Ecosyste.ms: Papers

10.1371/journal.pone.0048102

PPARG Binding Landscapes in Macrophages Suggest a Genome-Wide Contribution of PU.1 to Divergent PPARG Binding in Human and Mouse
Cited by: 18
Author(s): Sebastian Pott, Nima K. Kamrani, Guillaume Bourque, Sven Pettersson, Edison T. Liu
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pgen.1009296

A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation
Cited by: 9
Author(s): Ana Paula Azambujá, Marcos Simões-Costa
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1003728

The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option
Cited by: 33
Author(s): Aaron M. Wenger, Shoa L. Clarke, James H. Notwell, Tisha Chung, Geetu Tuteja, Harendra Guturu, Bruce T. Schaar, Gill Bejerano
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0071152

Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data
Cited by: 44
Author(s): Jie Lv, Wei Cui, Hongbo Liu, Hongbin He, Youcheng Xiu, Jing Guo, Hui Liu, Qi Liu, Tie-Bo Zeng, Yan Chen, Yan Zhang, Qiong Wu
Software Mentions: 2
Published: over 11 years ago

10.1167/iovs.61.10.13

Identification and Characterization of N⁶-Methyladenosine CircRNAs and Methyltransferases in the Lens Epithelium Cells From Age-Related Cataract
Cited by: 24
Author(s): Pengfei Li, Hualin Yu, Guowei Zhang, Lihua Kang, Bai Qin, Yu Cao, Jiawei Luo, Xiaojuan Chen, Ying Wang, Miaomiao Qin, Jian Wu, Yemeng Huang, Xi Zou, Huaijin Guan, Yong Wang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1004885

Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
Cited by: 49
Author(s): Dan Su, Xuting Wang, Michelle R. Campbell, Lingyun Song, Alexias Safi, Gregory E. Crawford, Douglas A. Bell
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pcbi.1002613

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
Cited by: 59
Author(s): Haipeng Xing, Yan Mo, Will Liao, Michael Q. Zhang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1004768

SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells
Cited by: 54
Author(s): Bastien Gerby, Cédric Tremblay, Mathieu Tremblay, Shanti Rojas-Sutterlin, Sabine Herblot, Josée Hébert, Guy Sauvageau, Sébastien Lemieux, Éric Lécuyer, Diogo Veiga, Trang Hoang
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12711-021-00631-4

A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations
Cited by: 7
Author(s): Zhongzi Wu, Haiming Gong, Mingpeng Zhang, Xinkai Tong, Huashui Ai, Shijun Xiao, Miguel Pérez‐Enciso, Bin Yang, Lusheng Huang
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.02559

Core promoter factor TAF9B regulates neuronal gene expression
Cited by: 33
Author(s): Francisco Herrera, Teppei Yamaguchi, Henk Roelink, Robert Tjian
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1002694

ELK1 Uses Different DNA Binding Modes to Regulate Functionally Distinct Classes of Target Genes
Cited by: 66
Author(s): Zaneta Odrowaz, Andrew D. Sharrocks
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1007109

SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells
Cited by: 49
Author(s): Sabine Jägle, Hauke Busch, Vivien Freihen, Sven Beyes, Monika Schrempp, Melanie Boerries, Andreas Hecht
Software Mentions: 2
Published: about 7 years ago

10.1186/gb-2008-9-9-r137

Model-based Analysis of ChIP-Seq (MACS)
Cited by: 12,473
Author(s): Yong Zhang, Tao Liu, Clifford A. Meyer, Jérôme Eeckhoute, D. S. Johnson, B Bernstein, Chad Nusbaum, R Myers, Myles Brown, Wei Li, X Shirley Liu
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pgen.1003244

A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis
Cited by: 321
Author(s): Yu Zhang, Oleg Mayba, Anne Pfeiffer, Hui Shi, James M. Tepperman, Terence P. Speed, Peter H. Quail
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1003778

Regulation of the Boundaries of Accessible Chromatin
Cited by: 16
Author(s): Xiaoran Chai, Sanjanaa Nagarajan, Kwoneel Kim, Kibaick Lee, Jung Kyoon Choi
Software Mentions: 2
Published: about 11 years ago

10.7554/eLife.05042

Response to Nodal morphogen gradient is determined by the kinetics of target gene induction
Cited by: 85
Author(s): Julien Dubrulle, Benjamin M Jordan, Laila Akhmetova, Jeffrey A. Farrell, Seok-Hyung Kim, Lilianna Solnica‐Krezel, Alexander F. Schier
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1002130

Graded Nodal/Activin Signaling Titrates Conversion of Quantitative Phospho-Smad2 Levels into Qualitative Embryonic Stem Cell Fate Decisions
Cited by: 80
Author(s): Kian Leong Lee, Sandy Lim, Yuriy L. Orlov, Le Yau Yit, Henry Yang, Lay Teng Ang, Lorenz Poellinger, Bing Lim
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.40806

Ovaries absent links dLsd1 to HP1a for local H3K4 demethylation required for heterochromatic gene silencing
Cited by: 24
Author(s): Yang Fu, Zhenghui Quan, Huanwei Huang, Minghui He, Xicheng Liu, Tao Cai, Rongwen Xi
Software Mentions: 2
Published: almost 6 years ago

10.1186/gb-2011-12-1-r2

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Cited by: 126
Author(s): Shaun Mahony, Esteban O. Mazzoni, Scott McCuine, Richard A. Young, Hynek Wichterle, David K. Gifford
Software Mentions: 2
Published: almost 14 years ago

10.1186/2040-2392-4-3

MeCP2 modulates gene expression pathways in astrocytes
Cited by: 74
Author(s): Dag H. Yasui, Huichun Xu, Keith W. Dunaway, Janine M. LaSalle, Lee‐Way Jin, Izumi Maezawa
Software Mentions: 2
Published: almost 12 years ago

10.7554/eLife.00426

Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice
Cited by: 67
Author(s): Kazuhiro Shimomura, Vivek Kumar, Nobuya Koike, Tae Kyung Kim, Jason Chong, Ethan D. Buhr, Andrew R. Whiteley, Sharon S. Low, Chiaki Omura, Deborah Fenner, Joseph R. Owens, Marc Richards, Seung Hee Yoo, Hee Kyung Hong, Martha Hotz Vitaterna, Joseph Bass, Mathew T. Pletcher, Tim Wiltshire, John B. Hogenesch, Phillip L. Lowrey, Joseph S. Takahashi
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1002624

A Genome-Wide Screen for Genetic Variants That Modify the Recruitment of REST to Its Target Genes
Cited by: 15
Author(s): Rory Johnson, Nadine Richter, Gireesh K. Bogu, Akshay Bhinge, Siaw Wei Teng, Siew Hua Choo, Lise O. Andrieux, Cinzia De Benedictis, Ralf Jauch, Lawrence W. Stanton
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1004079

C/EBPα Is Required for Long-Term Self-Renewal and Lineage Priming of Hematopoietic Stem Cells and for the Maintenance of Epigenetic Configurations in Multipotent Progenitors
Cited by: 80
Author(s): Marie Sigurd Hasemann, Felicia Kathrine Bratt Lauridsen, Johannes Waage, Janus Schou Jakobsen, Anne-Katrine Frank, Mikkel Bruhn Schuster, Nicolas Rapin, Frederik Otzen Bagger, Philipp S. Hoppe, Timm Schroeder, Bo T. Porse
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.37545

Tuned polymerization of the transcription factor Yan limits off-DNA sequestration to confer context-specific repression
Cited by: 3
Author(s): Charlene Hope, Jemma L. Webber, Sherzod A Tokamov, Ilaria Rebay
Software Mentions: 2
Published: about 6 years ago

10.1186/gb-2011-12-11-r113

Discovery of active enhancers through bidirectional expression of short transcripts
Cited by: 120
Author(s): Michael Melgar, Francis S. Collins, Praveen Sethupathy
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pgen.1003984

Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs
Cited by: 196
Author(s): Adam Auton, Ying Rui Li, Jeffrey M. Kidd, Kyle C. Oliveira, Julie Nadel, J. Kim Holloway, Jessica J. Hayward, Paula E. Cohen, John M. Greally, Jun Wang, Carlos D. Bustamante, Adam R. Boyko
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1006474

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis
Cited by: 42
Author(s): Reinhard Brunmeir, Jingyi Wu, Peng Xu, Sun-Yee Kim, Sylvain Julien, Qiongyi Zhang, Wei Xie, Feng Xu
Software Mentions: 2
Published: almost 8 years ago

10.1186/gb-2012-13-9-r50

Functional analysis of transcription factor binding sites in human promoters
Cited by: 140
Author(s): Troy W. Whitfield, Jie Wang, Patrick J. Collins, E. Christopher Partridge, Shelley Force Aldred, Nathan D. Trinklein, R Myers, Zhiping Weng
Software Mentions: 2
Published: almost 13 years ago

10.15252/emmm.201403927

Tumor cell‐specific inhibition of <scp>MYC</scp> function using small molecule inhibitors of the <scp>HUWE</scp>1 ubiquitin ligase
Cited by: 90
Author(s): Stefanie Peter, Jennyfer Bultinck, Kevin Myant, Laura A. Jaenicke, Susanne Walz, Judith Müller, Michael Gmachl, Matthias Treu, Guido Boehmelt, Carsten P. Ade, W. Schmitz, Armin Wiegering, Christoph Otto, Nikita Popov, Owen J. Sansom, Norbert Kraut, Martin Eilers
Software Mentions: 2
Published: about 10 years ago

10.1186/gb-2013-14-1-r6

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells
Cited by: 112
Author(s): Deborah A. Sanders, Caryn S. Ross-Innes, Dario Beraldi, Jason S. Carroll, Shankar Balasubramanian
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1007935

The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans
Cited by: 38
Author(s): Nicholas Peterson, Hilary K. Cheesman, Liu P, Sarah M. Anderson, Kyle J. Foster, Richa Chhaya, Paola N. Perrat, Jose Thekkiniath, Qiyuan Yang, Cole M. Haynes, Read Pukkila-Worley
Software Mentions: 2
Published: almost 6 years ago

10.1186/gb-2013-14-1-r3

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion
Cited by: 53
Author(s): Henar Hernando, Claire Shannon-Lowe, Abul B.M.M.K. Islam, Fátima Al‐Shahrour, Javier Rodríguez-Ubreva, Virginia C. Rodríguez-Cortez, Biola M. Javierre, Cristina Mangas, Agustín F. Fernández, Maribel Parra, Henri Jacques Delecluse, Manel Esteller, Eduardo López‐Granados, Mario F. Fraga, Núria López‐Bigas, Esteban Ballestar
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pgen.1006197

Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids
Cited by: 83
Author(s): Dae Kwan Ko, Dominica Rohozinski, Qingxin Song, Samuel H. Taylor, Thomas E. Juenger, Frank G. Harmon, Z Jeffrey Chen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1002972

Tethering of the Conserved piggyBac Transposase Fusion Protein CSB-PGBD3 to Chromosomal AP-1 Proteins Regulates Expression of Nearby Genes in Humans
Cited by: 30
Author(s): Lucas T. Gray, Kimberly K. Fong, Thomas Pavelitz, Alan M. Weiner
Software Mentions: 2
Published: about 12 years ago

10.1186/s12859-018-2516-4

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
Cited by: 93
Author(s): Yiqian Zhang, Michiaki Hamada
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1002841

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression
Cited by: 279
Author(s): Claudia Kutter, Stephen Watt, Klara Stefflova, Michael D. Wilson, Ângela Gonçalves, Chris P. Ponting, Duncan T. Odom, Ana C. Marques
Software Mentions: 2
Published: over 12 years ago

10.1186/s12867-018-0110-y

Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression
Cited by: 2
Author(s): Aleksandra Brzęk, Marlena Cichocka, Jakub Dolata, Wojciech Juzwa, Daniel Schümperli, Katarzyna Dorota Raczyńska
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1002111

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
Cited by: 80
Author(s): Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keleş
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1008339

A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure
Cited by: 5
Author(s): Mingguang Li, Ryan D. Fine, Manikarna Dinda, Stefan Bekiranov, Jeffrey S. Smith
Software Mentions: 2
Published: about 5 years ago

10.1007/s12031-020-01490-2

Unraveling Molecular Mechanisms of THAP1 Missense Mutations in DYT6 Dystonia
Cited by: 11
Author(s): Fu Bo Cheng, Michael Walter, Zinah Wassouf, Thomas Hentrich, Nicolas Casadei, Julia M. Schulze‐Hentrich, Peter A. Barbuti, Rejko Krüger, Olaf Rieß, Kathrin Grundmann-Hauser, Thomas Ott
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.10811

Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat
Cited by: 5
Author(s): Yanfeng Liu, Wei Wang
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0053880

Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells
Cited by: 91
Author(s): James A. Hagarman, Michael P. Motley, Katla Kristjánsdóttir, Paul D. Soloway
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2014-15-2-r23

Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts
Cited by: 46
Author(s): Helen Pemberton, Emma Anderton, Harshil Patel, Sharon Brookes, Hollie Chandler, Richard D. Palermo, Julie Stock, Marc Rodríguez‐Niedenführ, Tomáš Raček, Lucas de Breed, Aengus Stewart, Nik Matthews, Gordon Peters
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1003118

A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis
Cited by: 81
Author(s): Denes Hnisz, Anaïs F. Bardet, Clarissa J. Nobile, Andriy Petryshyn, Walter Glaser, Ulrike Schöck, Alexander Stark, Karl Kuchler
Software Mentions: 2
Published: almost 12 years ago

10.15252/embr.201643260

<scp>KMT</scp> 1 family methyltransferases regulate heterochromatin–nuclear periphery tethering via histone and non‐histone protein methylation
Cited by: 14
Author(s): Radhika Rao, Alhad Ashok Ketkar, Neelam Kedia, Vignesh K Krishnamoorthy, Vairavan Lakshmanan, Pankaj Kumar, Abhishek Mohanty, Shilpa Dilip Kumar, Sufi O. Raja, Akash Gulyani, Chandra Prakash Chaturvedi, Marjorie Brand, Dasaradhi Palakodeti, Shravanti Rampalli
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 7 years ago

10.1111/acel.13173

The NSD2/WHSC1/MMSET methyltransferase prevents cellular senescence‐associated epigenomic remodeling
Cited by: 19
Author(s): Hiroshi Tanaka, Tomoka Igata, Kan Etoh, Tomoaki Koga, Shin‐ichiro Takebayashi, Mitsuyoshi Nakao
Software Mentions: 2
Published: over 4 years ago

10.1186/1755-8794-6-50

ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer
Cited by: 8
Author(s): Madhu Sudhan Reddy Bysani, Ola Wallerman, Susanne Bornelöv, Kurt Zatloukal, Jan Komorowski, Claes Wadelius
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1008764

UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize
Cited by: 27
Author(s): Yanfang Du, Lei Liu, Yong Peng, Manfei Li, Yunfu Li, Dan Liu, Xingwang Li, Zuxin Zhang
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1005992

Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression
Cited by: 47
Author(s): Yichi Xu, Weimin Guo, Ping Li, Yan Zhang, Meng Zhao, Zenghua Fan, Zhihu Zhao, Jun Yan
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005108

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters
Cited by: 87
Author(s): Nicholas J. Fuda, Michael J. Guertin, Sumeet K. Sharma, Charles G. Danko, André L. Martins, Adam Siepel, John T. Lis
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1006650

SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer
Cited by: 15
Author(s): Shruthy Suresh, Deniz Durakoglugil, Xiaorong Zhou, Bokai Zhu, Sarah A. Comerford, Chao Xing, Xian Jin Xie, Brian York, Kathryn A. O’Donnell
Software Mentions: 2
Published: over 7 years ago

10.15252/embr.201642198

Capture‐C reveals preformed chromatin interactions between <scp>HIF</scp> ‐binding sites and distant promoters
Cited by: 58
Author(s): James L. Platt, Rafik Salama, James Smythies, Hani Choudhry, James O. J. Davies, Jim R. Hughes, Peter J. Ratcliffe, David R. Mole
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1007826

Downregulation of ERG and FLI1 expression in endothelial cells triggers endothelial-to-mesenchymal transition
Cited by: 50
Author(s): Naomi Nagai, Hiroto Ohguchi, Ryo Nakaki, Yoshihiro Matsumura, Yasuharu Kanki, Juro Sakai, Hiroyuki Aburatani, Takashi Minami
Software Mentions: 2
Published: almost 6 years ago

10.1038/celldisc.2016.37

Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation
Cited by: 23
Author(s): Sophie Beyer, Julien Pontis, Elija Schirwis, Valentine Battisti, Anja Rudolf, Fabien Le Grand, Slimane Ait‐Si‐Ali
Software Mentions: 2
Published: about 8 years ago

10.1038/celldisc.2015.46

Involvement of PARP1 in the regulation of alternative splicing
Cited by: 56
Author(s): Elena A. Matveeva, J. Nicholas Maiorano, Qingyang Zhang, Abdallah M. Eteleeb, Paolo Convertini, Jing Chen, Vittoria Infantino, Stefan Stamm, Jiping Wang, Eric C. Rouchka, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1006529

A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy
Cited by: 109
Author(s): Russell Corbett-Detig, Rasmus Nielsen
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12881-016-0292-4

Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57
Cited by: 25
Author(s): Mads Bak, Susanne E. Boonen, Christina Dahl, Johanne M D Hahnemann, Deborah J G Mackay, Zeynep Tümer, Karen Grønskov, I. Karen Temple, Per Guldberg, Niels Tommerup
Software Mentions: 2
Published: over 8 years ago

10.1186/gb-2013-14-9-r106

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples
Cited by: 96
Author(s): Abel González-Pérez, Alba Jené-Sanz, Núria López‐Bigas
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2013-14-8-r83

Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function
Cited by: 61
Author(s): Maxim Ivanov, Mart Kals, Marina Kacevska, Isabel Barragán, Kie Kasuga, Anders Rane, Andres Metspalu, Lili Milani, Magnus Ingelman‐Sundberg
Software Mentions: 2
Published: almost 12 years ago

10.4161/epi.29856

Methylome, transcriptome, and PPARγ cistrome analyses reveal two epigenetic transitions in fat cells
Cited by: 9
Author(s): Hitomi Takada, Yutaka Saitō, Toutai Mituyama, Zong Wei, Eiji Yoshihara, Sandra Jacinto, Michael Downes, Ronald M. Evans, Yasuyuki S. Kida
Software Mentions: 2
Published: over 10 years ago

10.1186/1756-8935-5-8

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner
Cited by: 81
Author(s): Frank Sleutels, Widia Soochit, Marek Bartkuhn, Helen Heath, Sven Dienstbach, Philipp Bergmaier, Vedran Franke, Manuel Rosa‐Garrido, Suzanne van de Nobelen, Lisa Caesar, Michael I.J.A. van der Reijden, Jan Christian Bryne, Wilfred F. J. van IJcken, J. Anton Grootegoed, M. Dolores Delgado, Boris Lenhard, Rainer Renkawitz, Frank Grosveld, Niels Galjart
Software Mentions: 2
Published: over 12 years ago

10.1186/gb-2014-15-4-r65

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens
Cited by: 144
Author(s): Jian Feng, Matthew B. Wilkinson, Xiaochuan Liu, Immanuel Purushothaman, Deveroux Ferguson, Vincent Vialou, Ian Maze, Ning‐Yi Shao, Pamela J. Kennedy, Ja Wook Koo, Caroline Dias, Benjamin M. Laitman, Victoria Stockman, Quincey LaPlant, Michael E. Cahill, Eric J. Nestler, Li Shen
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0085879

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis
Cited by: 92
Author(s): Fabrice David, Julien Delafontaine, Solenne Carat, Frederick J. Ross, Grégory Lefebvre, Yohan Jarosz, Lucas Sinclair, Daan Noordermeer, Jacques Rougemont, Marion Leleu
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13072-020-00376-2

Genome-wide occupancy reveals the localization of H1T2 (H1fnt) to repeat regions and a subset of transcriptionally active chromatin domains in rat spermatids
Cited by: 4
Author(s): Vasantha Shalini, Utsa Bhaduri, Anjhana C Ravikkumar, Anusha Rengarajan, R. Satyanarayana
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1005615

Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes
Cited by: 37
Author(s): Patompon Wongtrakoongate, Gregory Riddick, Suthat Fucharoen, Gary Felsenfeld
Software Mentions: 2
Published: about 9 years ago

10.1099/mgen.0.000081

The RegA regulon exhibits variability in response to altered growth conditions and differs markedly between Rhodobacter species
Cited by: 20
Author(s): Heidi S. Schindel, Carl E. Bauer
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0042761

A Novel Approach for Transcription Factor Analysis Using SELEX with High-Throughput Sequencing (TFAST)
Cited by: 14
Author(s): D. Reiss, Frederick M. Howard, Harry L. T. Mobley
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0023409

Systematic Clustering of Transcription Start Site Landscapes
Cited by: 58
Author(s): Xiaobei Zhao, Eivind Valen, Brian J. Parker, Albin Sandelin
Software Mentions: 2
Published: over 13 years ago

10.1038/s41421-018-0022-5

Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis
Cited by: 34
Author(s): Janet L. Manias Rothberg, Harinad Maganti, Hani Jrade, Christopher J. Porter, Gareth Palidwor, Christopher Cafariello, Hannah L. Battaion, Safwat T. Khan, Theodore J. Perkins, Robert F. Paulson, Caryn Y. Ito, William L. Stanford
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-1905-6

High-density P300 enhancers control cell state transitions
Cited by: 37
Author(s): Steven Witte, Allan Bradley, Anton J. Enright, Stefan A. Muljo
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.2339

CardioTF, a database of deconstructing transcriptional circuits in the heart system
Cited by: 1
Author(s): Yang Zhen
Software Mentions: 2
Published: over 8 years ago

10.1111/cpr.13045

SETD2 epidermal deficiency promotes cutaneous wound healing via activation of AKT/mTOR Signalling
Cited by: 8
Author(s): Xiaoxue Li, Changwei Liu, Yiwen Zhu, Hanyu Rao, Min Liu, Liming Gui, Wenlong Feng, Huayuan Tang, Jin Xu, Wei‐Qiang Gao, Li Li
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0117415

A Non-Parametric Peak Calling Algorithm for DamID-Seq
Cited by: 5
Author(s): Renhua Li, Leonie U. Hempel, Tingbo Jiang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0031621

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Cited by: 80
Author(s): Satish Sati, Vinay Singh Tanwar, Kalle Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, Sujatha Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1004319

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization
Cited by: 50
Author(s): Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica C. Mar, Chii M. Lin, Melvenia M. Martin, Michaël Ryan, Mirit I. Aladjem, Eric E. Bouhassira
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0200004

Activation of Nrf2 in the liver is associated with stress resistance mediated by suppression of the growth hormone-regulated STAT5b transcription factor
Cited by: 36
Author(s): John P. Rooney, Keiyu Oshida, Naresh Vasani, Beena Vallanat, Natalia Ryan, Brian N. Chorley, Xuting Wang, Douglas A. Bell, Kai Wu, Lauren M. Aleksunes, Curtis D. Klaassen, Thomas W. Kensler, J. Christopher Corton
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1008317

RNA Polymerase II CTD phosphatase Rtr1 fine-tunes transcription termination
Cited by: 11
Author(s): José Victorino, Melanie J. Fox, Whitney R. Smith-Kinnaman, Sarah A. Peck Justice, Katlyn Hughes Burriss, Asha K. Boyd, Megan A. Zimmerly, Rachel R. Chan, Gerald O. Hunter, Yunlong Liu, Amber L. Mosley
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-014-0576-y

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems
Cited by: 132
Author(s): Colm E. Nestor, Raffaele Ottaviano, Diana Reinhardt, Hazel A Cruickshanks, Heidi K. Mjoseng, Rhoanne C. McPherson, Antonio Lentini, John P. Thomson, Donncha S. Dunican, Sari Pennings, Stephen M. Anderton, Mikael Benson, Richard R. Meehan
Software Mentions: 2
Published: almost 10 years ago

10.7554/eLife.46269

Absolute quantification of cohesin, CTCF and their regulators in human cells
Cited by: 72
Author(s): Johann Holzmann, Antonio Z. Politi, Kota Nagasaka, Merle Hantsche-Grininger, Nike Walther, Birgit Koch, Johannes Fuchs, Gerhard Dürnberger, Wen Tang, René Ladurner, Roman R. Stocsits, Georg A. Busslinger, Béla Novák, Karl Mechtler, Iain F. Davidson, Jan Ellenberg, Jan‐Michael Peters
Software Mentions: 2
Published: over 5 years ago

10.1186/s40851-019-0148-9

Recapitulation-like developmental transitions of chromatin accessibility in vertebrates
Cited by: 22
Author(s): Masahiro Uesaka, Shigeru Kuratani, Hiroyuki Takeda, Naoki Irie
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-15-1042

Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes
Cited by: 36
Author(s): Isha Sethi, Satrajit Sinha, Michael Buck
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.celrep.2016.11.028

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3
Cited by: 111
Author(s): Kamila M. Jozwik, Igor Chernukhin, Aurélien A. Sérandour, Sankari Nagarajan, Jason S. Carroll
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.celrep.2018.03.056

Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism
Cited by: 134
Author(s): Jurian Schuijers, John C. Manteiga, Abraham S. Weintraub, Daniel S. Day, Alicia V. Zamudio, Denes Hnisz, Tong Ihn Lee, Richard A. Young
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1005669

Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination
Cited by: 73
Author(s): Xiaomin Dong, Kenian Chen, Raquel Cuevas-Diaz Duran, Yanan You, Steven A. Sloan, Ye Zhang, Shan Zong, Qilin Cao, Ben A. Barres, Jia Qian Wu
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00401-017-1783-x

Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness
Cited by: 19
Author(s): Alexandra Bogeas, Ghislaine Morvan-Dubois, Elias A. El-Habr, François Lejeune, Matthieu Defrance, Ashwin Narayanan, Klaudia Kuranda, Fanny Burel‐Vandenbos, Salwa Sayd, Virgile Delaunay, Luiz Gustavo Dubois, Hugues Parrinello, Stéphanie Rialle, Sylvie Fabrega, Ahmed Idbaïh, Jacques Haiech, Ivan Bièche, Thierry Virolle, Michèle Goodhardt, Hervé Chneiweiss, Marie Pierre Junier
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-015-0740-z

Predicting chromatin organization using histone marks
Cited by: 100
Author(s): Jialiang Huang, Eugenio Marco, Luca Pinello, Guo Cheng Yuan
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-015-0756-4

De novo ChIP-seq analysis
Cited by: 8
Author(s): Xin He, A. Ercüment Çiçek, Yuhao Wang, Marcel H. Schulz, Hai-Son Le, Ziv Bar‐Joseph
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1009368

Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
Cited by: 8
Author(s): Mar González-Ramírez, Cecilia Ballaré, Francesca Mugianesi, Malte Beringer, Alexandra Santanach, Enrique Blanco, Luciano Di Croce
Software Mentions: 2
Published: about 3 years ago

10.18632/oncotarget.12508

ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression
Cited by: 4
Author(s): Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M. Troy, Christopher H. Seward, Xing Lü, Lisa Stubbs
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.53381

Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation
Cited by: 58
Author(s): Tim D.D. Somerville, Giulia Biffi, Juliane Daßler-Plenker, Stella K. Hur, Xueyan He, Krysten E. Vance, Koji Miyabayashi, Yali Xu, Diogo Maia-Silva, Olaf Klingbeil, Osama E. Demerdash, Jonathan Preall, Michael A. Hollingsworth, Mikala Egeblad, David A. Tuveson, Christopher R. Vakoc
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0165581

Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome
Cited by: 10
Author(s): Jason Lin, Kiriko Hiraoka, Tomohiro Watanabe, Tony Kuo, Yoshinao Shinozaki, Atsushi Takatori, Nobuko Koshikawa, Anandhakumar Chandran, Joe Otsuki, Hiroshi Sugiyama, Paul Horton, Hiroki Nagase
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0028171

Dual Function of Histone H3 Lysine 36 Methyltransferase ASH1 in Regulation of Hox Gene Expression
Cited by: 43
Author(s): Yujiro Tanaka, Koji Kawahashi, Zen-ichiro Katagiri, Yasuhiro Nakayama, Milind Mahajan, Dimitris Kioussis
Software Mentions: 2
Published: almost 13 years ago

10.7554/eLife.02637

Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes
Cited by: 45
Author(s): Roberto Bonasio, Emilio Lecona, Varun Narendra, Philipp Voigt, Fulvio Parisi, Yuval Kluger, Danny Reinberg
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0084182

Epigenetic Reprogramming in Mist1−/− Mice Predicts the Molecular Response to Cerulein-Induced Pancreatitis
Cited by: 12
Author(s): Rashid Mehmood, Gábor Varga, Sonali Q. Mohanty, Scott W. Laing, Yuefeng Lu, C. L. Johnson, Alexei Kharitonenkov, Christopher L. Pin
Software Mentions: 2
Published: almost 11 years ago

10.7554/eLife.06068

Release of human cytomegalovirus from latency by a KAP1/TRIM28 phosphorylation switch
Cited by: 85
Author(s): Benjamin Rauwel, Suk Min Jang, Marco Cassano, Adamandia Kapopoulou, Isabelle Barde, Didier Trono
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-015-0819-6

P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis
Cited by: 57
Author(s): Chenghua Cui, Ying Gan, Lin Gu, James M. Wilson, Zhaojun Liu, Baozhen Zhang, Dajun Deng
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-015-0832-9

Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization
Cited by: 48
Author(s): Т. Н. Кузнецова, Shuang-Yin Wang, Nagesha A.S. Rao, Amit Mandoli, Joost H.A. Martens, Nils Rother, Aafke Aartse, Laszlo Groh, Eva M. Janssen-Megens, Guoliang Li, Yijun Ruan, Colin Logie, Hendrik G. Stunnenberg
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-017-4378-y

Genes uniquely expressed in human growth plate chondrocytes uncover a distinct regulatory network
Cited by: 11
Author(s): Bing Li, Karthika Balasubramanian, Deborah Krakow, Daniel H. Cohn
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-6-74

Cited by: 7
Author(s): Aba-Sah Dadzie, Albert Burger
Software Mentions: 2
Published: almost 20 years ago