User Publications

A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.

Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A.
Nature. 2012 Oct 18.

Rapid estrogen receptor signaling is essential for the protective effects of estrogen against vascular injury.

Bernelot Moens SJ, Schnitzler GR, Nickerson M, Guo H, Ueda K, Lu Q, Aronovitz MJ, Nickerson H, Baur WE, Hansen U, Iyer LK, Karas RH.
Circulation. 2012 Oct 16.

Analysis method of epigenetic DNA methylation to dynamically investigate the functional activity of transcription factors in gene expression.

Feng W, Dong Z, He B, Wang K.
BMC Genomics. 2012 Oct 5.

Role of the retinal vascular endothelial cell in ocular disease.

Bharadwaj AS, Appukuttan B, Wilmarth PA, Pan Y, Stempel AJ, Chipps TJ, Benedetti EE, Zamora DO, Choi D, David LL, Smith JR.
Prog Retin Eye Res. 2012 Sep 11.

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.

Alexandrov BS, Fukuyo Y, Lange M, Horikoshi N, Gelev V, Rasmussen KO, Bishop AR, Usheva A.
Nucleic Acids Res. 2012 Aug 16.

Decreased expression of synapse-related genes and loss of synapses in major depressive disorder.

Kang HJ, Voleti B, Hajszan T, Rajkowska G, Stockmeier CA, Licznerski P, Lepack A, Majik MS, Jeong LS, Banasr M, Son H, Duman RS.
Nat Med. 2012 Aug 12.

Transformation of a transposon into a derived prolactin promoter with function during human pregnancy.

Emera D, Wagner GP. Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11246-51. Epub 2012 Jun 25.

Rac1 signalling modulates a STAT5/BCL-6 transcriptional switch on cell-cycle-associated target gene promoters.

Barros P, Lam EW, Jordan P, Matos P. Nucleic Acids Res. 2012 Jun 20.

Promoter cloning and characterization of the human programmed cell death protein 4 (pdcd4) gene: evidence for ZBP-89 and Sp-binding motifs as essential Pdcd4 regulators.

Leupold JH, Asangani IA, Mudduluru G, Allgayer H. Biosci Rep. 2012 Jun;32(3):281-97.

Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.

Zacher B, Abnaof K, Gade S, Younesi E, Tresch A, Fröhlich H.
Bioinformatics. 2012 Jul 1;28(13):1714-1720. Epub 2012 May 4.

A single nucleotide polymorphism in the rabbit growth hormone (GH1) gene is associated with market weight in a commercial rabbit population

L. Fontanesi, S. Dall’Olio, E. Spaccapaniccia, E. Scotti, D. Fornasini, A. Frabetti, V. Russo
Livestock Science. 2012 April 26.

Hypoxia regulated gene transcription in human optic nerve lamina cribrosa cells in culture.

Kirwan RP, Felice L, Clark AF, O’Brien CJ, Leonard MO.
Invest Ophthalmol Vis Sci. 2012 Apr 24;53(4):2243-55. Print 2012 Apr.

Exploring the potential role of disease-causing mutation in a gene desert: duplication of noncoding elements 5′ of GRIA3 is associated with GRIA3 silencing and X-linked intellectual disability.

Bonnet C, Masurel-Paulet A, Khan AA, Béri-Dexheimer M, Callier P, Mugneret F, Philippe C, Thauvin-Robinet C, Faivre L, Jonveaux P.
Hum Mutat. 2012 Feb;33(2):355-8. doi: 10.1002/humu.21649. Epub 2011 Nov 28.

Sequence variation in promoter of Ica1 gene, which encodes protein implicated in type 1 diabetes, causes transcription factor autoimmune regulator (AIRE) to increase its binding and down-regulate expression.

Bonner SM, Pietropaolo SL, Fan Y, Chang Y, Sethupathy P, Morran MP, Beems M, Giannoukakis N, Trucco G, Palumbo MO, Solimena M, Pugliese A, Polychronakos C, Trucco M, Pietropaolo M.
J Biol Chem. 2012 May 18;287(21):17882-93. Epub 2012 Mar 24.

Identification of a melanocyte-specific, microphthalmia-associated transcription factor-dependent regulatory element in the intronic duplication causing hair greying and melanoma in horses.

Sundström E, Komisarczuk AZ, Jiang L, Golovko A, Navratilova P, Rinkwitz S, Becker TS, Andersson L.
Pigment Cell Melanoma Res. 2012 Jan;25(1):28-36. doi: 10.1111/j.1755-148X.2011.00902.x. Epub 2011 Sep 21.

Inflammatory changes in adipose tissue enhance expression of GPR84, a medium-chain fatty acid receptor: TNFa enhances GPR84 expression in adipocytes.

Nagasaki H, Kondo T, Fuchigami M, Hashimoto H, Sugimura Y, Ozaki N, Arima H, Ota A, Oiso Y, Hamada Y.
FEBS Lett. 2012 Feb 17;586(4):368-72. Epub 2012 Jan 10.

Increased expression of NuSAP in recurrent prostate cancer is mediated by E2F1.

Gulzar ZG, McKenney JK, Brooks JD.
Oncogene. 2012 Feb 20. doi: 10.1038/onc.2012.27.

Identification of polymorphisms in genes of the immune system in cynomolgus macaques.

Hong Wu, Karissa Adkins
Mammalian Genome Volume 23, Numbers 7-8 (2012)

Identification of a Gene Expression Signature Common to Distinct Cancer Pathways.

Niklaus Fankhauser, Igor Cima, Peter Wild, and Wilhelm Krek
Published online 2012 May 8. doi:  10.4137/CIN.S9542

SHP-2 and PTP-pest induction during Rb-E2F associated apoptosis.

Morales LD, Pena K, Kim DJ, Lieman JH.
Cell Mol Biol Lett. 2012 Sep;17(3):422-32. Epub 2012 May 29.

MYC-regulated genes involved in liver cell dysplasia identified in a transgenic model of liver cancer.

Hunecke D, Spanel R, Länger F, Nam SW, Borlak J.
J Pathol. 2012 May 31. doi: 10.1002/path.4059.

Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk.

Dunlop MG, Dobbins SE, Farrington SM, Jones AM, Palles C, Whiffin N, Tenesa A, Spain S, Broderick P, Ooi LY, Domingo E, Smillie C.
Nat Genet. 2012 May 27;44(7):770-776. doi: 10.1038/ng.2293.

Expression of Human Endogenous Retrovirus Type K (HML-2) Is Activated by the Tat Protein of HIV-1.

Gonzalez-Hernandez MJ, Swanson MD, Contreras-Galindo R, Cookinham S, King SR, Noel RJ Jr, Kaplan MH, Markovitz DM.
J Virol. 2012 Aug;86(15):7790-805. Epub 2012 May 16.

Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers.

Maia AT, Antoniou AC, O’Reilly M, Samarajiwa S, Dunning M, Kartsonaki C, Chin SF, Curtis CN, McGuffog L, Domchek SM; EMBRACE, Easton DF, Peock S, Frost D, Evans DG, Eeles R, Izatt L, Adlard J, Eccles D; GEMO Study Collaborators, Sinilnikova OM, Mazoyer S, Stoppa-Lyonnet D, Gauthier-Villars M, Faivre L, Venat-Bouvet L, Delnatte C, Nevanlinna H, Couch FJ, Godwin AK, Caligo MA; SWE-BRCA, Barkardottir RB; kConFab Investigators, Chen X, Beesley J, Healey S, Caldas C, Chenevix-Trench G, Ponder BA.

Breast Cancer Res. 2012 Apr 18;14(2):R63.Breast Cancer Res. 2012 Apr 18;14(2):R63.

Combinatorial activation and repression by seven transcription factors specify Drosophila odorant receptor expression.

Jafari S, Alkhori L, Schleiffer A, Brochtrup A, Hummel T, Alenius M. PLoS Biol. 2012;10(3):e1001280. Epub 2012 Mar 13.

A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes.

Dutta B, Pusztai L, Qi Y, André F, Lazar V, Bianchini G, Ueno N, Agarwal R, Wang B, Shiang CY, Hortobagyi GN, Mills GB, Symmans WF, Balázsi G.
Br J Cancer. 2012 Mar 13;106(6):1107-16. doi: 10.1038/bjc.2011.584. Epub 2012 Feb 16.

Genome-wide repression of NF-κB target genes by the transcription factor MIBP1 and its modulation by O-GlcNAc transferase.

Iwashita Y, Fukuchi N, Waki M, Hayashi K, Tahira T. J
Biol Chem. 2012 Jan 31.

Lead, calcium uptake, and related genetic variants in association with renal cell carcinoma risk in a cohort of male Finnish smokers.

Southard EB, Roff A, Fortugno T, Richie JP Jr, Kaag M, Chinchilli VM, Virtamo J, Albanes D, Weinstein S, Wilson RT.
Cancer Epidemiol Biomarkers Prev. 2012 Jan;21(1):191-201. Epub 2011 Nov 15

Ikaros represses and activates PU.1 cell-type-specifically through the multifunctional Sfpi1 URE and a myeloid specific enhancer.

Zarnegar MA, Rothenberg EV.
Oncogene. 2012 Jan 9. doi: 10.1038/onc.2011.597.

A single-nucleotide polymorphism in the EAP1 gene is associated with amenorrhea/oligomenorrhea in nonhuman primates.

Lomniczi A, Garcia-Rudaz C, Ramakrishnan R, Wilmot B, Khouangsathiene S, Ferguson B, Dissen GA, Ojeda SR.
Endocrinology. 2012 Jan;153(1):339-49. Epub 2011 Nov 29

Sclerostin expression is induced by BMPs in human Saos-2 osteosarcoma cells but not via direct effects on the sclerostin gene promoter or ECR5 element.

Yu L, der Valk M, Cao J, Han CY, Juan T, Bass MB, Deshpande C, Damore MA, Stanton R, Babij P.
Bone. 2011 Dec;49(6):1131-40. Epub 2011 Aug 26

Promoter cloning and characterization of the human programmed cell death protein 4 (pdcd4) gene: evidence for ZBP-89 and Sp-binding motifs as essential Pdcd4-regulators.

Leupold JH, Asangani IA, Mudduluru G, Allgayer H.
Biosci Rep. 2011 Nov 23.

Network analysis of microRNAs and their regulation in human ovarian cancer.

Schmeier S, Schaefer U, Essack M, Bajic VB.
BMC Syst Biol. 2011 Nov 3;5:183

Global Mapping of Cell Type-Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation.

Waki H, Nakamura M, Yamauchi T, Wakabayashi K, Yu J, Hirose-Yotsuya L, Take K, Sun W, Iwabu M, Okada-Iwabu M, Fujita T, Aoyama T, Tsutsumi S, Ueki K, Kodama T, Sakai J, Aburatani H, Kadowaki T.
PLoS Genet. 2011 Sep;7(10):e1002311. Epub 2011 Oct 20

Zinc-finger transcription factors are associated with guanine quadruplex motifs in human, chimpanzee, mouse and rat promoters genome-wide.

Kumar P, Yadav VK, Baral A, Kumar P, Saha D, Chowdhury S.
Nucleic Acids Res. 2011 Oct 1;39(18):8005-16. Epub 2011 Jul 4

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites.

Kulakovskiy IV, Belostotsky AA, Kasianov AS, Esipova NG, Medvedeva YA, Eliseeva IA, Makeev VJ.
Bioinformatics. 2011 Oct 1;27(19):2621-2624. Epub 2011 Aug 18

In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer.

Kaur M, Macpherson CR, Schmeier S, Narasimhan K, Choolani M, Bajic VB.
BMC Syst Biol. 2011 Sep 19;5:144

Characterization of STAT6 Target Genes in Human B Cells and Lung Epithelial Cells.

Kanai A, Suzuki K, Tanimoto K, Mizushima-Sugano J, Suzuki Y, Sugano S.
DNA Res. 2011 Epub Aug 9

Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators.

Mende S, Royer L, Herr A, Schmiedel J, Deschauer M, Klopstock T, Kostic VS, Schroeder M, Reichmann H, Storch A.
Neurol Res. 2011 Jul;33(6):638-55.

Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation.

Echeverría PC, Forafonov F, Pandey DP, Mühlebach G, Picard D.
BioData Min. 2011 Jun 14;4(1):15.

Comparative analysis of the ATRX promoter and 5′ regulatory region reveals conserved regulatory elements which are linked to roles in neurodevelopment, alpha-globin regulation and testicular function.

Tang P, Frankenberg S, Argentaro A, Graves JM, Familari M.
BMC Res Notes. 2011 Jun 15;4:200.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

Martin D, Pantoja C, Fernández Miñán A, Valdes-Quezada C, Moltó E, Matesanz F, Bogdanović O, de la Calle-Mustienes E, Domínguez O, Taher L, Furlan-Magaril M, Alcina A, Cañón S, Fedetz M, Blasco MA, Pereira PS, Ovcharenko I, Recillas-Targa F, Montoliu L, Manzanares M, Guigó R, Serrano M, Casares F, Gómez-Skarmeta JL.
Nat Struct Mol Biol. 2011 Jun;18(6):708-14. Epub 2011 May 22.

Regulation of hemocytes in Drosophila requires dappled cytochrome b5.

Kleinhesselink K, Conway C, Sholer D, Huang I, Kimbrell DA.
Biochem Genet. 2011 Jun;49(5-6):329-51. Epub 2011 Jan 30.

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

Annala M, Laurila K, Lähdesmäki H, Nykter M.
PLoS One. 2011;6(5):e20059. Epub 2011 May 26.

Dynamic regulation of PDX-1 and FoxO1 expression by FoxA2 in dexamethasone-induced pancreatic β-cells dysfunction.

Chen F, Zhu Y, Tang X, Sun Y, Jia W, Sun Y, Han X.
Endocrinology. 2011 May;152(5):1779-88. Epub 2011 Mar 8.

High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells.

Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q, Benos PV, Friedman N, Eickelberg O, Kaminski N.
PLoS One. 2011;6(5):e20319. Epub 2011 May 20.

Conservation of the ST6Gal I gene and its expression in the mammary gland.

Maksimovic J, Sharp JA, Nicholas KR, Cocks BG, Savin K.
Glycobiology. 2011 Apr;21(4):467-81. Epub 2010 Nov 22.

A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

Håndstad T, Rye MB, Drabløs F, Sætrom P.
PLoS One. 2011 Apr 14;6(4):e18430.

High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation.

Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, Zhang C, Morris K, Jenner C, Jackson S, Thomas B, Tabrett A, Legaie R, Moore JD, Wild DL, Ott S, Rand D, Beynon J, Denby K, Mead A, Buchanan-Wollaston V. Plant Cell. 2011 Mar;23(3):873-94. Epub 2011 Mar 29.

Discovering approximate-associated sequence patterns for protein-DNA interactions.

Chan TM, Wong KC, Lee KH, Wong MH, Lau CK, Tsui SK, Leung KS.
Bioinformatics. 2011 Feb 15;27(4):471-8. Epub 2010 Dec 30.

dPORE-miRNA: polymorphic regulation of microRNA genes.

Schmeier S, Schaefer U, MacPherson CR, Bajic VB.
PLoS One. 2011 Feb 4;6(2):e16657.

PCR DNA-array profiling of DNA-binding transcription factor activities in adult mouse tissues.

Sun Y, Cheng J, Mitchelson KR.
Methods Mol Biol. 2011;687:319-31.

Rb/E2F regulates expression of neogenin during neuronal migration.

Andrusiak MG, McClellan KA, Dugal-Tessier D, Julian LM, Rodrigues SP, Park DS, Kennedy TE, Slack RS.
Mol Cell Biol. 2011 Jan;31(2):238-47. Epub 2010 Nov 8.

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis.

Fang X, Yoon JG, Li L, Yu W, Shao J, Hua D, Zheng S, Hood L, Goodlett DR, Foltz G, Lin B.
BMC Genomics. 2011 Jan 6;12:11.

Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.

Ghedira K, Hornischer K, Konovalova T, Jenhani AZ, Benkahla A, Kel A.
Infect Genet Evol. 2010 Nov 18.

Systematic identification of conserved motif modules in the human genome.
Cai X, Hou L, Su N, Hu H, Deng M, Li X.
BMC Genomics. 2010 Oct 14;11:567.

The databases of transcription factors.
Chen HF, Wang JK.
Yi Chuan. 2010 Oct;32(10):1009-17.

A parallel scheme for comparing transcription factor binding sites matrices.
Carat S, Houlgatte R, Bourdon J.
Bioinform Comput Biol. 2010 Jun;8(3):485-502.

Discovering protein-DNA binding sequence patterns using association rule mining.
Leung KS, Wong KC, Chan TM, Wong MH, Lee KH, Lau CK, Tsui SK.
Nucleic Acids Res. 2010 Oct 1;38(19):6324-37. Epub 2010 Jun 6.

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J.
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W210-3. Epub 2010 May 16.

Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies.
Alamanova D, Stegmaier P, Kel A.
BMC Bioinformatics. 2010 May 3;11:225.

Variable structure motifs for transcription factor binding sites.
Reid JE, Evans KJ, Dyer N, Wernisch L, Ott S.
BMC Genomics. 2010 Jan 14;11:30.

Binding sites for ETS family of transcription factors dominate the promoter regions of differentially expressed genes in abdominal aortic aneurysms.
Nischan J, Gatalica Z, Curtis M, Lenk GM, Tromp G, Kuivaniemi H.
Circ Cardiovasc Genet. 2009 Dec;2(6):565-72. Epub 2009 Oct 19.

Evidence for coregulation of myocardial gene expression by MEF2 and NFAT in human heart failure.
Putt ME, Hannenhalli S, Lu Y, Haines P, Chandrupatla HR, Morrisey EE, Margulies KB, Cappola TP.
Circ Cardiovasc Genet. 2009 Jun;2(3):212-9. Epub 2009 Mar 31.

Proinflammatory phenotype with imbalance of KLF2 and RelA: risk of childhood stroke with sickle cell anemia.
Enenstein J, Milbauer L, Domingo E, Wells A, Roney M, Kiley J, Wei P, Hebbel RP.
Am J Hematol. 2010 Jan;85(1):18-23.

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices.
da Piedade I, Tang MH, Elemento O.
BMC Bioinformatics. 2009 Nov 26;10:388.

Protopia: a protein-protein interaction tool.
Real-Chicharro A, Ruiz-Mostazo I, Navas-Delgado I, Kerzazi A, Chniber O, Sánchez-Jiménez F, Medina MA, Aldana-Montes JF.
BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S17.

Identification of a novel functional deletion variant in the 5′-UTR of the DJ-1 gene.
Keyser RJ, van der Merwe L, Venter M, Kinnear C, Warnich L, Carr J, Bardien S.
BMC Med Genet. 2009 Oct 13;10:105.

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ.
Bioinformatics. 2009 Dec 1;25(23):3191-3. Epub 2009 Oct 1.

3D-footprint: a database for the structural analysis of protein-DNA complexes.
Contreras-Moreira B.
Nucleic Acids Res. 2010 Jan;38(Database issue):D91-7. Epub 2009 Sep 18.

D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.
Sen N, Mishra M, Khan F, Meena A, Sharma A.
Bioinformation. 2009 Jul 27;3(10):415-8.

Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor.
Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L.
PLoS One. 2009 Aug 11;4(8):e6589.

Functional analysis of promoter mutations in the ACTN4 and SYNPO genes in focal segmental glomerulosclerosis.
Dai S, Wang Z, Pan X, Wang W, Chen X, Ren H, Hao C, Han B, Chen N.
Nephrol Dial Transplant. 2010 Mar;25(3):824-35. Epub 2009 Aug 7.

A robust correlation estimator and nonlinear recurrent model to infer genetic interactions in Saccharomyces cerevisiae and pathways of pulmonary disease in Homo sapiens.
Chuang CL, Chen CM, Wong WS, Tsai KN, Chan EC, Jiang JA.
Biosystems. 2009 Dec;98(3):160-75. Epub 2009 Jun 13.

Assigning roles to protein mentions: the case of transcription factors.
Yang H, Keane J, Bergman CM, Nenadic G. J
Biomed Inform. 2009 Oct;42(5):887-94. Epub 2009 Apr 11.

The 15(S)-hydroxyeicosatetraenoic acid-induced angiogenesis requires Janus kinase 2-signal transducer and activator of transcription-5B-dependent expression of interleukin-8.
Cheranov SY, Wang D, Kundumani-Sridharan V, Karpurapu M, Zhang Q, Chava KR, Rao GN.
Blood. 2009 Jun 4;113(23):6023-33. Epub 2009 Apr 6.

New scoring schema for finding motifs in DNA Sequences.
Zare-Mirakabad F, Ahrabian H, Sadeghi M, Nowzari-Dalini A, Goliaei B.
BMC Bioinformatics. 2009 Mar 20;10:93.

Identification of two different length of beta-actin promoters of Tanichthys albonubes and comparison of their activity
Wang H, Ye X, Lao H, Xia S, Bai J, Jian Q.
Sheng Wu Gong Cheng Xue Bao. 2008 Oct;24(10):1768-75. Chinese.

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups.
Chang WC, Lee TY, Huang HD, Huang HY, Pan RL.
BMC Genomics. 2008 Nov 26;9:561.

Transcriptional regulation of EGR-1 by the interleukin-1-JNK-MKK7-c-Jun pathway.
Hoffmann E, Ashouri J, Wolter S, Doerrie A, Dittrich-Breiholz O, Schneider H, Wagner EF, Troppmair J, Mackman N, Kracht M.
J Biol Chem. 2008 May 2;283(18):12120-8. Epub 2008 Feb 15.

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species.
Wang X, Gu J, Zhang MQ, Li Y. Bioinformatics. 2008 Jan 15;24(2):165-71. Epub 2007 Nov 24.

Gene Expression Analysis of Forskolin Treated Basilar Papillae Identifies MicroRNA181a as a Mediator of Proliferation.
Frucht CS, Uduman M, Duke JL, Kleinstein SH, Santos-Sacchi J, Navaratnam DS.
PLoS One. 2010 Jul 9;5(7):e11502.

Gene set-based module discovery in the breast cancer transcriptome.
Niida A, Smith AD, Imoto S, Aburatani H, Zhang MQ, Akiyama T.
BMC Bioinformatics. 2009 Feb 26;10:71.

Discovery of transcriptional programs in cerebral ischemia by in silico promoter analysis.
Ridder DA, Bulashevska S, Chaitanya GV, Babu PP, Brors B, Eils R, Schneider A, Schwaninger M.
Brain Res. 2009 May 26;1272:3-13. Epub 2009 Mar 31.

Gene set-based module discovery in the breast cancer transcriptome.
Niida A, Smith AD, Imoto S, Aburatani H, Zhang MQ, Akiyama T.
BMC Bioinformatics. 2009 Feb 26;10:71.

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells.
Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T. BMC Bioinformatics. 2008 Sep 29;9:404.

GeneTrail–advanced gene set enrichment analysis.
Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92. Epub 2007 May 25.

Bladder inflammatory transcriptome in response to tachykinins: neurokinin 1 receptor-dependent genes and transcription regulatory elements.
Saban R, Simpson C, Vadigepalli R, Memet S, Dozmorov I, Saban MR.
BMC Urol. 2007 May 22;7:7.

Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis.
Liu Y, Ringnér M.
Genome Biol. 2007;8(5):R77.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6. Epub 2007 May 3.

Characterisation of the genomic canine Fgf8 locus and screen for genetic variants in 4 dogs with different face types.
Haworth KE, Healy C, McGonnell IM, Binns M, Sharpe PT.
DNA Seq. 2007 Jun;18(3):209-19.

Identification of nuclear factor-kappaB responsive element within the neuronal nitric oxide synthase exon 1f-specific promoter.
Li Y, Li G, Li C, Zhao Y.
Acta Biochim Biophys Sin. 2007 Apr;39(4):247-54.

KBERG: KnowledgeBase for Estrogen Responsive Genes.
Tang S, Zhang Z, Tan SL, Tang MH, Kumar AP, Ramadoss SK, Bajic VB.
Nucleic Acids Res. 2007 Jan;35(Database issue):D732-6. Epub 2006 Nov 7.

MUC1 gene overexpressed in breast cancer: structure and transcriptional activity of the MUC1 promoter and role of estrogen receptor alpha (ERalpha) in regulation of the MUC1 gene expression.
Zaretsky JZ, Barnea I, Aylon Y, Gorivodsky M, Wreschner DH, Keydar I.
Mol Cancer. 2006 Nov 5;5:57.

Aberrant low expression level of bovine beta-lactoglobulin is associated with a C to A transversion in the BLG promoter region.
Braunschweig MH, Leeb T.
J Dairy Sci. 2006 Nov;89(11):4414-9.

Characterization of binding sites of eukaryotic transcription factors.
Qian J, Lin J, Zack DJ. Genomics Proteomics Bioinformatics. 2006 May;4(2):67-79.

Comparative promoter analysis of doxorubicin resistance-associated genes suggests E47 as a key regulatory element.
Gyorffy A, Vásárhelyi B, Szöke D, Dietel M, Tulassay T, Györffy B.
Anticancer Res. 2006 Jul-Aug;26(4B):2971-6.

Informative priors based on transcription factor structural class improve de novo motif discovery.
Narlikar L, Gordân R, Ohler U, Hartemink AJ.
Bioinformatics. 2006 Jul 15;22(14):e384-92.

CRSD: a comprehensive web server for composite regulatory signature discovery.
Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W571-7.

Automatic transcription factor classifier based on functional domain composition.
Qian Z, Cai YD, Li Y.
Biochem Biophys Res Commun. 2006 Aug 18;347(1):141-4. Epub 2006 Jun 21.

The human kallikrein 10 promoter contains a functional retinoid response element.
Zeng M, Zhang Y, Bhat I, Wazer DE, Band H, Band V.
J Biol Chem. 2006 Jun;387(6):741-7.

Model-based identification of cis-acting elements from microarray data.
Liu Y, Taylor MW, Edenberg HJ.
Genomics. 2006 Oct;88(4):452-61. Epub 2006 May 23.

A polymorphism in the promoter region of the CD86 (B7.2) gene is associated with systemic sclerosis.
Abdallah AM, Renzoni EA, Anevlavis S, Lagan AL, Munkonge FM, Fonseca C, Black CM, Briggs D, Wells AU, Marshall SE, McHugh N, du Bois RM, Welsh KI.
Int J Immunogenet. 2006 Jun;33(3):155-61.

K-SPMM: a database of murine spermatogenic promoters modules & motifs.
Lu Y, Platts AE, Ostermeier GC, Krawetz SA.
BMC Bioinformatics. 2006 May 3;7:238.

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.
Huber BR, Bulyk ML.
BMC Bioinformatics. 2006 Apr 27;7:229.

Functional single nucleotide polymorphism haplotypes in the human equilibrative nucleoside transporter 1.
Myers SN, Goyal RK, Roy JD, Fairfull LD, Wilson JW, Ferrell RE.
Pharmacogenet Genomics. 2006 May;16(5):315-20.

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.
Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C, Deblois G, Giguère V, Ferretti V, Bergeron D, Coulombe B, Robert F. Genome Res. 2006 May;16(5):656-68. Epub 2006 Apr 10.

The -318 C>G single-nucleotide polymorphism in GNAI2 gene promoter region impairs transcriptional activity through specific binding of Sp1 transcription factor and is associated with high blood pressure in Caucasians from Italy.
Menzaghi C, Paroni G, De Bonis C, Soccio T, Marucci A, Bacci S, Trischitta V.
J Am Soc Nephrol. 2006 Apr;17(4 Suppl 2):S115-9.

A remote and highly conserved enhancer supports amygdala specific expression of the gene encoding the anxiogenic neuropeptide substance-P.
Davidson S, Miller KA, Dowell A, Gildea A, Mackenzie A.
Mol Psychiatry. 2006 Apr;11(4):323, 410-21.

Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences.
Fu Y, Weng Z.
Genome Inform. 2005;16(1):68-72.

Topology, tinkering and evolution of the human transcription factor network.
Rodriguez-Caso C, Medina MA, Solé RV.
FEBS J. 2005 Dec;272(24):6423-34.

Sequence features of DNA binding sites reveal structural class of associated transcription factor.
Narlikar L, Hartemink AJ.
Bioinformatics. 2006 Jan 15;22(2):157-63. Epub 2005 Nov 2.

Characterisation of the genomic structure of chick Fgf8.
Haworth KE, Healy C, Sharpe PT.
DNA Seq. 2005 Jun;16(3):180-6.

Detection and preliminary analysis of motifs in promoters of anaerobically induced genes of different plant species.
Mohanty B, Krishnan SP, Swarup S, Bajic VB.
Ann Bot. 2005 Sep;96(4):669-81. Epub 2005 Jul 18.

Differential regulation of the IL-10 gene in Th1 and Th2 T cells.
Kang KH, Im SH.
Ann N Y Acad Sci. 2005 Jun;1050:97-107.

Signal transduction pathway profiling of individual tumor samples.
Breslin T, Krogh M, Peterson C, Troein C.
BMC Bioinformatics. 2005 Jun 29;6:163.

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.
Hsiao A, Ideker T, Olefsky JM, Subramaniam S.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W627-32.

PromoterPlot: a graphical display of promoter similarities by pattern recognition.
Di Cara A, Schmidt K, Hemmings BA, Oakeley EJ.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W423-6.

The ferritin light-chain homologue promoter in Aedes aegypti.
Pham DQ, Chavez CA.
Insect Mol Biol. 2005 Jun;14(3):263-70.

Regulation of the ferritin heavy-chain homologue gene in the yellow fever mosquito, Aedes aegypti.
Pham DQ, Shaffer JJ.
Insect Mol Biol. 2005 Jun;14(3):223-36.

PathoPlant: a database on plant-pathogen interactions.
Bülow L, Schindler M, Choi C, Hehl R.
In Silico Biol. 2004;4(4):529-36.

Identifying regulatory subnetworks for a set of genes.
Scott MS, Perkins T, Bunnell S, Pepin F, Thomas DY, Hallett M.
Mol Cell Proteomics. 2005 May;4(5):683-92. Epub 2005 Feb 18.

Prediction of cis-regulatory elements of coregulated genes.
Kielbase SM, Blüthgen N, Sers C, Schäfer R, Herzel H.
Genome Inform. 2004;15(1):117-24.

Prediction of cis-regulatory elements of coregulated genes.
Kielbase SM, Blüthgen N, Sers C, Schäfer R, Herzel H.
Genome Inform. 2004;15(1):117-24.

Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays.
Yap YL, Lam DC, Luc G, Zhang XW, Hernandez D, Gras R, Wang E, Chiu SW, Chung LP, Lam WK, Smith DK, Minna JD, Danchin A, Wong MP.
Nucleic Acids Res. 2005 Jan 14;33(1):409-21.

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
Marinescu VD, Kohane IS, Riva A.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D91-7.

Annotating significant pairs of transcription factor binding sites in regulatory DNA.
Rateitschak K, Müller T, Vingron M.
In Silico Biol. 2004;4(4):479-87.

Genome-wide prediction and analysis of function-specific transcription factor binding sites.
Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A. In Silico Biol. 2004;4(4):395-410.

An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression.
Messina DN, Glasscock J, Gish W, Lovett M. Genome Res. 2004 Oct;14(10B):2041-7.

Binding matrix: a novel approach for binding site recognition.
Kim JT, Gewehr JE, Martinetz T. J
Bioinform Comput Biol. 2004 Jun;2(2):289-307.

MotifPrototyper: a Bayesian profile model for motif families.
Xing EP, Karp RM.
Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10523-8. Epub 2004 Jul 13.

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.
Loots GG, Ovcharenko I.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21.

Content analysis of the core promoter region of human genes.
Bajic VB, Choudhary V, Hock CK.
In Silico Biol. 2004;4(2):109-25.

Chromatin immunoprecipitation assay on the rainbow trout opsin proximal promoters illustrates binding of NF-kappaB and c-jun to the SWS1 promoter in the retina.
Dann SG, Allison WT, Veldhoen K, Johnson T, Hawryshyn CW. Exp Eye Res. 2004 May;78(5):1015-24.

Statistical analysis of over-represented words in human promoter sequences.
Mariño-Ramírez L, Spouge JL, Kanga GC, Landsman D.
Nucleic Acids Res. 2004 Feb 12;32(3):949-58. Print 2004. Erratum in: Nucleic Acids Res. 2004 Dec;32(22):6718. Nucleic Acids Res. 2004 Nov 8;32(19):5972.

Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways.
Tullai JW, Schaffer ME, Mullenbrock S, Kasif S, Cooper GM.
J Biol Chem. 2004 May 7;279(19):20167-77. Epub 2004 Feb 9.

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.
Steffens NO, Galuschka C, Schindler M, Bülow L, Hehl R.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D368-72.

Identification of novel anti-angiogenic factors by in silico functional gene screening method.
Lee SK, Choi YS, Cha J, Moon EJ, Lee SW, Bae MK, Sohn TK, Won Y, Ma S, Kong EB, Lee H, Lim S, Chang D, Kim YJ, Kim CW, Zhang BT, Kim KW.
J Biotechnol. 2003 Oct 9;105(1-2):51-60.

A non-parametric model for transcription factor binding sites.
King OD, Roth FP.
Nucleic Acids Res. 2003 Oct 1;31(19):e116.

Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes.
Bajic VB, Tan SL, Chong A, Tang S, Ström A, Gustafsson JA, Lin CY, Liu ET.
Nucleic Acids Res. 2003 Jul 1;31(13):3605-7.

SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences.
Boardman PE, Oliver SG, Hubbard SJ.
Nucleic Acids Res. 2003 Jul 1;31(13):3572-5.

Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters.
Santini S, Boore JL, Meyer A.
Genome Res. 2003 Jun;13(6A):1111-22. Erratum in: Genome Res. 2003 Aug;13(8):1973.

Comparative promoter analysis and its application in analysis of PTH-regulated gene expression.
Qiu P, Qin L, Sorrentino RP, Greene JR, Wang L, Partridge NC.
J Mol Biol. 2003 Mar 7;326(5):1327-36. Erratum in: J Mol Biol. 2003 May 16;328(5):1197.

BIOBASE Publications

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.

Wingender, E.
Brief Bioinform. 9, 326-332 (2008).

TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes.

Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E.
Nucleic Acids Res. 34, D108-D110 (2006).

TRANSFAC®, TRANSPATH® and CYTOMER® as starting points for an ontology of regulatory networks.

Wingender, E. In Silico Biol. 2004;4(1):55-61.

TRANSFAC: transcriptional regulation, from patterns to profiles.

Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E. Nucleic Acids Res. 31, 374-378 (2003).

From Transcriptional Regulation to Aggressive Behavior.

D’Souza UM, Kel A, Sluyter F. Behavior Genetics 33, 5 (2003).

S/MARt DB: a database on scaffold/matrix attached regions.

Liebich, I., Bode, J., Frisch, M., Wingender, E.
Nucleic Acids Res. 30, 372-374 (2002).

TRANSCompel: a database on composite regulatory elements in eukaryotic genes.

Kel-Margoulis, O.V., Kel, A.E., Reuter, I., Deineko, I.V., Wingender, E. Nucleic Acids Res. 30, 332-334 (2002).

The TRANSFAC system on gene expression regulation.

Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruess, M., Schacherer, F., Thiele, S., Urbach, S.
Nucleic Acids Res. 29, 281-3 (2001).

TRANSFAC: an integrated system for gene expression regulation.

Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruess, M., Reuter, I., Schacherer, F.
Nucleic Acids Res. 28, 316-319 (2000).