cran: JASPAR | Projects | Ecosyste.ms: Papers

10.1186/s13293-019-0259-1

The developmental origins of sex-biased expression in cardiac development
Cited by: 30
Author(s): Daniel F. Deegan, Reza Karbalaei, Jozef Madžo, Rob J. Kulathinal, Nora Engel
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-015-0797-4

Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
Cited by: 34
Author(s): Ralf Eggeling, Teemu Roos, Petri Myllymäki, Ivo Große
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-021-02499-5

Biologically relevant transfer learning improves transcription factor binding prediction
Cited by: 21
Author(s): Gherman Novakovsky, Manu Saraswat, Oriol Fornés, Sara Mostafavi, Wyeth W. Wasserman
Software Mentions: 2
Published: about 3 years ago

10.1186/s12929-018-0459-8

Identification of target genes in cardiomyopathy with fibrosis and cardiac remodeling
Cited by: 41
Author(s): Jinqiu Zhao, Tiewei Lv, Junjun Quan, Weian Zhao, Song Jing, Zhuolin Li, Han Lv, Wei Huang, Longke Ran
Software Mentions: 2
Published: over 6 years ago

10.1186/1745-6150-5-67

Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
Cited by: 5
Author(s): Georg Fuellen, Stephan Struckmann
Software Mentions: 2
Published: almost 15 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

10.1093/bioinformatics/btv017

Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets
Cited by: 20
Author(s): Hisaki Ikebata, Ryo Yoshida
Software Mentions: 2
Published: almost 10 years ago

10.1093/bioinformatics/bty372

REGGAE: a novel approach for the identification of key transcriptional regulators
Cited by: 8
Author(s): Tim Kehl, Lara Schneider, Kathrin Kattler, Daniel Stöckel, Jenny Wegert, Nico Gerstner, Nicole Ludwig, Ute Distler, Markus Schick, Ulrich Keller, Stefan Tenzer, Manfred Gessler, Jörn Walter, Andreas Keller, Norbert Graf, Eckart Meese, Hans‐Peter Lenhof
Software Mentions: 2
Published: over 6 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: over 6 years ago

10.1186/1471-2164-13-429

Identification and analysis of pig chimeric mRNAs using RNA sequencing data
Cited by: 15
Author(s): Lei Ma, Shulin Yang, Weihua Zhao, Zhonglin Tang, Tingting Zhang, Kui Li
Software Mentions: 2
Published: about 12 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: almost 7 years ago

10.1186/1471-2105-14-140

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
Cited by: 6
Author(s): Josef Laimer, Clemens J Zuzan, Tobias Ehrenberger, Monika Freudenberger, Simone Gschwandtner, Carina Lebherz, Peter Lackner
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-019-1728-x

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale
Cited by: 33
Author(s): Michał Sadowski, Agnieszka Kraft, Przemysław Szałaj, Michał Wlasnowolski, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-020-02225-7

Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression
Cited by: 35
Author(s): Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru, Yijing Zhang
Software Mentions: 2
Published: almost 4 years ago

10.1186/1756-0500-4-157

Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation
Cited by: 10
Author(s): Robab Hakim-Weber, Anne Krogsdam, Claus Jørgensen, Maria Fischer, Andreas Prokesch, Juliane Gertrude Bogner‐Strauß, Stefan R. Bornstein, Jacob B. Hansen, Lise Madsen, Karsten Kristiansen, Zlatko Trajanoski, Hubert Hackl
Software Mentions: 2
Published: over 13 years ago

10.1186/s13104-015-1039-6

A property-based analysis of human transcription factors
Cited by: 7
Author(s): Shahram Bahrami, Rezvan Ehsani, Finn Drabløs
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-018-2190-6

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks
Cited by: 10
Author(s): Ankit Jambusaria, Jeff Klomp, Zhigang Hong, Shahin Rafii, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 2
Published: over 6 years ago

10.1186/gb-2008-9-10-r148

Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases
Cited by: 96
Author(s): Monika Ray, Jianhua Ruan, Weixiong Zhang
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2008-9-2-r38

Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia
Cited by: 27
Author(s): Li Wei Chang, Jacqueline E. Payton, Wenlin Yuan, Timothy J. Ley, Rakesh Nagarajan, Gary D. Stormo
Software Mentions: 2
Published: almost 17 years ago

10.3390/genes11111363

Hes5.9 Coordinate FGF and Notch Signaling to Modulate Gastrulation via Regulating Cell Fate Specification and Cell Migration in Xenopus tropicalis
Cited by: 3
Author(s): Xiao Huang, Liyue Zhang, Shanshan Yang, Yongpu Zhang, Mingjiang Wu, Peichao Chen
Software Mentions: 2
Published: about 4 years ago

10.1186/s12860-021-00378-2

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity
Cited by: 2
Author(s): Atefeh Atefi, Pendar Shojaei kojouri, Fereshteh Karamali, Shiva Irani, Mohammad Hossein Nasr-Esfahani
Software Mentions: 2
Published: over 3 years ago

10.1186/s12863-020-00894-8

CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity
Cited by: 8
Author(s): Manthan Patel, Divyesh Patel, Subhamoy Datta, Uma Singh
Software Mentions: 2
Published: over 4 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: almost 18 years ago

10.1186/gb-2013-14-8-r84

PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs
Cited by: 102
Author(s): Annalisa Marsico, Matthew R. Huska, Julia Lasserre, Haiyang Hu, Dubravka Vučićević, Anne Musahl, Ulf Andersson Ørom, Martin Vingron
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2148-11-267

Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2
Cited by: 4
Author(s): Stephan Struckmann, Daniel Esch, Hans R. Schöler, Georg Fuellen
Software Mentions: 2
Published: about 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

10.1186/s12866-020-02072-3

First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach
Cited by: 5
Author(s): Abeer Babiker Idris, Einas Babiker Idris, Amany Eltayib Ataelmanan, Ali Elbagir Ali Mohamed, Bashir M. Osman Arbab, El-Amin Mohamed Ibrahim, Mohamed A. Hassan
Software Mentions: 2
Published: almost 4 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

10.3390/genes10020077

Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21
Cited by: 9
Author(s): Alina S. Ustiugova, Kirill V. Korneev, Dmitry V. Kuprash, Marina Afanasyeva
Software Mentions: 2
Published: almost 6 years ago

10.1186/1755-8794-6-45

Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression
Cited by: 8
Author(s): Adam E. Handel, Geir Kjetil Sandve, Giulio Disanto, Lahiru Handunnetthi, Gavin Giovannoni, Sreeram Ramagopalan
Software Mentions: 2
Published: about 11 years ago

10.1186/s12920-018-0439-6

“Omics” data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy
Cited by: 1
Author(s): Nzali Campbell, David Weitzenkamp, I. L. Campbell, Ronald F. Schmidt, Chindo Hicks, Michael J. Morgan, David Irwin, John J. Tentler
Software Mentions: 2
Published: almost 6 years ago

10.1186/1755-8794-7-34

On the identification of potential regulatory variants within genome wide association candidate SNP sets
Cited by: 42
Author(s): Chih-Yu Chen, I‐Shou Chang, Chao A. Hsiung, Wyeth W. Wasserman
Software Mentions: 2
Published: over 10 years ago

10.1186/s12920-019-0525-4

Impact of cancer mutational signatures on transcription factor motifs in the human genome
Cited by: 10
Author(s): Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann
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

10.3389/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

10.3390/genes10060406

Transcriptome Changes of Skeletal Muscle RNA-Seq Speculates the Mechanism of Postprandial Hyperglycemia in Diabetic Goto-Kakizaki Rats During the Early Stage of T2D
Cited by: 7
Author(s): Wenlu Zhang, Yuhuan Meng, Shuang Fu, Xingsong Li, Zixi Chen, Lizhen Huang, Hongli Du
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-021-00993-0

Diagnostic yield of rare skeletal dysplasia conditions in the radiogenomics era
Cited by: 5
Author(s): Ataf Sabir, Elizabeth Morley, Jameela Sheikh, Alistair Calder, Ana Beleza-Meireles, Moira Cheung, Alessandra Cocca, Mattias Jansson, Suzanne Lillis, Yogen Patel, Shu Yau, Christine Hall, A.C. Offiah, Melita Irving
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1006792

Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees
Cited by: 65
Author(s): Andreas Wållberg, Caspar Schöning, Matthew T. Webster, Martin Hasselmann
Software Mentions: 2
Published: over 7 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: about 5 years ago

10.1002/advs.201901380

Targeting YAP1/LINC00152/FSCN1 Signaling Axis Prevents the Progression of Colorectal Cancer
Cited by: 106
Author(s): Chunlin Ou, Zhenqiang Sun, Xiaoyun He, Xiaoling Li, Songqing Fan, Xiang Zheng, Ping Qiu, Guiyuan Li, Xiayu Li, Jian Ma
Software Mentions: 2
Published: almost 5 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: over 3 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/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: almost 4 years ago

10.1371/journal.pgen.1003195

Genome-Wide Screens for In Vivo Tinman Binding Sites Identify Cardiac Enhancers with Diverse Functional Architectures
Cited by: 61
Author(s): Hong Jin, Robert Stojnic, Boris Adryan, Anıl Özdemir, Angelike Stathopoulos, Manfred Frasch
Software Mentions: 2
Published: almost 12 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

10.1186/1471-2172-9-7

The Innate Immune Database (IIDB)
Cited by: 44
Author(s): Martin Korb, Alistair G. Rust, Vésteinn Thórsson, Christophe Battail, Bin Li, Daehee Hwang, Kathleen A. Kennedy, Jared C. Roach, Carrie M. Rosenberger, Mark Gilchrist, Daniel E. Zak, Carrie D. Johnson, Bruz Marzolf, Alan Aderem, Ilya Shmulevich, Hamid Bolouri
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-13-19

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
Cited by: 18
Author(s): Cyrille Lepoivre, Aurélie Bergon, Fabrice Lopez, Narayanan B. Perumal, Catherine Nguyen, Jean Imbert, Denis Puthier
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-12-365

Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver
Cited by: 114
Author(s): Edward Dere, Raymond Lo, Trine Celius, Jason Matthews, Timothy R. Zacharewski
Software Mentions: 2
Published: over 13 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: about 10 years ago

10.3390/genes11050482

Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans
Cited by: 8
Author(s): Massimiliano Chetta, Lorena Di Pietro, Nenad Bukvić, Wanda Lattanzi
Software Mentions: 2
Published: over 4 years ago

10.1111/jcmm.15625

CXXC finger protein 4 inhibits the CDK18‐ERK1/2 axis to suppress the immune escape of gastric cancer cells with involvement of ELK1/MIR100HG pathway
Cited by: 20
Author(s): Ping Li, Dongfang Ge, Pengfei Li, Fangyong Hu, Junfeng Chu, Xiaojun Chen, Wenbo Song, Ali Wang, Xiang Gu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-020-3348-6

BLAMM: BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs
Cited by: 3
Author(s): Jan Fostier
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1004894

Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors
Cited by: 4
Author(s): Andrew Wight, Doo Yang, Ilya Ioshikhes, Andrew P. Makrigiannis
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.0040005

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation
Cited by: 99
Author(s): Malin Andersen, Pär G. Engström, Stuart Lithwick, David J. Arenillas, Per Eriksson, Boris Lenhard, Wyeth W. Wasserman, Jacob Odeberg
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pcbi.1003490

A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
Cited by: 48
Author(s): Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino, Michele Caselle
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-13-S1-S3

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group
Cited by: 51
Author(s): Tzong-Yi Lee, Wen Chi Chang, Justin Bo Kai Hsu, Tzu Hao Chang, Dray Ming Shien
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-13-85

AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana
Cited by: 18
Author(s): Yi An Chen, Ying Chi Wen, Wen Chi Chang
Software Mentions: 2
Published: over 12 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/s12859-018-2441-6

Detection of long non–coding RNA homology, a comparative study on alignment and alignment–free metrics
Cited by: 30
Author(s): Teresa Maria Rosaria Noviello, Antonella Di Liddo, Giovanna Maria Ventola, Antonietta Spagnuolo, Salvatore D’Aniello, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 2
Published: about 6 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

10.3389/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

10.1016/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: almost 5 years ago

10.1371/journal.pcbi.0030007

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
Cited by: 67
Author(s): Thomas A. Down, Casey M. Bergman, Jing Su, Tim Hubbard
Software Mentions: 2
Published: almost 18 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: almost 8 years ago

10.1371/journal.pcbi.0030061

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
Cited by: 120
Author(s): Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pbio.2001069

Transcriptional regulatory logic of the diurnal cycle in the mouse liver
Cited by: 65
Author(s): Jonathan Sobel, Irina Krier, Teemu Andersin, Sunil K. Raghav, Donatella Canella, Federica Gilardi, Alexandra Styliani Kalantzi, Guillaume Rey, Benjamin D. Weger, Frédéric Gachon, Matteo Dal Peraro, Nouria Hernandez, Ueli Schibler, Bart Deplancke, Félix Naef
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-12-286

Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis
Cited by: 71
Author(s): Fred Y. Peng, Randall J. Weselake
Software Mentions: 2
Published: over 13 years ago

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

10.1093/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: almost 4 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: about 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: almost 5 years ago

10.1371/journal.pcbi.1002111

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

10.1038/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

10.1093/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

10.1093/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: almost 5 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: about 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

10.1093/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: almost 9 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

10.1186/1471-2105-15-336

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: about 10 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: almost 5 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

10.3390/cells8101281

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

10.1186/1471-2164-9-437

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: about 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

10.1038/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: almost 4 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: almost 12 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

10.3389/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

10.1038/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

10.1111/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: almost 4 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

10.1371/journal.pgen.1009309

Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder
Cited by: 11
Author(s): Kunling Huang, Yuchang Wu, Junha Shin, Yi Zheng, Alireza Fotuhi Siahpirani, Yunzhi Lin, Na Zheng, Jiawen Chen, Jianxin You, Sündüz Keleş, Daifeng Wang, Sushmita Roy, Qiongshi Lu
Software Mentions: 2
Published: almost 4 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: about 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

10.1038/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

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283