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Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq.

Chang YK, Zuo Z, Stormo GD.

BMC Mol Biol. 2018 Mar 27;19(1):5. doi: 10.1186/s12867-018-0106-7.


Comparison of discriminative motif optimization using matrix and DNA shape-based models.

Ruan S, Stormo GD.

BMC Bioinformatics. 2018 Mar 6;19(1):86. doi: 10.1186/s12859-018-2104-7.


Measuring quantitative effects of methylation on transcription factor-DNA binding affinity.

Zuo Z, Roy B, Chang YK, Granas D, Stormo GD.

Sci Adv. 2017 Nov 17;3(11):eaao1799. doi: 10.1126/sciadv.aao1799. eCollection 2017 Nov.


Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6.

Hu C, Malik V, Chang YK, Veerapandian V, Srivastava Y, Huang YH, Hou L, Cojocaru V, Stormo GD, Jauch R.

J Mol Biol. 2017 Nov 24;429(23):3626-3634. doi: 10.1016/j.jmb.2017.10.013. Epub 2017 Oct 16.


Inherent limitations of probabilistic models for protein-DNA binding specificity.

Ruan S, Stormo GD.

PLoS Comput Biol. 2017 Jul 7;13(7):e1005638. doi: 10.1371/journal.pcbi.1005638. eCollection 2017 Jul.


Quantitative specificity of STAT1 and several variants.

Roy B, Zuo Z, Stormo GD.

Nucleic Acids Res. 2017 Aug 21;45(14):8199-8207. doi: 10.1093/nar/gkx393.


BEESEM: estimation of binding energy models using HT-SELEX data.

Ruan S, Swamidass SJ, Stormo GD.

Bioinformatics. 2017 Aug 1;33(15):2288-2295. doi: 10.1093/bioinformatics/btx191.


Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq.

Chang YK, Srivastava Y, Hu C, Joyce A, Yang X, Zuo Z, Havranek JJ, Stormo GD, Jauch R.

Nucleic Acids Res. 2017 Jan 25;45(2):832-845. doi: 10.1093/nar/gkw1198. Epub 2016 Dec 2.


DNA Structure Helps Predict Protein Binding.

Stormo GD, Roy B.

Cell Syst. 2016 Sep 28;3(3):216-218. doi: 10.1016/j.cels.2016.09.004.


Combinatorial Cis-regulation in Saccharomyces Species.

Spivak AT, Stormo GD.

G3 (Bethesda). 2016 Jan 15;6(3):653-67. doi: 10.1534/g3.115.024331.


A quantitative understanding of lac repressor's binding specificity and flexibility.

Zuo Z, Chang Y, Stormo GD.

Quant Biol. 2015 Jun 1;3(2):69-80. Epub 2015 May 30.


DNA Motif Databases and Their Uses.

Stormo GD.

Curr Protoc Bioinformatics. 2015 Sep 3;51:2.15.1-6. doi: 10.1002/0471250953.bi0215s51. Review.


Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops.

Sasse SK, Zuo Z, Kadiyala V, Zhang L, Pufall MA, Jain MK, Phang TL, Stormo GD, Gerber AN.

J Biol Chem. 2015 Aug 7;290(32):19756-69. doi: 10.1074/jbc.M115.668558. Epub 2015 Jun 18.


Intermediate DNA methylation is a conserved signature of genome regulation.

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF.

Nat Commun. 2015 Feb 18;6:6363. doi: 10.1038/ncomms7363.


Spec-seq: determining protein-DNA-binding specificity by sequencing.

Stormo GD, Zuo Z, Chang YK.

Brief Funct Genomics. 2015 Jan;14(1):30-8. doi: 10.1093/bfgp/elu043. Epub 2014 Oct 30. Review.


High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding.

Zuo Z, Stormo GD.

Genetics. 2014 Nov;198(3):1329-43. doi: 10.1534/genetics.114.170100. Epub 2014 Sep 9.


Modeling the specificity of protein-DNA interactions.

Stormo GD.

Quant Biol. 2013 Jun;1(2):115-130.


Innate host defense requires TFEB-mediated transcription of cytoprotective and antimicrobial genes.

Visvikis O, Ihuegbu N, Labed SA, Luhachack LG, Alves AF, Wollenberg AC, Stuart LM, Stormo GD, Irazoqui JE.

Immunity. 2014 Jun 19;40(6):896-909. doi: 10.1016/j.immuni.2014.05.002. Epub 2014 May 29.


An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.

Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD.

Nucleic Acids Res. 2014 Apr;42(8):4800-12. doi: 10.1093/nar/gku132. Epub 2014 Feb 12.


Discriminative motif optimization based on perceptron training.

Patel RY, Stormo GD.

Bioinformatics. 2014 Apr 1;30(7):941-8. doi: 10.1093/bioinformatics/btt748. Epub 2013 Dec 24.


Identification of cilia genes that affect cell-cycle progression using whole-genome transcriptome analysis in Chlamydomonas reinhardtti.

Albee AJ, Kwan AL, Lin H, Granas D, Stormo GD, Dutcher SK.

G3 (Bethesda). 2013 Jun 21;3(6):979-91. doi: 10.1534/g3.113.006338.


Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA.

Genome Res. 2013 Jun;23(6):928-40. doi: 10.1101/gr.151472.112. Epub 2013 Mar 7.


Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases.

Zhu C, Gupta A, Hall VL, Rayla AL, Christensen RG, Dake B, Lakshmanan A, Kuperwasser C, Stormo GD, Wolfe SA.

Nucleic Acids Res. 2013 Feb 1;41(4):2455-65. doi: 10.1093/nar/gks1357. Epub 2013 Jan 8.


Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density.

Coronnello C, Hartmaier R, Arora A, Huleihel L, Pandit KV, Bais AS, Butterworth M, Kaminski N, Stormo GD, Oesterreich S, Benos PV.

PLoS Comput Biol. 2012;8(12):e1002830. doi: 10.1371/journal.pcbi.1002830. Epub 2012 Dec 20.


An Overview of RNA Sequence Analyses: Structure Prediction, ncRNA Gene Identification, and RNAi Design.

Stormo GD.

Curr Protoc Bioinformatics. 2013 Oct 15;43:12.1.1-3. doi: 10.1002/0471250953.bi1201s43.


Recognition models to predict DNA-binding specificities of homeodomain proteins.

Christensen RG, Enuameh MS, Noyes MB, Brodsky MH, Wolfe SA, Stormo GD.

Bioinformatics. 2012 Jun 15;28(12):i84-9. doi: 10.1093/bioinformatics/bts202.


An optimized two-finger archive for ZFN-mediated gene targeting.

Gupta A, Christensen RG, Rayla AL, Lakshmanan A, Stormo GD, Wolfe SA.

Nat Methods. 2012 Jun;9(6):588-90. doi: 10.1038/nmeth.1994. Epub 2012 Apr 29.


Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans.

Zhao G, Ihuegbu N, Lee M, Schriefer L, Wang T, Stormo GD.

G3 (Bethesda). 2012 Apr;2(4):469-81. doi: 10.1534/g3.111.001081. Epub 2012 Apr 1.


Exploring the DNA-recognition potential of homeodomains.

Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA.

Genome Res. 2012 Oct;22(10):1889-98. doi: 10.1101/gr.139014.112. Epub 2012 Apr 26.


Improved models for transcription factor binding site identification using nonindependent interactions.

Zhao Y, Ruan S, Pandey M, Stormo GD.

Genetics. 2012 Jul;191(3):781-90. doi: 10.1534/genetics.112.138685. Epub 2012 Apr 13.


Fast, sensitive discovery of conserved genome-wide motifs.

Ihuegbu NE, Stormo GD, Buhler J.

J Comput Biol. 2012 Feb;19(2):139-47. doi: 10.1089/cmb.2011.0249.


ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species.

Spivak AT, Stormo GD.

Nucleic Acids Res. 2012 Jan;40(Database issue):D162-8. doi: 10.1093/nar/gkr1180. Epub 2011 Dec 2.


Assessing the effects of symmetry on motif discovery and modeling.

Motlhabi LM, Stormo GD.

PLoS One. 2011;6(9):e24908. doi: 10.1371/journal.pone.0024908. Epub 2011 Sep 20.


Quantitative analysis demonstrates most transcription factors require only simple models of specificity.

Zhao Y, Stormo GD.

Nat Biotechnol. 2011 Jun 7;29(6):480-3. doi: 10.1038/nbt.1893. No abstract available.


An introduction to recognizing functional domains.

Stormo GD.

Curr Protoc Bioinformatics. 2011 Jun;Chapter 2:Unit 2.1. doi: 10.1002/0471250953.bi0201s34.


A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity.

Christensen RG, Gupta A, Zuo Z, Schriefer LA, Wolfe SA, Stormo GD.

Nucleic Acids Res. 2011 Jul;39(12):e83. doi: 10.1093/nar/gkr239. Epub 2011 Apr 20.


Maximally efficient modeling of DNA sequence motifs at all levels of complexity.

Stormo GD.

Genetics. 2011 Apr;187(4):1219-24. doi: 10.1534/genetics.110.126052. Epub 2011 Feb 7. Erratum in: Genetics. 2011 Dec;189(4):1525.


A nutrient-sensitive interaction between Sirt1 and HNF-1α regulates Crp expression.

Grimm AA, Brace CS, Wang T, Stormo GD, Imai S.

Aging Cell. 2011 Apr;10(2):305-17. doi: 10.1111/j.1474-9726.2010.00667.x. Epub 2011 Feb 1.


Determining the specificity of protein-DNA interactions.

Stormo GD, Zhao Y.

Nat Rev Genet. 2010 Nov;11(11):751-60. doi: 10.1038/nrg2845. Epub 2010 Sep 28. Review.


Motif discovery using expectation maximization and Gibbs' sampling.

Stormo GD.

Methods Mol Biol. 2010;674:85-95. doi: 10.1007/978-1-60761-854-6_6.


Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.

Sahota G, Stormo GD.

Bioinformatics. 2010 Nov 1;26(21):2672-7. doi: 10.1093/bioinformatics/btq501. Epub 2010 Aug 31.


Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation.

Kwan AL, Dutcher SK, Stormo GD.

Proc IEEE Int Symp Bioinformatics Bioeng. 2010:99-105.


Inferring binding energies from selected binding sites.

Zhao Y, Granas D, Stormo GD.

PLoS Comput Biol. 2009 Dec;5(12):e1000590. doi: 10.1371/journal.pcbi.1000590. Epub 2009 Dec 4.


An introduction to sequence similarity ("homology") searching.

Stormo GD.

Curr Protoc Bioinformatics. 2009 Sep;Chapter 3:Unit 3.1 3.1.1-7. doi: 10.1002/0471250953.bi0301s27.


Modeling the quantitative specificity of DNA-binding proteins from example binding sites.

Homsi DS, Gupta V, Stormo GD.

PLoS One. 2009 Aug 25;4(8):e6736. doi: 10.1371/journal.pone.0006736.


The AP-1 transcription factor Batf controls T(H)17 differentiation.

Schraml BU, Hildner K, Ise W, Lee WL, Smith WA, Solomon B, Sahota G, Sim J, Mukasa R, Cemerski S, Hatton RD, Stormo GD, Weaver CT, Russell JH, Murphy TL, Murphy KM.

Nature. 2009 Jul 16;460(7253):405-9. doi: 10.1038/nature08114. Epub 2009 Jul 5.


Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2.

Kwan AL, Li L, Kulp DC, Dutcher SK, Stormo GD.

BMC Genomics. 2009 May 7;10:210. doi: 10.1186/1471-2164-10-210.


Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs.

Foat BC, Stormo GD.

Mol Syst Biol. 2009;5:268. doi: 10.1038/msb.2009.24. Epub 2009 Apr 28.


Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines.

Xu X, Ji Y, Stormo GD.

PLoS Comput Biol. 2009 Apr;5(4):e1000338. doi: 10.1371/journal.pcbi.1000338. Epub 2009 Apr 3.


The cis-regulatory map of Shewanella genomes.

Liu J, Xu X, Stormo GD.

Nucleic Acids Res. 2008 Sep;36(16):5376-90. doi: 10.1093/nar/gkn515. Epub 2008 Aug 13.

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