bioconductor: DiffBind | Projects

10.1038/sdata.2016.4

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Cited by: 10
Author(s): Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 9 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

10.3389/fgene.2019.01386

Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection
Cited by: 17
Author(s): Thomas J. Hall, Douglas Vernimmen, John Andrew Browne, Michael P. Mullen, Stephen V. Gordon, David E. MacHugh, Alan M. O’Doherty
Software Mentions: 5
Published: almost 5 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPAR<i>γ</i>-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.51325

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
Cited by: 21
Author(s): Huan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yuchen Xiao, Jenna C. Carlson, Fabrice Darbellay, Axel Visel, Elizabeth J. Leslie, Patrick Breheny, Albert Erives, Robert A. Cornell
Software Mentions: 5
Published: almost 5 years ago

10.1242/jcs.232223

Tox4 modulates cell fate reprogramming
Cited by: 12
Author(s): Lotte Vanheer, Juan Song, Natalie De Geest, Adrian Janiszewski, Irene Talón, Caterina Provenzano, Taeho Oh, Joel Chappell, Vincent Pasque
Software Mentions: 5
Published: almost 6 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: over 3 years ago

10.7554/eLife.60191

MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor–1
Cited by: 33
Author(s): Tessa M. Popay, Jing Wang, Clare M. Adams, Gregory C. Howard, Simona G. Codreanu, Stacy D. Sherrod, John A. McLean, Lance R. Thomas, Shelly L. Lorey, Yuichi Machida, April M. Weissmiller, Christine M. Eischen, Qi Liu, William P. Tansey
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.51373

PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells
Cited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-015-0605-5

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
Cited by: 61
Author(s): Santiago Uribe-Lewis, Rory Stark, Thomas Carroll, Mark J. Dunning, Martin Bachman, Yoko Itō, Lovorka Stojic, Silvia Halim, Sarah L. Vowler, Andy G. Lynch, Benjamin Delatte, Eric James de Bony, Laurence Colin, Matthieu Defrance, Felix Krueger, Ana Luísa Silva, Rogier ten Hoopen, Ashraf E.K. Ibrahim, François Fuks, Adele Murrell
Software Mentions: 5
Published: over 9 years ago

10.1016/j.immuni.2017.12.010

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages
Cited by: 153
Author(s): Zsolt Czimmerer, Bence Dániel, Attila Horváth, Dominik Rückerl, Gergely Nagy, Máté Kiss, Matthew Peloquin, Marietta Margit Budai, Ixchelt Cuaranta-Monroy, Zoltán Simándi, László Steiner, Béla Nagy, Szilárd Póliska, Csaba Bankó, Zsolt Bacsó, Ira G. Schulman, Sascha Sauer, Jean Deleuze, Judith E. Allen, Szilvia Benkő, László Nagy
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pntd.0003853

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection
Cited by: 46
Author(s): David Roquis, Julie M. J. Lepesant, Marion Picard, Michael Freitag, Hugues Parrinello, Marco Groth, Rémi Emans, Céline Cosseau, Christoph Grunau
Software Mentions: 5
Published: about 9 years ago

10.1093/bioinformatics/btaa202

HiChIP-Peaks: a HiChIP peak calling algorithm
Cited by: 10
Author(s): Chenfu Shi, Magnus Rattray, Gisela Orozco
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2020.585746

Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium
Cited by: 7
Author(s): Peter McErlean, A. Paul Kelly, Jaideep Dhariwal, Max Kirtland, Julie Watson, Ismael Ranz, Janet L. Smith, Alka Saxena, David J. Cousins, Antoon van Oosterhout, Roberto Solari, Michael R. Edwards, Sebastian L. Johnston, Paul Lavender
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

10.1038/s41598-021-94186-5

Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties
Cited by: 6
Author(s): Sanshiro Kanazawa, H. Okada, Hironori Hojo, Shinsuke Ohba, Junichi Iwata, Makoto Komura, Atsuhiko Hikita
Software Mentions: 4
Published: over 3 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

10.1371/journal.pgen.1007466

Unique patterns of trimethylation of histone H3 lysine 4 are prone to changes during aging in Caenorhabditis elegans somatic cells
Cited by: 27
Author(s): Mintie Pu, Minghui Wang, Wenke Wang, Velayudhan Satheeja Santhi, Siu Sylvia Lee
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-021-02444-6

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network
Cited by: 12
Author(s): Zhonghua Du, Wei Xue, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Yang Wang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen, Ilkay Celik, Yanbo Zhu, Zi Yan, Changhao Fu, Shanshan Liu, Benzheng Jiao, Zhuo Wang, Hui Zhang, Günhan Gülsoy, Jianjun Luo, Baoming Qin, Sujun Gao, Philipp Kapranov, Miguel A. Esteban, Songling Zhang, Wei Li, Ferhat Ay, Runsheng Chen, Andrew R. Hoffman, Jiuwei Cui, Ji-Fan Hu
Software Mentions: 4
Published: over 3 years ago

10.1016/j.gpb.2019.05.005

Genome-wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer
Cited by: 8
Author(s): Shuang‐Ling Wu, Xiaoyi Zhang, Mengqi Chang, Changcai Huang, Jun Qian, Qing Li, Fang Yuan, Lihong Sun, Xinmiao Yu, Xinmiao Cui, Jiaxin Jiang, Meng-Yao Cui, Ye Liu, Hengchao Wu, Liang Zeng, Xiaoyue Wang, Yamei Niu, Wei‐Min Tong, Feng Jin
Software Mentions: 4
Published: almost 4 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: about 6 years ago

10.1084/jem.20181276

Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AML
Cited by: 78
Author(s): Faisal Basheer, George Giotopoulos, Eshwar Meduri, Haiyang Yun, Milena Mazan, Daniel Sasca, Paolo Gallipoli, Ludovica Marando, Malgorzata Gozdecka, Ryan Asby, Olivia Sheppard, Monika Dudek, Lars Bullinger, Hartmut Döhner, Richard Dillon, Sylvie Freeman, Oliver G. Ottmann, Alan Kenneth Burnett, Nigel H. Russell, Elli Papaemmanuil, Robert Kerrin Hills, Peter J. Campbell, George S. Vassiliou, Brian J. P. Huntly
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-020-02063-7

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize
Cited by: 57
Author(s): Yonghao Sun, Liang Dong, Ying Zhang, Dazhen Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li, Fang Yang
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: almost 4 years ago

10.3389/fphar.2019.00126

Making Sense of the Epigenome Using Data Integration Approaches
Cited by: 46
Author(s): Emma Cazaly, Joseph Saad, Wenyu Wang, Caroline A. Heckman, Miina Ollikainen, Jing Tang
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0130379

A FOXM1 Dependent Mesenchymal-Epithelial Transition in Retinal Pigment Epithelium Cells
Cited by: 13
Author(s): Parul Choudhary, Benjamin T Dodsworth, Ben S. Sidders, Alex Gutteridge, Christos Michaelides, Joshua K. Duckworth, Paul J. Whiting, Caroline Benn
Software Mentions: 4
Published: over 9 years ago

10.1186/s40478-021-01135-4

C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation
Cited by: 14
Author(s): Tatsuya Ozawa, Syuzo Kaneko, Frank Szulzewsky, Zhiwei Qiao, Mutsumi Takadera, Yoshitaka Narita, Tadashi Kondo, Eric C. Holland, Ryuji Hamamoto, Koichi Ichimura
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-5184-x

Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification
Cited by: 7
Author(s): Yung-Chih Lai, Ya-Chen Liang, Ting‐Xin Jiang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 4
Published: about 6 years ago

10.1016/j.cels.2020.05.003

Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons
Cited by: 24
Author(s): Daria Bunina, Nade Abazova, Nichole Diaz, Kyung‐Min Noh, Jeroen Krijgsveld, Judith B. Zaugg
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.27861

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer
Cited by: 124
Author(s): Neel Shah, Ping Wang, John Wongvipat, Wouter R. Karthaus, Wassim Abida, Joshua Armenia, Shira Rockowitz, Yotam Drier, B Bernstein, Henry W. Long, Matthew L. Freedman, Vivek Arora, Deyou Zheng, Charles L. Sawyers
Software Mentions: 4
Published: about 7 years ago

10.1038/srep33736

MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy
Cited by: 4
Author(s): Joanna Bednarczyk, Konrad J. Dębski, Anna Bot, Katarzyna Łukasiuk
Software Mentions: 4
Published: about 8 years ago

10.26508/lsa.201900331

Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis
Cited by: 18
Author(s): Florian Noack, Abhijeet Pataskar, Martin Schneider, Frank Buchholz, Vijay Tiwari, Federico Calegari
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008422

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
Cited by: 2
Author(s): Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka
Software Mentions: 4
Published: almost 4 years ago

10.1038/sdata.2018.255

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Cited by: 16
Author(s): Zhonghua Du, Lin Jia, Yichen Wang, Cong Wang, Wei Xue, Jingcheng Chen, Yanbo Zhu, Dehai Yu, Lei Zhou, Naifei Chen, Shilin Zhang, Ilkay Celik, Ferhat Ay, Sujun Gao, Songling Zhang, Wei Li, Andrew R. Hoffman, Jiuwei Cui
Software Mentions: 4
Published: about 6 years ago

10.1186/s13059-021-02375-2

Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation
Cited by: 8
Author(s): Nisha Padmanabhan, Kie Kyon Huang, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-O K Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Xuewen Ong, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee, Angie Lay Keng Tan, Shamaine Ho Wei Ting, Micah A. Luftig, Dennis Kappei, Warren D. Kruger, Jun Bian, Ying Swan Ho, Ming Teh, Steve Rozen, Patrick Tan
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0214559

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus cattle rumen tissue
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Zan Liu, Jiuzhou Song
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-017-1159-5

RNF40 regulates gene expression in an epigenetic context-dependent manner
Cited by: 38
Author(s): Wanhua Xie, Sankari Nagarajan, Simon J. Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri, Steven A. Johnsen
Software Mentions: 4
Published: almost 8 years ago

10.1126/sciadv.aaz4012

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion
Cited by: 13
Author(s): Gustavo A. Ruiz Buendía, Marion Leleu, Flavia Marzetta, Ludovica Vanzan, Jennifer Y. Tan, Victor Ythier, Emma Randall, Ana C. Marques, Tuncay Baubec, Rabih Murr, Ioannis Xénarios, Vincent Dion
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.68238

Neuronal calmodulin levels are controlled by CAMTA transcription factors
Cited by: 3
Author(s): Thanh Thi Kim Vuong-Brender, Sean M. Flynn, Yvonne Vallis, Mario de Bono
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-019-41639-7

Hox gene expression determines cell fate of adult periosteal stem/progenitor cells
Cited by: 22
Author(s): Vivian Bradaschia-Corrêa, Kevin Leclerc, Anne Marie Josephson, Sooyeon Lee, Laura Palma, Hannah P. Litwa, Shane S. Neibart, Jason C. Huo, Philipp Leucht
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.202439

A short deletion in the DNA-binding domain of STAT3 suppresses growth and progression of colon cancer cells
Cited by: 3
Author(s): Yijia Xiong, Dongyang Liu, Rongrong Shen, Yanbao Xiong
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-14-826

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets
Cited by: 29
Author(s): Gabriele Schweikert, Botond Cseke, Thomas Clouaire, Adrian Bird, Guido Sanguinetti
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-015-1495-3

Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila
Cited by: 11
Author(s): Sarah H. Carl, Steven Russell
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-5805-z

Corrupted DNA-binding specificity and ectopic transcription underpin dominant neomorphic mutations in KLF/SP transcription factors
Cited by: 19
Author(s): Melissa Ilsley, Stephen Huang, Graham Magor, Michael J. Landsberg, Kevin R. Gillinder, Andrew C. Perkins
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-2081-4

Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors
Cited by: 50
Author(s): Jason Piper, Salam A. Assi, Pierre Cauchy, Christophe Ladroue, Peter N. Cockerill, Constanze Bonifer, Sascha Ott
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12881-019-0835-6

Effect of prematurity on genome wide methylation in the placenta
Cited by: 13
Author(s): Jessica Schuster, Alper Uzun, Joan Stablia, Christoph Schorl, Mari Mori, Jamés F. Padbury
Software Mentions: 3
Published: over 5 years ago

10.1242/bio.042754

Defining the dynamic chromatin landscape of mouse nephron progenitors
Cited by: 17
Author(s): Sylvia Hilliard, Renming Song, Hongbing Liu, Chao‐Hui Chen, Yuwen Li, Melody Baddoo, Erik Flemington, Alanna Wanek, Jay K. Kolls, Zubaida Saifudeen, Samir S. El‐Dahr
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41375-019-0438-4

Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice
Cited by: 39
Author(s): Han Lin, Vikas Madan, Anand Mayakonda, Pushkar Dakle, Teoh Weoi Woon, S. Pavithra, Hazimah Binte Mohd Nordin, Zeya Cao, Janani Sundaresan, Ienglam Lei, Zhong Wang, H. Phillip Koeffler
Software Mentions: 3
Published: over 5 years ago

10.26508/lsa.202000762

Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution
Cited by: 40
Author(s): Oscar D. Villarreal, Sofiane Y Mersaoui, Zhenbao Yu, Jean–Yves Masson, Stéphane Richard
Software Mentions: 3
Published: over 4 years ago

10.1007/s12035-018-1377-1

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
Cited by: 17
Author(s): Patrick Bovio, Henriette Franz, Stefanie Heidrich, Tudor Rauleac, Fabian Kilpert, Thomas Manke, Tanja Vogel
Software Mentions: 3
Published: about 6 years ago

10.3390/v12080804

Respiratory Syncytial Virus Infection Induces Chromatin Remodeling to Activate Growth Factor and Extracellular Matrix Secretion Pathways
Cited by: 20
Author(s): Xiaofang Xu, Dianhua Qiao, Morgan Mann, Roberto P. Garofalo, Allan R. Brasier
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.9442

Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae
Cited by: 3
Author(s): Zachary J Waldrip, Piroon Jenjaroenpun, Oktawia A DeYoung, Intawat Nookaew, Sean D. Taverna, Kevin D. Raney, Alan J. Tackett
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1007224

SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs
Cited by: 44
Author(s): Daniel W. Hagey, Susanne Klum, Idha Kurtsdotter, Cécile Zaouter, Danijal Topcic, Olov Andersson, Maria Bergsland, Jonas Muhr
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1006745

GRHL3 binding and enhancers rearrange as epidermal keratinocytes transition between functional states
Cited by: 39
Author(s): Rachel Herndon Klein, Ziguang Lin, Amelia Soto Hopkin, William Gordon, Lam C. Tsoi, Yun Liang, Jóhann E. Guðjónsson, Bogi Andersen
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1009828

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II
Cited by: 11
Author(s): Mohammad S. Baig, Yimo Dou, Benjamin G. Bergey, Russell Bahar, Justin M. Burgener, Marjan Moallem, J B McNeil, Akhi Akhter, Giovanni L Burke, Veroni S. Sri Theivakadadcham, Patricia Richard, Damien D’Amours, Emanuel Rosonina
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1007088

Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB's innate function as the repressor of DREAM target genes
Cited by: 27
Author(s): Paul D. Goetsch, Jacob M. Garrigues, Susan Strome
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1007991

Sumoylation of DNA-bound transcription factor Sko1 prevents its association with nontarget promoters
Cited by: 12
Author(s): Veroni S. Sri Theivakadadcham, Benjamin G. Bergey, Emanuel Rosonina
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0100476

Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine
Cited by: 9
Author(s): José A. Carrillo, Yanghua He, Juan Luo, Kimberly R. Menendez, Nathaniel L. Tablante, Keji Zhao, Joseph N. Paulson, Bichun Li, Jiuzhou Song
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0155378

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
Cited by: 7
Author(s): Laurie A. Steiner, Vincent P. Schulz, Yelena Makismova, Kimberly Lezon-Geyda, Patrick G. Gallagher
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0196965

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5
Cited by: 8
Author(s): Brian H. Lee, Michael R. Stallcup
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0193126

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells
Cited by: 20
Author(s): Ting-Hsuan Wu, Lingfang Shi, Jessika Adrian, Minyi Shi, Ramesh V. Nair, M Snyder, Peter N. Kao
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0227116

Modeling the effect of prolonged ethanol exposure on global gene expression and chromatin accessibility in normal 3D colon organoids
Cited by: 20
Author(s): Matthew Devall, Lucas T. Jennelle, Jennifer Bryant, Stephanie A. Bien, Ulrike Peters, Steven M. Powell, Graham Casey
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41418-020-00647-1

RUNX3 methylation drives hypoxia-induced cell proliferation and antiapoptosis in early tumorigenesis
Cited by: 14
Author(s): Sun Hee Lee, Do Young Hyeon, San-Hyun Yoon, Ji Hak Jeong, Saeng Myung Han, Ju Won Jang, Minh Phương Nguyễn, Xin Zi, Soon Il An, Kwangbeom Hyun, Hee Jung Jung, Ji-Joon Song, Suk Chul Bae, Woo Ho Kim, Daehee Hwang, You Mie Lee
Software Mentions: 3
Published: about 4 years ago

10.1038/s41419-020-03081-w

The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis
Cited by: 7
Author(s): Florian Wegwitz, Evangelos Prokakis, Anastasija Pejkovska, Robyn Laura Kosinsky, Markus Glatzel, Klaus Pantel, Harriet Wikman, Steven A. Johnsen
Software Mentions: 3
Published: about 4 years ago

10.1038/s41419-021-04027-6

CRISPR screening identifies CDK12 as a conservative vulnerability of prostate cancer
Cited by: 16
Author(s): Hanqi Lei, Zifeng Wang, Donggen Jiang, Fang Liu, Meiling Liu, Xin‐Xing Lei, Yafei Yang, Bin He, Min Yan, Hai Huang, Quentin Liu, Jun Pang
Software Mentions: 3
Published: over 3 years ago

10.1016/j.jcmgh.2021.05.020

Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation
Cited by: 11
Author(s): Gaurav V. Sarode, Kari Neier, Noreene M. Shibata, Yuanjun Shen, Dmitry A. Goncharov, Elena A. Goncharova, Tagreed A. Mazi, Nikhil Joshi, Matthew L. Settles, Janine M. LaSalle, Valentina Medici
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13148-020-00921-6

Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues
Cited by: 12
Author(s): Hang Gyeong Chin, Zhiyi Sun, Udayakumar S. Vishnu, Pengying Hao, Paloma Cejas, George Spracklin, Pierre‐Olivier Estève, Shuang-yong Xu, Henry W. Long, Sriharsa Pradhan
Software Mentions: 3
Published: about 4 years ago

10.1186/s13148-020-00955-w

Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs
Cited by: 4
Author(s): Iraia Muñoa-Hoyos, John Halsall, Manu Araolaza, Carl Ward, Idoia García, Itziar Urizar-Arenaza, Marta Gianzo Citores, Paloma García, Bryan M. Turner, Nerea Subirán
Software Mentions: 3
Published: about 4 years ago

10.1186/s13148-016-0265-7

Neonatal monocytes exhibit a unique histone modification landscape
Cited by: 37
Author(s): Jennifer Bermick, Nathalie Lambrecht, Aaron D. denDekker, Steven L. Kunkel, Nicholas W. Lukacs, Cory M. Hogaboam, Matthew Schaller
Software Mentions: 3
Published: about 8 years ago

10.15252/embr.201745000

<scp>KAP</scp> 1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control
Cited by: 83
Author(s): Christopher H.C. Tie, Liane Fernandes, Lucía Conde, Luisa Robbez‐Masson, Rebecca P. Sumner, Thomas P. Peacock, Maria T. Rodriguez-Plata, Greta Mickute, Robert J. Gifford, Greg J. Towers, Javier Herrero, Helen M. Rowe
Software Mentions: 3
Published: over 6 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/fcell.2021.664545

Uniaxial Cyclic Stretching Promotes Chromatin Accessibility of Gene Loci Associated With Mesenchymal Stem Cells Morphogenesis and Osteogenesis
Cited by: 7
Author(s): Duo Zhang, Ran Zhang, Xiaoyuan Song, Karen Chang Yan, Haiyi Liang
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2018.00610

Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues
Cited by: 26
Author(s): Alexandre A. Lussier, Tamara S. Bodnar, Matthew Mingay, Alexandre Morin, Martin Hirst, Michæl S. Kobor, Joanne Weinberg
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2018.00346

Stable Histone Methylation Changes at Proteoglycan Network Genes Following Ethanol Exposure
Cited by: 9
Author(s): David P. Gavin, Joel G. Hashimoto, Nathan H. Lazar, Lucia Carbone, John C. Crabbe, Marina Guizzetti
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-017-1247-6

NicE-seq: high resolution open chromatin profiling
Cited by: 41
Author(s): V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre‐Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf, Sriharsa Pradhan
Software Mentions: 3
Published: over 7 years ago

10.1111/jcmm.15568

A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air‐liquid interface
Cited by: 10
Author(s): Jenny L. Kerschner, Alekh Paranjapye, Shiyi Yin, Dannielle L. Skander, Gürkan Bebek, Shih Hsing Leir, Ann Harris
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-37522-6

MITF has a central role in regulating starvation-induced autophagy in melanoma
Cited by: 60
Author(s): Katrín Möller, Sara Sigurbjörnsdóttir, Asgeir Ö. Arnthórsson, Vivian Pogenberg, Ramile Dilshat, Valerie Fock, Sólveig Hlín Brynjólfsdóttir, Christian Bindesbøll, M. Bessadóttir, Helga M. Ögmundsdóttir, Anne Simonsen, Lionel Larue, Matthias Wilmanns, Vésteinn Thórsson, Eiríkur Steingrimsson, Margrét H. Ögmundsdóttir
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-42292-w

Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis
Cited by: 19
Author(s): Marina R. Hadjicharalambous, Benoı̂t Roux, Eszter Csomor, Carol Feghali‐Bostwick, Lynne A. Murray, D. S. Clarke, Mark A. Lindsay
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-50927-1

TIP60/KAT5 is required for neuronal viability in hippocampal CA1
Cited by: 15
Author(s): Inga Urban, Cemil Kerimoğlu, M. Sadman Sakib, Haifang Wang, Eva Benito, Christina Thaller, Xunlei Zhou, Jun Yan, André Fischer, Gregor Eichele
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-67850-5

Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer
Cited by: 8
Author(s): Kristan E. van der Vos, Daniël J. Vis, Ekatarina Nevedomskaya, Y. Kim, Woonyoung Choi, David J. McConkey, Lodewyk Wessels, Bas W.G. van Rhijn, Wilbert Zwart, Michiel S. van der Heijden
Software Mentions: 3
Published: over 4 years ago

10.1186/s13287-021-02310-z

Hypoxic preconditioning induces epigenetic changes and modifies swine mesenchymal stem cell angiogenesis and senescence in experimental atherosclerotic renal artery stenosis
Cited by: 20
Author(s): Busra Isik, Roman Thaler, Busra B. Goksu, Sabena M. Conley, Hayder Al-Khafaji, Arjunmohan Mohan, Mohsen Afarideh, Abdelrhman Abumoawad, Xiang Yang Zhu, James D. Krier, Ishran M. Saadiq, Hui Tang, Alfonso Eirin, La Tonya J. Hickson, André J. van Wijnen, Stephen C. Textor, Lilach O. Lerman, Sandra M. Herrmann
Software Mentions: 3
Published: over 3 years ago

10.7150/thno.39093

Genome-wide interaction target profiling reveals a novel <i>Peblr20</i>-eRNA activation pathway to control stem cell pluripotency
Cited by: 22
Author(s): Cong Wang, Lin Jia, Yichen Wang, Zhonghua Du, Lei Zhou, Wei Xue, Hui Li, Shilin Zhang, Huiling Chen, Naifei Chen, Jingcheng Chen, Yanbo Zhu, Yuanyuan Nie, Ilkay Celic, Sujun Gao, Songling Zhang, Andrew R. Hoffman, Wei Li, Ji-Fan Hu, Jiuwei Cui
Software Mentions: 3
Published: almost 5 years ago

10.1093/hmg/ddx092

Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease
Cited by: 24
Author(s): Giuseppe Gallone, Wilfried Haerty, Giulio Disanto, Sreeram Ramagopalan, Chris P. Ponting, Antonio J. Berlanga‐Taylor
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.55124

Hox-dependent coordination of mouse cardiac progenitor cell patterning and differentiation
Cited by: 30
Author(s): Sonia Stefanovic, Brigitte Laforest, Jean-Pierre Desvignes, Fabienne Lescroart, Laurent Argiro, Corinne Maurel-Zaffran, David Salgado, Elise Plaindoux, Christopher De Bono, Kristijan Pažur, Magali Théveniau-Ruissy, Christophe Béroud, Michel Pucéat, Anthony Gavalas, Robert G. Kelly, Stéphane Zaffran
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.52370

Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity
Cited by: 14
Author(s): Erin Clark, Michael Rutlin, Lucia Capano, Samuel Aviles, Jordan R Saadon, Praveen Taneja, Qiyu Zhang, James B. Bullis, Timothy Lauer, Emma Myers, Anton Schulmann, Douglas Forrest, Sacha B. Nelson
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.55730

Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes
Cited by: 22
Author(s): Nora Yucel, Jessie Axsom, Yifan Yang, Li Li, Joshua H. Rhoades, Zoltàn Arany
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms221910204

Selective Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibition by the SCH772984 Compound Attenuates In Vitro and In Vivo Inflammatory Responses and Prolongs Survival in Murine Sepsis Models
Cited by: 7
Author(s): Michał Kopczyński, Izabela Rumieńczyk, Maria Kulecka, Małgorzata Statkiewicz, Kazimiera Pyśniak, Zuzanna Sandowska-Markiewicz, Urszula Wójcik-Trechcińska, Krzysztof Goryca, Karolina Pyziak, Eliza Majewska, Magdalena Masiejczyk, Katarzyna Wójcik-Jaszczyńska, Tomasz Rzymski, Karol Bomsztyk, Jerzy Ostrowski, Michał Mikula
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-020-60775-z

Neuron-specific analysis of histone modifications with post-mortem brains
Cited by: 6
Author(s): Kagari Koshi-Mano, Tatsuo Mano, Maho Morishima, Shigeo Murayama, Akira Tamaoka, Shoji Tsuji, Tatsushi Toda, Atsushi Iwata
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-55211-w

Mutant IDH1 confers resistance to energy stress in normal biliary cells through PFKP-induced aerobic glycolysis and AMPK activation
Cited by: 16
Author(s): Hiroaki Fujiwara, Keisuke Tateishi, Kento Misumi, Akimasa Hayashi, Kaori Igarashi, Hiroyuki Kato, Takuma Nakatsuka, Nobumi Suzuki, Keisuke Yamamoto, Yotaro Kudo, Yoku Hayakawa, Hayato Nakagawa, Yasuo Tanaka, Hideaki Ijichi, Hirofumi Kogure, Yosuke Nakai, Hiroyuki Isayama, Kiyoshi Hasegawa, Masashi Fukayama, Tomoyoshi Soga, Kazuhiko Koike
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.47691

Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2
Cited by: 43
Author(s): Emma J. Gehrke, Xiafei Zhang, Sheila Marie Pimentel‐Elardo, Andrew R. Johnson, Christiaan A. Rees, Stephanie E. Jones, Hindra Hindra, Sebastian S. Gehrke, Sonya Turvey, Suzanne Boursalie, Jane E. Hill, Erin E. Carlson, Justin R. Nodwell, Marie A. Elliot
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-017-12608-9

Nucleosome stability measured in situ by automated quantitative imaging
Cited by: 16
Author(s): László Imre, Zoltán Simándi, Attila Horváth, György Fenyőfalvi, Péter P. Nánási, Erfaneh Firouzi Niaki, Éva Hegedüs, Zsolt Bacsó, Urbain Weyemi, Rebekka Mauser, Juan Ausió, Albert Jeltsch, William M. Bonner, László Nagy, Hiroshi Kimurâ, Gábor Szabó
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.30201

Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B
Cited by: 43
Author(s): Chih Yung Sean Lee, Tu Lu, Géraldine Seydoux
Software Mentions: 2
Published: about 7 years ago

10.1534/g3.117.039586

The Saccharomyces cerevisiae Cdk8 Mediator Represses AQY1 Transcription by Inhibiting Set1p-Dependent Histone Methylation
Cited by: 5
Author(s): Michael J. Law, Michael A Finger
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4509-0

Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy
Cited by: 21
Author(s): Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L. Thomas, Alessandra Stella, J. L. Williams, Paolo Ajmone‐Marsan, Hasan Khatib
Software Mentions: 2
Published: almost 7 years ago

10.3389/fimmu.2020.00579

NCOR1 Orchestrates Transcriptional Landscapes and Effector Functions of CD4+ T Cells
Cited by: 10
Author(s): Daniela Hainberger, Valentina Stolz, Ci Zhu, Michael Schuster, Lena Müller, Patricia Hamminger, Ramona Rica, Darina Waltenberger, Marlis Alteneder, Thomas Krausgruber, Anastasiya Hladik, Sylvia Knapp, Christoph Bock, Michael Trauner, Michael A. Farrar, Wilfried Ellmeier
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.682094

H3K4me3 Histone ChIP-Seq Analysis Reveals Molecular Mechanisms Responsible for Neutrophil Dysfunction in HIV-Infected Individuals
Cited by: 3
Author(s): Paweł Piątek, Maciej Tarkowski, Magdalena Namiecińska, Agostino Riva, Marek Wieczorek, Sylwia Michlewska, Justyna Dulska, Małgorzata Domowicz, Małgorzata Majka Kulińska Michalska, Natalia Lewkowicz, Przemysław Lewkowicz
Software Mentions: 2
Published: over 3 years ago

10.1186/1756-8935-6-7

Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development
Cited by: 81
Author(s): Kelly Bush, Benjamin Yuen, Bonnie L. Barrilleaux, John W. Riggs, Henriette O’Geen, Rebecca Cotterman, Paul S. Knoepfler
Software Mentions: 2
Published: over 11 years ago

10.1038/s42003-020-1076-0

Reciprocal H3.3 gene editing identifies K27M and G34R mechanisms in pediatric glioma including NOTCH signaling
Cited by: 28
Author(s): Kuang-Yui Michael Chen, Kelly Bush, Rachel Herndon Klein, Vanessa Cervantes, Nichole Lewis, Aasim Naqvi, Ángel M. Carcaboso, Mirna Lechpammer, Paul S. Knoepfler
Software Mentions: 2
Published: over 4 years ago

10.1016/j.celrep.2018.07.077

Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming
Cited by: 28
Author(s): Anna D. Senft, Ita Costello, Hamish W King, Arne W. Mould, Elizabeth K. Bikoff, Elizabeth J. Robertson
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0098501

Rif1 Regulates Initiation Timing of Late Replication Origins throughout the S. cerevisiae Genome
Cited by: 84
Author(s): Jared M. Peace, Anna Ter‐Zakarian, Oscar M. Aparicio
Software Mentions: 2
Published: over 10 years ago

Projects: bioconductor: DiffBind

Papers Mentioning DiffBind 217