cran: JASPAR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0001821

Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16
Cited by: 10
Author(s): Ronald Yu, Jie Liu, Nick True, Wei Wang
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0063925

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci
Cited by: 42
Author(s): Suhn Kyong Rhie, Simon Coetzee, Houtan Noushmehr, Chunli Yan, Jae Mun Kim, Christopher A. Haiman
Software Mentions: 2
Published: over 11 years ago

10.1038/s41419-021-03425-0

The DNA-helicase HELLS drives ALK− ALCL proliferation by the transcriptional control of a cytokinesis-related program
Cited by: 9
Author(s): Annalisa Tameni, Elisabetta Sauta, Valentina Mularoni, Federica Torricelli, Gloria Manzotti, Giorgio Inghirami, Riccardo Bellazzi, Valentina Fragliasso, Alessia Ciarrocchi
Software Mentions: 2
Published: almost 4 years ago

10.1093/dnares/dsz004

FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets
Cited by: 4
Author(s): Shaoqiang Zhang, Ying Li, Xiangyun Wang, Zhengchang Su, Yong Chen
Software Mentions: 2
Published: over 5 years ago

10.3389/fphar.2021.700454

Evidence of Omics, Immune Infiltration, and Pharmacogenomic for SENP1 in the Pan-Cancer Cohort
Cited by: 12
Author(s): Somayye Taghvaei, Farzaneh Sabouni, Zarrin Minuchehr
Software Mentions: 2
Published: over 3 years ago

10.1186/s13045-019-0773-y

LINC01123, a c-Myc-activated long non-coding RNA, promotes proliferation and aerobic glycolysis of non-small cell lung cancer through miR-199a-5p/c-Myc axis
Cited by: 152
Author(s): Qian Hua, Mingming Jin, Baoming Mi, Fei Xu, Li Tian, Li Zhao, Jianjun Li, Gang Huang
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0046145

Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data
Cited by: 22
Author(s): Yaron Orenstein, Chaim Linhart, Ron Shamir
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0057520

cAMP Responsive Element Binding Protein-1 Is a Transcription Factor of Lysosomal-Associated Protein Transmembrane-4 beta in Human Breast Cancer Cells
Cited by: 22
Author(s): Meng Zhang, Jianjun Xu, Ruanbao Zhou, Qingyun Zhang
Software Mentions: 1
Published: over 11 years ago

10.1042/BSR20193299

STAT3-induced up-regulation of lncRNA NEAT1 as a ceRNA facilitates abdominal aortic aneurysm formation by elevating TULP3
Cited by: 18
Author(s): Bing Cai, Baihui Yang, Dong Huang, Di Wang, Jun Tian, Feiyun Chen, Xi Wang
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0198922

Fast sequence analysis based on diamond sampling
Cited by: 1
Author(s): Liangxin Gao, Wenzhen Bao, Hongbo Zhang, Changan Yuan, De-Shuang Huang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0152159

Identification of Regulatory Mutations in SERPINC1 Affecting Vitamin D Response Elements Associated with Antithrombin Deficiency
Cited by: 13
Author(s): Mara Toderici, María Eugenia de la Morena‐Barrio, José Padilla, Antonia Miñano, Ana Isabel Antón, Juan Antonio Iniesta, María Teresa Herranz, Núria Fernández, Vicente Vicente, Javier Corral
Software Mentions: 1
Published: over 8 years ago

10.1042/BSR20191203

Promoter polymorphisms in the lncRNA-MIAT gene associated with acute myocardial infarction in Chinese Han population: a case–control study
Cited by: 8
Author(s): Ruchao Ma, Xiaohui He, Xiaoli Zhu, Shuchao Pang, Bo Yan
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0051700

BMP-Mediated Functional Cooperation between Dlx5;Dlx6 and Msx1;Msx2 during Mammalian Limb Development
Cited by: 30
Author(s): Maxence Vieux-Rochas, Kamal Bouhali, Stefano Mantero, Giulia Garaffo, Paolo Provero, Simonetta Astigiano, Ottavia Barbieri, Mariano Francesco Caratozzolo, Apollonia Tullo, Luisa Guerrini, Yvan Lallemand, Benoît Robert, Giovanni Levi, Giorgio R. Merlo
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0213470

Gene expression profiling meta-analysis reveals novel gene signatures and pathways shared between tuberculosis and rheumatoid arthritis
Cited by: 15
Author(s): Mohamed Tarek Badr, Georg Häcker
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0107156

Chromatin Accessibility Mapping Identifies Mediators of Basal Transcription and Retinoid-Induced Repression of OTX2 in Medulloblastoma
Cited by: 7
Author(s): Matthew Wortham, Changcun Guo, Monica Zhang, Lingyun Song, Bum Kyu Lee, Vishwanath R. Iyer, Terrence S. Furey, Gregory E. Crawford, Hai Yan, Yiping He
Software Mentions: 1
Published: about 10 years ago

10.1042/BSR20190994

SP1–DLEU1–miR-4429 feedback loop promotes cell proliferative and anti-apoptotic abilities in human glioblastoma
Cited by: 15
Author(s): Xiaolei Liu, Ruwei Chen, Lijun Liu
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0013789

C/EBPδ Gene Targets in Human Keratinocytes
Cited by: 11
Author(s): S. Borrelli, Daniele Fanoni, Diletta Dolfini, Daniela Alotto, Maria Ravo, Olì Maria Victoria Grober, Alessandro Weisz, Carlotta Castagnoli, Emilio Berti, M. Alessandra Viganò, Roberto Mantovani
Software Mentions: 1
Published: about 14 years ago

10.3390/biom11050721

Glucocorticoid Receptor Alpha Targets SLC2A4 to Regulate Protein Synthesis and Breakdown in Porcine Skeletal Muscle Cells
Cited by: 0
Author(s): Xi Du, Weijing Xu, Jiali Shi, Kai Guo, Chang-Tong Guo, Rong Zheng, Siwen Jiang, Jin Choul Chai
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0107389

Defining Differential Genetic Signatures in CXCR4- and the CCR5-Utilizing HIV-1 Co-Linear Sequences
Cited by: 12
Author(s): Benjamas Aiamkitsumrit, Will Dampier, Julio Martín-García, Michael R. Nonnemacher, Vanessa Pirrone, Т. П. Иванова, Wenyi Zhong, Evelyn Kilareski, Hazeez Aldigun, Brian Frantz, Matthew Rimbey, Adam Wojno, Shendra Passic, Jennifer L. Williams, Sonia Shah, Brandon Blakey, Nirzari Parikh, Jeffrey M. Jacobson, Brian Moldover, Brian Wigdahl
Software Mentions: 1
Published: about 10 years ago

10.3390/biom10101382

Comparative Characterization of Two cxcl8 Homologs in Oplegnathus fasciatus: Genomic, Transcriptional and Functional Analyses
Cited by: 4
Author(s): Navaneethaiyer Umasuthan, S.D.N.K. Bathige, William Shanthakumar Thulasitha, Minyoung Oh, Jehee Lee
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0059607

rs12512631 on the Group Specific Complement (Vitamin D-Binding Protein GC) Implicated in Melanoma Susceptibility
Cited by: 23
Author(s): María Peña‐Chilet, Maider Ibarrola‐Villava, Manuel Martín-González, Marta Feito, Cristina Gómez‐Fernández, Dolores Planelles, G. Carretero, Aňa Lluch, Eduardo Nagore, Gloría Ribas
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0142147

From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach
Cited by: 2
Author(s): Gaurang Mahajan, Shekhar C. Mande
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0018475

Comprehensive Analysis of Transcript Start Sites in Ly49 Genes Reveals an Unexpected Relationship with Gene Function and a Lack Of Upstream Promoters
Cited by: 8
Author(s): Frances Gays, Alan Koh, Katarzyna Mickiewicz, Jonathan G. Aust, Colin G. Brooks
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0221650

17-β estradiol exerts anti-inflammatory effects through activation of Nrf2 in mouse embryonic fibroblasts
Cited by: 21
Author(s): Chin Hee Song, Nayoung Kim, Do Hee Kim, Ha Na Lee, Young Joon Surh
Software Mentions: 1
Published: over 5 years ago

10.3390/biomedicines7030071

Zebrafish: A Powerful Model for Understanding the Functional Relevance of Noncoding Region Mutations in Human Genetic Diseases
Cited by: 6
Author(s): Anita Mann, Shipra Bhatia
Software Mentions: 1
Published: about 5 years ago

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: about 5 years ago

10.1371/journal.pone.0078833

Detection of Regulatory SNPs in Human Genome Using ChIP-seq ENCODE Data
Cited by: 42
Author(s): L. O. Bryzgalov, E. V. Antontseva, M. Yu. Matveeva, A. A. Shilov, Е. В. Кашина, Viatcheslav A. Mordvinov, Т. И. Меркулова
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0118779

A Glycine Insertion in the Estrogen-Related Receptor (ERR) Is Associated with Enhanced Expression of Three Cytochrome P450 Genes in Transgenic Drosophila melanogaster
Cited by: 10
Author(s): Weilin Sun, M. Carmen Valero, Keon Mook Seong, Laura D. Steele, I-Ting Huang, Chien‐Hui Lee, J. Marshall Clark, Xinghui Qiu, Barry R. Pittendrigh
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0183433

Genetic dissection of endothelial transcriptional activity of zebrafish aryl hydrocarbon receptors (AHRs)
Cited by: 10
Author(s): Wade W. Sugden, Roberto Carlos Leonardo-Mendonça, Darío Acuña‐Castroviejo, Arndt F. Siekmann
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: almost 8 years ago

10.1371/journal.pone.0158036

A Common CYFIP1 Variant at the 15q11.2 Disease Locus Is Associated with Structural Variation at the Language-Related Left Supramarginal Gyrus
Cited by: 12
Author(s): Young Woon Woo, Tao Wang, Tulio Guadalupe, Rebecca A. Nebel, Arianna Vino, Victor A Del Bene, Sophie Molholm, Lars A. Ross, Marcel P. Zwiers, Simon E. Fisher, John J. Foxe, Brett S. Abrahams
Software Mentions: 1
Published: over 8 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: almost 8 years ago

10.1371/journal.pone.0195788

Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Cited by: 17
Author(s): D. Leland Taylor, David A. Knowles, Laura J. Scott, Andrea H. Ramirez, Francesco Paolo Casale, Brooke N. Wolford, Li Guan, Arushi Varshney, Ricardo D’Oliveira Albanus, Stephen C. J. Parker, Narisu Narisu, Peter S. Chines, Michael R. Erdos, Ryan Welch, Leena Kinnunen, Jouko Saramies, Jouko Sundvall, Timo A. Lakka, Markku Laakso, Jaakko Tuomilehto, Heikki A. Koistinen, Oliver Stegle, Michael Boehnke, Ewan Birney, Francis S. Collins
Software Mentions: 1
Published: over 6 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: almost 11 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

10.1371/journal.pone.0042779

Increasing Coverage of Transcription Factor Position Weight Matrices through Domain-level Homology
Cited by: 8
Author(s): Brady Bernard, Vésteinn Thórsson, Hector Rovira, Ilya Shmulevich
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0084002

Whole Blood Gene Expression Profiles in Insulin Resistant Latinos with the Metabolic Syndrome
Cited by: 11
Author(s): Samantha E. Tangen, Darwin Tsinajinnie, Martha Nuñez, Gabriel Q. Shaibi, Lawrence J. Mandarino, Dawn K. Coletta
Software Mentions: 1
Published: almost 11 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: over 3 years ago

10.1371/journal.pone.0012465

Identification of cis-Regulatory Elements in the Mammalian Genome: The cREMaG Database
Cited by: 29
Author(s): Marcin Piechota, Michał Korostyński, Ryszard Przewłocki
Software Mentions: 1
Published: about 14 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

10.1186/1471-2164-12-72

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: almost 14 years ago

10.3390/ani11020292

Long Noncoding RNA LncPGCR Mediated by TCF7L2 Regulates Primordial Germ Cell Formation in Chickens
Cited by: 4
Author(s): Jingyi Jiang, Chen Chen, Shaoze Cheng, Xia Yuan, Jing Jin, Chen Zhang, Xin Sun, Jiuzhou Song, Qisheng Zuo, Yani Zhang, Guohong Chen
Software Mentions: 1
Published: almost 4 years ago

10.18632/aging.203024

TCF-3-mediated transcription of lncRNA HNF1A-AS1 targeting oncostatin M expression inhibits epithelial-mesenchymal transition via TGFβ signaling in gastroenteropancreatic neuroendocrine neoplasms
Cited by: 6
Author(s): Jingwen Xue, Jianan Bai, Qin Long, Yue Wei, Jialing Pan, Xin Li, Qiyun Tang
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0093125

Two Enhancers Control Transcription of Drosophila muscleblind in the Embryonic Somatic Musculature and in the Central Nervous System
Cited by: 14
Author(s): Ariadna Bargiela, Beatriz Llamusí, Estefanía Cerro-Herreros, Rubén Artero
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0190457

Global mapping of transcription factor motifs in human aging
Cited by: 11
Author(s): David Alfego, Ulrich Rodeck, Andres Kriete
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0127089

Gene and MicroRNA Expression Responses to Exercise; Relationship with Insulin Sensitivity
Cited by: 50
Author(s): Carrie S. McLean, Clinton Mielke, Jeanine M. Cordova, Paul Langlais, Benjamin P. Bowen, Danielle N. Miranda, Dawn K. Coletta, Lawrence J. Mandarino
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0213013

Reproducible big data science: A case study in continuous FAIRness
Cited by: 31
Author(s): Ravi Madduri, Kyle Chard, Mike D’Arcy, Su-Young Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric W. Deutsch, Cory C. Funk, Benjamin D. Heavner, Matthew A. Richards, Paul Shannon, Gustavo Glusman, Nathan D. Price, Carl Kesselman, Ian Foster
Software Mentions: 1
Published: over 5 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: almost 16 years ago

10.1371/journal.pone.0020560

Inflammatory Gene Regulatory Networks in Amnion Cells Following Cytokine Stimulation: Translational Systems Approach to Modeling Human Parturition
Cited by: 19
Author(s): Ruth Li, William E. Ackerman, Taryn Summerfield, Lianbo Yu, Pooja Manchanda Gulati, Jie Zhang, Kun Huang, Roberto Romero, Douglas A. Kniss
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0150785

Genetic Variants of LDLR and PCSK9 Associated with Variations in Response to Antihypercholesterolemic Effects of Armolipid Plus with Berberine
Cited by: 20
Author(s): Isabel De Castro-Orós, Rosa Solà, Rosa M. Valls, Ángel Brea, Pilar Mozas, José Puzo, Miguel Pocovı́
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0071363

Rapid Cohort Generation and Analysis of Disease Spectrum of Large Animal Model of Cone Dystrophy
Cited by: 17
Author(s): Corinne Kostic, Simon Lillico, S. Crippa, Nicolas Grandchamp, Héloïse Pilet, Stéphanie Philippe, Zen H. Lu, Tim King, Jacques Mallet, Chamsy Sarkis, Yvan Arsenijévic, Bruce Whitelaw
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0096805

Genetic Association Study of Adiposity and Melanocortin-4 Receptor (MC4R) Common Variants: Replication and Functional Characterization of Non-Coding Regions
Cited by: 19
Author(s): Daniel S. Evans, Melissa A. Calton, Mee J. Kim, Pui‐Yan Kwok, Iva Miljkovic, Tamara B. Harris, Annemarie Koster, Yongmei Liu, Gregory J. Tranah, Nadav Ahituv, Wen-Chi Hsueh, Christian Vaisse
Software Mentions: 1
Published: over 10 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

10.1186/1471-2164-13-182

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: almost 13 years ago

10.1371/journal.pone.0176905

Combinatorial regulation of a Blimp1 (Prdm1) enhancer in the mouse retina
Cited by: 18
Author(s): Taylor Mills, Tatiana Eliseeva, Stephanie M. Bersie, Grace Randazzo, Jhenya Nahreini, Ko Uoon Park, Joseph A. Brzezinski
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0074637

Regulation of the F11, Klkb1, Cyp4v3 Gene Cluster in Livers of Metabolically Challenged Mice
Cited by: 7
Author(s): Huma Safdar, Audrey C. A. Cleuren, Ka Lei Cheung, Frank J. Gonzalez, Hans L. Vos, Yusuke Inoue, Pieter H. Reitsma, Bart J.M. van Vlijmen
Software Mentions: 1
Published: about 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: about 6 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

10.1186/1471-2105-13-215

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

10.1371/journal.pone.0113364

Oxytocin and Vasopressin Receptor Gene Variation as a Proximate Base for Inter- and Intraspecific Behavioral Differences in Bonobos and Chimpanzees
Cited by: 44
Author(s): Nicky Staes, Jeroen M. G. Stevens, Philippe Helsen, Mia J. Hillyer, Marisa L. Korody, Marcel Eens
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0150070

Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies
Cited by: 31
Author(s): Longjuan Qin, Yuyong Liu, Ya Wang, Guiju Wu, Jie Chen, Weiyuan Ye, Jiangke Yang, Qingyang Huang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0108065

CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining
Cited by: 9
Author(s): Carmen Navarro, Francisco J. López, Carlos Cano, Fernando García-Alcalde, Armando Blanco
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0035977

Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks
Cited by: 8
Author(s): Joana P. Gonçalves, Ricardo Santos Aires, Alexandre P. Francisco, Sara C. Madeira
Software Mentions: 1
Published: over 12 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

10.1186/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: over 5 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

10.1371/journal.pone.0099359

Transcriptional Regulation of the Tumor Suppressor FHL2 by p53 in Human Kidney and Liver Cells
Cited by: 13
Author(s): Jia‐Ying Xu, Junwei Zhou, Man-Shan Li, Chor-Fung Ng, Yuen-Keng Ng, Paul B.S. Lai, Stephen Kwok‐Wing Tsui
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0182373

CRISPR/Cas9-mediated knockout of c-REL in HeLa cells results in profound defects of the cell cycle
Cited by: 17
Author(s): Carsten Slotta, Thomas Schlüter, Lucia Mercedes Ruiz-Perera, Hussamadin M. Kadhim, Tobias Tertel, Elena Henkel, Wolfgang Hübner, Johannes F. W. Greiner, Thomas Huser, Barbara Kaltschmidt, Christian Kaltschmidt
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0040373

POWRS: Position-Sensitive Motif Discovery
Cited by: 7
Author(s): Ian Davis, Christopher C. Benninger, Philip N. Benfey, Tedd D. Elich
Software Mentions: 1
Published: over 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: over 9 years ago

10.1371/journal.pone.0215911

Allele-specific enhancers mediate associations between LCAT and ABCA1 polymorphisms and HDL metabolism
Cited by: 3
Author(s): Alicia Howard, Xiaochun Wang, Megana Prasad, Avinash Sahu, Radhouane Aniba, Michael Miller, Sridhar Hannenhalli, Yen-Pei C. Chang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0065498

Landscape of Transcriptional Deregulations in the Preeclamptic Placenta
Cited by: 69
Author(s): Daniel Vaiman, Rosamaria Calicchio, Francisco Miralles
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0140803

Differences in the Early Development of Human and Mouse Embryonic Stem Cells
Cited by: 14
Author(s): Razif Gabdoulline, Wolfgang Kaisers, Ana C. Gaspar, Kesavan Meganathan, Michael Xavier Doss, Smita Jagtap, Jürgen Hescheler, Agapios Sachinidis, Holger Schwender
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0017116

Sex Hormones in Autism: Androgens and Estrogens Differentially and Reciprocally Regulate RORA, a Novel Candidate Gene for Autism
Cited by: 185
Author(s): Tewarit Sarachana, Minyi Xu, Ray-Chang Wu, Valerie W. Hu
Software Mentions: 1
Published: almost 14 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: over 12 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/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

10.5713/ajas.19.1000

Regulation of chicken vanin1 gene expression by peroxisome proliferators activated receptor α and miRNA-181a-5p
Cited by: 0
Author(s): Zhongliang Wang, Jianfeng Yu, Nan Hua, Jie Li, Lei Xu, Wen Yao, Gu Z
Software Mentions: 1
Published: almost 4 years ago

10.18632/aging.103660

SP1-induced HOXD-AS1 promotes malignant progression of cholangiocarcinoma by regulating miR-520c-3p/MYCN
Cited by: 14
Author(s): Jinglin Li, Xingming Jiang, Zhenglong Li, Liyi Huang, Daolin Ji, Liang Yu, Yi Zhou, Yunfu Cui
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0037498

A Computational Profiling of Changes in Gene Expression and Transcription Factors Induced by vFLIP K13 in Primary Effusion Lymphoma
Cited by: 17
Author(s): Vasu Punj, Hittu Matta, Preet M. Chaudhary
Software Mentions: 1
Published: over 12 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/s12918-016-0304-1

Cross-species Conservation of context-specific networks
Cited by: 4
Author(s): Robert Pesch, Ralf Zimmer
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0109691

In Silico Pooling of ChIP-seq Control Experiments
Cited by: 2
Author(s): Guannan Sun, Rajini Srinivasan, Camila Lopez‐Anido, Holly A. Hung, John Svaren, Sündüz Keleş
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0000930

Neuroadaptations in Human Chronic Alcoholics: Dysregulation of the NF-κB System
Cited by: 80
Author(s): Anna Ökvist, Sofia Johansson, Alexander Kuzmin, Igor Bazov, Roxana Merino-Martinez, Igor Ponomarev, R. Dayne Mayfield, Donna Sheedy, Thomas Garrick, Clive Harper, Yasmin L. Hurd, Lars Terenius, Thomas J. Ekström, Georgy Bakalkin, Tatjana Yakovleva
Software Mentions: 1
Published: about 17 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: almost 12 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: over 18 years ago

10.1371/journal.pone.0068000

FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain
Cited by: 15
Author(s): Thais S. Rizzi, Sophie van der Sluis, Cathérine Derom, Evert Thiery, Ronald E. van Kesteren, Nele Jacobs, S Van Gestel, Robert Vlietinck, Matthijs Verhage, Peter Heutink, Daniëlle Posthuma
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0067752

Post-Zygotic and Inter-Individual Structural Genetic Variation in a Presumptive Enhancer Element of the Locus between the IL10Rβ and IFNAR1 Genes
Cited by: 1
Author(s): Hamid Reza Razzaghian, Lars A. Forsberg, Kancherla Reddy Prakash, Szymon Przerada, Hanna Paprocka, Anna Żywicka, Maxwell P. Westerman, Nancy L. Pedersen, Terrance P. O’Hanlon, Lisa G. Rider, Frederick W. Miller, Ewa Śrutek, Michał Jankowski, Wojciech Zegarski, Arkadiusz Piotrowski, Devin Absher, Jan P. Dumanski
Software Mentions: 1
Published: about 11 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: almost 12 years ago

10.1371/journal.pone.0173890

The microRNA-302b-inhibited insulin-like growth factor-binding protein 2 signaling pathway induces glioma cell apoptosis by targeting nuclear factor IA
Cited by: 14
Author(s): Chin Cheng Lee, Peng Hsu Chen, Kuo Hao Ho, Chwen Ming Shih, Chia Hsiung Cheng, Cheng Lin, Kur Ta Cheng, Ann Jeng Liu, Ku Chung Chen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0055521

Correlated Evolution of Positions within Mammalian cis Elements
Cited by: 2
Author(s): Rithun Mukherjee, Perry Evans, Larry N. Singh, Sridhar Hannenhalli
Software Mentions: 1
Published: almost 12 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: almost 13 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

10.1371/journal.pgen.1006441

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6
Cited by: 51
Author(s): Barbora Antosova, Smolikova Jana, Lucie Klimova, Jitka Láchová, Bendova Michaela, Iryna Kozmiková, Ondřej Machoň, Zbyněk Kozmík
Software Mentions: 1
Published: almost 8 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

10.1186/1748-7188-8-23

Jaccard index based similarity measure to compare transcription factor binding site models
Cited by: 52
Author(s): Ilya E. Vorontsov, Ivan V. Kulakovskiy, Vsevolod J. Makeev
Software Mentions: 1
Published: about 11 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

10.1371/journal.pgen.1004828

Epigenome-Guided Analysis of the Transcriptome of Plaque Macrophages during Atherosclerosis Regression Reveals Activation of the Wnt Signaling Pathway
Cited by: 30
Author(s): Stephen A. Ramsey, Yuliya Vengrenyuk, Prashanthi Menon, Irina Podolsky, Jonathan E. Feig, Alan Aderem, Edward A. Fisher, Elizabeth S. Gold
Software Mentions: 1
Published: almost 10 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: about 4 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

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283