cran: JASPAR | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-12-495

MotifMap: integrative genome-wide maps of regulatory motif sites for model species
Cited by: 151
Author(s): Kenneth Daily, Vishal R. Patel, Paul Rigor, Xiaohui Xie, Pierre Baldi
Software Mentions: 2
Published: almost 13 years ago

10.3390/genes9060278

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis
Cited by: 3
Author(s): Xin Chen, Anjun Ma, Adam McDermaid, Han-Yuan Zhang, Chao Liu, Huansheng Cao, Qin Ma
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1003652

Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus
Cited by: 60
Author(s): Clint L. Miller, Denise Anderson, Ramendra K. Kundu, Azad Raiesdana, Sylvia Nürnberg, Roxanne Diaz, Karen Cheng, Nicholas J. Leeper, Chung–Hsing Chen, I–Shou Chang, Eric E. Schadt, Chao A. Hsiung, Themistocles L. Assimes, Thomas Quertermous
Software Mentions: 2
Published: about 11 years ago

10.1186/gb-2007-8-2-r24

Quantifying similarity between motifs
Cited by: 1,493
Author(s): Sidhant Gupta, J Stamatoyannopoulos, Timothy L. Bailey, William Stafford Noble
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pgen.1009296

A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation
Cited by: 9
Author(s): Ana Paula Azambujá, Marcos Simões-Costa
Software Mentions: 2
Published: over 3 years ago

10.3389/fphys.2016.00615

Network Analysis-Based Approach for Exploring the Potential Diagnostic Biomarkers of Acute Myocardial Infarction
Cited by: 33
Author(s): Jiaqi Chen, Ling Yu, Siwei Zhang, Xia Chen
Software Mentions: 2
Published: almost 8 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: about 3 years ago

10.1371/journal.pgen.1002277

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development
Cited by: 59
Author(s): Jason A. Watts, Chaolin Zhang, Andres J. Klein‐Szanto, Jay D. Kormish, Junjiang Fu, Michael Q. Zhang, Kenneth S. Zaret
Software Mentions: 2
Published: about 13 years ago

10.7717/peerj.9954

The reuse of public datasets in the life sciences: potential risks and rewards
Cited by: 24
Author(s): Katharina Sielemann, Alenka Hafner, Boas Pucker
Software Mentions: 2
Published: almost 4 years ago

10.3389/fonc.2020.585551

MYBL2-Driven Transcriptional Programs Link Replication Stress and Error-prone DNA Repair With Genomic Instability in Lung Adenocarcinoma
Cited by: 7
Author(s): Benjamin B. Morris, Nolan A. Wages, Patrick A. Grant, P. Todd Stukenberg, Ryan D. Gentzler, Richard D. Hall, Wallace Akerley, Thomas K. Varghese, Susanne M. Arnold, Terence M. Williams, Vincenzo Coppola, David R. Jones, David T. Auble, Marty W. Mayo
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2019.01089

FA2H Exhibits Tumor Suppressive Roles on Breast Cancers via Cancer Stemness Control
Cited by: 18
Author(s): Xiaofeng Dai, Shuo Zhang, Hongye Cheng, Dongyan Cai, Chen Xiao, Zhaohui Huang
Software Mentions: 2
Published: almost 5 years ago

10.1534/g3.112.003202

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets
Cited by: 266
Author(s): Andrew Tae-Jun Kwon, David J. Arenillas, Rebecca Worsley Hunt, Wyeth W. Wasserman
Software Mentions: 2
Published: about 12 years ago

10.3389/fmicb.2019.00586

Sterol Regulatory Element-Binding Protein (Sre1) Promotes the Synthesis of Carotenoids and Sterols in Xanthophyllomyces dendrorhous
Cited by: 20
Author(s): María Soledad Gutiérrez, Sebastián Campusano, Ana María González, Melissa Gómez, Salvador Barahona, Dionisia Sepúlveda, Peter J. Espenshade, María Fernández‐Lobato, Marcelo Baeza, Víctor Cifuentes, Jennifer Alcaı́no
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-15-336

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection
Cited by: 34
Author(s): Zhi Ping Liu, Hulin Wu, Jian Zhu, Hongyu Miao
Software Mentions: 2
Published: almost 10 years ago

10.3389/fmolb.2021.668402

Expression and Prognostic Value of MCM Family Genes in Osteosarcoma
Cited by: 12
Author(s): Jian Zhou, Mingyong Wang, Zhen Zhou, Wanchun Wang, Juan Duan, Gen Sheng Wu
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2105-7-396

Predicting transcription factor binding sites using local over-representation and comparative genomics
Cited by: 53
Author(s): Matthieu Defrance, Hélène Touzet
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2164-16-S5-S4

Direct ChIP-Seq significance analysis improves target prediction
Cited by: 8
Author(s): Mukesh Bansal, Geetu Mendiratta, Santosh Anand, Ritu Kushwaha, Hyunjae R. Kim, Manjunath Kustagi, Archana Iyer, R. S. K. Chaganti, Andrea Califano, Pavel Sumazin
Software Mentions: 2
Published: over 9 years ago

10.3389/fnmol.2016.00013

Recombinant Human Myelin-Associated Glycoprotein Promoter Drives Selective AAV-Mediated Transgene Expression in Oligodendrocytes
Cited by: 35
Author(s): Georg von Jonquières, Dominik Fröhlich, Claudia B. Klugmann, Xin Wen, Anne E. Harasta, Roshini Ramkumar, Ziggy H. T. Spencer, Gary D. Housley, Matthias Klugmann
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2019.00152

Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes
Cited by: 4
Author(s): Yueer Lu, Xiao Wang, Hang Yu, Jianlin Li, Zhiqiang Jiang, Bangwei Chen, Yueqi Lu, Wei Wang, Chongyin Han, Ying Ouyang, Lizhen Huang, Chunbo Chen, Weidong Tian, Fei Ling
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-9-437

Analysis of Porcine Transcriptional Response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the Mesenteric Lymph Node
Cited by: 44
Author(s): Yanfang Wang, Oliver Couture, Long Qu, Jolita J. Uthe, Shawn M. D. Bearson, Daniel Kuhar, Joan K. Lunney, Dan Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 2
Published: almost 16 years ago

10.18632/aging.102583

lncRNA Rmst acts as an important mediator of BMP9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) by antagonizing Notch-targeting microRNAs
Cited by: 18
Author(s): Zhicai Zhang, Jianxiang Liu, Zongyue Zeng, Jiaming Fan, Shifeng Huang, Linghuan Zhang, Bo Zhang, Xi Wang, Yixiao Feng, Zhenyu Ye, Ling Zhao, Du Cao, Lijuan Yang, Mikhail Pakvasa, Bin Liu, William Wagstaff, Xiaoxing Wu, Han Luo, Jing Zhang, Meng Zhang, Fang He, Yukun Mao, Huimin Ding, Yongtao Zhang, Chunping Niu, Rex C. Haydon, Hue H. Luu, Michael J. Lee, Jennifer Moriatis Wolf, Zengwu Shao, Tong‐Chuan He
Software Mentions: 2
Published: almost 5 years ago

10.3389/fncel.2014.00373

De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus
Cited by: 87
Author(s): Roman M. Stilling, Eva Benito, Michael Gertig, Jonas Barth, Vincenzo Capece, Susanne Burkhardt, Stefan Bonn, André Fischer
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-14-4

Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules
Cited by: 61
Author(s): Keunsoo Kang, Gertraud W. Robinson, Lothar Hennighausen
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-016-2468-x

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti
Cited by: 23
Author(s): Susanta K. Behura, Joseph Sarro, Ping Li, Keshava Mysore, David W. Severson, Scott J. Emrich, Molly Duman-Scheel
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-10-71

Gene set-based module discovery in the breast cancer transcriptome
Cited by: 35
Author(s): Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
Software Mentions: 2
Published: over 15 years ago

10.1038/srep03041

Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival
Cited by: 12
Author(s): Amir Feizi, Sergio Bordel
Software Mentions: 2
Published: almost 11 years ago

10.15252/msb.20188430

A resource of variant effect predictions of single nucleotide variants in model organisms
Cited by: 79
Author(s): Omar Wagih, Marco Galardini, Bede P. Busby, Danish Memon, Athanasios Typas, Pedro Beltrão
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-020-07079-8

Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data
Cited by: 1
Author(s): Ming Shi, Sheng Tan, Xueping Xie, Ao Li, Wulin Yang, Tao Zhu, Hongqiang Wang
Software Mentions: 2
Published: almost 4 years ago

10.1002/1878-0261.12657

Norepinephrine‐CREB1‐miR‐373 axis promotes progression of colon cancer
Cited by: 13
Author(s): Jing Han, Qingwei Jiang, Ruili Ma, Huahua Zhang, Dongdong Tong, Kaijie Tang, Xiaofei Wang, Lei Ni, Jiyu Miao, Baojun Duan, Yang Yang, Yanke Chen, Fei Wu, Jianbo Han, Mengchang Wang, Ni Hou, Chen Huang
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-019-2735-3

MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites
Cited by: 10
Author(s): Jialu Hu, Jingru Wang, Jianan Lin, Tianwei Liu, Yuanke Zhong, Jie Liu, Yanyan Zheng, Yiqun Gao, Junhao He, Xuequn Shang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-5277-6

Constructing tissue-specific transcriptional regulatory networks via a Markov random field
Cited by: 6
Author(s): Shuping Ma, Tao Jiang, Rui Jiang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-018-2215-1

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data
Cited by: 2
Author(s): Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie‐Pierre Buisine, Hélène Touzet, Martin Figeac
Software Mentions: 2
Published: over 6 years ago

10.1186/s13072-015-0043-3

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors
Cited by: 32
Author(s): Andreas Lennartsson, Peter Arner, Michela Fagiolini, Alka Saxena, Robin Andersson, Hazuki Takahashi, Yukihiko Noro, Judy Sng, Albin Sandelin, Takao K. Hensch, Piero Carninci
Software Mentions: 2
Published: almost 9 years ago

10.1186/1756-8935-8-8

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements
Cited by: 57
Author(s): Matthew S. Wilken, Joseph A. Brzezinski, Anna La Torre, Kyle Siebenthall, Robert E. Thurman, Peter J. Sabo, Richard Sandstrom, Jeff Vierstra, Theresa K. Canfield, R. Scott Hansen, Michael A. Bender, J Stamatoyannopoulos, Thomas A. Reh
Software Mentions: 2
Published: over 9 years ago

10.1016/j.mcn.2015.04.007

The Dlx5 and Foxg1 transcription factors, linked via miRNA-9 and -200, are required for the development of the olfactory and GnRH system
Cited by: 49
Author(s): Giulia Garaffo, Daniele Conte, Paolo Provero, Daniela Tomaiuolo, Zheng Luo, Patrizia Pinciroli, Clelia Peano, Ilaria D’Atri, Yorick Gitton, Talya Etzion, Yoav Gothilf, Dafne Gays, Massimo Santoro, Giorgio R. Merlo
Software Mentions: 2
Published: about 9 years ago

10.1186/s12943-020-01217-2

LINC00173.v1 promotes angiogenesis and progression of lung squamous cell carcinoma by sponging miR-511-5p to regulate VEGFA expression
Cited by: 85
Author(s): Jia‐Rong Chen, Aibin Liu, Zhihui Wang, Bin Wang, Xingxing Chai, Wenjie Lu, Ting Cao, Ronggang Li, Mingyan Wu, Zhuming Lu, Wei Pang, Lin Xiao, Xiangmeng Chen, Yan Zheng, Qiong Chen, Jincheng Zeng, Jun Li, Xin Zhang, Dong Ren, Yanming Huang
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2021.651913

The Transcription Factor C/EBPβ Promotes HFL-1 Cell Migration, Proliferation, and Inflammation by Activating lncRNA HAS2-AS1 in Hypoxia
Cited by: 5
Author(s): Xue Yang, Fei Qi, Shanchen Wei, Lin Li, Xinmin Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-10-218

Transcriptional programs: Modelling higher order structure in transcriptional control
Cited by: 3
Author(s): John E. Reid, Sascha Ott, Lorenz Wernisch
Software Mentions: 2
Published: about 15 years ago

10.1093/database/bav119

Ensembl regulation resources
Cited by: 43
Author(s): Daniel R. Zerbino, Nathan Johnson, Thomas Juetteman, Dan Sheppard, Steven P. Wilder, Ilias Lavidas, Michael Nuhn, Emily Perry, Quentin Raffaillac-Desfosses, Daniel Sobral, Damian Keefe, Stefan Gräf, Ikhlak Ahmed, Rhoda Kinsella, Bethan Pritchard, Simon Brent, Ridwan M Amode, Anne Parker, Stephen J. Trevanion, Ewan Birney, Ian Dunham, Paul Flicek
Software Mentions: 2
Published: over 8 years ago

10.1093/database/baab022

IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease
Cited by: 7
Author(s): Farhat Aziz Khan, Aleksandar Radovanović, Takashi Gojobori, Mandeep Kaur
Software Mentions: 2
Published: over 3 years ago

10.1016/j.ydbio.2019.09.006

Enhancer activation by FGF signalling during otic induction
Cited by: 11
Author(s): Monica Tambalo, Maryam Anwar, Mustafa Ahmed, Andrea Streit
Software Mentions: 2
Published: over 4 years ago

10.1016/j.csbj.2020.11.006

Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework
Cited by: 5
Author(s): Patrick Martin, Nicolae Radu Zabet
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-018-5409-z

RNA sequencing identifies common pathways between cigarette smoke exposure and replicative senescence in human airway epithelia
Cited by: 10
Author(s): Hannah Voic, Xiuying Li, Jun Ho Jang, Chunbin Zou, Prithu Sundd, Jonathan K. Alder, Mauricio Rojas, Divay Chandra, Scott H. Randell, Rama K. Mallampalli, Yohannes Tesfaigzi, Tyrone Ryba, Toru Nyunoya
Software Mentions: 2
Published: over 5 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

10.1186/s12943-016-0510-x

ITGA6 is directly regulated by hypoxia-inducible factors and enriches for cancer stem cell activity and invasion in metastatic breast cancer models
Cited by: 143
Author(s): Danielle L. Brooks, Luciana P. Schwab, Raisa I. Krutilina, Deanna N. Parke, Aarti Sethuraman, David Hoogewijs, Alexandra Schörg, Lauren Gotwald, Meiyun Fan, Roland H. Wenger, Tiffany N. Seagroves
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-12-238

MotifClick: prediction of cis-regulatory binding sites via merging cliques
Cited by: 10
Author(s): Shaoqiang Zhang, Shan Li, Meng Niu, Phuc Pham, Zhengchang Su
Software Mentions: 2
Published: over 13 years ago

10.1093/database/baz141

ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
Cited by: 11
Author(s): Erik Czipa, Mátyás Schiller, Tibor Nagy, Levente Kontra, László Steiner, Júlia Koller, Orsolya Pálné-Szén
Software Mentions: 2
Published: over 4 years ago

10.1242/dev.147322

Functional characterisation of cis-regulatory elements governing dynamic <i>Eomes</i> expression in the early mouse embryo
Cited by: 31
Author(s): Claire Simon, Damien J. Downes, M Gosden, Jelena Telenius, Douglas R. Higgs, Jim R. Hughes, Ita Costello, Elizabeth K. Bikoff, Elizabeth J. Robertson
Software Mentions: 2
Published: over 7 years ago

10.1186/s12943-019-1104-1

TEAD4 modulated LncRNA MNX1-AS1 contributes to gastric cancer progression partly through suppressing BTG2 and activating BCL2
Cited by: 78
Author(s): You Shuai, Zhonghua Ma, Weitao Liu, Yu Tao, Changsheng Yan, Hua Jiang, Shasha Tian, Tongpeng Xu, Yongqian Shu
Software Mentions: 2
Published: over 4 years ago

10.1186/s13148-019-0666-5

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer
Cited by: 20
Author(s): Christoph Weigel, Jittiporn Chaisaingmongkol, Yassen Assenov, Christine Kuhmann, Volker Winkler, Irene Santi, Olga Bogatyrova, Simone Kaucher, Justo Lorenzo Bermejo, Suet Yi Leung, Tsun Leung Chan, Felix Lasitschka, M. Bohrer, Alexander Marx, Roland Heyny-von Haußen, Christel Herold‐Mende, Gerhard Dyckhoff, Petra Boukamp, K.-W. Delank, K. Hörmann, Burkhard M. Lippert, G. Baier, Andreas Dietz, Christopher C. Oakes, Christoph Plass, Heiko Becher, Peter Schmezer, Heribert Ramroth, Odilia Popanda
Software Mentions: 2
Published: over 5 years ago

10.3390/cells9122690

The PARP Inhibitor Olaparib Modulates the Transcriptional Regulatory Networks of Long Non-Coding RNAs during Vasculogenic Mimicry
Cited by: 5
Author(s): Mónica Fernández-Cortés, Eduardo Andrés-León, F. Javier Oliver
Software Mentions: 2
Published: almost 4 years ago

10.3390/cells9010147

IGF-1 Signalling Regulates Mitochondria Dynamics and Turnover through a Conserved GSK-3β–Nrf2–BNIP3 Pathway
Cited by: 46
Author(s): Sarah Riis, Jack Murray, Rosemary O’Connor
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-017-4339-5

Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes
Cited by: 7
Author(s): Naoki Osato
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-017-3785-4

Transversions have larger regulatory effects than transitions
Cited by: 65
Author(s): Cong Guo, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe, Timothy E. Reddy
Software Mentions: 2
Published: over 7 years ago

10.3390/cells8101281

Enhancer Dysfunction in 3D Genome and Disease
Cited by: 15
Author(s): Ji‐Han Xia, Gong-Hong Wei
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-9-495

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
Cited by: 34
Author(s): Matthew S. Hestand, M.A. van Galen, Michel P. Villerius, Gert‐Jan B. van Ommen, Johan T. den Dunnen, Peter A C ‘t Hoen
Software Mentions: 2
Published: almost 16 years ago

10.3390/cells8121498

Gene Expression Profiles Controlled by the Alternative Splicing Factor Nova2 in Endothelial Cells
Cited by: 9
Author(s): Elisa Belloni, Anna Di Matteo, Davide Pradella, Margherita Vacca, Christopher D R Wyatt, Roberta Alfieri, Antonio Maffia, Simone Sabbioneda, Claudia Ghigna
Software Mentions: 2
Published: almost 5 years ago

10.3390/cells8040298

miR-1306 Mediates the Feedback Regulation of the TGF-β/SMAD Signaling Pathway in Granulosa Cells
Cited by: 22
Author(s): Liu Yang, Xiaohong Du, Lu Liu, Qiuyu Cao, Zengxiang Pan, Qifa Li
Software Mentions: 2
Published: over 5 years ago

10.1016/j.bbagrm.2018.06.010

Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells
Cited by: 16
Author(s): Ioanna Pavlaki, Igor Chernukhin, Georgia Kita, Svetlana Gretton, Christopher T. Clarkson, Vladimir B. Teif, Elena Klenova
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-021-02211-0

Functional in vivo characterization of sox10 enhancers in neural crest and melanoma development
Cited by: 6
Author(s): Rebecca L. Cunningham, Eva T. Kramer, Sophia K. DeGeorgia, Paula M. Godoy, Anna P. Zarov, Shayana Seneviratne, Vadim Grigura, Charles K. Kaufman
Software Mentions: 2
Published: over 3 years ago

10.1111/cpr.12981

Circ_SMAD4 promotes gastric carcinogenesis by activating wnt/β‐catenin pathway
Cited by: 27
Author(s): Liyan Wang, Bin Li, Xiaoyuan Yi, Xuejun Xiao, Qianqian Zheng, Lei Ma
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0096320

Prediction of Potential Cancer-Risk Regions Based on Transcriptome Data: Towards a Comprehensive View
Cited by: 22
Author(s): Arghavan Alisoltani, Hossein Fallahi, Mahdi Ebrahimi, Mansour Ebrahimi, Esmaeil Ebrahimie
Software Mentions: 2
Published: over 10 years ago

10.1038/s41420-021-00575-0

Long noncoding RNA LINC00261 upregulates ITIH5 to impair tumorigenic ability of pancreatic cancer stem cells
Cited by: 4
Author(s): Lijuan Zou, Hengpeng He, Zhiguo Li, Ou Chen, Xiukun Jia, Hao Zhang
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2105-12-S10-S19

Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets
Cited by: 18
Author(s): Sujoy Roy, Kevin Heinrich, Vinhthuy Phan, Michael W. Berry, Ramin Homayouni
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12859-018-2421-x

SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines
Cited by: 25
Author(s): Giulia Fiscon, Federica Conte, Paola Paci
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-14-84

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury
Cited by: 34
Author(s): Li‐Wei Chang, Andreu Viader, Nobish Varghese, Jacqueline E. Payton, Jeffrey Milbrandt, Rakesh Nagarajan
Software Mentions: 2
Published: over 11 years ago

10.1038/s41419-020-03300-4

STAT1-induced regulation of lncRNA ZFPM2-AS1 predicts poor prognosis and contributes to hepatocellular carcinoma progression via the miR-653/GOLM1 axis
Cited by: 30
Author(s): Xiwu Zhang, Qiu-Han Li, Zuo-di Xu, Dou Jinjin
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-017-3942-9

Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous
Cited by: 29
Author(s): Pamela Córdova, A Scheidegger Gonzalez, David R. Nelson, María-Soledad Gutiérrez, Marcelo Baeza, Víctor Cifuentes, Jennifer Alcaı́no
Software Mentions: 2
Published: about 7 years ago

10.1038/s41419-020-2735-2

Low GAS5 expression may predict poor survival and cisplatin resistance in cervical cancer
Cited by: 26
Author(s): Xingyu Fang, Guangyu Zhong, Yuhan Wang, Zhongqiu Lin, Rong Lin, Tingting Yao
Software Mentions: 2
Published: about 4 years ago

10.1038/s41419-018-0966-2

The MYB/miR-130a/NDRG2 axis modulates tumor proliferation and metastatic potential in salivary adenoid cystic carcinoma
Cited by: 35
Author(s): Yu Wang, Chun-ye Zhang, Ronghui Xia, Jing Han, Bei Sun, Shuyang Sun, Jiang Li
Software Mentions: 2
Published: about 6 years ago

10.1038/s41419-021-03523-z

Long noncoding RNA LINC00518 induces radioresistance by regulating glycolysis through an miR-33a-3p/HIF-1α negative feedback loop in melanoma
Cited by: 28
Author(s): Yan Liu, Dong He, Mengqing Xiao, Yuxing Zhu, Jianda Zhou, Ke Cao
Software Mentions: 2
Published: over 3 years ago

10.1038/s41419-018-1205-6

p73 regulates ependymal planar cell polarity by modulating actin and microtubule cytoskeleton
Cited by: 29
Author(s): Sandra Fuertes-Álvarez, Laura Maeso‐Alonso, Javier Villoch-Fernández, Merit Wildung, Marta Martín-López, Clayton B. Marshall, A. Villena, Inmaculada Diez-Prieto, Jennifer A. Pietenpol, Fadel Tissir, Muriel Lizé, Margarita M Marqués, Maria C. Marin
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2105-12-171

TAFFEL: Independent Enrichment Analysis of gene sets
Cited by: 1
Author(s): Mitja Kurki, Jussi Paananen, Markus Storvik, Seppo Ylä‐Herttuala, Juha E. Jääskeläinen, Mikael von und zu Fraunberg, Garry Wong, Petri Pehkonen
Software Mentions: 2
Published: over 13 years ago

10.17179/excli2020-2934

Genome-wide expression changes induced by bisphenol A, F and S in human stem cell derived hepatocyte-like cells.
Cited by: 2
Author(s): Baltasar Lucendo‐Villarin, Patrick Nell, Birte Hellwig, Panagiotis Filis, David Feuerborn, Peter J. O’Shaughnessy, Patrício Godoy, Jörg Rahnenführer, Jan G. Hengstler, Anna Cherianidou, Agapios Sachinidis, Paul A. Fowler, David C. Hay
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41419-020-2556-3

Galectin-3 modulates epithelial cell adaptation to stress at the ER-mitochondria interface
Cited by: 19
Author(s): Lucie Coppin, Arnaud Jannin, Emilie Ait Yahya, C. Thuillier, Céline Villenet, Meryem Tardivel, Antonino Bongiovanni, Cécile Gaston, Simon de Beco, Nicolas Barois, Isabelle Van Seuningen, Emmanuelle Durand, Amélie Bonnefond, Jean-Claude Vienne, Jòseph Vamecq, Martin Figeac, Audrey Vincent, Delphine Delacour, Nicole Porchet, Pascal Pigny
Software Mentions: 2
Published: over 4 years ago

10.1189/jlb.6TA1014-477RR

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells
Cited by: 21
Author(s): Anagha Joshi, Christopher Pooley, Tom C. Freeman, Andreas Lennartsson, Magda Babina, Christian Schmidl, Teunis B. H. Geijtenbeek, Tom Michoel, Jessica Severin, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji, Yoshihide Hayashizaki, Piero Carninci, Michael Rehli, David Hume
Software Mentions: 2
Published: over 9 years ago

10.1038/s41419-021-03882-7

Prrx1 promotes stemness and angiogenesis via activating TGF-β/smad pathway and upregulating proangiogenic factors in glioma
Cited by: 19
Author(s): Zetao Chen, Yihong Chen, Yan Li, Weidong Lian, Kaiyu Zheng, Yuxuan Zhang, Yujie Zhang, Lin Cao, Chaoqun Liu, Fei Sun, Xinlin Sun, Jihui Wang, Liang Zhao, Yiquan Ke
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.69765

Sex-specific pubertal and metabolic regulation of Kiss1 neurons via Nhlh2
Cited by: 11
Author(s): Silvia León, Rajae Talbi, Elizabeth McCarthy, Kaitlin Ferrari, Chrysanthi Fergani, Lydie Naulé, Ji Hae Choi, Rona S. Carroll, Ursula B. Kaiser, Carlos F. Aylwin, Alejandro Lomniczi, Víctor Navarro
Software Mentions: 2
Published: about 3 years ago

10.1186/s13578-021-00675-5

RETRACTED ARTICLE: Long noncoding RNA SNHG1 promotes TERT expression by sponging miR-18b-5p in breast cancer
Cited by: 7
Author(s): Yujuan Kang, Lin Wan, Qin Wang, Yanling Yin, Jiena Liu, Lei Liu, Hao Wu, Lei Zhang, Xin Zhang, Shouping Xu, Da Pang
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2164-11-145

Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs
Cited by: 33
Author(s): Srinivas Veerla, Markus Ringnér, Mattias Höglund
Software Mentions: 2
Published: over 14 years ago

10.1038/s41418-018-0204-6

Oncogenic zinc finger protein ZNF322A promotes stem cell-like properties in lung cancer through transcriptional suppression of c-Myc expression
Cited by: 18
Author(s): Chauying J. Jen, Chun Yen Liu, Yuting Chen, Li Wu, Yang Chih Shieh, Wu‐Wei Lai, Yi‐Ching Wang
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-020-2435-y

CCL5 derived from tumor-associated macrophages promotes prostate cancer stem cells and metastasis via activating β-catenin/STAT3 signaling
Cited by: 131
Author(s): Renlun Huang, Shengqi Wang, Neng Wang, Yifeng Zheng, Jianfu Zhou, Bowen Yang, Xuan Wang, Juping Zhang, Lang Guo, Shusheng Wang, Zhiqiang Chen, Zhiyu Wang, Shulin Xiang
Software Mentions: 2
Published: over 4 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: over 3 years ago

10.3390/cancers13184577

The Stress-Inducible BCL2A1 Is Required for Ovarian Cancer Metastatic Progression in the Peritoneal Microenvironment
Cited by: 5
Author(s): Rui Liang, Mingo M. H. Yung, Fengjiao He, Peili Jiao, Ki Chan, Hextan Ys Ngan, David W. Chan
Software Mentions: 2
Published: about 3 years ago

10.1186/s12935-021-02180-8

LINC01605, regulated by the EP300-SMYD2 complex, potentiates the binding between METTL3 and SPTBN2 in colorectal cancer
Cited by: 9
Author(s): Meng Yue, Tao Liu, Guoqiang Yan, Xiaofan Luo, Lei Wang
Software Mentions: 2
Published: about 3 years ago

10.1186/1471-2164-13-S8-S18

CTF: a CRF-based transcription factor binding sites finding system
Cited by: 6
Author(s): Yiping He, Yizhe Zhang, Guangyong Zheng, Chaochun Wei
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0212063

Impact of miR-223-3p and miR-2909 on inflammatory factors IL-6, IL-1ß, and TNF-α, and the TLR4/TLR2/NF-κB/STAT3 signaling pathway induced by lipopolysaccharide in human adipose stem cells
Cited by: 48
Author(s): Juan Wu, Ping Niu, Yang Zhao, Cheng Yan, Weiping Chen, Lan Lin, Jing-Mei Lu, Xue Cheng, Zhiliang Xu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0033617

Identification and Analysis of Conserved cis-Regulatory Regions of the MEIS1 Gene
Cited by: 20
Author(s): José Luis Royo, José Bessa, Carmen Herrera Hidalgo, Ana Fernández-Miñán, Juan J. Tena, Yolanda Roncero, José Luis Gómez-Skármeta, Fernando Casares
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-019-5450-6

Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection
Cited by: 14
Author(s): Elena Denisenko, Reto Guler, Musa M. Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0164752

Inhibition of Snail Family Transcriptional Repressor 2 (SNAI2) Enhances Multidrug Resistance of Hepatocellular Carcinoma Cells
Cited by: 11
Author(s): Xinyu Zhao, Lei Li, Xiao-Bo Wang, Rongjie Fu, Yaping Lv, Wei Jin, Chao Meng, Guoqiang Chen, Lei Huang, Ke-Wen Zhao
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-15-1161

Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates
Cited by: 31
Author(s): Christian Selinger, Jennifer Tisoncik-Go, Vineet D. Menachery, Sudhakar Agnihothram, G. Lynn Law, Jean Chang, Sara M. Kelly, Pavel Sova, Ralph S. Baric, Michael G. Katze
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0079011

Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots
Cited by: 45
Author(s): Sunita Kumari, Doreen Ware
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2105-11-366

Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster
Cited by: 19
Author(s): Denis C. Bauer, Fabian A. Buske, Timothy L. Bailey
Software Mentions: 2
Published: about 14 years ago

10.1093/bib/bbv107

Systematic dissection of dysregulated transcription factor–miRNA feed-forward loops across tumor types
Cited by: 45
Author(s): Wei Jiang, Ramkrishna Mitra, Lin Chen, Quan Wang, Feixiong Cheng, Zhongming Zhao
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0024153

Inactivation of a Single Copy of Crebbp Selectively Alters Pre-mRNA Processing in Mouse Hematopoietic Stem Cells
Cited by: 6
Author(s): Madeleine E. Lemieux, Zhongqing Cheng, Qing Zhou, Ruth White, John E. Cornell, Andrew L. Kung, Vivienne I. Rebel
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0185570

The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies
Cited by: 4
Author(s): Abdulkadir Elmas, Xiaodong Wang, Jacqueline M. Dresch
Software Mentions: 2
Published: almost 7 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

10.1371/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

10.1038/s41416-019-0395-8

MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer
Cited by: 28
Author(s): Michael J. G. Milevskiy, Udai Gujral, Carolina Marques, Andrew Stone, Korinne Northwood, Les J. Burke, Julia M. Gee, Kenneth P. Nephew, Susan J. Clark, Melissa A. Brown
Software Mentions: 2
Published: over 5 years ago

10.1002/advs.202100106

3D Adipose Tissue Culture Links the Organotypic Microenvironment to Improved Adipogenesis
Cited by: 28
Author(s): Joanne X. Shen, Morgane Couchet, Jérémy Dufau, Thaís de Castro Barbosa, Maximilian H. Ulbrich, Martin Helmstädter, Aurino M. Kemas, Reza Zandi Shafagh, Marie-Adeline Marquès, Jacob B. Hansen, Niklas Mejhert, Dominique Langin, Mikael Rydén, Volker M. Lauschke
Software Mentions: 2
Published: about 3 years ago

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283