bioconductor: bsseq | Projects | Ecosyste.ms: Papers

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: almost 5 years ago

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 3 years ago

10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: almost 6 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: over 6 years ago

10.3389/fnmol.2021.664912

Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition
Cited by: 9
Author(s): Sergio Espeso‐Gil, Aliaksei Z. Holik, Sarah Bonnin, Shalu Jhanwar, Sandhya Chandrasekaran, Roger Piqué-Regi, Júlia Albaigès-Ràfols, Michael P. Maher, Jon Permanyer, Manuel Irimia, Marc R. Friedländer, Meritxell Pons-Espinal, Schahram Akbarian, Mara Dierssen, Philipp G. Maass, Charlotte N. Hor, Stephan Ossowski
Software Mentions: 9
Published: about 3 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: almost 6 years ago

10.3390/ijms21114014

Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in Zebrafish
Cited by: 6
Author(s): Sophia Murat El Houdigui, Christelle Adam-Guillermin, Olivier Armant
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0132866

swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing
Cited by: 43
Author(s): Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, Bingyu Chen, Dongsheng Huang
Software Mentions: 7
Published: about 9 years ago

10.1186/s12864-019-6047-9

Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni
Cited by: 9
Author(s): Austin T. Hilliard, Dan Xie, Zhihai Ma, M Snyder, Russell D. Fernald
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12859-015-0742-6

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
Cited by: 60
Author(s): Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J. Morelli, Valerio Bianchi, Bruno Amati, Joseph R. Ecker, Mattia Pelizzola
Software Mentions: 7
Published: almost 9 years ago

10.15252/msb.20156520

Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children
Cited by: 93
Author(s): Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan‐Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M. Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanné, Stefan Wiemann, Christina Geörg, Hendrik G. Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann
Software Mentions: 6
Published: over 8 years ago

10.7554/eLife.37110

Genetic predisposition to uterine leiomyoma is determined by loci for genitourinary development and genome stability
Cited by: 50
Author(s): Niko Välimäki, Heli Kuisma, Annukka Pasanen, Oskari Heikinheimo, Jari Sjöberg, Ralf Bützow, Nanna Sarvilinna, Hanna-Riikka Heinonen, Jaana Tolvanen, Simona Bramante, Tomas Tanskanen, Juha Auvinen, Outi Uimari, Amjad Alkodsi, Rainer Lehtonen, Eevi Kaasinen, Kimmo Palin, Lauri A. Aaltonen
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-019-5578-4

Genome-wide methylation is modified by caloric restriction in Daphnia magna
Cited by: 20
Author(s): Jack Hearn, Marianne Pearson, Mark Blaxter, Philip J. Wilson, Tom J. Little
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-017-1909-0

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
Cited by: 52
Author(s): John Gaspar, Ronald P. Hart
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-020-3470-5

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
Cited by: 8
Author(s): Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder
Software Mentions: 5
Published: about 4 years ago

10.1186/s13072-018-0186-0

Transient reduction of DNA methylation at the onset of meiosis in male mice
Cited by: 36
Author(s): Valeriya Gaysinskaya, Brendan Miller, Chiara De Luca, Godfried W. van der Heijden, Kasper D. Hansen, Alex Bortvin
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-019-2845-y

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions
Cited by: 29
Author(s): Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz, Ryan Lister
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-019-1827-8

methylCC: technology-independent estimation of cell type composition using differentially methylated regions
Cited by: 12
Author(s): Stephanie Hicks, Rafael A. Irizarry
Software Mentions: 4
Published: over 4 years ago

10.1007/s00204-016-1879-4

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women
Cited by: 24
Author(s): Karin Engström, Tomasz K. Wojdacz, Francesco Marabita, Philip Ewels, Max Käller, Francesco Vezzi, Nicola Prezza, Joel Gruselius, Marie Vahter, Karin Broberg
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1008894

AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization
Cited by: 5
Author(s): Nicolas Christophorou, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, Aurélie Chambon, Victor Solier, Daniel Vezon, Mathilde Grelon, Xiaoqi Feng, Nicolas Bouché, Christine Mézard
Software Mentions: 3
Published: about 4 years ago

10.1186/s13073-018-0534-5

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Cited by: 108
Author(s): Wei-Hung Pan, Felix Sommer, Maren Falk-Paulsen, Thomas Ulas, Lena Best, Antonella Fazio, Priyadarshini Kachroo, Anne Luzius, Marlene Jentzsch, Ateequr Rehman, Fabian Müller, Thomas Lengauer, Joern Walter, Sven Künzel, John F. Baines, Stefan Schreiber, André Franke, Joachim L. Schultze, Fredrik Bäckhed, Philip Rosenstiel
Software Mentions: 3
Published: over 6 years ago

10.1186/s13073-020-00785-8

Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes
Cited by: 44
Author(s): Charles E. Mordaunt, Julia M. Jianu, Benjamin I. Laufer, Yihui Zhu, Keith W. Dunaway, Kelly M. Bakulski, Jason I. Feinberg, Heather E. Volk, Kristen Lyall, Lisa Croen, Craig J. Newschaffer, Sally J Ozonoff, Irva Hertz‐Picciotto, M. Daniele Fallin, Rebecca J. Schmidt, Janine M. LaSalle
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-37618-z

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis
Cited by: 9
Author(s): Alan M. O’Doherty, Kévin Rue-Albrecht, David A. Magee, Simone Ahting, Rachelle E Irwin, Thomas Jonathan Hall, John A. Browne, Nicolas C. Nalpas, Colum P. Walsh, Stephen V. Gordon, Marcin W. Wojewodzic, David E. MacHugh
Software Mentions: 3
Published: over 5 years ago

10.1186/s12915-015-0128-2

The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers
Cited by: 14
Author(s): Sarah K. Harten, Harald Oey, Lauren M. Bourke, Vandhana Bharti, Luke Isbel, Lucia Daxinger, Pierre Faou, Neil O. Robertson, Jacqueline M. Matthews, Emma Whitelaw
Software Mentions: 3
Published: over 9 years ago

10.1186/s13148-021-01110-9

Altered DNA methylation pattern reveals epigenetic regulation of Hox genes in thoracic aortic dissection and serves as a biomarker in disease diagnosis
Cited by: 5
Author(s): Peiru Liu, Jing Zhang, Duo Du, Dandan Zhang, Zelin Jin, Qiu Wan-hua, Xinchen Zhou, Sujun Dong, Mengyu Zhou, Heyu Zhao, Wei Zhang, Jiakang Ma, Song Sun, Weiguo Fu, Yun Liu, Lixin Wang
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0168623

Site-Dependent Differences in DNA Methylation and Their Impact on Plant Establishment and Phosphorus Nutrition in Populus trichocarpa
Cited by: 23
Author(s): Brigitte Schönberger, Xianfeng Chen, Svenja Mager, Uwe Ludewig
Software Mentions: 2
Published: over 7 years ago

10.1172/jci.insight.147610

Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury
Cited by: 75
Author(s): Temesgen E. Andargie, Takayuki Tsuji, Fayaz Seifuddin, Moon Kyoo Jang, Peter S.T. Yuen, Hyesik Kong, Ilker Tunc, Komudi Singh, Ananth V. Charya, Kenneth J. Wilkins, Steven D. Nathan, Andrea L. Cox, Mehdi Pirooznia, Robert A. Star, Sean Agbor‐Enoh
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-019-2750-4

A (fire)cloud-based DNA methylation data preprocessing and quality control platform
Cited by: 5
Author(s): Divy Kangeyan, Andrew Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz, Martin J. Aryee
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.34423

The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium
Cited by: 39
Author(s): Katharina Schlereth, Dieter Weichenhan, Tobias Bauer, Tina Heumann, Evangelia Giannakouri, Daniel B. Lipka, Samira Jaeger, Matthias Schlesner, Patrick Aloy, Roland Eils, Christoph Plass, Hellmut G. Augustin
Software Mentions: 2
Published: about 6 years ago

10.1038/srep28616

Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation
Cited by: 52
Author(s): Saskia Trump, Matthias Bieg, Zuguang Gu, Loreen Thürmann, Tobias Bauer, Mario Bauer, Naveed Ishaque, Stefan Röder, Lei Gu, Gunda Herberth, Christian Lawerenz, Michael Borte, Matthias Schlesner, Christoph Plass, Nicolle Diessl, Markus Eszlinger, Oliver Mücke, Horst Dietrich Elvers, Dirk K. Wissenbach, Martin von Bergen, Carl Herrmann, Dieter Weichenhan, Rosalind J. Wright, Irina Lehmann, Roland Eils
Software Mentions: 1
Published: about 8 years ago

10.1186/s13148-020-00880-y

Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels
Cited by: 15
Author(s): Dilys Lam, Phuc-Loi Luu, Jenny Z. Song, Wenjia Qu, Gail P. Risbridger, Mitchell G. Lawrence, Jennifer Lu, Matt Trau, Darren Korbie, Susan J. Clark, Ruth Pidsley, Clare Stirzaker
Software Mentions: 1
Published: about 4 years ago

10.1186/s13148-020-0819-6

Methylation silencing of TGF-β receptor type II is involved in malignant transformation of esophageal squamous cell carcinoma
Cited by: 15
Author(s): Yarui Ma, Siyuan He, Aiai Gao, Ying Zhang, Qing Zhu, Pei Wang, Baofeng Yang, Huihui Yin, Yifei Li, Jinge Song, Pinli Yue, Mo Li, Dandan Zhang, Yun Liu, Xiaobing Wang, Mingzhou Guo, Yuchen Jiao
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1003946

Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana
Cited by: 63
Author(s): Maxim V. C. Greenberg, Angélique Deleris, Christopher J. Hale, Ao Liu, Suhua Feng, Steven E. Jacobsen
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-5002-5

Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling
Cited by: 27
Author(s): Chao Li, Yan Li, Guangxian Zhou, Ye Gao, Sen Ma, Yulin Chen, Jiuzhou Song, Xiaolong Wang
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41388-021-01657-0

DNA methylome profiling of circulating tumor cells in lung cancer at single base-pair resolution
Cited by: 25
Author(s): Lei Zhao, Xiaohong Wu, Junnian Zheng, Dong Dong
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.3560

Herbicide injury induces DNA methylome alterations in <i>Arabidopsis</i>
Cited by: 24
Author(s): Gunjune Kim, Christopher R. Clarke, Hailey Larose, Hong T. Tran, David C. Haak, Liqing Zhang, Shawn D. Askew, Jacob N. Barney, James H. Westwood
Software Mentions: 1
Published: about 7 years ago

10.1038/sdata.2017.148

Whole genome DNA methylation sequencing of the chicken retina, cornea and brain
Cited by: 17
Author(s): Isac Lee, Bejan Rasoul, Ashton S Holub, Alannah Lejeune, Ray A. Enke, Winston Timp
Software Mentions: 1
Published: almost 7 years ago

Projects: bioconductor: bsseq

Papers Mentioning bsseq 38