cran: JASPAR | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009403

Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron pest, Spodoptera exigua
Cited by: 42
Author(s): Bo Hu, He Huang, Songzhu Hu, Miaomiao Ren, Wei Qi, Xiangrui Tian, Mohammed Esmail Abdalla Elzaki, Chris Bass, Jianya Su, Subba Reddy Palli
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1004200

Lsd1 Restricts the Number of Germline Stem Cells by Regulating Multiple Targets in Escort Cells
Cited by: 57
Author(s): Susan Eliazer, Víctor Palacios, Zhaohui Wang, Rahul K. Kollipara, Ralf Kittler, Michael Buszczak
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1003252

Antagonism Versus Cooperativity with TALE Cofactors at the Base of the Functional Diversification of Hox Protein Function
Cited by: 28
Author(s): María Luisa Rivas, José Manuel Espinosa-Vázquez, Nagraj Sambrani, Stephen Greig, Samir Merabet, Yacine Graba, James Castelli-Gair Hombría
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pgen.1007137

Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element
Cited by: 12
Author(s): Jessica Zuin, Valentina Casà, Jelena Pozojevic, Petros Kolovos, Mirjam C G N van den Hout, Wilfred F. J. van IJcken, Ilaria Parenti, Diana Braunholz, Yorann Baron, Erwan Watrin, Frank J. Kaiser, Kerstin S. Wendt
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pgen.1005368

RFX2 Is a Major Transcriptional Regulator of Spermiogenesis
Cited by: 55
Author(s): W S Kistler, Dominique Baas, Sylvain Lemeille, Marie Paschaki, Queralt Seguín-Estévez, Emmanuèle Barras, Wei Ma, Jean-Luc Duteyrat, Laurette Morlé, Bénédicte Durand, Walter Reith
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1004981

Eye Selector Logic for a Coordinated Cell Cycle Exit
Cited by: 18
Author(s): Carla S. Lopes, Fernando Casares
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006787

Common variants upstream of MLF1 at 3q25 and within CPZ at 4p16 associated with neuroblastoma
Cited by: 57
Author(s): Lee McDaniel, Karina L. Conkrite, Xiao Chang, Mario Capasso, Zalman Vaksman, Derek A. Oldridge, Anna Zachariou, Millicent Horn, Maura Diamond, Cuiping Hou, Achille Iolascon, Hákon Hákonarson, Nazneen Rahman, Marcella Devoto, Sharon J. Diskin
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1007320

A Distalless-responsive enhancer of the Hox gene Sex combs reduced is required for segment- and sex-specific sensory organ development in Drosophila
Cited by: 17
Author(s): Sebnem Ece Eksi, Olga Barmina, Christopher Lee McCallough, Artyom Kopp, Teresa V. Orenic
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1005386

A Novel Locus Harbouring a Functional CD164 Nonsense Mutation Identified in a Large Danish Family with Nonsyndromic Hearing Impairment
Cited by: 18
Author(s): Mette Nyegaard, Nanna Dahl Rendtorff, Morten S. Nielsen, Thomas J. Corydon, Ditte Demontis, Anna Starnawska, Anne Hedemand, Annalisa Buniello, Francesco Niola, Michael Toft Overgaard, Suzanne M. Leal, Wasim Ahmad, Friedrik P. Wikman, K. Brorson Petersen, Dorthe Gylling Crüger, Jaap Oostrik, Hannie Kremer, Niels Tommerup, Morten Frödin, Karen P. Steel, Lisbeth Tranebjærg, Anders D. Børglum
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1007738

Unraveling the transcriptional regulation of TWIST1 in limb development
Cited by: 27
Author(s): Naama Hirsch, Reut Eshel, Reut Bar Yaacov, Tal Shahar, Fania Shmulevich, Idit Dahan, Noam Levaot, Tommy Kaplan, Darío G. Lupiáñez, Ramon Y. Birnbaum
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1002629

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population
Cited by: 603
Author(s): Jordana T. Bell, Pei-Chien Tsai, Tsun-Po Yang, Ruth Pidsley, James Nisbet, Daniel Glass, Massimo Mangino, Guangju Zhai, Feng Zhang, Ana M. Valdes, So–Youn Shin, Emma Dempster, Robin M. Murray, Elin Grundberg, Åsa K. Hedman, Alexandra C. Nica, Kerrin S. Small, Emmanouil T. Dermitzakis, Mark I. McCarthy, Jonathan Mill, Tim D. Spector, Panos Deloukas
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1004828

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

10.1371/journal.pgen.1006441

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

10.1371/journal.pone.0055521

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

10.1371/journal.pone.0173890

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

10.1371/journal.pone.0067752

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

10.1371/journal.pone.0068000

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

10.1371/journal.pone.0000930

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

10.1371/journal.pone.0109691

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

10.1371/journal.pone.0037498

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

10.1371/journal.pone.0017116

Sex Hormones in Autism: Androgens and Estrogens Differentially and Reciprocally Regulate RORA, a Novel Candidate Gene for Autism
Cited by: 185
Author(s): Tewarit Sarachana, Minyi Xu, Ray-Chang Wu, Valerie W. Hu
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0140803

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

10.1371/journal.pone.0065498

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

10.1371/journal.pone.0215911

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

10.1371/journal.pone.0040373

POWRS: Position-Sensitive Motif Discovery
Cited by: 7
Author(s): Ian Davis, Christopher C. Benninger, Philip N. Benfey, Tedd D. Elich
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0182373

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

10.1371/journal.pone.0099359

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

10.1371/journal.pone.0035977

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

10.1371/journal.pone.0108065

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

10.1371/journal.pone.0150070

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

10.1371/journal.pone.0113364

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

10.1371/journal.pone.0074637

Regulation of the F11, Klkb1, Cyp4v3 Gene Cluster in Livers of Metabolically Challenged Mice
Cited by: 7
Author(s): Huma Safdar, Audrey C. A. Cleuren, Ka Lei Cheung, Frank J. Gonzalez, Hans L. Vos, Yusuke Inoue, Pieter H. Reitsma, Bart J.M. van Vlijmen
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0176905

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

10.1371/journal.pone.0096805

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

10.1371/journal.pone.0071363

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

10.1371/journal.pone.0150785

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

10.1371/journal.pone.0020560

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

10.1371/journal.pone.0213013

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

10.1371/journal.pone.0127089

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

10.1371/journal.pone.0190457

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

10.1371/journal.pone.0093125

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

10.1371/journal.pone.0012465

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

10.1371/journal.pone.0084002

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

10.1371/journal.pone.0042779

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

10.1371/journal.pone.0195788

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

10.1371/journal.pone.0158036

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

10.1371/journal.pone.0183433

Genetic dissection of endothelial transcriptional activity of zebrafish aryl hydrocarbon receptors (AHRs)
Cited by: 10
Author(s): Wade W. Sugden, Roberto Carlos Leonardo-Mendonça, Darío Acuña‐Castroviejo, Arndt F. Siekmann
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0118779

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

10.1371/journal.pone.0078833

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

10.1371/journal.pone.0221650

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

10.1371/journal.pone.0018475

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

10.1371/journal.pone.0142147

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

10.1371/journal.pone.0059607

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

10.1371/journal.pone.0107389

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

10.1371/journal.pone.0013789

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

10.1371/journal.pone.0107156

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

10.1371/journal.pone.0213470

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

10.1371/journal.pone.0051700

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

10.1371/journal.pone.0152159

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

10.1371/journal.pone.0198922

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

10.1371/journal.pone.0057520

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

10.1371/journal.pone.0046145

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

10.1371/journal.pone.0202778

c-Myb regulates transcriptional activation of miR-143/145 in vascular smooth muscle cells
Cited by: 9
Author(s): Mark Chandy, Masaharu Ishida, Eric A. Shikatani, Omar El-Mounayri, Lawrence Changsu Park, Talat Afroze, Tao Wang, Philip A. Marsden, Mansoor Husain
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0252816

Vitamin D3 attenuates doxorubicin-induced senescence of human aortic endothelial cells by upregulation of IL-10 via the pAMPKα/Sirt1/Foxo3a signaling pathway
Cited by: 15
Author(s): Lei Chen, Rachel Holder, Charles B. Porter, Zubair Shah
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0083364

A Provisional Gene Regulatory Atlas for Mouse Heart Development
Cited by: 9
Author(s): Hailin Chen, Vincent VanBuren
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0104687

Genome-Wide Modulation of Gene Transcription in Ovarian Carcinoma Cells by a New Mithramycin Analogue
Cited by: 19
Author(s): Carolina Vizcaíno, Luz-Elena Núñez, Francisco Morís, José Portugal
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0068712

Optimized Position Weight Matrices in Prediction of Novel Putative Binding Sites for Transcription Factors in the Drosophila melanogaster Genome
Cited by: 1
Author(s): Vyacheslav Morozov, Ilya Ioshikhes
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0194252

CCAAT-enhancer binding protein-α (C/EBPα) and hepatocyte nuclear factor 4α (HNF4α) regulate expression of the human fructose-1,6-bisphosphatase 1 (FBP1) gene in human hepatocellular carcinoma HepG2 cells
Cited by: 11
Author(s): Siriluck Wattanavanitchakorn, Pinnara Rojvirat, Tanit Chavalit, Michael J. MacDonald, Sarawut Jitrapakdee
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0001820

Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources
Cited by: 49
Author(s): Harri Lähdesmäki, Alistair G. Rust, Ilya Shmulevich
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0090155

A Compensatory Role of NF-κB to p53 in Response to 5-FU–Based Chemotherapy for Gastric Cancer Cell Lines
Cited by: 24
Author(s): Fumitaka Endo, Satoshi Nishizuka, Kohei Kume, Kazushige Ishida, Hirokatsu Katagiri, Kazunari Ishida, Kei Sato, Takeshi Iwaya, Keisuke Koeda, Go Wakabayashi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0162681

Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors
Cited by: 7
Author(s): Yuriy Korostelev, Ilya A. Zharov, Andrey A. Mironov, Alexandra B. Rakhmaininova, Mikhail S. Gelfand
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0009084

Regulation of Gene Expression in Hepatic Cells by the Mammalian Target of Rapamycin (mTOR)
Cited by: 21
Author(s): Rosa H. Jimenez, Ju Seog Lee, Mirko Francesconi, Gastone Castellani, Nicola Neretti, Jennifer Sanders, John M. Sedivy, Philip A. Gruppuso
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0117607

Gene Co-Expression Network Analysis Provides Novel Insights into Myostatin Regulation at Three Different Mouse Developmental Timepoints
Cited by: 11
Author(s): Xuerong Yang, James E. Koltes, Carissa A. Park, Shuai Chen, James M. Reecy
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0157265

Histone Methyltransferase Enhancer of Zeste Homolog 2-Mediated ABCA1 Promoter DNA Methylation Contributes to the Progression of Atherosclerosis
Cited by: 59
Author(s): Yun-Cheng Lv, Yue Tang, Ping Zhang, Wei Keat Wan, Feng Yao, Ping He, Wei Xie, Mo Zhang, Jinfeng Shi, Jianfeng Wu, Juan Peng, Dan Liu, Francisco S. Cayabyab, Xi-Long Zheng, Xiangyang Tang, Xin Ouyang, Chao-Ke Tang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0001623

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites
Cited by: 40
Author(s): Troels Marstrand, Jes Frellsen, Ida Moltke, Martin Thiim, Eivind Valen, Dorota Retelska, Anders Krogh
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0172219

DNA methylation of the Fthl17 5’-upstream region regulates differential Fthl17 expression in lung cancer cells and germline stem cells
Cited by: 4
Author(s): Nana Aoki, Kentaro Mochizuki, Yasuhisa Matsui
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0020059

A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays
Cited by: 42
Author(s): Matti Annala, Kirsti Laurila, Harri Lähdesmäki, Matti Nykter
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0207275

Broad-complex Z3 contributes to the ecdysone-mediated transcriptional regulation of the vitellogenin gene in Bombus lantschouensis
Cited by: 3
Author(s): Congai Zhen, Huipeng Yang, Shudong Luo, Jiaxing Huang, Jie Wu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0052055

COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets
Cited by: 16
Author(s): Nati Ha, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0052460

A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites
Cited by: 14
Author(s): Beisi Xu, Dustin E. Schones, Yongmei Wang, Haojun Liang, Guohui Li
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0020022

Identification of Novel Targets of CSL-Dependent Notch Signaling in Hematopoiesis
Cited by: 38
Author(s): Habib Hamidi, Derek Gustafason, Matteo Pellegrini, Judith C. Gasson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0004544

Biological Convergence of Cancer Signatures
Cited by: 22
Author(s): Xavier Solé, Núria Bonifaci, Núria López‐Bigas, Antoni Berenguer, Pilar Hernández, Oscar Reina, Christopher A. Maxwell, Helena Aguilar, Ander Urruticoechea, Sílvia de Sanjosé, Francesc Comellas, Gabriel Capellá, Vı́ctor Moreno, Miguel Ángel Pujana
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0047836

The Limits of De Novo DNA Motif Discovery
Cited by: 25
Author(s): David Simcha, Nathan D. Price, Donald Geman
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0067605

Selective Methylation of CpGs at Regulatory Binding Sites Controls NNAT Expression in Wilms Tumors
Cited by: 23
Author(s): Jochen Hubertus, Ferdinand Zitzmann, Franziska Trippel, Josef Müller‐Höcker, Maximilian Stehr, Dietrich von Schweinitz, Roland Kappler
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0084320

Estradiol Reduces Ferrous Citrate Complex-Induced NOS2 Up-Regulation in Cerebral Endothelial Cells by Interfering the Nuclear Factor Kappa B Transactivation through an Estrogen Receptor β–Mediated Pathway
Cited by: 4
Author(s): Li Ching Chen, Wen Sen Lee
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0180579

Transcriptional role of androgen receptor in the expression of long non-coding RNA Sox2OT in neurogenesis
Cited by: 18
Author(s): Valentina Tosetti, Jenny Sassone, Luca Ferri, Michela Taiana, Gloria Bedini, Sara Nava, Greta Brenna, Chiara Di Resta, Davide Pareyson, Anna Maria Di Giulio, Stephana Carelli, Eugenio Parati, Alfredo Gorio
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0051478

The ChIP-seq-Defined Networks of Bcl-3 Gene Binding Support Its Required Role in Skeletal Muscle Atrophy
Cited by: 21
Author(s): Robert W. Jackman, Chia‐Ling Wu, Susan C. Kandarian
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0155637

Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots
Cited by: 16
Author(s): Yupeng Wang, Stephen P. Ficklin, Xiyin Wang, F. Alex Feltus, Andrew H. Paterson
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0008155

A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data
Cited by: 56
Author(s): Xin He, Chieh Chun Chen, Feng Hong, Fang Fang, Saurabh Sinha, Huck Hui Ng, Sheng Zhong
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0022519

MIRTFnet: Analysis of miRNA Regulated Transcription Factors
Cited by: 24
Author(s): Haroon Naeem, Robert Küffner, Ralf Zimmer
Software Mentions: 1
Published: about 13 years ago

10.3390/cancers12030758

MeCP2 Promotes Colorectal Cancer Metastasis by Modulating ZEB1 Transcription
Cited by: 21
Author(s): Dan Luo, Wei Ge
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers13153752

rs10514231 Leads to Breast Cancer Predisposition by Altering ATP6AP1L Gene Expression
Cited by: 5
Author(s): Shumin Ma, Naixia Ren, Qilai Huang
Software Mentions: 1
Published: over 3 years ago

10.3390/cancers12113363

The 40bp Indel Polymorphism rs150550023 in the MDM2 Promoter is Associated with Intriguing Shifts in Gene Expression in the p53-MDM2 Regulatory Hub
Cited by: 3
Author(s): Heidi Miedl, Bianca Dietrich, Klaus Kaserer, Martin Schreiber
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers12123864

Adipocyte-Derived Leptin Promotes PAI-1-Mediated Breast Cancer Metastasis in a STAT3/miR-34a Dependent Manner
Cited by: 13
Author(s): Sijing Li, Xiaohui Wei, Xiaoman Zhan, Junqi He, Yu-Qi Zeng, Xuemei Tian, Shengtao Yuan, Li Sun
Software Mentions: 1
Published: almost 4 years ago

10.3390/cancers13163993

PPAR-Responsive Elements Enriched with Alu Repeats May Contribute to Distinctive PPARγ–DNMT1 Interactions in the Genome
Cited by: 2
Author(s): Ingo G. H. Schmidt‐Wolf, Fabián Tobar-Tosse, Tikam Chand Dakal, Hongde Liu, Arijit Biswas, Athira M. Menon, Anoosha Paruchuri, Panagiotis Katsonis, Olivier Lichtarge, M. Michael Gromiha, Michael Ludwig, Ingo G. H. Schmidt‐Wolf, Frank G. Holz, Karin U. Loeffler, Martina C. Herwig‐Carl
Software Mentions: 1
Published: over 3 years ago

10.3390/cancers12082005

Clinical and Pre-Clinical Evidence of Carbonic Anhydrase IX in Pancreatic Cancer and Its High Expression in Pre-Cancerous Lesions
Cited by: 16
Author(s): Sabina Strapcova, Martina Takáčová, Lucia Csáderová, Paola Martinelli, Ľubomíra Lukáčiková, Viliam Gál, Juraj Kopáček, Eliška Švastová
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers12020493

Knockdown of TFAM in Tumor Cells Retarded Autophagic Flux through Regulating p53 Acetylation and PISD Expression
Cited by: 5
Author(s): Xu Jiang, Jun Wang
Software Mentions: 1
Published: over 4 years ago

10.3390/cancers13102403

Aldo-Keto Reductase 1C3 Mediates Chemotherapy Resistance in Esophageal Adenocarcinoma via ROS Detoxification
Cited by: 10
Author(s): Chengke Zhou, Zhefang Wang, Jiahui Li, Xiaolin Wu, Ningbo Fan, Dai Li, Fanyu Liu, Patrick Sven Plum, Sascha Hoppe, Axel M. Hillmer, A Quaas, Florian Gebauer, Seung‐Hun Chon, Christiane Bruns, Yue Zhao
Software Mentions: 1
Published: over 3 years ago

10.1186/s13578-021-00678-2

A novel mechanism for C1GALT1 in the regulation of gastric cancer progression
Cited by: 9
Author(s): Dong Xiao, Chunli Chen, Xinzhou Deng, Yongyu Liu, Qiwen Duan, Zhen Peng, Zhiguo Luo, Li Shen
Software Mentions: 1
Published: about 3 years ago

10.1186/s13578-021-00671-9

FOXD1 promotes EMT and cell stemness of oral squamous cell carcinoma by transcriptional activation of SNAI2
Cited by: 17
Author(s): Yang Chen, Weilian Liang, Ke Liu, Zhengjun Shang
Software Mentions: 1
Published: over 3 years ago

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283