pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1534/g3.115.022889

Generation of a Maize B Centromere Minimal Map Containing the Central Core Domain
Cited by: 2
Author(s): Nathanael A. Ellis, Ryan N. Douglas, Caroline E. Jackson, James A. Birchler, R. Kelly Dawe
Software Mentions: 1
Published: almost 9 years ago

10.3390/ijms19123987

Therapeutic Vulnerabilities in FLT3-Mutant AML Unmasked by Palbociclib
Cited by: 12
Author(s): Iris Z. Uras, Barbara Maurer, Sofie Nebenfuehr, Markus Zojer, Peter Valent, Veronika Sexl
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms20071704

Improved Prediction of Regulatory Element Using Hybrid Abelian Complexity Features with DNA Sequences
Cited by: 3
Author(s): Chengchao Wu, Jin Chen, Yunxia Liu, Xuehai Hu
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-31835-2

Targeting a phospho-STAT3-miRNAs pathway improves vesicular hepatic steatosis in an in vitro and in vivo model
Cited by: 13
Author(s): Laura Belloni, Silvia Di Cocco, Francesca Guerrieri, Abigail Nunn, Silvia Piconese, Debora Salerno, Barbara Testoni, Claudio Pulito, Federica Mori, Matteo Pallocca, Andrea Sacconi, Elisa Vivoli, Fabio Marra, Sabrina Strano, Giovanni Blandino, Massimo Levrero, Natalia Pediconi
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-64655-4

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection
Cited by: 14
Author(s): Dongpin Oh, J. Seth Strattan, Junho K. Hur, José Bento, Alexander Urban, Giltae Song, J. Michael Cherry
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms9030485

Genome-Wide Mapping Reveals Complex Regulatory Activities of BfmR in Pseudomonas aeruginosa
Cited by: 10
Author(s): Kebin Fan, Qiao Cao, Lefu Lan
Software Mentions: 1
Published: over 3 years ago

10.3390/microorganisms9020344

Identification of Novel phoP-phoQ Regulated Genes that Contribute to Polymyxin B Tolerance in Pseudomonas aeruginosa
Cited by: 18
Author(s): Baopeng Yang, Chang Liu, Xiaolei Pan, Wei Fu, Zheng Fan, Yongxin Jin, Fang Bai, Zhihui Cheng, Weihui Wu
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-018-24956-1

Mouse medulloblastoma driven by CRISPR activation of cellular Myc
Cited by: 16
Author(s): BaoHan T. Vo, Jin Ah Kwon, Chunliang Li, David Finkelstein, Beisi Xu, Brent A. Orr, Charles J. Sherr, Martine F. Roussel
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-23774-9

Global dynamics of stage-specific transcription factor binding during thymocyte development
Cited by: 12
Author(s): Takamitsu Hosoya, Ricardo D’Oliveira Albanus, John Hensley, Greggory Myers, Yasuhiro Kyono, Jacob O. Kitzman, Stephen C. J. Parker, James Douglas Engel
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers13040764

IRF8 Is an AML-Specific Susceptibility Factor That Regulates Signaling Pathways and Proliferation of AML Cells
Cited by: 12
Author(s): Franziska Liss, Miriam Frech, Ying Wang, Gavin Giel, Sabrina Fischer, Clara Simon, Lisa Marie Weber, Andrea Nist, Thorsten Stiewe, Andreas Neubauer, Andreas Burchert, Robert Liefke
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-70610-0

The ubiquitin ligase Cullin-1 associates with chromatin and regulates transcription of specific c-MYC target genes
Cited by: 13
Author(s): Melanie Sweeney, Polina Iakova, Laure Maneix, Frank Y. Shih, Hannah E. Cho, Ergün Sahin, André Catic
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-017-18106-2

Convergent microevolution of Cryptococcus neoformans hypervirulence in the laboratory and the clinic
Cited by: 29
Author(s): Samantha D. M. Arras, Kate L. Ormerod, Paige E. Erpf, Monica I. Espinosa, Alex C. Carpenter, Ross Blundell, Samantha R. Stowasser, Benjamin L. Schulz, Miloš Tanurdžić, James A. Fraser
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-14389-7

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin
Cited by: 39
Author(s): Asa Thibodeau, Eladio J. Márquez, Dong-Guk Shin, Paola Vera-Licona, Duygu Ucar
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.25781

Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1
Cited by: 6
Author(s): William Hankey, Zhong Chen, Maxwell Bergman, Max O. Fernandez, Baris Hancioglu, Xun Lan, Anil G. Jegga, Jie Zhang, Victor X. Jin, Bruce J. Aronow, Qianben Wang, Joanna Groden
Software Mentions: 1
Published: over 6 years ago

10.1016/j.molcel.2020.03.013

Cohesin Causes Replicative DNA Damage by Trapping DNA Topological Stress
Cited by: 36
Author(s): Nicola E. Minchell, Andrea Keszthelyi, Jonathan Baxter
Software Mentions: 1
Published: over 4 years ago

10.1186/s40478-020-01092-4

Effects of H3.3G34V mutation on genomic H3K36 and H3K27 methylation patterns in isogenic pediatric glioma cells
Cited by: 11
Author(s): Tina Huang, Andrea Piunti, Jin Qi, Marc A. Morgan, Elizabeth Bartom, Ali Shilatifard, Amanda Saratsis
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-017-11800-1

Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s
Cited by: 56
Author(s): Jong-Hun Lee, Sung‐Joon Park, Kenta Nakai
Software Mentions: 1
Published: about 7 years ago

10.1038/cr.2016.4

SIRT6 safeguards human mesenchymal stem cells from oxidative stress by coactivating NRF2
Cited by: 242
Author(s): Huize Pan, Di Guan, Xiaomeng Liu, Jingyi Li, Lixia Wang, Jun Wu, Junzhi Zhou, Weizhou Zhang, Rui Ren, Weiqi Zhang, Ying Liu, Jiping Yang, Ying Hao, Tingting Yuan, Gang Yuan, Hu Wang, Zhenyu Ju, Zhiyong Mao, Jian Li, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-020-80650-1

The negative elongation factor NELF promotes induced transcriptional response of Drosophila ecdysone-dependent genes
Cited by: 12
Author(s): M. Yu. Mazina, Elena V. Kovalenko, Nadezhda E. Vorobyeva
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-017-06859-9

Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation
Cited by: 16
Author(s): Andrew C. Nelson, Arne W. Mould, Elizabeth K. Bikoff, Elizabeth J. Robertson
Software Mentions: 1
Published: over 7 years ago

10.1038/cr.2017.55

5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader
Cited by: 559
Author(s): Xin Yang, Ying Yang, Bao‐Fa Sun, Yu‐Sheng Chen, Jiawei Xu, Weiyi Lai, Ang Li, Xing Wang, Devi Prasad Bhattarai, Wen Xiao, Hui Sun, Qin Zhu, Haili Ma, Samir Adhikari, Min Sun, Yajuan Hao, Bing Zhang, Chih-Hsien Huang, Niu Huang, Guibin Jiang, Yongliang Zhao, Hailin Wang, Yingpu Sun, Yun‐Gui Yang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-79539-w

Histone acetyltransferase PfGCN5 regulates stress responsive and artemisinin resistance related genes in Plasmodium falciparum
Cited by: 15
Author(s): Mukul Rawat, Abhishek Kanyal, Aishwarya Sahasrabudhe, Shruthi S. Vembar, José-Juan Lopez-Rubio, Krishanpal Karmodiya
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-79666-4

A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition
Cited by: 9
Author(s): Federico Pecori, Ikuko Yokota, Hisatoshi Hanamatsu, Taichi Miura, Chika Ogura, Hayato Ota, Yoshihiro Furukawa, Shinya Oki, Kazuo Yamamoto, Osamu Yoshie, Shoko Nishihara
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-017-04506-x

CTCF binding landscape in jawless fish with reference to Hox cluster evolution
Cited by: 34
Author(s): Mitsutaka Kadota, Yuichiro Hara, Kaori Tanaka, Wataru Takagi, Chiharu Tanegashima, Osamu Nishimura, Shigehiro Kuraku
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-81975-1

Epigenetic silencing directs expression heterogeneity of stably integrated multi-transcript unit genetic circuits
Cited by: 7
Author(s): Jan Zimak, Zachary W. Wagoner, Nellie Nelson, Brooke Waechtler, Hana Schlosser, Morgan Kopecky, Jie Wu, Weian Zhao
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpsyt.2019.00362

Potential Mechanism for HIV-Associated Depression: Upregulation of Serotonin Transporters in SIV-Infected Macaques Detected by 11C-DASB PET
Cited by: 9
Author(s): Swati Shah, Sanhita Sinharay, Kenta Matsuda, William Schreiber-Stainthorp, Siva Muthusamy, Dianne Lee, Paul Wakim, Vanessa M. Hirsch, Avindra Nath, Michele Di Mascio, Dima A. Hammoud
Software Mentions: 1
Published: over 5 years ago

10.1038/s41421-019-0088-8

Optimizing genome editing strategy by primer-extension-mediated sequencing
Cited by: 57
Author(s): Jianhang Yin, Mengzhu Liu, Yang Liu, Jinchun Wu, Tingting Gan, Weiwei Zhang, Yinghui Li, Yaxuan Zhou, Jiazhi Hu
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2019.00982

Genome-Wide Identification of SNAC1-Targeted Genes Involved in Drought Response in Rice
Cited by: 31
Author(s): Li Xu, Yu Sun Chang, Siqi Ma, Jianqiang Shen, Honghong Hu, Lizhong Xiong
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-03534-x

Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis
Cited by: 9
Author(s): Utkarsh Raj, Imlimaong Aier, Rahul Semwal, Pritish Kumar Varadwaj
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms21072294

MYC-Associated Factor MAX is a Regulator of the Circadian Clock
Cited by: 10
Author(s): Olga Blaževitš, Nityanand Bolshette, Donatella Vecchio, Ana Guijarro, Ottavio Croci, Stefano Campaner, Benedetto Grimaldi
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-017-02547-w

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
Cited by: 46
Author(s): Lindsey Montefiori, Liana Hernandez, Zijie Zhang, Yoav Gilad, Carole Ober, Gregory E. Crawford, Marcelo A. Nóbrega, Noboru Jo Sakabe
Software Mentions: 1
Published: over 7 years ago

10.3390/cells9071661

Inhibition of HDAC1/2 Along with TRAP1 Causes Synthetic Lethality in Glioblastoma Model Systems
Cited by: 18
Author(s): Trang Nguyen, Yiru Zhang, Enyuan Shang, Chang Shu, Catarina M. Quinzii, Mike‐Andrew Westhoff, Georg Karpel‐Massler, Markus D. Siegelin
Software Mentions: 1
Published: over 4 years ago

10.3389/fpls.2021.712713

ALKBH10B, an mRNA m6A Demethylase, Modulates ABA Response During Seed Germination in Arabidopsis
Cited by: 14
Author(s): Jinming Tang, Junbo Yang, Hong-Chao Duan, Guifang Jia
Software Mentions: 1
Published: over 3 years ago

10.3389/fphar.2020.605967

The Role of Bone Morphogenetic Protein 9 in Nonalcoholic Fatty Liver Disease in Mice
Cited by: 6
Author(s): Qin-Juan Sun, Ling-Yan Cai, Jie Jian, Yalu Cui, Chia-Chi Flora Huang, Shuqing Liu, Jiasun Lu, Wei Wang, Xin Zeng, Li-Ye Zhong
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-95165-6

A CpG island promoter drives the CXXC5 gene expression
Cited by: 2
Author(s): Pelin Yaşar, Gizem Kars, Kerim Yavuz, Gamze Ayaz, Çerağ Oğuztüzün, Ecenaz Bilgen, Zeynep Suvacı, Özgül Persil Çetinkol, Tolga Can, Mesut Muyan
Software Mentions: 1
Published: over 3 years ago

10.1186/s13020-021-00502-6

Hierarchical chromatin features reveal the toxin production in Bungarus multicinctus
Cited by: 4
Author(s): Xuejiao Liao, Shuai Guo, Xiao Yin, Baosheng Liao, Mingqian Li, He Su, Qiushi Li, Jin Pei, Jihai Gao, Juan Lei, Xiwen Li, Zhixing Huang, Jiang Xu, Shilin Chen
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-017-00973-4

Dynamics of chromatin accessibility during TGF-β-induced EMT of Ras-transformed mammary gland epithelial cells
Cited by: 20
Author(s): Mayu Arase, Yusuke Tamura, Natsumi Kawasaki, Kazunobu Isogaya, Ryo Nakaki, Atsushi Mizutani, Sadami Tsutsumi, Hiroyuki Aburatani, Kohei Miyazono, Daizo Koinuma
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-97060-6

A prelude to the proximity interaction mapping of CXXC5
Cited by: 3
Author(s): Gamze Ayaz, Gizem Turan, Çağla Ece Olgun, Gizem Kars, Burcu Karakaya, Kerim Yavuz, Öykü Deniz Demiralay, Tolga Can, Mesut Muyan, Pelin Yaşar
Software Mentions: 1
Published: about 3 years ago

10.26508/lsa.201800108

BZLF1 interacts with chromatin remodelers promoting escape from latent infections with EBV
Cited by: 30
Author(s): Marisa Schaeffner, Paulina Mrozek-Górska, Alexander Buschle, Anne Woellmer, Takanobu Tagawa, Filippo M. Cernilogar, Gunnar Schotta, Nils Krietenstein, Corinna Lieleg, Philipp Korber, Wolfgang Hammerschmidt
Software Mentions: 1
Published: over 5 years ago

10.1186/s12915-020-00883-4

Hyperactivated Wnt-β-catenin signaling in the absence of sFRP1 and sFRP5 disrupts trophoblast differentiation through repression of Ascl2
Cited by: 10
Author(s): Haili Bao, Dong Liu, Yingchun Xu, Yang Sun, Change Mu, Yongqin Yu, Chunping Wang, Qian Han, Sanmei Liu, Han Cai, Fan Liu, Shuangbo Kong, Wenbo Deng, Bin Cao, Haibin Wang, Qiang Wang, Jinhua Lu
Software Mentions: 1
Published: about 4 years ago

10.1186/s13287-019-1228-7

OCT4 and PAX6 determine the dual function of SOX2 in human ESCs as a key pluripotent or neural factor
Cited by: 25
Author(s): Shuchen Zhang, Emma Bell, Huihan Zhi, Stephen D. Brown, Siti A. M. Imran, Véronique Azuara, Wei Cui
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.27584

Clinical implications of chromatin accessibility in human cancers
Cited by: 7
Author(s): Yuexin Liu
Software Mentions: 1
Published: over 4 years ago

10.1038/s41420-020-00400-0

Dual EZH2 and G9a inhibition suppresses multiple myeloma cell proliferation by regulating the interferon signal and IRF4-MYC axis
Cited by: 33
Author(s): Kazuya Ishiguro, Hiroshi Kitajima, Takeshi Niinuma, Reo Maruyama, Naotaka Nishiyama, Hitoshi Ohtani, Gota Sudo, Mutsumi Toyota, Hajime Sasaki, Eiko Yamamoto, Masahiro Kai, Hiroshi Nakase, Hiromu Suzuki
Software Mentions: 1
Published: almost 4 years ago

10.1111/acel.13382

C/EBP homologous protein deficiency enhances hematopoietic stem cell function via reducing ATF3/ROS‐induced cell apoptosis
Cited by: 8
Author(s): Zhencan Shi, Daojun Diao, Yanan Zhao, Ying Luo, Yafei Li, Dingdong Liu, Kai Zhang, Yugang Qiu, Li Yu, Zhangfa Song, Zhenyu Ju
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0139672

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture
Cited by: 27
Author(s): Soichi Inagaki, Isabelle Henry, Meric Lieberman, Luca Comai
Software Mentions: 1
Published: about 9 years ago

10.1038/srep18472

SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins
Cited by: 22
Author(s): Linda Mannini, Francesco Cucco, Valentina Quarantotti, Clelia Amato, Mara Tinti, L. Tana, Annalisa Frattini, Domenico Delia, Ian D. Krantz, Rolf Jessberger, Antonio Musio
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep16567

Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation
Cited by: 12
Author(s): Daishi Inoue, Hitoshi Aihara, Tatsuharu Sato, Hirofumi Mizusaki, Masamichi Doiguchi, Miki Higashi, Yuko Imamura, Mitsuhiro Yoneda, Takayuki Miyanishi, Satoshi Fujii, Akihiko Okuda, Takeya Nakagawa, Takashi Ito
Software Mentions: 1
Published: about 9 years ago

10.1186/s13058-019-1164-6

Glucocorticoid receptor modulation decreases ER-positive breast cancer cell proliferation and suppresses wild-type and mutant ER chromatin association
Cited by: 31
Author(s): Eva Tonsing-Carter, Kyle M. Hernandez, Caroline R. Kim, Ryan V. Harkless, Alyce Oh, Kathleen R. Bowie, Diana C. West-Szymanski, Mayra A. Betancourt-Ponce, Bradley D. Green, Ricardo R. Lastra, Gini F. Fleming, Sarat Chandarlapaty, Suzanne D. Conzen
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.00244

The CagRS Two-Component System Regulates Clavulanic Acid Metabolism via Multiple Pathways in Streptomyces clavuligerus F613-1
Cited by: 21
Author(s): Jiafang Fu, Ronghuo Qin, Guanghua Zong, Cheng Liu, Ni Kang, Chunlong Zhong, Guangxiang Cao
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41419-019-1417-4

m6A methylation controls pluripotency of porcine induced pluripotent stem cells by targeting SOCS3/JAK2/STAT3 pathway in a YTHDF1/YTHDF2-orchestrated manner
Cited by: 66
Author(s): Ruifan Wu, Youhua Liu, Youbing Zhao, Zhen Bi, Yuan Yao, Qing Liu, Fengqin Wang, Yizhen Wang, Xinxia Wang
Software Mentions: 1
Published: almost 6 years ago

10.7150/thno.51857

Smad3 deficiency promotes beta cell proliferation and function in db/db mice via restoring Pax6 expression
Cited by: 11
Author(s): Jingyi Sheng, Li Wang, Patrick Ming‐Kuen Tang, Hong‐Lian Wang, Jianchun Li, Bihua Xu, Vivian Weiwen Xue, Ruizhi Tan, Nana Jin, Ting‐Fung Chan, Xiao‐Ru Huang, Rong Ma, Hui‐Yao Lan
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.pt.2017.08.002

Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems
Cited by: 31
Author(s): Marcelo S. da Silva, Raphael Souza Pavani, Jeziel D. Damasceno, Catarina A. Marques, Richard McCulloch, Luíz Ricardo Orsini Tosi, Maria Carolina Elias
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2020.00413

Involvement of Transcription Elongation Factor GreA in Mycobacterium Viability, Antibiotic Susceptibility, and Intracellular Fitness
Cited by: 11
Author(s): Siyuan Feng, Yan Liu, Wanfei Liang, Mohamed Abd El-Gawad El-Sayed Ahmed, Zihan Zhao, Shan Cong, Adam P. Roberts, Lujie Liang, Liya Liao, Zhijuan Zhong, Zhaowang Guo, Yongqiang Yang, Wen Xing, Hongtao Chen, Guo‐Bao Tian
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0163035

E2F1 Orchestrates Transcriptomics and Oxidative Metabolism in Wharton’s Jelly-Derived Mesenchymal Stem Cells from Growth-Restricted Infants
Cited by: 6
Author(s): Peck Yean Tan, Chien-Chi Chang, Kaibo Duan, Michael Poidinger, Kar Hui Ng, Yap Seng Chong, Peter D. Gluckman, Walter Stünkel
Software Mentions: 1
Published: about 8 years ago

10.1128/mBio.02563-18

AtrR Is an Essential Determinant of Azole Resistance in Aspergillus fumigatus
Cited by: 52
Author(s): Sanjoy Paul, Mark Stamnes, Grace Heredge Thomas, Hong Liu, Daisuke Hagiwara, Katsuya Gomi, Scott G. Filler, W. Scott Moye‐Rowley
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-021-03769-7

IL-4 inhibits regulatory T cells differentiation by HDAC9-mediated epigenetic regulation
Cited by: 10
Author(s): Jikai Cui, Heng Xu, Jizhang Yu, Yuan Li, Zhang Chen, Yanqiang Zou, Xi Zhang, Yifan Du, Jiahong Xia, Jie Wu
Software Mentions: 1
Published: over 3 years ago

10.1128/mBio.03054-19

CRISPR Interference of a Clonally Variant GC-Rich Noncoding RNA Family Leads to General Repression of var Genes in Plasmodium falciparum
Cited by: 31
Author(s): Anna Barcons-Simon, Carlos Cordón-Obras, Julien Guizetti, Jessica M. Bryant, Artur Scherf
Software Mentions: 1
Published: over 4 years ago

10.1186/s13148-020-00835-3

Crosstalk between DNA methylation and histone acetylation triggers GDNF high transcription in glioblastoma cells
Cited by: 21
Author(s): Baole Zhang, Xiao-He Gu, Xiao Han, Dianshuai Gao, Jie Liu, Ting-Wen Guo
Software Mentions: 1
Published: over 4 years ago

10.1242/dev.127936

Activation of a T-box-Otx2-Gsc gene network independent of TBP and TBP-related factors
Cited by: 9
Author(s): Emese Gazdag, U. Jacobi, Ila van Kruijsbergen, Daniel L. Weeks, Gert Jan C. Veenstra
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.46314

Improved CUT&RUN chromatin profiling tools
Cited by: 253
Author(s): Michael P. Meers, Terri D. Bryson, Steven Henikoff, Steven Henikoff
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.03128-20

Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores
Cited by: 24
Author(s): Ming-Yueh Wu, Matthew E. Mead, Mi-Kyung Lee, George F. Neuhaus, Donovon A. Adpressa, Julia Martien, Ye-Eun Son, Heungyun Moon, Daniel Amador‐Noguez, Kap-Hoon Han, Antonis Rokas, Sandra Loesgen, Jae‐Hyuk Yu, Hee-Soo Park
Software Mentions: 1
Published: over 3 years ago

10.1128/MCB.00252-18

O-GlcNAcylation Signal Mediates Proteasome Inhibitor Resistance in Cancer Cells by Stabilizing NRF1
Cited by: 40
Author(s): Hiroshi Sekine, Kazuyuki Okazaki, Koichiro Kato, Md. Morshedul Alam, Hiroki Shima, Fumiki Katsuoka, Teppei Tsujita, Norio Suzuki, Akira Kobayashi, Kazuhiko Igarashi, Masayuki Yamamoto, Hozumi Motohashi
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0222329

Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation
Cited by: 8
Author(s): Mariângela Bueno Cordeiro Maldonado, Nelson B. de Rezende Neto, Sheila Tiemi Nagamatsu, Marcelo Falsarella Carazzolle, Jesse L. Hoff, Lynsey K. Whitacre, Robert D. Schnabel, Susanta K. Behura, Stephanie McKay, Taylor Jf, Flávia L. Lopes
Software Mentions: 1
Published: about 5 years ago

10.1038/s41408-021-00541-0

ASXL1 mutations are associated with distinct epigenomic alterations that lead to sensitivity to venetoclax and azacytidine
Cited by: 20
Author(s): Nora E. Rahmani, Nandini Ramachandra, Srabani Sahu, Nadege Gitego, Andrea López, Kith Pradhan, Tushar D. Bhagat, Shanisha Gordon-Mitchell, B. Peña, Mohammad Kazemi, K. Visweswara Rao, Orsi Giricz, Shahina Maqbool, Raul Olea, Yongmei Zhao, Jinghang Zhang, Hamid Dolatshad, Vickram Tittrea, Dharamveer Tatwavedi, Shalini Singh, Juseong Lee, Tianyu Sun, Ulrich Steidl, Aditi Shastri, Daichi Inoue, Omar Abdel‐Wahab, Andrea Pellagatti, Evripidis Gavathiotis, Jacqueline Boultwood, Amit Verma
Software Mentions: 1
Published: about 3 years ago

10.1038/s41597-019-0313-1

Transcriptome and chromatin accessibility in porcine intestinal epithelial cells upon Zearalenone exposure
Cited by: 8
Author(s): Haifei Wang, Jian Jin, Jiayun Wu, Huan Qu, Shenglong Wu, Wenbin Bao
Software Mentions: 1
Published: almost 5 years ago

10.1128/mBio.01636-21

Expression Patterns of Plasmodium falciparum Clonally Variant Genes at the Onset of a Blood Infection in Malaria-Naive Humans
Cited by: 11
Author(s): Anastasia K. Pickford, Lucas Michel-Todó, Florian Dupuy, Alfredo Mayor, Pedro Luis Cano Alonso, Catherine Lavazec, Alfred Cortés
Software Mentions: 1
Published: about 3 years ago

10.1128/mBio.01458-21

Screening of Chemical Libraries for New Antifungal Drugs against Aspergillus fumigatus Reveals Sphingolipids Are Involved in the Mechanism of Action of Miltefosine
Cited by: 10
Author(s): Thaila Fernanda dos Reis, Maria Augusta Crivelente Horta, Ana Cristina Colabardini, Caroline Mota Fernandes, Lilian Pereira Silva, Rafael Wesley Bastos, Maria Vitória de Lazari Fonseca, Fang Wang, Celso Martins, Márcio L. Rodrigues, Cristina Silva Pereira, Maurizio Del Poeta, Koon Ho Wong, Gustavo Henrique Goldman
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0145531

DNA-Binding Motif of the Imprinted Transcription Factor PEG3
Cited by: 18
Author(s): Suman Lee, Yingli An, Joomyeong Kim
Software Mentions: 1
Published: almost 9 years ago

10.1128/mSphere.00646-20

High-Resolution Genome-Wide Occupancy in Candida spp. Using ChEC-seq
Cited by: 4
Author(s): Faïza Tebbji, Inès Khemiri, Adnane Sellam
Software Mentions: 1
Published: about 4 years ago

10.1128/MCB.00498-13

The PR/SET Domain Zinc Finger Protein Prdm4 Regulates Gene Expression in Embryonic Stem Cells but Plays a Nonessential Role in the Developing Mouse Embryo
Cited by: 25
Author(s): Debora Bogani, Marc A. Morgan, Andrew C. Nelson, Ita Costello, Joanna F. McGouran, Benedikt M. Kessler, Elizabeth J. Robertson, Elizabeth K. Bikoff
Software Mentions: 1
Published: about 11 years ago

10.3389/fcell.2021.621374

METTL3-Mediated N6-Methyladenosine Modification Is Involved in the Dysregulation of NRIP1 Expression in Down Syndrome
Cited by: 4
Author(s): Weili Shi, Fan Yang, Ranran Dai, Yuchun Sun, Chaowu Yan, Shixiu Liao, Bingtao Hao
Software Mentions: 1
Published: over 3 years ago

10.1093/hmg/ddw423

GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps
Cited by: 1
Author(s): Miloš Nikolić, Argyris Papantonis, Álvaro Rada-Iglesias
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12931-021-01728-6

The role of RNA m6A methylation in the regulation of postnatal hypoxia-induced pulmonary hypertension
Cited by: 17
Author(s): Shanshan Xu, Xuefeng Xu, Ziming Zhang, Lingling Yan, Liyan Zhang, Lizhong Du
Software Mentions: 1
Published: over 3 years ago

10.1186/s13148-021-01126-1

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes
Cited by: 60
Author(s): Tasnim H. Beacon, Geneviève P. Delcuve, Camila López, Gino Nardocci, Igor Kovalchuk, André J. van Wijnen, James R. Davie
Software Mentions: 1
Published: over 3 years ago

10.1186/s13046-018-0832-1

Osteopontin alters DNA methylation through up-regulating DNMT1 and sensitizes CD133+/CD44+ cancer stem cells to 5 azacytidine in hepatocellular carcinoma
Cited by: 39
Author(s): Xiaomei Gao, Yuanyuan Sheng, Jing Yang, Chaoqun Wang, Rui Zhang, Ying Zhu, Ze Zhang, Kaili Zhang, Sijia Yan, Haoting Sun, Jie Wei, Xuan Wang, Xinxin Yu, Yu Zhang, Qin Luo, Yan Zheng, Peng Qiao, Yue Zhao, Qiongzhu Dong, Lun–Xiu Qin
Software Mentions: 1
Published: over 6 years ago

10.1186/s13046-019-1477-4

MFAP5 facilitates the aggressiveness of intrahepatic Cholangiocarcinoma by activating the Notch1 signaling pathway
Cited by: 16
Author(s): Jianhui Li, Xiao‐Xu Zhu, Fu-Xi Li, Chen‐Song Huang, Xi‐Tai Huang, Jie‐Qin Wang, Zhuoxing Gao, Shijin Li, Qiong‐Cong Xu, Wei Zhao
Software Mentions: 1
Published: almost 5 years ago

10.1084/jem.20190490

KLRG1 and NKp46 discriminate subpopulations of human CD117+CRTH2− ILCs biased toward ILC2 or ILC3
Cited by: 84
Author(s): Maho Nagasawa, Balthasar A. Heesters, Chantal M. A. Kradolfer, Lisette Krabbendam, Itziar Martínez-González, Marjolein J. W. de Bruijn, Korneliusz Golebski, Ralph Stadhouders, Hergen Spits, Suzanne M. Bal
Software Mentions: 1
Published: over 5 years ago

10.3390/biomedicines8010010

Meta-Analysis of Hypoxic Transcriptomes from Public Databases
Cited by: 34
Author(s): Hidemasa Bono, Kiichi Hirota
Software Mentions: 1
Published: almost 5 years ago

10.3389/fcell.2021.586150

PATZ1 (MAZR) Co-occupies Genomic Sites With p53 and Inhibits Liver Cancer Cell Proliferation via Regulating p27
Cited by: 2
Author(s): Zhen Long Ng, Jiamin Siew, Jia Li, Guanxu Ji, Min Huang, Xiali Liao, Shiguang Yu, Yuanyuan Chew, Chin Wen Png, Yongliang Zhang, Shijun Wen, Henry C. Yang, Yixi Zhou, Yun Long, Zhi‐Hong Jiang, Qiang Wu
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13072-017-0152-2

Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
Cited by: 10
Author(s): Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Shinichi Morishita, Hiroyuki Takeda
Software Mentions: 1
Published: about 7 years ago

10.3390/jof6020052

Identification of AflR Binding Sites in the Genome of Aspergillus flavus by ChIP-Seq
Cited by: 8
Author(s): Qing Kong, Perng‐Kuang Chang, Chunjuan Li, Zhaorong Hu, Zheng Ma, Quanxi Sun, Shiguang Shan
Software Mentions: 1
Published: over 4 years ago

10.1242/bio.026120

GATA6 is essential for endoderm formation from human pluripotent stem cells
Cited by: 38
Author(s): Joseph B. Fisher, Kirthi Pulakanti, Sridhar Rao, Stephen A. Duncan
Software Mentions: 1
Published: almost 8 years ago

10.3389/fcell.2021.690079

Transcription-Based Multidimensional Regulation of Fatty Acid Metabolism by HIF1α in Renal Tubules
Cited by: 6
Author(s): Wenju Li, Aiping Duan, Yufei Xing, Lina Xu, Jingping Yang
Software Mentions: 1
Published: over 3 years ago

10.1002/ctm2.553

Interplay of m6A and histone modifications contributes to temozolomide resistance in glioblastoma
Cited by: 31
Author(s): Fuxi Li, Siyun Chen, J. Yu, Zhuoxing Gao, Ziqi Sun, Yi Yang, Long Teng, Chuanxia Zhang, Yuzhe Li, Yimin Pan, Chaoying Qin, Wenyong Long, Qing Liu, Wei Zhao
Software Mentions: 1
Published: about 3 years ago

10.1111/cpr.12826

B‐cell lymphoma 2 family genes show a molecular pattern of spatiotemporal heterogeneity in gynaecologic and breast cancer
Cited by: 5
Author(s): Jiajian Wang, Sidi Li, Shudai Lin, Shuang Fu, Qiu Li, Ke Ding, Keying Liang, Hongli Du
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0252354

PEG3 controls lipogenesis through ACLY
Cited by: 2
Author(s): Subash Ghimire, Joomyeong Kim
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0180922

Direct targets of pSTAT5 signalling in erythropoiesis
Cited by: 31
Author(s): Kevin R. Gillinder, Hugh Tuckey, Charles C. Bell, Graham Magor, Stephen Huang, Melissa Ilsley, Andrew C. Perkins
Software Mentions: 1
Published: over 7 years ago

10.1038/s41421-018-0061-y

Tetratricopeptide repeat domain 7A is a nuclear factor that modulates transcription and chromatin structure
Cited by: 7
Author(s): Marie‐Thérèse El‐Daher, Nicolas Cagnard, Marine Gil, Marie Chansel Da Cruz, Claire Leveau, Fernando E. Sepulveda, Mohammed Zarhrate, Frédéric Torès, Patricia Legoix, Sylvain Baulande, Jean‐Pierre de Villartay, Geneviève Almouzni, Jean‐Pierre Quivy, Alain Fischer, Geneviève de Saint Basile
Software Mentions: 1
Published: about 6 years ago

10.1038/onc.2016.184

The BET inhibitor JQ1 selectively impairs tumour response to hypoxia and downregulates CA9 and angiogenesis in triple negative breast cancer
Cited by: 111
Author(s): Leonardo Lisbôa da Motta, Ioanna Ledaki, Karin Purshouse, Syed Haider, Marco Antônio De Bastiani, Dilair Baban, Matteo Morotti, Graham Steers, Simon Wigfield, Esther Bridges, JL Li, Stefan Knapp, Daniel Ebner, Fábio Klamt, Adrian L. Harris, Alan McIntyre
Software Mentions: 1
Published: over 8 years ago

10.1038/s41388-019-0743-4

PKNOX2 suppresses gastric cancer through the transcriptional activation of IGFBP5 and p53
Cited by: 31
Author(s): Li Zhang, Weilin Li, Lei Cao, Jia‐Ying Xu, Yun Qian, Huarong Chen, Yanquan Zhang, Wei Kang, Hongyan Gou, Chi Chun Wong
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41388-019-0969-1

LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells
Cited by: 24
Author(s): Joan Pau Cebrià-Costa, Laura Pascual-Reguant, Abel González-Pérez, Gemma Serra-Bardenys, Jessica Querol, Marc Cosín, Gaetano Verde, Riccardo Aiese Cigliano, Walter Sanseverino, Sandra Segura-Bayona, Ane Iturbide, David Andreu, Paolo Nuciforo, Cristina Bernadó-Morales, Verónica Rodilla, Joaquı́n Arribas, José Yélamos, Antonio Garcı́a de Herreros, Travis H. Stracker, Sandra Peiró
Software Mentions: 1
Published: about 5 years ago

10.1098/rsif.2017.0034

The circadian dynamics of small nucleolar RNA in the mouse liver
Cited by: 13
Author(s): Stuart Aitken, Colin A. Semple
Software Mentions: 1
Published: over 7 years ago

10.1073/pnas.2018615118

ARABIDOPSIS THALIANA HOMEOBOX GENE 1 controls plant architecture by locally restricting environmental responses
Cited by: 19
Author(s): Mahwish Ejaz, Stefano Bencivenga, Rafael Garcia Tavares, Maxwell S. Bush, Robert Sablowski
Software Mentions: 1
Published: over 3 years ago

10.1038/s41421-020-00241-2

N6-methyladenosine regulates RNA abundance of SARS-CoV-2
Cited by: 6
Author(s): Ting Zhang, Ying Yang, Xiang Zou, Chun-Chun Gao, Wenjing Wang, Conghui Wang, Xia Xiao, Xing Wang, Weinan Qiu, Wenjie Li, Lili Ren, Mingkun Li, Yongliang Zhao, Yu-Sheng Chen, Jianwei Wang, Ying Yang
Software Mentions: 1
Published: almost 4 years ago

10.1111/mmi.14667

Genome‐wide analysis of in vivo CcpA binding with and without its key co‐factor HPr in the major human pathogen group A Streptococcus
Cited by: 9
Author(s): Sruti DebRoy, Víctor Aliaga-Tobar, Gabriel Galvez, Srishtee Arora, Xiaowen Liang, Nicola Horstmann, Vinícius Maracaja-Coutinho, Mauricio Latorre, Magnus Höök, Anthony R. Flores, Samuel A. Shelburne
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41389-020-0232-1

SOX9 interacts with FOXC1 to activate MYC and regulate CDK7 inhibitor sensitivity in triple-negative breast cancer
Cited by: 23
Author(s): Lin Tang, Juan Jin, Kun Xu, Xin Wang, Jinhai Tang, Xiaoxiang Guan
Software Mentions: 1
Published: over 4 years ago

10.1002/1878-0261.12098

<scp>ZEB</scp> 1‐regulated inflammatory phenotype in breast cancer cells
Cited by: 81
Author(s): Akihiro Katsura, Yusuke Tamura, Satoshi Hokari, Masaru Harada, Masato Morikawa, Tsubasa Sakurai, Kei Takahashi, Atsushi Mizutani, Jun Nishida, Yuichiro Yokoyama, Yasuyuki Morishita, Takashi Murakami, Shogo Ehata, Kohei Miyazono, Daizo Koinuma
Software Mentions: 1
Published: over 7 years ago

10.1242/dev.163147

Gli3controls the onset of cortical neurogenesis by regulating the radial glial cell cycle throughCdk6expression
Cited by: 30
Author(s): Kerstin Hasenpusch‐Theil, Stephen C. West, Alexandra Kelman, Zrinko Kozić, Sophie Horrocks, Andrew P. McMahon, David J. Price, John O. Mason, Thomas Theil
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13072-020-00337-9

The histone methyltransferase Setd8 alters the chromatin landscape and regulates the expression of key transcription factors during erythroid differentiation
Cited by: 14
Author(s): Jason Myers, Tyler Couch, Zachary C. Murphy, Jeffrey Malik, Michael Getman, Laurie A. Steiner
Software Mentions: 1
Published: over 4 years ago

10.1186/s13075-016-1169-9

Chromatin landscapes and genetic risk in systemic lupus
Cited by: 17
Author(s): Joyce Hui-Yuen, Lisha Zhu, Lai Ping Wong, Kaiyu Jiang, Yanmin Chen, Tao Liu, James N. Jarvis
Software Mentions: 1
Published: almost 8 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203