pypi: deepTools | Projects | Ecosyste.ms: Papers

10.12688/wellcomeopenres.16911.2

Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018
Cited by: 0
Author(s): Martha M Luka, Everlyn Kamau, Zaydah R. de Laurent, John M. Morobe, Leonard K. Alii, D. James Nokes, Charles N. Agoti
Software Mentions: 1
Published: about 3 years ago

10.1002/advs.202004504

OTUD7B Deubiquitinates LSD1 to Govern Its Binding Partner Specificity, Homeostasis, and Breast Cancer Metastasis
Cited by: 19
Author(s): Zhicheng Gong, Aicun Li, Jian Ding, Qing Li, Lei Zhang, Yuanpei Li, Zhe Meng, Fei Chen, Jialiang Huang, Dawang Zhou, Ronggui Hu, Jing Ye, Wen Li, Han You
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1009225

The H3.3K27M oncohistone antagonizes reprogramming in Drosophila
Cited by: 8
Author(s): Kami Ahmad, Steven Henikoff
Software Mentions: 1
Published: over 3 years ago

10.3390/plants9040523

Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance
Cited by: 4
Author(s): Medhat Mahmoud, Joanna Gracz‐Bernaciak, Marek Żywicki, Wojciech M. Karłowski, Tomasz Twardowski, Agata Tyczewska
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pbio.2005886

Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock
Cited by: 103
Author(s): Kenneth A. Dyar, Michael Hubert, Ashfaq Ali Mir, Stefano Ciciliot, Dominik Lutter, Franziska Greulich, Fabiana Quagliarini, Maximilian Kleinert, Katrin Fischer, Thomas O. Eichmann, Lauren E. Wright, Marcia Ivonne Peña Paz, Alberto Casarin, Vanessa Pertegato, Vanina Romanello, Mattia Albiero, Sara Mazzucco, Gaudenzio Meneghesso, Leonardo Salviati, Gianni Biolo, Bert Blaauw, Stefano Schiaffino, N. Henriette Uhlenhaut
Software Mentions: 1
Published: over 6 years ago

10.1186/s13072-020-00364-6

Epigenomic landscape of enhancer elements during Hydra head organizer formation
Cited by: 10
Author(s): Puli Chandramouli Reddy, Akhila Gungi, Suyog Ubhe, Sanjeev Galande
Software Mentions: 1
Published: about 4 years ago

10.1016/j.celrep.2018.10.079

BET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication
Cited by: 38
Author(s): Akhil Bowry, Ann Liza Piberger, Patricia Rojas, Marco Saponaro, Eva Petermann
Software Mentions: 1
Published: about 6 years ago

10.1016/j.celrep.2021.108797

Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts
Cited by: 14
Author(s): Kevin S. Lang, Houra Merrikh
Software Mentions: 1
Published: over 3 years ago

10.1186/s13072-020-00381-5

Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes
Cited by: 7
Author(s): Luke T. Marr, Josefina Ocampo, David Clark, Jeffrey J. Hayes
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pgen.1004853

Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
Cited by: 17
Author(s): О. С. Новікова, Dorie Smith, Ingrid Hahn, Arthur Beauregard, Marlene Belfort
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.celrep.2020.108319

Integrator-Dependent and Allosteric/Intrinsic Mechanisms Ensure Efficient Termination of snRNA Transcription
Cited by: 15
Author(s): Lee Davidson, Laura Francis, Joshua D. Eaton, Steven West
Software Mentions: 1
Published: about 4 years ago

10.1186/s40478-021-01124-7

Differentiated glioblastoma cells accelerate tumor progression by shaping the tumor microenvironment via CCN1-mediated macrophage infiltration
Cited by: 23
Author(s): Atsuhito Uneda, Kazuhiko Kurozumi, Akiko Fujimura, Kentaro Fujii, Joji Ishida, Yosuke Shimazu, Yoshihiro Otani, Yusuke Tomita, Yasuhiko Hattori, Yuji Matsumoto, Nobushige Tsuboi, Keigo Makino, Shuichiro Hirano, Atsunori Kamiya, Isao Date
Software Mentions: 1
Published: over 3 years ago

10.3390/genes12071018

Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites
Cited by: 5
Author(s): Amr Galal Abd El-Raheem Ibrahim, Ricardo Zorzetto Nicoliello Vêncio, Alan Péricles Rodrigues Lorenzetti, Tie Koide
Software Mentions: 1
Published: over 3 years ago

10.3390/ani11051315

Genomic Imprinting at the Porcine DIRAS3 Locus
Cited by: 4
Author(s): Jinsoo Ahn, In-Sul Hwang, Mi-Ryung Park, Seongsoo Hwang, Kichoon Lee
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1009433

Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria
Cited by: 7
Author(s): Satish Adhikari, Ivan Erill, Patrick D. Curtis
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0184500

Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers
Cited by: 8
Author(s): Julie M. Lander, Dorothy M. Supp, Hua He, Lisa J. Martin, Marc E. Rothenberg, Matthew T. Weirauch, Steven T. Boyce, Raphael Kopan
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.66290

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay
Cited by: 6
Author(s): Hiroaki Tachiwana, Mariko Dacher, Kazuhira Maehara, Akihito Harada, Yosuke Seto, Ryohei Katayama, Yasuyuki Ohkawa, Hiroshi Kimurâ, Hitoshi Kurumizaka, Noriko Saitoh
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.679854

A Master Regulator BrpR Coordinates the Expression of Multiple Loci for Robust Biofilm and Rugose Colony Development in Vibrio vulnificus
Cited by: 6
Author(s): Seung-Ho Hwang, Ha Na Im, Sang Ho Choi
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.31706

Revised roles of ISL1 in a hES cell-based model of human heart chamber specification
Cited by: 31
Author(s): Roberto Quaranta, Jakob Fell, Frank Rühle, Jyoti Rao, Ilaria Piccini, Marcos J. Araúzo-Bravo, Arie O. Verkerk, Monika Stoll, Boris Greber
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.16384

Elevated TATA-binding protein expression drives vascular endothelial growth factor expression in colon cancer
Cited by: 11
Author(s): Sandra Johnson, Justin J. Lin, Christopher J. Walkey, Michael P. Leathers, Cristian Coarfa, Deborah L. Johnson
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.28042

Pim kinase inhibitor co-treatment decreases alternative non-homologous end-joining DNA repair and genomic instability induced by topoisomerase 2 inhibitors in cells with FLT3 internal tandem duplication
Cited by: 2
Author(s): Mario Scarpa, Shivani Kapoor, Eric S. Tvedte, Kshama A. Doshi, Ying Zou, Pratibha Singh, Jonelle K. Lee, Aditi Chatterjee, Muhamad Ali, Robin E. Bromley, Julie C. Dunning Hotopp, Feyruz V. Rassool, Maria R. Baer
Software Mentions: 1
Published: about 3 years ago

10.1186/s12916-020-01736-1

Immediate and durable effects of maternal tobacco consumption alter placental DNA methylation in enhancer and imprinted gene-containing regions
Cited by: 24
Author(s): Sophie Rousseaux, Emie Seyve, Florent Chuffart, Ekaterina Bourova-Flin, Mériem Benmerad, Charles Munier, Anne Forhan, Barbara Heude, Valérie Siroux, Rémy Slama, Jörg Tost, Daniel Vaiman, Saadi Khochbin, Johanna Lepeule, Isabella Annesi‐Maesano, Julien Bernard, Jérémie Botton, Charles Munier, Patricia Dargent‐Molina, Blandine de Lauzon‐Guillain, Pierre Ducimetière, Maria De Agostini, B Foliguet, Anne Forhan, Xavier Fritel, Alice Germa, Valérie Goua, R. Hankard, Barbara Heude, Monique Kaminski, Béatrice Larroque, Nathalie Lelong, Johanna Lepeule, G Magnin, Laëtitia Marchand, Cathy Nabet, Fabrice H.F. Pierre, Rémy Slama, Marie‐Josèphe Saurel‐Cubizolles, M. Schweitzer, O. Thiébaugeorges
Software Mentions: 1
Published: about 4 years ago

10.1038/s42003-021-02282-z

Loss of histone methyltransferase ASH1L in the developing mouse brain causes autistic-like behaviors
Cited by: 16
Author(s): Yuen Gao, Natalia Duque-Wilckens, Mohammad B. Aljazi, Yan Wu, Adam J. Moeser, George I. Mias, Alfred J. Robison, Jun He
Software Mentions: 1
Published: over 3 years ago

10.1186/s13104-018-3516-1

Dynamic bimodal changes in CpG and non-CpG methylation genome-wide upon CGGBP1 loss-of-function
Cited by: 14
Author(s): Divyesh Patel, Manthan Patel, Bengt Westermark, Uma Singh
Software Mentions: 1
Published: over 6 years ago

10.1242/dmm.046573

Disruption of a Hedgehog-Foxf1-Rspo2 signaling axis leads to tracheomalacia and a loss of Sox9+ tracheal chondrocytes
Cited by: 13
Author(s): Talia Nasr, Andrea M. Holderbaum, Praneet Chaturvedi, Kavita Agarwal, Jessica L. Kinney, Keziah Daniels, Stephen L. Trisno, Vladimir Ustiyan, John M. Shannon, James M. Wells, Débora Sinner, Vladimir V. Kalinichenko, Aaron M. Zorn
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13059-020-02040-0

Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae
Cited by: 31
Author(s): Chenxi Qiu, Hailing Jin, Irina O. Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William Lai, Richard P. Metz, Charles D. Johnson, Sing Hoi Sze, B. Franklin Pugh, Bryce E. Nickels, Craig D. Kaplan
Software Mentions: 1
Published: over 4 years ago

10.1186/s13059-019-1767-3

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis
Cited by: 59
Author(s): Kinga Rutowicz, Maciej Lirski, Benoît Mermaz, Gianluca Teano, Jasmin Schubert, Imen Mestiri, Magdalena A. Kroteń, Tohnyui Ndinyanka Fabrice, Simon Fritz, Stefan Grob, Christoph Ringli, Lusik Cherkezyan, Frédy Barneche, Andrzej Jerzmanowski, Célia Baroux
Software Mentions: 1
Published: over 5 years ago

10.1042/BSR20201053

Integrative analysis of DNA methylation and gene expression profiles identified potential breast cancer-specific diagnostic markers
Cited by: 10
Author(s): Xinhua Liu, Yonglin Peng, Ju Wang
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8010105

Rules and Exceptions: The Role of Chromosomal ParB in DNA Segregation and Other Cellular Processes
Cited by: 27
Author(s): Adam Kawałek, Paweł Wawrzyniak, Aneta Agnieszka Bartosik, Grażyna Jagura-Burdzy
Software Mentions: 1
Published: almost 5 years ago

10.1093/femsre/fuz018

Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete?
Cited by: 52
Author(s): Jérôme Collemare, Michael Seidl
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-018-1564-4

Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions
Cited by: 43
Author(s): Han Chen, Haidong Shu, Liyuan Wang, Fan Zhang, Xi Li, Sylvans Ochieng Ochola, Fei Mao, Hongyu Ma, Wenwu Ye, Tingting Gu, Lubin Jiang, Yufeng Wu, Yuanchao Wang, Sophien Kamoun, Suomeng Dong
Software Mentions: 1
Published: about 6 years ago

10.1186/s13100-021-00237-z

Methylation of rRNA as a host defense against rampant group II intron retrotransposition
Cited by: 2
Author(s): Justin M Waldern, Dorie Smith, Carol Lyn Piazza, E. Bailey, Nicholas J. Schiraldi, Reza Nemati, Dan Fabris, Marlene Belfort, О. С. Новікова
Software Mentions: 1
Published: over 3 years ago

10.1186/s12964-020-0510-8

Epigenetic induction of tumor stemness via the lipopolysaccharide-TET3-HOXB2 signaling axis in esophageal squamous cell carcinoma
Cited by: 16
Author(s): Fan Xu, Zhonghe Liu, Ronghua Liu, Lu Chen, Lin Wang, Wei Mao, Qinqing Zhu, Huankai Shou, Xiaoying Zhang, Yin Li, Yiwei Chu, Jie Gu
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-80846-5

Transcriptome-wide high-throughput mapping of protein–RNA occupancy profiles using POP-seq
Cited by: 6
Author(s): Mansi Srivastava, Rajneesh Srivastava, Sarath Chandra Janga
Software Mentions: 1
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: pypi: deepTools

Papers Mentioning deepTools 435