Ecosyste.ms: Papers

10.1371/journal.pone.0251354

Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling
Cited by: 3
Author(s): Ramalingam Radhakrishnan, Upasana Bedi Chanana, Saddam Hussain, Soni Sharma, Kaveri Goel, Deepa Bisht, Ketki Patne, Pynskhem Bok Swer, Joel W. Hockensmith, Rohini Muthuswami
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.66524

Extracellular signal-regulated kinase mediates chromatin rewiring and lineage transformation in lung cancer
Cited by: 14
Author(s): Yusuke Inoue, Ana Nikolić, Dylan Farnsworth, Rocky Shi, Fraser Johnson, Alvin Liu, Marc Ladanyi, Romel Somwar, Marco Gallo, William W. Lockwood
Software Mentions: 6
Published: almost 3 years ago

10.7554/eLife.37078

Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes
Cited by: 31
Author(s): Corinna Speth, Emese Szabó, Cláudia Martinho, Silvio Collani, Sven zur Oven-Krockhaus, Sandra Richter, Irina Droste-Borel, Boris Maček, York‐Dieter Stierhof, Markus Schmid, Chang Liu, Sascha Laubinger
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.40197

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Cited by: 61
Author(s): Chongyuan Luo, Qian Yi Lee, Orly L. Wapinski, Rosa Castanon, Joseph R. Nery, Moritz Mall, Michael S. Kareta, Shay Cullen, Margaret A. Goodell, Howard Y. Chang, Marius Wernig, Joseph R. Ecker
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.18591

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes
Cited by: 105
Author(s): Nathan R. Rose, Hamish W King, Neil P. Blackledge, Nadezda A. Fursova, Katherine Ji Ember, Román Fischer, Benedikt M. Kessler, Robert J. Klose
Software Mentions: 6
Published: over 7 years ago

10.1016/j.cell.2018.09.040

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
Cited by: 116
Author(s): Vicki Metzis, Sebastian Steinhauser, Edvinas Pakanavicius, Mina Gouti, Despina Stamataki, Kenzo Ivanovitch, Thomas Watson, Teresa Rayón, S. Neda Mousavy Gharavy, Robin Lovell-Badge, Nicholas M. Luscombe, James Briscoe
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0123380

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)
Cited by: 41
Author(s): Christopher Terranova, Sridhar T. Narla, Yu Wei Lee, Jonathan Bard, Abhirath Parikh, Ewa K. Stachowiak, Emmanuel S. Tzanakakis, Michael Buck, Barbara Birkaya, Michal K. Stachowiak
Software Mentions: 6
Published: about 9 years ago

10.1186/s13059-021-02300-7

riboCIRC: a comprehensive database of translatable circRNAs
Cited by: 39
Author(s): Huihui Li, Mingzhe Xie, Yan Wang, Ludong Yang, Zhi Xie
Software Mentions: 6
Published: about 3 years ago

10.3389/fcell.2021.723676

Integrative Epigenome Map of the Normal Human Prostate Provides Insights Into Prostate Cancer Predisposition
Cited by: 5
Author(s): Tao Wang, Juan Song, Min Qu, Xu Gao, Wenhui Zhang, Ziwei Wang, Lin Zhao, Yan Wang, Bing Li, Jing Li, Jinjian Yang
Software Mentions: 6
Published: over 2 years ago

10.7554/eLife.47898

CTCF confers local nucleosome resiliency after DNA replication and during mitosis
Cited by: 52
Author(s): Nick Owens, Thaleia Papadopoulou, Nicola Festuccia, Alexandra Tachtsidi, Inma González, Agnès Dubois, Sandrine Vandormael-Pournin, Elphège P. Nora, Benoit G. Bruneau, Michel Cohen-Tannoudji, Pablo Navarro
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.52648

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
Cited by: 34
Author(s): Anneke Dixie Kakebeen, Alexander Daniel Chitsazan, Madison Corinne Williams, Lauren Saunders, Andrea E. Wills
Software Mentions: 6
Published: about 4 years ago

10.1186/s13072-021-00411-w

Sensitivity of cohesin–chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion
Cited by: 4
Author(s): Arkadiy K. Golov, Anastasia V. Golova, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 6
Published: almost 3 years ago

10.7554/eLife.58123

TBX3 acts as tissue-specific component of the Wnt/β-catenin transcriptional complex
Cited by: 28
Author(s): Dario Zimmerli, Costanza Borrelli, Amaia Jauregi-Miguel, Simon Söderholm, Salome Brütsch, Nikolaos Doumpas, Jan Reichmuth, Fabienne Murphy-Seiler, Michel Aguet, Konrad Basler, Andreas E. Moor, Claudio Cantù
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13072-018-0250-9

Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection
Cited by: 29
Author(s): José Luis Ruiz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Jean-Bosco Ouédraogo, Victor G. Corcés, Elena Gómez-Díaz
Software Mentions: 6
Published: over 5 years ago

10.1186/s13059-020-02190-1

DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis
Cited by: 12
Author(s): Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed, Olivier Mathieu
Software Mentions: 6
Published: over 3 years ago

10.15252/embj.2019102808

HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer
Cited by: 36
Author(s): Jorge Ferrer, Edgar Bernardo, Anthony Beucher, Miguel A. Maestro, Natalia del Pozo, I.R. Hernández Millán, Lena Haeberle, Martin Schlensog, Sami-Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías De Vas, Karl B. Shpargel, Eva C. Vaquero, Terry Magnuson, Sagrario Ortega, Irene Espósito, Francisco X. Real, Jorge Ferrer
Software Mentions: 6
Published: about 4 years ago

10.7554/eLife.57189

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma
Cited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-020-02216-8

Histone modifications during the life cycle of the brown alga Ectocarpus
Cited by: 21
Author(s): Simon Bourdareau, Leïla Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho, J. Mark Cock
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.10150

ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation
Cited by: 50
Author(s): Nataliya Nady, Ankit Gupta, Ziyang Ma, Tomek Swigut, Akiko Koide, Shohei Koide, Joanna Wysocka
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1009432

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans
Cited by: 12
Author(s): Chenglin Li, Mintie Pu, Wenke Wang, Amaresh Chaturbedi, Felicity J Emerson, Siu Sylvia Lee
Software Mentions: 6
Published: over 2 years ago

10.1242/dev.199604

The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency
Cited by: 16
Author(s): Nicola Festuccia, Nick Owens, Almira Chervova, Agnès Dubois, Pablo Navarro
Software Mentions: 6
Published: over 2 years ago

10.1016/j.devcel.2021.02.007

Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization
Cited by: 15
Author(s): Fabio M D'Orazio, Piotr J. Balwierz, Ada Jimenez González, Yixuan Guo, Benjamín Hernández-Rodríguez, Lucy Wheatley, Aleksandra Jasiulewicz, Yavor Hadzhiev, Juan M. Vaquerizas, Bradley R. Cairns, Boris Lenhard, Ferenc Müller
Software Mentions: 6
Published: about 3 years ago

10.7554/eLife.59388

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals
Cited by: 10
Author(s): Eric M. Sanford, Benjamin Emert, Allison Coté, Arjun Raj
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2020.00553

ADNP Controls Gene Expression Through Local Chromatin Architecture by Association With BRG1 and CHD4
Cited by: 22
Author(s): Xiaoyun Sun, Wenjun Yu, Li Li, Yuhua Sun
Software Mentions: 6
Published: almost 4 years ago

10.3389/fmicb.2019.01408

Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6A
Cited by: 19
Author(s): Anthony J. Saviola, Cosima Zimmermann, Michael Mariani, Sylvia Signorelli, Diana L. Gerrard, Joseph R. Boyd, Darren J. Wight, Guillaume Morissette, Annie Gravel, Isabelle Dubuc, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 6
Published: almost 5 years ago

10.26508/lsa.202000976

Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Cited by: 5
Author(s): Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pgen.1009338

Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization
Cited by: 15
Author(s): Margarita V. Brovkina, Rachel Duffié, Abbigayl E. C. Burtis, E. Josephine Clowney
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1004994

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling
Cited by: 147
Author(s): Kristofer Davie, Jelle Jacobs, Mardelle Atkins, Delphine Potier, Valerie Christiaens, Georg Halder, Stein Aerts
Software Mentions: 6
Published: over 9 years ago

10.7554/eLife.57345

Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
Cited by: 37
Author(s): Michelle C. Ward, Nicholas E. Banovich, Abhishek Sarkar, Matthew Stephens, Yoav Gilad
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1008905

Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase
Cited by: 5
Author(s): Richard Silva, María Ascensión Villar-Fernández, Gerben Vader
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms22116034

mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex
Cited by: 9
Author(s): Martin Schüle, Tamer Butto, Sri Dewi, Laura Schlichtholz, Susanne Strand, Susanne Gerber, Kristina Endres, Susann Schweiger, Jennifer Winter
Software Mentions: 6
Published: almost 3 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 6 years ago

10.1128/mSystems.00550-20

A Comprehensive Coexpression Network Analysis in Vibrio cholerae
Cited by: 4
Author(s): Cory D. DuPai, Claus O. Wilke, Bryan William Davies
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-020-03927-2

WACS: improving ChIP-seq peak calling by optimally weighting controls
Cited by: 2
Author(s): Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins
Software Mentions: 5
Published: over 3 years ago

10.1084/jem.20191257

Combined deletion of <i>Bap1</i>, <i>Nf2</i>, and <i>Cdkn2ab</i> causes rapid onset of malignant mesothelioma in mice
Cited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-018-1602-2

RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs
Cited by: 107
Author(s): Pierre Murat, Giovanni Marsico, Barbara Herdy, Avazeh T. Ghanbarian, Guillem Portella, Shankar Balasubramanian
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-019-1721-4

Chromatin accessibility plays a key role in selective targeting of Hox proteins
Cited by: 35
Author(s): Damiano Porcelli, Bettina Fischer, Steven Russell, Robert A. White
Software Mentions: 5
Published: almost 5 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: over 4 years ago

10.1186/s13059-017-1310-3

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation
Cited by: 26
Author(s): Kevin Van Bortle, Douglas H. Phanstiel, M Snyder
Software Mentions: 5
Published: over 6 years ago

10.1016/j.stemcr.2019.04.012

Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci
Cited by: 31
Author(s): Erin N. Smith, Agnieszka D’Antonio‐Chronowska, William W. Greenwald, Victor Borja, Lana Ribeiro Aguiar, Robert Pogue, Hiroko Matsui, Paola Benaglio, Shyamanga Borooah, Matteo D’Antonio, Radha Ayyagari, Kelly A. Frazer
Software Mentions: 5
Published: almost 5 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-017-3589-6

Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity
Cited by: 14
Author(s): Michael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D. Gallaher, Albert J. Courey
Software Mentions: 5
Published: about 7 years ago

10.1038/s42003-021-02116-y

DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift
Cited by: 22
Author(s): Julia Franzen, Theodoros Georgomanolis, Anton Selich, Chao-Chung Kuo, Reinhard Stöger, Lilija Brant, Melita Sara Mulabdić, Eduardo Fernández-Rebollo, Clara Grezella, Alina Ostrowska, Matthias Begemann, Miloš Nikolić, Björn Rath, Anthony D. Ho, Michael Rothe, Axel Schambach, Argyris Papantonis, Wolfgang Wagner
Software Mentions: 5
Published: about 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: almost 3 years ago

10.1186/s13059-017-1281-4

Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid
Cited by: 77
Author(s): Weiren Zhu, Bo Hu, Claude Becker, Ezgi Sueheyla Dogan, Kenneth W. Berendzen, Detlef Weigel, Chang Liu
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-020-1001-6

Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation
Cited by: 25
Author(s): Christina N Vallianatos, Brynne Raines, Robert S. Porter, Katherine M Bonefas, Michael C. Wu, Patricia M. Garay, Katie M. Collette, Young Ah Seo, Yali Dou, Catherine E. Keegan, Natalie C. Tronson, Shigeki Iwase
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-016-1057-2

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
Cited by: 52
Author(s): Nina Koenecke, Jeff Johnston, Bjoern Gaertner, Malini Natarajan, Julia Zeitlinger
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-018-1489-y

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells
Cited by: 25
Author(s): Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jérémy Denizot, Raquel Manzano García, Steven Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip T. Hawkins, Len R. Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick Varga‐Weisz
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1007114

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus
Cited by: 62
Author(s): Steven P. Barrett, Kevin R. Parker, Caroline Horn, Miguel A. Mata, Julia Salzman
Software Mentions: 5
Published: over 6 years ago

10.1038/s41392-020-00378-2

Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis
Cited by: 11
Author(s): Mingsen Li, Liqiong Zhu, Jiafeng Liu, Huaxing Huang, Huizhen Guo, Li Wang, Lingyu Li, Sijie Gu, Jieying Tan, Jing Zhong, Bowen Wang, Zhen Mao, Yong Fan, Chunqiao Liu, Jing Yuan, Hong Ouyang
Software Mentions: 5
Published: over 3 years ago

10.7150/thno.47081

Targeted inhibition of KDM6 histone demethylases eradicates tumor-initiating cells via enhancer reprogramming in colorectal cancer
Cited by: 20
Author(s): Junbao Zhang, Ying Ying, Meiqi Li, Maolin Wang, Xiaoyan Huang, Min Jia, Junhui Zeng, Canjie Ma, Yixiang Zhang, Chen Li, Xiaomei Wang, Xing-sheng Shu
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-66377-z

Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation
Cited by: 10
Author(s): Marine Barthez, Mathilde Poplineau, Marwa Elrefaey, Nathalie Caruso, Yacine Graba, Andrew J. Saurin
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-018-4746-2

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Cited by: 19
Author(s): Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann‐Kristin Östlund Farrants, Neus Visa
Software Mentions: 5
Published: about 6 years ago

10.1186/s13148-020-00970-x

Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming
Cited by: 15
Author(s): Karen L. Leung, Smriti Sanchita, Catherine T. Pham, Brett A. Davis, Mariam Okhovat, Xiangming Ding, Phillip A. Dumesic, Tristan Grogan, Kevin J. Williams, Marco Morselli, Feiyang Ma, Lucia Carbone, Xinmin Li, Matteo Pellegrini, Daniel A. Dumesic, Gregorio D. Chazenbalk
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1006731

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
Cited by: 19
Author(s): Ivar Grytten, Knut Dagestad Rand, Alexander J. Nederbragt, Geir Storvik, Ingrid K. Glad, Geir Kjetil Sandve
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-34115-1

Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster
Cited by: 8
Author(s): Ezequiel Názer, Ryan Dale, Cameron D. Palmer, Elissa P. Lei
Software Mentions: 5
Published: over 5 years ago

10.1002/ctm2.133

Analysis of single‐cell RNAseq identifies transitional states of T cells associated with hepatocellular carcinoma
Cited by: 12
Author(s): Yang Yz, Fangming Liu, Weiren Liu, Mingyue Ma, Jie Gao, Yan Lu, Li-Hao Huang, Xiaoying Li, Ying–Hong Shi, Xiangdong Wang, Duojiao Wu
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1006982

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Cited by: 83
Author(s): Ivan Jurić, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Maowen Hu
Software Mentions: 5
Published: about 5 years ago

10.1016/j.cell.2021.03.062

Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13059-015-0720-3

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
Cited by: 70
Author(s): Andrey V. Kartashov, Artem Barski
Software Mentions: 5
Published: almost 9 years ago

10.1038/s41598-019-45515-2

Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea
Cited by: 13
Author(s): Brent A. Wilkerson, Alex Chitsazan, Leah S. VandenBosch, Matthew S. Wilken, Thomas A. Reh, Olivia Bermingham‐McDonogh
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pbio.2006347

Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation
Cited by: 33
Author(s): Mingming Zhao, Jaimy Joy, Weiqiang Zhou, Supriyo De, William H. Wood, Kevin G. Becker, Hongkai Ji, Ranjan Sen
Software Mentions: 5
Published: over 5 years ago

10.3390/cells8070698

Single Cell Gene Co-Expression Network Reveals FECH/CROT Signature as a Prognostic Marker
Cited by: 19
Author(s): Xin Chen, Lingling Hu, Yuan Wang, Weijun Sun, Chao Yang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12885-019-5537-0

Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma
Cited by: 8
Author(s): Karsten Kleo, Lora Dimitrova, Elisabeth Oker, Nancy Tomaszewski, Erika Gebel Berg, Franziska Taruttis, Julia C. Engelmann, Philipp Schwarzfischer, Jörg Reinders, Rainer Spang, Wolfram Gronwald, Peter J. Oefner, Michael Hummel
Software Mentions: 5
Published: about 5 years ago

10.18632/aging.101341

Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: over 6 years ago

10.1038/sdata.2018.142

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research
Cited by: 306
Author(s): Philip L. De Jager, Yiyi Ma, Cristin McCabe, Jishu Xu, Badri N. Vardarajan, Daniel Felsky, Hans‐Ulrich Klein, Charles C. White, Mette A. Peters, Ben Lodgson, Parham Nejad, Ao Tang, Lara M. Mangravite, Lei Yu, Chris Gaiteri, Sara Mostafavi, Julie A. Schneider, David A. Bennett
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pbio.3000710

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice
Cited by: 18
Author(s): Virlana M. Shchuka, Luis E. Abatti, Huayun Hou, Nawrah Khader, Anna Dorogin, Michael D. Wilson, Oksana Shynlova, Jennifer A. Mitchell
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-016-1248-6

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
Cited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: over 7 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPAR<i>γ</i>-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: over 3 years ago

10.3389/fnmol.2018.00481

Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency
Cited by: 30
Author(s): A. Ayanna Wade, Kenneth J. Lim, Rinaldo Catta-Preta, Alexander Nord
Software Mentions: 5
Published: over 5 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: over 2 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: over 3 years ago

10.1167/iovs.18-24101

Ascorbate Suppresses VEGF Expression in Retinal Pigment Epithelial Cells
Cited by: 20
Author(s): David W. Sant, Vladimir Camarena, Sushmita Mustafi, Yiwen Li, Zachary Wilkes, Derek Van Booven, Rong Wen, Gaofeng Wang
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.stem.2019.03.017

Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Cited by: 78
Author(s): Tüzer Kalkan, Susanne Bornelöv, Carla Mulas, Evangelia Diamanti, Tim Lohoff, Markus Ralser, Sjors Middelkamp, Patrick Lombard, Jennifer Nichols, Austin Smith
Software Mentions: 5
Published: about 5 years ago

10.3389/fimmu.2021.633654

The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition
Cited by: 11
Author(s): Xiaofang Xu, Dianhua Qiao, Chenyang Dong, Morgan Mann, Roberto P. Garofalo, Sündüz Keleş, Allan R. Brasier
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.ppat.1008221

PDGFRA defines the mesenchymal stem cell Kaposi’s sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment
Cited by: 23
Author(s): Julián Naipauer, Santas Rosario, Sachin Gupta, Courtney Premer, Omayra Méndez-Solís, Mariana Schlesinger, Virginia Ponzinibbio, Vaibhav Jain, Rolf Renne, Ho Lam Chan, Lluís Morey, Daria Salyakina, Martı́n C. Abba, Siôn L. Williams, Joshua M. Hare, Pascal J. Goldschmidt‐Clermont, Enrique A. Mesri
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2021.613808

Characterization of SALL2 Gene Isoforms and Targets Across Cell Types Reveals Highly Conserved Networks
Cited by: 3
Author(s): Carlos Farkas, Aracelly Quiroz, Claudia Álvarez, Viviana E. Hermosilla, Carlos F. Aylwin, Alejandro Lomniczi, Ariel F. Castro, Matías I. Hepp, Roxana Pincheira
Software Mentions: 5
Published: about 3 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: over 2 years ago

10.3389/fgene.2019.01386

Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection
Cited by: 17
Author(s): Thomas J. Hall, Douglas Vernimmen, John Andrew Browne, Michael P. Mullen, Stephen V. Gordon, David E. MacHugh, Alan M. O’Doherty
Software Mentions: 5
Published: over 4 years ago

10.15252/msb.20145123

Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast
Cited by: 61
Author(s): Mathieu Clément-Ziza, Xavi Marsellach, Sandra Codlin, Manos A. Papadakis, Susanne Reinhardt, María Rodríguez-López, Stuart Martin, Samuel Marguerat, Alexander Schmidt, Eun‐Hye Lee, Christopher T. Workman, Jürg Bähler, Andreas Beyer
Software Mentions: 5
Published: over 9 years ago

10.1016/j.immuni.2017.12.010

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages
Cited by: 153
Author(s): Zsolt Czimmerer, Bence Dániel, Attila Horváth, Dominik Rückerl, Gergely Nagy, Máté Kiss, Matthew Peloquin, Marietta Margit Budai, Ixchelt Cuaranta-Monroy, Zoltán Simándi, László Steiner, Béla Nagy, Szilárd Póliska, Csaba Bankó, Zsolt Bacsó, Ira G. Schulman, Sascha Sauer, Jean Deleuze, Judith E. Allen, Szilvia Benkő, László Nagy
Software Mentions: 5
Published: over 6 years ago

10.15252/msb.20209885

Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function
Cited by: 12
Author(s): Wim J. de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2019.00277

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs
Cited by: 19
Author(s): Kun Han, Ruimin Ren, Jianhua Cao, Shuhong Zhao, Mei Yu
Software Mentions: 5
Published: about 5 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: about 3 years ago

10.1016/j.stem.2020.09.001

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Cited by: 86
Author(s): Hannah K. Long, Marco Osterwalder, Ian Welsh, Karissa Hansen, James O. J. Davies, Yiran E. Liu, Mervenaz Koska, Alexander T. Adams, Robert Aho, Neiha Arora, Kazuya Ikeda, Ruth M. Williams, Tatjana Sauka‐Spengler, Matthew H. Porteus, Tim Mohun, Diane E. Dickel, Tomek Swigut, Jim R. Hughes, Douglas R. Higgs, Axel Visel, Licia Selleri, Joanna Wysocka
Software Mentions: 5
Published: over 3 years ago

10.1002/hep4.1749

Meta‐analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions
Cited by: 4
Author(s): Emilian Jungwirth, Katrin Panzitt, Hanns‐Ulrich Marschall, Gerhard Thallinger, Martin Wagner
Software Mentions: 5
Published: almost 3 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: over 3 years ago

10.3389/fgene.2021.648701

Multiomics Analysis Reveals Molecular Abnormalities in Granulosa Cells of Women With Polycystic Ovary Syndrome
Cited by: 14
Author(s): Ru-Song Zhao, Yonghui Jiang, Shigang Zhao, Han Zhao
Software Mentions: 5
Published: about 3 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: over 4 years ago

10.3389/fgene.2020.508809

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes
Cited by: 16
Author(s): Fábio Pértille, A. M. G. Ibelli, Maj El Sharif, Mirele Daiana Poleti, Anna Sophie Fröhlich, Shiva Rezaei, Mônica Corrêa Ledur, Per Jensen, Carlos Guerrero-Bosagna, Luiz Lehmann Coutinho
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-017-3817-0

lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets
Cited by: 22
Author(s): Yixiao Gong, Hsin‐Chun Huang, Yu Liang, Thomas Trimarchi, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 5
Published: almost 7 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: about 6 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: almost 4 years ago

10.1093/gigascience/giy117

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation
Cited by: 16
Author(s): Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Junyan Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J. Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-021-00863-5

Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation
Cited by: 69
Author(s): Bin Han, Wei Jiang, Pan Cui, Kai Zheng, Chun Dang, Junjie Wang, He Li, Lin Chen, Rongxin Zhang, Qing Mei Wang, Zhenyu Ju, Junwei Hao
Software Mentions: 5
Published: about 3 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: almost 4 years ago

10.3389/fimmu.2021.647688

Epigenetic Features of HIV-Induced T-Cell Exhaustion Persist Despite Early Antiretroviral Therapy
Cited by: 12
Author(s): Geneviève Martin, Debattama R. Sen, Matthew Pace, Nicola Robinson, Jodi Meyerowitz, Emily Adland, John Thornhill, Mathew Jones, Ane Ogbe, Lucia Parolini, Natalia Olejniczak, Panagiota Zacharopoulou, Helen Brown, Christian Willberg, Nneka Nwokolo, Julie Fox, Sarah Fidler, W. Nicholas Haining, John Frater
Software Mentions: 5
Published: almost 3 years ago

10.3389/fcimb.2021.612656

Higher-Order Chromatin Structures of Chromosomally Integrated HHV-6A Predict Integration Sites
Cited by: 2
Author(s): Michael Mariani, Cosima Zimmerman, Princess D. Rodriguez, Ellie Hasenohr, Giulia Aimola, Diana L. Gerrard, Alyssa Richman, Andrea Dest, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 5
Published: about 3 years ago

10.3389/fgene.2019.00684

Increase in DNA Damage by MYCN Knockdown Through Regulating Nucleosome Organization and Chromatin State in Neuroblastoma
Cited by: 3
Author(s): Xinjie Hu, Weisheng Zheng, Qianshu Zhu, Liang Gu, Yanhua Du, Zhe Han, Xiaobai Zhang, Daniel Carter, Belamy B. Cheung, Andong Qiu, Cizhong Jiang
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13073-020-00749-y

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome
Cited by: 36
Author(s): Florian Köhler, Felix Bormann, Günter Raddatz, Julian Gutekunst, Nick Gilbert, Tanja Musch, Anke S. Lonsdorf, Sylvia Erhardt, Frank Lyko, Manuel Rodríguez-Paredes
Software Mentions: 5
Published: almost 4 years ago