pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1186/s12284-021-00515-7

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling
Cited by: 5
Author(s): Chao Zhou, Xiaoyun Liu, Xinglei Li, Hanlin Zhou, Sijia Wang, Yanfei Zhu, Yonghong Zhang, Sanhe Li, Aiqing You, Lei Zhou, Zhengquan He
Software Mentions: 3
Published: over 3 years ago

10.1016/j.xpro.2020.100187

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation
Cited by: 2
Author(s): Wei Xu, Ying Ye, Andrew D. Sharrocks, Wensheng Zhang, Xi Chen
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0228590

Genome-wide analysis of HOXC4 and HOXC6 regulated genes and binding sites in prostate cancer cells
Cited by: 8
Author(s): Zhifei Luo, Peggy J. Farnham
Software Mentions: 3
Published: almost 5 years ago

10.1111/mmi.12345

The <scp>APSES</scp> transcription factor <scp>Efg</scp>1 is a global regulator that controls morphogenesis and biofilm formation in <scp>C</scp>andida parapsilosis
Cited by: 42
Author(s): Leona A. Connolly, Alessandro Riccombeni, Zsuzsana Grózer, Linda Holland, Denise B. Lynch, David R. Andes, Attila Gácser, Geraldine Butler
Software Mentions: 3
Published: over 11 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

10.1038/sdata.2016.109

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development
Cited by: 47
Author(s): Pang Wei Koh, Rahul Sinha, Amira Barkal, Rachel M. Morganti, Angela C Chen, Irving L. Weissman, Lay Teng Ang, Anshul Kundaje, Kyle M. Loh
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.24859

MYCN acts as a direct co-regulator of p53 in MYCN amplified neuroblastoma
Cited by: 25
Author(s): Saurabh Agarwal, Giorgio Milazzo, Kimal Rajapakshe, R Bernardi, Zaowen Chen, Eveline Barberi, Jan Koster, Giovanni Perini, Cristian Coarfa, Jason M. Shohet
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00208-20

Combined RNAseq and ChIPseq Analyses of the BvgA Virulence Regulator of Bordetella pertussis
Cited by: 7
Author(s): Loïc Coutte, Rudy Antoine, Stéphanie Slupek, Luis Solans, Julien Derop, Amélie Bonnefond, David Hot, Camille Locht
Software Mentions: 3
Published: over 4 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

10.1002/bit.26891

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture
Cited by: 35
Author(s): Inmaculada Hernández, Heena Dhiman, Gerald Klanert, Vaibhav Jadhav, Norbert Auer, Michael Hanscho, Martina Baumann, Anna Esteve‐Codina, Marc Dabad, Jessica Gómez, Tyler Alioto, Angelika Merkel, Emanuele Raineri, Simon Heath, Daniel Rico, Nicole Borth
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.03457-20

The Transcription Factor Pdr802 Regulates Titan Cell Formation and Pathogenicity of Cryptococcus neoformans
Cited by: 10
Author(s): Júlia Catarina Vieira Reuwsaat, Daniel Paiva Agustinho, Heryk Motta, Andrew L. Chang, Holly Brown, Michael R. Brent, Lívia Kmetzsch, Tamara L. Doering
Software Mentions: 3
Published: over 3 years ago

10.1038/s41597-020-0556-x

Chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain
Cited by: 9
Author(s): Mingyue Wang, Yang Liu, Tinggang Wen, Weiwei Liu, Qionghua Gao, Jie Zhao, Zijun Xiong, Zhifeng Wang, Wei Jiang, Yeya Yu, Liang Wu, Yue Yuan, Xiaoyü Wei, Jiangshan Xu, Mengnan Cheng, Pei Zhang, Panyi Li, Yong Hou, Huanming Yang, Guojie Zhang, Qiye Li, Chuanyu Liu, Longqi Liu
Software Mentions: 3
Published: over 4 years ago

10.1038/s41408-021-00421-7

Myeloma-specific superenhancers affect genes of biological and clinical relevance in myeloma
Cited by: 11
Author(s): Yunlu Jia, Jianbiao Zhou, Tze King Tan, Tae-Hoon Chung, Regina Wan Ju Wong, Jing-Yuan Chooi, Julia S.L. Lim, Takaomi Sanda, Melissa Ooi, Sanjay de Mel, Cinnie Yentia Soekojo, Yongxia Chen, Enfan Zhang, Zhen Cai, Peng Shen, Jian Ruan, Wee‐Joo Chng
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.ccell.2020.03.022

C/EBPα and GATA-2 Mutations Induce Bilineage Acute Erythroid Leukemia through Transformation of a Neomorphic Neutrophil-Erythroid Progenitor
Cited by: 14
Author(s): Cristina Di Genua, Simona Valletta, Mario Buono, Bilyana Stoilova, Connor Sweeney, Alba Rodríguez-Meira, Amit Grover, Roy Drissen, Yiran Meng, Ryan Beveridge, Zahra Aboukhalil, Dimitris Karamitros, Mirjam E. Belderbos, Leonid Bystrykh, Supat Thongjuea, Paresh Vyas, Claus Nerlov
Software Mentions: 3
Published: over 4 years ago

10.1186/s12915-021-01114-0

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species
Cited by: 7
Author(s): Lianggang Huang, Xuejie Li, Lü Dong, Bin Wang, Li Pan
Software Mentions: 3
Published: about 3 years ago

10.7150/thno.39093

Genome-wide interaction target profiling reveals a novel Peblr20-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

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 8 years ago

10.3389/fonc.2020.00302

CAMKV Is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma
Cited by: 7
Author(s): Robyn T. Sussman, Jo Lynne Rokita, Kevin Huang, Pichai Raman, Komal S. Rathi, Daniel Martı́nez, Kristopher R. Bosse, Maria Lane, Lori S. Hart, Tricia R. Bhatti, Bruce Pawel, John M. Maris
Software Mentions: 3
Published: over 4 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: about 8 years ago

10.1016/j.celrep.2021.109349

IL-7R signaling activates widespread VH and DH gene usage to drive antibody diversity in bone marrow B cells
Cited by: 4
Author(s): Amanda Baizan-Edge, Bryony A. Stubbs, Michael J T Stubbington, Daniel J. Bolland, Kristina A. Tabbada, Simon Andrews, Anne E. Corcoran
Software Mentions: 3
Published: over 3 years ago

10.1096/fj.201902061RR

Histone ChIP‐Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell‐type specificity
Cited by: 14
Author(s): Kathleen Cheung, M.J. Barter, Julia Falk, Carole J. Proctor, Louise N. Reynard, David A. Young
Software Mentions: 3
Published: almost 5 years ago

10.3390/cells10061271

Nucleoporin TPR Affects C2C12 Myogenic Differentiation via Regulation of Myh4 Expression
Cited by: 3
Author(s): Jana Uhlířová, Lenka Šebestová, Karel Fišer, Tomáš Sieger, Jindřiška Fišerová, Pavel Hozák
Software Mentions: 3
Published: over 3 years ago

10.1016/j.celrep.2019.08.040

RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction
Cited by: 23
Author(s): Anetta Ptasińska, Anna Pickin, Salam A. Assi, Paulynn Suyin Chin, Luke Ames, Roberto Avellino, Stephan Gröschel, Ruud Delwel, Peter N. Cockerill, Cameron S. Osborne, Constanze Bonifer
Software Mentions: 3
Published: about 5 years ago

10.1186/1756-8935-7-33

Chromatin accessibility: a window into the genome
Cited by: 306
Author(s): Maria Tsompana, Michael Buck
Software Mentions: 3
Published: about 10 years ago

10.3390/cells9061435

Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats
Cited by: 13
Author(s): Yu‐Chin Lien, Paul Zhiping Wang, Xueqing Maggie Lu, Rebecca A. Simmons
Software Mentions: 3
Published: over 4 years ago

10.1016/j.isci.2021.102435

The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia
Cited by: 14
Author(s): Henny Maat, Tjerk Jan Atsma, Shanna M. Hogeling, Aida Rodríguez López, Jennifer Jaques, Mirjam Olthuis, Marcel P. de Vries, Chantal Gravesteijn, Annet Z. Brouwers-Vos, Nisha van der Meer, Suzan Datema, Jonas B Salzbrunn, Gerwin Huls, Roy Baas, Joost H.A. Martens, Vincent van den Boom, Jan Jacob Schuringa
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-96263-1

Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons
Cited by: 7
Author(s): César Meléndez-Ramírez, Raquel Cuevas-Diaz Duran, Tonatiuh Barrios-García, Mayela Giacoman-Lozano, Adolfo López-Ornelas, Jessica Herrera-Gamboa, Enrique Estudillo, Ernesto Soto-Reyes, Iván Velasco, Víctor Treviño
Software Mentions: 3
Published: over 3 years ago

10.1534/g3.115.019828

Enrichment of H3K9me2 on Unsynapsed Chromatin inCaenorhabditis elegansDoes Not Targetde NovoSites
Cited by: 14
Author(s): Yiqing Guo, Bing Yang, Yini Li, Xia Xu, Eleanor M. Maine
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-021-88003-2

Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation
Cited by: 5
Author(s): Jonathan Sobel, Claudiane Guay, Ofer Elhanani, Adriana Rodríguez-Trejo, Lisa Stoll, Véronique Menoud, Cécile Jacovetti, Michael D. Walker, Romano Regazzi
Software Mentions: 3
Published: over 3 years ago

10.1038/s41422-018-0074-y

Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis
Cited by: 228
Author(s): Yao Chen, Yuxuan Zheng, Yun Gao, Zhen Lin, Suming Yang, Tongtong Wang, Qiu Wang, Nannan Xie, Rong Hua, Mingxi Liu, Jiahao Sha, Michael D. Griswold, Jinsong Li, Fuchou Tang, Ming-Han Tong
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms21061993

Time-Course Transcriptome Study Reveals Mode of bZIP Transcription Factors on Light Exposure in Arabidopsis
Cited by: 15
Author(s): Y. Kurihara, Yuko Makita, Haruka Shimohira, Minami Matsui
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-017-04370-9

A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a
Cited by: 2
Author(s): Anna C. Aschenbrenner, Kevin Baßler, Mirco Brondolin, Lorenzo Bonaguro, Pilar Carrera, Kathrin Klee, Thomas Ulas, Joachim L. Schultze, Michael Hoch
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-81577-x

The combination of the tubulin binding small molecule PTC596 and proteasome inhibitors suppresses the growth of myeloma cells
Cited by: 3
Author(s): Yurie Nagai, Naoya Mimura, Ola Rizq, Yusuke Isshiki, Motohiko Oshima, Mohamed Rizk, Atsunori Saraya, Shuhei Koide, Yaeko Nakajima‐Takagi, Makiko Miyota, Tetsuhiro Chiba, Nagisa Oshima-Hasegawa, Tomoya Muto, Shokichi Tsukamoto, Shio Mitsukawa, Yusuke Takeda, Chikako Ohwada, Masahiro Takeuchi, Tohru Iseki, Chiaki Nakaseko, William Lennox, Josephine Sheedy, Marla Weetall, Koutaro Yokote, Atsushi Iwama, Emiko Sakaida
Software Mentions: 3
Published: almost 4 years ago

10.26508/lsa.202000654

A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition
Cited by: 4
Author(s): Mario Cocco, Matthew A. Care, Amel Saadi, Muna Al-Maskari, Gina M. Doody, Reuben Tooze
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms21041248

NCAPG Dynamically Coordinates the Myogenesis of Fetal Bovine Tissue by Adjusting Chromatin Accessibility
Cited by: 5
Author(s): Xin Hu, Yishen Xing, Xing Fu, Qiyuan Yang, Ling Ren, Yahui Wang, Qian Li, Junya Li, Lupei Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-017-13186-6

Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori
Cited by: 13
Author(s): Quan Zhang, Tingcai Cheng, Shengkai Jin, Youbing Guo, Yuqian Wu, Duolian Liu, Xiaomin Xu, Yueting Sun, Zhiqing Li, Huawei He, Qingyou Xia
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-020-74537-4

CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression
Cited by: 21
Author(s): Hui Yao, D. Ford Hannum, Yiwen Zhai, Sophie F. Hill, Ricardo D’Oliveira Albanus, Wenjia Lou, Jennifer Skidmore, Gilson J Sanchez, Alina Saiakhova, Stephanie Bielas, Peter C. Scacheri, Mats Ljungman, Stephen C. J. Parker, Donna M. Martin
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms20194951

Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module
Cited by: 26
Author(s): Nicholas Gladman, Yinping Jiao, Young Koung Lee, Lifang Zhang, Ratan Chopra, Michael Regulski, Gloria Burow, Chad Hayes, Shawn A. Christensen, Lavanya Dampanaboina, Junping Chen, John J. Burke, Doreen Ware, Zhanguo Xin
Software Mentions: 3
Published: about 5 years ago

10.3389/fbioe.2019.00427

A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
Cited by: 1
Author(s): Liu Hui, Tiantongfei Jiang, Shuyuan Wang, Xiang Chen, Xiaoyan Jin, Qi Wang, Xinhui Li, Jiaqi Yin, Tingting Shao, Yongsheng Li, Juan Xu, Qiong Wu
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-71447-3

Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells
Cited by: 8
Author(s): Christian F. Deschepper
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-69443-8

AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq
Cited by: 0
Author(s): Laura Arrigoni, F. Ferrari, Juliane Weller, Chiara Bella, Ulrike Bönisch, Thomas Manke
Software Mentions: 3
Published: over 4 years ago

10.1242/dev.199628

LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells
Cited by: 8
Author(s): Juli Liu, Sheng Liu, Lei Han, Sheng Yi, Yucheng Zhang, Il-man Kim, Jun Wan, Lei Yang
Software Mentions: 3
Published: over 3 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

10.1242/dev.190181

TCF7L2 regulates postmitotic differentiation programs and excitability patterns in the thalamus
Cited by: 13
Author(s): Marcin Andrzej Lipiec, Joanna Bem, Kamil Koziński, Chaitali Chakraborty, Joanna Urban-Ciećko, Tomasz Zajkowski, Michał Dąbrowski, Łukasz Mateusz Szewczyk, Ángel Toval, José Luis Ferrán, Andrzej Nagalski, M. Wisniewska
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.stem.2019.02.004

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance
Cited by: 66
Author(s): Jessica Bertolini, Rebecca Favaro, Yanfen Zhu, Miriam Pagin, Chew Yee Ngan, Chee-Hong Wong, Harianto Tjong, Marit W. Vermunt, Ben Martynoga, Cristiana Barone, Jessica Mariani, Marcos J. Cardozo, Noemí Tabanera, Federico Zambelli, Sara Mercurio, Sergio Ottolenghi, Paul Robson, Menno P. Creyghton, Paola Bovolenta, Giulio Pavesi, François Guillemot, Silvia K. Nicolis, Chia‐Lin Wei
Software Mentions: 3
Published: over 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

10.1038/s41598-018-29865-x

EPO does not promote interaction between the erythropoietin and beta-common receptors
Cited by: 18
Author(s): Karen S. Cheung Tung Shing, Sophie E. Broughton, Tracy L. Nero, Kevin R. Gillinder, Melissa Ilsley, Hayley S. Ramshaw, Angel F. Lopez, Michael D. W. Griffin, Michael W. Parker, Andrew C. Perkins, Urmi Dhagat
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-31101-5

KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons
Cited by: 33
Author(s): Zimei Wang, Vatsal Mehra, Matthew T. Simpson, Brian Maunze, Advaita Chakraborty, Lyndsey Holan, Erik Eastwood, Murray G. Blackmore, Ishwariya Venkatesh
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.33333

Zfp281 is essential for mouse epiblast maturation through transcriptional and epigenetic control of Nodal signaling
Cited by: 25
Author(s): Xin Huang, Sophie Balmer, Fan Yang, Miguel Fidalgo, Dan Li, Diana Guallar, Anna-Katerina Hadjantonakis, Jianlong Wang
Software Mentions: 3
Published: almost 7 years ago

10.1093/molbev/msab131

Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes
Cited by: 9
Author(s): Colin J. Shew, Paulina Carmona-Mora, Daniela C. Soto, Mira Mastoras, Elizabeth S. Roberts, Joseph Rosas, Dhriti Jagannathan, Gulhan Kaya, Henriette O’Geen, Megan Y. Dennis
Software Mentions: 3
Published: over 3 years ago

10.1186/s13072-017-0158-9

Genome-wide profiling of transcribed enhancers during macrophage activation
Cited by: 21
Author(s): Elena Denisenko, Reto Guler, Musa M. Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
Software Mentions: 3
Published: about 7 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

10.1186/s12943-020-01301-7

Targeting CDK7 suppresses super enhancer-linked inflammatory genes and alleviates CAR T cell-induced cytokine release syndrome
Cited by: 12
Author(s): Wei Ye, Chong Li, Huifang Bian, Wei Qian, Kaizhou Jin, Tianmin Xu, Xiaomao Guo, Lu Xia, Fengtao Su
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-34420-9

A neural network based model effectively predicts enhancers from clinical ATAC-seq samples
Cited by: 21
Author(s): Asa Thibodeau, Asli Uyar, Shubham Khetan, Michael L. Stitzel, Duygu Ucar
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-35868-5

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
Cited by: 11
Author(s): Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Franki Speleman, Katleen De Preter
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-36057-0

Chromatin accessibility identifies diversity in mesenchymal stem cells from different tissue origins
Cited by: 27
Author(s): Yen-Ting Ho, Takashi Shimbo, Edward Wijaya, Yuya Ouchi, Eiichi Takaki, Ryusuke Yamamoto, Yasushi Kikuchi, Yasufumi Kaneda, Katsuto Tamai
Software Mentions: 3
Published: almost 6 years ago

10.3390/genes11010003

Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq
Cited by: 28
Author(s): Nicole B. Kingsley, Colin Kern, Catherine Creppe, Erin N. Hales, Huaijun Zhou, Theodore S. Kalbfleisch, James N. MacLeod, Jessica L Petersen, Carrie J. Finno, Rebecca R. Bellone
Software Mentions: 3
Published: almost 5 years ago

10.3390/ani9080523

Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs
Cited by: 12
Author(s): Haifei Wang, Yang Li, Huan Qu, Hanping Feng, Shenglong Wu, Wenbin Bao
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-61514-0

Proximity-dependent biotin labelling reveals CP190 as an EcR/Usp molecular partner
Cited by: 17
Author(s): M. Yu. Mazina, Rustam H. Ziganshin, Mikhail D. Magnitov, Anton Golovnin, Nadezhda E. Vorobyeva
Software Mentions: 3
Published: over 4 years ago

10.1007/s00401-020-02225-8

C11orf95-RELA reprograms 3D epigenome in supratentorial ependymoma
Cited by: 11
Author(s): Jacqueline Jufen Zhu, Nathaniel Jillette, Xiao Nan Li, Albert W. Cheng, Ching C. Lau
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-59469-3

Targeting Oncogenic Super Enhancers in MYC-Dependent AML Using a Small Molecule Activator of NR4A Nuclear Receptors
Cited by: 18
Author(s): S. Greg Call, Ryan P. Duren, Anil K. Panigrahi, Huu Lam Nguyen, Pablo R. Freire, Sandra L. Grimm, Cristian Coarfa, Orla M. Conneely
Software Mentions: 3
Published: almost 5 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

10.1186/s12915-019-0687-8

Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations
Cited by: 45
Author(s): Lingzhao Fang, Shuli Liu, Mei Liu, Xiaolong Kang, Shudai Lin, Bingjie Li, Erin E. Connor, VI Ransom L. Baldwin, Albert Tenesa, Li Ma, George E. Liu, Congjun Li
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-56277-2

ONECUT2 overexpression promotes RAS-driven lung adenocarcinoma progression
Cited by: 20
Author(s): Qingyang Ma, Kai Wu, Hui Li, Huichun Li, Yong Zhu, Guohong Hu, Landian Hu, Xiangyin Kong
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-45841-5

Etv2 transcriptionally regulates Yes1 and promotes cell proliferation during embryogenesis
Cited by: 12
Author(s): Bhairab N. Singh, Wuming Gong, Satyabrata Das, Joshua W. M. Theisen, Javier Sierra-Pagan, Demetris Yannopoulos, Erik Skie, Pruthvi Shah, Mary G. Garry, Daniel J. Garry
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.17462

Klf5 regulates muscle differentiation by directly targeting muscle-specific genes in cooperation with MyoD in mice
Cited by: 59
Author(s): Shinichiro Hayashi, Ichiro Manabe, Yumi Suzuki, Frédéric Relaix, Yumiko Oishi
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0233044

Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes
Cited by: 13
Author(s): Shay Hantisteanu, Yosef Dicken, Varda Negreanu, Dalia Goldenberg, Ori Brenner, Dena Leshkowitz, Joseph Lotem, Ditsa Levanon, Yoram Groner
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers12020458

Misregulation of ELK1, AP1, and E12 Transcription Factor Networks Is Associated with Melanoma Progression
Cited by: 5
Author(s): Komudi Singh, Michelle A. Baird, R. Fischer, Vijender Chaitankar, Fayaz Seifuddin, Yunching Chen, Ilker Tunc, Clare M. Waterman, Mehdi Pirooznia
Software Mentions: 3
Published: almost 5 years ago

10.1534/genetics.119.302929

Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes
Cited by: 7
Author(s): Wei Zhou, Michael W. Dorrity, Kerry L Bubb, Christine Queitsch, Stanley Fields
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.59464

Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function
Cited by: 18
Author(s): Yinan Li, Anthony Osuma, Edgar Correa, Munachiso A Okebalama, Pauline Dao, Olivia Gaylord, Jihad Aburas, Priota Islam, André Ex Brown, Paschalis Kratsios
Software Mentions: 3
Published: about 4 years ago

10.18632/oncotarget.6922

Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes
Cited by: 88
Author(s): Terri L. Messier, Jonathan A. R. Gordon, Joseph R. Boyd, Coralee E. Tye, Gillian Browne, Janet L. Stein, Jane B. Lian
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0238742

A hypothetical trivalent epigenetic code that affects the nature of human ESCs
Cited by: 2
Author(s): Yasuhisa Ishikawa, Kenta Nakai
Software Mentions: 3
Published: about 4 years ago

10.1093/database/bav050

A general concept for consistent documentation of computational analyses
Cited by: 9
Author(s): Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12915-018-0573-9

UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells
Cited by: 32
Author(s): Cong Xiong, Zengqi Wen, Juan Yu, Jun Chen, Chao-Pei Liu, Xiaodong Zhang, Ping Chen, Rui-Ming Xu, Guohong Li
Software Mentions: 3
Published: about 6 years ago

10.1038/s41419-019-1792-x

The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes
Cited by: 32
Author(s): Noelia Luna-Peláez, Rosana March-Díaz, María Ceballos-Chávez, José A. Guerrero-Martínez, Paolo Grazioli, Pablo García-Gutiérrez, Thomas Vaccari, Valentina Massa, José Carlos Castañeda Reyes, Mario García-Domínguez
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0215340

Identification of ChIP-seq and RIME grade antibodies for Estrogen Receptor alpha
Cited by: 8
Author(s): Silvia-E. Glont, Evangelia K. Papachristou, Ashley Sawle, Kelly A. Holmes, Jason S. Carroll, Rasmus Siersbæk
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.44306

PAX8 regulon in human ovarian cancer links lineage dependency with epigenetic vulnerability to HDAC inhibitors
Cited by: 31
Author(s): Kaixuan Shi, Xiang Yin, Mei-Chun Cai, Yan Yan, Chenqiang Jia, Ping Ma, Shengzhe Zhang, Zhenfeng Zhang, Zhenyu Gu, Meiying Zhang, Wen Di, Guanglei Zhuang
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.561804

CYP27B1 Downregulation: A New Molecular Mechanism Regulating EZH2 in Ovarian Cancer Tumorigenicity
Cited by: 7
Author(s): Xiao Huo, Hengzi Sun, Qiuhong Qian, Xiangwen Ma, Peng Peng, Mei Yu, Ying Zhang, Jiaxin Yang, Dongyan Cao, Ting Gui, Keng Shen
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-017-1173-7

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
Cited by: 70
Author(s): Warren A. Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Simon Maguire, Elodie Boulier, Adriana Redensek, Stephen Watt, Avik Datta, Laura Clarke, Paul Flicek, Daniel Mead, Dirk S. Paul, Stephan Beck, Guillaume Bourque, Mark Lathrop, André Tchernof, Marie‐Claude Vohl, Florence Demenais, Isabelle Pin, Kate Downes, Hendrick G. Stunnenberg, Nicole Soranzo, Tomi Pastinen, Elin Grundberg
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2021.717555

Systematic Analysis of Monoallelic Gene Expression and Chromatin Accessibility Across Multiple Tissues in Hybrid Mice
Cited by: 0
Author(s): Weizheng Liang, Xudong Zou, Guipeng Li, Shaojie Zhou, Chi Tian, Bernhard Schaefke
Software Mentions: 3
Published: about 3 years ago

10.1186/s13072-019-0325-2

Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans
Cited by: 10
Author(s): Alexis V. Stutzman, April S. Liang, Vera Beilinson, Kohta Ikegami
Software Mentions: 3
Published: almost 5 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

10.1186/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

10.1186/s13072-016-0051-y

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis
Cited by: 51
Author(s): Takashi Urahama, Akihito Harada, Kazuhira Maehara, Naoki Horikoshi, Koichi Sato, Yuko Sato, Koji Shiraishi, Norihiro Sugino, Akihisa Osakabe, Hiroaki Tachiwana, Wataru Kagawa, Hiroshi Kimurâ, Yasuyuki Ohkawa, Hitoshi Kurumizaka
Software Mentions: 3
Published: almost 9 years ago

10.3389/fcell.2021.615098

Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation
Cited by: 2
Author(s): Chih-Yi Yang, Rita Jui-Hsien Lu, Ming-Kang Lee, Felix Shih-Hsian Hsiao, Ya-Ping Yen, Chi‐Feng Cheng, Pu-Sheng Hsu, Yi-Tzang Tsai, Shih‐Kuo Chen, I-Hsuan Liu, Pao‐Yang Chen, Shau-Ping Lin
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.29518

Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state
Cited by: 32
Author(s): Yixuan Wang, Chengchen Zhao, Zhenzhen Hou, Yuanyuan Yang, Yan Bi, Hong Wang, Yong Zhang, Shaorong Gao
Software Mentions: 3
Published: almost 7 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

10.1186/s13072-019-0312-7

Folate deficiency induced H2A ubiquitination to lead to downregulated expression of genes involved in neural tube defects
Cited by: 16
Author(s): Pei Pei, Xiyue Cheng, Jianhua Yu, Jinying Shen, Xue Li, Jianxin Wu, Shan Wang, Ting Zhang
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-017-1376-y

SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells
Cited by: 26
Author(s): Özgen Deniz, Lorenzo de la Rica, Kevin Cheng, Dominik Spensberger, Miguel R. Branco
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13059-018-1430-4

OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks
Cited by: 46
Author(s): Tingting Li, Lumeng Jia, Yong Cao, Qing Chen, Cheng Li
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.18290

Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
Cited by: 109
Author(s): Chan-Wang Jerry Lio, Jiayuan Zhang, Edahí González-Avalos, Patrick G. Hogan, Xing Chang, Anjana Rao
Software Mentions: 3
Published: about 8 years ago

10.1186/s13059-018-1463-8

Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human
Cited by: 38
Author(s): Karol Szlachta, Ryan G. Thys, Naomi D Atkin, Levi C. T. Pierce, Stefan Bekiranov, Yuh‐Hwa Wang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-018-1464-7

DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells
Cited by: 109
Author(s): Tianpeng Gu, Xueqiu Lin, Shay Cullen, Min Luo, Mira Jeong, Marcos R.H. Estécio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Qi, Jiajia Chen, Michael Kyba, Yun Huang, Taiping Chen, Wei Li, Margaret A. Goodell
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-018-1483-4

Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline
Cited by: 42
Author(s): Vera B. Kaiser, Colin A. Semple
Software Mentions: 3
Published: over 6 years ago

10.15252/emmm.201911099

Vulnerability of drug‐resistant EML4‐ALK rearranged lung cancer to transcriptional inhibition
Cited by: 9
Author(s): Athanasios R. Paliouras, Marta Buzzetti, Lei Shi, Ian J. Donaldson, Peter Magee, Sudhakar Sahoo, Hui-Sun Leong, Matteo Fassan, Matthew Carter, Gianpiero Di Leva, Matthew Krebs, Fiona Blackhall, Christine M. Lovly, Michela Garofalo
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.37084

FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment
Cited by: 21
Author(s): Emilia Dimitrova, Takashi Kondo, Angelika Feldmann, Manabu Nakayama, Haruhiko Koseki, Rebecca Konietzny, Benedikt M. Kessler, Robert J. Klose
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.51754

Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells
Cited by: 20
Author(s): Ana Filipa Domingues, Rashmi Kulkarni, George Giotopoulos, Shikha Gupta, Laura Vinnenberg, Liliana Arede, Elena Foerner, Mitra Khalili, Rita Romano Adao, Ayona Johns, Sophie Tan, Keti Zeka, Brian J. P. Huntly, Sudhakaran Prabakaran, Cristina Pina
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.53916

Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network
Cited by: 36
Author(s): Isabella V. Soluri, Lauren M Zumerling, Omar A Payan Parra, Eleanor G. Clark, Shelby A. Blythe
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-018-1531-0

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
Cited by: 54
Author(s): Yu Guo, Andrew A. Perez, Dennis J. Hazelett, Gerhard A. Coetzee, Suhn Kyong Rhie, Peggy J. Farnham
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-021-07373-z

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data
Cited by: 2
Author(s): Henriette Miko, Yunjiang Qiu, Bjoern Gaertner, Maike Sander, Uwe Ohler
Software Mentions: 3
Published: almost 4 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203