Ecosyste.ms: Papers

10.1186/s13059-014-0456-5

RRHP: a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution
Cited by: 45
Author(s): Adam Petterson, Tzu Hung Chung, Darany Tan, Xueguang Sun, Xiaoteng Jia
Software Mentions: 1
Published: about 10 years ago

10.1186/gb-2014-15-5-r82

Insulator function and topological domain border strength scale with architectural protein occupancy
Cited by: 255
Author(s): Kevin Van Bortle, Michael H. Nichols, L i Li, Chin‐Tong Ong, Naomi Takenaka, Zhaohui S. Qin, Victor G. Corcés
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13059-014-0474-3

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework
Cited by: 59
Author(s): Arif Harmanci, Joel Rozowsky, Mark Gerstein
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-019-5609-1

Genome-wide analysis of three histone marks and gene expression in Paulownia fortunei with phytoplasma infection
Cited by: 12
Author(s): Lijun Yan, Guoqiang Fan, Xiaoyü Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-014-0547-3

Epigenetic modifications are associated with inter-species gene expression variation in primates
Cited by: 70
Author(s): Xiang Zhou, Carolyn E. Cain, Marsha Myrthil, Noah Lewellen, Katelyn Michelini, Emily Davenport, Matthew Stephens, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-015-1882-9

Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation
Cited by: 42
Author(s): Efil Bayam, Gulcan Semra Sahin, Gizem Guzelsoy, Gökhan Güner, Alkan Kabakçıoğlu, Gulayse Ince-Dunn
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-11-396

Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression
Cited by: 74
Author(s): Xiaojiang Xu, Stephen A. Hoang, Marty W. Mayo, Stefan Bekiranov
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-14-575

The role of retinoic acid in hepatic lipid homeostasis defined by genomic binding and transcriptome profiling
Cited by: 53
Author(s): Yuqi He, Lei Gong, Yaping Fang, Qimin Zhan, Hui‐Xin Liu, Yuqi He, Grace L. Guo, Lois D. Lehman‐McKeeman, Jianwen Fang, Yu‐Jui Yvonne Wan
Software Mentions: 1
Published: about 11 years ago

10.1186/s13059-015-0760-8

Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells
Cited by: 53
Author(s): Anna Mattout, Yair Aaronson, Badi Sri Sailaja, Raghu Ram Edupuganti, Arigela Harikumar, Jan‐Philipp Mallm, Kae Hwan Sim, Malka Nissim-Rafinia, Emmanuelle Supper, Prim B. Singh, Siu Kwan Sze, Susan M. Gasser, Karsten Rippe, Eran Meshorer
Software Mentions: 1
Published: about 9 years ago

10.1186/s13059-016-0919-y

Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets
Cited by: 14
Author(s): Aurélien A. Sérandour, Stéphane Avner, Elise A. Mahé, Thierry Madigou, Sylvain Guibert, Michaël Weber, Gilles Salbert
Software Mentions: 1
Published: over 8 years ago

10.1186/s13059-016-1001-5

In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine
Cited by: 57
Author(s): Mario Iurlaro, Gordon R. McInroy, Heather E. Burgess, Wendy Dean, Eun‐Ang Raiber, Martin Bachman, Dario Beraldi, Shankar Balasubramanian, Wolf Reik
Software Mentions: 1
Published: over 8 years ago

10.1098/rsob.140043

Eic1 links Mis18 with the CCAN/Mis6/Ctf19 complex to promote CENP-A assembly
Cited by: 41
Author(s): Lakxmi Subramanian, Nicholas R. T. Toda, Juri Rappsilber, Robin C. Allshire
Software Mentions: 1
Published: over 10 years ago

10.1186/s13059-016-1089-7

Choosing panels of genomics assays using submodular optimization
Cited by: 17
Author(s): Kai Wei, Maxwell W. Libbrecht, Jeffrey A. Bilmes, William Stafford Noble
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-016-1144-4

Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects
Cited by: 147
Author(s): Yuanpeng Gao, Haibo Wu, Yongsheng Wang, Xin Liu, Linlin Chen, Qian Li, Chenchen Cui, Li Xu, Jingcheng Zhang, Yong Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-016-2731-1

Genome-wide alteration of 5-hydroxymenthylcytosine in a mouse model of Alzheimer’s disease
Cited by: 45
Author(s): Liqi Shu, Wenjia Sun, Liping Li, Zihui Xu, Li Lin, Pei Xie, Hui Shen, Luoxiu Huang, Qi Xu, Peng Jin, Xuekun Li
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-12-134

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
Cited by: 144
Author(s): Joshua W. K. Ho, Eric Bishop, Peter Karchenko, Nicolas Nègre, Kevin P. White, Peter J. Park
Software Mentions: 1
Published: over 13 years ago

10.1186/s13059-018-1411-7

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution
Cited by: 23
Author(s): Raphaël Mourad, Krzysztof Ginalski, Gaëlle Legube, Olivier Cuvier
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-018-5375-5

Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEX-Seq and microarray data
Cited by: 10
Author(s): Hideyuki Oka, Takaaki Kojima, Kenji Ihara, Tetsuo Kobayashi, Hideo Nakano
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.67259

TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells
Cited by: 16
Author(s): Anna Osnato, Stephanie Brown, Christel Krueger, Simon Andrews, Amanda J. Collier, Shota Nakanoh, Mariana Quiroga Londoño, Brandon T Wesley, Daniele Muraro, A Sophie Brumm, Kathy K. Niakan, Ludovic Vallier, Daniel Ortmann, Peter J. Rugg‐Gunn
Software Mentions: 1
Published: about 3 years ago

10.1186/s13059-019-1771-7

RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
Cited by: 151
Author(s): Leilei Zhou, Shiping Tian, Guozheng Qin
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-10-618

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
Cited by: 119
Author(s): Teemu D. Laajala, Sunil K. Raghav, Soile Tuomela, Riitta Lahesmaa, Tero Aittokallio, Laura L. Elo
Software Mentions: 1
Published: almost 15 years ago

10.1098/rsob.150263

ParA and ParB coordinate chromosome segregation with cell elongation and division during <i>Streptomyces</i> sporulation
Cited by: 67
Author(s): Magdalena Donczew, Dorota Mackiewicz, Agnieszka Wróbel, Klas Flärdh, Jolanta Zakrzewska‐Czerwińska, Dagmara Jakimowicz
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-14-232

A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples
Cited by: 52
Author(s): Wilbert Zwart, Rutger H.T. Koornstra, Jelle Wesseling, Emiel J. Rutgers, Sabine C. Linn, Jason S. Carroll
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-237

AmrZ is a global transcriptional regulator implicated in iron uptake and environmental adaption in P. fluorescensF113
Cited by: 35
Author(s): Francisco Martínez‐Granero, Miguel Redondo‐Nieto, Pilar Vesga, Marta Martín, Rafael Rivilla
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-2125-9

EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions
Cited by: 17
Author(s): Yonglun Luo, Jenny Blechingberg, Ana Miguel Fernandes, Shengting Li, Tue Fryland, Anders D. Børglum, Lars Bolund, Anders Lade Nielsen
Software Mentions: 1
Published: about 9 years ago

10.1186/s13059-021-02385-0

N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner
Cited by: 60
Author(s): Leilei Zhou, Renkun Tang, Xiaojing Li, Shiping Tian, Bingbing Li, Guozheng Qin
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-018-5187-7

High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division
Cited by: 6
Author(s): Daniel G. Mediati, Catherine Burke, Shirin Ansari, Elizabeth J. Harry, Iain G. Duggin
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms151223537

The Dynamics of DNA Methylation in Maize Roots under Pb Stress
Cited by: 35
Author(s): Haiping Ding, Junying Gao, Cheng Qin, Hui Ma, Hong Huang, Song Pan, Xiao‐Dong Luo, Hung-Ching Lin, Yaou Shen, Guangtang Pan, Zhiming Zhang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13073-016-0280-5

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses
Cited by: 43
Author(s): Kivia Aparecida Pontes de Oliveira, Eva Kaergel, Matthias Heinig, Jean-Fred Fontaine, Giannino Patone, Enrique M. Muro, Stephan Mathas, Michael Hummel, Miguel A. Andrade‐Navarro, Norbert Hübner, Claus Scheidereit
Software Mentions: 1
Published: over 8 years ago

10.1186/s13073-016-0308-x

Identification of the BRD1 interaction network and its impact on mental disorder risk
Cited by: 27
Author(s): Tue Fryland, Jane H. Christensen, Jonatan Pallesen, Manuel Mattheisen, Johan Palmfeldt, Mads Bak, Jakob Grove, Ditte Demontis, Jenny Blechingberg, Hong Ooi, Mette Nyegaard, Mads E. Hauberg, Niels Tommerup, Niels Gregersen, Ole Mors, Thomas J. Corydon, Anders Lade Nielsen, Anders D. Børglum
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-11-415

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
Cited by: 217
Author(s): Mali Salmon‐Divon, Heidi Dvinge, Kairi Tammoja, Paul Bertone
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-015-1358-y

Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance
Cited by: 37
Author(s): Sho Maekawa, Naoto Imamachi, Takuma Irie, Hidenori Tani, K Matsumoto, Ryuta Mizutani, Katsutoshi Imamura, Miho Kakeda, Tetsushi Yada, Sumio Sugano, Yutaka Suzuki, Nobuyoshi Akimitsu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12859-015-0579-z

Is this the right normalization? A diagnostic tool for ChIP-seq normalization
Cited by: 9
Author(s): Claudia Angelini, Ruth Heller, Rita Volkinshtein, Daniel Yekutieli
Software Mentions: 1
Published: over 9 years ago

10.1186/s13742-015-0050-0

Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears
Cited by: 1
Author(s): Nicholas C. Wong, Gavin Meredith, George Marnellos, Miroslav Dudas, Mandy Parkinson-Bates, Minhee S. Halemba, Zac Chatterton, Jovana Maksimovic, David M. Ashley, Françoise Méchinaud, Jeffrey M. Craig, Richard Saffery
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-5932-6

NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions
Cited by: 1
Author(s): Daoshan Zheng, Justyna Trynda, Zhifu Sun, Zhaoyu Li
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-821

Genome-wide Twist1 occupancy in endocardial cushion cells, embryonic limb buds, and peripheral nerve sheath tumor cells
Cited by: 13
Author(s): Mary P. Lee, Nancy Ratner, Katherine E. Yutzey
Software Mentions: 1
Published: about 10 years ago

10.1186/s41065-016-0012-2

eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines
Cited by: 4
Author(s): Fang Huang, Jiawei Shen, Qingli Guo, Yongyong Shi
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-9-537

Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq
Cited by: 126
Author(s): Yong Zhang, Hyunjin Shin, Jun S. Song, Ying Lei, X Shirley Liu
Software Mentions: 1
Published: about 16 years ago

10.3390/ijms21186557

FACS-Based Proteomics Enables Profiling of Proteins in Rare Cell Populations
Cited by: 9
Author(s): Evelyne Maes, Nathalie Cools, Hanny Willems, Geert Baggerman
Software Mentions: 1
Published: about 4 years ago

10.1002/acm2.13207

Impact of slice thickness, pixel size, and CT dose on the performance of automatic contouring algorithms
Cited by: 16
Author(s): Kai Huang, Dong Joo Rhee, Rachel B. Ger, Rick R. Layman, Jinzhong Yang, Carlos Cárdenas, Laurence Edward Court
Software Mentions: 1
Published: over 3 years ago

10.1074/jbc.RA119.008687

Telomere repeat–binding factor 2 binds extensively to extra-telomeric G-quadruplexes and regulates the epigenetic status of several gene promoters
Cited by: 26
Author(s): Ananda Kishore Mukherjee, Shalu Sharma, Sulochana Bagri, Rintu Kutum, Pankaj Kumar, Asgar Hussain, Prateek Singh, Dhurjhoti Saha, Anirban Kar, Debasis Dash, Shantanu Chowdhury
Software Mentions: 1
Published: about 5 years ago

10.1111/jcmm.14424

Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer
Cited by: 15
Author(s): Kening Li, Congling Xu, Yuxin Du, Muhammad Junaid, Aman-Chandra Kaushik, Dong‐Qing Wei
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21239061

ChIP-Seq-Based Approach in Mouse Enteric Precursor Cells Reveals New Potential Genes with a Role in Enteric Nervous System Development and Hirschsprung Disease
Cited by: 4
Author(s): Leticia Villalba‐Benito, Ana Torroglosa, Berta Lasa, Raquel M. Fernández, María José Moya-Jiménez, Guillermo Antiñolo, Salud Borrego
Software Mentions: 1
Published: almost 4 years ago

10.1093/jxb/erw496

Cold acclimation alters DNA methylation patterns and confers tolerance to heat and increases growth rate in Brassica rapa
Cited by: 72
Author(s): Xilin Hou, Ying Liu, Weike Duan, Feiyi Huang, Xilin Hou
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1000985

Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome
Cited by: 72
Author(s): Daniela Hüser, Andreas Gogol-Döring, Timo Lutter, Stefan Weger, Kerstin Winter, Eva-Maria Hammer, Toni Cathomen, Knut Reinert, Regine Heilbronn
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.ppat.1003636

Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming
Cited by: 80
Author(s): Michael J. McClellan, C. David Wood, Opeoluwa O. Ojeniyi, Tim J. Cooper, Aditi Kanhere, Aaron Arvey, Helen Webb, Richard D. Palermo, Marie L. Harth-Hertle, Bettina Kempkes, Richard G. Jenner, Michelle J. West
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms22083902

Detection of Genomic Uracil Patterns
Cited by: 6
Author(s): Angéla Békési, Eszter Holub, Hajnalka Laura Pálinkás, Beáta G. Vértessy
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.ppat.1004511

Specific Dysregulation of IFNγ Production by Natural Killer Cells Confers Susceptibility to Viral Infection
Cited by: 12
Author(s): Nassima Fodil, David Langlais, Peter Moussa, Gregory A. Boivin, Tania Di Pietrantonio, Irena Radovanovic, Anne Dumaine, Mathieu Blanchette, Erwin Schurr, Philippe Gros, Silvia M. Vidal
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1006167

Epigenetic Landscape of Kaposi's Sarcoma-Associated Herpesvirus Genome in Classic Kaposi's Sarcoma Tissues
Cited by: 30
Author(s): Rui Sun, Xiaohua Tan, Xing Wang, Xiaodong Wang, Lei Yang, Erle S. Robertson, Ke Lan
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-015-2248-z

Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development
Cited by: 5
Author(s): Qian Dong, Mingxu Fang, Sugata Roychowdhury, Carl E. Bauer
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-015-1824-6

Functional diversity of CTCFs is encoded in their binding motifs
Cited by: 10
Author(s): Rongxin Fang, Chengqi Wang, Geir Skogerbø, Zhihua Zhang
Software Mentions: 1
Published: about 9 years ago

10.1530/REP-16-0441

A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa
Cited by: 23
Author(s): Gerly Sillaste, Lauris Kaplinski, Riho Meier, Uelle Jaakma, Elo Eriste, Andres Salumets
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22094959

Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing
Cited by: 3
Author(s): Lilas Courtot, Elodie Bournique, Chrystelle Maric, Laure Guitton-Sert, Miguel Madrid-Mencía, Véra Pancaldi, Jean‐Charles Cadoret, Jean-Sébastien Hoffmann, Valérie Bergoglio
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-13-S6-S6

A modulator based regulatory network for ERα signaling pathway
Cited by: 5
Author(s): Hui Wu, Pengyue Zheng, Guanglong Jiang, Yunlong Liu, Kenneth P. Nephew, Tim Hui-Ming Huang, Lang Li
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-13-51

Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR
Cited by: 42
Author(s): Hansook Kim Chong, Jacob Biesinger, Young‐Kyo Seo, Xiaohui Xie, Timothy F. Osborne
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2105-10-299

BayesPeak: Bayesian analysis of ChIP-seq data
Cited by: 125
Author(s): Christiana Spyrou, Rory Stark, Andy G. Lynch, Simon Tavaré
Software Mentions: 1
Published: about 15 years ago

10.1038/srep08635

Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq)
Cited by: 5
Author(s): Wilberforce Zachary Ouma, Maria Katherine Mejía‐Guerra, Alper Yılmaz, Pablo Pareja-Tobes, Wei Li, Andrea I. Doseff, Erich Grotewold
Software Mentions: 1
Published: over 9 years ago

10.1038/srep17568

TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer
Cited by: 49
Author(s): Christopher G. Chapman, Christopher J. Mariani, Feng Wu, Katherine Meckel, Fatma Ayaloglu Butun, Alice Chuang, Jozef Madžo, Marc Bissonnette, John H. Kwon, Lucy A. Godley
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep19620

Exploration of nucleosome positioning patterns in transcription factor function
Cited by: 13
Author(s): Kazuhira Maehara, Yasuyuki Ohkawa
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep21598

Oscillating primary transcripts harbor miRNAs with circadian functions
Cited by: 26
Author(s): Haifang Wang, Zenghua Fan, Meng Zhao, Juan Li, Minghua Lü, Wei Liu, Hao Ying, Mofang Liu, Jun Yan
Software Mentions: 1
Published: over 8 years ago

10.1038/srep24318

Histone H4 lysine 20 acetylation is associated with gene repression in human cells
Cited by: 40
Author(s): Jun Ya Kaimori, Kazuhira Maehara, Yoko Hayashi‐Takanaka, Akihito Harada, Masafumi Fukuda, Shuichi Yamamoto, Naotsugu Ichimaru, Takashi Umehara, Shigeyuki Yokoyama, Ryotaro Matsuda, Tsuyoshi Ikura, Koji Nagao, Chikashi Obuse, Naohito Nozaki, Shiro Takahara, Toshifumi Takao, Yasuyuki Ohkawa, Hiroshi Kimurâ, Yoshitaka Isaka
Software Mentions: 1
Published: over 8 years ago

10.1038/srep26566

TLR signals posttranscriptionally regulate the cytokine trafficking mediator sortilin
Cited by: 19
Author(s): Toshiki Yabe-Wada, Shintaro Matsuba, Kazuya Takeda, Tetsuya Sato, Mikita Suyama, Yasuyuki Ohkawa, Toshiyuki Takai, Haifeng Shi, Caroline C. Philpott, Akira Nakamura
Software Mentions: 1
Published: over 8 years ago

10.1038/srep28112

Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells
Cited by: 16
Author(s): Yoko Itahana, Jinqiu Zhang, Jonathan Göke, Leah A. Vardy, Rachel Han, Kozue Iwamoto, Engin Cukuroglu, Paul Robson, Mahmoud A. Pouladi, Alan Colman, Koji Itahana
Software Mentions: 1
Published: over 8 years ago

10.1038/srep30255

NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes
Cited by: 24
Author(s): Chongzhi Zang, Annouck Luyten, Justina Chen, X. Shirley Liu, Ramesh A. Shivdasani
Software Mentions: 1
Published: over 8 years ago

10.1038/srep31785

Novel O-GlcNAcylation on Ser40 of canonical H2A isoforms specific to viviparity
Cited by: 31
Author(s): Mitsuko Hirosawa, Koji Hayakawa, Chikako Yoneda, Daisuke Arai, Hitoshi Shiota, Takehiro Suzuki, Satoshi Tanaka, Naoshi Dohmae, Kunio Shiota
Software Mentions: 1
Published: about 8 years ago

10.1038/srep32611

Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines
Cited by: 87
Author(s): Stephen Wilson, Jianfei Qi, Fabian V. Filipp
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-017-3561-5

Genome-wide identification of direct HBx genomic targets
Cited by: 50
Author(s): Francesca Guerrieri, Laura Belloni, Daniel D’Andrea, Natalia Pediconi, Loredana Le Pera, Barbara Testoni, C. Scisciani, Océane Floriot, Fabien Zoulim, Anna Tramontano, Massimo Levrero
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-14-680

A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer
Cited by: 56
Author(s): Haiyun Wang, Clifford A. Meyer, Fei Teng, Gang Wang, Fan Zhang, X Shirley Liu
Software Mentions: 1
Published: almost 12 years ago

10.1038/srep41938

Fe doped Magnetic Nanodiamonds made by Ion Implantation
Cited by: 12
Author(s): C.H. Chen, I. C. Cho, Hui-Shan Jian, Huan Niu
Software Mentions: 1
Published: almost 8 years ago

10.1038/srep42875

Altered enhancer transcription underlies Huntington’s disease striatal transcriptional signature
Cited by: 40
Author(s): Stéphanie Le Gras, Céline Keime, Anne Anthony, Caroline Lotz, Lucie de Longprez, Emmanuel Brouillet, Jean‐Christophe Cassel, Anne‐Laurence Boutillier, Karine Mérienne
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-01138-z

Transcription Factor Antagonism Controls Enteroendocrine Cell Specification from Intestinal Stem Cells
Cited by: 14
Author(s): Yumei Li, Zhimin Pang, Huanwei Huang, Chenhui Wang, Tao Cai, Rongwen Xi
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-12-152

Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites
Cited by: 86
Author(s): Søren Fisker Schmidt, Mette Jørgensen, Yun Chen, Ronni Nielsen, Albin Sandelin, Susanne Mandrup
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-017-04929-6

Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data
Cited by: 5
Author(s): Sascha Jung, Vladimir Espinosa Angarica, Miguel A. Andrade‐Navarro, Noel J. Buckley, Antonio del Sol
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-06539-8

Overexpression of DNMT3b target genes during Enteric Nervous System development contribute to the onset of Hirschsprung disease
Cited by: 15
Author(s): Leticia Villalba‐Benito, Ana Torroglosa, Raquel M. Fernández, Macarena Ruíz-Ferrer, María José Moya-Jiménez, Guillermo Antiñolo, Salud Borrego
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22126254

Transcriptome Profiling of m6A mRNA Modification in Bovine Mammary Epithelial Cells Treated with Escherichia coli
Cited by: 12
Author(s): Ting Li, Changjie Lin, Yifan Zhu, Haojun Xu, Yiya Yin, Chaohao Wang, Xin Tang, Tongxing Song, Aizhen Guo, Yingyu Chen, Changmin Hu
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-11-81

An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Cited by: 24
Author(s): Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson, Dabing Zhang
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-017-13442-9

Genetic and Epigenetic Profiling Reveals EZH2-mediated Down Regulation of OCT-4 Involves NR2F2 during Cardiac Differentiation of Human Embryonic Stem Cells
Cited by: 12
Author(s): Varsha Pursani, Prasad Pethe, Mohsin Bashir, Prabha Sampath, Vivek Tanavde, Deepa Bhartiya
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-13-S8-S12

Combining multiple ChIP-seq peak detection systems using combinatorial fusion
Cited by: 22
Author(s): Christina Schweikert, Stuart M. Brown, Zuojian Tang, PR Smith, David Hsu
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-017-15634-9

DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma
Cited by: 20
Author(s): Andrey Finegersh, Scott Kulich, Theresa Guo, Alexander V. Favorov, Elana J. Fertig, Ludmila Danilova, Daria A. Gaykalova, Joseph A. Califano, Umamaheswar Duvvuri
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-15828-1

Prep1 prevents premature adipogenesis of mesenchymal progenitors
Cited by: 14
Author(s): Giorgia Maroni, В. А. Ткачук, Alexander Egorov, Marco J. Morelli, Raffaele Luongo, Elena Levantini, Francesco Blasi, Maria Cristina Magli, Dmitry Penkov
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-20043-7

Necessity of p53-binding to the CDH1 locus for its expression defines two epithelial cell types differing in their integrity
Cited by: 12
Author(s): Tsukasa Oikawa, Yutaro Otsuka, Yasuhito Onodera, Mei Horikawa, Haruka Handa, Shigeru Hashimoto, Yutaka Suzuki, Hisataka Sabe
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-25308-9

Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles
Cited by: 20
Author(s): Svitlana Vdovikova, Siv Gilfillan, Shixiong Wang, Mitesh Dongre, Sun Nyunt Wai, Antoni Hurtado
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-32927-9

Histone deacetylase (HDAC) 1 and 2 complexes regulate both histone acetylation and crotonylation in vivo
Cited by: 76
Author(s): Rdw Kelly, Aditya Chandru, P. Marc Watson, Yun Song, Matthew Blades, Naomi Robertson, AG Jamieson, John W. R. Schwabe, Shaun M. Cowley
Software Mentions: 1
Published: about 6 years ago

10.1186/1743-0003-10-57

Contribution of hip joint proprioception to static and dynamic balance in cerebral palsy: a case control study
Cited by: 55
Author(s): Diane L. Damiano, Jason R. Wingert, Christopher J. Stanley, Lindsey A. Curatalo
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-018-36698-1

Considerations for high-yield, high-throughput cell enrichment: fluorescence versus magnetic sorting
Cited by: 96
Author(s): Bryan A. Sutermaster, Eric M. Darling
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-018-38017-0

FOXM1 modulates 5-FU resistance in colorectal cancer through regulating TYMS expression
Cited by: 80
Author(s): Vidhya Varghese, Luca Magnani, Narumi Harada-Shoji, Francesco Mauri, Richard Szydlo, Shang J. Yao, Eric W.‐F. Lam, Laura Kenny
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-15-598

Genome-wide analysis of DNA methylation patterns in horse
Cited by: 31
Author(s): Ja-Rang Lee, Chang Pyo Hong, Jae-Woo Moon, Yun‐Hoa Jung, Dae-Soo Kim, Tae-Hyung Kim, Jeong‐An Gim, Jin-Han Bae, Yuri Choi, Jungwoo Eo, Yun-Jeong Kwon, Sanghoon Song, Junsu Ko, Young Mok Yang, Hak-Kyo Lee, Kyung-Do Park, Kung Ahn, Kyoung-Tag Do, Hong-Seok Ha, Kyudong Han, Joo Mi Yi, Hee‐Jae Cha, Byung-Wook Cho, Jong Bhak, Heui‐Soo Kim
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-019-44278-0

Quantification of very low-abundant proteins in bacteria using the HaloTag and epi-fluorescence microscopy
Cited by: 23
Author(s): Alessia Lepore, Hannah N. Taylor, Dirk Landgraf, Burak Okumuş, Alfonso Jaramillo, Lorna McLaren, Somenath Bakshi, Johan Paulsson, Meriem El Karoui
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-51018-x

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer
Cited by: 8
Author(s): Emily Flam, Ludmila Danilova, Dylan Z. Kelley, Elena Stavrovskaya, Theresa Guo, Michael Considine, Jiang Qian, Joseph A. Califano, Alexander V. Favorov, Elana J. Fertig, Daria A. Gaykalova
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-87683-0

Comparative analysis of histone H3K4me3 modifications between blastocysts and somatic tissues in cattle
Cited by: 7
Author(s): Mao Ishibashi, Shuntaro Ikeda, Naojiro Minami
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-016-2890-0

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius
Cited by: 16
Author(s): Han Liu, Kun Wang, Ann-Christin Lindås, Eveline Peeters
Software Mentions: 1
Published: over 8 years ago

10.3390/s100504521

A Multipath Routing Protocol Based on Clustering and Ant Colony Optimization for Wireless Sensor Networks
Cited by: 118
Author(s): Jing Yang, Mingwei Xu, Wei Zhao, XU Bao-guo
Software Mentions: 1
Published: over 14 years ago

10.1186/2044-5040-1-25

Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer
Cited by: 27
Author(s): Phillip W. L. Tai, Katherine I. Fisher-Aylor, Charis L. Himeda, Catherine L. Smith, Alexandra P. MacKenzie, Deri Helterline, John C. Angello, Robert E. Welikson, B Wold, Stephen D. Hauschka
Software Mentions: 1
Published: over 13 years ago

10.1016/j.stemcr.2017.04.016

RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells
Cited by: 14
Author(s): Riikka Lund, Nelly Rahkonen, Maia Malonzo, Leni Kauko, Maheswarareddy Emani, Virpi Kivinen, Elisa Närvä, Esko Kemppainen, Asta Laiho, Heli Skottman, Outi Hovatta, Omid Rasool, Matti Nykter, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 1
Published: over 7 years ago

10.1186/s13287-016-0466-1

Integrated analysis of hematopoietic differentiation outcomes and molecular characterization reveals unbiased differentiation capacity and minor transcriptional memory in HPC/HSC-iPSCs
Cited by: 2
Author(s): Shuai Gao, Xinfeng Hou, Yonghua Jiang, Zijian Xu, Tao Cai, Jiajie Chen, Gang Chang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13287-018-0810-8

Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage
Cited by: 18
Author(s): Varsha Pursani, Deepa Bhartiya, Vivek Tanavde, Mohsin Bashir, Prabha Sampath
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.6644

Cell cycle-dependent resolution of DNA double-strand breaks
Cited by: 19
Author(s): Susanna Ambrosio, Giacomo Di Palo, Giuliana Napolitano, Stefano Amente, Gaetano Ivan Dellino, Mario Faretta, Pier Giuseppe Pelicci, Luigi Lania, Barbara Majello
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-016-3450-3

Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data
Cited by: 2
Author(s): Chi Yang, Min-Hsuan Chen, Shengrong Lin, Erik H. Andrews, Chao Cheng, Chun-Chi Liu, Jeremy J.W. Chen
Software Mentions: 1
Published: almost 8 years ago

10.1155/2016/3162363

Dynamic Changes in Occupancy of Histone Variant H2A.Z during Induced Somatic Cell Reprogramming
Cited by: 4
Author(s): Fenglin Dong, Zhenwei Song, Jiali Yu, Baole Zhang, Bao‐Chun Jiang, Ying Shen, Youde Lu, Chunlei Song, Cong Peng, Honglin Liu
Software Mentions: 1
Published: almost 9 years ago

10.1155/2020/8837654

Mesenchymal Stem/Progenitor Cells: The Prospect of Human Clinical Translation
Cited by: 25
Author(s): Dina Rady, Marwa M. S. Abbass, Aiah A. El-Rashidy, Sara El Moshy, Israa Ahmed Radwan, Christof E. Dörfer, Karim M. Fawzy El‐Sayed
Software Mentions: 1
Published: over 4 years ago