pypi: deepTools | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0218458

p73 regulates epidermal wound healing and induced keratinocyte programming
Cited by: 18
Author(s): J. Scott Beeler, Clayton B. Marshall, Paula I. González-Ericsson, Timothy M. Shaver, Gabriela L. Santos Guasch, Spencer Lea, Kimberly N. Johnson, Hailing Jin, Bryan J. Venters, Melinda E. Sanders, Jennifer A. Pietenpol
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-021-07774-0

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
Cited by: 10
Author(s): Aileen R Ferraro, Abigail J Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-020-00760-3

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
Cited by: 32
Author(s): Aileen P. Szczepanski, Zibo Zhao, Victoria Sosnowski, Young Ah Goo, Elizabeth T. Bartom, Lu Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-3100-2

RACS: rapid analysis of ChIP-Seq data for contig based genomes
Cited by: 4
Author(s): Marcelo Ponce, Alejandro Saettone, Syed Nabeel‐Shah, Jeffrey Fillingham
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-015-0597-1

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis
Cited by: 127
Author(s): Julieta L. Mateos, Pedro Madrigal, Kazuhiko Tsuda, Vimal Rawat, René Richter, Maida Romera-Branchat, Fabio Fornara, Korbinian Schneeberger, Paweł Krajewski, George Coupland
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0238924

Exploring the potential of comparative de novo transcriptomics to classify Saccharomyces brewing yeasts
Cited by: 1
Author(s): Jürgen Behr, Meike Kliche, Andreas Geißler, Rudi F. Vogel
Software Mentions: 5
Published: about 4 years ago

10.3390/genes12081291

Regional Specific Differentiation of Integumentary Organs: Regulation of Gene Clusters within the Avian Epidermal Differentiation Complex and Impacts of SATB2 Overexpression
Cited by: 3
Author(s): Gee-Way Lin, Yung-Chih Lai, Ya-Chen Liang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.61894

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
Cited by: 45
Author(s): Michael Borg, Ranjith Papareddy, Rodolphe Dombey, Elin Axelsson, Michael D. Nodine, David Twell, Frédéric Berger
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.50541

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Cited by: 62
Author(s): Rita A Batista, Jordi Moreno‐Romero, Yue Qiu, Joram van Boven, Juan Santos‐González, Duarte D. Figueiredo, Claudia Köhler
Software Mentions: 5
Published: almost 5 years ago

10.1016/j.stem.2017.10.013

Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming
Cited by: 34
Author(s): Tyson Joel Ruetz, Ulrich Pfisterer, Bruno Di Stefano, James Ashmore, Meryam Beniazza, Tian V. Tian, Daniel F. Kaemena, Luca Tosti, Wenfang Tan, Jonathan Manning, Eleni Chantzoura, Daniella Rylander Ottosson, Samuel Collombet, Anna Johnsson, Erez Cohen, Kosuke Yusa, Sten Linnarsson, Thomas Graf, Malin Parmar, Keisuke Kaji
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41422-020-0385-7

Stabilization of heterochromatin by CLOCK promotes stem cell rejuvenation and cartilage regeneration
Cited by: 51
Author(s): Chuqian Liang, Zunpeng Liu, Moshi Song, Wei Li, Zeming Wu, Zehua Wang, Qiaoran Wang, Si Wang, Yan Ke, Liang Sun, Tomoaki Hishida, Yanning Cai, Juan Carlos Izpisúa Belmonte, Pedro Guillén, Piu Chan, Qi Zhou, Weiqi Zhang, Jing Qu, Guanghui Liu
Software Mentions: 5
Published: over 4 years ago

10.26508/lsa.202000864

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories
Cited by: 12
Author(s): Sophie G Kellaway, Peter Keane, Benjamin Edginton-White, Kakkad Regha, Ella Kennett, Constanze Bonifer
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1008799

BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1
Cited by: 9
Author(s): Shu Wu, Yuanlong Ge, Xiaocui Li, Yiding Yang, Huan Zhou, Kaixuan Lin, Zepeng Zhang, Yong Zhao
Software Mentions: 5
Published: over 4 years ago

10.1186/s40478-018-0614-1

Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, H3 K27M-mutant’ discriminate two subgroups based on the type of histone H3 mutated and not supratentorial or infratentorial location
Cited by: 78
Author(s): David Castel, Cathy Philippe, Thomas Kergrohen, Martin Sill, Jane Merlevede, E. Barret, Stéphanie Puget, Christian Sainte‐Rose, Christof M. Kramm, Chris Jones, Pascale Varlet, Stefan M. Pfister, Jacques Grill, David Jones, Marie‐Anne Debily
Software Mentions: 5
Published: about 6 years ago

10.26508/lsa.201900318

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
Cited by: 11
Author(s): Junaid Akhtar, Piyush More, Steffen Albrecht, Fédérico Marini, Walter Kaiser, Apurva Kulkarni, Leszek Wojnowski, Jean-Fred Fontaine, Miguel A. Andrade‐Navarro, Marion Silies, Christian Berger
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-018-4943-z

ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference
Cited by: 19
Author(s): Thomas Pranzatelli, Drew G. Michael, John A. Chiorini
Software Mentions: 5
Published: over 6 years ago

10.1186/s13072-017-0137-1

Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid
Cited by: 32
Author(s): Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, Julie Jaquiéry, Gaël Le Trionnaire
Software Mentions: 5
Published: over 7 years ago

10.1186/s13072-019-0285-6

H3K4me2 functions as a repressive epigenetic mark in plants
Cited by: 46
Author(s): Kun Wang, Kunpeng Liu, Liufan Yin, Yu Yu, Ji Qi, Wen‐Hui Shen, Jun Zhu, Yijing Zhang, Dong Ao
Software Mentions: 5
Published: over 5 years ago

10.15252/emmm.201911115

Disease modeling of a mutation in α‐actinin 2 guides clinical therapy in hypertrophic cardiomyopathy
Cited by: 77
Author(s): Maksymilian Prondzynski, Marc D. Lemoine, Antonia T.L. Zech, András Horváth, Vittoria Di Mauro, Jussi T. Koivumäki, Nico Kresin, Josefine Busch, T. Krause, Elisabeth Krämer, Saskia Schlossarek, Michael Spohn, Felix W. Friedrich, Julia Münch, Sandra D. Laufer, Charles Redwood, Alexander E Volk, Arne Hansen, Giulia Mearini, Daniele Catalucci, Christian Meyer, Torsten Christ, Monica Patten, Thomas Eschenhagen, Lucie Carrier
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1009705

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis
Cited by: 22
Author(s): Masatoshi Nakamoto, Toshitaka Uchino, Eriko Koshimizu, Yudai Kuchiishi, Ryota Sekiguchi, Liu Wang, Ryusuke Sudo, Masato Endo, Yann Guiguen, Manfred Schartl, John H. Postlethwait, Takashi Sakamoto
Software Mentions: 5
Published: about 3 years ago

10.1016/j.devcel.2018.10.004

SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
Cited by: 60
Author(s): Takayuki Hirota, Paul Blakeley, Mahesh N. Sangrithi, Shantha K. Mahadevaiah, Vesela Encheva, Ambrosius P. Snijders, Elias ElInati, Obah A. Ojarikre, Dirk G. de Rooij, Kathy K. Niakan, James M. A. Turner
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.ccell.2020.03.001

Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation
Cited by: 84
Author(s): Zeda Zhang, Chuanli Zhou, Xiaoling Li, Spencer Barnes, Su Deng, Elizabeth Hoover, Chi Chao Chen, Young Sun Lee, Yanxiao Zhang, Choushi Wang, Lauren Metang, Chao Wu, Carla Rodriguez Tirado, Nickolas A. Johnson, John Wongvipat, Kristina Navrazhina, Zhen Cao, Danielle Choi, Chen‐Hung Huang, Eliot Linton, Xiaoping Chen, Yupu Liang, Christopher E. Mason, Elisa de Stanchina, Wassim Abida, Amaia Lujambio, Sheng Li, Scott W. Lowe, Joshua T. Mendell, Venkat S. Malladi, Charles L. Sawyers, Ping Mu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12915-021-00996-4

Reorganization of the 3D chromatin architecture of rice genomes during heat stress
Cited by: 39
Author(s): Zhe Liang, Qian Zhang, Changmian Ji, Guihua Hu, Pingxian Zhang, Yifan Wang, Liwen Yang, Xiaofeng Gu
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-021-02501-7

Phase separation of Epstein-Barr virus EBNA2 protein reorganizes chromatin topology for epigenetic regulation
Cited by: 12
Author(s): Yiting Yang, Xidong Ye, Ranran Dai, Zhaoqiang Li, Yan Zhang, Wei Xue, Yafang Zhu, Delong Feng, Litao Qin, Xin Wang, Bo Lei, Shixiu Liao, Bingtao Hao
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-019-1860-7

CRUP: a comprehensive framework to predict condition-specific regulatory units
Cited by: 26
Author(s): Anna Ramisch, Verena Heinrich, Laura V. Glaser, Alisa Fuchs, Xinyi Yang, Philipp Benner, Robert Schöpflin, Na Li, Sarah Kinkley, Anja Römer-Hillmann, John Longinotto, Steffen Heyne, Beate Czepukojc, Sonja M. Kessler, Alexandra K. Kiemer, Cristina Cadenas, Laura Arrigoni, Nina Gasparoni, Thomas Manke, Thomas Pap, J. Andrew Pospisilik, Jan G. Hengstler, Jörn Walter, Sebastiaan H. Meijsing, Ho‐Ryun Chung, Martin Vingron
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2021.705848

Brg1 Supports B Cell Proliferation and Germinal Center Formation Through Enhancer Activation
Cited by: 6
Author(s): Dominik Schmiedel, Hadas Hezroni, Amit Hamburg, Ziv Shulman
Software Mentions: 5
Published: about 3 years ago

10.1038/s42003-021-01859-y

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology
Cited by: 16
Author(s): Sara Calhoun, Tisza Ann Szeremy Bell, Lukas R. Dahlin, Yuliya A. Kunde, Kurt LaButti, Katherine Louie, Andrea Kuftin, Daniel Treen, David Dilworth, Sirma Mihaltcheva, Christopher Daum, Benjamin P. Bowen, Trent Northen, Michael T. Guarnieri, Shawn R. Starkenburg, Igor V. Grigoriev
Software Mentions: 5
Published: over 3 years ago

10.1186/s13072-016-0079-z

Epigenetic dynamics of monocyte-to-macrophage differentiation
Cited by: 71
Author(s): Stefan Wallner, Christopher Schröder, Elsa Leitão, Tea Berulava, Claudia Haak, Daniela Beißer, Sven Rahmann, Andreas S. Richter, Thomas Manke, Ulrike Bönisch, Laura Arrigoni, Sebastian Fröhler, Filippos Klironomos, Wei Chen, Nikolaus Rajewsky, Fabian Müller, Peter Ebert, Thomas Lengauer, Matthias Barann, Philip Rosenstiel, Gilles Gasparoni, Karl Nordström, Jörn Walter, Benedikt Brors, Gideon Zipprich, Bärbel Felder, Ludger Klein-Hitpaß, Corinna Attenberger, Gerd Schmitz, Bernhard Horsthemke
Software Mentions: 5
Published: over 8 years ago

10.1186/s13072-018-0230-0

CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands
Cited by: 19
Author(s): Louie N. van de Lagemaat, Maria Flenley, Magnus Lynch, David Garrick, Simon R. Tomlinson, Kamil R. Kranc, Douglas Vernimmen
Software Mentions: 5
Published: about 6 years ago

10.1073/pnas.2005330117

Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism
Cited by: 31
Author(s): Louise Hunter, Charlotte E Pelekanou, Antony Adamson, Polly Downton, Nichola J Barron, Thomas Cornfield, Toryn Poolman, Neil Humphreys, Peter Cunningham, Leanne Hodson, A. S. I. Loudon, Mudassar Iqbal, David A. Bechtold, David Ray
Software Mentions: 5
Published: about 4 years ago

10.1016/j.stem.2017.09.003

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development
Cited by: 190
Author(s): Jingtao Guo, Edward J. Grow, Chongil Yi, Hana Mlčochová, Geoffrey J. Maher, Cecilia Lindskog, Patrick J. Murphy, Candice L. Wike, Douglas T. Carrell, Anne Goriely, James M. Hotaling, Bradley R. Cairns
Software Mentions: 5
Published: about 7 years ago

10.1016/j.gpb.2020.08.001

G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments
Cited by: 3
Author(s): Zixiang Yan, Luzhang Ji, Xiangru Huo, Qianfeng Wang, Yuwen Zhang, Bo Wen
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.02024

MOF-associated complexes ensure stem cell identity and Xist repression
Cited by: 73
Author(s): Tomasz Chelmicki, Friederike Dündar, Matthew James Turley, Tasneem Khanam, Tuğçe Aktaş, Fidel Ramírez, Anne-Valérie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke, Asifa Akhtar
Software Mentions: 5
Published: over 10 years ago

10.1038/s41422-018-0099-2

The adult human testis transcriptional cell atlas
Cited by: 381
Author(s): Jingtao Guo, Edward J. Grow, Hana Mlčochová, Geoffrey J. Maher, Cecilia Lindskog, Xiaolu Nie, Yixuan Guo, Yodai Takei, Jina Yun, Long Cai, Robin Kim, Douglas T. Carrell, Anne Goriely, James M. Hotaling, Bradley R. Cairns
Software Mentions: 5
Published: about 6 years ago

10.1016/j.celrep.2018.04.004

mRNA Cap Methyltransferase, RNMT-RAM, Promotes RNA Pol II-Dependent Transcription
Cited by: 32
Author(s): Dhaval Varshney, Olivia Lombardi, Gabriele Schweikert, Sianadh Dunn, Olga Suska, Victoria H. Cowling
Software Mentions: 5
Published: over 6 years ago

10.1016/j.celrep.2018.04.047

Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription
Cited by: 68
Author(s): David L.V. Bauer, Michael Tellier, Maira Martínez-Alonso, Takayuki Nojima, Nick J. Proudfoot, Shona Murphy, Ervin Fodor
Software Mentions: 5
Published: over 6 years ago

10.3389/fcimb.2020.600325

Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
Cited by: 12
Author(s): Charlotte Michaux, Elisabeth E Hansen, Laura Jenniches, Milan Gerovac, Lars Barquist, Jörg Vogel
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13072-021-00399-3

The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome
Cited by: 8
Author(s): William T. Jordan, Erica Larschan
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.47605

Toxoplasma gondii infection drives conversion of NK cells into ILC1-like cells
Cited by: 79
Author(s): Eugene Park, Sanket Patel, Qiuling Wang, Prabhakar S. Andhey, Konstantin Zaitsev, Sophia Porter, Maxwell Hershey, Michael D. Bern, Béatrice Plougastel-Douglas, Patrick L. Collins, Marco Colonna, Kenneth M. Murphy, Eugene M. Oltz, Maxim N. Artyomov, L. David Sibley, Wayne M. Yokoyama
Software Mentions: 5
Published: over 5 years ago

10.3389/fncel.2020.00131

Loss of Arid1a Promotes Neuronal Survival Following Optic Nerve Injury
Cited by: 3
Author(s): Xue-Qi Peng, Shang-Kun Dai, Changping Li, Peipei Li, Zhimeng Wang, Heng Du, Zhao‐Qian Teng, Shuguang Yang, Chang‐Mei Liu
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.567812

Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line
Cited by: 13
Author(s): Ganrea Chanthavixay, Colin Kern, Ying Wang, Perot Saelao, Susan J. Lamont, Rodrigo A. Gallardo, Gonzalo Rincón, Huaijun Zhou
Software Mentions: 5
Published: about 4 years ago

10.1016/j.celrep.2020.107691

Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells
Cited by: 17
Author(s): Monica Nafria, Peter Keane, Elizabeth Ng, Edouard G. Stanley, Andrew G. Elefanty, Constanze Bonifer
Software Mentions: 5
Published: over 4 years ago

10.1186/s13072-015-0046-0

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia
Cited by: 16
Author(s): Jiansheng Wu, Luca Pinello, Elinor Yissachar, Jonathan W. Wischhusen, Guo‐Cheng Yuan, Charles W.M. Roberts
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-021-02348-5

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
Cited by: 65
Author(s): Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Pedro Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-016-3135-y

A comparative study of ChIP-seq sequencing library preparation methods
Cited by: 21
Author(s): Arvind Sundaram, Timothy R. Hughes, Shea Biondi, Nathalie Bolduc, Sarah K. Bowman, Andrew Camilli, Yap Ching Chew, Catherine Couture, Andrew Farmer, John P. Jerome, David W. Lazinski, Andrew McUsic, Peng Xu, Kamran Shazand, Feng Xu, Robert Lyle, Gregor D. Gilfillan
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.63274

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
Cited by: 68
Author(s): Steven Henikoff, Hatice S Kaya-Okur, Kami Ahmad
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-021-86919-3

Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: over 3 years ago

10.1016/j.cell.2021.06.007

Polyamine metabolism is a central determinant of helper T cell lineage fidelity
Cited by: 96
Author(s): Daniel J. Puleston, Francesc Baixauli, David E. Sanin, Joy Edwards-Hicks, Matteo Villa, Agnieszka M. Kabat, Marcin M. Kamiński, Michal Stanckzak, Hauke J. Weiss, Katarzyna M. Grzes, Klara Piletič, Cameron S. Field, Mauro Corrado, Fabian Haessler, Chao Wang, Yaarub Musa, L Schimmelpfennig, Lea J. Flachsmann, Gerhard Mittler, Nir Yosef, Vijay K. Kuchroo, Joerg M. Buescher, Stefan Balabanov, Edward J. Pearce, Douglas R. Green, Erika L. Pearce
Software Mentions: 5
Published: over 3 years ago

10.1016/j.molcel.2019.11.021

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression
Cited by: 208
Author(s): Simone Tamburri, Elisa Lavarone, Daniel Fernández-Pérez, E. J. Conway, Marika Zanotti, Daria Manganaro, Diego Pasini
Software Mentions: 5
Published: almost 5 years ago

10.3389/fgene.2019.01207

Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus
Cited by: 26
Author(s): Sarah-Anne David, Anaïs Vitorino Carvalho, Coralie Gimonnet, Aurélien Brionne, Christelle Hennequet-Antier, Benoît Piégu, Sabine Crochet, Nathalie Couroussé, Thierry Bordeau, Yves Bigot, Anne Collin, Vincent Coustham
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.63036

Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants
Cited by: 5
Author(s): J. Roman Arguello, Liliane Abuin, Jan Armida, Kaan Mika, Phing Chian Chai, Richard Benton
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0232715

PIWI-interacting RNAs are differentially expressed during cardiac differentiation of human pluripotent stem cells
Cited by: 11
Author(s): Alejandro La Greca, María Agustina Scarafia, María Clara Hernández Cañás, Nelba Pérez, Sheila Castañeda, Carolina Colli, Alan Miqueas Möbbs, Natalia Lucía Santín Velazque, Gabriel Neiman, Ximena Garate, Cyntia Abán, Ariel Waisman, Lucía Moro, Gustavo Sevlever, Carlos Luzzani, Santiago Gabriel Miriuka
Software Mentions: 4
Published: over 4 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/s13059-017-1159-5

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

10.1371/journal.pgen.1009349

Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription
Cited by: 3
Author(s): Shih-Ying Tsai, Fu Huang
Software Mentions: 4
Published: almost 4 years ago

10.4049/jimmunol.2000450

Exhausted CD4+ T Cells during Malaria Exhibit Reduced mTORc1 Activity Correlated with Loss of T-bet Expression
Cited by: 9
Author(s): Ana Villegas-Méndez, Garima Khandelwal, Lucy M McGowan, Rebecca S Dookie, Michael Haley, Charlotte George, David Sims, Graham Lord, Linda V. Sinclair, Richard G. Jenner, Kevin N. Couper
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.55102

The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway
Cited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1008908

An expanded cell wall damage signaling network is comprised of the transcription factors Rlm1 and Sko1 in Candida albicans
Cited by: 19
Author(s): Marienela Y. Heredia, Mélanie Ikeh, Deepika Gunasekaran, Karen A. Conrad, Sviatlana Filimonava, Dawn H. Marotta, Clarissa J. Nobile, Jason M. Rauceo
Software Mentions: 4
Published: over 4 years ago

10.3390/epigenomes3020011

Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors
Cited by: 11
Author(s): Diana L. Gerrard, Joseph R. Boyd, Gary S. Stein, Victor X. Jin, Seth Frietze
Software Mentions: 4
Published: over 5 years ago

10.26508/lsa.201900331

Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis
Cited by: 18
Author(s): Florian Noack, Abhijeet Pataskar, Martin Schneider, Frank Buchholz, Vijay Tiwari, Federico Calegari
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2021.649634

Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf
Cited by: 5
Author(s): Jiafu Zhu, Han Zhao, Fanjiang Kong, Baohui Liu, Min Liu, Zhicheng Dong
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1008326

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome
Cited by: 31
Author(s): Paja Sijacic, Dylan H Holder, Marko Bajic, Roger B. Deal
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1007466

Unique patterns of trimethylation of histone H3 lysine 4 are prone to changes during aging in Caenorhabditis elegans somatic cells
Cited by: 27
Author(s): Mintie Pu, Minghui Wang, Wenke Wang, Velayudhan Satheeja Santhi, Siu Sylvia Lee
Software Mentions: 4
Published: over 6 years ago

10.26508/lsa.202000809

Reduced RNA turnover as a driver of cellular senescence
Cited by: 9
Author(s): Nowsheen Mullani, Yevheniia Porozhan, Adèle Mangelinck, Christophe Rachez, Mickaël Costallat, Éric Batsché, Michèle Goodhardt, Giovanni Cenci, Carl Mann, Christian Muchardt
Software Mentions: 4
Published: almost 4 years ago

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-97909-w

Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation
Cited by: 7
Author(s): Siv Anita Hegre, Helle Samdal, Antonin Klima, Endre Bakken Stovner, Kristin G. Nørsett, Nina Beate Liabakk, Lene Christin Olsen, Konika Chawla, Per Arne, Pål Sætrom
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1006903

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
Cited by: 17
Author(s): Elodie Thierion, Johan Le Men, Samuel Collombet, Céline Hernandez, Fanny Coulpier, Patrick Torbey, Morgane Thomas‐Chollier, Daan Noordermeer, Patrick Charnay, Pascale Gilardi-Hebenstreit
Software Mentions: 4
Published: over 7 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

10.1186/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

10.1084/jem.20150907

Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells
Cited by: 76
Author(s): Alejandro V. Villarino, Giuseppe Sciumè, Fred P. Davis, S. Iwata, Beatrice Zitti, Gertraud W. Robinson, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: about 7 years ago

10.15252/embr.201744059

Transposon‐driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution
Cited by: 33
Author(s): Matthew P Davis, Claudia Carrieri, Harpreet K. Saini, Stijn van Dongen, Tommaso Leonardi, Giovanni Bussotti, Jack Monahan, Tania Auchynnikava, Angelo Bitetti, Juri Rappsilber, Robin C. Allshire, Alena Shkumatava, Dónal O’Carroll, Anton J. Enright
Software Mentions: 4
Published: over 7 years ago

10.26508/lsa.202000961

A role for condensin in mediating transcriptional adaptation to environmental stimuli
Cited by: 4
Author(s): Lucy Lancaster, Harshil Patel, Gavin Kelly, Frank Uhlmann
Software Mentions: 4
Published: over 3 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.2019.02451

Pan-Cancer Analysis Reveals Disrupted Circadian Clock Associates With T Cell Exhaustion
Cited by: 51
Author(s): Yingcheng Wu, Baorui Tao, Tianyang Zhang, Yihui Fan, Renfang Mao
Software Mentions: 4
Published: about 5 years ago

10.3389/fnmol.2017.00185

Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq
Cited by: 18
Author(s): Shannon Farris, Yu Wang, James M. Ward, Serena M. Dudek
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-48979-4

Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken
Cited by: 22
Author(s): Satoshi Yamashita, Kensuke Kataoka, Hiroto Yamamoto, Tomoko Kato, Satoshi Hara, Katsushi Yamaguchi, Claire Renard-Guillet, Yuki Katou, Katsuhiko Shirahige, Haruki Ochi, Hitoshi Ogino, Tatsuo Uchida, Masafumi Inui, Shuji Takada, Shuji Shigenobu, Hiroshi Asahara
Software Mentions: 4
Published: about 5 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

10.1126/sciadv.abf7346

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome
Cited by: 4
Author(s): Seung Kyoon Kim, Xihui Liu, Jong-Min Park, Dahun Um, Gokhul Kilaru, Cheng Ming Chiang, Min-Hee Kang, Kimberly M. Huber, Keunsoo Kang, Tae Kyung Kim
Software Mentions: 4
Published: over 3 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

10.1186/s13072-016-0070-8

Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Cited by: 18
Author(s): Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine Broberg Vågbø, Robert Lyle, Marianne Kristiansen Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland, Judith Staerk
Software Mentions: 4
Published: over 8 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

10.3389/fgene.2020.595550

An Enhancer-Based Analysis Revealed a New Function of Androgen Receptor in Tumor Cell Immune Evasion
Cited by: 3
Author(s): Yuan Wang, Jiajia Li, Jingjing Li, Peipei Li, Li Wang, Lijun Di
Software Mentions: 4
Published: almost 4 years ago

10.1038/s42003-021-01661-w

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
Cited by: 16
Author(s): Christoph Niemöller, Julius Wehrle, Julian Riba, Rainer Claus, Nathalie Renz, Janika Rhein, Sabine Bleul, Juliane M. Stosch, Justus Duyster, Christoph Plass, Pavlo Lutsik, Daniel B. Lipka, Michael Lübbert, Heiko Becker
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-020-3386-0

GsmPlot: a web server to visualize epigenome data in NCBI
Cited by: 2
Author(s): Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-018-0576-y

Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology
Cited by: 14
Author(s): Stefano Amatori, Giuseppe Persico, Claudio Paolicelli, Roman Hillje, Nora Sahnane, Francesco Corini, Daniela Furlan, Lucilla Luzi, Saverio Minucci, Marco Giorgio, Pier Giuseppe Pelicci, Mirco Fanelli
Software Mentions: 4
Published: about 6 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

10.3389/fpls.2021.715820

Genome-Wide Identification of the ARF Gene Family and ARF3 Target Genes Regulating Ovary Initiation in Hazel via ChIP Sequencing
Cited by: 8
Author(s): Wei Heng, Yufei Cheng, Ying Sun, Xingzheng Zhang, Hailong He, Jianfeng Liu
Software Mentions: 4
Published: over 3 years ago

10.1007/s10577-020-09643-0

CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites
Cited by: 4
Author(s): Michi Miura, Honglin Chen
Software Mentions: 4
Published: about 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 <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

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: about 6 years ago

10.1186/s13072-020-00341-z

EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications
Cited by: 1
Author(s): Anshupa Sahu, Na Li, Ilona Dunkel, Ho‐Ryun Chung
Software Mentions: 4
Published: over 4 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: over 4 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

10.1126/sciadv.abe3516

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor
Cited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: almost 4 years ago

10.3390/v12080817

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain
Cited by: 6
Author(s): Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M. Workman, Jean-Jack M. Riethoven, David Steffen, Sarah Sillman, Hiep L.X. Vu
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/s13072-019-0319-0

Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Cited by: 29
Author(s): Ryuichiro Nakato, Youichiro Wada, Ryo Nakaki, Genta Nagae, Yuki Katou, Sadami Tsutsumi, N. Nakajima, Hiroshi Fukuhara, Atsushi Iguchi, Takahide Kohro, Yasuharu Kanki, Yutaka Saitô, Mika Kobayashi, Akashi Izumi-Taguchi, Naoki Osato, Kenji Tatsuno, Asuka Kamio, Yoko Hayashi‐Takanaka, Hiromi Wada, Shinzo Ohta, Masamichi Aikawa, Hiroyuki Nakajima, Masaki Nakamura, Rebecca C. McGee, Kyle W. Heppner, Tatsuo Kawakatsu, Michiru Genno, Hiroshi Yanase, Haruki Kume, Takaaki Senbonmatsu, Yukio Homma, Shigeyuki Nishimura, Toutai Mitsuyama, Hiroyuki Aburatani, Hiroshi Kimurâ, Katsuhiko Shirahige
Software Mentions: 4
Published: almost 5 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

10.1016/j.immuni.2021.05.016

A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression
Cited by: 22
Author(s): Francesco Cilenti, Giulia Barbiera, Nicoletta Caronni, Dario Iodice, Elisa Montaldo, Simona Barresi, Eleonora Lusito, Vincenzo Cuzzola, Francesco Maria Vittoria, Luca Mezzanzanica, Paolo Miotto, Pietro Di Lucia, Dejan Lazarevic, Daniela María Cirillo, Matteo Iannacone, Marco Genua, Renato Ostuni
Software Mentions: 4
Published: over 3 years ago

Projects: pypi: deepTools

Papers Mentioning deepTools 435