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Magee JA, Chang LW, Stormo GD, Milbrandt J.
Direct, Androgen Receptor-Mediated Regulation of the FKBP5 Gene via a Distal
Enhancer Element.
Endocrinology. 2006 Jan;147(1):590-8. Epub 2005 Oct 6.
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Ong C, Cheng H, Chang LW, Ohtsuka T, Kageyama R, Stormo GD, Kopan R.
Collaboration between discrete protein domains and binding site architecture on
the promoter determine target selectivity of vertebrate notch proteins.
J Biol Chem. 2005 Dec 19; [Epub ahead of print]
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Wang T, Stormo GD.
Identifying the conserved network of cis-regulatory sites of a eukaryotic
genome.
Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17400-5. Epub 2005 Nov 21.
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Liu J, Stormo GD.
Combining SELEX with quantitative assays to rapidly obtain accurate models of
protein-DNA interactions.
Nucleic Acids Res. 2005 Sep 25;33(17):e141.
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Liu J, Stormo GD.
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.
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Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92.
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Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J.
Pairwise local structural alignment of RNA sequences with sequence similarity
less than 40%.
Bioinformatics. 2005 May 1;21(9):1815-24. Epub 2005 Jan 18.
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Agrawal R, Stormo GD.
Editing efficiency of a Drosophila gene correlates with a distant splice site
selection.
RNA. 2005 May;11(5):563-6.
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Gershenzon NI, Stormo GD, Ioshikhes IP.
Computational technique for improvement of the position-weight matrices for the
DNA/protein binding sites.
Nucleic Acids Res. 2005 Apr 22;33(7):2290-301. Print 2005.
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Li JB, Zhang M, Dutcher SK, Stormo GD.
Procom: a web-based tool to compare multiple eukaryotic proteomes.
Bioinformatics. 2005 Apr 15;21(8):1693-4. Epub 2004 Nov 25.
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Tan K, McCue LA, Stormo GD.
Making connections between novel transcription factors and their DNA motifs.
Genome Res. 2005 Feb;15(2):312-20. Epub 2005 Jan 14.
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Freimuth RR, Stormo GD, McLeod HL.
PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis.
Hum Mutat. 2005 Feb;25(2):110-7.
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2004
GuhaThakurta D, Schriefer LA, Waterston RH, Stormo GD.
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes.
Genome Res. 2004 Dec;14(12):2457-68.
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Li JB, Gerdes JM, Haycraft CJ, Fan Y, Teslovich TM, May-Simera H, Li H, Blacque OE, Li L, Leitch CC, Lewis RA, Green JS, Parfrey PS, Leroux MR, Davidson WS, Beales PL, Guay-Woodford LM, Yoder BK, Stormo GD, Katsanis N, Dutcher SK.
Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.
Cell. 2004 May 14;117(4):541-52.
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Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG, Shortliffe EH, Stormo GD, Szczepaniak MC, Tuck D, Williamson J;
American College of Medical Informatics. Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics.
J Am Med Inform Assoc. 2004 May-Jun;11(3):167-72. Epub 2004 Feb 5.
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Hu Y, Wang T, Stormo GD, Gordon JI.
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 13;101(15):5559-64. Epub 2004 Apr 1.
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Ruan J, Stormo GD, Zhang W.
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.
Bioinformatics. 2004 Jan 1;20(1):58-66.
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Lin Y, Stormo GD, Taghert PH.
The neuropeptide pigment-dispersing factor coordinates pacemaker interactions in the Drosophila circadian system.
J Neurosci. 2004 Sep 8;24(36):7951-7.
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Man TK, Yang JS, Stormo GD
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding
specificity of the Mnt repressor.
Nucleic Acids Res. 2004 32(13):4026-4032.
PDF
Ruan J, Stormo GD, Zhang W
ILM: a web server for predicting RNA secondary structures with pseudoknots.
Nucleic Acids Res. 2004 32:W146-149.
PDF
Akopyants NS, Matlib RS, Bukanova EN, Smedes MR, Brownstein BH, Stormo GD, Beverley SM
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 136(1):71-86.
PDF
Zhao T, Chang LW, McLeod HL, Stormo GD.
PromoLign:A database for upstream region analysis and SNPs.
Human Mutation 2004 Jun23(6):534-539.
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Li JB, Gerdes JM, Haycraft CJ, Fan Y, Teslovich TM, May-Simera H, Li H, Blacque OE, Li L, Leitch CC, Lewis RA,
Green JS, Parfrey PS, Leroux MR, Davidson WS, Beales PL, Guay-Woodford LM, Yoder BK, Stormo GD, Katsanis N,
Dutcher SK
Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.
Cell 2004 117(4):541-552.
PDF
Hu Y, Wang T, Stormo GD, Gordon JI
RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its
gene targets and DNA binding sites.
Proc. Natl. Acad. Sci. USA 2004 101(15):5559-5564.
PDF
Ji Y, Xu X, Stormo GD
A graph theoretical approach to predict common RNA secondary structure motifs including
pseudoknots in unaligned sequences.
bioinformatics 2004 20(10):1591-1602.
PDF
Friedman CP, Altman RB, Kohane IS, McCormick KA, Miller PL, Ozbolt JG, Shortliffe EH, Stormo GD,
Szczepaniak MC, Tuck D, Williamson J
Training the Next Generation of Informaticians: The Impact of "BISTI" and Bioinformatics--A
Report from the American College of Medical Informatics.
J Am Med Inform Assoc. 2004 11(3):167-172.
PDF
Ruan J, Stormo GD, Zhang W
An iterated loop matching approach to the prediction of RNA secondary structures
with pseudoknots.
bioinformatics 2004 20(1):58-66.
PDF
2003
Wang T, Stormo GD
Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
bioinformatics 2003 19(18):2369-2380.
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Liu J, Tan K, Stormo GD.
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 31(23):6891-6903.
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Johnston M, Stormo GD.
Evolution. Heirlooms in the attic.
Science 2003 302(5647):997-999.
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Li JB, Lin S, Jia H, Wu H, Roe BA, Kulp D, Stormo GD, Dutcher SK.
Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III.
J Eukaryot Microbiol. 2003 50(3):145-155.
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Stormo GD
New tricks for an old dogma: riboswitches as cis-only regulatory systems.
Molecular cell 2003 11(6):1419-1420.
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2002
Silbaq FS, Ruttenberg SE, Stormo GD.
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections.
Nucleic Acids Res. 2002 30(24):5539-5548.
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Cobb JP, Laramie JM, Stormo GD, Morrissey JJ, Shannon WD, Qiu Y, Karl IE, Buchman TG, Hotchkiss RS.
Sepsis gene expression profiling: Murine splenic compared with hepatic responses determined by using
complementary DNA microarrays.
Crit Care Med. 2002 30(12):2711-2721.
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Benos PV, Lapedes AS, Stormo GD.
Probabilistic code for DNA recognition by proteins of the EGR family.
J. Mol. Biol. 2002 323(4):701-727,
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Benos PV, Bulyk ML, Stormo GD.
Additivity in protein-DNA interactions: how good an approximation is it?
Nucleic Acids Res. 2002 30(20):4442-4451.
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Lin Y, Han M, Shimada B, Wang L, Gibler TM, Amarakone A, Awad TA, Stormo GD, Van Gelder
RN, and Taghert PH.
Influence of the period-dependent circadian clock on diurnal, circadian, and
aperiodic gene expression in Drosophila melanogaster.
Proc. Natl. Acad. Sci. USA 2002 99(14):9562-9567.
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GuhaThakurta D, Palomar L, Stormo GD, Tedesco P, Johnson TE, Walker D, Lithgow G, Kim S and Link
CD
Identification of a novel cis regulatory element involved in
heat shock response in C. elegans using microarray gene
expression and computational methods.
Genome Research 2002 12(5):701-712.
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Benos PV, Lapedes AS and Stormo GD
Protein meets DNA. Is there a ``code'' for recognition? Probab(ilistical)ly.
Bioessays 2002 24(5):466-475.
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Stormo GD and Tan K
Mining Genome Databases to Identify and Understand New Gene Regulatory
Systems.
Current Opinion in Microbiology 2002 5:149-153.
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Beverley SM, Akopyants NS, Goyard S, Matlib RS, Gordon JL, Brownstein BH, Stormo GD, Bukanova EN, Hott CT, Li F, MacMillan S, Muo JN,
Schwertman LA, Smeds MR and Wang Y.
Putting the Leishmania genome to work: functional
genomics by transposon mapping and expression profiling.
Philo. Trans. Royal Society Lond B Biol Sci. 2002 357:47-53.
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GuhaThakurta D, Schriefer LA, Hresko MC, Waterston RH, and Stormo GD
Identifying Muscle Regulatory Elements And Genes in the Nematode
Caenorhabditis elegans
Pacific Symposium on Biocomputing 2002 7:425-436.
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2001
Li F and Stormo GD
Selection of optimal DNA oligos for gene expression arrays.
Bioinformatics 2001 17(11):1067-1076.
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GuhaThakurta D, and Stormo GD
Identifying target sites for cooperatively binding factors.
Bioinformatics 2001 17(7):608-621.
Abstract
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Man TK and Stormo GD
Non-independence of Mnt repressor-operator interaction determined by a new
quantitative multiple fluorescence relative affinity (QuMFRA) assay.
Nucleic Acids Research 2001. 29(12):2471-8.
Abstract
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Gorodkin J, Stricklin SL, Stormo GD
Discovering common stem-loop motifs in unaligned RNA sequences.
Nucleic Acids Research 2001 29(10):2135-44.
Abstract
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Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo, GD
A comparative genomics approach to prediction of new members of regulons.
Genome Research 2001. 11(4):566-84.
Abstract
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Benos PV, Lapedes AS, Fields DS, Stormo GD
SAMIE: statistical algorithm for modeling interaction energies.
Pacific Symposium on Biocomputing 2001 6:115-26.
Abstract
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Cobb JP, Brownstein BH, Watson MA, Shannon WD, Laramie JM, Qiu Y, Stormo GD, Morrissey JJ, Buchman TG, Karl IE, Hotchkiss RS
Injury in the ear of genomics.
Shock 2001 15(3):165-70.
Abstract
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2000
Li F and Stormo GD
Selecting optimum DNA oligos for microarrays.
BIBE 2000
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Akmaev VR, Kelley ST, Stormo GD
Phylogenetically enhanced statistical tools for RNA structure prediction.
Bioinformatics 2000 16(6):501-12.
Abstract
PDF
Workman CT, Stormo GD
ANN-Spec: a method for discovering transcription factor binding sites with improved specificity.
Pacific Symposium on Biocomputing 2000: 467-78.
Abstract
PDF
Stormo GD
DNA binding sites: representation and discovery.
Bioinformatics 2000. 16(1):16-23.
Abstract
PDF
Stormo GD
Gene-finding approaches for eukaryotes.
Genome Research 2000. 10(4):394-7.
Abstract
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Kelly ST, Akmaev VR, Stormo GD
Improved statistical methods reveal direct interactions between 16S and 23S rRNA.
Nucleic Acids Research 2000. 28(24):4938-43.
Abstract
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1999
Hertz GZ, Stormo GD
Identifying DNA and protein patterns with statistically significant alignments of multiple
sequences.
Bioinformatics 1999. 15(7-8):563-77.
Abstract
PDF
Weaver DC, Workman CT, Stormo GD
Modeling regulatory networks with weight matrices.
Pacific Symposium on Biocomputing 1999:112-23.
Abstract
PDF
Akmaev VR, Kelly ST, Stormo GD
A phylogenetic approach to RNA structure prediction.
Proc Int Conf Intell Syst Mol Biol. 1999:10-7.
Abstract
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1998
Stormo GD
Information content and free energy in DNA--protein interactions.
Journal of Theoretical Biology 1998. 195(1):135-7.
Abstract
PDF
Tabaska JE, Cary RB, Gabow HN, Stormo GD
An RNA folding method capable of identifying pseudoknots and base triples.
Bioinformatics 1998. 14(8):691-9.
Abstract
PDF
Stormo GD, Fields DS
Specificity, free energy and information content in protein-DNA interactions.
Trends in Biochemical Sciences 1998. 23(3):109-13.
Abstract
PDF
Levy S, Compagnoni L, Myers EW, Stormo GD
Xlandscape: the graphical display of word frequencies in sequences.
Bioinformatics 1998. 14(1):
Abstract
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1997
Gorodkin J, Heyer LJ, Brunak S, Stormo GD
Displaying the information contents of structural RNA alignments: the structure logos.
CABIOS(now Bioinformatics) 1997. 13(6):583-6.
Abstract
PDF
Tabaska JE and Stormo GD
Automated alignment of RNA sequences to pseudoknotted structures.
Proc Int Conf Intell Syst Mol Biol. 1997:311-8.
Abstract
PDF
Gorodkin J, Heyer LJ, Stormo GD
Finding common sequence and structure motifs in a set of RNA sequences.
Proc Int Conf Intell Syst Mol Biol.
Abstract
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Gorodkin J, Heyer LJ, Stormo GD
Finding the most significant common sequence and structure motifs in a set of RNA sequences.
Nucleic Acids Research 1997. 25(18):3724-32.
Abstract
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Fields DS, He Y, Al-Uzri AY, Stormo GD
Quantitative specificity of the Mnt repressor.
Journal of Molecular Biology 1997. 271(2):178-94.
Abstract
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Chen QK, Hertz GZ, Stormo GD
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD
matrices.
CABIOS(now Bioinformatics) 1997. 13(1):29-35.
Abstract
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Before 1997
Hertz GZ and Stormo GD
Escherichia coli promoter sequences: analysis and prediction.
Methods in Enzymology 1996. 273:30-42.
Abstract
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Chen QK, Hertz GZ, Stormo GD
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a
database of weight matrices.
CABIOS(now Bioinformatics) 1995. 11(5):563-6.
Abstract
PDF
Cui Y, Wang Q, Stormo GD, Calvo JM
A consensus sequence for binding of Lrp to DNA.
Journal of Bacteriology 1995. 177(17):4872-80.
Abstract
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Ulyanov Av and Stormo GD
Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions.
Nucleic Acids Research 1995. 23(8):1434-40.
Abstract
PDF
Snyder EE and Stormo GD
Identification of protein coding regions in genomic DNA.
Journal of Molecular Biology 1995. 248(1):1-18.
Abstract
PDF
Cary RB and Stormo GD
Graph-theoretic approach to RNA modeling using comparative data.
Proc Int Conf Intell Syst Mol Biol. 1995: 75-8.
Abstract
PDF
Fields DS and Stormo GD
Quantitative DNA sequencing to determine the relative protein-DNA binding constants to multiple DNA
sequences.
Analytical Biochemistry 1994. 219(2):230-9.
Abstract
PDF
Barrick D, Villanueba K, Childs J, Kalil R, Schneider TD, Lawrence CE, Gold L, Stormo GD
Quantitative analysis of ribosome binding sites in E.coli.
Nucleic Acids Research 1994. 22(7):1287-95.
Abstract
PDF
Melov S, Hertz GZ, Stormo GD, Johnson TE
Detection of deletions in the mitochondrial genome of Caenorhabditis elegans.
Nucleic Acids Research 1994. 22(6):1075-8.
Abstract
PDF
Stormo GD and Haussler D
Optimally parsing a sequence into different classes based on multiple types of evidence.
Proc Int Conf Intell Syst Mol Biol. 1994: 369-75.
Abstract
PDF
Heumann JM, Lapedes AS, Stormo GD
Neural networks for determining protein specificity and multiple alignment of binding sites.
Proc Int Conf Intell Syst Mol Biol. 1994: 188-94.
Abstract
PDF
Selick HE, Stormo GD, Dyson RL, Alberts BM
Analysis of five presumptive protein-coding sequences clustered between the primosome genes, 41 and 61,
of bacteriophages T4, T2, and T6.
Journal of Virology 1993. 67(4):2305-6.
Abstract
PDF
Stormo GD, Strobl S, Yoshioka M, Lee JS
Specificity of the Mnt protein. Independent effects of mutations at different positions in the
operator.
Journal of Molecular Biology 1993. 229(4):821-6.
Abstract
PDF
Snyder EE, Stormo GD
Identification of coding regions in genomic DNA sequences: an application of dynamic programming and
neural networks.
Nucleic Acids Research 1993. 21(3):607-13.
Abstract
PDF
Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD
Identifying constraints on the higher-order structure of RNA: continued development and application of
comparative sequence analysis methods.
Nucleic Acids Research 1992. 20(21):5785-95.
Abstract
PDF
Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C
Splicing signals in Drosophila: intron size, information content, and consensus sequences.
Nucleic Acids Research 1992. 20(16):4255-62.
Abstract
PDF
Ringquist S, Shinedling S, Barrick D, Green L, Binkley J, Stormo GD, Gold L
Translation initiation in Escherichia coli: sequences within the ribosome-binding site.
Molecular Microbiology 1992. 6(9):1219-29.
Abstract
PDF
Cardon LR, Stormo GD
Expectation maximization algorithm for identifying protein-binding sites with variable lengths from
unaligned DNA fragments.
Journal of Molecular Biology 1992. 223(1):159-70.
Abstract
PDF
Arvidson DN, Youderian P, Schneider TD, Stormo GD
Automated kinetic assay of beta-galactosidase activity.
Biotechniques 1991. 11(6):733-4.
Abstract
PDF
Stormo GD, Yoshioka M
Specificity of the Mnt protein determined by binding to randomized operators.
Proc Natl Acad Sci USA. 1991. 88(13):5699-703.
Abstract
PDF
Stormo GD
Probing information content of DNA-binding sites.
Methods in Enzymology 1991. 208:458-68.
Abstract
PDF
Ruffner DE, Stormo GD, Uhlenbeck OC
Sequence requirements of the hammerhead RNA self-cleavage reaction.
Biochemistry 1990. 29(47):10695-702.
Abstract
PDF
Hertz GZ, Hartzell GW 3rd, Stormo GD
Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
CABIOS(now Bioinformatics) 1990. 6(2):81-92.
Abstract
PDF
Gold L, Stormo GD
High-level translation initiation.
Methods in Enzymology 1990. 185:89-93.
Abstract
PDF
Stormo GD
Consensus patterns in DNA.
Methods in Enzymology 1990. 183:211-21.
Abstract
PDF
Stormo GD, Hartzell GW 3rd
Identifying protein-binding sites from unaligned DNA fragments.
Proc Natl Acad Sci USA. 1989. 86(4):1183-7.
Abstract
PDF
Schneider TD, Stormo GD
Excess information at bacteriophage T7 genomic promoters detected by a random
cloning technique.
Nucleic Acids Research 1989. 17(2):659-74.
Abstract
PDF
McPheeters DS, Stormo GD, Gold L
Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA.
Journal of Molecular Biology 1988. 201(3):517-35.
Abstract
PDF
Stormo GD
Computer methods for analyzing sequence recognition of nucleic acids.
Annual Review of Biochemistry 1988. 17:241-63.
Abstract
PDF
Stormo GD, Schneider TD, Gold L
Quantitative analysis of the relationship between nucleotide sequence and functional activity.
Nucleic Acids Research 1986. 14(16):6661-79.
Abstract
PDF
Schneider TD, Stormo GD, Gold L, Ehrenfeucht A
Information content of binding sites on nucleotide sequences.
Journal of Molecular Biology 1986. 188(3):415-31.
Abstract
PDF
Clift B, Haussler D, McConnell R, Schneider TD, Stormo GD
Sequence landscapes.
Nucleic Acids Research 1986. 14(1):141-58.
Abstract
Munson LM, Stormo GD, Niece RL, Reznikoff WS
lacZ translation initiation mutations.
Journal of Molecular Biology 1984. 177(4):663-83.
Abstract
PDF
Schneider TD, Stormo GD, Yarus MA, Gold L
Delila system tools.
Nucleic Acids Research 1984. 12(1):129-40.
Abstract
PDF
von Hippel PH, Kowalczykowski SC, Lonberg N, Newport JW, Paul LS, Stormo GD, Gold L
Autoregulation of gene expression. Quantitative evaluation of the expression and function of the
bacteriophage T4 gene 32 (single-stranded DNA
binding) protein system.
Journal of Molecular Biology 1982. 162(4):795-818.
Abstract
PDF
Schneider TD, Stormo GD, Haemer JS, Gold L
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation.
Nucleic Acids Research 1982. 10(9):3013-24.
Abstract
PDF
Stormo GD, Schneider TD, Gold L, Ehrenfeucht A
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
Nucleic Acids Research 1982. 10(9):2997-3011.
Abstract
PDF
Stormo GD, Schneider TD, Gold LM
Characterization of translational initiation sites in E. coli.
Nucleic Acids Research 1982. 10(9):2971-96.
Abstract
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