bioconductor: MethylSeekR | Projects

10.1186/s13059-019-1805-1

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: about 5 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 8 years ago

10.1186/s12864-021-07493-6

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Cited by: 19
Author(s): Richard Edwards, Matthew A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina D. Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanović, Robert A. Zammit, E Aiden, Wesley C. Warren, J. William O. Ballard
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pgen.1007102

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
Cited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: almost 7 years ago

10.7554/eLife.36187

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: about 6 years ago

10.1038/srep35903

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: about 8 years ago

10.1186/s13148-021-01144-z

Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes
Cited by: 9
Author(s): Sara Di Persio, Elsa Leitão, Marius Wöste, Tobias Tekath, Jann‐Frederik Cremers, Martin Dugas, Xiaolin Liao, Gerd Meyer zu Hörste, Sabine Kliesch, Sandra Laurentino, Nina Neuhaus, Bernhard Horsthemke
Software Mentions: 8
Published: over 3 years ago

10.1186/1471-2105-15-337

Bison: bisulfite alignment on nodes of a cluster
Cited by: 12
Author(s): Devon P. Ryan, Dan Ehninger
Software Mentions: 6
Published: about 10 years ago

10.3389/fcell.2021.723676

Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition
Cited by: 5
Author(s): Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li, Jing Li, Jinjian Yang
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.40197

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Cited by: 61
Author(s): Chongyuan Luo, Qian Yi Lee, Orly L. Wapinski, Rosa Castanon, Joseph R. Nery, Moritz Mall, Michael S. Kareta, Shay Cullen, Margaret A. Goodell, Howard Y. Chang, Marius Wernig, Joseph R. Ecker
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-015-0856-1

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
Cited by: 85
Author(s): Stephan Busche, Xiaojian Shao, Maxime Caron, Tony Kwan, Fiona Allum, Warren A. Cheung, Bing Ge, Susan Westfall, Simon Maguire, Amy Barrett, Jordana T. Bell, Mark I. McCarthy, Panos Deloukas, Mathieu Blanchette, Guillaume Bourque, Timothy D. Spector, Mark Lathrop, Tomi Pastinen, Elin Grundberg
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-019-6019-0

Identification of methylation states of DNA regions for Illumina methylation BeadChip
Cited by: 12
Author(s): Ximei Luo, Fang Wang, Guohua Wang, Yuming Zhao
Software Mentions: 5
Published: over 4 years ago

10.1186/s13072-016-0079-z

Epigenetic dynamics of monocyte-to-macrophage differentiation
Cited by: 71
Author(s): Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S. Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller, Peter Ebert, Thomas Lengauer, Matthias Barann, Philip Rosenstiel, Gilles Gasparoni, Karl Nordström, Jörn Walter, Benedikt Brors, Gideon Zipprich, Bärbel Felder, Ludger Klein-Hitpaß, Corinna Attenberger, Gerd Schmitz, Bernhard Horsthemke
Software Mentions: 5
Published: over 8 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: over 4 years ago

10.1186/s13073-021-00938-3

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability
Cited by: 9
Author(s): Jennifer Derrien, Catherine Guérin‐Charbonnel, Victor Gaborit, Loı̈c Campion, Martine Devic, Elise Douillard, Nathalie Roi, Hervé Avet‐Loiseau, Olivier Decaux, Thierry Facon, Jan‐Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas, Stέphane Minvielle
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-017-1273-4

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
Cited by: 131
Author(s): Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck, Maike Stam
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0163491

LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines
Cited by: 3
Author(s): Jingting Xu, Hong Hu, Yang Dai
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-016-0911-6

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
Cited by: 15
Author(s): Tarmo Äijö, Yun Huang, Henrik Mannerström, Lukas Chávez, Ageliki Tsagaratou, Anjana Rao, Harri Lähdesmäki
Software Mentions: 4
Published: over 8 years ago

10.1093/gigascience/giaa027

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C
Cited by: 43
Author(s): Matthew A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva Chan, André E. Minoche, Richard J. Edwards, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Martin A. Smith, E Aiden, Timothy P. L. Smith, Robert A. Zammit, J. William O. Ballard
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-018-1510-5

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains
Cited by: 65
Author(s): Abdulrahman Salhab, Karl Nordström, Gilles Gasparoni, Kathrin Kattler, Peter Ebert, Fidel Ramírez, Laura Arrigoni, Fabian Müller, Julia K. Polansky, Cristina Cadenas, Jan G. Hengstler, Thomas Lengauer, Thomas Manke, Jörn Walter
Software Mentions: 3
Published: about 6 years ago

10.1186/s13072-020-00363-7

Characterization of universal features of partially methylated domains across tissues and species
Cited by: 12
Author(s): Benjamin E. Decato, Jianghan Qu, Xiaojing Ji, Elvin Wagenblast, Simon Knott, Gregory J. Hannon, Andrew D. Smith
Software Mentions: 3
Published: about 4 years ago

10.1038/s41422-018-0125-4

Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Cited by: 99
Author(s): Chan Gu, Shanling Liu, Qihong Wu, Lin Zhang, Fan Guo
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1004143

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes
Cited by: 62
Author(s): Dimos Gaidatzis, Lukas Burger, Rabih Murr, Anita Lerch, Sophie Dessus-Babus, Dirk Schübeler, Michael Stadler
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-015-1833-5

DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis
Cited by: 110
Author(s): Naoki Kubo, Y. Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Tetsuya Sato, Hirohito Sone, Yasuyuki Sato, Shin-ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Mikita Suyama, Toru Kono, Kazuyuki Ohbo, Hidetada Sasaki
Software Mentions: 2
Published: over 9 years ago

10.1038/s12276-019-0215-5

Epigenetic analysis in rheumatoid arthritis synoviocytes
Cited by: 23
Author(s): Seokjin Ham, Jonghee Bae, Suman Lee, Bong-Jo Kim, Bok‐Ghee Han, Seung‐Ki Kwok, Tae-Young Roh
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-40262-w

The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue
Cited by: 21
Author(s): Galina Dvoriantchikova, Rajeev J. Seemungal, Dmitry Ivanov
Software Mentions: 2
Published: over 5 years ago

10.3389/fnmol.2019.00182

DNA Methylation Dynamics During the Differentiation of Retinal Progenitor Cells Into Retinal Neurons Reveal a Role for the DNA Demethylation Pathway
Cited by: 11
Author(s): Galina Dvoriantchikova, Rajeev J. Seemungal, Dmitry Ivanov
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-3617-6

Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia
Cited by: 10
Author(s): Di Huang, Ivan Ovcharenko
Software Mentions: 1
Published: over 7 years ago

10.1038/s42003-020-01608-7

A chicken DNA methylation clock for the prediction of broiler health
Cited by: 18
Author(s): Günter Raddatz, Ryan J. Arsenault, Bridget Aylward, Rose Whelan, Florian Böhl, Frank Lyko
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-015-1809-5

Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape
Cited by: 8
Author(s): Takehito Yokoyama, Fumihito Miura, Hiromitsu Araki, Koji Okamura, Takashi Ito
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.04094

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
Cited by: 65
Author(s): Arnaud R Krebs, Sophie Dessus-Babus, Lukas Burger, Dirk Schübeler
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-019-45777-w

Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes
Cited by: 22
Author(s): Stephen Bradford, Shalima S. Nair, Aaron L. Statham, Susan J. van Dijk, Timothy J. Peters, Firoz Anwar, Hugh J. French, Julius Z. H. von Martels, Brodie Sutcliffe, Madhavi P. Maddugoda, Michelle Peranec, Hilal Varinli, Rosanna Arnoldy, Michael Buckley, Jason P. Ross, Elena Zotenko, Jenny Z. Song, Clare Stirzaker, Denis C. Bauer, Wenjia Qu, Michael M. Swarbrick, Helen L. Lutgers, Reginald V. Lord, Katherine Samaras, Peter L. Molloy, Susan J. Clark
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-63572-w

Vitamin C supports conversion of human γδ T cells into FOXP3-expressing regulatory cells by epigenetic regulation
Cited by: 24
Author(s): Léonce Kouakanou, Christian Peters, Qiwei Sun, Stefan Floess, Jaydeep Bhat, Jochen Huehn, Dieter Kabelitz
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: MethylSeekR

Papers Mentioning MethylSeekR 33