, Elaine Murray
Software Mentions: 4
Published: over 4 years ago

10.1186/s13148-017-0316-8

Immunomethylomic approach to explore the blood neutrophil lymphocyte ratio (NLR) in glioma survival
Cited by: 50
Author(s): John K. Wiencke, Devin C. Koestler, Lucas A. Salas, Joseph L. Wiemels, Ritu Roy, Helen M. Hansen, Terri Rice, Lucie McCoy, Paige M. Bracci, Annette M. Molinaro, Karl T. Kelsey, Margaret Wrensch, Brock C. Christensen
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes11010034

Genome-Wide Tiling Array Analysis of HPV-Induced Warts Reveals Aberrant Methylation of Protein-Coding and Non-Coding Regions
Cited by: 3
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-018-0581-1

Methylome profiling of healthy and central precocious puberty girls
Cited by: 28
Author(s): Danielle Bessa, Mariana Maschietto, Carlos F. Aylwin, Ana Pinheiro Machado Canton, Vinícius Nahime Brito, Delanie B Macedo, Marina Cunha-Silva, Heloísa Marcelina Cunha Palhares, Elisabete Aparecida Mantovani Rodrigues de Resende, Maria de Fátima Borges, Berenice B. Mendonca, Irène Netchine, Ana Cristina Victorino Krepischi, Alejandro Lomniczi, Sergio R. Ojeda, Ana Cláudia Latronico
Software Mentions: 4
Published: about 6 years ago

10.1172/JCI94509

STAT5BN642H is a driver mutation for T cell neoplasia
Cited by: 52
Author(s): Hà Phạm, Barbara Maurer, Michaela Prchal-Murphy, Reinhard Grausenburger, Eva Grundschober, Tahereh Javaheri, Harini Nivarthi, Auke Boersma, Thomas Kolbe, Mohamed Elabd, Florian Halbritter, Jan Pěnčík, Zahra Kazemi, Florian Grebien, Markus Hengstschläger, Lukas Kenner, Stefan Kubicek, Matthias Farlik, Christoph Bock, Peter Valent, Mathias Müller, Thomas Rülicke, Veronika Sexl, Richard Moriggl
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20174094

Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae
Cited by: 18
Author(s): Eliah Overbey, Amber M. Paul, Willian A. da Silveira, Candice Tahimic, Sigrid Reinsch, Nathaniel J. Szewczyk, Seta Stanbouly, Charles Wang, Jonathan M. Galazka, Xiao Wen Mao
Software Mentions: 4
Published: over 5 years ago

10.1186/s12967-021-02858-7

Deconvolution of sarcoma methylomes reveals varying degrees of immune cell infiltrates with association to genomic aberrations
Cited by: 5
Author(s): Malte Simon, Sadaf S. Mughal, Peter Horak, Sebastian Uhrig, Jonas Buchloh, Bogac Aybey, Albrecht Stenzinger, Hanno Glimm, Stefan Fröhling, Benedikt Brors, Charles D. Imbusch
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-020-06886-3

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data
Cited by: 8
Author(s): Yadollah Shahryary, Rashmi R. Hazarika, Frank Johannes
Software Mentions: 4
Published: over 4 years ago

10.1186/s13148-018-0504-1

Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO
Cited by: 82
Author(s): Jonathan Heiss, Allan C. Just
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-46930-1

Distinct epigenetic profiles in children with perinatally-acquired HIV on antiretroviral therapy
Cited by: 17
Author(s): Stephanie Shiau, Renate Strehlau, Shuang Wang, Avy Violari, Catherine Do, Faeezah Patel, Afaaf Liberty, Izabela Krupska, Stephen M. Arpadi, Marc Foca, Ashraf Coovadia, Elaine J. Abrams, Benjamin Tycko, Mary Beth Terry, Louise Kuhn
Software Mentions: 4
Published: over 5 years ago

10.1093/cdn/nzaa097

Nutritional Epigenomics and Age-Related Disease
Cited by: 18
Author(s): Sophia Amenyah, Mary Ward, James J. Strain, Helene McNulty, Catherine F Hughes, Caitlin Dollin, Colum P. Walsh, Diane J. Lees-Murdock
Software Mentions: 4
Published: over 4 years ago

10.1038/s42003-021-01661-w

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
Cited by: 16
Author(s): Christoph Niemöller, Julius Wehrle, Julian Riba, Rainer Claus, Nathalie Renz, Janika Rhein, Sabine Bleul, Juliane M. Stosch, Justus Duyster, Christoph Plass, Pavlo Lutsik, Daniel B. Lipka, Michael Lübbert, Heiko Becker
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers11020263

Integrative Omic Profiling Reveals Unique Hypoxia Induced Signatures in Gastric Cancer Associated Myofibroblasts
Cited by: 2
Author(s): Hanna Najgebauer, Andrew F. Jarnuczak, Andrea Varró, Christopher M. Sanderson
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41388-018-0659-4

Histoepigenetic analysis of HPV- and tobacco-associated head and neck cancer identifies both subtype-specific and common therapeutic targets despite divergent microenvironments
Cited by: 20
Author(s): Ivenise Carrero, Hsuan-Chen Liu, Andrew G. Sikora, Aleksandar Milosavljevic
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-018-2037-1

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus
Cited by: 25
Author(s): David E. Condon, Phu V. Tran, Yu‐Chin Lien, Jonathan Schug, Michael Georgieff, Rebecca A. Simmons, Kyoung Jae Won
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12859-015-0641-x

An evaluation of statistical methods for DNA methylation microarray data analysis
Cited by: 51
Author(s): Dongmei Li, Zidian Xie, Marc A. Le Pape, Timothy D. Dye
Software Mentions: 3
Published: over 9 years ago

10.1002/1878-0261.12684

<i>SST</i> gene hypermethylation acts as a pan‐cancer marker for pancreatic ductal adenocarcinoma and multiple other tumors: toward its use for blood‐based diagnosis
Cited by: 18
Author(s): Mehdi Manoochehri, Yenan Wu, Nathalia A. Giese, Oliver Strobel, Stefanie Kutschmann, Florian Haller, Jörg D. Hoheisel, Evgeny A. Moskalev, Thilo Hackert, Andrea S. Bauer
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0165548

Are Epigenetic Factors Implicated in Chronic Widespread Pain?
Cited by: 17
Author(s): Andrea Burri, Zoya Marinova, Mark D. Robinson, Brigitte Kühnel, Mélanie Waldenberger, Simone Wahl, Sonja Kunze, Christian Gieger, Gregory Livshits, Frances Williams
Software Mentions: 3
Published: about 8 years ago

10.3390/cancers12030764

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability
Cited by: 41
Author(s): Wa Zhang, David Klinkebiel, Carter J. Barger, Sanjit Pandey, Chittibabu Guda, Austin Miller, Stacey N. Akers, Kunle Odunsi, Adam R. Karpf
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-017-0376-9

Long-term prenatal exposure to paracetamol is associated with DNA methylation differences in children diagnosed with ADHD
Cited by: 50
Author(s): Kristina Gervin, Hedvig Nordeng, Eivind Ystrøm, Ted Reichborn‐Kjennerud, Robert Lyle
Software Mentions: 3
Published: over 7 years ago

10.1186/s13148-019-0618-0

A randomized controlled trial of folic acid intervention in pregnancy highlights a putative methylation-regulated control element at ZFP57
Cited by: 32
Author(s): Rachelle E Irwin, Sara-Jayne Thursby, Miroslava Ondičová, Kristina Pentieva, Helene McNulty, Rebecca C Richmond, Aoife Caffrey, Diane J. Lees-Murdock, Marian McLaughlin, Tony Cassidy, Matthew Suderman, Caroline L Relton, Colum P. Walsh
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13148-018-0440-0

DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling
Cited by: 29
Author(s): Leonardo De Boni, Gilles Gasparoni, Carolin Haubenreich, Sascha Tierling, Imke Schmitt, Michael Peitz, Philipp Koch, Jörn Walter, Ullrich Wüllner, Oliver Brüstle
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13148-016-0235-0

Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas
Cited by: 7
Author(s): Annette Lim, Nicholas C. Wong, Ruth Pidsley, Elena Zotenko, June Corry, Alexander Dobrovic, Susan J. Clark, Danny Rischin, Benjamin Solomon
Software Mentions: 3
Published: over 8 years ago

10.1080/15592294.2018.1429857

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta
Cited by: 34
Author(s): Sungsam Gong, Michelle D. Johnson, Justyna Dopierała, Francesca Gaccioli, Ulla Sovio, Miguel Constância, Gordon C. S. Smith, D. Stephen Charnock-Jones
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13072-018-0182-4

Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression
Cited by: 18
Author(s): Karla O’Neill, Rachelle E Irwin, Sarah Jayne Mackin, Sara Jayne Thursby, Avinash Thakur, Ciske Bertens, Laura Masala, Jayne Loughery, Darragh G. McArt, Colum P. Walsh
Software Mentions: 3
Published: over 6 years ago

10.1038/s12276-020-00493-8

Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer
Cited by: 78
Author(s): Jae Won Cho, Min Hee Hong, Sang Jun Ha, Young-Joon Kim, Byoung Chul Cho, Insuk Lee, Hye Ryun Kim
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2019.01050

Maternal Intake of n-3 Polyunsaturated Fatty Acids During Pregnancy Is Associated With Differential Methylation Profiles in Cord Blood White Cells
Cited by: 16
Author(s): Marzia Bianchi, Anna Alisi, Marta Fabrizi, Cristina Vallone, Lucilla Ravà, Riccardo Giannico, Pamela Vernocchi, Fabrizio Signore, Melania Manco
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.00907

Epigenetic Delay in the Neurodevelopmental Trajectory of DNA Methylation States in Autism Spectrum Disorders
Cited by: 28
Author(s): Michael J. Corley, Naurú Idalia Vargas-Maya, Alina P.S. Pang, Annette Lum-Jones, Dongmei Li, Vedbar S. Khadka, Răzvan Sultana, D. Caroline Blanchard, Alika K. Maunakea
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2019.02136

Identification and Characterization of Post-activated B Cells in Systemic Autoimmune Diseases
Cited by: 37
Author(s): Sarah Y. Weißenberg, Franziska Szelinski, Eva Schrezenmeier, Ana‐Luisa Stefanski, Annika Wiedemann, Héctor Rincón‐Arévalo, Anna Welle, Annemarie Jungmann, Karl Nordström, Jörn Walter, Juliana Imgenberg‐Kreuz, Gunnel Nordmark, Lars Rönnblom, Prathyusha Bachali, Michelle D. Catalina, Amrie C. Grammer, Peter E. Lipsky, Andreia C. Lino, Thomas Dörner
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2017.00030

Combinatorial Ranking of Gene Sets to Predict Disease Relapse: The Retinoic Acid Pathway in Early Prostate Cancer
Cited by: 4
Author(s): Hieu T. Nim, Milena B. Furtado, Mirana Ramialison, Sarah Boyd
Software Mentions: 3
Published: almost 8 years ago

10.3390/genes12020129

Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis
Cited by: 11
Author(s): DeAnna Baker Frost, Willian A. da Silveira, E. Starr Hazard, Ilia Atanelishvili, Robert Wilson, Jonathan Flume, Kayleigh L. Day, Jim C. Oates, Galina S. Bogatkevich, Carol Feghali‐Bostwick, Gary Hardiman, Paula S. Ramos
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13073-020-00724-7

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL
Cited by: 14
Author(s): Justyna A. Wierzbińska, Réka Tóth, Naveed Ishaque, Karsten Rippe, Jan‐Philipp Mallm, Lara Klett, Daniel Mertens, Thorsten Zenz, Thomas Hielscher, Marc Seifert, Ralf Küppers, Yassen Assenov, Pavlo Lutsik, Stephan Stilgenbauer, Philipp M. Roessner, Martina Seiffert, John C. Byrd, Christopher C. Oakes, Christoph Plass, Daniel B. Lipka
Software Mentions: 3
Published: almost 5 years ago

10.1038/srep33310

Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment
Cited by: 32
Author(s): Michael J. Corley, Christian K. Dye, Michelle L DʼAntoni, Mary Margaret Byron, Ka'ahukane Leite-Ah Yo, Annette Lum-Jones, Beau K. Nakamoto, Victor Valcour, Ivo N. SahBandar, Cecilia Shikuma, Lishomwa C. Ndhlovu, Alika K. Maunakea
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-25085-5

RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Cited by: 67
Author(s): Anda R. Gliga, Sebastiano Di Bucchianico, Jessica M. Lindvall, Bengt Fadeel, Hanna Karlsson
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-83016-3

Identification of epigenetic memory candidates associated with gestational age at birth through analysis of methylome and transcriptional data
Cited by: 6
Author(s): Kohei Kashima, Tomoko Kawai, Riki Nishimura, Yuh Shiwa, Kevin Y. Urayama, Hiromi Kamura, Kazue Takeda, Saki Aoto, Atsushi Ito, Kazuo Matsubara, Takeshi Nagamatsu, Tomoyuki Fujii, Isaku Omori, Mitsumasa Shimizu, Hironobu Hyodo, Koji Kugu, Kenji Matsumoto, Atsushi Shimizu, Akira Oka, Masashi Mizuguchi, Kazuhiko Nakabayashi, Kenichiro Hata, Naoto Takahashi
Software Mentions: 3
Published: almost 4 years ago

10.1155/2018/8076397

The Influence of Metabolic Syndrome and Sex on the DNA Methylome in Schizophrenia
Cited by: 12
Author(s): Kyle J. Burghardt, Jaclyn M. Goodrich, Brittany N Lines, Vicki L. Ellingrod
Software Mentions: 3
Published: almost 7 years ago

10.1155/2017/2913648

Differential Analysis of Genetic, Epigenetic, and Cytogenetic Abnormalities in AML
Cited by: 7
Author(s): Mirazul Islam, Zahurin Mohamed, Yassen Assenov
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.65715

Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status
Cited by: 8
Author(s): Ilhame Diboun, Sachin Wani, Stuart H. Ralston, Omar Albagha
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms20194822

Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection
Cited by: 4
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22042136

Extensive Placental Methylation Profiling in Normal Pregnancies
Cited by: 8
Author(s): Ornella Rondinone, Alessio Murgia, Jole Costanza, Silvia Tabano, Margherita Camanni, Luigi Corsaro, Laura Fontana, Patrizia Colapietro, Luciano Calzari, S. Motta, Carlo Santaniello, Tatjana Radaelli, Enrico Ferrazzi, Silvano Bòsari, Davide Gentilini, Silvia Maria Sirchia, Monica Miozzo
Software Mentions: 3
Published: almost 4 years ago

10.18632/oncotarget.14330

c-Jun-N-terminal phosphorylation regulates DNMT1 expression and genome wide methylation in gliomas
Cited by: 20
Author(s): Dieter Henrik Heiland, Roberto Ferrarese, Rainer Claus, Fangping Dai, Anie P. Masilamani, Eva Kling, Astrid Weyerbrock, Teresia Kling, Sven Nelander, Maria Stella Carro
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33959-x

A systems biology network analysis of nutri(epi)genomic changes in endothelial cells exposed to epicatechin metabolites
Cited by: 31
Author(s): Dragan Milenković, Wim Vanden Berghe, Christine Morand, Sylvain Claude, Annette van de Sandt, Simone Gorreßen, Laurent-Emmanuel Monfoulet, Chandra Sekhar Chirumamilla, Ken Declerck, Katarzyna Szarc vel Szic, Maija Lahtela‐Kakkonen, Clarissa Gerhäuser, Marc W. Merx, Malte Kelm
Software Mentions: 2
Published: about 6 years ago

10.3390/jcm10122680

Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer
Cited by: 8
Author(s): Μαρία Παναγοπούλου, Antonia Cheretaki, Makrina Karaglani, Ioanna Balgkouranidou, Eirini Biziota, Kyriakos Amarantidis, Nikolaos Xenidis, Stylianos Kakolyris, Stavroula Baritaki, Εkaterini Chatzaki
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0204371

LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer
Cited by: 5
Author(s): Konstantin Babalyan, Rinat Sultanov, Edward V. Generozov, Е. И. Шарова, Elena S. Kostryukova, Andrey K. Larin, Alexandra Kanygina, Vadim M. Govorun, Georgij Arapidi
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.27080

Methylation alteration of <i>SHANK1</i> as a predictive, diagnostic and prognostic biomarker for chronic lymphocytic leukemia
Cited by: 16
Author(s): Eleonora Loi, Loredana Moi, Antonio Fadda, Giannina Satta, Mariagrazia Zucca, Sonia Sanna, Shadi Amini Nia, Giuseppina Cabras, Marina Padoan, Corrado Magnani, Lucia Miligi, Sara Piro, Davide Gentilini, Maria Grazia Ennas, Melissa C. Southey, Graham G. Giles, Nicole Wong Doo, Pierluigi Cocco, Patrizia Zavattari
Software Mentions: 2
Published: over 5 years ago

10.1007/s00018-019-03358-0

Direct conversion of human fibroblasts into therapeutically active vascular wall-typical mesenchymal stem cells
Cited by: 13
Author(s): Jennifer Steens, Kristian Unger, Lea Klar, Anika Neureiter, Karolin Wieber, Julia Heß, Heinz Jakob, Hannes Klump, Diana Klein
Software Mentions: 2
Published: about 5 years ago

10.1186/s12935-020-01458-7

Napabucasin overcomes cisplatin resistance in ovarian germ cell tumor-derived cell line by inhibiting cancer stemness
Cited by: 15
Author(s): Silvia Schmidtova, Lambert C. J. Dorssers, Katarína Kalavska, Ad J. M. Gillis, J. Wolter Oosterhuis, Hans Stoop, Svetlana Miklikova, Zuzana Kozovská, Monika Buríková, Katarina Gercakova, Erika Durinikova, Michal Chovanec, Michal Mego, Lucia Kučerová, Leendert Looijenga
Software Mentions: 2
Published: over 4 years ago

10.1186/s12931-018-0850-8

SERPINA1 methylation and lung function in tobacco-smoke exposed European children and adults: a meta-analysis of ALEC population-based cohorts
Cited by: 10
Author(s): Anna Beckmeyer-Borowko, Medea Imboden, Faisal I. Rezwan, Matthias Wielscher, André Amaral, Ayoung Jeong, Emmanuel Schaffner, Juha Auvinen, Sylvain Sebért, Ville Karhunen, Robert Bettschart, Alexander Turk, Marco Pons, Daiana Stolz, Florian Kronenberg, Ryan Arathimos, Gemma C Sharp, Caroline L Relton, A. John Henderson, Marjo Riitta Järvelin, Déborah Jarvis, John W. Holloway, Nicole Probst‐Hensch
Software Mentions: 2
Published: over 6 years ago

10.1038/s41597-020-0456-0

DNA methylation of chronic lymphocytic leukemia with differential response to chemotherapy
Cited by: 5
Author(s): Deyan Yordanov Yosifov, Johannes Bloehdorn, Hartmut Döhner, Peter Lichter, Stephan Stilgenbauer, Daniel Mertens
Software Mentions: 2
Published: over 4 years ago

10.1038/s41398-017-0070-x

Genetic estimators of DNA methylation provide insights into the molecular basis of polygenic traits
Cited by: 12
Author(s): Virginie Freytag, Vanja Vukojević, Holger Wagner-Thelen, Annette Milnik, Christian Vogler, Markus Leber, Leonie Weinhold, Anne C. Böhmer, Steffi G. Riedel‐Heller, Wolfgang Maier, Dominique J.‐F. de Quervain, Alfredo Ramı́rez, Andreas Papassotiropoulos
Software Mentions: 2
Published: almost 7 years ago

10.3390/cancers12071799

Comprehensive Constitutional Genetic and Epigenetic Characterization of Lynch-Like Individuals
Cited by: 12
Author(s): Estela Dámaso, Maribel González‐Acosta, Gardenia Vargas-Parra, Matilde Navarro, Judith Balmañà, Teresa Ramón y Cajal, N Tuset, Bryony A. Thompson, Fátima Marín, Anna Fernández, Carolina Gómez, Àngela Velasco, Ares Solanes, Sílvia Iglesias, Gisela Urgel, Consol López, Jesús Del Valle, Olga Campos, Maria Santacana, Xavier Matías‐Guiu, Conxi Lázaro, Laura Valle, Joan Brunet, Marta Pineda, Gabriel Capellá
Software Mentions: 2
Published: over 4 years ago

10.1186/s40478-018-0561-x

Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs
Cited by: 59
Author(s): Markus Schulze, Annika Sommer, Sonja Plötz, Michaela Farrell, Beate Winner, Janina Grosch, Jürgen Winkler, Markus J. Riemenschneider
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.16437

Promoter DNA methylation analysis reveals a combined diagnosis of CpG-based biomarker for prostate cancer
Cited by: 10
Author(s): Yuanyuan Tang, Sanyuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
Software Mentions: 2
Published: almost 8 years ago

10.7150/ijms.39261

Epigenome-wide analysis of common warts reveals aberrant promoter methylation
Cited by: 5
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 2
Published: almost 5 years ago

10.3390/biomedicines8070181

Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars
Cited by: 11
Author(s): Mansour A. Alghamdi, Hilary Wallace, Phillip E. Melton, Eric K. Moses, Andrew Stevenson, Laith N. AL-Eitan, Suzanne Rea, Janine M. Duke, Patricia L Danielsen, Cecilia M. Prêle, Fiona Wood, Mark W. Fear
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.14208

DNA methylation landscape of hepatoblastomas reveals arrest at early stages of liver differentiation and cancer-related alterations
Cited by: 20
Author(s): Mariana Maschietto, T. Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araújo, Talita Ferreira Marques Aguiar, Cecília Maria Lima da Costa, Isabela Werneck da Cunha, Luciana dos Reis Vasques, Mônica Cypriano, Helena Brentani, Sílvia Regina Caminada de Toledo, P. L. Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana Cristina Victorino Krepischi
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.stem.2016.10.019

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation
Cited by: 189
Author(s): Matthias Farlik, Florian Halbritter, Fabian Müller, Fizzah Choudry, Peter Ebert, Johanna Klughammer, Samantha Farrow, Antonella Santoro, Valerio Ciaurro, Anthony Mathur, Rakesh Uppal, Hendrik G. Stunnenberg, Willem H. Ouwehand, Elisa Laurenti, Thomas Lengauer, Mattia Frontini, Christoph Bock
Software Mentions: 2
Published: about 8 years ago

10.3390/cancers13071677

Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning
Cited by: 23
Author(s): Μαρία Παναγοπούλου, Makrina Karaglani, Vangelis G. Manolopoulos, Ioannis Iliopoulos, Ioannis Tsamardinos, Εkaterini Chatzaki
Software Mentions: 2
Published: over 3 years ago

10.1038/srep44547

Sex differences in DNA methylation of the cord blood are related to sex-bias psychiatric diseases
Cited by: 61
Author(s): Mariana Maschietto, Laura Caroline Bastos, Ana Carolina Tahira, Elen Pereira Bastos, Veronica Luiza Vale Euclydes, Alexandra Brentani, Günther Fink, Angelica de Baumont, Aloísio Felipe-Silva, Rossana Pulcineli Vieira Francisco, Gisele Rodrigues Gouveia, Sandra Grisi, Ana Maria de Ulhôa Escobar, Carlos Alberto Moreira-Filho, Guilherme Polanczyk, Eurı́pedes Constantino Miguel, Helena Brentani
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms19103172

sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data
Cited by: 7
Author(s): Chol Hee Jung, Daniel J. Park, Peter Georgeson, Khalid Mahmood, Roger L. Milne, Melissa C. Southey, Bernard J. Pope
Software Mentions: 2
Published: about 6 years ago

10.1186/s13148-021-01055-z

An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies
Cited by: 20
Author(s): Kristine L. Haftorn, Yunsung Lee, William Robert Paul Denault, Christian M. Page, Haakon E. Nustad, Robert Lyle, Håkon K. Gjessing, Anni Malmberg, Maria C Magnus, Øyvind Næss, Darina Czamara, Katri Räikkönen, Jari Lahti, Per Magnus, Siri Eldevik Håberg, Astanand Jugessur, Jon Bohlin
Software Mentions: 2
Published: over 3 years ago

10.18632/aging.202621

An aging and p53 related marker: HOXA5 promoter methylation negatively correlates with mRNA and protein expression in old age
Cited by: 1
Author(s): Laura-Kim Feiner, Sascha Tierling, Sebastian Holländer, Matthias Glanemann, Claudia Rubie
Software Mentions: 2
Published: almost 4 years ago

Projects: bioconductor: RnBeads

Papers Mentioning RnBeads 145