cran: JASPAR | Projects | Ecosyste.ms: Papers

10.3390/cancers12082261

MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer
Cited by: 12
Author(s): Alessandra Cataldo, Sandra Romero-Córdoba, Ilaria Plantamura, Giulia Cosentino, Alfredo Hidalgo‐Miranda, Elda Tagliabue, Marilena V. Iorio
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-019-1721-4

Chromatin accessibility plays a key role in selective targeting of Hox proteins
Cited by: 35
Author(s): Damiano Porcelli, Bettina Fischer, Steven Russell, Robert A. White
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-018-4564-6

Characterization of the human RFX transcription factor family by regulatory and target gene analysis
Cited by: 57
Author(s): Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Santosh Misra, Carsten O. Daub, Juha Kere, Peter Swoboda
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-15-1047

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets
Cited by: 13
Author(s): Meng Niu, Ehsan Tabari, Zhengchang Su
Software Mentions: 4
Published: about 10 years ago

10.1534/g3.119.400294

Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits
Cited by: 18
Author(s): Maren E. Cannon, Kevin W. Currin, Kristin L. Young, Hannah J. Perrin, Swarooparani Vadlamudi, Alexias Safi, Lingyun Song, Ying Wu, Martin Wabitsch, Markku Laakso, Gregory E. Crawford, Karen L. Mohlke
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006636

TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Cited by: 69
Author(s): Hannah Seberg, Eric Van Otterloo, Stacie K. Loftus, Huan Liu, Greg Bonde, Ramakrishna Sompallae, Derek Gildea, Juan Francisco de Paz Santana, J. Robert Manak, William J. Pavan, Trevor Williams, Robert A. Cornell
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pgen.1006778

Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
Cited by: 11
Author(s): Adi Hendler, Edgar M. Medina, Anastasiya Kishkevich, Mehtap Abu-Qarn, Steffi Klier, Nicolas E. Buchler, Robertus A.M. de Bruin, Amir Aharoni
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-15-910

Transcriptomic portrait of human Mesenchymal Stromal/Stem cells isolated from bone marrow and placenta
Cited by: 50
Author(s): Beatriz Rosón-Burgo, Fermín Sánchez‐Guijo, Consuelo del Cañizo, Javier De Las Rivas
Software Mentions: 4
Published: about 10 years ago

10.18632/aging.203030

Downregulation of USP18 reduces tumor-infiltrating activated dendritic cells in extranodal diffuse large B cell lymphoma patients
Cited by: 5
Author(s): Chong Zhao, Runzhi Huang, Zhiwei Zeng, Siqi Yang, Wei Lü, Jiali Liu, Yanyu Wei, Hong Guo, Yanjie Zhang, Penghui Yan, Zongqiang Huang, Jun Shi
Software Mentions: 4
Published: over 3 years ago

10.1186/gb-2012-13-10-r88

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Cited by: 72
Author(s): Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo
Software Mentions: 4
Published: almost 13 years ago

10.1186/1471-2164-8-265

Inference of transcriptional regulation using gene expression data from the bovine and human genomes
Cited by: 8
Author(s): Amonida Zadissa, John C. McEwan, Chris M. Brown
Software Mentions: 4
Published: over 17 years ago

10.1186/s12864-016-2729-8

A systematic, large-scale comparison of transcription factor binding site models
Cited by: 13
Author(s): Daniela Hombach, Jana Marie Schwarz, Peter N. Robinson, Markus Schuelke, Dominik Seelow
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2020.01228

Targeting Nuclear LSD1 to Reprogram Cancer Cells and Reinvigorate Exhausted T Cells via a Novel LSD1-EOMES Switch
Cited by: 30
Author(s): Wen Juan Tu, Robert McCuaig, Abel Tan, Kristine Hardy, Nabila Seddiki, Sayed Ali, Jane E. Dahlstrom, Elaine Bean, Jenny C. Dunn, Jade K. Forwood, S. Tsimbalyuk, Kate Smith, Desmond Yip, Laeeq Malik, Thiru Prasanna, Peter J. Milburn, Sudha Rao
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2019.01253

Signal Integration of IFN-I and IFN-II With TLR4 Involves Sequential Recruitment of STAT1-Complexes and NFκB to Enhance Pro-inflammatory Transcription
Cited by: 32
Author(s): Anna Piaszyk-Borychowska, Lajos Széles, Attila Csermely, Hsüch‐Ching Chiang, Joanna Wesoły, Chien‐Kuo Lee, László Nagy, Hans A.R. Bluyssen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009229

3D genome evolution and reorganization in the Drosophila melanogaster species group
Cited by: 24
Author(s): Nicole S. Torosin, Aparna Anand, Tirupathi Rao Golla, Weihuan Cao, Chris Ellison
Software Mentions: 4
Published: almost 4 years ago

10.3389/fnins.2021.671249

Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury
Cited by: 7
Author(s): Victor Gourain, Olivier Armant, Luisa Lübke, Nicolas Diotel, Sepand Rastegar, Uwe Strähle
Software Mentions: 4
Published: over 3 years ago

10.1111/acer.14259

Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46
Cited by: 4
Author(s): Nicole A.R. Walter, Christina Zheng, Robert P. Searles, Shannon K. McWeeney, Kathleen A. Grant, Robert Hitzemann
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2021.667013

The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses
Cited by: 11
Author(s): José Ribamar Costa Ferreira‐Neto, Artemisa Nazaré da Costa Borges, Manassés Daniel da Silva, David Anderson de Lima Morais, João Pacífico Bezerra-Neto, Guillaume Bourque, Éderson Akio Kido, Ana Maria Benko‐Iseppon
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2019.01214

Weighted Gene Co-Expression Network Analysis Identifies Critical Genes in the Development of Heart Failure After Acute Myocardial Infarction
Cited by: 59
Author(s): Xiaowei Niu, Jingjing Zhang, Lanlan Zhang, Yufei Hou, Shuangshuang Pu, Ai-Ai Chu, Ming Bai, Zheng Zhang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1002789

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
Cited by: 125
Author(s): Yoichiro Shibata, Nathan C. Sheffield, Olivier Fédrigo, Courtney C. Babbitt, Matthew Wortham, Alok K. Tewari, Darin London, Lingyun Song, Bum Kyu Lee, Vishwanath R. Iyer, Stephen C. J. Parker, Elliott H. Margulies, Gregory A. Wray, Terrence S. Furey, Gregory E. Crawford
Software Mentions: 4
Published: over 12 years ago

10.3389/fgene.2015.00331

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
Cited by: 12
Author(s): Marina Lizio, Yuri Ishizu, Masayoshi Itoh, Timo Lassmann, Akira Hasegawa, Atsutaka Kubosaki, Jessica Severin, Hideya Kawaji, Yukio Nakamura, Harukazu Suzuki, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
Software Mentions: 4
Published: about 9 years ago

10.1186/1741-7015-11-163

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
Cited by: 56
Author(s): Adam E. Handel, Geir Kjetil Sandve, Giulio Disanto, Antonio J. Berlanga‐Taylor, Giuseppe Gallone, Heather Hanwell, Finn Drabløs, Gavin Giovannoni, George C. Ebers, Sreeram Ramagopalan
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pcbi.1006090

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
Cited by: 12
Author(s): Sneha Mitra, Anushua Biswas, Leelavati Narlikar
Software Mentions: 4
Published: over 6 years ago

10.1186/s12915-021-01009-0

Multi-omic profiling of pituitary thyrotropic cells and progenitors
Cited by: 4
Author(s): Alexandre Z. Daly, L Dudley, Michael T. Peel, Stephen A. Liebhaber, Stephen C. J. Parker, Sally A. Camper
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22157810

Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis
Cited by: 4
Author(s): Shital Kumar Mishra, Taole Liu, Han Wang
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-6-68

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals
Cited by: 45
Author(s): Sven Nelander, Erik Larsson, Erik Kristiansson, Robert Månsson, Olle Nerman, Mikael Sigvardsson, Petter Mostad, Per Lindahl
Software Mentions: 4
Published: over 19 years ago

10.1186/1471-2164-16-S7-S13

MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures
Cited by: 6
Author(s): Yizhe Zhang, Yiping He, Guangyong Zheng, Chaochun Wei
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-11-365

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Cited by: 39
Author(s): Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn, Ole Kiehn
Software Mentions: 4
Published: almost 15 years ago

10.1186/1471-2164-12-110

Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1
Cited by: 16
Author(s): Zen H. Lu, Alex di Domenico, Steven H. Wright, Pamela Knight, Bruce Whitelaw, Alan D. Pemberton
Software Mentions: 4
Published: almost 14 years ago

10.1080/15592294.2016.1182272

Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio)
Cited by: 138
Author(s): Lauren V. Laing, Joana Viana, Emma Dempster, Maciej Trznadel, L. A. Trunkfield, Tamsyn M. Uren Webster, Ronny van Aerle, Gregory C. Paull, Robert J. Wilson, Jonathan Mill, Eduarda M. Santos
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-015-0846-z

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features
Cited by: 28
Author(s): Sunil Kumar, Philipp Bücher
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijms20143425

Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network
Cited by: 17
Author(s): Lan Gongqiang, Jiyun Zhou, Ruifeng Xu, Qin Lu, Hongpeng Wang
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.67312

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation
Cited by: 43
Author(s): Lizhi He, Henry E. Pratt, Mingshi Gao, Fengxiang Wei, Zhiping Weng, Kevin Struhl
Software Mentions: 4
Published: over 3 years ago

10.7150/thno.47830

LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network
Cited by: 68
Author(s): Yin Zhang, Yong-Xin Huang, Dan-Lan Wang, Bing Yang, Haiyan Yan, Lehang Lin, Yun Li, Jie Chen, Lisha Xie, Yongsheng Huang, Jian-You Liao, Kaishun Hu, Jun He, Phei Er Saw, Xiaoding Xu, Yin Ding
Software Mentions: 4
Published: almost 5 years ago

10.1002/1878-0261.12982

CDX2 expression in the hematopoietic lineage promotes leukemogenesis via TGFβ inhibition
Cited by: 6
Author(s): Anne Galland, Victor Gourain, Karima Habbas, Yonca Güler, Elisabeth Martin, Claudine Ebel, Manuela Tavian, Laurent Vallat, Marie‐Pierre Chenard, Laurent Mauvieux, Jean–Noël Freund, Isabelle Duluc, Claire Domon‐Dell
Software Mentions: 4
Published: over 3 years ago

10.1186/s13029-015-0040-8

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence
Cited by: 3
Author(s): Connor H. Fortin, Katharina Schulze, Gregory A. Babbitt
Software Mentions: 4
Published: about 9 years ago

10.1186/s13046-021-02122-2

Mutant NPM1-regulated lncRNA HOTAIRM1 promotes leukemia cell autophagy and proliferation by targeting EGR1 and ULK3
Cited by: 19
Author(s): Yipei Jing, Xueke Jiang, Lei Li, Meixi Peng, Jun Ren, Qiaoling Xiao, Tao Yao, Yonghong Tao, Junpeng Huang, Lu Wang, Yuting Tang, Zailin Yang, Yang Zhou, Ling Zhang
Software Mentions: 4
Published: about 3 years ago

10.1038/s41419-019-2040-0

Severe head dysgenesis resulting from imbalance between anterior and posterior ontogenetic programs
Cited by: 2
Author(s): Emmanuelle Grall, Victor Gourain, Asmaa Naïr, Elisabeth Martin, Marie‐Christine Birling, Jean–Noël Freund, Isabelle Duluc
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-70368-5

Transcriptomic analysis delineates potential signature genes and miRNAs associated with the pathogenesis of asthma
Cited by: 16
Author(s): Prithvi Singh, Archana Sharma, Jha R, Shweta Arora, Rafiq Ahmad, Arshad Husain Rahmani, Saleh A. Almatroodi, Ravins Dohare, Mansoor Ali Syed
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-79740-x

Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer’s Disease
Cited by: 12
Author(s): Travis Johnson, Shunian Xiang, Tianhan Dong, Zhi Huang, Michael Cheng, Tianfu Wang, Kai Yang, Dong Ni, Kun Huang, Jie Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1093/molbev/msab197

Functional Characterization of the Cnidarian Antiviral Immune Response Reveals Ancestral Complexity
Cited by: 13
Author(s): Magda Lewandowska, Ton Sharoni, Yael Admoni, Reuven Aharoni, Yehu Moran
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers13020208

Interferon Regulatory Factor 9 Promotes Lung Cancer Progression via Regulation of Versican
Cited by: 11
Author(s): David Brunn, Kati Turkowski, Stefan Günther, Andreas Weigert, Thomas Muley, Mark Kriegsmann, Hauke Winter, Reinhard Dammann, Georgios T. Stathopoulos, Michael Thomas, Andreas Güenther, Friedrich Grimminger, Soni Savai Pullamsetti, Werner Seeger, Rajkumar Savai
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-23207-7

Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation
Cited by: 10
Author(s): Leila Taher, Julia Beck, Wen Li, Catrin Roolf, Jan T. Soller, Barbara C. Rütgen, Sabine E. Hammer, Murali Chodisetti, Sina Sender, Katharina A Sterenczak, Georg Fuellen, Christian Junghanß, Bertram Brenig, Ingo Nolte, Ekkehard Schütz, Hugo Murua Escobar
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-25302-1

Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells
Cited by: 8
Author(s): Shuzo Teruya, Tomohisa Okamura, Takashi Komai, Mariko Inoue, Yukiko Iwasaki, Shuji Sumitomo, Hirofumi Shoda, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 4
Published: over 6 years ago

10.1038/sdata.2018.141

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations
Cited by: 12
Author(s): Oriol Fornés, Marius Gheorghe, Phillip A. Richmond, David J. Arenillas, Wyeth W. Wasserman, Anthony Mathelier
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0045708

Cooperativity of Stress-Responsive Transcription Factors in Core Hypoxia-Inducible Factor Binding Regions
Cited by: 32
Author(s): Diego Villar, Amaya Ortiz-Barahona, Laura Gómez-Maldonado, Nuria Pescador, Fátima Sánchez-Cabo, Hubert Hackl, Blanca Rodriguez, Zlatko Trajanoski, Ana Dopazo, Tim Hui-Ming Huang, Pearlly S. Yan, Luis del Peso
Software Mentions: 4
Published: about 12 years ago

10.1186/s12935-020-01632-x

Targeting Lymphotoxin Beta and Paired Box 5: a potential therapeutic strategy for soft tissue sarcoma metastasis
Cited by: 0
Author(s): Runzhi Huang, Zhiwei Zeng, Penghui Yan, Huabin Yin, Xiaolong Zhu, Peng Hu, Juanwei Zhuang, Jiaju Li, Siqi Li, Dianwen Song, Tong Meng, Zongqiang Huang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-020-07257-8

Intricate genetic variation networks control the adventitious root growth angle in apple
Cited by: 5
Author(s): Caixia Zheng, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang, Zhenhai Han
Software Mentions: 4
Published: about 4 years ago

10.1186/gm122

Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia
Cited by: 105
Author(s): Nathan Stephens, Iain J. Gallagher, Olav Rooyackers, Richard J.E. Skipworth, Ben Tan, Troels Marstrand, James A. Ross, Denis C. Guttridge, Lars Lundell, Kenneth C. H. Fearon, James A. Timmons
Software Mentions: 4
Published: almost 15 years ago

10.1093/jxb/eru119

Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences
Cited by: 81
Author(s): Salma Balazadeh, Jörg Schildhauer, Wagner L. Araújo, Sergi Munné‐Bosch, Alisdair R. Fernie, Sebastian Proost, Klaus Humbeck, Bernd Mueller‐Roeber
Software Mentions: 4
Published: over 10 years ago

10.1093/bioinformatics/btv470

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites
Cited by: 179
Author(s): Simon Coetzee, Gerhard A. Coetzee, Dennis J. Hazelett
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0221760

Population size estimation for quality control of ChIP-Seq datasets
Cited by: 4
Author(s): Semyon Kolmykov, Yury V. Kondrakhin, Ivan S. Yevshin, Ruslan N. Sharipov, Anna S. Ryabova, Fedor A. Kolpakov
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-019-2732-6

The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation
Cited by: 4
Author(s): Yance Feng, Sheng Zhang, Liang Li, Lei M. Li
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0255971

TCF21 regulates miR-10a-5p/LIN28B signaling to block the proliferation and invasion of melanoma cells
Cited by: 5
Author(s): Hongxia Zhu, Mengshi Kang, Xinping Bai
Software Mentions: 4
Published: over 3 years ago

10.1016/j.redox.2019.101321

Cannabidiol induces antioxidant pathways in keratinocytes by targeting BACH1
Cited by: 94
Author(s): Laura Casares, Víctor García, Martín Garrido‐Rodriguez, Estrella Millán, Juan A. Collado, Adela García‐Martín, Jon Peñarando, Marco A. Calzado, Laureano de la Vega, Eduardo Muñóz
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-43881-5

Comprehensive and Systematic Analysis of Gene Expression Patterns Associated with Body Mass Index
Cited by: 13
Author(s): Paule V. Joseph, Rosario B. Jaime-Lara, Yupeng Wang, Lichen Xiang, Wendy A. Henderson
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-349

NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data
Cited by: 3
Author(s): Nak-Kyeong Kim, Rasika V Jayatillake, John L. Spouge
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-6-79

Cited by: 189
Author(s): Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva
Software Mentions: 4
Published: almost 20 years ago

10.1186/1752-0509-3-93

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
Cited by: 11
Author(s): Pierre R. Bushel, Nicholas A. Heard, Roee Gutman, Liwen Liu, Shyamal D. Peddada, Saumyadipta Pyne
Software Mentions: 4
Published: about 15 years ago

10.1186/s12864-018-4800-0

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits
Cited by: 20
Author(s): Min Wang, Tim Hancock, Amanda J. Chamberlain, Christy J. Vander Jagt, J.E. Pryce, Benjamin G. Cocks, Michael E. Goddard, Ben J. Hayes
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0158936

LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome
Cited by: 91
Author(s): Alaguraj Veluchamy, Teddy Jégu, Federico Ariel, David Latrasse, Kadarkaraisamy Mariappan, Soon-Kap Kim, Martín Crespi, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-017-4086-7

The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
Cited by: 59
Author(s): Victoria A. Ingham, Patricia Pignatelli, Jonathan D. Moore, Simon C. Wagstaff, Hilary Ranson
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-015-0811-x

Sequence information gain based motif analysis
Cited by: 1
Author(s): Joan Maynou, Erola Pairó, S. Marco, Alexandre Perera
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0143627

Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells
Cited by: 17
Author(s): Elena Grassi, Ettore Zapparoli, Ivan Molineris, Paolo Provero
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0041374

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Cited by: 121
Author(s): Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0029021

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells
Cited by: 72
Author(s): Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antònia Navarro, Diana Monsivais, John S. Coon, Julie Kim, Yang Dai, Serdar E. Bulun
Software Mentions: 4
Published: almost 13 years ago

10.1186/s13059-014-0534-8

Prioritizing causal disease genes using unbiased genomic features
Cited by: 39
Author(s): Rahul C. Deo, Gabriel Musso, Murat Taşan, Paul Ling-Fung Tang, Annie Poon, Christiana Yuan, Janine F. Felix, Ramachandran S. Vasan, Rameen Beroukhim, Teresa De Marco, Pui‐Yan Kwok, Calum A. MacRae, Frederick P. Roth
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0236771

Transcriptome analysis of sevoflurane exposure effects at the different brain regions
Cited by: 6
Author(s): Hiroto Yamamoto, Yasuzo Uchida, Tomoki Chiba, Ryota Kurimoto, Taijiro Matsushima, Maiko Inotsume, Chihiro Ishikawa, Haiyan Li, Takashi Shiga, Masafumi Muratani, Tatsuo Uchida, Hiroshi Asahara
Software Mentions: 4
Published: almost 4 years ago

10.1186/gb-2014-15-3-r52

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis
Cited by: 120
Author(s): Hai Wu, Troy W. Whitfield, Jonathan A. R. Gordon, Jason R. Dobson, Phillip W. L. Tai, André J. van Wijnen, Janet L. Stein, Jane B. Lian
Software Mentions: 4
Published: almost 11 years ago

10.3389/fcell.2021.568660

Transcriptional Repression of MFG-E8 Causes Disturbance in the Homeostasis of Cell Cycle Through DOCK/ZP4/STAT Signaling in Buffalo Mammary Epithelial Cells
Cited by: 5
Author(s): Arvind Verma, Syed Azmal Ali, Parul Singh, Sanjay Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-14-72

Identification of germ cell-specific genes in mammalian meiotic prophase
Cited by: 12
Author(s): Yunfei Li, Debjit Ray, Ping Ye
Software Mentions: 3
Published: almost 12 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/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

10.1371/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/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

10.1371/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

10.3389/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

10.1371/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

10.1186/1471-2105-14-128

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Cited by: 4,562
Author(s): Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma’ayan
Software Mentions: 3
Published: over 11 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

10.3389/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

10.1186/1471-2164-9-561

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: about 16 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.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

10.1186/1471-2105-10-S1-S13

DNA motif alignment by evolving a population of Markov chains
Cited by: 6
Author(s): Chengpeng Bi
Software Mentions: 3
Published: almost 16 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

10.3389/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: over 3 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

10.12688/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: over 5 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

10.1371/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

10.3389/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: almost 9 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

10.1093/database/bav007

PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples
Cited by: 3
Author(s): Yiyu Zheng, Xiaoman Li, Haiyan Hu
Software Mentions: 3
Published: almost 10 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

10.3390/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

10.3390/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

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283