cran: JASPAR | Projects | Ecosyste.ms: Papers

10.1038/cddis.2017.426

Common microRNA–mRNA interactions exist among distinct porcine iPSC lines independent of their metastable pluripotent states
Cited by: 8
Author(s): Shiqiang Zhang, Youlong Xie, Hongxia Cao, Huayan Wang
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-44882-0

Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Cited by: 15
Author(s): Elo Madissoon, Anastasios Damdimopoulos, Shintaro Katayama, Kaarel Krjutškov, Elisabet Einarsdottir, Katariina Mamia, Bert De Groef, Outi Hovatta, Juha Kere, Pauliina Damdimopoulou
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0163128

Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers
Cited by: 8
Author(s): Amanda Field, Jie Xiang, W. Ray Anderson, Patricia L. Graham, Leslie Pick
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-31101-5

KLF6 and STAT3 co-occupy regulatory DNA and functionally synergize to promote axon growth in CNS neurons
Cited by: 33
Author(s): Zimei Wang, Vatsal Mehra, Matthew T. Simpson, Brian Maunze, Advaita Chakraborty, Lyndsey Holan, Erik Eastwood, Murray G. Blackmore, Ishwariya Venkatesh
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-06099-x

Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum
Cited by: 18
Author(s): Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka‐Spengler
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-03554-7

WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data
Cited by: 21
Author(s): Hongbo Zhang, Lin Zhu, De-Shuang Huang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-13186-6

Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori
Cited by: 13
Author(s): Quan Zhang, Tingcai Cheng, Shengkai Jin, Youbing Guo, Yuqian Wu, Duolian Liu, Xiaomin Xu, Yueting Sun, Zhiqing Li, Huawei He, Qingyou Xia
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0130413

A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes
Cited by: 11
Author(s): J. Watson Grice, Boris Noyvert, Laura Doglio, Greg Elgar
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-15221-y

Deconvolution of Transcriptional Networks in Post-Traumatic Stress Disorder Uncovers Master Regulators Driving Innate Immune System Function
Cited by: 12
Author(s): Abolfazl Doostparast Torshizi, Kai Wang
Software Mentions: 3
Published: about 7 years ago

10.1186/1755-8794-5-27

Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics
Cited by: 19
Author(s): Diego Díez, Susumu Goto, John V. Fahy, David J. Erle, Prescott G. Woodruff, Åsa M. Wheelock, Craig E. Wheelock
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0160228

Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach
Cited by: 5
Author(s): Rajneesh Srivastava, Yang Zhang, Xin Xiong, Xiaoning Zhang, Xiaoyan Pan, X. Charlie Dong, Suthat Liangpunsakul, Sarath Chandra Janga
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0148526

Tinman Regulates NetrinB in the Cardioblasts of the Drosophila Dorsal Vessel
Cited by: 6
Author(s): Jamshid Asadzadeh, Niamh Neligan, Sunita G. Kramer, Juan-Pablo Labrador
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0155099

Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids
Cited by: 13
Author(s): Sara L. Svahn, Leif Väremo, Britt G. Gabrielsson, Eduard Peris, Intawat Nookaew, Louise Grahnemo, Ann‐Sofie Sandberg, Ingrid Wernstedt Asterholm, John‐Olov Jansson, Jens Nielsen, Maria Johansson
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0215495

CiiiDER: A tool for predicting and analysing transcription factor binding sites
Cited by: 120
Author(s): Linden J. Gearing, Helen E. Cumming, R. A. Chapman, Alexander M. Finkel, Isaac Woodhouse, Kevin Luu, Jodee Gould, Samuel C. Forster, Paul J. Hertzog
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1004869

Host Transcriptional Response to Influenza and Other Acute Respiratory Viral Infections – A Prospective Cohort Study
Cited by: 108
Author(s): Yijie Zhai, Luis M. Franco, Robert L. Atmar, John Quarles, Nancy H. Arden, Kristine L. Bucasas, Janet Wells, Diane Niño, Xueqing Wang, Gladys Zapata, Chad A. Shaw, John W. Belmont, Robert B. Couch
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-83742-8

Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
Cited by: 2
Author(s): Hanze Guo, Chun‐Hua Yan, Naiyu Chi
Software Mentions: 3
Published: over 3 years ago

10.1186/s12284-017-0177-y

Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs
Cited by: 17
Author(s): Dongliang Yu, Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Huizhong Wang, Yijun Meng
Software Mentions: 3
Published: over 7 years ago

10.1038/s41419-021-03676-x

Cellular fate of intersex differentiation
Cited by: 7
Author(s): Xin Wang, Fengling Lai, Dantong Shang, Yang Cheng, Tian Lan, Hanhua Cheng, Rongjia Zhou
Software Mentions: 3
Published: over 3 years ago

10.26508/lsa.202000810

DGCR8 deficiency impairs macrophage growth and unleashes the interferon response to mycobacteria
Cited by: 0
Author(s): Barbara Killy, Barbara Bodendorfer, Jörg Mages, Kristina Ritter, Jonathan Schreiber, Christoph Hölscher, Katharina Pracht, Arif B. Ekici, Hans‐Martin Jäck, Roland Lang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0247402

DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis
Cited by: 0
Author(s): Davide Noto, Antonina Giammanco, Rossella Spina, Francesca Fayer, Angelo B. Cefalù, Maurizio Averna
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-9-561

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups
Cited by: 250
Author(s): Wen Chi Chang, Tzong-Yi Lee, Hsien Da Huang, His Yuan Huang, Rong Pan
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0183874

Sex-based differences in myocardial gene expression in recently deceased organ donors with no prior cardiovascular disease
Cited by: 37
Author(s): Kolsoum InanlooRahatloo, Grace Liang, Davis Vo, Antje Ebert, Ivy Nguyen, Patricia K. Nguyen
Software Mentions: 3
Published: about 7 years ago

10.1093/gigascience/gix136

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data
Cited by: 24
Author(s): Quan Nguyen, Ross L. Tellam, Marina Naval-Sánchez, Laércio R. Porto-Neto, W. Barendse, Antônio Reverter, Ben J. Hayes, James W. Kijas, Brian P. Dalrymple
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0013897

A Bayesian Search for Transcriptional Motifs
Cited by: 6
Author(s): Andrew Miller, Cristin G. Print, Poul M. F. Nielsen, Edmund J. Crampin
Software Mentions: 3
Published: about 14 years ago

10.1172/jci.insight.136477

Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs
Cited by: 10
Author(s): Xiaofeng Chen, Mingrui Guo, Yuanyuan Duan, Feng Jiang, Hao Wu, Shanshan Dong, Xiaorong Zhou, Hlaing Nwe Thynn, C.C. Liu, Lin Zhang, Yan Guo, Tie‐Lin Yang
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0155338

Composing a Tumor Specific Bacterial Promoter
Cited by: 7
Author(s): Igor V. Deyneko, Nadine Kasnitz, Sara Leschner, Siegfried Weiß
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-021-02323-0

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Cited by: 46
Author(s): Gareth Benjamin Gillard, Lars Grønvold, Line Lieblein Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, J. Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen Rød Sandve, Torgeir R. Hvidsten
Software Mentions: 3
Published: over 3 years ago

10.1093/gbe/evu210

Transcription Factors Bind Negatively Selected Sites within Human mtDNA Genes
Cited by: 46
Author(s): Amit Blumberg, Badi Sri Sailaja, Anshul Kundaje, Liron Levin, Sara Dadon, Shimrit Shmorak, Eitan Shaulian, Eran Meshorer, Dan Mo
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2105-12-365

Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns
Cited by: 2
Author(s): Jérémy Gruel, Michel LeBorgne, Nolwenn Le Meur, Nathalie Théret
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0167165

Effective Feature Selection for Classification of Promoter Sequences
Cited by: 5
Author(s): K. Kouser, P. G. Lavanya, Lalitha Rangarajan, K Acharya Kshitish
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0013876

Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors
Cited by: 9
Author(s): Adrian Schröder, Johannes Eichner, Jochen Supper, Jonas Eichner, Dierk Wanke, Carsten Henneges, Andreas Zell
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0024210

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles
Cited by: 21
Author(s): Yingtao Bi, Hyunsoo Kim, Ravi P. Gupta, Ramana V. Davuluri
Software Mentions: 3
Published: about 13 years ago

10.1016/j.jbc.2021.100456

Binding of Gtf2i-β/δ transcription factors to the ARMS2 gene leads to increased circulating HTRA1 in AMD patients and in vitro
Cited by: 6
Author(s): Yang Pan, Daisuke Iejima, Mao Nakayama, Akiko Suga, Tomoyuki Noda, Inderjeet Kaur, Taraprasad Das, Subhabrata Chakrabarti, Robyn H. Guymer, Margaret M. DeAngelis, Megumi Yamamoto, Paul N. Baird, Takeshi Iwata
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-13-50

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages
Cited by: 68
Author(s): Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R. Steffensen, Carsten Carlberg
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0079402

Linear Decay of Retrotransposon Antisense Bias across Genes Is Contingent upon Tissue Specificity
Cited by: 1
Author(s): Sara B. Linker, Dale J. Hedges
Software Mentions: 3
Published: about 11 years ago

10.1186/s13059-020-02164-3

Tissue-specific usage of transposable element-derived promoters in mouse development
Cited by: 48
Author(s): Benpeng Miao, Shuhua Fu, Cheng Lyu, Paul Gontarz, Ting Wang, Bo Zhang
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-020-01996-3

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study
Cited by: 37
Author(s): Giovanna Ambrosini, Ilya E. Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornés, Daria D. Nikolaeva, Benoît Ballester, Jan Grau, Ivo Große, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Philipp Bücher
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0079118

Discovering Transcription and Splicing Networks in Myelodysplastic Syndromes
Cited by: 11
Author(s): Hongyan Wang, Jianguo Wen, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: about 11 years ago

10.1186/s13059-020-02186-x

Cis-acting lnc-eRNA SEELA directly binds histone H4 to promote histone recognition and leukemia progression
Cited by: 17
Author(s): Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qianqian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang, Yue‐Qin Chen
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0169687

Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO)
Cited by: 59
Author(s): Allison Cox, Benjamin W. Darbro, Ronald M. Laxer, Gabriel Vélez, Xinyu Bing, Alexis L. Finer, Albert Erives, Vinit B. Mahajan, Alexander G. Bassuk, Polly J. Ferguson
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-10-388

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices
Cited by: 9
Author(s): Isabelle da Piedade, Man-Hung Eric Tang, Olivier Elemento
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12864-018-5241-5

The impact of genome evolution on the allotetraploid Nicotiana rustica – an intriguing story of enhanced alkaloid production
Cited by: 22
Author(s): Nicolas Sierro, James N. D. Battey, Lucien Bovet, Verena Liedschulte, Sonia Ouadi, JH Thomas, Hervé Broye, Hélène Laparra, Aline Vuarnoz, Gerhard K. Lang, Simon Goepfert, Manuel C. Peitsch, Nikolai V. Ivanov
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0153658

Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci
Cited by: 8
Author(s): Emmanuela Falcone, Luca Grandoni, Francesca Garibaldi, Isabella Manni, G. Filligoi, Giulia Piaggio, Aymone Gurtner
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-019-1847-4

RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants
Cited by: 43
Author(s): Hai Lin, Katherine A. Hargreaves, Rudong Li, Jill L. Reiter, Yue Wang, Matthew Mort, David Neil Cooper, Yaoqi Zhou, Chi Zhang, Michael T. Eadon, M. Eileen Dolan, Joseph Ipe, Todd C. Skaar, Yunlong Liu
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-016-1051-8

Novel regional age-associated DNA methylation changes within human common disease-associated loci
Cited by: 27
Author(s): Christopher G. Bell, Yudong Xia, Wei Yuan, Fei Gao, Kirsten Ward, Leonie Roos, Massimo Mangino, Pirro G. Hysi, Jordana T. Bell, Jun Wang, Timothy D. Spector
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0017286

Identification of Anchor Genes during Kidney Development Defines Ontological Relationships, Molecular Subcompartments and Regulatory Pathways
Cited by: 77
Author(s): Rathi D Thiagarajan, Kylie Georgas, Bree Rumballe, Emmanuelle Lesieur, Han Sheng Chiu, Darrin Taylor, Dave Tang, Sean M. Grimmond, Melissa H. Little
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0078032

Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population
Cited by: 16
Author(s): Sung Chun, Jevon Plunkett, Kari Teramo, Louis J. Muglia, Justin C. Fay
Software Mentions: 3
Published: about 11 years ago

10.1186/s13059-019-1642-2

Identification of transcription factor binding sites using ATAC-seq
Cited by: 284
Author(s): Li Z, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-019-1877-y

Chromatin interactome mapping at 139 independent breast cancer risk signals
Cited by: 22
Author(s): Jonathan Beesley, Haran Sivakumaran, Mahdi Moradi Marjaneh, Luize Gonçalves Lima, Kristine M. Hillman, Susanne Kaufmann, Natasha Tuano, Nehal Hussein, Sunyoung Ham, Pamela Mukhopadhyay, Stephen H. Kazakoff, Jason S. Lee, Kyriaki Michailidou, Daniel R. Barnes, Antonis C. Antoniou, Laura Fachal, Alison M. Dunning, Douglas F. Easton, Nicola Waddell, Joseph Rosenbluh, Andreas Möller, Georgia Chenevix-Trench, Juliet D. French, Stacey L. Edwards
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-020-02208-8

Evolution of regulatory networks associated with traits under selection in cichlids
Cited by: 14
Author(s): Tarang K. Mehta, Christopher Koch, William G. Nash, Sara Knaack, Padhmanand Sudhakar, Márton Ölbei, Sarah Bastkowski, Luca Penso-Dolfin, Wilfried Haerty, Sushmita Roy, Federica Di-Palma
Software Mentions: 3
Published: almost 4 years ago

10.7150/jca.60647

FOXD3-induced miR-133a blocks progression and metastasis of colorectal cancer through regulating UBA2
Cited by: 4
Author(s): Yuanfang Cheng, Yajuan Wang, Yuanzun Cheng, Qingmei Yang, Lejing Zhang, Zhaoxi Li, Jiancheng Cheng
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008645

The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes
Cited by: 9
Author(s): Charles S. Omura, Susan E. Lott
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-14-178

Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis
Cited by: 7
Author(s): Florent Baty, Jochen J. Rüdiger, Nicola Miglino, Lukas Kern, Pieter Borger, Martin Brutsche
Software Mentions: 3
Published: over 11 years ago

10.1186/gb-2013-14-7-r72

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design
Cited by: 18
Author(s): Robin P. Smith, Samantha J. Riesenfeld, Alisha K. Holloway, Qiang Li, Karl K. Murphy, Natalie M. Feliciano, Lorenzo Orecchia, Nir Oksenberg, Katherine S. Pollard, Nadav Ahituv
Software Mentions: 3
Published: almost 12 years ago

10.1186/s13059-014-0412-4

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets
Cited by: 55
Author(s): Rebecca Worsley Hunt, Wyeth W. Wasserman
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-15-331

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
Cited by: 40
Author(s): Suhn Kyong Rhie, Dennis J. Hazelett, Simon Coetzee, Chunli Yan, Houtan Noushmehr
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1004339

Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells
Cited by: 6
Author(s): Lihong Shi, Michael C. Sierant, Katherine Gurdziel, Fan Zhu, Shuaiying Cui, Katarzyna Ewa Kolodziej, John Strouboulis, Yuanfang Guan, Osamu Takahashi, Kim Chew Lim, James Douglas Engel
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1007755

Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus
Cited by: 30
Author(s): Vivek Nanda, Ting Wang, Milos Pjanic, Boxiang Liu, Trieu Nguyen, Ljubica Matic, Ulf Hedin, Simon Koplev, Lijiang Ma, Oscar Franzén, Arno Ruusalepp, Eric E. Schadt, Johan Björkegren, Stephen B. Montgomery, M Snyder, Thomas Quertermous, Nicholas J. Leeper, Clint L. Miller
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-017-1680-2

CircularLogo: A lightweight web application to visualize intra-motif dependencies
Cited by: 5
Author(s): Zhenqing Ye, Tao Ma, Michael Kalmbach, Surendra Dasari, Jean Pierre A. Kocher, Liguo Wang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1009681

Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage
Cited by: 9
Author(s): Neta Degani, Yoav Lubelsky, Rotem Ben-Tov Perry, Elena Ainbinder, Igor Ulitsky
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009090

A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer
Cited by: 2
Author(s): Anaïs Assouvie, Maxime Rotival, Juliette Hamroune, Didier Busso, Paul-Henri Roméo, Lluís Quintana‐Murci, Germain Rousselet
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1002688

YY1 Regulates Melanocyte Development and Function by Cooperating with MITF
Cited by: 42
Author(s): Juying Li, Jun S. Song, Robert J.A. Bell, Thanh Nga Tran, Rizwan Haq, Huifei Liu, Kevin T. Love, Robert Langer, Daniel G. Anderson, Lionel Larue, David E. Fisher
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.0010016

Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Cited by: 194
Author(s): Panin Le, Joshua R. Friedman, Jonathan Schug, John Brestelli, J. Brandon Parker, Irina M. Bochkis, Klaus H. Kaestner
Software Mentions: 3
Published: over 19 years ago

10.1186/gb-2007-8-5-r84

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome
Cited by: 31
Author(s): Shaun Mahony, David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos
Software Mentions: 3
Published: almost 18 years ago

10.3389/fonc.2019.01340

The TGFβ-Induced Long Non-coding RNA TBULC Promotes the Invasion and Migration of Non-small Cell Lung Cancer Cells and Indicates Poor Prognosis
Cited by: 4
Author(s): Sufei Zheng, Zhiliang Lu, Chengming Liu, Xinfeng Wang, Runsen Jin, Shuangshuang Mao, Jianbing Huang, Yuanyuan Lei, Chaoqi Zhang, Nan Sun, Jie He
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1006224

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters
Cited by: 16
Author(s): Christopher A. Lavender, Kimberly R. Cannady, Jackson A. Hoffman, Kevin W. Trotter, Daniel A. Gilchrist, Brian D. Bennett, Adam Burkholder, Craig J. Burd, David C. Fargo, Trevor Archer
Software Mentions: 3
Published: over 8 years ago

10.3389/fphys.2021.711645

In silico Characterization of the Heme Oxygenase 1 From Bottlenose Dolphin (Tursiops truncatus): Evidence of Changes in the Active Site and Purifying Selection
Cited by: 2
Author(s): Carlos A. Reyes-Ramos, Ramón Gaxiola-Robles, José Pablo Vázquez‐Medina, Luis Javier Ramírez-Jirano, Oscar Kurt Bitzer-Quintero, Tania Zenteno‐Savín
Software Mentions: 3
Published: over 3 years ago

10.1002/cam4.2468

Comprehensive analysis of five long noncoding RNAs expression as competing endogenous RNAs in regulating hepatoma carcinoma
Cited by: 13
Author(s): Xin Lou, Jun Li, Yu Dong, Yaqing Wei, Feng Shan, Jinjin Sun
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1008659

A putative silencer variant in a spontaneous canine model of retinitis pigmentosa
Cited by: 9
Author(s): Maria Kaukonen, Ileana B. Quintero, Abdul Kadir Mukarram, Marjo K. Hytönen, Saila Holopainen, Kaisa Wickström, Kaisa Kyöstilä, Meharji Arumilli, Sari Jalomäki, Carsten O. Daub, Juha Kere, Hannes Lohi
Software Mentions: 3
Published: over 4 years ago

10.1186/gb-2009-10-4-r38

Transcriptional features of genomic regulatory blocks
Cited by: 100
Author(s): Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O. Daub, Yoshihide Hayashizaki, Boris Lenhard
Software Mentions: 3
Published: almost 16 years ago

10.3389/fgene.2016.00024

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells
Cited by: 98
Author(s): Valentina Boeva
Software Mentions: 3
Published: over 8 years ago

10.3389/fimmu.2021.636289

Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing
Cited by: 7
Author(s): Daniel J. B. Clarke, Alison W. Rebman, Allison Bailey, Megan L. Wojciechowicz, Sherry L. Jenkins, John Erol Evangelista, Matteo Danieletto, Jinshui Fan, Mark W. Eshoo, Michael R. Mosel, William H. Robinson, Nitya S. Ramadoss, Jason Bobe, Mark J. Soloski, Avi Ma’ayan
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1003214

The Next Generation of Transcription Factor Binding Site Prediction
Cited by: 159
Author(s): Anthony Mathelier, Wyeth W. Wasserman
Software Mentions: 3
Published: about 11 years ago

10.3389/fcell.2021.633035

Co-treatment With Everolimus, an mTOR-Specific Antagonist, or Downregulation of ELK1 Enhances the Sensitivity of Pancreatic Cancer Cells to Genistein
Cited by: 1
Author(s): Tianyu Li, Tiantao Kuang, Zhao-Shuo Yang, Qiqi Zhang, Wen Zhang, Yue Fan
Software Mentions: 3
Published: about 3 years ago

10.3390/ph12040156

C3orf70 Is Involved in Neural and Neurobehavioral Development
Cited by: 8
Author(s): Yoshifumi Ashikawa, Takashi Shiromizu, Koki Miura, Yoshiyuki Adachi, Takaaki Matsui, Yasumasa Bessho, Toshio Tanaka, Yuhei Nishimura
Software Mentions: 3
Published: about 5 years ago

10.1002/wsbm.1467

Functional genomic approaches to elucidate the role of enhancers during development
Cited by: 13
Author(s): Genevieve E. Ryan, Emma K. Farley
Software Mentions: 3
Published: almost 5 years ago

10.3390/pathogens10091127

Delineating the Role of Aedes aegypti ABC Transporter Gene Family during Mosquito Development and Arboviral Infection via Transcriptome Analyses
Cited by: 8
Author(s): Vijoy Kumar, Shilpi Garg, Lalita Gupta, Kuldeep Gupta, Cheikh Tidiane Diagne, Dorothée Missé, Julien Pompon, Sanjeev Kumar, Vishal Saxena
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2105-8-385

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm
Cited by: 94
Author(s): Emma Redhead, Timothy L. Bailey
Software Mentions: 3
Published: about 17 years ago

10.12688/f1000research.16200.2

Predicting transcription factor binding using ensemble random forest models
Cited by: 7
Author(s): Fatemeh Behjati Ardakani, Florian Schmidt, Marcel H. Schulz
Software Mentions: 3
Published: about 5 years ago

10.1016/j.omtn.2021.03.001

lncRNA LOC102724169 plus cisplatin exhibit the synergistic anti-tumor effect in ovarian cancer with chronic stress
Cited by: 6
Author(s): Xiaofang Zhou, Mu Liu, Guanming Deng, Le Chen, Lijuan Sun, Yun Zhang, Chenhui Luo, Jie Tang
Software Mentions: 3
Published: over 3 years ago

10.3389/fbioe.2019.00427

A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
Cited by: 1
Author(s): Liu Hui, Tiantongfei Jiang, Shuyuan Wang, Xiang Chen, Xiaoyan Jin, Qi Wang, Xinhui Li, Jiaqi Yin, Tingting Shao, Yongsheng Li, Juan Xu, Qiong Wu
Software Mentions: 3
Published: almost 5 years ago

10.1186/bcr3587

Progesterone receptor assembly of a transcriptional complex along with activator protein 1, signal transducer and activator of transcription 3 and ErbB-2 governs breast cancer growth and predicts response to endocrine therapy
Cited by: 30
Author(s): María Celeste Díaz Flaqué, Natalia M. Galigniana, Wendy Béguelin, Rocío Vicario, Cecilia J. Proietti, Rosalía Cordo Russo, Martín A. Rivas, Mercedes Tkach, Pablo Guzmán, Juan Carlos Roa, Esteban Maronna, Viviana Pineda, Sergio Muñoz, María F. Mercogliano, Eduardo H. Charreau, Patricio Yankilevich, Roxana Schillaci, Patricia V. Elizalde
Software Mentions: 3
Published: almost 11 years ago

10.1016/j.mce.2020.111007

Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107
Cited by: 11
Author(s): Nan Yang, Andrew Berry, Carolin M Sauer, Matthew Baxter, Ian J. Donaldson, Karen Forbes, Rachelle Donn, Laura Matthews, David Ray
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-14-337

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver
Cited by: 48
Author(s): Logan J. Everett, John Le Lay, Sabina Lukovac, Diana Bernstein, David J. Steger, Mitchell A. Lazar, Klaus H. Kaestner
Software Mentions: 3
Published: over 11 years ago

10.15252/emmm.202012104

Chromatin accessibility landscape of pediatric T‐lymphoblastic leukemia and human T‐cell precursors
Cited by: 10
Author(s): Büşra Erarslan-Uysal, Joachim Kunz, Tobias Rausch, Paulina Richter-Pechańska, Ianthe Aem van Belzen, Viktoras Frismantas, Beat Bornhäuser, Diana Ordoñez-Rueada, Malte Paulsen, Vladimı́r Beneš, Martin Stanulla, Martin Schrappe, Gunnar Cario, Gabriele Escherich, Kseniya Bakharevich, Renate Kirschner-Schwabe, Cornelia Eckert, Tsvetomir Loukanov, Matthias Gorenflo, Sebastian M. Waszak, Jean‐Pierre Bourquin, Martina U. Muckenthaler, Jan O. Korbel, Andreas E. Kulozik
Software Mentions: 3
Published: over 4 years ago

10.1186/s13072-015-0028-2

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates
Cited by: 16
Author(s): Parameswaran Ramachandran, Gareth Palidwor, Theodore J. Perkins
Software Mentions: 3
Published: about 9 years ago

10.1002/1878-0261.12683

Long noncoding RNA SNHG12 induces proliferation, migration, epithelial–mesenchymal transition, and stemness of esophageal squamous cell carcinoma cells via post‐transcriptional regulation of BMI1 and CTNNB1
Cited by: 29
Author(s): Duoguang Wu, Xiaotian He, Wenjian Wang, Xueqiang Hu, Kefeng Wang, Minghui Wang
Software Mentions: 3
Published: over 4 years ago

10.3390/v13040544

Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis
Cited by: 4
Author(s): Liana V. Basova, Alexander Lindsey, Anne Marie McGovern, Ronald J. Ellis, Maria Cecília Garibaldi Marcondes
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-8-189

MATLIGN: a motif clustering, comparison and matching tool
Cited by: 24
Author(s): Matti Kankainen, Ari Löytynoja
Software Mentions: 3
Published: over 17 years ago

10.1186/s12864-018-5408-0

Probing transcription factor combinatorics in different promoter classes and in enhancers
Cited by: 24
Author(s): Jimmy Vandel, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, Laurent Bréhélin
Software Mentions: 3
Published: almost 6 years ago

10.1186/1756-8935-7-33

Chromatin accessibility: a window into the genome
Cited by: 306
Author(s): Maria Tsompana, Michael Buck
Software Mentions: 3
Published: about 10 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

10.1042/BSR20200487

The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1
Cited by: 21
Author(s): Juntong Wang, Jingshun Gu, Aiwu You, Jun Li, Yuyan Zhang, Guomin Rao, Xuehua Ge, Kun Zhang, Jianfeng Li, Xiaohui Lu, Qianchao Wang, Tzu Chen Lin, Ling Cheng, Meiying Zhu, Xiaotang Wu, Dongchun Wang
Software Mentions: 2
Published: over 4 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

10.1038/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

10.1186/1471-2105-14-9

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis
Cited by: 27
Author(s): Kjetil Klepper, Finn Drabløs
Software Mentions: 2
Published: almost 12 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

10.1093/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

10.1186/s12864-016-3163-7

Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron
Cited by: 31
Author(s): William J Gammerdinger, Matthew A. Conte, Jean‐François Baroiller, Hélèna D'Cotta, Thomas D. Kocher
Software Mentions: 2
Published: about 8 years ago

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283