Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: JASPAR

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/JASPAR

R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices
1 version
Latest release: almost 12 years ago
0 downloads

Papers Mentioning JASPAR 1,283

10.3390/ani9110874
Characteristics of the BMP7 Promoter in Hu Sheep
Cited by: 5
Author(s): Xiaoyang Lv, Wei Sun, Shuangxia Zou, Ling Chen, Joram M. Mwacharo, Jinyu Wang
Software Mentions: 1
Published: almost 5 years ago
10.3390/ani11061572
H3K4me2 Promotes the Activation of lncCPSET1 by Jun in the Chicken PGC Formation
Cited by: 2
Author(s): Chen Zhang, Qisheng Zuo, Xiaomin Gao, Cai Hu, Shujian Zhou, Chen Chen, Yichen Zou, Juanjuan Zhao, Yani Zhang, Bichun Li
Software Mentions: 1
Published: over 3 years ago
10.1186/s13075-018-1713-x
E2F2 directly regulates the STAT1 and PI3K/AKT/NF-κB pathways to exacerbate the inflammatory phenotype in rheumatoid arthritis synovial fibroblasts and mouse embryonic fibroblasts
Cited by: 51
Author(s): Shiguan Wang, Lin Wang, Changliang Wu, Shaohua Sun, Jihong Pan
Software Mentions: 1
Published: almost 6 years ago
10.1002/art.39278
Correlation of the Osteoarthritis Susceptibility Variants That Map to Chromosome 20q13 With an Expression Quantitative Trait Locus Operating on<i>NCOA3</i>and With Functional Variation at the Polymorphism rs116855380
Cited by: 22
Author(s): Fiona Gee, Michael D. Rushton, John Loughlin, Louise N. Reynard
Software Mentions: 1
Published: almost 9 years ago
10.1186/1471-2105-11-551
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs
Cited by: 8
Author(s): Fernando García-Alcalde, Armando Blanco, Adrian J. Shepherd
Software Mentions: 1
Published: almost 14 years ago
10.1186/1471-2105-8-138
Multiple non-collinear TF-map alignments of promoter regions
Cited by: 11
Author(s): Enrique Blanco, Roderic Guigó, Xavier Messeguer
Software Mentions: 1
Published: over 17 years ago
10.1186/1471-2105-8-100
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs
Cited by: 4
Author(s): Mamoru Kato, Tatsuhiko Tsunoda
Software Mentions: 1
Published: over 17 years ago
10.1186/s12859-016-1354-5
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules
Cited by: 1
Author(s): Natalia Acevedo-Luna, Leonardo Mariño-Ramírez, Armand Halbert, Ulla Hansen, David Landsman, John L. Spouge
Software Mentions: 1
Published: almost 8 years ago
10.1186/1471-2105-10-93
New scoring schema for finding motifs in DNA Sequences
Cited by: 9
Author(s): Fatemeh Zare-Mirakabad, H. Ahrabian, M. Sadeghi, Abbas Nowzari-Dalini, Bahram Goliaei
Software Mentions: 1
Published: over 15 years ago
10.1186/1471-2105-7-238
K-SPMM: a database of murine spermatogenic promoters modules & motifs
Cited by: 5
Author(s): Yi Lu, Adrian E. Platts, G. Charles Ostermeier, Stephen A. Krawetz
Software Mentions: 1
Published: over 18 years ago
10.1186/1471-2105-14-108
LASAGNA: A novel algorithm for transcription factor binding site alignment
Cited by: 24
Author(s): Chih Lee, Chun-Hsi Huang
Software Mentions: 1
Published: over 11 years ago
10.1186/1471-2105-7-389
Fast index based algorithms and software for matching position specific scoring matrices
Cited by: 126
Author(s): Michael Beckstette, Robert Homann, Robert Giegerich, Stefan Kurtz
Software Mentions: 1
Published: about 18 years ago
10.1186/1471-2105-13-215
Searching for transcription factor binding sites in vector spaces
Cited by: 12
Author(s): Chih Lee, Chun-Hsi Huang
Software Mentions: 1
Published: about 12 years ago
10.1186/1471-2105-10-224
FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral
Cited by: 13
Author(s): Fernando García, Francisco J. López, Carlos Cano, Armando Blanco
Software Mentions: 1
Published: about 15 years ago
10.1186/s12859-017-2005-1
Sequence motif finder using memetic algorithm
Cited by: 11
Author(s): Jader M. Caldonazzo Garbelini, André Yoshiaki Kashiwabara, Danilo Sipoli Sanches
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2105-10-82
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
Cited by: 24
Author(s): Bartosz Wilczyński, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn
Software Mentions: 1
Published: over 15 years ago
10.1186/1471-2105-10-339
Transcription factor site dependencies in human, mouse and rat genomes
Cited by: 3
Author(s): Andrija Tomović, Michael Stadler, Edward J. Oakeley
Software Mentions: 1
Published: almost 15 years ago
10.1186/1471-2105-10-S6-S6
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
Cited by: 5
Author(s): Endre Sebestyén, Tibor Nagy, Sándor Suhai, Endre Barta
Software Mentions: 1
Published: over 15 years ago
10.1186/1471-2105-14-26
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites
Cited by: 4
Author(s): Alexis Vandenbon, Yutaro Kumagai, Shunsuke Teraguchi, Karlou Mar Amada, Shizuo Akira, Daron M. Standley
Software Mentions: 1
Published: over 11 years ago
10.1186/s12859-018-2104-7
Comparison of discriminative motif optimization using matrix and DNA shape-based models
Cited by: 10
Author(s): Shuxiang Ruan, Gary D. Stormo
Software Mentions: 1
Published: over 6 years ago
10.1186/s12859-017-1755-0
An efficient algorithm for improving structure-based prediction of transcription factor binding sites
Cited by: 12
Author(s): Alvin Farrel, Jun‐tao Guo
Software Mentions: 1
Published: about 7 years ago
10.1186/s12859-015-0666-1
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors
Cited by: 6
Author(s): Xiaoyan Ma, Daphne Ezer, Carmen Navarro, Boris Adryan
Software Mentions: 1
Published: about 9 years ago
10.1186/1471-2105-14-298
Flanking sequence context-dependent transcription factor binding in early Drosophila development
Cited by: 10
Author(s): Jessica L. Stringham, Adam S. Brown, Robert A. Drewell, Jacqueline M. Dresch
Software Mentions: 1
Published: almost 11 years ago
10.1186/1471-2105-12-67
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model
Cited by: 65
Author(s): Antony Le Béchec, Élodie Portales-Casamar, Guillaume Vetter, Michèle Moes, Pierre-Joachim Zindy, Anne Saumet, David J. Arenillas, Charles Theillet, Wyeth W. Wasserman, Charles-Henri Lecellier, Evelyne Friederich
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2407-14-708
Large differences in global transcriptional regulatory programs of normal and tumor colon cells
Cited by: 30
Author(s): David Cordero, Xavier Solé, Marta Crous‐Bou, Rebeca Sanz‐Pamplona, Laia Paré, Elisabet Guinó, David Olivares, Antonio Berenguer, Cristina Santos, Ramón Salazar, Sebastiano Biondo, Vı́ctor Moreno
Software Mentions: 1
Published: almost 10 years ago
10.1186/1471-2407-9-279
Identification of target genes of transcription factor activator protein 2 gamma in breast cancer cells
Cited by: 27
Author(s): Anbang He, Xingcheng Xiao, Ren Daolong, Liu Gan, Xiaojuan Ding, Xi Qiao, Xinyang Hu, Ru‐Shi Liu, Jian Zhang, Sheng Xiang
Software Mentions: 1
Published: about 15 years ago
10.1186/s12885-021-08552-7
Oncogenic role of ALX3 in cervical cancer cells through KDM2B-mediated histone demethylation of CDC25A
Cited by: 3
Author(s): Jinhong Qi, Li Zhou, Dongqing Li, Jingyuan Yang, He Wang, Haipeng Cao, Yunlan Huang, Zhiming Zhang, Ling‐Sai Chang, Chen Zhu, Zuanming Jin, Yong Yuan
Software Mentions: 1
Published: about 3 years ago
10.1186/1471-2407-11-119
A Kallikrein 15 (KLK15) single nucleotide polymorphism located close to a novel exon shows evidence of association with poor ovarian cancer survival
Cited by: 18
Author(s): Jyotsna Batra, Christina M. Nagle, Tracy A. O’Mara, M.A. Higgins, Ying Dong, Olivia L. Tan, Felicity Lose, Lene Marie Skeie, Srilakshmi Srinivasan, Kelly L. Bolton, Honglin Song, Susan J. Ramus, Simon A. Gayther, Paul D.P. Pharoah, Mary-Anne Kedda, Amanda B. Spurdle, Judith A. Clements
Software Mentions: 1
Published: over 13 years ago
10.1186/s12872-021-01939-1
Comprehensive analysis of autophagy-related genes and patterns of immune cell infiltration in valvular atrial fibrillation
Cited by: 6
Author(s): Ao Liu, Kangni Jia, Hong‐Qing Liang, Jin Qi
Software Mentions: 1
Published: over 3 years ago
10.1186/s12872-021-02136-w
Identification and functional study of GATA4 gene regulatory variants in atrial septal defects
Cited by: 2
Author(s): Dongchen Fan, Shuchao Pang, Jing Chen, Jiping Shan, Qianjin Cheng, Bo Yan
Software Mentions: 1
Published: about 3 years ago
10.1186/1471-2121-14-47
New insights in osteogenic differentiation revealed by mass spectrometric assessment of phosphorylated substrates in murine skin mesenchymal cells
Cited by: 11
Author(s): Erik Halcsik, Maria Fernanda Forni, André Fujita, Thiago Verano‐Braga, Ole N. Jensen, Mari Cleide Sogayar
Software Mentions: 1
Published: almost 11 years ago
10.1186/1471-213X-11-5
The nephrogenic potential of the transcription factors osr1, osr2, hnf1b, lhx1 and pax8 assessed in Xenopus animal caps
Cited by: 26
Author(s): Christiane Drews, Sabine Senkel, Gerhart U. Ryffel
Software Mentions: 1
Published: over 13 years ago
10.1186/s12863-017-0573-8
Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle
Cited by: 10
Author(s): Taichi Arishima, Shinji Sasaki, Takeshi Isobe, Yoshihisa Ikebata, Shinichi Shimbara, Shogo Ikeda, Keisuke Kawashima, Yutaka Suzuki, Masao Watanabe, Sumio Sugano, Kazunori Mizoshita, Yoshikazu Sugimoto
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12863-018-0701-0
Polymorphisms of HOMER1 gene are associated with piglet splay leg syndrome and one significant SNP can affect its intronic promoter activity in vitro
Cited by: 3
Author(s): Sutong Xu, Xingjie Hao, Min Zhang, Kai Wang, Shuaifeng Li, Xing Chen, Lu Yang, Lin Hu, Shujun Zhang
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12863-017-0516-4
Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population
Cited by: 10
Author(s): Bo Han, Weijun Liang, Liu Lin, Yanhua Li, Dan Sun
Software Mentions: 1
Published: over 7 years ago
10.1186/s12863-018-0708-6
Characterization and functional analyses of the human HTR1A gene: 5’ regulatory region modulates gene expression in vitro
Cited by: 1
Author(s): Xue Wu, Feng‐ling Xu, Mei Ding, Jingjing Zhang, Jun Yao, Baojie Wang
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12864-017-3750-2
In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants
Cited by: 16
Author(s): Lenora W. M. Loo, Mathieu Lemire, Loı̈c Le Marchand
Software Mentions: 1
Published: over 7 years ago
10.1186/1471-2164-13-437
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells
Cited by: 21
Author(s): Mingzhu Zhu, Xin Deng, Trupti Joshi, Dong Xu, Gary Stacey, Jianlin Cheng
Software Mentions: 1
Published: about 12 years ago
10.1186/1471-2164-13-182
The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3′ UTR
Cited by: 16
Author(s): Marta Iwanaszko, Allan R. Brasier, Marek Kimmel
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2164-10-S1-S18
Word-based characterization of promoters involved in human DNA repair pathways
Cited by: 11
Author(s): Jens Lichtenberg, Edwin Jacox, Joshua D. Welch, Kyle Kurz, Xiaoyu Liang, Mary Qu Yang, Frank A. Drews, Klaus Ecker, Stephen S. Lee, Laura Elnitski, Lonnie R. Welch
Software Mentions: 1
Published: over 15 years ago
10.1186/1471-2164-12-72
Analysis of nucleosome positioning determined by DNA helix curvature in the human genome
Cited by: 19
Author(s): Hongde Liu, Xueye Duan, Shuangxin Yu, Xiao Sun
Software Mentions: 1
Published: over 13 years ago
10.1186/s12864-018-4469-4
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli
Cited by: 17
Author(s): Chi Nga Chow, Yi Fan Chiang-Hsieh, Chia Hung Chien, Han Zheng, Tzong-Yi Lee, Nai Wu, Kuan Chieh Tseng, Ping Hou, Wen Chi Chang
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2164-11-355
Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes
Cited by: 29
Author(s): Francesca Orso, Davide Corà, Benedetta Ubezio, Paolo Provero, Michele Caselle, Daniela Taverna
Software Mentions: 1
Published: over 14 years ago
10.1186/s12864-019-6299-4
A generative model for constructing nucleic acid sequences binding to a protein
Cited by: 8
Author(s): Jinho Im, Byungkyu Park, Kyungsook Han
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12864-015-1673-3
HIV-1 gp120 influences the expression of microRNAs in human monocyte-derived dendritic cells via STAT3 activation
Cited by: 9
Author(s): Andrea Masotti, Gloria Donninelli, Letizia Da Sacco, Barbara Varano, Manuela Del Cornò, Sandra Gessani
Software Mentions: 1
Published: about 9 years ago
10.1186/s12864-016-2818-8
Erratum to: A systematic, large-scale comparison of transcription factor binding site models
Cited by: 0
Author(s): Daniela Hombach, Jana Marie Schwarz, Peter N. Robinson, Markus Schuelke, Dominik Seelow
Software Mentions: 1
Published: about 8 years ago
10.1186/1471-2164-14-S2-S3
miRNA-target prediction based on transcriptional regulation
Cited by: 23
Author(s): Toyofumi Fujiwara, Tetsushi Yada
Software Mentions: 1
Published: over 11 years ago
10.1186/1471-2164-11-30
Variable structure motifs for transcription factor binding sites
Cited by: 21
Author(s): John E. Reid, Katharine Evans, Nigel P. Dyer, Lorenz Wernisch, Sascha Ott
Software Mentions: 1
Published: over 14 years ago
10.1186/1471-2164-9-510
An optimized procedure for the design and evaluation of Ecotilling assays
Cited by: 7
Author(s): Stefan Coassin, Anita Brandstätter, Florian Kronenberg
Software Mentions: 1
Published: almost 16 years ago
10.1186/s12864-015-1643-9
Whole-genome cartography of p53 response elements ranked on transactivation potential
Cited by: 56
Author(s): Toma Tebaldi, Sara Zaccara, Federica Alessandrini, Alessandra Bisio, Yari Ciribilli, Alberto Inga
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-017-4023-9
Logo2PWM: a tool to convert sequence logo to position weight matrix
Cited by: 4
Author(s): Gao Z, Lu Liu, Jianhua Ruan
Software Mentions: 1
Published: almost 7 years ago
10.1186/1471-2164-11-257
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns
Cited by: 28
Author(s): Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki, Carsten O. Daub
Software Mentions: 1
Published: over 14 years ago
10.1186/1471-2164-12-128
Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α
Cited by: 28
Author(s): Zhongyan Wang, Eric Bishop, Patricia A. Burke
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2164-16-S7-S12
Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation
Cited by: 21
Author(s): Junbai Wang, Agnieszka Małecka, Gunhild Trøen, Jan Delabie
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2164-13-405
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions
Cited by: 229
Author(s): Luiz Augusto Bovolenta, Márcio Luís Acencio, Ney Lemke
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2164-15-752
Differential motif enrichment analysis of paired ChIP-seq experiments
Cited by: 22
Author(s): Tom Lesluyes, James E. Johnson, Philip Machanick, Timothy L. Bailey
Software Mentions: 1
Published: about 10 years ago
10.1186/s12864-019-6063-9
Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis
Cited by: 9
Author(s): Thomas Ha, Peter G. Y. Zhang, Rémi Robert, Joanna Yeung, Douglas J. Swanson, Anthony Mathelier, Wyeth W. Wasserman, Su-Jin Im, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Peter Arner, Piero Carninci, Yoshihide Hayashizaki, Daniel Goldowitz
Software Mentions: 1
Published: about 5 years ago
10.1186/1471-2164-15-900
Abundance, arrangement, and function of sequence motifs in the chicken promoters
Cited by: 19
Author(s): Hideaki Abe, Neil J. Gemmell
Software Mentions: 1
Published: over 10 years ago
10.1186/s12864-016-2916-7
Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants
Cited by: 7
Author(s): Fred Y. Peng, Zhiqiu Hu, Rong‐Cai Yang
Software Mentions: 1
Published: about 8 years ago
10.1186/s12864-015-1271-4
Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation
Cited by: 122
Author(s): Jun Wan, Verity F. Oliver, Guohua Wang, Heng Zhu, Donald J. Zack, Shannath L. Merbs, Jiang Qian
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-016-2564-y
ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage
Cited by: 31
Author(s): Francisco J. Romero–Campero, Ignacio Pérez–Hurtado, Eva Lucas-Reina, Javier Romero, Federico Valverde
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2164-12-353
The differential disease regulome
Cited by: 9
Author(s): Geir Kjetil Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K. Glad, Lars Holden, Matthew T. G. Holden, Knut Liestøl, Trevor Clancy, Finn Drabløs, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi, Eivind Hovig
Software Mentions: 1
Published: about 13 years ago
10.1186/1471-2164-13-152
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features
Cited by: 61
Author(s): Chih-Yu Chen, Quaid Morris, Jennifer A. Mitchell
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2164-15-1155
Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss
Cited by: 26
Author(s): Rajini Haraksingh, Fereshteh Jahanbani, Juan Rodriguez-Paris, Joel Gelernter, Kari Nadeau, John S. Oghalai, Iris Schrijver, M Snyder
Software Mentions: 1
Published: almost 10 years ago
10.1186/s12864-017-4305-2
CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors
Cited by: 4
Author(s): Jing Qin, Yaohua Hu, Ka Yan, Xiaoying Jiang, Ching Hei Ho, Ling Ming Tsang, Yi Liu, Ricky Wai Tak Leung, Ka Hou Chu
Software Mentions: 1
Published: almost 7 years ago
10.1186/1471-2164-15-80
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data
Cited by: 32
Author(s): Victor G. Levitsky, Ivan V. Kulakovskiy, Nikita I. Ershov, Dmitry Oshchepkov, Vsevolod J. Makeev, Charlie Hodgman, Т. И. Меркулова
Software Mentions: 1
Published: over 10 years ago
10.1186/s12864-019-6051-0
SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes
Cited by: 10
Author(s): Teshome Dagne Mulugeta, Torfinn Nome, Thu‐Hien To, Manu Kumar Gundappa, Daniel J. Macqueen, Dag Inge Våge, Simen Rød Sandve, Torgeir R. Hvidsten
Software Mentions: 1
Published: about 5 years ago
10.1186/1471-2164-8-459
Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters
Cited by: 24
Author(s): Nicolás Bellora, Domènec Farré, M. Mar Albà
Software Mentions: 1
Published: almost 17 years ago
10.1186/1471-2164-15-208
TACO: a general-purpose tool for predicting cell-type–specific transcription factor dimers
Cited by: 23
Author(s): Aleksander Jankowski, Shyam Prabhakar, Jerzy Tiuryn
Software Mentions: 1
Published: over 10 years ago
10.1186/1471-2164-14-796
Predicting tissue specific transcription factor binding sites
Cited by: 28
Author(s): Shan Zhong, Xin He, Ziv Bar‐Joseph
Software Mentions: 1
Published: almost 11 years ago
10.1186/s12879-016-1632-x
PU.1 is involved in the immune response to Aspergillus fumigatus through upregulating Dectin-1 expression
Cited by: 10
Author(s): Min Wang, Zhicheng Liu, Chenyang Liu, Ting Wu, Feng Cai, Quan Wang, Xin Su, Yi Shi
Software Mentions: 1
Published: over 8 years ago
10.1186/s12916-017-0792-x
Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects
Cited by: 45
Author(s): Cajsa Davegårdh, Christa Broholm, Alexander Perfilyev, Tora Ida Henriksen, Sonia García-Calzón, Lone Peijs, Ninna S. Hansen, Petr Volkov, Rasmus Kjøbsted, Jørgen F. P. Wojtaszewski, Maria Pedersen, Bente Klarlund Pedersen, Dov B. Ballak, Charles A. Dinarello, Bas Heinhuis, Leo A. B. Joosten, Erika Nilsson, Allan Vaag, Camilla Schéele, Charlotte Ling
Software Mentions: 1
Published: over 7 years ago
10.1186/1755-8794-1-46
A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining
Cited by: 49
Author(s): Bor‐Sen Chen, Shih-Kuang Yang, Chung-Yu Lan
Software Mentions: 1
Published: almost 16 years ago
10.1186/1471-2199-7-4
Regulation of the human LAT gene by the Elf-1 transcription factor
Cited by: 20
Author(s): Timothy S. Finco, Geri E Justice-Healy, Sarah Patel, Victoria Hamilton
Software Mentions: 1
Published: over 18 years ago
10.1186/s12867-018-0104-9
pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor
Cited by: 3
Author(s): Yi­hui Zhai, Hong Xu, Qian Shen, Franz Schaefer, Claus Peter Schmitt, Jing Chen, Haimei Liu, Jialu Liu, Jiaojiao Liu
Software Mentions: 1
Published: over 6 years ago
10.1186/s12860-020-00276-z
Retinoic acid receptor-related orphan receptor α reduces lipid droplets by upregulating neutral cholesterol ester hydrolase 1 in macrophages
Cited by: 14
Author(s): Hiroshi Matsuoka, Riki TOKUNAGA, Miyu KATAYAMA, Yuichiro HOSODA, Kaoruko MIYA, Kento SUMI, Ami OHISHI, Jun Kamishikiryo, Akiho Shima, Akihiro Michihara
Software Mentions: 1
Published: over 4 years ago
10.1186/1471-2202-11-46
Genomic and neural analysis of the estradiol-synthetic pathway in the zebra finch
Cited by: 23
Author(s): Sarah E. London, David F. Clayton
Software Mentions: 1
Published: over 14 years ago
10.1186/s12870-014-0300-9
Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction
Cited by: 29
Author(s): Parsa Hosseini, Benjamin F. Matthews
Software Mentions: 1
Published: almost 10 years ago
10.1186/s12870-021-02859-0
Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes
Cited by: 12
Author(s): Zhengwen Liu, Xingfen Wang, Zhengwen Sun, Yan Zhang, Chengsheng Meng, Bin Chen, Guoning Wang, Huifeng Ke, Jing Wu, Yuanyuan Yan, Liqiang Wu, Zhikun Li, Jun‐Bo Yang, Guiyin Zhang, Zhiying Ma
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2393-9-56
Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study
Cited by: 29
Author(s): Daniel A. Enquobahrie, Michelle A. Williams, Chunfang Qiu, Seid Muhie, Kimberly Slentz-Kesler, Zhaoping Ge, Tanya Sorenson
Software Mentions: 1
Published: almost 15 years ago
10.1186/s12888-020-02906-4
Functional polymorphisms and transcriptional analysis in the 5′ region of the human serotonin receptor 1B gene (HTR1B) and their associations with psychiatric disorders
Cited by: 3
Author(s): Xi Xia, Mei Ding, Jin‐feng Xuan, Jiaxin Xing, Jun Yao, Xue Wu, Baojie Wang
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12890-021-01657-6
LncRNA LINC00520 aggravates cell proliferation and migration in lung adenocarcinoma via a positive feedback loop
Cited by: 9
Author(s): Wenyu Huang, Xinxing Wang, Fengjie Wu, Fanggui Xu
Software Mentions: 1
Published: about 3 years ago
10.1186/1752-0509-6-S2-S4
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences
Cited by: 9
Author(s): Dianhui Wang, Sarwar Tapan
Software Mentions: 1
Published: over 12 years ago
10.1186/1752-0509-7-S2-S11
Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits
Cited by: 7
Author(s): Juan Liu, Xinghuo Ye, Fang‐Xiang Wu
Software Mentions: 1
Published: over 11 years ago
10.1186/1752-0509-7-7
SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks
Cited by: 165
Author(s): Dávid Fazekas, Mihály Koltai, Dénes Türei, Dezső Módos, Máté Pálfy, Zoltán Dúl, Lilián Zsákai, Máté Szalay-Bekő, Katalin Lenti, Illés J. Farkas, Tibor Vellai, Péter Csermely, Tamás Korcsmáros
Software Mentions: 1
Published: over 11 years ago
10.1186/s12918-016-0304-1
Cross-species Conservation of context-specific networks
Cited by: 4
Author(s): Robert Pesch, Ralf Zimmer
Software Mentions: 1
Published: about 8 years ago
10.1186/1752-0509-5-S1-S2
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs
Cited by: 22
Author(s): Bingchuan Liu, Jiajia Chen, Bairong Shen
Software Mentions: 1
Published: over 13 years ago
10.1186/s12918-014-0118-y
Sexually-dimorphic targeting of functionally-related genes in COPD
Cited by: 46
Author(s): Kimberly Glass, John Quackenbush, Edwin K. Silverman, Bartolomé R. Celli, Stephen I. Rennard, Guo Cheng Yuan, Dawn L. DeMeo
Software Mentions: 1
Published: almost 10 years ago
10.1186/1752-0509-6-90
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs
Cited by: 15
Author(s): Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin
Software Mentions: 1
Published: about 12 years ago
10.1186/s12917-015-0428-3
Putative regulation mechanism for the MSTN gene by a CpG island generated by the SINE marker Ins227bp
Cited by: 8
Author(s): R. van den Hoven, Emre Gür, Manuela Schlamanig, Martin Hofer, Ali Cesur Onmaz, Ralf Steinborn
Software Mentions: 1
Published: about 9 years ago
10.1186/s12917-019-1979-5
A single nucleotide variant in the promoter region of the CCR5 gene increases susceptibility to arthritis encephalitis virus in goats
Cited by: 11
Author(s): Silvia Colussi, Rosanna Desiato, Chiara Beltramo, Simone Peletto, Paola Modesto, Maria Grazia Maniaci, Valentina Campia, Antonio Quasso, Sergio Rosati, Luigi Bertolotti, Giuseppe Ru, Pier Luigi Acutis
Software Mentions: 1
Published: about 5 years ago
10.1186/s12610-021-00126-8
miR-122-5p regulates the tight junction of the blood-testis barrier of mice via occludin
Cited by: 2
Author(s): Limin Liu, Man Zhu, Xiaoli Liu, Lu-Min Fei, Jianyun Shen, Deyu Chen
Software Mentions: 1
Published: over 3 years ago
10.1093/bioinformatics/btt248
MEME-LaB: motif analysis in clusters
Cited by: 50
Author(s): Paul E. Brown, Laura Baxter, Richard Hickman, Jim Beynon, Jonathan D. Moore, Sascha Ott
Software Mentions: 1
Published: over 11 years ago
10.1093/bioinformatics/bty856
TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis
Cited by: 31
Author(s): Florian Schmidt, Fabian Kern, Peter Ebert, Nina Baumgarten, Marcel H. Schulz
Software Mentions: 1
Published: almost 6 years ago
10.1093/bioinformatics/bty964
An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs
Cited by: 14
Author(s): Richard C. Brown, Gerton Lunter
Software Mentions: 1
Published: almost 6 years ago
10.1186/s40659-015-0019-6
A possible role of Drosophila CTCF in mitotic bookmarking and maintaining chromatin domains during the cell cycle
Cited by: 18
Author(s): Wenlong Shen, Dong Wang, Bingyu Ye, Minglei Shi, Yan Zhang, Zhihu Zhao
Software Mentions: 1
Published: over 9 years ago
10.1186/s12938-021-00912-5
The significance of homeodomain transcription factor 2 in colon cancer cells
Cited by: 3
Author(s): Yang He, Peng Gong, Sitong Wang, Qing Xu, Jianhua Chen
Software Mentions: 1
Published: about 3 years ago
10.1155/2014/623078
Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles
Cited by: 9
Author(s): Chia Hung Chien, Yi Fan Chiang-Hsieh, Ann-Ping Tsou, Shun Long Weng, Wen Chi Chang, Hsien Da Huang
Software Mentions: 1
Published: over 10 years ago
10.1155/2017/5251236
Expression of MicroRNA-29a Regulated by Yes-Associated Protein Modulates the Neurite Outgrowth in N2a Cells
Cited by: 11
Author(s): Chunye Tan, Chengbin Yu, Zhiwen Song, Hongjun Zou, Xu Xu, Zhibin Wang
Software Mentions: 1
Published: over 7 years ago
10.1155/2017/6274513
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model
Cited by: 0
Author(s): Haitao Guo, Hongwei Huo
Software Mentions: 1
Published: over 7 years ago