pypi: MAnorm | Projects | Ecosyste.ms: Papers

10.1186/s12864-017-4353-7

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
Cited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Software Mentions: 21
Published: almost 7 years ago

10.1186/s13072-021-00390-y

Molecular and computational approaches to map regulatory elements in 3D chromatin structure
Cited by: 7
Author(s): Beoung Hun Lee, Suhn Kyong Rhie
Software Mentions: 21
Published: over 3 years ago

10.1371/journal.pone.0251032

Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation
Cited by: 2
Author(s): Y-h. Taguchi, Turki Turki
Software Mentions: 8
Published: over 3 years ago

10.1093/gigascience/giz147

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
Cited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 5 years ago

10.3389/fgene.2021.664654

Integrative Ranking of Enhancer Networks Facilitates the Discovery of Epigenetic Markers in Cancer
Cited by: 0
Author(s): Qi Wang, Yonghe Wu, Tim Vorberg, Roland Eils, Carl Herrmann
Software Mentions: 8
Published: over 3 years ago

10.1002/pld3.159

The HAC1 histone acetyltransferase promotes leaf senescence and regulates the expression of ERF022
Cited by: 28
Author(s): Will E. Hinckley, Keykhosrow Keymanesh, Jaime Cordova, Judy A. Brusslan
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0083506

Widespread Misinterpretable ChIP-seq Bias in Yeast
Cited by: 128
Author(s): Daechan Park, Yaelim Lee, Gurvani Bhupindersingh, Vishwanath R. Iyer
Software Mentions: 5
Published: almost 11 years ago

10.3389/fgene.2015.00169

Identifying differential transcription factor binding in ChIP-seq
Cited by: 21
Author(s): Dai-Ying Wu, Danielle Bittencourt, Michael R. Stallcup, Kimberly D. Siegmund
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-015-0720-3

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
Cited by: 70
Author(s): Andrey V. Kartashov, Artem Barski
Software Mentions: 5
Published: over 9 years ago

10.1002/1878-0261.12491

A 17 gene panel for non‐small‐cell lung cancer prognosis identified through integrative epigenomic‐transcriptomic analyses of hypoxia‐induced epithelial–mesenchymal transition
Cited by: 21
Author(s): Yue‐Lei Chen, Yihe Zhang, Junwen Wang, Na Chen, Weiying Fang, Jianing Zhong, Yi Liu, Rui Qin, Xinxin Yu, Zhen Sun, Fei Gao
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1007233

RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes
Cited by: 43
Author(s): Shannel R. Adams, So Maezawa, Kris G. Alavattam, Hironori Abe, Akihiko Sakashita, Megan Shroder, Tyler J. Broering, Julie Sroga Rios, Michael A. Thomas, Xinhua Lin, Carolyn M. Price, Artem Barski, Paul R. Andreassen, Satoshi H. Namekawa
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-017-3929-6

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis
Cited by: 42
Author(s): Likai Wang, Fan Zhang, Siddharth Rode, Kevin Chin, Eun Esther Ko, Jonghwan Kim, Vishwanath R. Iyer, Hong Qiao
Software Mentions: 4
Published: over 7 years ago

10.1242/jcs.181248

Nuclear PKC-θ facilitates rapid transcriptional responses in human memory CD4+ T cells via p65 and H2B phosphorylation
Cited by: 11
Author(s): Jasmine Li, Kristine Hardy, Chansavath Phetsouphanh, Wen Juan Tu, Elissa L Sutcliffe, Robert McCuaig, Christopher R Sutton, Anjum Zafar, C. Mee Ling Munier, John Zaunders, Xu Yin, Angelo Theodoratos, Abel Tan, Pek Siew Lim, Tobias Knaute, Antonia Masch, Johannes Zerweck, Vedran Brezar, Peter J. Milburn, Jenny C. Dunn, Marco G. Casarotto, Stephen J. Turner, Nabila Seddiki, Anthony D. Kelleher, Sudha Rao
Software Mentions: 4
Published: almost 9 years ago

10.1186/gb-2014-15-1-r11

dCLIP: a computational approach for comparative CLIP-seq analyses
Cited by: 46
Author(s): Tao Wang, Yang Xie, Guanghua Xiao
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pcbi.1003326

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Cited by: 228
Author(s): Timonthy Bailey, Paweł Krajewski, István Ladunga, Céline Lefèbvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0186435

Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response
Cited by: 14
Author(s): Bernardo Pérez-Zamorano, Sandra Rosas‐Madrigal, Oscar Arturo Migueles Lozano, Manuel Castillo Méndez, Verónica Valverde-Garduño
Software Mentions: 4
Published: about 7 years ago

10.1186/s13059-020-02062-8

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis
Cited by: 26
Author(s): Lejon E. M. Kralemann, S. Liu, Minerva S. Trejo-Arellano, Rafael Muñoz‐Viana, Claudia Köhler, Lars Hennig
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-01973-w

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Cited by: 27
Author(s): Xin Liu, Yong Chen, Yuannyu Zhang, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu
Software Mentions: 4
Published: over 4 years ago

10.18632/aging.103442

TCF7L2 rs290487 C allele aberrantly enhances hepatic gluconeogenesis through allele-specific changes in transcription and chromatin binding
Cited by: 4
Author(s): Xueyou Zhang, Panpan Ye, Haitao Huang, Baohong Wang, Fengqin Dong, Qi Ling
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.38080

Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity
Cited by: 40
Author(s): Yu-Chun Yen, Wen Fu Hsieh, Ya-Yin Tsai, Ya Lin Lu, Ee Shan Liau, Ho Chiang Hsu, Yen‐Chung Chen, Ting Chun Liu, Mien Chang, Joye Li, Shau Ping Lin, Jui-Hung Hung, Jun-An Chen
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-017-3719-1

Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
Cited by: 42
Author(s): Xiaochun Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Chen Yan, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen, Qin Wang, Guangxiang Zhu, Meng Xie, Jiayun Wu, Tao He, Chunyu Huang, Xiang Gao, Xuewei Li
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-S9-S12

dCaP: detecting differential binding events in multiple conditions and proteins
Cited by: 4
Author(s): Kuan Bei Chen, Ross C. Hardison, Yu Zhang
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41419-021-03897-0

G-protein-coupled receptor GPR17 inhibits glioma development by increasing polycomb repressive complex 1-mediated ROS production
Cited by: 10
Author(s): Huiqing Liu, Rui Xing, Zhimin Ou, Jintong Zhao, Guolin Hong, Tong‐Jin Zhao, Han Ying, Ying Chen
Software Mentions: 3
Published: over 3 years ago

10.1038/s41421-018-0045-y

Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters
Cited by: 16
Author(s): Hongduo Sun, Jiawei Wang, Zheng Gong, Jiaying Yao, Yuangao Wang, Jian Xu, Guo Cheng Yuan, Yijing Zhang, Zongshu Shao
Software Mentions: 3
Published: over 6 years ago

10.1186/s13072-020-00350-y

Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver
Cited by: 15
Author(s): Bryan J. Matthews, David J. Waxman
Software Mentions: 3
Published: over 4 years ago

10.1016/j.febslet.2015.11.027

Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource
Cited by: 12
Author(s): Guillaume Devailly, Anna Mantsoki, Tom Michoel, Anagha Joshi
Software Mentions: 3
Published: almost 9 years ago

10.3389/fcvm.2020.594325

The Regulatory Role of Histone Modification on Gene Expression in the Early Stage of Myocardial Infarction
Cited by: 5
Author(s): Jinyu Wang, Bo Lin, Yanping Zhang, Le Ni, Lingjie Hu, Jian Yang, Liang Xu, Dan Shi, Yihan Chen
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13073-017-0481-6

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells
Cited by: 16
Author(s): Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M.S. Oliveira, Márton Keszei, Scott B. Snapper, Piergiorgio Percipalle, Lisa S. Westerberg
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-30781-3

Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke
Cited by: 11
Author(s): Kimberly Glass, Derek Thibault, Feng Guo, Joseph F. Mitchel, Brandon Pham, Weiliang Qiu, Yan Li, Zhiqiang Jiang, Peter J. Castaldi, Edwin K. Silverman, Benjamin A. Raby, Jin‐Ah Park, Guo‐Cheng Yuan, Xiaobo Zhou
Software Mentions: 3
Published: about 6 years ago

10.1186/s13287-020-01711-w

TATA box-binding protein-related factor 3 drives the mesendoderm specification of human embryonic stem cells by globally interacting with the TATA box of key mesendodermal genes
Cited by: 3
Author(s): He Liang, Peng Zhang, Hua-Jun Bai, Jingsong Huang, Huang‐Tian Yang
Software Mentions: 3
Published: over 4 years ago

10.1111/jipb.12871

The transcription factor GATA10 regulates fertility conversion of a two‐line hybrid tms5 mutant rice via the modulation of UbL40 expression
Cited by: 15
Author(s): Jing Jin, Songtao Gui, Qian Li, Ying Wāng, Hongyuan Zhang, Zhixuan Zhu, Hao Chen, Yueyang Sun, Yu Zeng, Xingguo Huang, Yi Ding
Software Mentions: 3
Published: about 5 years ago

10.1038/s41416-021-01499-3

Aspirin enhances the therapeutic efficacy of cisplatin in oesophageal squamous cell carcinoma by inhibition of putative cancer stem cells
Cited by: 7
Author(s): Zhigeng Zou, Wei Zheng, Hongjun Fan, Guohua Deng, Shuaiyao Lu, Wei Jiang, Xiying Yu
Software Mentions: 2
Published: over 3 years ago

10.1126/sciadv.abd7459

Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer
Cited by: 34
Author(s): Nicole Oatman, Nupur Dasgupta, Priyanka Arora, Kwangmin Choi, Mruniya V. Gawali, Neeraj Gupta, Sreeja Parameswaran, Joseph Salomone, Julie A. Reisz, Sean E. Lawler, Frank B. Furnari, Cameron Brennan, Jianqiang Wu, Larry Sallans, Gary A. Gudelsky, Pankaj B. Desai, Brian Gebelein, Matthew T. Weirauch, Angelo D’Alessandro, Kakajan Komurov, Biplab Dasgupta
Software Mentions: 2
Published: almost 4 years ago

10.1038/srep42522

Myotonic dystrophy type 1 patient-derived iPSCs for the investigation of CTG repeat instability
Cited by: 33
Author(s): Junko Ueki, Mikihito Nakamori, Masahiro Nakamura, Misato Nishikawa, Yoshinori Yoshida, Azusa Tanaka, Asuka Morizane, Masayoshi Kamon, Toshiyuki Araki, Masanori Takahashi, Akira Watanabe, Nobuya Inagaki, Hiroyuki Sakurai
Software Mentions: 2
Published: almost 8 years ago

10.7150/thno.48744

Proteasome activator PA200 maintains stability of histone marks during transcription and aging
Cited by: 14
Author(s): Tiancai Jiang, Shuang Ma, Xia Han, Zi-Yu Luo, Qianqian Zhu, Tomoki Chiba, Wei Xie, Kui Lin, Xiao‐Bo Qiu
Software Mentions: 2
Published: almost 4 years ago

10.1155/2016/3172093

Genome-Wide DNA Methylation in Mixed Ancestry Individuals with Diabetes and Prediabetes from South Africa
Cited by: 12
Author(s): Tandi E. Matsha, Carmen Pheiffer, Steve E. Humphries, Junaid Gamieldien, Rajiv T Erasmus, André Pascal Kengne
Software Mentions: 2
Published: almost 9 years ago

10.3390/cancers13040739

Metformin Reduces Histone H3K4me3 at the Promoter Regions of Positive Cell Cycle Regulatory Genes in Lung Cancer Cells
Cited by: 13
Author(s): Dongho Kim, Yujin Kim, Bo Bin Lee, Eun Yoon Cho, Joungho Han, Young Mog Shim, Duk-Hwan Kim
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0125156

Identifying TF-MiRNA Regulatory Relationships Using Multiple Features
Cited by: 3
Author(s): Mingyu Shao, Yanni Sun, Shuigeng Zhou
Software Mentions: 2
Published: over 9 years ago

10.1093/jmcb/mjaa079

Testosterone attenuates pulmonary epithelial inflammation in male rats of COPD model through preventing NRF1-derived NF-κB signaling
Cited by: 16
Author(s): Xueting Wang, Lijie Huang, Shan Jiang, Kang Cheng, Dan Wang, Qianqian Luo, Xiaomei Wu, Li Zhu
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.00633

Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation
Cited by: 212
Author(s): Marc Kerényi, Zongshu Shao, Yuan-Nian Hsu, Guoji Guo, Sidinh Luc, Kassandra O'Brien, Yuko Fujiwara, Cong Peng, Minh Nguyen, Stuart H. Orkin
Software Mentions: 1
Published: over 11 years ago

10.1186/s12868-019-0546-0

The Bdnf and Npas4 genes are targets of HDAC3-mediated transcriptional repression
Cited by: 7
Author(s): Anto Sam Crosslee Louis Sam Titus, Dharmendra Sharma, Min Soo Kim, Santosh R. D’Mello
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pgen.1005771

Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements
Cited by: 106
Author(s): Hua Wang, Chunmei Liu, Jingfei Cheng, Jian Liu, Lei Zhang, Chongsheng He, Wenhui Shen, Hong Jin, Lin Xu, Yijing Zhang
Software Mentions: 1
Published: almost 9 years ago

Projects: pypi: MAnorm

Papers Mentioning MAnorm 42