Ecosyste.ms: Papers

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: almost 7 years ago

10.1186/s13148-019-0795-x

DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis
Cited by: 50
Author(s): Ieva Rauluševičiūtė, Finn Drabløs, Morten Rye
Software Mentions: 10
Published: almost 5 years ago

10.1155/2014/910390

<i>biomvRhsmm:</i>Genomic Segmentation with Hidden Semi-Markov Model
Cited by: 4
Author(s): Yang Du, Eduard Muráni, Siriluck Ponsuksili, Klaus Wimmers
Software Mentions: 10
Published: almost 11 years ago

10.3389/fgene.2014.00324

Statistical methods for detecting differentially methylated loci and regions
Cited by: 90
Author(s): Mark D. Robinson, Abdullah Kahraman, Charity W. Law, Helen Lindsay, Małgorzata Nowicka, Lukas M. Weber, Xiaobei Zhou
Software Mentions: 9
Published: about 10 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/s12885-020-06777-6

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers
Cited by: 11
Author(s): Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson, Giancarlo Marra
Software Mentions: 7
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 Sequencing
Cited 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/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: about 9 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: about 5 years ago

10.1186/s12864-016-3326-6

TEA: the epigenome platform for Arabidopsis methylome study
Cited by: 3
Author(s): Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yubin Wang, Pao‐Yang Chen, Chung‐Yen Lin
Software Mentions: 7
Published: almost 8 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

10.1534/genetics.116.195008

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation
Cited by: 12
Author(s): Owen J. L. Rackham, Sarah R. Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K. Srivastava, Jacques Behmoaras, Πέτρος Δελλαπόρτας, Leonardo Bottolo, Enrico Petretto
Software Mentions: 6
Published: over 7 years ago

10.1016/j.ebiom.2021.103383

Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Cited by: 4
Author(s): Kevin A. Roth, Louis Coussement, Elena V. Knatko, Maureen Higgins, Sandra Steyaert, Charlotte M. Proby, Tim De Meyer, Albena T. Dinkova‐Kostova
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0220934

Profiling DNA methylation patterns of zebrafish liver associated with parental high dietary arachidonic acid
Cited by: 18
Author(s): Anne‐Catrin Adam, Kai Kristoffer Lie, Paul Whatmore, Lars Martin Jakt, Mari Moren, Kaja H. Skjærven
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: almost 7 years ago

10.3390/ijms20215343

Discrimination of DNA Methylation Signal from Background Variation for Clinical Diagnostics
Cited by: 8
Author(s): Robersy Sánchez, Xiaodong Yang, Thomas A. Maher, Sally A. Mackenzie
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2086-5

An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
Cited by: 23
Author(s): W. Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg, John Goutsias
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07845-2

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
Cited by: 4
Author(s): Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro Shimizu, Rie Shimizu‐Inatsugi, Mark D. Robinson
Software Mentions: 4
Published: over 3 years ago

10.1093/bioinformatics/btu749

M3D: a kernel-based test for spatially correlated changes in methylation profiles
Cited by: 27
Author(s): Tom Mayo, Gabriele Schweikert, Guido Sanguinetti
Software Mentions: 4
Published: about 10 years ago

10.1186/s13072-016-0075-3

Profiling genome-wide DNA methylation
Cited by: 245
Author(s): Wai-Shin Yong, Fei‐Man Hsu, Pao‐Yang Chen
Software Mentions: 4
Published: over 8 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: over 5 years ago

10.1515/jib-2020-0031

Differentially methylated CpG sites associated with the high-risk group of prostate cancer
Cited by: 2
Author(s): Anastasiya A. Kobelyatskaya, Elena A. Pudova, Maria Fedorova, K. M. Nyushko, B. Ya. Alekseev, А. Д. Каприн, Д. Ю. Трофимов, Г. Т. Сухих, Anastasiya V. Snezhkina, George S. Krasnov, S. V. Razin, Anna V. Kudryavtseva
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-15420-7

Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans
Cited by: 47
Author(s): Rhianna C. Laker, Christian Garde, Donny M. Camera, William J. Smiles, Juleen R. Zierath, John A. Hawley, Romain Barrès
Software Mentions: 3
Published: about 7 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

10.1111/biom.13307

A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation
Cited by: 3
Author(s): Kaiqiong Zhao, Karim Oualkacha, Lajmi Lakhal‐Chaieb, Aurélie Labbe, Kathleen Klein, Antonio Ciampi, Marie Hudson, Inés Colmegna, Tomi Pastinen, Tieyuan Zhang, Denise Daley, Celia Greenwood
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-15-215

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments
Cited by: 139
Author(s): Egor Dolzhenko, Andrew D. Smith
Software Mentions: 2
Published: over 10 years ago

10.3390/genes10040298

Computational Methods for Detection of Differentially Methylated Regions Using Kernel Distance and Scan Statistics
Cited by: 2
Author(s): Faith Dunbar, Hongyan Xu, Dongseok Ryu, Santu Ghosh, Huidong Shi, Varghese George
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-017-3482-3

Quantitation of DNA methylation in Epstein-Barr virus–associated nasopharyngeal carcinoma by bisulfite amplicon sequencing
Cited by: 23
Author(s): Weilin Zhao, Yuchang Mo, Shumin Wang, Katsumi Midorikawa, Ning Ma, Yusuke Hiraku, Shinji Oikawa, Guangwu Huang, Zhe Zhang, Mariko Murata, Kazuhiko Takeuchi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0214307

DNA methylome of human neonatal umbilical cord: Enrichment of differentially methylated regions compared to umbilical cord blood DNA at transcription factor genes involved in body patterning and effects of maternal folate deficiency or children’s sex
Cited by: 11
Author(s): Kenichi Sakurai, Keiko Shioda, Akifumi Eguchi, Masahiro Watanabe, Hidenobu Miyaso, Chisato Mori, Toshi Shioda
Software Mentions: 1
Published: over 5 years ago

10.1002/hbm.24817

Age of acquisition impacts the brain differently depending on neuroanatomical metric
Cited by: 16
Author(s): Hannah Claussenius-Kalman, Kelly A. Vaughn, Pilar Archila‐Suerte, Arturo E. Hernández
Software Mentions: 1
Published: about 5 years ago

10.1038/s41597-019-0202-7

STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
Cited by: 22
Author(s): David Green, Sonia Tarazona, Isabel Ferreirós-Vidal, Ricardo N. Ramirez, Andreas Schmidt, Theo H. Reijmers, Veronica von Saint Paul, Francesco Marabita, Javier Rodríguez-Ubreva, Antonio García-Gómez, Thomas Carroll, Lee Cooper, Ziwei Liang, Gopuraja Dharmalingam, Frans van der Kloet, Amy C. Harms, Leandro Balzano‐Nogueira, Vincenzo Lagani, Ioannis Tsamardinos, Michael Lappé, Dieter Maier, Johan A. Westerhuis, Thomas Hankemeier, Axel Imhof, Esteban Ballestar, A Mortazavi, Matthias Merkenschlager, Jesper Tegnér, Ana Conesa
Software Mentions: 1
Published: about 5 years ago

10.1038/s41366-018-0219-6

Adipose tissue mitochondrial dysfunction in human obesity is linked to a specific DNA methylation signature in adipose-derived stem cells
Cited by: 47
Author(s): Miriam Ejarque, Victòria Ceperuelo-Mallafré, Carolina Serena, Elsa Maymó-Masip, Xevi Duran, Àngels Díaz-Ramos, Mónica Millán-Scheiding, Yaiza Núñez‐Álvarez, Catalina Núñez‐Roa, P. Da Gama, Pablo M. García-Rovés, Miguel A. Peinado, Jeffrey M. Gimble, António Zorzano, Joan Vendrell, Sonia Fernández‐Veledo
Software Mentions: 1
Published: about 6 years ago

10.1096/fba.2020-00101

Identification of methylation changes associated with positive and negative growth deviance in Gambian infants using a targeted methyl sequencing approach of genomic DNA
Cited by: 3
Author(s): Claire R. Quilter, K. M. Harvey, Julien Bauer, Benjamin M. Skinner, Marı́a Gómez, Manu Shrivastava, Andrew M. Doel, Saikou Drammeh, David Dunger, Sophie E. Moore, Ken K. Ong, Andrew M. Prentice, Robin M. Bernstein, Carole A. Sargent, Nabeel A. Affara
Software Mentions: 1
Published: almost 4 years ago