Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: bsseq
https://packages.ecosyste.ms/registries/bioconductor.org/packages/bsseq
Analyze, manage and store bisulfite sequencing data
1 version
Latest release: about 1 year ago
11 dependent packages
182,319 downloads total
Papers Mentioning bsseq 38
10.3389/fonc.2020.00423
Computational Oncology in the Multi-Omics Era: State of the ArtCited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago
10.1186/s13059-019-1805-1
Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylationCited 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: about 5 years ago
10.1186/s13059-021-02335-w
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traitsCited 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 GuixCited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago
10.1038/s41598-018-19655-w
msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing dataCited 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: almost 7 years ago
10.3389/fnmol.2021.664912
Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for CognitionCited 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: over 3 years ago
10.12688/f1000research.13196.2
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeRCited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: about 6 years ago
10.3390/ijms21114014
Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in ZebrafishCited by: 6
Author(s): Sophia Murat El Houdigui, Christelle Adam-Guillermin, Olivier Armant
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pone.0132866
swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite SequencingCited by: 43
Author(s): Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, Bingyu Chen, Dongsheng Huang
Software Mentions: 7
Published: over 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 burtoniCited by: 9
Author(s): Austin T. Hilliard, Dan Xie, Zhihai Ma, M Snyder, Russell D. Fernald
Software Mentions: 7
Published: about 5 years ago
10.1186/s12859-015-0742-6
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics dataCited 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: about 9 years ago
10.15252/msb.20156520
Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their childrenCited 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 stabilityCited 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: about 6 years ago
10.1186/s12864-019-5578-4
Genome-wide methylation is modified by caloric restriction in Daphnia magnaCited 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 dataCited by: 52
Author(s): John Gaspar, Ronald P. Hart
Software Mentions: 5
Published: almost 7 years ago
10.1186/s12859-020-3470-5
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing dataCited by: 8
Author(s): Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder
Software Mentions: 5
Published: over 4 years ago
10.1186/s13072-018-0186-0
Transient reduction of DNA methylation at the onset of meiosis in male miceCited 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 regionsCited by: 29
Author(s): Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz, Ryan Lister
Software Mentions: 4
Published: over 5 years ago
10.1186/s13059-019-1827-8
methylCC: technology-independent estimation of cell type composition using differentially methylated regionsCited by: 12
Author(s): Stephanie Hicks, Rafael A. Irizarry
Software Mentions: 4
Published: almost 5 years ago
10.1007/s00204-016-1879-4
Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed womenCited 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: about 8 years ago
10.1371/journal.pgen.1008894
AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localizationCited 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: over 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 developmentCited 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 genesCited 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: about 4 years ago
10.1038/s41598-018-37618-z
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovisCited 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: almost 6 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 enhancersCited 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 diagnosisCited 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: over 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 trichocarpaCited by: 23
Author(s): Brigitte Schönberger, Xianfeng Chen, Svenja Mager, Uwe Ludewig
Software Mentions: 2
Published: almost 8 years ago
10.1172/jci.insight.147610
Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injuryCited 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 platformCited 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 endotheliumCited 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: over 6 years ago
10.1038/srep28616
Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulationCited 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: over 8 years ago
10.1186/s13148-020-00880-y
Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panelsCited 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: over 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 carcinomaCited 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: almost 5 years ago
10.1371/journal.pgen.1003946
Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thalianaCited by: 63
Author(s): Maxim V. C. Greenberg, Angélique Deleris, Christopher J. Hale, Ao Liu, Suhua Feng, Steven E. Jacobsen
Software Mentions: 1
Published: about 11 years ago
10.1186/s12864-018-5002-5
Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cyclingCited by: 27
Author(s): Chao Li, Yan Li, Guangxian Zhou, Ye Gao, Sen Ma, Yulin Chen, Jiuzhou Song, Xiaolong Wang
Software Mentions: 1
Published: about 6 years ago
10.1038/s41388-021-01657-0
DNA methylome profiling of circulating tumor cells in lung cancer at single base-pair resolutionCited by: 25
Author(s): Lei Zhao, Xiaohong Wu, Junnian Zheng, Dong Dong
Software Mentions: 1
Published: almost 4 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: over 7 years ago
10.1038/sdata.2017.148
Whole genome DNA methylation sequencing of the chicken retina, cornea and brainCited by: 17
Author(s): Isac Lee, Bejan Rasoul, Ashton S Holub, Alannah Lejeune, Ray A. Enke, Winston Timp
Software Mentions: 1
Published: about 7 years ago