bioconductor: Ringo | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.1186/1471-2105-11-194

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Cited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: over 14 years ago

10.1186/1471-2105-8-221

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: over 17 years ago

10.1371/journal.pone.0096376

Large Sex Differences in Chicken Behavior and Brain Gene Expression Coincide with Few Differences in Promoter DNA-Methylation
Cited by: 38
Author(s): Daniel Nätt, Beatrix Agnvall, Per Jensen
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0145585

Epigenetic Alterations in Density Selected Human Spermatozoa for Assisted Reproduction
Cited by: 20
Author(s): Bolan Yu, Hua Zhou, Min Liu, Ting Zheng, Lu Jiang, Mei Zhao, Xiaohong Xu, Zhaofeng Huang
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2164-11-441

Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties
Cited by: 80
Author(s): Marika Vitikainen, Mikko Arvas, Tiina Pakula, Merja Oja, Merja Penttilä, Markku Saloheimo
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-13-42

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
Cited by: 17
Author(s): Michiel E. Adriaens, Magali Jaillard, Lars Eijssen, Claus Mayer, Chris T. Evelo
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0154836

Alteration of Gene Expression, DNA Methylation, and Histone Methylation in Free Radical Scavenging Networks in Adult Mouse Hippocampus following Fetal Alcohol Exposure
Cited by: 44
Author(s): Eric Chater‐Diehl, Benjamin I. Laufer, Christina A Castellani, Bonnie Alberry, Shiva M. Singh
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0045708

Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions
Cited by: 32
Author(s): Diego Villar, Amaya Ortiz-Barahona, Laura Gómez-Maldonado, Nuria Pescador, Fátima Sánchez-Cabo, Hubert Hackl, Blanca Rodriguez, Zlatko Trajanoski, Ana Dopazo, Tim Hui-Ming Huang, Pearlly S. Yan, Luis del Peso
Software Mentions: 4
Published: about 12 years ago

10.1038/celldisc.2015.45

Mapping gene regulatory circuitry of Pax6 during neurogenesis
Cited by: 56
Author(s): Sudhir Thakurela, Neha Tiwari, Sandra Schick, Angela Garding, Robert Ivánek, Benedikt Berninger, Vijay Tiwari
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13148-019-0791-1

DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways
Cited by: 21
Author(s): Faiza Noreen, Taya Küng, Luigi Tornillo, Helen L. Parker, Miguel G. Silva, Stefan Weis, Giancarlo Marra, Roland Rad, Kaspar Truninger, Primo Schär
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1007909

Dual role of DMXL2 in olfactory information transmission and the first wave of spermatogenesis
Cited by: 10
Author(s): Clara Gobé, Maëva Elzaïat, Nicolas Meunier, Marjolaine André, Eli Sellem, Patrice Congar, Luc Jouneau, Aurélie Allais‐Bonnet, Ikrame Naciri, Bruno Passet, Eric Pailhoux, Maëlle Pannetier
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1004619

Interplay of dFOXO and Two ETS-Family Transcription Factors Determines Lifespan in Drosophila melanogaster
Cited by: 56
Author(s): Nazif Alic, MMaria Giannakou, Irene Papatheodorou, Matthew P. Hoddinott, T. Daniel Andrews, Ekin Bolukbasi, Linda Partridge
Software Mentions: 3
Published: about 10 years ago

10.1186/1868-7083-6-1

The effects of olanzapine on genome-wide DNA methylation in the hippocampus and cerebellum
Cited by: 55
Author(s): Melkaye G Melka, Benjamin I. Laufer, Patrick P. McDonald, Christina A Castellani, Nagalingam Rajakumar, Richard O’Reilly, Shiva M. Singh
Software Mentions: 3
Published: almost 11 years ago

10.1242/dmm.010975

Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice
Cited by: 105
Author(s): Benjamin I. Laufer, Katarzyna Mantha, Morgan L. Kleiber, Eric J. Diehl, Sean M. F. Addison, Shiva M. Singh
Software Mentions: 3
Published: almost 12 years ago

10.3389/fcimb.2020.00250

Combined Analysis of DNA Methylome and Transcriptome Reveal Novel Candidate Genes Related to Porcine Escherichia coli F4ab/ac-Induced Diarrhea
Cited by: 7
Author(s): Wenwen Wang, Chuanli Zhou, Hui Tang, Ying Yu, Qin Zhang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12263-020-00681-1

Maternal folic acid impacts DNA methylation profile in male rat offspring implicated in neurodevelopment and learning/memory abilities
Cited by: 15
Author(s): Xinyan Wang, Zhenshu Li, Yun Zhu, Jing Yan, Huan Liu, Guowei Huang, Wen Li
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40537-021-00443-9

An analysis of the graph processing landscape
Cited by: 8
Author(s): Miguel E. Coimbra, Alexandre P. Francisco, Luís Veiga
Software Mentions: 3
Published: over 3 years ago

10.1038/srep08748

Genome-wide Mapping Reveals Conservation of Promoter DNA Methylation Following Chicken Domestication
Cited by: 16
Author(s): Qinghe Li, Yuanyuan Wang, Xiaoxiang Hu, Yaofeng Zhao, Ning Li
Software Mentions: 3
Published: over 9 years ago

10.1038/srep19162

DNA methylation is critical for tooth agenesis: implications for sporadic non-syndromic anodontia and hypodontia
Cited by: 37
Author(s): Jing Wang, Ke Sun, Yin Shen, Yuanzhi Xu, Jing Xie, Ru Huang, Yiming Zhang, Chenyuan Xu, Xu Zhang, Raorao Wang, Yunfeng Lin
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12920-015-0093-1

DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks
Cited by: 43
Author(s): Christina A Castellani, Benjamin I. Laufer, Melkaye G Melka, Eric J. Diehl, Richard O’Reilly, Shiva M. Singh
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-4992-3

Dynamic changes in ORC localization and replication fork progression during tissue differentiation
Cited by: 9
Author(s): Brian L Hua, George W. Bell, Helena Kashevsky, Jessica R. Von Stetina, Terry L. Orr‐Weaver
Software Mentions: 3
Published: over 6 years ago

10.1155/2018/8929057

The Effect of Citalopram on Genome-Wide DNA Methylation of Human Cells
Cited by: 10
Author(s): Riya R. Kanherkar, Bruk Getachew, Joseph Ben-Sheetrit, Sudhir Varma, Thomas Heinbockel, Yousef Tizabi, Antonei B. Csóka
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0258193

Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes
Cited by: 0
Author(s): Gabriel A. Preising, Joshua J. Faber-Hammond, Suzy C. P. Renn
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0203155

Integrated analysis of DNA methylation profiling and gene expression profiling identifies novel markers in lung cancer in Xuanwei, China
Cited by: 16
Author(s): Juan Wang, Yong Duan, Qinghe Meng, Rong Gong, Chong Guo, Ying Zhao, Yanliang Zhang
Software Mentions: 3
Published: about 6 years ago

10.1186/s40303-015-0013-5

Insights into the origin of DNA methylation differences between monozygotic twins discordant for schizophrenia
Cited by: 9
Author(s): Melkaye G Melka, Christina A Castellani, Richard O’Reilly, Shiva M. Singh
Software Mentions: 3
Published: over 9 years ago

10.1038/srep29390

Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis
Cited by: 40
Author(s): Mengyuan Song, Yanghua He, Huangkai Zhou, Yi Zhang, Xizhi Li, Ying Yu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0113784

Hypermethylation of Cox5a Promoter Is Associated with Mitochondrial Dysfunction in Skeletal Muscle of High Fat Diet-Induced Insulin Resistant Rats
Cited by: 14
Author(s): Yingying Gong, Yuan-yuan Liu, Jin Li, Lei Su, Shuang Yu, Xiao‐Feng Zhu, Xiaopei Cao, Hang Xiao
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-13-563

Hepatitis B viral core protein disrupts human host gene expression by binding to promoter regions
Cited by: 46
Author(s): Yanhai Guo, Wei Kang, Xiaoying Li, Yong-Nian Li, Xiang An, Yonglan Liu, Jingbo Zhao, Ju Zhang, Yan Zhang
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-14-76

BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data
Cited by: 3
Author(s): Jerry Guintivano, Michal Arad, Kellie L.K. Tamashiro, Todd D. Gould, Zachary Kaminsky
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1004658

Telomeric ORFs (TLOs) in Candida spp. Encode Mediator Subunits That Regulate Distinct Virulence Traits
Cited by: 32
Author(s): Haran John, Boyle Hannah, Karsten Hokamp, Tim Yeomans, Zhongle Liu, Michael Church, Alastair B. Fleming, Matthew Anderson, Judith Berman, Lawrence C. Myers, Derek J. Sullivan, Gary P. Moran
Software Mentions: 1
Published: about 10 years ago

10.3390/ijms160511229

Transcriptional (ChIP-Chip) Analysis of ELF1, ETS2, RUNX1 and STAT5 in Human Abdominal Aortic Aneurysm
Cited by: 16
Author(s): Matthew C Pahl, Robert Erdman, Helena Kuivaniemi, John H. Lillvis, James R. Elmore, Gerard Tromp
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0030515

The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression
Cited by: 162
Author(s): Andriy Bilichak, Yaroslav Ilnystkyy, Jens Hollunder, Igor Kovalchuk
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1002040

Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation
Cited by: 302
Author(s): Marcel Lafos, Phillip Kroll, Mareike L. Hohenstatt, Frazer Thorpe, Oliver Clarenz, Daniel Schubert
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2105-8-443

Erratum to: Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 7
Author(s): Joern Toedling, Oleg Skylar, Tammo Krueger, Jenny J. Fischer, Silke Sperling, Wolfgang Huber
Software Mentions: 1
Published: about 17 years ago

Ecosyste.ms: Papers

Projects: bioconductor: Ringo

Papers Mentioning Ringo 36