pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1038/s41419-019-2201-1

Epigenetic priming by Dot1l in lymphatic endothelial progenitors ensures normal lymphatic development and function
Cited by: 11
Author(s): Hyunjin Yoo, Young Jae Lee, Chanhyeok Park, Dabin Son, Dong Yoon Choi, Ji Hyun Park, Hee-Jin Choi, Hyun Woo La, Yun Jung Choi, Eun Hye Moon, Dieter Saur, Hyung Min Chung, Hyuk Song, Jeong Tae, Hoon Jang, Dong Ryul Lee, Chankyu Park, Ok Hee Lee, Ssang-Goo Cho, Seok Ho Hong, Gu Kong, Jin‐Hoi Kim, Yun‐Sang Choi, Kwonho Hong
Software Mentions: 2
Published: almost 5 years ago

10.15252/embj.201798219

The long non‐coding <scp>RNA</scp> Paupar promotes <scp>KAP</scp> 1‐dependent chromatin changes and regulates olfactory bulb neurogenesis
Cited by: 43
Author(s): Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil R. Clark, Tamara Sirey, Sheena Lee, Dan J. Woodcock, Chris P. Ponting, Francis G. Szele, Keith W. Vance
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.44656

TERRA regulate the transcriptional landscape of pluripotent cells through TRF1-dependent recruitment of PRC2
Cited by: 36
Author(s): Rosa M. Marión, Juan Montero, Isabel López de Silanes, Osvaldo Graña‐Castro, Paula Martínez, Stefan Schoeftner, José Alejandro Palacios-Fábrega, Marı́a A. Blasco
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-03810-9

Pericentromeric Satellite III transcripts induce etoposide resistance
Cited by: 6
Author(s): Julian Kanne, Michelle Hussong, Jörg Isensee, Álvaro Muñoz‐López, Jan Wolffgramm, Felix Heß, Christina Grimm, Sergey Bessonov, Lydia Meder, Jie Wang, Hans Christian Reinhardt, Margarete Odenthal, Tim Hucho, Reinhard Büttner, Daniel Summerer, Michal R. Schweiger
Software Mentions: 2
Published: over 3 years ago

10.15252/embr.201846255

Ch <scp>IP</scp> ‐Atlas: a data‐mining suite powered by full integration of public Ch <scp>IP</scp> ‐seq data
Cited by: 473
Author(s): Shinya Oki, Toshio Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno
Software Mentions: 2
Published: about 6 years ago

10.15252/embr.202051989

H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing
Cited by: 33
Author(s): Sjoerd J D Tjalsma, Mayako Hori, Yuko Sato, Aurélie Bousard, Akito Ohi, Ana Raposo, Julia Roensch, Agnès Le Saux, Jumpei Nogami, Kazuhira Maehara, Tomoya Kujirai, Tetsuya Handa, Sandra Bagés-Arnal, Yasuyuki Ohkawa, Hitoshi Kurumizaka, Simão Teixeira da Rocha, J. Ż̷ylicz, Hiroshi Kimurâ, Edith Heard
Software Mentions: 2
Published: almost 4 years ago

10.15252/embr.201846222

Budding yeast Rif1 binds to replication origins and protects <scp>DNA</scp> at blocked replication forks
Cited by: 30
Author(s): Shin‐ichiro Hiraga, Chandre Monerawela, Yuki Katou, Sophie Shaw, Kate Rosalind Mary Clark, Katsuhiko Shirahige, Anne Donaldson
Software Mentions: 2
Published: over 6 years ago

10.15252/embr.201948019

The role of Xist ‐mediated Polycomb recruitment in the initiation of X‐chromosome inactivation
Cited by: 72
Author(s): Aurélie Bousard, Ana Raposo, J. Ż̷ylicz, Christel Picard, Vanessa Borges Pires, Yanyan Qi, Cláudia Raquel Estopa Gil, Laurène Syx, Howard Y. Chang, Edith Heard, Simão Teixeira da Rocha
Software Mentions: 2
Published: about 5 years ago

10.1210/en.2018-00819

Glucocorticoid Receptor–Tethered Mineralocorticoid Receptors Increase Glucocorticoid-Induced Transcriptional Responses
Cited by: 31
Author(s): Caroline A Rivers, Mark F. Rogers, Felicity Stubbs, Becky Conway-Campbell, Stafford L. Lightman, John R. Pooley
Software Mentions: 2
Published: over 5 years ago

10.1186/s13072-019-0287-4

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
Cited by: 210
Author(s): Michael P. Meers, Dan Tenenbaum, Steven Henikoff
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-021-03817-2

Muscle regeneration controlled by a designated DNA dioxygenase
Cited by: 10
Author(s): Hongye Wang, Youhua Huang, Ming Yu, Yu Ye, Sheng Li, Huating Wang, Hao Sun, Bing Li, Guoliang Xu, Ping Hu
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.ppat.1006133

Two-Component Signaling System VgrRS Directly Senses Extracytoplasmic and Intracellular Iron to Control Bacterial Adaptation under Iron Depleted Stress
Cited by: 35
Author(s): Li Wang, Yue Pan, Zuoqiang Yuan, Huan Zhang, Peng Bao-Yu, Fangfang Wang, Wenyuan Qian
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12920-020-0662-9

An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer
Cited by: 6
Author(s): Naoto Kubota, Mikita Suyama
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2018.00731

Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells
Cited by: 8
Author(s): Sharmi Banerjee, Hongxiao Zhu, Man Lai Tang, Wu-chun Feng, Xiaowei Wu, Hehuang Xie
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.ppat.1004905

Genome-Wide Identification of the Target Genes of AP2-O, a Plasmodium AP2-Family Transcription Factor
Cited by: 79
Author(s): Ikuyo Kaneko, Shiro Iwanaga, Tomomi Kato, Issei Kobayashi, Masao Yuda
Software Mentions: 1
Published: over 9 years ago

10.1093/jxb/erab074

Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize
Cited by: 21
Author(s): Jinhong Luo, Min Wang, Guifang Jia, Yan He
Software Mentions: 1
Published: almost 4 years ago

10.12688/f1000research.53926.1

PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals
Cited by: 5
Author(s): Peter Briggs, Louise Hunter, Shen-Hsi Yang, Andrew D. Sharrocks, Mudassar Iqbal
Software Mentions: 1
Published: over 3 years ago

10.1093/jxb/erw409

Rice aleurone layer specific OsNF-YB1 regulates grain filling and endosperm development by interacting with an ERF transcription factor
Cited by: 87
Author(s): Jingjing Xu, Xiaofan Zhang, Xue Hou
Software Mentions: 1
Published: about 8 years ago

10.3390/cancers13030387

A Regulatory Loop of FBXW7-MYC-PLK1 Controls Tumorigenesis of MYC-Driven Medulloblastoma
Cited by: 9
Author(s): Dong Wang, Angela Pierce, Bethany Veo, Susan Fosmire, Etienne Danis, Andrew M. Donson, Sujatha Venkataraman, Rajeev Vibhakar
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.36696

H3.3K27M mutant proteins reprogram epigenome by sequestering the PRC2 complex to poised enhancers
Cited by: 69
Author(s): Fang Dong, Haiyun Gan, Cheng Liu, Jeong Heon Lee, Hui Zhou, Jann N. Sarkaria, David J. Daniels, Zhiguo Zhang
Software Mentions: 1
Published: over 6 years ago

10.1038/s42003-021-02307-7

Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring
Cited by: 3
Author(s): Junfeng Chen, Huijuan Bi, Mats E. Pettersson, Daiki X. Sato, Angela P. Fuentes‐Pardo, Chunheng Mo, Shady Younis, Ola Wallerman, Patric Jern, Gregorio Molés, Ana Gómez, Gunnar Kleinau, Patrick Scheerer, Leif Andersson
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2019.00754

The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment
Cited by: 19
Author(s): Yi Zhang, Mohith Manjunath, Jialu Yan, Brittany Baur, Shilu Zhang, Sushmita Roy, Jun S. Song
Software Mentions: 1
Published: about 5 years ago

10.1038/cddis.2015.117

Che-1 modulates the decision between cell cycle arrest and apoptosis by its binding to p53
Cited by: 36
Author(s): Agata Desantis, Tiziana Bruno, Valeria Catena, Francesca De Nicola, Frauke Goeman, Simona Iezzi, Cristina Socolovschi, Maria Pia Gentileschi, Sabrina Germoni, Valentina Monteleone, Marsha Pellegrino, Martin Kann, Paolo D’Onorio De Meo, Matteo Pallocca, Katja Höpker, Fabiola Moretti, Elisabetta Mattei, Hans Christian Reinhardt, Aristide Floridi, Claudio Passananti, Thomas Benzing, Giovanni Blandino, Maurizio Fanciulli
Software Mentions: 1
Published: over 9 years ago

10.3390/cancers10100371

Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
Cited by: 15
Author(s): Gaetano Verde, Lara Isabel de Llobet Cucalon, Javier Quilez, Sandra Peiró, François Le Dily, Miguel Beato
Software Mentions: 1
Published: about 6 years ago

10.1111/jcmm.15807

Altered m 6 A modification is involved in up‐regulated expression of FOXO3 in luteinized granulosa cells of non‐obese polycystic ovary syndrome patients
Cited by: 23
Author(s): Shen Zhang, Wen-Li Deng, Qiongyou Liu, Peiyu Wang, Wei Yang, Wuhua Ni
Software Mentions: 1
Published: about 4 years ago

10.7554/eLife.44360

Transcriptional down-regulation of ccr5 in a subset of HIV+ controllers and their family members
Cited by: 17
Author(s): Elena Gonzalo-Gil, Patrick B Rapuano, Uchenna Ikediobi, Rebecca Leibowitz, Sameet Mehta, Ayse K. Coskun, J Zachary Porterfield, Teagan D Lampkin, Vincent C. Marconi, David Rimland, Bruce D. Walker, Steven G. Deeks, Richard E. Sutton
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.21064

PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes
Cited by: 88
Author(s): Mitsuhiro Endoh, Takaho A. Endo, Jun Shinga, Kozaburo Hayashi, Anca M. Farcas, Kit-Wan Ma, Shinsuke Ito, Jafar Sharif, Tamie Endoh, Naoko Onaga, Manabu Nakayama, Tomoyuki Ishikura, Osamu Masui, Benedikt M. Kessler, Toshio Suda, Osamu Ohara, Akihiko Okuda, Robert J. Klose, Haruhiko Koseki
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.21130

YAP is essential for mechanical force production and epithelial cell proliferation during lung branching morphogenesis
Cited by: 95
Author(s): Chuwen Lin, Erica Yao, Kuan Zhang, Xuan Jiang, Stacey Croll, Katherine L. Thompson-Peer, Pao-Tien Chuang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-020-03798-7

MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification
Cited by: 4
Author(s): Qiangwei Zhou, Ze Wang, Jing Li, Wing‐Kin Sung, Guoliang Li
Software Mentions: 1
Published: about 4 years ago

10.1074/jbc.RA120.015824

The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase
Cited by: 13
Author(s): Manisha Yadav, Ravi Shankar Singh, Daniel J. Hogan, Venkatasubramanian Vidhyasagar, Shizhuo Yang, Ivy Yeuk Wah Chung, Anthony Kusalik, Oleg Y. Dmitriev, Mirosław Cygler, Yuliang Wu
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.47333

Telomere dysfunction cooperates with epigenetic alterations to impair murine embryonic stem cell fate commitment
Cited by: 9
Author(s): Mélanie Criqui, Aditi Qamra, Tsz Wai Chu, Monika Sharma, Jeffrey Tsao, Danielle Henry, Dalia Baršytė-Lovejoy, C.H. Arrowsmith, Neil Winegarden, Mathieu Lupien, Lea Harrington
Software Mentions: 1
Published: over 4 years ago

10.12688/wellcomeopenres.15091.2

ELK1 has a dual activating and repressive role in human embryonic stem cells
Cited by: 4
Author(s): Ian Prise, Andrew D. Sharrocks
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-021-01756-4

Annotation of chromatin states in 66 complete mouse epigenomes during development
Cited by: 26
Author(s): Arjan van der Velde, Kaili Fan, Junko Tsuji, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Zhiping Weng
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-018-4697-7

Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions
Cited by: 9
Author(s): Rahul Jangid, Ashwin Kelkar, Vijaykumar Yogesh Muley, Sanjeev Galande
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.23084

Atrophin controls developmental signaling pathways via interactions with Trithorax-like
Cited by: 13
Author(s): K.W.K. Yeung, Ann Boija, Edvin Karlsson, Per-Henrik Holmqvist, Yonit Tsatskis, Ilaria Nisoli, Damian Yap, Alireza Lorzadeh, Michelle Moksa, Martin Hirst, Samuel Aparicio, Manolis Fanto, Per Stenberg, Mattias Mannervik, Helen McNeill
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.35216

Arid1a restrains Kras-dependent changes in acinar cell identity
Cited by: 35
Author(s): Geulah Livshits, Direna Alonso-Curbelo, John P. Morris, Richard P. Koche, Michael Saborowski, John E. Wilkinson, Scott W. Lowe
Software Mentions: 1
Published: over 6 years ago

10.1074/jbc.RA120.015353

A physical basis for quantitative ChIP-sequencing
Cited by: 10
Author(s): Bradley M. Dickson, Rochelle L. Tiedemann, Alison A. Chomiak, Evan M. Cornett, Robert M. Vaughan, Scott B. Rothbart
Software Mentions: 1
Published: about 4 years ago

10.18632/oncotarget.9513

BET bromodomain-mediated interaction between ERG and BRD4 promotes prostate cancer cell invasion
Cited by: 41
Author(s): Alexandra M. Blee, Shujun Liu, Liguo Wang, Haojie Huang
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2014.00252

Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches
Cited by: 13
Author(s): Michael R. Foret, Richard Sandstrom, C. T. Rhodes, Yufeng Wang, Mitchel S. Berger, Chin Hsing Lin
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.41913

GREB1 amplifies androgen receptor output in human prostate cancer and contributes to antiandrogen resistance
Cited by: 17
Author(s): Eugine Lee, John Wongvipat, Danielle Choi, Ping Wang, Young Sun Lee, Deyou Zheng, Philip A. Watson, Anuradha Gopalan, Charles L. Sawyers
Software Mentions: 1
Published: almost 6 years ago

10.1172/jci.insight.142577

GRHL3 activates FSCN1 to relax cell-cell adhesions between migrating keratinocytes during wound reepithelialization
Cited by: 5
Author(s): Ghaidaa Kashgari, Sanan Venkatesh, Samuel Refuerzo, Brandon Pham, A Bayat, Rachel Herndon Klein, Raúl Ramos, Albert Ta, Maksim V. Plikus, Ping H. Wang, Bogi Andersen
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-019-5989-2

Cut-C: cleavage under tethered nuclease for conformational capture
Cited by: 3
Author(s): Takashi Shimbo, Machika Kawamura, Edward Wijaya, Eiichi Takaki, Yasufumi Kaneda, Katsuto Tamai
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.29145

A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development
Cited by: 24
Author(s): Christie Ciarlo, Charles Kaufman, Beste Kınıkoğlu, Jonathan Michael, Song Yang, Christopher R. D'Amato, Sasja Blokzijl-Franke, Jeroen den Hertog, Thorsten M. Schlaeger, Yi Zhou, Eric C. Liao, Leonard I. Zon
Software Mentions: 1
Published: about 7 years ago

10.1111/pbi.13255

ZmILI1 regulates leaf angle by directly affecting liguleless1 expression in maize
Cited by: 25
Author(s): Zhenzhen Ren, Liancheng Wu, Lixia Ku, Huitao Wang, Haixia Zeng, Huihui Su, Wei Li, Deqiang Dou, Huafeng Liu, Yingying Cao, Dongling Zhang, Shengbo Han, Yanhui Chen
Software Mentions: 1
Published: about 5 years ago

10.7554/eLife.30433

LAST, a c-Myc-inducible long noncoding RNA, cooperates with CNBP to promote CCND1 mRNA stability in human cells
Cited by: 63
Author(s): Limian Cao, Pengfei Zhang, Jinming Li, Mian Wu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13007-020-0556-z

A native chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in strawberry fruits
Cited by: 8
Author(s): Xiaorong Huang, Qunxing Pan, Ying‐Chung Jimmy Lin, Tingting Gu, Yang Li
Software Mentions: 1
Published: almost 5 years ago

10.1038/s42003-019-0522-3

Functional D-box sequences reset the circadian clock and drive mRNA rhythms
Cited by: 51
Author(s): Hikari Yoshitane, Yoshimasa Asano, Aya Sagami, Seinosuke Sakai, Yutaka Suzuki, Hitoshi Okamura, Wataru Iwasaki, Haruka Ozaki, Yoshitaka Fukada
Software Mentions: 1
Published: over 5 years ago

10.3389/fcell.2021.714383

Suppression of Cell Tumorigenicity by Non-neural Pro-differentiation Factors via Inhibition of Neural Property in Tumorigenic Cells
Cited by: 6
Author(s): Xiaoli Yang, Ning Cao, Lü Chen, Lin Liu, Min Zhang, Ying Cao
Software Mentions: 1
Published: about 3 years ago

10.1016/j.gpb.2018.12.007

m6A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2
Cited by: 120
Author(s): Junchen Chen, Yi-Chang Zhang, Chih-Hsien Huang, Hui Shen, Bao‐Fa Sun, Xiaowen Cheng, Yujie Zhang, Yun‐Gui Yang, Qiang Shu, Ying Yang, Xuekun Li
Software Mentions: 1
Published: over 5 years ago

10.1111/acel.12996

Elevated H3K27ac in aged skeletal muscle leads to increase in extracellular matrix and fibrogenic conversion of muscle satellite cells
Cited by: 25
Author(s): Jiajian Zhou, Kam-Hei So, Yuying Li, Yang Li, Jie Yuan, Yudan Ding, Fengyuan Chen, Youhua Huang, Jin Liu, Wayne Lee, Gang Li, Zhenyu Ju, Hao Sun, Huating Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-020-0984-3

The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells
Cited by: 16
Author(s): Azra Fatima, Dilber Irmak, Alireza Noormohammadi, Markus M. Rinschen, Aniruddha Das, Orsolya Leidecker, Christina Schindler, Víctor Sánchez-Gaya, Prerana Wagle, Wojciech Pokrzywa, Thorsten Hoppe, Álvaro Rada-Iglesias, David Vı́lchez
Software Mentions: 1
Published: over 4 years ago

10.5808/gi.21020

Analysis of H3K4me3-ChIP-Seq and RNA-Seq data to understand the putative role of miRNAs and their target genes in breast cancer cell lines
Cited by: 1
Author(s): Aneesh Kotipalli, Ruma Banerjee, Sunitha Manjari Kasibhatla, Rajendra Joshi
Software Mentions: 1
Published: over 3 years ago

10.1038/s41421-021-00301-1

Interception of host fatty acid metabolism by mycobacteria under hypoxia to suppress anti-TB immunity
Cited by: 9
Author(s): Hua Yang, Fei Wang, Xinya Guo, Feng Liu, Liu Z, Xiangyang Wu, Mengmeng Zhao, Mingtong Ma, Haipeng Liu, Lianhua Qin, Lin Wang, Tianqi Tang, Sha Wang, Yang Wang, Jianxia Chen, Xiaochen Huang, Jie Wang, Cheng Peng, Ruijuan Zheng, Fengyan Tang, Lu Zhang, Chunyan Wu, Stefan H. Oehlers, Zhigang Song, Jia-Lei She, Feng Huang, Xunwei Xie, Baoxue Ge
Software Mentions: 1
Published: about 3 years ago

10.5808/GI.2020.18.4.e42

Comparative analysis of commonly used peak calling programs for ChIP-Seq analysis
Cited by: 11
Author(s): Hyeongrin Jeon, Hyunji Lee, Byung Ha Kang, Insoon Jang, Tae-Young Roh
Software Mentions: 1
Published: almost 4 years ago

10.1038/s42003-021-02280-1

The γ-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells
Cited by: 6
Author(s): Matthieu Corvaisier, Jingkai Zhou, Darina Malycheva, Nicola Cornella, Dimitrios Chioureas, Nina Gustafsson, Catalina Ana Rosselló, Silvia Ayora, Tongbin Li, Kristina Ekström‐Holka, Karin Jirström, Lisa Lindström, María Alvarado-Kristensson
Software Mentions: 1
Published: over 3 years ago

10.1186/s13072-019-0263-z

Targeted in vivo epigenome editing of H3K27me3
Cited by: 18
Author(s): Harumi Fukushima, Hiroyuki Takeda, Ryohei Nakamura
Software Mentions: 1
Published: over 5 years ago

10.1111/cgf.12924

AVOCADO: Visualization of Workflow–Derived Data Provenance for Reproducible Biomedical Research
Cited by: 29
Author(s): Holger Stitz, Stefan Luger, Marc Streit, Nils Gehlenborg
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.3001378

Regulation of integrin and extracellular matrix genes by HNRNPL is necessary for epidermal renewal
Cited by: 6
Author(s): Jingting Li, Yifang Chen, Manisha Tiwari, Varun Bansal, George L. Sen
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-014-1195-4

Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq
Cited by: 28
Author(s): Janus Schou Jakobsen, Frederik Otzen Bagger, Marie Sigurd Hasemann, Mikkel Bruhn Schuster, Anne-Katrine Frank, Johannes Waage, Kristoffer Vitting-Seerup, Bo T. Porse
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41421-021-00261-6

Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations
Cited by: 14
Author(s): Yingying Liu, Yanjun Zhang, Xue Han, Mei Cao, Guohui Bai, Zhongcheng Mu, Yanli Yao, Shuyang Sun, Fang Dong, Jing Huang
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.15082

Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse
Cited by: 19
Author(s): Luke Isbel, Lexie Prokopuk, Haoyu Wu, Lucia Daxinger, Harald Oey, Alex Spurling, Adam J. Lawther, Matthew W. Hale, Emma Whitelaw
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.2001333

Environmental change drives accelerated adaptation through stimulated copy number variation
Cited by: 86
Author(s): Ryan M. Hull, Cristina Cruz, Carmen V. Jack, Jonathan Houseley
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1006591

Multi-study inference of regulatory networks for more accurate models of gene regulation
Cited by: 56
Author(s): Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1006673

A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
Cited by: 4
Author(s): Jia Lee, Xiaoyi Cao, Sheng Zhong
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-5934-4

Genome-wide mapping and profiling of γH2AX binding hotspots in response to different replication stress inducers
Cited by: 16
Author(s): Xinxing Lyu, Megan Chastain, Weihang Chai
Software Mentions: 1
Published: over 5 years ago

10.15252/embj.201899793

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming
Cited by: 66
Author(s): Saša Šviković, Alastair Crisp, Sue Mei Tan-Wong, Thomas A. Guilliam, Aidan J. Doherty, Nicholas J. Proudfoot, Guillaume Guilbaud, Julian E. Sale
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.06073

The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism
Cited by: 66
Author(s): Timothy J. Parnell, Alisha Schlichter, Barbara G. Wilson, Bradley R. Cairns
Software Mentions: 1
Published: over 9 years ago

10.1038/s41419-020-03019-2

Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation
Cited by: 26
Author(s): Guoping Ding, Xiaodong Xu, Dan Li, Yuhao Chen, Weimin Wang, Dongnan Ping, Shengnan Jia, Liping Cao
Software Mentions: 1
Published: about 4 years ago

10.18632/oncotarget.8696

ΔNp63α induces the expression of FAT2 and Slug to promote tumor invasion
Cited by: 45
Author(s): Tuyen T. Dang, Jill M. Westcott, Erin A. Maine, Mohammed Kanchwala, Chao Xing, Gray W. Pearson
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005088

NLRC5 Exclusively Transactivates MHC Class I and Related Genes through a Distinctive SXY Module
Cited by: 73
Author(s): Kristina Ludigs, Queralt Seguín-Estévez, Sylvain Lemeille, Isabel Ferrero, Giorgia Rota, Sonia T. Chelbi, Chantal Mattmann, H. Robson MacDonald, Walter Reith, Greta Guarda
Software Mentions: 1
Published: over 9 years ago

10.1016/j.dib.2016.09.001

Dataset of TWIST1-regulated genes in the cranial mesoderm and a transcriptome comparison of cranial mesoderm and cranial neural crest
Cited by: 1
Author(s): Heidi Bildsoe, Xiaochen Fan, Emilie Wilkie, Ator Ashoti, Vanessa Jones, Melinda Power, Jin Qin, Junwen Wang, Patrick Tam, David A.F. Loebel
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13059-020-02095-z

The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos
Cited by: 16
Author(s): Feifei Li, Danyang Wang, Ruigao Song, Chenglong Cao, Zhihua Zhang, Yu Wang, Xiaoli Li, Jiaojiao Huang, Qiang Liu, Naipeng Hou, Bingxiang Xu, Li Xiao, Xiaomeng Gao, Yan Jia, Jianguo Zhao, Yanfang Wang
Software Mentions: 1
Published: over 4 years ago

10.1186/s13072-018-0220-2

Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions
Cited by: 5
Author(s): Idan Nurick, Ron Shamir, Ran Elkon
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.08955

HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells
Cited by: 41
Author(s): Jonathan E. Reeder, Youn Tae Kwak, Ryan P. McNamara, Christian V. Forst, Iván D’Orso
Software Mentions: 1
Published: about 9 years ago

10.1038/s41419-021-04082-z

Malat-1-PRC2-EZH1 interaction supports adaptive oxidative stress dependent epigenome remodeling in skeletal myotubes
Cited by: 9
Author(s): Nadine Hosny El Said, Francesco Della Valle, Peng Liu, Andreu Paytuví-Gallart, Sabir A. Adroub, Juliette Gimenez
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-016-2940-7

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA
Cited by: 23
Author(s): Gergely Nagy, Erik Czipa, László Steiner, Tibor Nagy, Sándor Pongor, László Nagy, Endre Barta
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.22718

The PAX8 cistrome in epithelial ovarian cancer
Cited by: 37
Author(s): Emily Adler, Rosario I. Corona, Janet M. Lee, Norma I. Rodríguez-Malavé, Paulette Mhawech‐Fauceglia, Heidi M. Sowter, Dennis J. Hazelett, Kate Lawrenson, Simon A. Gayther
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2975-9

Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat
Cited by: 12
Author(s): Minako Yoshihara, Daisuke Saito, Tetsuya Sato, Osamu Ohara, Takashi Kuramoto, Mikita Suyama
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-019-1802-4

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
Cited by: 73
Author(s): Qi Zhu, Nan Liu, Stuart H. Orkin, Guo‐Cheng Yuan
Software Mentions: 1
Published: about 5 years ago

10.1186/s13059-018-1573-3

N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA
Cited by: 42
Author(s): Guan‐Zheng Luo, Ziyang Hao, Liangzhi Luo, Mei‐Hua Shen, Daniela Sparvoli, Yuqing Zheng, Zijie Zhang, Xiaocheng Weng, Kai Chen, Qiang Cui, Aaron P. Turkewitz, Chuan He
Software Mentions: 1
Published: about 6 years ago

10.1186/s13059-018-1512-3

Alternative splicing links histone modifications to stem cell fate decision
Cited by: 50
Author(s): Yungang Xu, Weiling Zhao, Scott D. Olson, Karthik S. Prabhakara, Xiaobo Zhou
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.12713

Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients
Cited by: 29
Author(s): Mark A. Applebaum, Aashish R. Jha, Clara Kao, Kyle M. Hernandez, Gillian DeWane, Helen R. Salwen, Alexandre Chlenski, Marija Dobratic, Christopher J. Mariani, Lucy A. Godley, Nanduri R. Prabhakar, Kevin P. White, Barbara Elaine Stranger, Susan L. Cohn
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0241515

Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq
Cited by: 4
Author(s): Ying Shi, Weihua Gong, Xiangrong Gong, Ping Wang, Xin Zhao
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13059-018-1485-2

ChromTime: modeling spatio-temporal dynamics of chromatin marks
Cited by: 10
Author(s): Petko Fiziev, Jason Ernst
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0102612

Single Nucleotide Polymorphisms with Cis-Regulatory Effects on Long Non-Coding Transcripts in Human Primary Monocytes
Cited by: 5
Author(s): Jonas Carlsson Almlöf, Per Lundmark, Anders Lundmark, Bing Ge, Tomi Pastinen, Alison H. Goodall, François Cambien, Panos Deloukas, Willem H. Ouwehand, Ann‐Christine Syvänen
Software Mentions: 1
Published: over 10 years ago

10.1093/database/baw138

IRNdb: the database of immunologically relevant non-coding RNAs
Cited by: 11
Author(s): Elena Denisenko, Ho D, Ousman Tamgue, Mumin Ozturk, Harukazu Suzuki, Frank Brombacher, Reto Guler, Sebastian Schmeier
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0194420

Chromatin immunoprecipitation (ChIP) method for non-model fruit flies (Diptera: Tephritidae) and evidence of histone modifications
Cited by: 4
Author(s): Nagalingam Kumaran, Michał T. Lorenc, Sahana Manoli, Stephen L. Cameron, Anthony R. Clarke, Kevin J. Dudley
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-017-1246-7

The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility
Cited by: 50
Author(s): Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magali Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Frédy Barneche, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Heribert Hirt, Cécile Raynaud, Moussa Benhamed
Software Mentions: 1
Published: over 7 years ago

10.1186/s12863-020-0809-x

The effects of the DNA Demethylating reagent, 5-azacytidine on SMCHD1 genomic localization
Cited by: 0
Author(s): Shabnam Massah, J. Jubene, Frank J.S. Lee, Timothy V. Beischlag, Gratien G. Préfontaine
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13059-016-1133-7

Single-cell epigenomic variability reveals functional cancer heterogeneity
Cited by: 83
Author(s): Ulrike M. Litzenburger, Jason D. Buenrostro, Beijing Wu, Ying Shen, Nathan C. Sheffield, Arwa S. Kathiria, William J. Greenleaf, Howard Y. Chang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12863-017-0497-3

A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
Cited by: 8
Author(s): Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama
Software Mentions: 1
Published: over 7 years ago

10.1016/j.gdata.2016.01.019

Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II
Cited by: 10
Author(s): Ryan P. McNamara, Carlos Guzmán, Jonathan E. Reeder, Iván D’Orso
Software Mentions: 1
Published: over 8 years ago

10.3390/genes12050640

Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions
Cited by: 8
Author(s): Mingkun Huang, Ling Zhang, Limeng Zhou, Wai‐Shing Yung, Man-Wah Li, Hon‐Ming Lam
Software Mentions: 1
Published: over 3 years ago

10.3390/genes12030441

DNA Methylation at ATP11A cg11702988 Is a Biomarker of Lung Disease Severity in Cystic Fibrosis: A Longitudinal Study
Cited by: 2
Author(s): Fanny Pineau, Davide Caimmi, Sylvie Taviaux, Maurane Reveil, Laura Brosseau, Isabelle Rivals, Margot Drevait, Isabelle Vachier, Mireille Claustres, R. Chiron, Albertina De Sario
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0152918

Identification of Epigenetic Biomarkers of Lung Adenocarcinoma through Multi-Omics Data Analysis
Cited by: 16
Author(s): Chie Kikutake, Koji Yahara
Software Mentions: 1
Published: over 8 years ago

10.1093/molbev/msab033

B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and Histone Modifications in the Mouse
Cited by: 19
Author(s): Tomoko Ichiyanagi, Hirokazu Katoh, Yoshinobu Mori, Keigo Hirafuku, Beverly Ann Boyboy, Masaki Kawase, Kenji Ichiyanagi
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13072-015-0024-6

Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage
Cited by: 75
Author(s): Michael Walker, Timothy Billings, Christopher L. Baker, Natalie R. Powers, Hui Tian, Ruth L. Saxl, Kwangbom Choi, Matthew A. Hibbs, Gregory W. Carter, Mary Ann Handel, Kenneth Paigen, Petko M. Petkov
Software Mentions: 1
Published: about 9 years ago

10.1186/s13072-020-0329-y

Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish
Cited by: 7
Author(s): Marjo J. den Broeder, Jarle Ballangby, Leonie M. Kamminga, Peter Aleström, Juliette Legler, Leif C. Lindeman, Jorke H. Kamstra
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13041-019-0429-4

Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains
Cited by: 20
Author(s): Eilís Hannon, Sarah Marzi, Leonard Schalkwyk, Jonathan Mill
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12943-019-1088-x

m6A modification suppresses ocular melanoma through modulating HINT2 mRNA translation
Cited by: 102
Author(s): Ruobing Jia, Peiwei Chai, Shanzheng Wang, Bao‐Fa Sun, Yangfan Xu, Ying Yang, Shengfang Ge, Renbing Jia, Yun‐Gui Yang
Software Mentions: 1
Published: about 5 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203