Gary Stormo

Gary Stormo

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Gary Stormo

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

BMC Bioinformatics 2018 03 6;19(1):86. Epub 2018 Mar 6.

Department of Genetics and Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA.

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http://dx.doi.org/10.1186/s12859-018-2104-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840810PMC
March 2018

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

BMC Mol Biol 2018 03 27;19(1). Epub 2018 Mar 27.

Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1186/s12867-018-0106-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869772PMC
March 2018

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

J Mol Biol 2017 11 16;429(23):3626-3634. Epub 2017 Oct 16.

CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China; Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2017.10.013DOI Listing
November 2017

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

Sci Adv 2017 11 17;3(11):eaao1799. Epub 2017 Nov 17.

Department of Genetics and The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108-8510, USA.

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http://dx.doi.org/10.1126/sciadv.aao1799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694663PMC
November 2017

Quantitative specificity of STAT1 and several variants.

Nucleic Acids Res 2017 Aug;45(14):8199-8207

Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108-8510, USA.

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http://dx.doi.org/10.1093/nar/gkx393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737217PMC
August 2017

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

PLoS Comput Biol 2017 Jul 7;13(7):e1005638. Epub 2017 Jul 7.

Department of Genetics and The Edison Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521849PMC
July 2017

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

Nucleic Acids Res 2017 01 2;45(2):832-845. Epub 2016 Dec 2.

Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

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http://dx.doi.org/10.1093/nar/gkw1198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314778PMC
January 2017

DNA Structure Helps Predict Protein Binding.

Cell Syst 2016 Sep;3(3):216-218

Department of Genetics and Center for Genome Science and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1016/j.cels.2016.09.004DOI Listing
September 2016

Combinatorial Cis-regulation in Saccharomyces Species.

G3 (Bethesda) 2016 Jan 15;6(3):653-67. Epub 2016 Jan 15.

Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108

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http://dx.doi.org/10.1534/g3.115.024331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777128PMC
January 2016

DNA Motif Databases and Their Uses.

Authors:
Gary D Stormo

Curr Protoc Bioinformatics 2015 Sep 3;51:2.15.1-2.15.6. Epub 2015 Sep 3.

Washington University School of Medicine, St. Louis, Missouri.

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http://dx.doi.org/10.1002/0471250953.bi0215s51DOI Listing
September 2015

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

J Biol Chem 2015 Aug 18;290(32):19756-69. Epub 2015 Jun 18.

From the Department of Medicine, National Jewish Health, Denver, Colorado 80206, Department of Medicine, University of Colorado, Denver, Colorado 80045

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http://www.jbc.org/content/290/32/19756.full.pdf
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http://www.jbc.org/lookup/doi/10.1074/jbc.M115.668558
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http://dx.doi.org/10.1074/jbc.M115.668558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528137PMC
August 2015

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

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

Department of Genetics and Center for Genomic Sciences and Systems Biology, School of Medicine, Washington University, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1007/s40484-015-0044-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704127PMC
June 2015

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

Genetics 2014 Nov 9;198(3):1329-43. Epub 2014 Sep 9.

Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108-8510

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http://dx.doi.org/10.1534/genetics.114.170100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224169PMC
November 2014

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

Immunity 2014 Jun 29;40(6):896-909. Epub 2014 May 29.

Laboratory of Comparative Immunology, Center for the Study of Inflammatory Bowel Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1016/j.immuni.2014.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104614PMC
June 2014

Discriminative motif optimization based on perceptron training.

Bioinformatics 2014 Apr 24;30(7):941-8. Epub 2013 Dec 24.

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967114PMC
April 2014

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

Nucleic Acids Res 2014 Apr 12;42(8):4800-12. Epub 2014 Feb 12.

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/nar/gku132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005693PMC
April 2014

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

Authors:
Gary D Stormo

Curr Protoc Bioinformatics 2013 Oct 15;43:12.1.1-12.1.3. Epub 2013 Oct 15.

Washington University School of Medicine, Saint Louis, Missouri.

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http://dx.doi.org/10.1002/0471250953.bi1201s43DOI Listing
October 2013

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

G3 (Bethesda) 2013 Jun 21;3(6):979-91. Epub 2013 Jun 21.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1534/g3.113.006338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689809PMC
June 2013

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

Nucleic Acids Res 2013 Feb 8;41(4):2455-65. Epub 2013 Jan 8.

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1093/nar/gks1357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575815PMC
February 2013

Exploring the DNA-recognition potential of homeodomains.

Genome Res 2012 Oct 26;22(10):1889-98. Epub 2012 Apr 26.

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1101/gr.139014.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460184PMC
October 2012

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

Genetics 2012 Jul 13;191(3):781-90. Epub 2012 Apr 13.

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1534/genetics.112.138685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389974PMC
July 2012

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

Nat Methods 2012 Jun 29;9(6):588-90. Epub 2012 Apr 29.

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, USA.

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http://dx.doi.org/10.1038/nmeth.1994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443678PMC
June 2012

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

Bioinformatics 2012 Jun;28(12):i84-9

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371834PMC
June 2012

Fast, sensitive discovery of conserved genome-wide motifs.

J Comput Biol 2012 Feb;19(2):139-47

Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1089/cmb.2011.0249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272693PMC
February 2012

Assessing the effects of symmetry on motif discovery and modeling.

PLoS One 2011 20;6(9):e24908. Epub 2011 Sep 20.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024908PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176789PMC
January 2012

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

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

Department of Genetics, Washington University Medical School, St Louis, MO, USA.

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http://dx.doi.org/10.1093/nar/gkr1180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245033PMC
January 2012

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

Nucleic Acids Res 2011 Jul 20;39(12):e83. Epub 2011 Apr 20.

Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/nar/gkr239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130293PMC
July 2011

An introduction to recognizing functional domains.

Authors:
Gary D Stormo

Curr Protoc Bioinformatics 2011 Jun;Chapter 2:Unit 2.1

Washington University School of Medicine, St. Louis, MO, USA.

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http://dx.doi.org/10.1002/0471250953.bi0201s34DOI Listing
June 2011

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

Aging Cell 2011 Apr 1;10(2):305-17. Epub 2011 Feb 1.

Department of Developmental Biology Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1111/j.1474-9726.2010.00667.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079228PMC
April 2011

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

Authors:
Gary D Stormo

Genetics 2011 Apr 7;187(4):1219-24. Epub 2011 Feb 7.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1534/genetics.110.126052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070529PMC
April 2011

Motif discovery using expectation maximization and Gibbs' sampling.

Authors:
Gary D Stormo

Methods Mol Biol 2010 ;674:85-95

Department of Genetics, School of Medicine, Washington University, St. Louis, MO, USA.

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http://dx.doi.org/10.1007/978-1-60761-854-6_6DOI Listing
December 2010

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

Bioinformatics 2010 Nov 31;26(21):2672-7. Epub 2010 Aug 31.

Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981494PMC
November 2010

Determining the specificity of protein-DNA interactions.

Nat Rev Genet 2010 Nov 28;11(11):751-60. Epub 2010 Sep 28.

Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd, St. Louis, Missouri 63110-8510, USA.

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http://dx.doi.org/10.1038/nrg2845DOI Listing
November 2010

Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation.

Proc IEEE Int Symp Bioinformatics Bioeng 2010 :99-105

Dept. Computer Science & Engineering, Washington University in St. Louis, St. Louis, Missouri,

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http://dx.doi.org/10.1109/BIBE.2010.24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108062PMC
January 2010

Inferring binding energies from selected binding sites.

PLoS Comput Biol 2009 Dec 4;5(12):e1000590. Epub 2009 Dec 4.

Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777355PMC
December 2009

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

Authors:
Gary D Stormo

Curr Protoc Bioinformatics 2009 Sep;Chapter 3:Unit 3.1 3.1.1-7

Washington University, School of Medicine, St Louis, Missouri, USA.

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http://dx.doi.org/10.1002/0471250953.bi0301s27DOI Listing
September 2009

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

PLoS One 2009 Aug 25;4(8):e6736. Epub 2009 Aug 25.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006736PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726951PMC
August 2009

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

Nature 2009 Jul 5;460(7253):405-9. Epub 2009 Jul 5.

Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1038/nature08114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716014PMC
July 2009

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

Mol Syst Biol 2009 28;5:268. Epub 2009 Apr 28.

Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA.

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http://dx.doi.org/10.1038/msb.2009.24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683727PMC
June 2009

Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2.

BMC Genomics 2009 May 7;10:210. Epub 2009 May 7.

Department of Computer Science and Engineering, Washington University in Saint Louis, Saint Louis, MO, USA.

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http://dx.doi.org/10.1186/1471-2164-10-210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694837PMC
May 2009

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

PLoS Comput Biol 2009 Apr 3;5(4):e1000338. Epub 2009 Apr 3.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659441PMC
April 2009

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.

Bioinformatics 2008 Sep 27;24(17):1850-7. Epub 2008 Jun 27.

Department of Genetics, Washington University School of Medicine, 660 S Euclid, Box 8232, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732218PMC
September 2008

The cis-regulatory map of Shewanella genomes.

Nucleic Acids Res 2008 Sep 13;36(16):5376-90. Epub 2008 Aug 13.

Department of Genetics, Washington University School of Medicine, 660 S Euclid, Box 8232, St Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/nar/gkn515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532739PMC
September 2008

Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.

Cell 2008 Jun;133(7):1277-89

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1016/j.cell.2008.05.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478728PMC
June 2008

An iterative method for selecting degenerate multiplex PCR primers.

Methods Mol Biol 2007 ;402:245-68

Department of Computer Science and Engineering, Washington University in St. Louis, MO, USA.

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http://dx.doi.org/10.1007/978-1-59745-528-2_12DOI Listing
November 2007

Computational identification and functional validation of regulatory motifs in cartilage-expressed genes.

Genome Res 2007 Oct 4;17(10):1438-47. Epub 2007 Sep 4.

Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1101/gr.6224007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1987341PMC
October 2007

RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment.

Bioinformatics 2007 Aug 30;23(15):1883-91. Epub 2007 May 30.

Department of Genetics, Washington University, School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm272DOI Listing
August 2007

A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments.

Bioinformatics 2007 Aug 5;23(16):2073-9. Epub 2007 Jun 5.

Division of Endocrinology, Metabolism and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btm292DOI Listing
August 2007

Putting numbers on the network connections.

Bioessays 2007 Aug;29(8):717-21

Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA.

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http://dx.doi.org/10.1002/bies.20617DOI Listing
August 2007

PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis.

Nucleic Acids Res 2007 Jul 21;35(Web Server issue):W238-44. Epub 2007 May 21.

Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1093/nar/gkm308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933204PMC
July 2007

Identification of muscle-specific regulatory modules in Caenorhabditis elegans.

Genome Res 2007 Mar 6;17(3):348-57. Epub 2007 Feb 6.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1101/gr.5989907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800926PMC
March 2007

Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach.

PLoS One 2007 Feb 28;2(2):e262. Epub 2007 Feb 28.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000262PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1803023PMC
February 2007

Molecular diagnostics in sepsis: from bedside to bench.

J Am Coll Surg 2006 Nov 11;203(5):585-598. Epub 2006 Sep 11.

Department of Surgery, School of Medicine, Washington University, St Louis, MO 63110, USA.

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http://dx.doi.org/10.1016/j.jamcollsurg.2006.06.028DOI Listing
November 2006

Training of the next generation of biostatisticians: a call to action in the U.S.

Stat Med 2006 Oct;25(20):3415-29

Department of Biostatistics and Medical Informatics, University of Wisconsin, School of Medicine & Public Health, 600 Highland Avenue, Box 4675, Madison, WI 53792, USA.

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http://dx.doi.org/10.1002/sim.2668DOI Listing
October 2006

An introduction to recognizing functional domains.

Authors:
Gary D Stormo

Curr Protoc Bioinformatics 2006 Oct;Chapter 2:Unit 2.1

Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1002/0471250953.bi0201s15DOI Listing
October 2006

Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans.

Bioinformatics 2006 May 4;22(10):1239-44. Epub 2006 Apr 4.

Department of Genetics, Washington University School of Medicine 660 S. Euclid, Campus Box 8232, St. Louis, MO 63110, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl076DOI Listing
May 2006

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.

Genome Res 2006 Mar 31;16(3):405-13. Epub 2006 Jan 31.

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1101/gr.4303406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1415218PMC
March 2006

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

BMC Bioinformatics 2006 Mar 7;7:113. Epub 2006 Mar 7.

Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1186/1471-2105-7-113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435934PMC
March 2006

An overview of RNA structure prediction and applications to RNA gene prediction and RNAi design.

Authors:
Gary D Stormo

Curr Protoc Bioinformatics 2006 Mar;Chapter 12:Unit 12.1

Washington University School of Medicine, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1002/0471250953.bi1201s13DOI Listing
March 2006

Target selectivity of vertebrate notch proteins. Collaboration between discrete domains and CSL-binding site architecture determines activation probability.

J Biol Chem 2006 Feb 19;281(8):5106-19. Epub 2005 Dec 19.

Department of Molecular Biology and Pharmacology, Division of Dermatology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1074/jbc.M506108200DOI Listing
February 2006

Direct, androgen receptor-mediated regulation of the FKBP5 gene via a distal enhancer element.

Endocrinology 2006 Jan 6;147(1):590-8. Epub 2005 Oct 6.

Department of Pathology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1210/en.2005-1001DOI Listing
January 2006

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome.

Proc Natl Acad Sci U S A 2005 Nov 21;102(48):17400-5. Epub 2005 Nov 21.

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1073/pnas.0505147102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1297658PMC
November 2005

Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions.

Nucleic Acids Res 2005 Sep 25;33(17):e141. Epub 2005 Sep 25.

Department of Genetics, Washington University School of Medicine, 660 S Euclid, Box 8232, St Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/nar/gni139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236725PMC
September 2005

enoLOGOS: a versatile web tool for energy normalized sequence logos.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W389-92

Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/nar/gki439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160200PMC
July 2005

Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.

BMC Bioinformatics 2005 Jul 13;6:176. Epub 2005 Jul 13.

Department of Genetics, Washington University School of Medicine, St, Louis, MO 63110, USA.

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http://dx.doi.org/10.1186/1471-2105-6-176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184061PMC
July 2005

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.

Bioinformatics 2005 May 18;21(9):1815-24. Epub 2005 Jan 18.

Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/bti279DOI Listing
May 2005

Editing efficiency of a Drosophila gene correlates with a distant splice site selection.

RNA 2005 May;11(5):563-6

Department of Genetics, Washington University Medical School, 660 S. Euclid, Box 8232, St. Louis, MO 63110-8232, USA.

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http://dx.doi.org/10.1261/rna.7280605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370744PMC
May 2005

Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites.

Nucleic Acids Res 2005 22;33(7):2290-301. Epub 2005 Apr 22.

Department of Biomedical Informatics, The Ohio State University 3184 Graves Hall, 333 W. 10th Avenue, Columbus, OH 43210, USA.

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http://dx.doi.org/10.1093/nar/gki519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1084321PMC
May 2005

Procom: a web-based tool to compare multiple eukaryotic proteomes.

Bioinformatics 2005 Apr 25;21(8):1693-4. Epub 2004 Nov 25.

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti161DOI Listing
April 2005

PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis.

Hum Mutat 2005 Feb;25(2):110-7

Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1002/humu.20123DOI Listing
February 2005

Making connections between novel transcription factors and their DNA motifs.

Genome Res 2005 Feb 14;15(2):312-20. Epub 2005 Jan 14.

Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1101/gr.3069205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546533PMC
February 2005

Novel transcription regulatory elements in Caenorhabditis elegans muscle genes.

Genome Res 2004 Dec;14(12):2457-68

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1101/gr.2961104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534670PMC
December 2004

The neuropeptide pigment-dispersing factor coordinates pacemaker interactions in the Drosophila circadian system.

J Neurosci 2004 Sep;24(36):7951-7

Department of Genetics, Washington University Medical School, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1523/JNEUROSCI.2370-04.2004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6729918PMC
September 2004

Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor.

Nucleic Acids Res 2004 2;32(13):4026-32. Epub 2004 Aug 2.

Department of Genetics, Washington University, 660 S. Euclid, Box 8232, St Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/nar/gkh729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC506813PMC
August 2004

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.

Bioinformatics 2004 Jul 12;20(10):1591-602. Epub 2004 Feb 12.

Department of Genetics, Washington University, School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth131DOI Listing
July 2004

Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major.

Mol Biochem Parasitol 2004 Jul;136(1):71-86

Department of Molecular Microbiology, Center for Infectious Disease Research, Washington University School of Medicine, Campus Box 8230, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.

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http://dx.doi.org/10.1016/j.molbiopara.2004.03.002DOI Listing
July 2004

ILM: a web server for predicting RNA secondary structures with pseudoknots.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W146-9

Department of Computer Science and Engineering, Washington University in St Louis, St Louis, MO 63130, USA.

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http://dx.doi.org/10.1093/nar/gkh444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441582PMC
July 2004

PromoLign: a database for upstream region analysis and SNPs.

Hum Mutat 2004 Jun;23(6):534-9

Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1002/humu.20049DOI Listing
June 2004

RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites.

Proc Natl Acad Sci U S A 2004 Apr 1;101(15):5559-64. Epub 2004 Apr 1.

Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1073/pnas.0306988101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC397422PMC
April 2004

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.

Bioinformatics 2004 Jan;20(1):58-66

Department of Computer Science, Washington University in St. Louis, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg373DOI Listing
January 2004

Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria.

Nucleic Acids Res 2003 Dec;31(23):6891-903

Department of Genetics, Washington University Medical School, St Louis, MO 63110, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC290249PMC
http://dx.doi.org/10.1093/nar/gkg879DOI Listing
December 2003

Combining phylogenetic data with co-regulated genes to identify regulatory motifs.

Bioinformatics 2003 Dec;19(18):2369-80

Department of Genetics, Washington University Medical School, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg329DOI Listing
December 2003

Evolution. Heirlooms in the attic.

Science 2003 Nov;302(5647):997-9

Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1126/science.1092271DOI Listing
November 2003

Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III.

J Eukaryot Microbiol 2003 May-Jun;50(3):145-55

Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA.

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http://dx.doi.org/10.1111/j.1550-7408.2003.tb00109.xDOI Listing
August 2003

New tricks for an old dogma: riboswitches as cis-only regulatory systems.

Authors:
Gary D Stormo

Mol Cell 2003 Jun;11(6):1419-20

Department of Genetics, Washington University School of Medicine, 660 S. Euclid, St. Louis, MO 63110, USA.

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http://dx.doi.org/10.1016/s1097-2765(03)00240-5DOI Listing
June 2003