pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1038/s41598-018-36927-7

High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue
Cited by: 23
Author(s): Saori Fujiwara, Songjoon Baek, Lyuba Varticovski, Sohyoung Kim, Gordon L. Hager
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-41672-6

Utilization of NGS technologies to investigate transcriptomic and epigenomic mechanisms in trastuzumab resistance
Cited by: 7
Author(s): Miguel Nava, Pranabananda Dutta, Robin Farias‐Eisner, Jaydutt V. Vadgama, Yanyuan Wu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-43021-z

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages
Cited by: 27
Author(s): Kazuhide Watanabe, Ye Liu, Shuhei Noguchi, Madeleine Murray, Jen-Chien Chang, Mami Kishima, Hajime Nishimura, Kosuke Hashimoto, Aki Minoda, Harukazu Suzuki
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-47521-w

A principled strategy for mapping enhancers to genes
Cited by: 13
Author(s): Dongkyeong Kim, Hongjoo An, Randall S. Shearer, Mohamed Sharif, Chuandong Fan, Jinok Choi, Sun Hwa Ryu, Yungki Park
Software Mentions: 2
Published: over 5 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

10.1038/s41598-019-55692-9

Characterization of cancer omics and drug perturbations in panels of lung cancer cells
Cited by: 13
Author(s): Ayako Suzuki, Keiichi Onodera, Kazuma Matsui, Masahide Seki, Hiroyasu Esumi, Tomoyoshi Soga, Sumio Sugano, Takashi Kohno, Yutaka Suzuki, Katsuya Tsuchihara
Software Mentions: 2
Published: almost 5 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

10.1099/mgen.0.000031

Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073
Cited by: 14
Author(s): Heer H. Mehta, Yuxuan Liu, Michael Q. Zhang, Stephen Spiro
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-020-76574-5

Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay
Cited by: 9
Author(s): Haiyan Yu, Hongwei Wu, Fengping Zheng, Chaowei Zhu, Yin Li, Weier Dai, Dongzhou Liu, Donge Tang, Xiaoping Hong, Yong Dai
Software Mentions: 2
Published: about 4 years ago

10.1016/j.mex.2020.101165

High-performance method for identification of super enhancers from ChIP-Seq data with configurable cloud virtual machines
Cited by: 5
Author(s): Н. Н. Орлова, Olga V. Bogatova, А. В. Орлов
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-79601-7

Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells
Cited by: 10
Author(s): Kylie Hin-Man Mak, Yuk Man Lam, Ray Kit Ng
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-83431-6

Retinoic acid regulates erythropoietin production cooperatively with hypoxia-inducible factors in human iPSC-derived erythropoietin-producing cells
Cited by: 1
Author(s): Naoko Katagiri, Hirofumi Hitomi, Shin-Ichi Mae, Maki Kotaka, Lei Li, Takuya Yamamoto, Akira Nishiyama, Kenji Osafune
Software Mentions: 2
Published: almost 4 years ago

10.26508/lsa.201900529

Oscillatory cAMP signaling rapidly alters H3K4 methylation
Cited by: 5
Author(s): Tyler C. Huff, Vladimir Camarena, David W. Sant, Zachary Wilkes, Derek Van Booven, Allegra T. Aron, Ryan K Muir, Adam R. Renslo, Christopher J. Chang, Paula V. Monje, Gaofeng Wang
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21051819

Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?
Cited by: 11
Author(s): Xiaoru Fan, Jingguang G. Chen, Yufeng Wu, Chee How Teo, Guohua Xu, Xing Fan
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21239052

Impact of AHR Ligand TCDD on Human Embryonic Stem Cells and Early Differentiation
Cited by: 4
Author(s): Indrek Teino, Antti Matvere, Martin Pook, Inge Varik, Laura Pajusaar, Keyt Uudeküll, Helen Vaher, Annika Trei, Arnold Kristjuhan, Tõnis Org, Toivo Maimets
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-89852-7

Identification of a PadR-type regulator essential for intracellular pathogenesis of Burkholderia pseudomallei
Cited by: 1
Author(s): Ian McMillan, Michael H. Norris, Jan Zarzycki-Siek, Yun Heacock-Kang, Zhenxin Sun, Bradley R. Borlee, Tung T. Hoang
Software Mentions: 2
Published: over 3 years ago

10.26508/lsa.201800115

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors
Cited by: 40
Author(s): Abhishek A. Singh, Karianne Schuurman, Ekaterina Nevedomskaya, Suzan Stelloo, Simon Linder, Marjolein Droog, Yongsoo Kim, Joyce Sanders, Henk van der Poel, Andries M. Bergman, Lodewyk Wessels, Wilbert Zwart
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-021-96488-0

Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation
Cited by: 5
Author(s): Nadezhda E. Vorobyeva, Maksim Erokhin, Darya Chetverina, А. Н. Краснов, M. Yu. Mazina
Software Mentions: 2
Published: over 3 years ago

10.26508/lsa.201900516

Endogenous epitope-tagging of Tet1, Tet2 and Tet3 identifies TET2 as a naïve pluripotency marker
Cited by: 13
Author(s): Raphaël Pantier, Tülin Tatar, Douglas Colby, Ian Chambers
Software Mentions: 2
Published: about 5 years ago

10.1038/s41375-018-0184-z

Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism
Cited by: 18
Author(s): James B. Studd, Minjun Yang, Zhenhua Li, Jayaram Vijayakrishnan, Yi Lü, Allen Eng Juh Yeoh, Kajsa Paulsson, Richard S. Houlston
Software Mentions: 2
Published: over 6 years ago

10.7150/thno.35882

HIF-1α/Wnt signaling-dependent control of gene transcription regulates neuronal differentiation of glioblastoma stem cells
Cited by: 28
Author(s): Daniele Boso, Elena Rampazzo, Carlo Zanon, Silvia Bresolin, Francesca Maule, Elena Porcù, Alice Cani, Alessandro Della Puppa, Luca Trentin, Giuseppe Basso, Luca Persano
Software Mentions: 2
Published: almost 6 years ago

10.7150/thno.49345

IGF2BP1 overexpression stabilizes PEG10 mRNA in an m6A-dependent manner and promotes endometrial cancer progression
Cited by: 90
Author(s): Lin Zhang, Yicong Wan, Zihan Zhang, Yi Jiang, Zhifeng Gu, Xiaoling Ma, Song Nie, Jing Yang, Jinghe Lang, Wenjun Cheng, Lan Zhu
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41416-021-01499-3

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

10.1128/mBio.01272-17

HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail
Cited by: 35
Author(s): Joanna Hołówka, Damian Trojanowski, Katarzyna Ginda, Bartosz Wojtaś, Bartłomiej Gielniewski, Dagmara Jakimowicz, Jolanta Zakrzewska‐Czerwińska
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.01130-18

Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi
Cited by: 51
Author(s): Ming-Jiuan Wu, Matthew E. Mead, Mi Kyung Lee, Erin M. Ostrem Loss, Sun Chang Kim, Antonis Rokas, Jae Hyuk Yu
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.01376-19

Chromatin Profiling of the Repetitive and Nonrepetitive Genomes of the Human Fungal Pathogen Candida albicans
Cited by: 19
Author(s): R. Jordan Price, Esther Weindling, Judith Berman, Alessia Buscaino
Software Mentions: 2
Published: about 5 years ago

10.1038/s41416-020-0907-6

BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene
Cited by: 12
Author(s): Takaya Yamamoto, Akiyuki Hirosue, Masafumi Nakamoto, Ryoji Yoshida, Junki Sakata, Yuichiro Matsuoka, Katsunobu Kawahara, Yuka Nagao, Masashi Nagata, Nobuhiro Takahashi, Akimitsu Hiraki, Masanori Shinohara, Mitsuyoshi Nakao, Noriko Saitoh, Hideki Nakayama
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.00142-20

Merkel Cell Polyomavirus DNA Replication Induces Senescence in Human Dermal Fibroblasts in a Kap1/Trim28-Dependent Manner
Cited by: 15
Author(s): Svenja Siebels, Manja Czech-Sioli, Michael Spohn, Claudia Schmidt, Juliane Theiß, Daniela Indenbirken, Thomas Günther, Adam Grundhoff, Nicole Fischer
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.00633-21

Genome Scale Analysis Reveals IscR Directly and Indirectly Regulates Virulence Factor Genes in Pathogenic <i>Yersinia</i>
Cited by: 4
Author(s): David Balderas, Erin L. Mettert, Hanh Lam, Rajdeep Banerjee, Tomas Gverzdys, Pablo Álvarez, Geetha Saarunya, N. Kyle Tanner, Adam Zoubedi, Yahan Wei, Patricia J. Kiley, Victoria Auerbuch
Software Mentions: 2
Published: over 3 years ago

10.1128/mBio.01067-21

Methyltransferase-like 3 Modulates Severe Acute Respiratory Syndrome Coronavirus-2 RNA N6-Methyladenosine Modification and Replication
Cited by: 43
Author(s): Xueyan Zhang, Haojie Hao, Li Ma, Yecheng Zhang, Xiao Hu, Zhe Chen, Di Liu, Jun Yuan, Zhangli Hu, Wuxiang Guan
Software Mentions: 2
Published: about 3 years ago

10.1042/BSR20210691

Histone H3K4me1 strongly activates the DNase I hypersensitive sites in super-enhancers than those in typical enhancers
Cited by: 2
Author(s): Young-Seok Kang, Jin Gu Kang, AeRi Kim
Software Mentions: 2
Published: over 3 years ago

10.7150/ijbs.45112

<i>Osblr8</i> orchestrates intrachromosomal loop structure required for maintaining stem cell pluripotency
Cited by: 6
Author(s): Yanbo Zhu, Zi Yan, Zhonghua Du, Shilin Zhang, Changhao Fu, Ying Meng, Wei Xue, Yizhuo Wang, Andrew R. Hoffman, Ji-Fan Hu, Jiuwei Cui, Wei Li
Software Mentions: 2
Published: almost 5 years ago

10.3390/biology9120428

ATP-Dependent Chromatin Remodeler CHD9 Controls the Proliferation of Embryonic Stem Cells in a Cell Culture Condition-Dependent Manner
Cited by: 4
Author(s): Hyunjin Yoo, Hyeonwoo La, Eun Joo Lee, Heejin Choi, Jeongheon Oh, Nguyen Xuan Thang, Kwonho Hong
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12575-017-0059-0

An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue
Cited by: 9
Author(s): Sarah-Anne David, Benoît Piégu, Christelle Hennequet-Antier, Maëlle Pannetier, Tiphaine Aguirre-Lavin, Sabine Crochet, Thierry Bordeau, Nathalie Couroussé, Aurélien Brionne, Yves Bigot, Anne Collin, Vincent Coustham
Software Mentions: 2
Published: about 7 years ago

10.1155/2016/3172093

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

10.1186/s13045-020-00933-y

The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma
Cited by: 17
Author(s): Samrat Roy Choudhury, Cody Ashby, Ruslana G. Tytarenko, Michael Bauer, Yan Wang, Shayu Deshpande, Judith Den, Carolina Schinke, Maurizio Zangari, Sharmilan Thanendrarajan, Faith E. Davies, Frits van Rhee, Gareth J. Morgan, Brian A Walker
Software Mentions: 2
Published: over 4 years ago

10.1242/bio.043638

Unique trophoblast chromatin environment mediated by the PcG protein SFMBT2
Cited by: 3
Author(s): Priscilla Tang, Kamelia Miri, Susannah Varmuza
Software Mentions: 2
Published: almost 6 years ago

10.4049/jimmunol.2000367

The Zinc Finger Protein Zbtb18 Represses Expression of Class I Phosphatidylinositol 3-Kinase Subunits and Inhibits Plasma Cell Differentiation
Cited by: 2
Author(s): Bingteng Xie, Tariq E. Khoyratty, Enas Abu-Shah, Pablo F. Céspedes, Andrew J. MacLean, Gabriela Pirgova, Zhiyuan Hu, Ahmed A. Ahmed, Michael L. Dustin, Irina A. Udalova, Tal I. Arnon
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/btab269

Bayesian information sharing enhances detection of regulatory associations in rare cell types
Cited by: 1
Author(s): Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
Software Mentions: 2
Published: over 3 years ago

10.1098/rsob.200050

Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer
Cited by: 3
Author(s): Maritere Urióstegui-Arcos, Rodrigo Aguayo‐Ortiz, María del Pilar Valencia-Morales, Erika Melchy-Pérez, Yvonne Rosenstein, Laura Domı́nguez, Mario Zurita
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btab274

Resolving diverse protein–DNA footprints from exonuclease-based ChIP experiments
Cited by: 3
Author(s): Anushua Biswas, Leelavati Narlikar
Software Mentions: 2
Published: over 3 years ago

10.1016/j.jmb.2020.10.008

TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues
Cited by: 2
Author(s): Raphaël Pantier, Nicholas P. Mullin, Elisa Hall-Ponselé, Ian Chambers
Software Mentions: 2
Published: about 4 years ago

10.1093/jmcb/mjz092

Isoform-specific involvement of Brpf1 in expansion of adult hematopoietic stem and progenitor cells
Cited by: 4
Author(s): Qiuping He, Ming Hong, Jincan He, Weixin Chen, Meng Zhao, Wei Zhao
Software Mentions: 2
Published: about 5 years ago

10.1186/s12870-018-1403-5

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)
Cited by: 37
Author(s): Tiago Capote, Pedro Barbosa, Ana Usié, A. M. Ramos, Vera Inácio, Ricardo J. Ordás, Sónia Gonçalves, Leonor Morais-Cecílio
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.44344

Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
Cited by: 102
Author(s): Christopher D. Todd, Özgen Deniz, Darren Taylor, Miguel R. Branco
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.13964

ERG signaling in prostate cancer is driven through PRMT5-dependent methylation of the Androgen Receptor
Cited by: 57
Author(s): Zineb Mounir, Joshua M. Korn, Thomas Westerling, Fallon Lin, C.A. Kirby, Markus Schirle, Gregg McAllister, Greg Hoffman, Nadire Ramadan, Anke Hartung, Feng Yuan, D. Randal Kipp, Christopher Quinn, Michelle Fodor, Jason R. Baird, Marie Schoumacher, Ronald A. Meyer, James Deeds, Gilles Buchwalter, Travis Stams, Nicholas Keen, William R. Sellers, Myles Brown, Raymond Pagliarini
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.35073

BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome
Cited by: 52
Author(s): Jackson A. Hoffman, Kevin W. Trotter, James M. Ward, Trevor Archer
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-019-0477-8

Transcriptomic and ChIP-sequence interrogation of EGFR signaling in HER2+ breast cancer cells reveals a dynamic chromatin landscape and S100 genes as targets
Cited by: 8
Author(s): Miguel Nava, Pranabananda Dutta, Nathan R. Zemke, Robin Farias‐Eisner, Jaydutt V. Vadgama, Yanyuan Wu
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.58029

Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network
Cited by: 32
Author(s): Shreyasi Mukherjee, Praneet Chaturvedi, Scott A. Rankin, Margaret Fish, Marcin Wlizla, Kitt D. Paraiso, Melissa MacDonald, Marc E. Rothenberg, Matthew T. Weirauch, Ira L. Blitz, Ken Wy. Cho, Aaron M. Zorn
Software Mentions: 2
Published: about 4 years ago

10.1186/s12920-021-01007-9

Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression
Cited by: 5
Author(s): Kerry E. Poppenberg, Haley R Zebraski, Naval Avasthi, Muhammad Waqas, Adnan H. Siddiqui, James N. Jarvis, Vincent M. Tutino
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-5274-9

Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model
Cited by: 0
Author(s): Can Wang, Shihua Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-6072-8

Deciphering epigenomic code for cell differentiation using deep learning
Cited by: 5
Author(s): Pengyu Ni
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.23250

Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator
Cited by: 44
Author(s): Isabel Nocedal, Eugenio Mancera, Alexander D. Johnson
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-020-06803-8

Replication origin location might contribute to genetic variability in Trypanosoma cruzi
Cited by: 7
Author(s): Christiane B. de Araujo, Júlia Pinheiro Chagas da Cunha, Davi Toshio Inada, Jeziel D. Damasceno, Alex Ranieri Jerônimo Lima, Priscila Mazzocchi Hiraiwa, Catarina A. Marques, Evonnildo Costa Gonçalves, Milton Yutaka Nishiyama-Jr, Richard McCulloch, Maria Carolina Elias
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-018-5326-1

Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming
Cited by: 12
Author(s): Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T. Smale, Kenneth S. Zaret, Kathrin Plath, Matteo Pellegrini
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-016-2428-5

Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms
Cited by: 26
Author(s): Nirmalya Saha, Mengying Liu, Ambikai Gajan, Lori A. Pile
Software Mentions: 2
Published: almost 9 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

10.3390/ijms22147454

Chromatin Dynamics and Gene Expression Response to Heat Exposure in Field-Conditioned versus Laboratory-Cultured Nematostella vectensis
Cited by: 4
Author(s): Eviatar Weizman, Mieka Rinsky, Noa Simon‐Blecher, Sarit Lampert-Karako, Orly Yaron, Ann M. Tarrant, Oren Levy
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-016-2468-x

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
Cited by: 23
Author(s): Susanta K. Behura, Joseph Sarro, Ping Li, Keshava Mysore, David W. Severson, Scott J. Emrich, Molly Duman-Scheel
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-5611-7

Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos
Cited by: 24
Author(s): Wei Zhu, Xiaocui Xu, Xinxin Wang, Jiang Liu
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.35621

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes
Cited by: 89
Author(s): Sheila S Teves, Luye An, Aarohi Bhargava-Shah, Liangqi Xie, Xavier Darzacq, Robert Tjian
Software Mentions: 2
Published: over 6 years ago

10.1111/acel.13147

PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome
Cited by: 9
Author(s): Ming Wang, Lulu Wang, Minxian Qian, Xiaolong Tang, Zuojun Liu, Yiwei Lai, Ying Ao, Yinghua Huang, Yuan Meng, Lei Shi, Peng Li, Xinyue Cao, Zimei Wang, Baoming Qin, Baohua Liu
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.25776

CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Cited by: 446
Author(s): Anders S. Hansen, Iryna Pustova, Claudia Cattoglio, Robert Tjian, Xavier Darzacq
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-017-4218-0

Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
Cited by: 7
Author(s): Mollee Dworkin, Shaojun Xie, Malay C. Saha, Jyothi Thimmapuram, Venu Kalavacharla
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-019-5966-9

Genome-wide localization of the polyphenol quercetin in human monocytes
Cited by: 8
Author(s): Dana Atrahimovich, Avraham O. Samson, Yifthah Barsheshet, Jacob Vaya, Soliman Khatib, Eli Reuveni
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-1258-1

Spatial features for Escherichia coli genome organization
Cited by: 19
Author(s): Ting Xie, Liang-Yu Fu, Qingyong Yang, Heng Xiong, H. Eric Xu, Bin-Guang Ma, Hongyu Zhang
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.14470

PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells
Cited by: 54
Author(s): María Inés Pérez Millán, Michelle L. Brinkmeier, Amanda H. Mortensen, Sally A. Camper
Software Mentions: 2
Published: over 8 years ago

10.1002/advs.202002680

USP38 Couples Histone Ubiquitination and Methylation via KDM5B to Resolve Inflammation
Cited by: 17
Author(s): Zhiyao Zhao, Zexiong Su, Puping Liang, Di Liu, Shuai Yang, Yiming Wu, Ling Ma, Jiayi Feng, Xiya Zhang, Chenglei Wu, Junjiu Huang, Jun Cui
Software Mentions: 2
Published: about 4 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

10.1186/s12864-020-07220-7

NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors
Cited by: 2
Author(s): Bronte Wen, Hyun Jun Jung, Lihe Chen, Fahad Saeed, Mark A. Knepper
Software Mentions: 2
Published: about 4 years ago

10.1186/s12863-021-00972-5

Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis
Cited by: 4
Author(s): Junlin Zhang, Bao Liu, Yan Song, Chen Yang, Jiao Fu, Jianquan Liu, Tao Ma, Zhenxiang Xi, Huanhuan Liu
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.22194

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity
Cited by: 48
Author(s): Federico Gaiti, Katia Jindrich, Selene L. Fernández-Valverde, Kathrein E. Roper, Bernard M. Degnan, Miloš Tanurdžić
Software Mentions: 2
Published: over 7 years ago

10.1038/s41422-021-00515-8

RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability
Cited by: 38
Author(s): Feng Xiong, Ruo–Yu Wang, Joo-Hyung Lee, Shenglan Li, Shin-Fu Chen, Z. Liao, Lana Al Hasani, Phuoc T. Nguyen, Xiaoyu Zhu, Joanna Krakowiak, Dung‐Fang Lee, Leng Han, Kuang‐Lei Tsai, Ying Liu, Wenbo Li
Software Mentions: 2
Published: over 3 years ago

10.1038/s41422-018-0113-8

A novel m6A reader Prrc2a controls oligodendroglial specification and myelination
Cited by: 222
Author(s): Rong Wu, Ang Li, Bao‐Fa Sun, Jianguang Sun, Jinhua Zhang, Ting Zhang, Yu‐Sheng Chen, Yujie Xiao, Yuhao Gao, Qingyang Zhang, Jun Ma, Xin Yang, Yuhe Liao, Weiyi Lai, Xiaolong Qi, Shukun Wang, Yousheng Shu, Hailin Wang, Fengchao Wang, Yun‐Gui Yang, Zengqiang Yuan
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells8111393

rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment
Cited by: 12
Author(s): Nickolai A. Tchurikov, Д. М. Федосеева, Elena S. Klushevskaya, I. Y. Slovohotov, V. R. Chechetkin, Yuri V. Kravatsky, О. В. Кретова
Software Mentions: 2
Published: about 5 years ago

10.1016/j.celrep.2018.11.100

LXR Suppresses Inflammatory Gene Expression and Neutrophil Migration through cis-Repression and Cholesterol Efflux
Cited by: 63
Author(s): D. G. Thomas, Amanda C. Doran, Panagiotis Fotakis, Marit Westerterp, Per Antonson, Hui Jiang, Xian Cheng Jiang, Jan Åke Gustafsson, Ira Tabas, Alan R. Tall
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.56922

Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins
Cited by: 18
Author(s): Steven Z DeLuca, Megha Ghildiyal, Liang-Yu Pang, Allan C. Spradling
Software Mentions: 2
Published: over 4 years ago

10.1186/s12915-021-00977-7

Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants
Cited by: 10
Author(s): Aiping Duan, Hong Wang, Yan Zhu, Qi Wang, Jing Zhang, Qi Hou, Yufei Xing, Jin‐Song Shi, Jinhua Hou, Zhaohui Qin, Zhaohong Chen, Zhihong Liu, Jingping Yang
Software Mentions: 2
Published: over 3 years ago

10.1186/s13148-021-01105-6

Chromatin accessibility changes at intergenic regions are associated with ovarian cancer drug resistance
Cited by: 7
Author(s): John Gallon, Erick Loomis, Edward Curry, Nicholas G. Martin, Leigh Brody, Ian Garner, Robert E. Brown, James M. Flanagan
Software Mentions: 2
Published: over 3 years ago

10.1186/s13148-019-0645-x

The hyper-activation of transcriptional enhancers in breast cancer
Cited by: 38
Author(s): Qinglan Li, Danya Wang, Lingao Ju, Jie Yao, Chuan Gao, Pin‐Ji Lei, Lianyun Li, Xiaolu Zhao, Min Wu
Software Mentions: 2
Published: over 5 years ago

10.1016/j.celrep.2016.11.028

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3
Cited by: 111
Author(s): Kamila M. Jozwik, Igor Chernukhin, Aurélien A. Sérandour, Sankari Nagarajan, Jason S. Carroll
Software Mentions: 2
Published: almost 8 years ago

10.1002/ctm2.416

C/EBPδ drives key endocrine signals in the human amnion at parturition
Cited by: 12
Author(s): Jiayue Lu, Wangsheng Wang, Qiong Zhou, Liuyi Ling, Ying Hao, Yun Sun, Leslie Myatt, Kang Sun
Software Mentions: 2
Published: over 3 years ago

10.1111/cpr.13080

Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming
Cited by: 4
Author(s): Liying Wang, Zhiliang Xu, Yunlong Wang, Chao Liu, Haixia Wei, Ruidan Zhang, Yinghong Chen, Lina Wang, Wenwen Liu, Shu-Hua Xiao, Wei Li
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-021-02153-7

Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment
Cited by: 18
Author(s): Jonathan Rubin, Jacob T. Stanley, Rutendo F Sigauke, Cecilia B. Levandowski, Zachary L. Maas, Jessica Westfall, Dylan J. Taatjes, Robin D. Dowell
Software Mentions: 2
Published: over 3 years ago

10.1038/s41421-019-0116-8

Pwp1 regulates telomere length by stabilizing shelterin complex and maintaining histone H4K20 trimethylation
Cited by: 5
Author(s): Yangyang Yu, Wenwen Jia, Yao Lyu, Dingwen Su, Mingliang Bai, Junwei Shen, Jing Qiao, Tong Han, Wenqiang Liu, Jiayu Chen, Wen Chen, Dan Ye, Xudong Guo, Shifeng Zhu, Jiajie Xi, Rong Zhu, Xiaoping Wan, Shaorong Gao, Jiyue Zhu, Jiuhong Kang
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-020-01411-4

Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma
Cited by: 11
Author(s): Britney A. Helling, Débora R. Sobreira, Grace Hansen, Noboru Jo Sakabe, Kaixuan Luo, Christine Billstrand, Bharathi Laxman, Raluca Nicolae, Dan L. Nicolae, Yury A. Bochkov, James E. Gern, Marcelo A. Nóbrega, Steven R. White, Carole Ober
Software Mentions: 2
Published: about 4 years ago

10.1038/s41421-017-0004-z

Loss of ASXL1 in the bone marrow niche dysregulates hematopoietic stem and progenitor cell fates
Cited by: 21
Author(s): Peng Zhang, Zizhen Chen, Rong Li, Ying Guo, Hui Shi, Jie Bai, Hui Yang, Mengyao Sheng, Zhaomin Li, Zhuo Li, Jianping Li, Shi Chen, Weiping Yuan, Tao Cheng, Mingjiang Xu, Yuan Zhou, Feng Chun Yang
Software Mentions: 2
Published: almost 7 years ago

10.1038/s42003-021-02211-0

Functional in vivo characterization of sox10 enhancers in neural crest and melanoma development
Cited by: 6
Author(s): Rebecca L. Cunningham, Eva T. Kramer, Sophia K. DeGeorgia, Paula M. Godoy, Anna P. Zarov, Shayana Seneviratne, Vadim Grigura, Charles K. Kaufman
Software Mentions: 2
Published: over 3 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

10.1038/s42003-020-01403-4

ATAC-seq with unique molecular identifiers improves quantification and footprinting
Cited by: 15
Author(s): Tao Zhu, Keyan Liao, Rongfang Zhou, Chen Xia, Weibo Xie
Software Mentions: 2
Published: about 4 years ago

10.5936/csbj.201401002

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS
Cited by: 54
Author(s): Yong Yang, Justin M. Fear, Jianhong Hu, Irina Haecker, Lei Zhou, Rolf Renne, David C. Bloom, Lauren M. McIntyre
Software Mentions: 2
Published: almost 11 years ago

10.1016/j.csbj.2018.02.003

Computational Methods for Assessing Chromatin Hierarchy
Cited by: 20
Author(s): Pearl Chang, Moloya Gohain, Ming‐Ren Yen, Pao‐Yang Chen
Software Mentions: 2
Published: almost 7 years ago

10.1093/dnares/dsz004

FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets
Cited by: 4
Author(s): Shaoqiang Zhang, Ying Li, Xiangyun Wang, Zhengchang Su, Yong Chen
Software Mentions: 2
Published: over 5 years ago

10.1016/j.dib.2020.106365

Data of correlation analysis between the density of H3K4me3 in promoters of genes and gene expression: Data from RNA-seq and ChIP-seq analyses of the murine prefrontal cortex
Cited by: 1
Author(s): Vasiliy V. Reshetnikov, Polina E. Kisaretova, Nikita I. Ershov, T. I. Merkulova, Natalia P. Bondar
Software Mentions: 2
Published: almost 4 years ago

10.1093/database/bay140

RAEdb: a database of enhancers identified by high-throughput reporter assays
Cited by: 13
Author(s): Zena Cai, Ya Cui, Zhiying Tan, Gaihua Zhang, Zhongyang Tan, Xinlei Zhang, Yousong Peng
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/baab030

Integration of 1:1 orthology maps and updated datasets into Echinobase
Cited by: 8
Author(s): Saoirse Foley, Carolyn J Ku, Brad Arshinoff, Vaneet Lotay, Kamran Karimi, Peter D. Vize, Veronica F. Hinman
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.ydbio.2019.09.006

Enhancer activation by FGF signalling during otic induction
Cited by: 11
Author(s): Monica Tambalo, Maryam Anwar, Mustafa Ahmed, Andrea Streit
Software Mentions: 2
Published: almost 5 years ago

10.1242/dev.139261

iDamIDseq and iDEAR: An improved method and computational pipeline to profile chromatin-binding proteins
Cited by: 14
Author(s): José Arturo Gutierrez-Triana, Juan L. Mateo, David Ibberson, Soojin Ryu, Joachim Wittbrodt
Software Mentions: 2
Published: almost 9 years ago

10.1242/dev.178582

Canonical Notch signaling controls the early thymic epithelial progenitor cell state and emergence of the medullary epithelial lineage in fetal thymus development
Cited by: 24
Author(s): Dong Liu, Anastasia I. Kousa, Kathy E. O’Neill, Paul Rouse, Martyna Popis, Alison Farley, Simon R. Tomlinson, Svetlana Ulyanchenko, François Guillemot, Philip A. Seymour, Mette C. Jørgensen, Palle Serup, Ute Koch, Freddy Radtke, C. Clare Blackburn
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41419-020-2482-4

The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming
Cited by: 11
Author(s): Wanhua Xie, Michaela Miehe, Sandra D. Laufer, Steven A. Johnsen
Software Mentions: 2
Published: over 4 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203