bioconductor: ChIPseeker | Projects

10.1186/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: over 4 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

Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1high memory phenotype CD4 T cells
Cited by: 6
Author(s): Alistair L. J. Symonds, Wei Zheng, Tizong Miao, Ang Li, Tieshang Wang, Ruth Kiome, Xiaofeng Hou, Suling Li, Ping Wang
Software Mentions: 15
Published: about 4 years ago

10.3390/cells8111321

Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets
Cited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: almost 5 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: about 5 years ago

10.1038/s41598-019-41601-7

Characteristics and homogeneity of N6-methylation in human genomes
Cited by: 13
Author(s): Clare Pacini, Charles R. Bradshaw, Nigel Garrett, Magdalena J. Koziol
Software Mentions: 11
Published: over 5 years ago

10.1080/21623945.2019.1697563

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: over 5 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: almost 4 years ago

10.3390/jof6030182

ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans
Cited by: 14
Author(s): Sabrina Jenull, Michael Tscherner, Theresia Mair, Karl Kuchler
Software Mentions: 9
Published: almost 4 years ago

10.7554/eLife.42675

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila
Cited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: about 5 years ago

10.1016/j.celrep.2020.108546

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions
Cited by: 33
Author(s): Panagiotis Kotsantis, Sandra Segura-Bayona, Pol Margalef, Paulina Marzec, Phil Ruis, Graeme Hewitt, Roberto Bellelli, Harshil Patel, Robert Goldstone, Anna R. Poetsch, Simon J. Boulton
Software Mentions: 9
Published: over 3 years ago

10.15252/embj.2020104983

Interactions between lineage‐associated transcription factors govern haematopoietic progenitor states
Cited by: 17
Author(s): Iwo Kuciński, Nicola K. Wilson, Rebecca Hannah, Sarah Kinston, Pierre Cauchy, Aurelie Lenaerts, Rudolf Grosschedl, Berthold Göttgens
Software Mentions: 9
Published: almost 4 years ago

10.3389/fonc.2021.575425

Systematic Chromatin Accessibility Analysis Based on Different Immunological Subtypes of Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Shiqiang Zhang, Wenzhong Zheng, Donggen Jiang, Haiyun Xiong, Guolong Liao, Xiangwei Yang, He Ma, Jun Li, Miaojuan Qiu, Binbin Li, Chunhui Sun, Jing Zhao, Liling Wang, Jun Pang
Software Mentions: 9
Published: over 3 years ago

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-021-98889-7

Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
Cited by: 7
Author(s): Enrique Blanco, Mar González-Ramírez, Luciano Di Croce
Software Mentions: 8
Published: almost 3 years ago

10.1186/s13148-020-00996-1

Integrated analysis reveals the alterations that LMNA interacts with euchromatin in LMNA mutation-associated dilated cardiomyopathy
Cited by: 9
Author(s): Xiaolin Zhang, Xiuli Shao, Ruijia Zhang, Rongli Zhu, Rui Feng
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-019-3090-0

CSA: a web service for the complete process of ChIP-Seq analysis
Cited by: 2
Author(s): Min Li, Li Tang, Fang‐Xiang Wu, Yi Pan, Jianxin Wang
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pcbi.1007814

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility
Cited by: 4
Author(s): Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado‐Sainz, Felipe Cortés‐Ledesma
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.56980

m6A RNA methylation impacts fate choices during skin morphogenesis
Cited by: 18
Author(s): Linghe Xi, Thomas Carroll, Irina Matos, Ji‐Dung Luo, Lisa Polak, H. Amalia Pasolli, Samie R. Jaffrey, Elaine Fuchs
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-021-07760-6

UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Cited by: 31
Author(s): Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime A Castro-Mondragón, Anthony Mathelier
Software Mentions: 8
Published: about 3 years ago

10.26508/lsa.202101113

Statistical guidelines for quality control of next-generation sequencing techniques
Cited by: 1
Author(s): Maximilian Sprang, Matteo Krüger, Miguel A. Andrade‐Navarro, Jean-Fred Fontaine
Software Mentions: 8
Published: almost 3 years ago

10.1186/s13059-021-02450-8

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Cited by: 3
Author(s): Chenyang Dong, Shane P. Simonett, Sun‐Young Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Huan Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller, Sündüz Keleş
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12859-016-1274-4

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Cited by: 95
Author(s): Qian Qin, Shenglin Mei, Qiu Liang Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Xu Han, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long, X. Shirley Liu
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pntd.0008262

Global changes in nitration levels and DNA binding profile of Trypanosoma cruzi histones induced by incubation with host extracellular matrix
Cited by: 5
Author(s): Rubens Daniel Miserani Magalhães, Eliciane Cevolani Mattos, Andrei Rozanski, Pedro A. F. Galante, Giuseppe Palmisano, Ângela K. Cruz, Walter Colli, Anamaria A. Camargo, Maria Júlia M. Alves
Software Mentions: 7
Published: about 4 years ago

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: about 3 years ago

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: almost 3 years ago

10.1093/gigascience/giaa068

Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution
Cited by: 8
Author(s): Michael Kluge, Marie-Sophie Friedl, Amrei L Menzel, Caroline C. Friedel
Software Mentions: 7
Published: about 4 years ago

10.3390/genes10030231

H3K27me3 Depletion during Differentiation Promotes Myogenic Transcription in Porcine Satellite Cells
Cited by: 12
Author(s): Sheng Wang, Yan Sun, Ruimin Ren, Junhui Xie, Xiaohuan Tian, Shuhong Zhao, Xinyun Li, Jianhua Cao
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.58123

TBX3 acts as tissue-specific component of the Wnt/β-catenin transcriptional complex
Cited by: 28
Author(s): Dario Zimmerli, Costanza Borrelli, Amaia Jauregi-Miguel, Simon Söderholm, Salome Brütsch, Nikolaos Doumpas, Jan Reichmuth, Fabienne Murphy-Seiler, Michel Aguet, Konrad Basler, Andreas E. Moor, Claudio Cantù
Software Mentions: 6
Published: almost 4 years ago

10.1093/hmg/ddv449

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation
Cited by: 42
Author(s): Isabel Mendizabal, Soojin V. Yi
Software Mentions: 6
Published: over 8 years ago

10.1128/mSystems.01006-20

Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Cited by: 6
Author(s): A. K. M. Firoj Mahmud, K. Peter R. Nilsson, Anna Fahlgren, Roberto Navais, Rajdeep Choudhury, Kemal Avican, Maria Fällman
Software Mentions: 6
Published: over 3 years ago

10.1186/s12967-018-1751-9

Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
Cited by: 37
Author(s): Raúl Fernández Pérez, Pablo Santamarina, Juan Ramón Tejedor, Rocío G. Urdinguio, Julio Álvarez, P. Redon, Agustín F. Fernández, Mario F. Fraga, Empar Lurbe
Software Mentions: 6
Published: over 5 years ago

10.1186/s13287-020-01983-2

IRF-1 expressed in the inner cell mass of the porcine early blastocyst enhances the pluripotency of induced pluripotent stem cells
Cited by: 8
Author(s): Bingbo Shi, Dengfeng Gao, Zhong Liu, Minglei Zhi, Xiaogang Weng, Junjun Xu, Junhong Li, Xuguang Du, Yanli Xin, Jie Gao, Qianqian Zhu, Suying Cao, Liu Z
Software Mentions: 6
Published: over 3 years ago

10.26508/lsa.202000976

Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Cited by: 5
Author(s): Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
Software Mentions: 6
Published: about 3 years ago

10.1002/1878-0261.12954

The evolutionarily conserved long non‐coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms
Cited by: 21
Author(s): Rebecca Mather, Abhijit Parolia, Sandra E. Carson, Erik Venalainen, David Roig-Carles, Mustapha Jaber, Shih‐Chun Chu, Ilaria Alborelli, Rebecca Wu, Dong Lin, Noushin Nabavi, Elena Jachetti, Mario P. Colombo, Hui Xue, Perla Pucci, Xinpei Ci, Cheryl A. Hawkes, Yinglei Li, Hardev Pandha, Igor Ulitsky, Crystal N. Marconett, Luca Quagliata, Wei Jiang, Ignacio A. Romero, Yuzhuo Wang, Francesco Crea
Software Mentions: 6
Published: over 3 years ago

10.1002/1878-0261.12968

Phosphorylation of the androgen receptor at Ser81 is co‐sustained by CDK1 and CDK9 and leads to AR‐mediated transactivation in prostate cancer
Cited by: 14
Author(s): Xintao Gao, Jintai Liang, LiYang Wang, Zhaoyang Zhang, Peipei Yuan, Jiaxin Wang, Youhe Gao, Fen Ma, Carla Calagua, Huihui Ye, Olga Voznesensky, Shaogang Wang, Tao Wang, Jihong Liu, Shaoyong Chen, Xiaohui Liu
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-021-94805-1

AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators
Cited by: 4
Author(s): Arno Meiler, Fabio Marchianò, Margaux Haering, Manuela Weitkunat, Frank Schnorrer, Bianca Habermann
Software Mentions: 6
Published: almost 3 years ago

10.1038/s41598-020-80111-9

FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs
Cited by: 13
Author(s): Billie G. C. Griffith, Rosanna Upstill-Goddard, Holly Brunton, Graeme R. Grimes, Andrew V. Biankin, Bryan Serrels, Adam Byron, Margaret C. Frame
Software Mentions: 6
Published: over 3 years ago

10.3390/cancers13133330

Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer
Cited by: 1
Author(s): Rui-chao Zeng, Ahmed Mohamed, Kum Kum Khanna, Michelle M. Hill
Software Mentions: 6
Published: about 3 years ago

10.1126/sciadv.abe8978

Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming
Cited by: 56
Author(s): Álvaro Herrero-Navarro, Lorenzo Puche-Aroca, Verónica Moreno‐Juan, Alejandro Sempere-Ferràndez, Ana Espinosa, Rafael Susín, Laia Torres-Masjoan, Eduardo Leyva-Díaz, Marisa Karow, María Figueres-Oñate, Laura López‐Mascaraque, José P. López‐Atalaya, Benedikt Berninger, Guillermina López‐Bendito
Software Mentions: 6
Published: over 3 years ago

10.1038/s42003-020-01616-7

Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons
Cited by: 24
Author(s): Dong Won Kim, Kai Li, Zoe Qianyi Wang, Yi Stephanie Zhang, Abhijith Bathini, Matthew Brown, Sonia Hao Lin, Parris Whitney Washington, Cuiyun Sun, Susan Lindtner, Bora Lee, Hong Wang, Tomomi Shimogori, John L.R. Rubenstein, Seth Blackshaw
Software Mentions: 6
Published: over 3 years ago

10.1016/j.xpro.2020.100079

Using Chromatin Accessibility to Delineate Therapeutic Subtypes in Pancreatic Cancer Patient-Derived Cell Lines
Cited by: 4
Author(s): Holly Brunton, Ian Garner, Ulla-Maja Bailey, Rosanna Upstill-Goddard, Peter J. Bailey
Software Mentions: 6
Published: almost 4 years ago

10.1242/jcs.259051

The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription
Cited by: 0
Author(s): David Z. Kochan, Julia S. P. Mawer, Jennifer Massen, Kiril Tishinov, Swati Parekh, Martin Graef, Anne Spang, Peter Tessarz
Software Mentions: 6
Published: almost 3 years ago

10.1186/s13072-021-00391-x

Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster
Cited by: 15
Author(s): Marat Sabirov, Olga Kyrchanova, Galina V. Pokholkova, Artem Bonchuk, Natalia Klimenko, Elena Belova, И. Ф. Жимулев, Oksana Maksimenko, Pavel Georgiev
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giy117

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation
Cited by: 16
Author(s): Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Junyan Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J. Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-25748-3

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9
Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-017-14942-4

Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Cited by: 6
Author(s): Yusuke Morita, Mikiko Ohno, Kiyoto Nishi, Yutaka Hiraoka, Sayaka Saijo, Shintaro Matsuda, Toru Kita, Takeshi Kimura, Eiichiro Nishi
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2020.00199

Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing
Cited by: 3
Author(s): Christopher Lee, Kai Wang, Tingting Qin, Maureen A. Sartor
Software Mentions: 5
Published: over 4 years ago

10.26508/lsa.201900318

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
Cited by: 11
Author(s): Junaid Akhtar, Piyush More, Steffen Albrecht, Fédérico Marini, Walter Kaiser, Apurva Kulkarni, Leszek Wojnowski, Jean-Fred Fontaine, Miguel A. Andrade‐Navarro, Marion Silies, Christian Berger
Software Mentions: 5
Published: about 5 years ago

10.1002/bit.25990

Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time
Cited by: 109
Author(s): Julia Feichtinger, Inmaculada Hernández, Christoph Fischer, Michael Hanscho, Norbert Auer, Matthias Hackl, Vaibhav Jadhav, Martina Baumann, Peter M. Krempl, Christian Schmidl, Matthias Farlik, Michael Schuster, Angelika Merkel, Andreas Sommer, Simon Heath, Daniel Rico, Christoph Bock, Gerhard Thallinger, Nicole Borth
Software Mentions: 5
Published: about 8 years ago

10.1186/s13287-021-02508-1

Transcriptome-wide m6A methylome during osteogenic differentiation of human adipose-derived stem cells
Cited by: 4
Author(s): Weihao Sun, Yidan Song, Kai Xia, Liyuan Yu, Xinqi Huang, Zhihe Zhao, Jun Liu
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12864-021-07774-0

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
Cited by: 10
Author(s): Aileen R Ferraro, Abigail J Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.62857

TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex
Cited by: 23
Author(s): Nicole Merritt, Keith Garcia, Dushyandi Rajendran, Zhen‐Yuan Lin, Xiaomeng Zhang, Katrina A. Mitchell, Nicholas Borcherding, Colleen Fullenkamp, Michael S. Chimenti, Anne‐Claude Gingras, Kieran F. Harvey, Munir R. Tanas
Software Mentions: 5
Published: about 3 years ago

10.3389/fgene.2020.508809

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes
Cited by: 16
Author(s): Fábio Pértille, A. M. G. Ibelli, Maj El Sharif, Mirele Daiana Poleti, Anna Sophie Fröhlich, Shiva Rezaei, Mônica Corrêa Ledur, Per Jensen, Carlos Guerrero-Bosagna, Luiz Lehmann Coutinho
Software Mentions: 5
Published: over 3 years ago

10.1186/s13148-020-00970-x

Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming
Cited by: 15
Author(s): Karen L. Leung, Smriti Sanchita, Catherine T. Pham, Brett A. Davis, Mariam Okhovat, Xiangming Ding, Phillip A. Dumesic, Tristan Grogan, Kevin J. Williams, Marco Morselli, Feiyang Ma, Lucia Carbone, Xinmin Li, Matteo Pellegrini, Daniel A. Dumesic, Gregorio D. Chazenbalk
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-020-1001-6

Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation
Cited by: 25
Author(s): Christina N Vallianatos, Brynne Raines, Robert S. Porter, Katherine M Bonefas, Michael C. Wu, Patricia M. Garay, Katie M. Collette, Young Ah Seo, Yali Dou, Catherine E. Keegan, Natalie C. Tronson, Shigeki Iwase
Software Mentions: 5
Published: about 4 years ago

10.3389/fncel.2020.00131

Loss of Arid1a Promotes Neuronal Survival Following Optic Nerve Injury
Cited by: 3
Author(s): Xue-Qi Peng, Shang-Kun Dai, Changping Li, Peipei Li, Zhimeng Wang, Heng Du, Zhao‐Qian Teng, Shuguang Yang, Chang‐Mei Liu
Software Mentions: 5
Published: about 4 years ago

10.1534/g3.119.400986

Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate
Cited by: 1
Author(s): Dane Vassiliadis, Koon Ho Wong, Jo Anne Blinco, Geoff Dumsday, Alex Andrianopoulos, Brendon J. Monahan
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.57683

EHMT2 epigenetically suppresses Wnt signaling and is a potential target in embryonal rhabdomyosarcoma
Cited by: 14
Author(s): Ananya Pal, Jia Yu Leung, Gareth Chin Khye Ang, Vinay Kumar Rao, Luca Pignata, Huey Jin Lim, Maxime Hebrard, Kenneth Tou En Chang, Victor Kwan Min Lee, Ernesto Guccione, Reshma Taneja
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2019.00277

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs
Cited by: 19
Author(s): Kun Han, Ruimin Ren, Jianhua Cao, Shuhong Zhao, Mei Yu
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2021.662707

PLXNC1: A Novel Potential Immune-Related Target for Stomach Adenocarcinoma
Cited by: 12
Author(s): Zhizhan Ni, Chenshen Huang, Hongmei Zhao, Jinzhe Zhou, Muren Hu, Qing Chen, Bujun Ge, Qi Huang
Software Mentions: 5
Published: about 3 years ago

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: about 3 years ago

10.3389/fimmu.2021.633654

The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition
Cited by: 11
Author(s): Xiaofang Xu, Dianhua Qiao, Chenyang Dong, Morgan Mann, Roberto P. Garofalo, Sündüz Keleş, Allan R. Brasier
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1009260

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage
Cited by: 43
Author(s): Marta Gianini, Aleix Bayona-Feliú, Daisy Sproviero, Sónia Barroso, Cristina Cereda, Andrés Aguilera
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1004751

metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns
Cited by: 11
Author(s): Charles Joly Beauparlant, Fabien C. Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau, Arnaud Droit
Software Mentions: 5
Published: almost 8 years ago

10.1186/s40478-018-0614-1

Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, H3 K27M-mutant’ discriminate two subgroups based on the type of histone H3 mutated and not supratentorial or infratentorial location
Cited by: 78
Author(s): David Castel, Cathy Philippe, Thomas Kergrohen, Martin Sill, Jane Merlevede, E. Barret, Stéphanie Puget, Christian Sainte‐Rose, Christof M. Kramm, Chris Jones, Pascale Varlet, Stefan M. Pfister, Jacques Grill, David Jones, Marie‐Anne Debily
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-64700-2

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro differentiation of a putative hepatocyte progenitor
Cited by: 16
Author(s): Jesús Rafael Rodríguez‐Aguilera, Szilvia Ecsedi, Chloe D. Goldsmith, Marie-Pierre Cros, Mariana Domínguez‐López, Nuria Guerrero‐Celis, Rebeca Pérez‐Cabeza de Vaca, Isabelle Chemin, Félix Recillas‐Targa, Victoria Chagoya de Sánchez, Héctor Hernández-Vargas
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-021-86919-3

Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: over 3 years ago

10.1038/s41392-020-00378-2

Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis
Cited by: 11
Author(s): Mingsen Li, Liqiong Zhu, Jiafeng Liu, Huaxing Huang, Huizhen Guo, Li Wang, Lingyu Li, Sijie Gu, Jieying Tan, Jing Zhong, Bowen Wang, Zhen Mao, Yong Fan, Chunqiao Liu, Jing Yuan, Hong Ouyang
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0214677

PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues
Cited by: 8
Author(s): Samadrita Bhattacharyya, Adwait Amod Sathe, Minoti Bhakta, Chao Xing, Nikhil V. Munshi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5170-3

Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin
Cited by: 19
Author(s): Jinhee Park, William J. Belden
Software Mentions: 4
Published: over 5 years ago

10.1186/s12920-020-00749-2

Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression
Cited by: 6
Author(s): Damien Kaukonen, Riina Kaukonen, Lélia Polit, Bryan T. Hennessy, Riikka Lund, Stephen F. Madden
Software Mentions: 4
Published: about 4 years ago

10.1155/2020/9031723

Identification and Analysis of Estrogen Receptor α Promoting Tamoxifen Resistance-Related lncRNAs
Cited by: 11
Author(s): Xiulei Zhang, Shanjun Gao, Zhen Li, Wei Wang, Guangzhi Liu
Software Mentions: 4
Published: about 4 years ago

10.3390/cancers12082003

Methylation Patterns and Chromatin Accessibility in Neuroendocrine Lung Cancer
Cited by: 5
Author(s): Elsa Arbajian, Mattias Aine, Anna Karlsson, Johan Vallon‐Christersson, Hans Brunnström, Josef Davidsson, Sofie Mohlin, Maria Planck, Johan Staaf
Software Mentions: 4
Published: about 4 years ago

10.1186/s13148-020-00973-8

5-Hydroxymethylcytosine profiles of cfDNA are highly predictive of R-CHOP treatment response in diffuse large B cell lymphoma patients
Cited by: 9
Author(s): Hangyu Chen, Weilong Zhang, Lei Zhang, Ping Yang, Fang Li, Zeruo Yang, Jing Wang, Pei Meng, Yun Hong, Changjian Yan, Wei Li, Jia Liu, Nuo Xu, Long Chen, Xiu-Bing Xiao, Yan Qin, Xiaohong He, Hui Liu, Haichuan Zhu, Chuan He, Jian Lin, Hongmei Jing
Software Mentions: 4
Published: over 3 years ago

10.1186/s13148-018-0576-y

Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology
Cited by: 14
Author(s): Stefano Amatori, Giuseppe Persico, Claudio Paolicelli, Roman Hillje, Nora Sahnane, Francesco Corini, Daniela Furlan, Lucilla Luzi, Saverio Minucci, Marco Giorgio, Pier Giuseppe Pelicci, Mirco Fanelli
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2020.571501

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells
Cited by: 4
Author(s): Andrea Cirino, Ilaria Aurigemma, Monica Franzese, Gabriella Lania, Dario Righelli, Rosa Ferrentino, Elizabeth Illingworth, Claudia Angelini, Antonio Baldini
Software Mentions: 4
Published: almost 4 years ago

10.3389/fphar.2021.673831

MMP24 Contributes to Neuropathic Pain in an FTO-Dependent Manner in the Spinal Cord Neurons
Cited by: 6
Author(s): Longfei Ma, Yangyuxin Huang, Fengjiang Zhang, Dave Schwinn Gao, Na Sun, Jinxuan Ren, Suyun Xia, Jia Li, Xiujuan Peng, Yu Lu, Bao‐Chun Jiang, Min Yan
Software Mentions: 4
Published: about 3 years ago

10.3389/fpls.2021.715820

Genome-Wide Identification of the ARF Gene Family and ARF3 Target Genes Regulating Ovary Initiation in Hazel via ChIP Sequencing
Cited by: 8
Author(s): Wei Heng, Yufei Cheng, Ying Sun, Xingzheng Zhang, Hailong He, Jianfeng Liu
Software Mentions: 4
Published: almost 3 years ago

10.3390/genes10060433

BarkBase: Epigenomic Annotation of Canine Genomes
Cited by: 26
Author(s): Kate Megquier, Diane P. Genereux, Jessica P. Hekman, Ross Swofford, Jason Turner-Maier, Jeremy Johnson, Jacob Alonso, Li Xue, Kathleen M. Morrill, Lynne J. Anguish, Michele Koltookian, Brittney Logan, Claire R. Sharp, Lluís Ferrer, Kerstin Lindblad‐Toh, Vicki N. Meyers-Wallen, Andrew M. Hoffman, Elinor K. Karlsson
Software Mentions: 4
Published: about 5 years ago

10.1038/s41597-020-00713-w

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq
Cited by: 2
Author(s): Xiaomeng Zhao, Long Su, Weilin Xu, Sarah Schaack, Cheng Sun
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-73146-5

Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development
Cited by: 9
Author(s): David Brena, Joan Bertran, Montserrat Porta-de-la-Riva, Yolanda Guillén, Eric Cornes, Dmytro Kukhtar, Lluís Campos-Vicens, Lierni Fernández, Irene Pecharromán, Albert García-López, Abul B.M.M.K. Islam, Laura Marruecos, Anna Bigas, Julián Cerón, Lluís Espinosa
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-87635-8

H3K4me2 ChIP-Seq reveals the epigenetic landscape during mushroom formation and novel developmental regulators of Schizophyllum commune
Cited by: 9
Author(s): Peter Jan Vonk, Robin A. Ohm
Software Mentions: 4
Published: over 3 years ago

10.1186/s13287-019-1323-9

Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells
Cited by: 8
Author(s): Yingying Wang, Baosen Guo, Zengrong Xiao, Haijun Lin, Xi Zhang, Yueqiang Song, Yalei Li, Xuehu Gao, Jin-Jun Yu, Zhihua Shao, Xuekun Li, Yuan Luo, Siguang Li
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.67305

ZC3H4 restricts non-coding transcription in human cells
Cited by: 24
Author(s): Chris Estell, Lee Davidson, Pieter C. Steketee, Adam Monier, Steven West
Software Mentions: 4
Published: about 3 years ago

10.7554/eLife.51109

Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
Cited by: 47
Author(s): Sarah E Dremel, Neal A. DeLuca
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.40199

Cellular acidosis triggers human MondoA transcriptional activity by driving mitochondrial ATP production
Cited by: 38
Author(s): Blake R. Wilde, Zhizhou Ye, Tian-Yeh Lim
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21082800

Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Cited by: 13
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Tengyu Wei, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms22020530

Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes
Cited by: 14
Author(s): Anna Johanna Wiese, Lenka Steinbachová, Ljudmilla Timofejeva, Vojtěch Čermák, Božena Klodová, Ranjani Sri Ganji, Mariana Limones-Méndez, Pavel Bokvaj, Said Hafidh, David Potěšil, David Honys
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22052679

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model
Cited by: 15
Author(s): Fábio Pértille, Manuel Álvarez‐Rodríguez, Arthur Nery da Silva, Isabel Barranco, Jordi Roca, Carlos Guerrero-Bosagna, Heriberto Rodríguez-Martinez
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22126503

Comparative Analysis of Histone H3K4me3 Distribution in Mouse Liver in Different Diets Reveals the Epigenetic Efficacy of Cyanidin-3-O-glucoside Dietary Intake
Cited by: 5
Author(s): Giuseppe Persico, Francesca Casciaro, Alessandra Marinelli, Chiara Tonelli, Katia Petroni, Marco Giorgio
Software Mentions: 4
Published: about 3 years ago

10.3390/ijms221910403

MMP14 Contributes to HDAC Inhibition-Induced Radiosensitization of Glioblastoma
Cited by: 1
Author(s): Yuchuan Zhou, Hongxia Liu, Zheng Wang, Qianping Chen, Songling Hu, Yan Pan, Yang Bai, Jianghong Zhang, Chunlin Shao
Software Mentions: 4
Published: almost 3 years ago

10.18632/oncotarget.13169

Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA and lncRNA expression by ChIP sequencing and RNA sequencing
Cited by: 6
Author(s): Yuan Li, Mei Luo, Xuejiao Shi, Zhiliang Lu, Shengrong Sun, Jianbing Huang, Zhaoli Chen, Jié He
Software Mentions: 4
Published: over 7 years ago

10.1128/JVI.01399-20

Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level
Cited by: 22
Author(s): Caroline C. Friedel, Adam W. Whisnant, Lara Djaković, Andrzej Rutkowski, Marie-Sophie Friedl, Michael Kluge, James C Williamson, Somesh Sai, Ramón Vidal, Sascha Sauer, Thomas Hennig, Arnhild Grothey, Andrea Milić, Bhupesh K. Prusty, Paul J. Lehner, Nicholas J Matheson, Florian Erhard, Lars Dölken
Software Mentions: 4
Published: over 3 years ago

10.3389/fcell.2021.740866

Interplay Between BALL and CREB Binding Protein Maintains H3K27 Acetylation on Active Genes in Drosophila
Cited by: 2
Author(s): Ammad Shaukat, Muhammad Haider Farooq Khan, Hina Ahmad, Zain Umer, Muhammad Tariq
Software Mentions: 3
Published: almost 3 years ago

10.3390/molecules26041194

Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua
Cited by: 2
Author(s): Limeng Zhou, Yingzhang Huang, Qi Wang, Dianjing Guo
Software Mentions: 3
Published: over 3 years ago

10.3389/fmolb.2020.618088

DNA Damage Induces Dynamic Associations of BRD4/P-TEFb With Chromatin and Modulates Gene Transcription in a BRD4-Dependent and -Independent Manner
Cited by: 5
Author(s): Yawei Song, Gongcheng Hu, Jinping Jia, Maojin Yao, Xiaoshan Wang, Wenliang Lu, Andrew P. Hutchins, Jiekai Chen, Keiko Ozato, Hongjie Yao
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.00220

The DNA Methylation Status of Wnt and Tgfβ Signals Is a Key Factor on Functional Regulation of Skeletal Muscle Satellite Cell Development
Cited by: 13
Author(s): Weiya Zhang, Saixian Zhang, Yongming Xu, Yunlong Ma, Dingxiao Zhang, Xinyun Li, Shuhong Zhao
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-019-0306-5

Early-life DNA methylation profiles are indicative of age-related transcriptome changes
Cited by: 17
Author(s): Niran Hadad, Dustin R. Masser, Laura Blanco-Berdugo, David R. Stanford, Willard M. Freeman
Software Mentions: 3
Published: almost 5 years ago

Projects: bioconductor: ChIPseeker

Papers Mentioning ChIPseeker 161