pypi: MACS2 | Projects | Ecosyste.ms: Papers

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

10.7554/eLife.24570

EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Cited by: 36
Author(s): Shanshan Ai, Yong Peng, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence Prendiville, Wen Zheng, Yuli Liu, Stuart H. Orkin, Dazhi Wang, Jia Yu, William T. Pu, Aibin He
Software Mentions: 4
Published: over 7 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

10.7554/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

10.7554/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

10.26508/lsa.202000944

In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood
Cited by: 6
Author(s): Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fátima Smagulova
Software Mentions: 4
Published: over 3 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

10.26508/lsa.202000848

Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis
Cited by: 19
Author(s): Martin Rougée, Leandro Quadrana, Jérôme Zervudacki, Valentin Hure, Vincent Colot, Lionel Navarro, Angélique Deleris
Software Mentions: 4
Published: almost 4 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

10.3390/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

10.1186/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

10.1038/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/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

10.1186/s13059-020-02062-8

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis
Cited by: 26
Author(s): Lejon E. M. Kralemann, S. Liu, Minerva S. Trejo-Arellano, Rafael Muñoz‐Viana, Claudia Köhler, Lars Hennig
Software Mentions: 4
Published: over 4 years ago

10.1186/s13072-021-00393-9

H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum
Cited by: 10
Author(s): Jessica Connacher, Gabrielle A. Josling, Lindsey M. Orchard, Janette Reader, Manuel Llinás, Lyn‐Marié Birkholtz
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

10.1186/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/s13059-019-1880-3

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/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

10.15252/embr.201846331

Clipped histone H3 is integrated into nucleosomes of <scp>DNA</scp> replication genes in the human malaria parasite Plasmodium falciparum
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

10.7554/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

10.1128/JVI.01399-20

Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level
Cited by: 22
Author(s): Caroline C. Friedel, Adam W. Whisnant, Lara Djaković, Andrzej Rutkowski, Marie-Sophie Friedl, Michael Kluge, James C Williamson, Somesh Sai, Ramón Vidal, Sascha Sauer, Thomas Hennig, Arnhild Grothey, Andrea Milić, Bhupesh K. Prusty, Paul J. Lehner, Nicholas J Matheson, Florian Erhard, Lars Dölken
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1004290

Copy Number Variation Is a Fundamental Aspect of the Placental Genome
Cited by: 55
Author(s): Roberta L. Hannibal, Edward B. Chuong, Juan Carlos Rivera-Mulia, David M. Gilbert, Anton Valouev, Julie C. Baker
Software Mentions: 3
Published: over 10 years ago

10.15252/emmm.201911099

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

10.15252/emmm.202012574

Cooperation of LIM domain‐binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia
Cited by: 2
Author(s): Tetsuo Ohnishi, Yuji Kiyama, Fumiko Arima-Yoshida, Mitsutaka Kadota, Tomoe Ichikawa, Kazuyuki Yamada, Akïharu Watanabe, Hideki Ohba, Kaori Tanaka, Akihiro Nakaya, Yasue Horiuchi, Yoshimi Iwayama, Manabu Toyoshima, Itone Ogawa, Chie Shimamoto-Mitsuyama, Motoko Maekawa, Shabeesh Balan, Makoto Arai, Mitsuhiro Miyashita, Kazuya Toriumi, Yayoi Nozaki, Rumi Kurokawa, Kazuhiro Suzuki, Akane Yoshikawa, Tomoko Toyota, Toshihiko Hosoya, Hiroyuki Okuno, Haruhiko Bito, Masanari Itokawa, Shigehiro Kuraku, Toshiya Manabe, Takeo Yoshikawa
Software Mentions: 3
Published: over 3 years ago

10.3390/ani9080523

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

10.15252/emmm.202012112

Resolving mechanisms of immune‐mediated disease in primary <scp>CD</scp> 4 T cells
Cited by: 27
Author(s): Christophe Bourges, Abigail F. Groff, Oliver S. Burren, Chiara Gerhardinger, Kaia Mattioli, Anna Hutchinson, Theodore Hu, Tanmay Anand, Madeline Epping, Chris Wallace, Kenneth G. C. Smith, John L. Rinn, James C. Lee
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009708

Ras/ERK and PI3K/AKT signaling differentially regulate oncogenic ERG mediated transcription in prostate cells
Cited by: 6
Author(s): Brady G. Strittmatter, Travis J. Jerde, Peter C. Hollenhorst
Software Mentions: 3
Published: over 3 years ago

10.15252/embj.201899016

miR‐200/375 control epithelial plasticity‐associated alternative splicing by repressing the <scp>RNA</scp> ‐binding protein Quaking
Cited by: 75
Author(s): Katherine A. Pillman, C. Phillips, Suraya Roslan, John Toubia, B Kate Dredge, Andrew G. Bert, Rachael Lumb, Daniel Neumann, Xiaochun Li, Simon J. Conn, Dawei Liu, Cameron P. Bracken, David Lawrence, Nataly Stylianou, Andreas W. Schreiber, Wayne D. Tilley, Brett G. Hollier, Yeesim Khew‐Goodall, Luke A. Selth, Gregory J. Goodall, Philip A. Gregory
Software Mentions: 3
Published: over 6 years ago

10.1016/j.ebiom.2016.06.048

Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies
Cited by: 33
Author(s): Karin Hellner, Fabrizio Miranda, Donatien Fotso Chedom, Sandra Herrero-González, Daniel M. Hayden, Rick Tearle, Mara Artibani, Mohammad KaramiNejadRanjbar, Ruth M. Williams, Kezia Gaitskell, Samar Elorbany, Ruoyan Xu, Alexandros Laios, Petronela Buiga, Karim Ahmed, Sunanda Dhar, Rebecca Yu Zhang, Leticia Campo, Kevin A. Myers, M. Luz Lozano, Maria Ruiz‐Miró, Sònia Gatius, Alba Mota, Gema Moreno‐Bueno, Xavier Matías‐Guiu, Javier Benı́tez, Lorna Witty, Gil McVean, Simon J. Leedham, Ian Tomlinson, Radoje Drmanac, Jean‐Baptiste Cazier, Robert J. Klein, Kevin Dunne, Robert C. Bast, Stephen Kennedy, A. Bassim Hassan, Stefano Lise, María José García, Brock A. Peters, Christopher Yau, Tatjana Sauka‐Spengler, Ahmed A. Ahmed
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-020-07268-5

ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus
Cited by: 9
Author(s): Dayle Johnston, JaeWoo Kim, Jeremy F. Taylor, Bernadette Earley, Matthew S. McCabe, Ken Lemon, Catherine Duffy, Michael McMenamy, S. L. Cosby, Sinéad M. Waters
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1009044

NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation
Cited by: 18
Author(s): Yuta Hiraike, Hironori Waki, Kana Miyake, Takahito Wada, Misato Oguchi, Kaede Saito, Sadami Tsutsumi, Hiroyuki Aburatani, Toshimasa Yamauchi, Takashi Kadowaki
Software Mentions: 3
Published: about 4 years ago

10.7150/thno.39093

Genome-wide interaction target profiling reveals a novel Peblr20-eRNA activation pathway to control stem cell pluripotency
Cited by: 22
Author(s): Cong Wang, Lin Jia, Yichen Wang, Zhonghua Du, Lei Zhou, Wei Xue, Hui Li, Shilin Zhang, Huiling Chen, Naifei Chen, Jingcheng Chen, Yanbo Zhu, Yuanyuan Nie, Ilkay Celic, Sujun Gao, Songling Zhang, Andrew R. Hoffman, Wei Li, Ji-Fan Hu, Jiuwei Cui
Software Mentions: 3
Published: almost 5 years ago

10.1242/dev.199628

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

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: almost 8 years ago

10.1242/dev.190181

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

10.1371/journal.pgen.1008002

Deletion of Cdkn1b in ACI rats leads to increased proliferation and pregnancy-associated changes in the mammary gland due to perturbed systemic endocrine environment
Cited by: 10
Author(s): Ling Ding, Lauren B. Shunkwiler, Nicholas W. Harper, Yang Zhao, Kunihiko Hinohara, Sung Jin Huh, Muhammad B. Ekram, Jan Guz, Michael J. Kern, Alexander Awgulewitsch, James D. Shull, Bart M. G. Smits, Kornélia Polyák
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07373-z

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

10.1093/database/bav050

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

10.1016/j.ccell.2020.03.022

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

10.1038/s41598-021-88003-2

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

10.1038/s41598-021-96263-1

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

10.1371/journal.pgen.1007884

Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi
Cited by: 12
Author(s): Valentina del Olmo Toledo, Robert Puccinelli, Polly M. Fordyce, J. Christian Pérez
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-018-1531-0

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

10.1038/s41598-021-81577-x

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

10.1038/s41598-020-74537-4

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

10.1186/s12864-018-4992-3

Dynamic changes in ORC localization and replication fork progression during tissue differentiation
Cited by: 9
Author(s): Brian L Hua, George W. Bell, Helena Kashevsky, Jessica R. Von Stetina, Terry L. Orr‐Weaver
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008540

MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen
Cited by: 8
Author(s): Hannah Weber, Rachel Ruoff, Michael J. Garabedian
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-018-1483-4

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

10.1038/s41598-020-71447-3

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

10.1038/s42003-019-0543-y

The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia
Cited by: 23
Author(s): Eviatar Weizman, Oren Levy
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-019-1642-2

Identification of transcription factor binding sites using ATAC-seq
Cited by: 284
Author(s): Li Z, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-69443-8

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

10.1038/s42003-019-0718-6

Monocytes undergo multi-step differentiation in mice during oral infection by Toxoplasma gondii
Cited by: 8
Author(s): Aurélie Detavernier, Abdulkader Azouz, Hussein Shehade, Marion Splittgerber, Laurye Van Maele, Muriel Nguyen, Séverine Thomas, Younès Achouri, David Švec, Emilie Calonne, François Fuks, Guillaume Oldenhove, Stanislas Goriely
Software Mentions: 3
Published: almost 5 years ago

10.1038/s42003-021-02209-8

Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes
Cited by: 4
Author(s): Hong Wang, Aiping Duan, Jing Zhang, Qi Wang, Yufei Xing, Zhaohui S. Qin, Zhihong Liu, Jingping Yang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009318

Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis
Cited by: 10
Author(s): Jonathan Lenz, Robert Liefke, Julianne Funk, Samuel Shoup, Andrea Nist, Thorsten Stiewe, Robert A. Schulz, Yumiko Tokusumi, Lea Albert, Hartmann Raifer, Klaus Förstemann, Olalla Vázquez, Tsuyoshi Tokusumi, Nancy Fossett, Alexander Brehm
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-018-1463-8

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

10.1038/s42003-019-0665-2

Transcription factor Znf2 coordinates with the chromatin remodeling SWI/SNF complex to regulate cryptococcal cellular differentiation
Cited by: 18
Author(s): Jianfeng Lin, Youbao Zhao, Aileen R Ferraro, Ence Yang, Zachary A. Lewis, Xiaorong Lin
Software Mentions: 3
Published: about 5 years ago

10.1038/s41408-021-00421-7

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

10.1371/journal.pgen.1007681

Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
Cited by: 37
Author(s): Dharini Iyer, Quanyi Zhao, Robert Wirka, Ameay V. Naravane, Trieu Nguyen, Boxiang Liu, Manabu Nagao, Paul Cheng, Clint L. Miller, Juyong Brian Kim, Milos Pjanic, Thomas Quertermous
Software Mentions: 3
Published: about 6 years ago

10.1002/bit.26891

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

10.1186/s13059-019-1694-3

Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery
Cited by: 77
Author(s): Bo Hu, Nan Wang, Xiuli Bi, Ezgi Süheyla Karaaslan, Anna-Lena Weber, Weiren Zhu, Kenneth W. Berendzen, Chang Liu
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-018-1464-7

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

10.1038/s41598-020-67850-5

Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer
Cited by: 8
Author(s): Kristan E. van der Vos, Daniël J. Vis, Ekatarina Nevedomskaya, Y. Kim, Woonyoung Choi, David J. McConkey, Lodewyk Wessels, Bas W.G. van Rhijn, Wilbert Zwart, Michiel S. van der Heijden
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-45841-5

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

10.1186/s13148-020-00965-8

5-Hydroxymethylation highlights the heterogeneity in keratinization and cell junctions in head and neck cancers
Cited by: 8
Author(s): Siyu Liu, Marcell Costa de Medeiros, Evan Fernandez, Katie R. Zarins, Raymond G. Cavalcante, Tingting Qin, Gregory T. Wolf, María E. Figueroa, Nisha J. D’Silva, Laura S. Rozek, Maureen A. Sartor
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-019-42292-w

Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis
Cited by: 19
Author(s): Marina R. Hadjicharalambous, Benoı̂t Roux, Eszter Csomor, Carol Feghali‐Bostwick, Lynne A. Murray, D. S. Clarke, Mark A. Lindsay
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-56277-2

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

10.1186/s13148-020-00921-6

Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues
Cited by: 12
Author(s): Hang Gyeong Chin, Zhiyi Sun, Udayakumar S. Vishnu, Pengying Hao, Paloma Cejas, George Spracklin, Pierre‐Olivier Estève, Shuang-yong Xu, Henry W. Long, Sriharsa Pradhan
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-020-59469-3

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

10.3390/cells10061271

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

10.1186/s13059-017-1247-6

NicE-seq: high resolution open chromatin profiling
Cited by: 41
Author(s): V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre‐Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf, Sriharsa Pradhan
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-34420-9

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

10.3390/cells9061435

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

10.1038/s41598-018-35868-5

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

10.1016/j.stem.2019.02.004

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance
Cited by: 66
Author(s): Jessica Bertolini, Rebecca Favaro, Yanfen Zhu, Miriam Pagin, Chew Yee Ngan, Chee-Hong Wong, Harianto Tjong, Marit W. Vermunt, Ben Martynoga, Cristiana Barone, Jessica Mariani, Marcos J. Cardozo, Noemí Tabanera, Federico Zambelli, Sara Mercurio, Sergio Ottolenghi, Paul Robson, Menno P. Creyghton, Paola Bovolenta, Giulio Pavesi, François Guillemot, Silvia K. Nicolis, Chia‐Lin Wei
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-017-1376-y

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

10.1038/s41598-018-36057-0

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

10.1038/s41598-020-61514-0

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

10.1038/s41422-018-0074-y

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

10.1371/journal.pbio.3001364

The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation
Cited by: 14
Author(s): Cecilia B. Levandowski, Taylor Jones, Margaret Gruca, Sivapriya Ramamoorthy, Robin D. Dowell, Dylan J. Taatjes
Software Mentions: 3
Published: over 3 years ago

10.1093/bioinformatics/btw127

SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Cited by: 3
Author(s): Christian Arnold, Pooja Bhat, Judith B. Zaugg
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-13186-6

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

10.1371/journal.pbio.3000580

12-h clock regulation of genetic information flow by XBP1s
Cited by: 34
Author(s): Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C. Dacso, Colleen A. McClung, Bert W. O’Malley, Silvia Liu, Bokai Zhu
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.celrep.2019.08.040

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

10.1186/s12915-019-0687-8

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

10.1038/s41598-018-29865-x

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

10.1016/j.celrep.2021.109349

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

10.1186/s12860-020-00251-8

Identification of universal and cell-type specific p53 DNA binding
Cited by: 14
Author(s): Antonina Hafner, Lyubov Kublo, Michael Tsabar, Galit Lahav, Jacob Stewart-Ornstein
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-020-3510-1

A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks
Cited by: 3
Author(s): Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva, Riccardo Bellazzi
Software Mentions: 3
Published: over 4 years ago

10.1016/j.celrep.2018.06.003

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development
Cited by: 115
Author(s): Lucas J.T. Kaaij, Robin H. van der Weide, René F. Ketting, Elzo de Wit
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2021.108759

Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M
Cited by: 22
Author(s): Jianming Wang, Patricia Rojas, Jingwen Mao, Martina Mustè Sadurnì, Olivia Garnier, Songshu Xiao, Martin R. Higgs, Paloma García, Marco Saponaro
Software Mentions: 3
Published: almost 4 years ago

10.1016/j.celrep.2021.109725

Enhancer recruitment of transcription repressors RUNX1 and TLE3 by mis-expressed FOXC1 blocks differentiation in acute myeloid leukemia
Cited by: 10
Author(s): Fabrizio Simeoni, Isabel Romero-Camarero, Francesco Camera, Fabio Amaral, Oliver Sinclair, Evangelia K. Papachristou, Gary J. Spencer, Michael Lie-A-Ling, Georges Lacaud, Daniel H. Wiseman, Jason S. Carroll, Tim C. P. Somervaille
Software Mentions: 3
Published: about 3 years ago

10.1186/s13059-018-1430-4

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

10.1038/srep32417

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

10.1038/s41423-019-0219-z

The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection
Cited by: 32
Author(s): Xiangyu Chen, Guoshuai Cao, Jialin Wu, Xinxin Wang, Zhiwei Pan, Jianbao Gao, Tian Qin, Lifan Xu, Zhirong Li, Yaxing Hao, Qizhao Huang, Pengcheng Wang, Minglu Xiao, Luoyingzi Xie, Shupei Tang, Zhenyu Liu, Li Hu, Jianfang Tang, Ran He, Li Wang, Xinyuan Zhou, Yuzhang Wu, Mengjie Chen, Beicheng Sun, Bo Zhu, Jun Huang, Lilin Ye
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-017-1173-7

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

10.1038/s41598-017-04370-9

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

10.1038/s41598-018-31101-5

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

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203