pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1186/s13072-021-00418-3

Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation
Cited by: 5
Author(s): Yujuan Gui, Kamil Grzyb, Mélanie Thomas, Jochen Ohnmacht, Pierre Garcia, Manuel Buttini, Alexander Skupin, Thomas Sauter, Lasse Sinkkonen
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-020-02063-7

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

10.1186/s13195-020-00598-2

Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model
Cited by: 24
Author(s): Yaqi Wang, Xiaomin Zhang, Shan Qiao, Yuli Hou, Jing Liu, Yu Sun, Peichang Wang
Software Mentions: 4
Published: over 4 years ago

10.1016/j.stem.2020.06.020

Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration
Cited by: 251
Author(s): Jinwook Choi, Jong-Eun Park, Georgia Tsagkogeorga, Motoko Yanagita, Bon‐Kyoung Koo, Namshik Han, Joo Hyeon Lee
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1008926

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads
Cited by: 6
Author(s): Ramila Shah, Alexander J. Ruthenburg
Software Mentions: 4
Published: over 3 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pcbi.1008422

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

10.7554/eLife.64204

Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence
Cited by: 5
Author(s): Shou Liu, Wenjian Cao, Yichi Niu, Jiayi Luo, Yanhua Zhao, Zheng Hu, Chenghang Zong
Software Mentions: 4
Published: over 3 years ago

10.1093/bioinformatics/btaa202

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

10.1038/s41422-020-0281-1

Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks
Cited by: 34
Author(s): Yao Chen, Ruitu Lyu, Bowen Rong, Yuxuan Zheng, Zhen Lin, Ruofei Dai, Xi Zhang, Nannan Xie, Siqing Wang, Fuchou Tang, Fei Lan, Ming-Han Tong
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.29750

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool
Cited by: 29
Author(s): Vladimir Camarena, David W. Sant, Tyler C. Huff, Sushmita Mustafi, Ryan K Muir, Allegra T. Aron, Christopher J. Chang, Adam R. Renslo, Paula V. Monje, Gaofeng Wang
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41422-020-00465-7

The m6A methylome of SARS-CoV-2 in host cells
Cited by: 87
Author(s): June Liu, Yixin Xu, Kai Li, Qing Ye, Hang Zhou, Hai Sun, Xiaoyu Li, Yu Liu, Yong Qiang Deng, Rui Ting Li, Miao Cheng, Bo He, Jia Zhou, Xiao Feng Li, Aiping Wu, Chengqi Yi, Qi Cheng
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13059-020-01983-8

High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells
Cited by: 73
Author(s): Peiyao A. Zhao, Takayo Sasaki, David M. Gilbert
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.60498

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments
Cited by: 11
Author(s): Hajnalka Laura Pálinkás, Angéla Békési, Gergely Róna, Lőrinc Sándor Pongor, Gábor Papp, Gergely Tihanyi, Eszter Holub, Ádám Póti, Carolina Gemma, Simak Ali, Michael J. Morten, Eli Rothenberg, Michele Pagano, Dávid Szűts, Balázs Győrffy, Beáta G. Vértessy
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.67305

ZC3H4 restricts non-coding transcription in human cells
Cited by: 24
Author(s): Chris Estell, Lee Davidson, Pieter C. Steketee, Adam Monier, Steven West
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02012-4

REPIC: a database for exploring the N6-methyladenosine methylome
Cited by: 65
Author(s): Shun Liu, Allen Zhu, Chuan He, Mengjie Chen
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.55526

Delineating the early transcriptional specification of the mammalian trachea and esophagus
Cited by: 27
Author(s): Akela Kuwahara, Ace E. Lewis, Coohleen Coombes, Fang-Shiuan Leung, Michelle Percharde, Jeffrey O. Bush
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2019.02.012

Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Cited by: 56
Author(s): Lee Davidson, Laura Francis, Ross A. Cordiner, Joshua D. Eaton, Chris Estell, Sara Macías, Javier F. Cáceres, Steven West
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pbio.3000153

Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm
Cited by: 17
Author(s): Alessandro Magli, June Baik, Lauren J. Mills, Il-Youp Kwak, Bridget S. Dillon, Ricardo Mondragón-González, David Stafford, Scott Swanson, Ron Stewart, James A. Thomson, Daniel J. Garry, Brian David Dynlacht, Rita C.R. Perlingeiro
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.67312

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation
Cited by: 43
Author(s): Lizhi He, Henry E. Pratt, Mingshi Gao, Fengxiang Wei, Zhiping Weng, Kevin Struhl
Software Mentions: 4
Published: about 3 years ago

10.1016/j.celrep.2021.108758

SOX17 integrates HOXA and arterial programs in hemogenic endothelium to drive definitive lympho-myeloid hematopoiesis
Cited by: 23
Author(s): Ho Sun Jung, Gene I. Uenishi, Mi Ae Park, Peng Liu, Kran Suknuntha, Matthew Raymond, Yoon Jung Choi, James A. Thomson, Irene M. Ong, Igor I. Slukvin
Software Mentions: 4
Published: almost 4 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.27024

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts
Cited by: 113
Author(s): Jason C. Bell, David Jukam, Nicole A Teran, Viviana I. Risca, Owen K. Smith, Whitney L. Johnson, Jan M. Skotheim, William J. Greenleaf, Aaron F. Straight
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-019-1869-y

Characterizing the interplay between gene nucleotide composition bias and splicing
Cited by: 16
Author(s): Sébastien Lemaire, Nicolas Fontrodona, Fabien Aubé, Jean‐Baptiste Claude, Hélène Polvèche, Laurent Modolo, Cyril F. Bourgeois, Franck Mortreux, Didier Auboeuf
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Cited by: 17
Author(s): Jingwen Fang, Qing Ma, Constance R. Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13072-020-00368-2

Chromatin accessibility dynamics of Chlamydia-infected epithelial cells
Cited by: 4
Author(s): Regan J. Hayward, J. Wallis Marsh, Michael S. Humphrys, Wilhelmina M. Huston, Garry S. A. Myers
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-020-03729-6

Theoretical characterisation of strand cross-correlation in ChIP-seq
Cited by: 2
Author(s): Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-019-1894-x

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Cited by: 76
Author(s): Elissavet Kentepozidou, Sarah J. Aitken, Christine Feig, Klara Stefflova, Ximena Ibarra-Soria, Duncan T. Odom, Maša Roller, Paul Flicek
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13059-020-02249-z

N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease
Cited by: 112
Author(s): Andrew M Shafik, Feiran Zhang, Zhiqin Guo, Qing Dai, Kinga Pajdzik, Yangping Li, Yunhee Kang, Bing Yao, Hao Wu, Chuan He, Emily G. Allen, Ranhui Duan, Peng Jin
Software Mentions: 4
Published: almost 4 years ago

10.1161/CIRCULATIONAHA.120.046672

Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis
Cited by: 192
Author(s): Gabriel F. Alencar, Katherine Owsiany, Santosh Karnewar, Katyayani Sukhavasi, Giuseppe Mocci, Anh Nguyen, Corey Williams, Sohel Shamsuzzaman, Michal Mokrý, Christopher A. Henderson, Ryan M. Haskins, Richard A. Baylis, Aloke V. Finn, Coleen A. McNamara, Eli R. Zunder, Vamsidhar R M Venkata, Gérard Pasterkamp, Johan Björkegren, Stefan Bekiranov, Gary K. Owens
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.33084

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
Cited by: 23
Author(s): Michelle C. Ward, Siming Zhao, Kaixuan Luo, Bryan J. Pavlovic, Mehdi Karimi, Matthew Stephens, Yoav Gilad
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-017-0153-1

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state
Cited by: 25
Author(s): Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
Software Mentions: 4
Published: about 7 years ago

10.1186/s12915-021-01009-0

Multi-omic profiling of pituitary thyrotropic cells and progenitors
Cited by: 4
Author(s): Alexandre Z. Daly, L Dudley, Michael T. Peel, Stephen A. Liebhaber, Stephen C. J. Parker, Sally A. Camper
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-019-0286-5

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity
Cited by: 20
Author(s): Pierre Khoueiry, Aoife Ward Gahlawat, Massimo Petretich, Anne-Marie Michon, Daniel F. Simola, Enid Y.N. Lam, Eileen E. M. Furlong, Vladimı́r Beneš, Mark A. Dawson, Rab K. Prinjha, Gerard Drewes, Paola Grandi
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: about 4 years ago

10.1038/s41388-019-1005-1

Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines
Cited by: 12
Author(s): Li Wang, Hongying Zhao, Jing Li, Yingqi Xu, Yujia Lan, Wenkang Yin, Xiaoqin Liu, Lei Yu, Shan Lin, Michael Yifei Du, Xia Li, Yun Xiao, Yunpeng Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-019-1705-4

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination
Cited by: 31
Author(s): Anne-Sophie Fiorucci, Clara Bourbousse, Lorenzo Concia, Martin Rougée, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Elodie Layat, David Latrasse, Soon Kap Kim, Nicole Chaumont, Bérangère Lombard, David Stroebel, Sophie Lemoine, Ammara Mohammad, Corinne Blugeon, Damarys Loew, Christophe Bailly, Chris Bowler, Moussa Benhamed, Frédy Barneche
Software Mentions: 4
Published: over 5 years ago

10.1186/s13287-021-02601-5

Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias
Cited by: 0
Author(s): Gajendra W. Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, Yoojin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P. Presson, Dong-Sung An, Irvin S. Y. Chen
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-017-1273-4

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
Cited by: 131
Author(s): Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck, Maike Stam
Software Mentions: 4
Published: over 7 years ago

10.1038/s41419-017-0173-6

Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation
Cited by: 22
Author(s): Yanjian Li, Yi He, Zhengyu Liang, Yang Wang, Fengling Chen, Mohamed Nadhir Djekidel, Guipeng Li, Xu Zhang, Shuqin Xiang, Zejun Wang, Juntao Gao, Michael Q. Zhang, Chen Yang
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13287-019-1323-9

Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells
Cited by: 8
Author(s): Yingying Wang, Baosen Guo, Zengrong Xiao, Haijun Lin, Xi Zhang, Yueqiang Song, Yalei Li, Xuehu Gao, Jin-Jun Yu, Zhihua Shao, Xuekun Li, Yuan Luo, Siguang Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s13072-021-00395-7

Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina
Cited by: 13
Author(s): Florian Carlier, M. Li, Laetitia Maroc, Robert Debuchy, Charbel Souaid, Daan Noordermeer, Pierre Grognet, Fabienne Malagnac
Software Mentions: 4
Published: over 3 years ago

10.1038/s41380-020-0767-8

AP-1 controls the p11-dependent antidepressant response
Cited by: 25
Author(s): Revathy U. Chottekalapanda, Salina Kalik, Jodi Gresack, Alyssa Ayala, Melanie Gao, Wei Wang, Sarah J. Meller, Ammar Aly, Anne Schaefer, Paul Greengard
Software Mentions: 4
Published: over 4 years ago

10.1038/s41418-019-0285-x

CBP and SRF co-regulate dendritic growth and synaptic maturation
Cited by: 25
Author(s): Beatriz del Blanco, Deisy Guiretti, Romana Tomasoni, María T. Lopez-Cascales, Rafael Muñoz‐Viana, Michał Lipiński, Marilyn Scandaglia, Yaiza Coca, Román Olivares, Luis M. Valor, Eloı́sa Herrera, Ángel Barco
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-83851-4

Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice
Cited by: 30
Author(s): Payel Kundu, Eileen Ruth S. Torres, Keaton Stagaman, Kristin B. Kasschau, Mariam Okhovat, Sarah Holden, Samantha Ward, Kimberly A. Nevonen, Brett A. Davis, Takashi Saito, Takaomi C. Saido, Lucia Carbone, Thomas J. Sharpton, Jacob Raber
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-84647-2

Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)
Cited by: 8
Author(s): Timothy I. Shaw, Li Dong, Liqing Tian, Chenxi Qian, Yu Liu, Bensheng Ju, Anthony A. High, Kanisha Kavdia, Vishwajeeth Pagala, Bridget Shaner, Deqing Pei, John Easton, Laura J. Janke, Shaina N. Porter, Xiaotu Ma, Cheng Cheng, Shondra M. Pruett-Miller, John K. Choi, Jiyang Yu, Junmin Peng, Wei Gu, A. Thomas Look, James R. Downing, Jinghui Zhang
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-017-1159-5

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

10.1038/s41598-021-86821-y

Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach
Cited by: 3
Author(s): Momoko Hamano, Seitaro Nomura, Midori Iida, Issei Komuro, Yoshihiro Yamanishi
Software Mentions: 4
Published: over 3 years ago

10.1016/j.cell.2018.11.041

The Implication of Early Chromatin Changes in X Chromosome Inactivation
Cited by: 188
Author(s): J. Ż̷ylicz, Aurélie Bousard, Kristina Žumer, François Dossin, Eusra Mohammad, Simão Teixeira da Rocha, Björn Schwalb, Laurène Syx, Florent Dingli, Damarys Loew, Patrick Cramer, Edith Heard
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.cell.2018.11.044

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation
Cited by: 115
Author(s): Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B. Meyer, Ricardo J. Miragaia, Graham Dy, Jhuma Pramanik, Kosuke Yusa, Riitta Lahesmaa, Sarah A. Teichmann
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.cell.2019.01.029

Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis
Cited by: 109
Author(s): Javier Gallego-Bartolomé, Wanlu Liu, Peggy Hsuanyu Kuo, Suhua Feng, Basudev Ghoshal, Jason Gardiner, Jiannan Zhao, Soo Young Park, Joanne Chory, Steven E. Jacobsen
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-88516-w

Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB
Cited by: 11
Author(s): Roza Berhanu Lemma, Marit Ledsaak, Bettina M. Fuglerud, Geir Kjetil Sandve, Ragnhild Eskeland, Odd S. Gabrielsen
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-021-07679-y

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens
Cited by: 14
Author(s): Jingyao Ren, Weihua Tian, Keren Jiang, Zhang Wang, Dandan Wang, Zhuanjian Li, Fengbin Yan, Yanbin Wang, Yadong Tian, Kepeng Ou, Hongjun Wang, Xiangtao Kang, Hong Li, Xiaojun Liu
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-019-0258-9

Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups
Cited by: 21
Author(s): Katherine A. Giles, Cathryn M. Gould, Qian Du, Ksenia Skvortsova, Jenny Z. Song, Madhavi P. Maddugoda, Joanna Achinger-Kawecka, Clare Stirzaker, Susan J. Clark, Phillippa C. Taberlay
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-73146-5

Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development
Cited by: 9
Author(s): David Brena, Joan Bertran, Montserrat Porta-de-la-Riva, Yolanda Guillén, Eric Cornes, Dmytro Kukhtar, Lluís Campos-Vicens, Lierni Fernández, Irene Pecharromán, Albert García-López, Abul B.M.M.K. Islam, Laura Marruecos, Anna Bigas, Julián Cerón, Lluís Espinosa
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-78682-8

Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
Cited by: 1
Author(s): Tatsuhiko Yamanaka, Haruko Miyazaki, Asako Tosaki, Sankar N. Maity, Tomomi Shimogori, Nobutaka Hattori, Nobuyuki Nukina
Software Mentions: 4
Published: almost 4 years ago

10.1093/g3journal/jkab190

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes
Cited by: 3
Author(s): Jaclyn M. Noshay, Zhikai Liang, Peng Zhou, Peter A. Crisp, Alexandre P. Marand, Candice N. Hirsch, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers11010025

Stemness, Pluripotentiality, and Wnt Antagonism: sFRP4, a Wnt antagonist Mediates Pluripotency and Stemness in Glioblastoma
Cited by: 51
Author(s): G Bhuvanalakshmi, Naisarg Gamit, Manasi Patil, Frank Arfuso, Gautam Sethi, Arun Dharmarajan, Alan Prem Kumar, Sudha Warrier
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.molmet.2019.12.006

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures
Cited by: 91
Author(s): Vivek Rai, Daniel Quang, Michael R. Erdos, Darren A. Cusanovich, Riza M. Daza, Narisu Narisu, Luli S. Zou, John P. Didion, Yuanfang Guan, Jay Shendure, Stephen C. J. Parker, Francis S. Collins
Software Mentions: 4
Published: almost 5 years ago

10.3390/cancers13112561

Global Chromatin Changes Resulting from Single-Gene Inactivation—The Role of SMARCB1 in Malignant Rhabdoid Tumor
Cited by: 6
Author(s): Colin Kenny, Elaine O’Meara, Mevlüt Ulaş, Karsten Hokamp, Maureen O’Sullivan
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.113.009514

Genomics of CpG Methylation in Developing and Developed Zebrafish
Cited by: 40
Author(s): David McGaughey, Hatice Özel Abaan, Ryan M. Miller, Peter Kropp, Lawrence C. Brody
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-61678-9

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues
Cited by: 23
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ganrea Chanthavixay, Y. Wang, Mary E. Delany, Huaijun Zhou, Pablo J. Ross
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-37872-1

Long non-coding RNA repertoire and open chromatin regions constitute midbrain dopaminergic neuron - specific molecular signatures
Cited by: 10
Author(s): Joshua M. Gendron, Claire Sauty-Colace, Nicolas Beaume, Hugues Cartonnet, Justine Guégan, Damien Ulveling, Corinne Pardanaud-Glavieux, Ivan Moszer, Hélène Cheval, Philippe Ravassard
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-39395-9

Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages
Cited by: 24
Author(s): Cheng Wang, Luca Nanni, Boris Novakovic, Wout Megchelenbrink, Т. Н. Кузнецова, Hendrik G. Stunnenberg, Stefano Ceri, Colin Logie
Software Mentions: 4
Published: over 5 years ago

10.1016/j.molcel.2019.04.002

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities
Cited by: 116
Author(s): Andrea Scelfo, Daniel Fernández-Pérez, Simone Tamburri, Marika Zanotti, Elisa Lavarone, Monica Soldi, Tiziana Bonaldi, Karin Johanna Ferrari, Diego Pasini
Software Mentions: 4
Published: over 5 years ago

10.1016/j.molcel.2021.06.020

BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation
Cited by: 38
Author(s): E. J. Conway, Federico Rossi, Daniel Fernández-Pérez, Eleonora Ponzo, Karin Johanna Ferrari, Marika Zanotti, Daria Manganaro, Simona Rodighiero, Simone Tamburri, Diego Pasini
Software Mentions: 4
Published: about 3 years ago

10.1111/acel.13012

The conserved histone chaperone LIN‐53 is required for normal lifespan and maintenance of muscle integrity in <i>Caenorhabditis elegans</i>
Cited by: 11
Author(s): Stefanie Müthel, Bora Uyar, Ming He, Anne Krause, Burcu Vitrinel, Selman Bulut, Djordje Vasiljevic, Iris Marchal, Stefan Kempa, Altuna Akalin, Baris Tursun
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.673831

MMP24 Contributes to Neuropathic Pain in an FTO-Dependent Manner in the Spinal Cord Neurons
Cited by: 6
Author(s): Longfei Ma, Yangyuxin Huang, Fengjiang Zhang, Dave Schwinn Gao, Na Sun, Jinxuan Ren, Suyun Xia, Jia Li, Xiujuan Peng, Yu Lu, Bao‐Chun Jiang, Min Yan
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-73116-x

Base-resolution methylomes of gliomas bearing histone H3.3 mutations reveal a G34 mutant-specific signature shared with bone tumors
Cited by: 10
Author(s): Yuhei Sangatsuda, Fumihito Miura, Hiromitsu Araki, Masahiro Mizoguchi, Nobuhiro Hata, Daisuke Kuga, Ryusuke Hatae, Yojiro Akagi, Takeo Amemiya, Yutaka Fujioka, Yasuhito Arai, Akihiko Yoshida, Tatsuhiro Shibata, Koji Yoshimoto, Koji Iihara, Takashi Ito
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0235748

Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information
Cited by: 8
Author(s): Koh Onimaru, Osamu Nishimura, Shigehiro Kuraku
Software Mentions: 4
Published: over 4 years ago

10.1016/j.molcel.2021.06.016

Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination
Cited by: 31
Author(s): Ashwin Narain, Pranjali Bhandare, Bikash Adhikari, Simone Backes, Martin Eilers, Lars Dölken, Andreas Schlösser, Florian Erhard, Apoorva Baluapuri, Elmar Wolf
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0145585

Epigenetic Alterations in Density Selected Human Spermatozoa for Assisted Reproduction
Cited by: 20
Author(s): Bolan Yu, Hua Zhou, Min Liu, Ting Zheng, Lu Jiang, Mei Zhao, Xiaohong Xu, Zhaofeng Huang
Software Mentions: 4
Published: almost 9 years ago

10.1038/srep33736

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

10.1038/s41598-017-15822-7

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease
Cited by: 23
Author(s): Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Software Mentions: 4
Published: about 7 years ago

10.1186/s13058-016-0728-y

Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer
Cited by: 11
Author(s): Zhi Hu, Jian‐Hua Mao, Christina Curtis, Ge Huang, Shenda Gu, Laura M. Heiser, Marc E. Lenburg, James E. Korkola, Nora Bayani, Shamith A. Samarajiwa, José A. Seoane, Mark Dane, Amanda Esch, Heidi S. Feiler, Nicholas J. Wang, Mary Ann Hardwicke, Sylvie Laquerre, Jeff W. Jackson, Kenneth W. Wood, Barbara Weber, Paul T. Spellman, Samuel Aparicio, Richard Wooster, Carlos Caldas, Joe W. Gray
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2020.571501

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells
Cited by: 4
Author(s): Andrea Cirino, Ilaria Aurigemma, Monica Franzese, Gabriella Lania, Dario Righelli, Rosa Ferrentino, Elizabeth Illingworth, Claudia Angelini, Antonio Baldini
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0129350

Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection
Cited by: 0
Author(s): Thadeous J. Kacmarczyk, Caitlin Bourque, Xihui Zhang, Yanwen Jiang, Yariv Houvras, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 9 years ago

10.1038/s41597-020-00713-w

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq
Cited by: 2
Author(s): Xiaomeng Zhao, Long Su, Weilin Xu, Sarah Schaack, Cheng Sun
Software Mentions: 4
Published: about 4 years ago

10.1038/sdata.2018.141

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations
Cited by: 12
Author(s): Oriol Fornés, Marius Gheorghe, Phillip A. Richmond, David J. Arenillas, Wyeth W. Wasserman, Anthony Mathelier
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2018.03075

Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis
Cited by: 22
Author(s): Andrea Iannello, Simona Rolla, Alessandro Maglione, Giulio Ferrero, Valentina Bardina, Ilenia Inaudi, Stefania De Mercanti, Francesco Novelli, Lucrezia D'Antuono, Simona Cardaropoli, Tullia Todros, Maria Vittoria Turrini, Cinzia Cordioli, Giorgia Puorro, Angela Marsili, Roberta Lanzillo, Vincenzo Brescia Morra, Francesca Cordero, Michele De Bortoli, Luca Durelli, Andrea Visconti, Santina Cutrupi, Marinella Clerico
Software Mentions: 4
Published: almost 6 years ago

10.1038/sdata.2018.255

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

10.1038/srep25864

Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events
Cited by: 19
Author(s): Graham D. Johnson, Meritxell Jodar, Roger Piqué-Regi, Stephen A. Krawetz
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2019.01253

Signal Integration of IFN-I and IFN-II With TLR4 Involves Sequential Recruitment of STAT1-Complexes and NFκB to Enhance Pro-inflammatory Transcription
Cited by: 32
Author(s): Anna Piaszyk-Borychowska, Lajos Széles, Attila Csermely, Hsüch‐Ching Chiang, Joanna Wesoły, Chien‐Kuo Lee, László Nagy, Hans A.R. Bluyssen
Software Mentions: 4
Published: over 5 years ago

10.1007/s13238-020-00728-4

SIRT7 antagonizes human stem cell aging as a heterochromatin stabilizer
Cited by: 69
Author(s): Shijia Bi, Zunpeng Liu, Zeming Wu, Zehua Wang, Xiaoqian Liu, Si Wang, Jie Ren, Yan Yao, Weiqi Zhang, Moshi Song, Guanghui Liu, Jing Qu
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0214677

PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues
Cited by: 8
Author(s): Samadrita Bhattacharyya, Adwait Amod Sathe, Minoti Bhakta, Chao Xing, Nikhil V. Munshi
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0158936

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome
Cited by: 91
Author(s): Alaguraj Veluchamy, Teddy Jégu, Federico Ariel, David Latrasse, Kadarkaraisamy Mariappan, Soon-Kap Kim, Martín Crespi, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed
Software Mentions: 4
Published: over 8 years ago

10.15252/embr.201846331

Clipped histone H3 is integrated into nucleosomes of <scp>DNA</scp> replication genes in the human malaria parasite <i>Plasmodium falciparum</i>
Cited by: 8
Author(s): Abril Marcela Herrera‐Solorio, Shruthi S. Vembar, Cameron Ross MacPherson, Daniela Lozano-Amado, Gabriela Romero Meza, Beatriz Xoconostle‐Cázares, Rafael Miyazawa Martins, Patty Chen, Miguel Vargas, Artur Scherf, Rosaura Hernández‐Rivas
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0208054

Agnostic detection of genomic alterations by holistic DNA structural interrogation
Cited by: 1
Author(s): Ryan K. Shultzaberger, Rachel E. Abrams, Challise J. Sullivan, Anthony Schmitt, T. W. Thompson, John Dresios
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13100-021-00235-1

Genomic properties of variably methylated retrotransposons in mouse
Cited by: 13
Author(s): Jessica L. Elmer, Amir D. Hay, Noah J. Kessler, Tessa M. Bertozzi, Eve Ainscough, Anne C. Ferguson-Smith
Software Mentions: 4
Published: over 3 years ago

10.1186/s13072-020-00355-7

N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum
Cited by: 11
Author(s): Gayathri Govindaraju, Rajashekar Varma Kadumuri, Devadathan Valiyamangalath Sethumadhavan, C. A. Jabeena, Sreenivas Chavali, Arumugam Rajavelu
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.ppat.1009132

Memory like NK cells display stem cell like properties after Zika virus infection
Cited by: 8
Author(s): Weshely Kujur, Oscar Murillo, Sitaramaraju Adduri, Ramakrishna Vankayalapati, Nagarjun V. Konduru, Sachin Mulik
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2020.566734

Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging
Cited by: 4
Author(s): Yujuan Gui, Mélanie Thomas, Pierre Garcia, Mona Karout, Rashi Halder, Alessandro Michelucci, Heike Kollmus, Cuiqi Zhou, Shlomo Melmed, Klaus Schughart, Rudi Balling, Michel Mittelbronn, Joseph H. Nadeau, Robert W. Williams, Thomas Sauter, Manuel Buttini, Lasse Sinkkonen
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2020.585746

Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium
Cited by: 7
Author(s): Peter McErlean, A. Paul Kelly, Jaideep Dhariwal, Max Kirtland, Julie Watson, Ismael Ranz, Janet L. Smith, Alka Saxena, David J. Cousins, Antoon van Oosterhout, Roberto Solari, Michael R. Edwards, Sebastian L. Johnston, Paul Lavender
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0238076

Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration
Cited by: 3
Author(s): Yuko Oda, Thai Nguyen, Akiko Hata, Mark B. Meyer, J. Wesley Pike, Daniel Bikle
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-018-5170-3

Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin
Cited by: 19
Author(s): Jinhee Park, William J. Belden
Software Mentions: 4
Published: about 6 years ago

10.15252/emmm.201606198

<scp>LIMT</scp> is a novel metastasis inhibiting lnc<scp>RNA</scp> suppressed by <scp>EGF</scp> and downregulated in aggressive breast cancer
Cited by: 68
Author(s): Aldema Sas‐Chen, Miriam Ragle Aure, Limor Leibovich, Sílvia Carvalho, Yehoshua Enuka, Cindy Körner, Maria Polycarpou‐Schwarz, Sara Lavi, Nava Nevo, Yuri Kuznetsov, Justin C. Yuan, Francisco Azuaje, Igor Ulitsky, Sven Diederichs, Stefan Wiemann, Zohar Yakhini, Vessela N. Kristensen, Anne‐Lise Børresen‐Dale, Yosef Yarden, Torill Sauer, Jürgen Geisler, Solveig Hofvind, Tone Frost Bathen, Elin Borgen, Olav Engebråten, Øystein Fodstad, Øystein Garred, Gry Aarum Geitvik, Rolf Kåresen, Bjørn Naume, Gunhild Mari Mælandsmo, Hege G. Russnes, Ellen Schlichting, Thérese Sørlie, Ole Christian Lingjærde, Kristine Kleivi Sahlberg, Helle Skjerven, Britt Fritzman
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-018-5184-x

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

10.1371/journal.pgen.1004604

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Cited by: 77
Author(s): Andrew D. Hoffmann, Xinan Yang, Ozanna Burnicka-Turek, Joshua D. Bosman, Xiaomeng Ren, Jeffrey D. Steimle, Steven A. Vokes, Andrew P. McMahon, Vladimir V. Kalinichenko, Ivan P. Moskowitz
Software Mentions: 4
Published: about 10 years ago

10.1083/jcb.202008101

DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A
Cited by: 30
Author(s): Kelly E. Leon, Raquel Buj, Elizabeth Lesko, Erika S. Dahl, Chi‐Wei Chen, Naveen K. Tangudu, Yuka Imamura‐Kawasawa, Andrew V. Kossenkov, Ryan P. Hobbs, Katherine M. Aird
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1008633

Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection
Cited by: 9
Author(s): Xiaodong Kong, Guisheng Wei, Nan Chen, Shudi Zhao, Yongrong Shen, Jianjia Zhang, Li Yang, Xiaoqun Zeng, Xiaoxia Wu
Software Mentions: 4
Published: over 4 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203