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Gary stormo

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TOP 3
Cong Zhu; Ryan Christensen; Benjamin Dake; Ankit Gupta; Victoria L Hall; Charlotte Kuperwasser; Abirami Lakshmanan; Amy L Rayla; Gary stormo; Scot A Wolfe
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases.
Ryan Christensen; Metewo Selase Enuameh; Marcus B Noyes; Michael H Brodsky; Scot A Wolfe; Gary stormo
Recognition models to predict DNA-binding specificities of homeodomain proteins.
Ryan Christensen; Ankit Gupta; Lawrence A Schriefer; Scot A Wolfe; Zheng Zuo; Gary stormo
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity.

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All Publications

2013: Cong Zhu; Ryan Christensen; Benjamin Dake; Ankit Gupta; Victoria L Hall; Charlotte Kuperwasser; Abirami Lakshmanan; Amy L Rayla; Gary stormo; Scot A Wolfe
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases.
Nucleic acids research 2013;41(4):2455-65.
2012: Ryan Christensen; Metewo Selase Enuameh; Marcus B Noyes; Michael H Brodsky; Scot A Wolfe; Gary stormo
Recognition models to predict DNA-binding specificities of homeodomain proteins.
Bioinformatics (Oxford, England) 2012;28(12):i84-9.
2011: Ryan Christensen; Ankit Gupta; Lawrence A Schriefer; Scot A Wolfe; Zheng Zuo; Gary stormo
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity.
Nucleic acids research 2011;39(12):e83.
2009: Yue Zhao; David Granas; Gary stormo
Inferring binding energies from selected binding sites.
PLoS computational biology 2009;5(12):e1000590.
2009: Xing Xu; Yongmei Ji; Gary stormo
Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines.
PLoS computational biology 2009;5(4):e1000338.
2008: Jiajian Liu; Xing Xu; Gary stormo
The cis-regulatory map of Shewanella genomes.
Nucleic acids research 2008;36(16):5376-90.
2008: Jiajian Liu; Gary stormo
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.
Bioinformatics (Oxford, England) 2008;24(17):1850-7.
2008: Marcus B Noyes; Ryan Christensen; Atsuya Wakabayashi; Gary stormo; Michael H Brodsky; Scot A Wolfe
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.
Cell 2008;133(7):1277-89.
2008: Jason M Laramie; T Philip Chung; Buddy Brownstein; Gary stormo; J Perren Cobb
Transcriptional profiles of human epithelial cells in response to heat: computational evidence for novel heat shock proteins.
Shock (Augusta, Ga.) 2008;29(5):623-30.
2008: Li Wei Chang; Jacqueline E Payton; Wenlin Yuan; Timothy J Ley; Rakesh Nagarajan; Gary stormo
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia.
Genome biology 2008;9(2):R38.
2008: Jue Zeng; Jizhou Yan; Ting Wang; Deborah Mosbrook-Davis; Kyle T Dolan; Ryan Christensen; Gary stormo; David Haussler; Richard H Lathrop; Rainer K Brachmann; Shawn M Burgess
Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins.
Nucleic acids research 2008;36(1):e8.
2007: Sherri R Davies; Li-Wei Chang; Debabrata Patra; Xiaoyun Xing; Karen L Posey; Jacqueline Hecht; Gary stormo; Linda J Sandell
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes.
Genome research 2007;17(10):1438-47.
2007: Yiyong Zhou; Corentin Cras-Méneur; Mitsuru Ohsugi; Gary stormo; M Alan Permutt
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments.
Bioinformatics (Oxford, England) 2007;23(16):2073-9.
2007: Gary stormo; Yue Zhao
Putting numbers on the network connections.
BioEssays : news and reviews in molecular, cellular and developmental biology 2007;29(8):717-21.
2007: Xing Xu; Yongmei Ji; Gary stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment.
Bioinformatics (Oxford, England) 2007;23(15):1883-91.
2007: Li-Wei Chang; Burr R Fontaine; Gary stormo; Rakesh Nagarajan
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis.
Nucleic acids research 2007;35(Web Server issue):W238-44.
2007: Guoyan Zhao; Lawrence A Schriefer; Gary stormo
Identification of muscle-specific regulatory modules in Caenorhabditis elegans.
Genome research 2007;17(3):348-57.
2007: Richard Souvenir; Jeremy Buhler; Gary stormo; Weixiong Zhang
An iterative method for selecting degenerate multiplex PCR primers.
Methods in molecular biology (Clifton, N.J.) 2007;402():245-68.
2007: R H Rochat; Lisa de las Fuentes; Gary stormo; Victor G Davila-Roman; C Charles Gu
A novel method combining linkage disequilibrium information and imputed functional knowledge for tagSNP selection.
Human heredity 2007;64(4):243-9.
2007: Guoyan Zhao; Kuan Y Chang; Katherine Varley; Gary stormo
Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach.
PloS one 2007;2(2):e262.
2006: T Philip Chung; Jason M Laramie; Donald J Meyer; Thomas J Downey; Laurence H Y Tam; Huashi Ding; Timothy G Buchman; Irene E Karl; Gary stormo; Richard S Hotchkiss; J Perren Cobb
Molecular diagnostics in sepsis: from bedside to bench.
Journal of the American College of Surgeons 2006;203(5):585-598.
2006: David L DeMets; Gary stormo; Michael Boehnke; Thomas A Louis; Jeremy Taylor; Dennis Dixon
Training of the next generation of biostatisticians: a call to action in the U.S.
Statistics in medicine 2006;25(20):3415-29.
2006: Gary stormo
An introduction to recognizing functional domains.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2006;Chapter 2():Unit 2.1.
2006: Ritesh Agrawal; Gary stormo
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans.
Bioinformatics (Oxford, England) 2006;22(10):1239-44.
2006: Gary stormo
An overview of RNA structure prediction and applications to RNA gene prediction and RNAi design.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2006;Chapter 12():Unit 12.1.
2006: Li-Wei Chang; Rakesh Nagarajan; Jeffrey A Magee; Jeffrey Milbrandt; Gary stormo
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.
Genome research 2006;16(3):405-13.
2006: Chin-Tong Ong; Hui-Teng Cheng; Li-Wei Chang; Toshiyuki Ohtsuka; Ryoichiro Kageyama; Gary stormo; Raphael Kopan
Target selectivity of vertebrate notch proteins. Collaboration between discrete domains and CSL-binding site architecture determines activation probability.
The Journal of biological chemistry 2006;281(8):5106-19.
2006: Kenzie D Macisaac; Ting Wang; D Benjamin Gordon; David K Gifford; Gary stormo; Ernest Fraenkel
An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
BMC bioinformatics 2006;7():113.
2006: Jeffrey A Magee; Li-Wei Chang; Gary stormo; Jeffrey Milbrandt
Direct, androgen receptor-mediated regulation of the FKBP5 gene via a distal enhancer element.
Endocrinology 2006;147(1):590-8.
2005: Ting Wang; Gary stormo
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(48):17400-5.
2005: Christopher T Workman; Yutong Yin; David L Corcoran; Trey Ideker; Gary stormo; Panayiotis V Benos
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Nucleic acids research 2005;33(Web Server issue):W389-92.
2005: Ritesh Agrawal; Gary stormo
Editing efficiency of a Drosophila gene correlates with a distant splice site selection.
RNA (New York, N.Y.) 2005;11(5):563-6.
2005: Jakob H Havgaard; Rune B Lyngsø; Gary stormo; Jan Gorodkin
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
Bioinformatics (Oxford, England) 2005;21(9):1815-24.
2005: Jin Billy Li; Miao Zhang; Susan Dutcher; Gary stormo
Procom: a web-based tool to compare multiple eukaryotic proteomes.
Bioinformatics (Oxford, England) 2005;21(8):1693-4.
2005: J Perren Cobb; Michael N Mindrinos; Carol Miller-Graziano; Steve E Calvano; Henry V Baker; wenzhong xiao; Krzysztof Laudanski; Bernard H Brownstein; Constance M Elson; Douglas L Hayden; David N Herndon; Stephen F Lowry; Ronald V Maier; David A Schoenfeld; Lyle L Moldawer; Ronald W Davis; Ronald G Tompkins; Henry V Baker; Paul Bankey; Timothy Billiar; Bernard H Brownstein; Steve E Calvano; David Camp; Irshad Chaudry; J Perren Cobb; Ronald W Davis; Constance M Elson; Bradley Freeman; Richard Gamelli; Nicole Gibran; Brian Harbrecht; Douglas L Hayden; Wyrta Heagy; David Heimbach; David N Herndon; Jureta Horton; John Hunt; Krzysztof Laudanski; James Lederer; Stephen F Lowry; Ronald V Maier; John Mannick; Bruce McKinley; Carol Miller-Graziano; Michael Mindrinos; Joseph Minei; Lyle L Moldawer; Ernest Moore; Frederick Moore; Robert Munford; Avery Nathens; Grant O'keefe; Gary Purdue; Laurence Rahme; Daniel Remick; Matthew Sailors; David A Schoenfeld; Michael Shapiro; Geoffrey Silver; Richard Smith; Gregory Stephanopoulos; Gary stormo; Ronald G Tompkins; Mehmet Toner; Shaw Warren; Michael West; Steven Wolfe; Wenzhong Xiao; Vernon Young
Application of genome-wide expression analysis to human health and disease.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(13):4801-6.
2005: Kai Tan; Lee Ann McCue; Gary stormo
Making connections between novel transcription factors and their DNA motifs.
Genome research 2005;15(2):312-20.
2005: Robert R Freimuth; Gary stormo; howard mcleod
PolyMAPr: programs for polymorphism database mining, annotation, and functional analysis.
Human mutation 2005;25(2):110-7.
2005: Jiajian Liu; Gary stormo
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions.
Nucleic acids research 2005;33(17):e141.
2005: Jiajian Liu; Gary stormo
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.
BMC bioinformatics 2005;6():176.
2005: Naum I Gershenzon; Gary stormo; Ilya P Ioshikhes
Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites.
Nucleic acids research 2005;33(7):2290-301.
2004: Debraj GuhaThakurta; Lawrence A Schriefer; Robert H Waterston; Gary stormo
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes.
Genome research 2004;14(12):2457-68.
2004: Yiing Lin; Gary stormo; Paul H Taghert
The neuropeptide pigment-dispersing factor coordinates pacemaker interactions in the Drosophila circadian system.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2004;24(36):7951-7.
2004: Yongmei Ji; Xing Xu; Gary stormo
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.
Bioinformatics (Oxford, England) 2004;20(10):1591-602.
2004: Jianhua Ruan; Gary stormo; Weixiong Zhang
ILM: a web server for predicting RNA secondary structures with pseudoknots.
Nucleic acids research 2004;32(Web Server issue):W146-9.
2004: Natalia S Akopyants; Robin S Matlib; Elena N Bukanova; Matthew R Smeds; Bernard H Brownstein; Gary stormo; Stephen M Beverley
Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major.
Molecular and biochemical parasitology 2004;136(1):71-86.
2004: Tao Zhao; Li-Wei Chang; howard mcleod; Gary stormo
PromoLign: a database for upstream region analysis and SNPs.
Human mutation 2004;23(6):534-9.
2004: Jin Billy Li; Jantje M Gerdes; Courtney J. Haycraft; Yanli Fan; Tanya M Teslovich; Helen May-Simera; Haitao Li; Oliver E Blacque; Linya Li; Carmen C Leitch; Richard Allan Lewis; Jane S Green; Patrick S Parfrey; Michel R Leroux; William S Davidson; Philip L Beales; Lisa M Guay-Woodford; Bradley K Yoder; Gary stormo; Nicholas Katsanis; Susan Dutcher
Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.
Cell 2004;117(4):541-52.
2004: Charles P Friedman; Russ B Altman; Isaac S Kohane; Kathleen A McCormick; Perry L Miller; Judy Ozbolt; Edward H Shortliffe; Gary stormo; M Cleat Szczepaniak; David Tuck; Jeffrey Williamson
Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics.
Journal of the American Medical Informatics Association : JAMIA 2004;11(3):167-72.
2004: Yan Hu; Ting Wang; Gary stormo; Jeffrey I Gordon
RNA interference of achaete-scute homolog 1 in mouse prostate neuroendocrine cells reveals its gene targets and DNA binding sites.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(15):5559-64.
2004: Tsz-Kwong Man; Joshua SungWoo Yang; Gary stormo
Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor.
Nucleic acids research 2004;32(13):4026-32.
2004: Jianhua Ruan; Gary stormo; Weixiong Zhang
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots.
Bioinformatics (Oxford, England) 2004;20(1):58-66.
2003: Ting Wang; Gary stormo
Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
Bioinformatics (Oxford, England) 2003;19(18):2369-80.
2003: Jiajian Liu; Kai Tan; Gary stormo
Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria.
Nucleic acids research 2003;31(23):6891-903.
2003: Mark Johnston; Gary stormo
Evolution. Heirlooms in the attic.
Science (New York, N.Y.) 2003;302(5647):997-9.
2003: Gary stormo
New tricks for an old dogma: riboswitches as cis-only regulatory systems.
Molecular cell 2003;11(6):1419-20.
2003: Jin Billy Li; Shaoping Lin; Honggui Jia; Hongmin Wu; Bruce A Roe; David Kulp; Gary stormo; Susan Dutcher
Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III.
The Journal of eukaryotic microbiology 2003;50(3):145-55.
2002: Fauzi S Silbaq; Steven E Ruttenberg; Gary stormo
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections.
Nucleic acids research 2002;30(24):5539-48.
2002: J Perren Cobb; Jason M Laramie; Gary stormo; Jerry J Morrissey; William D Shannon; Yuyu Qiu; Irene E Karl; Timothy G Buchman; Richard S Hotchkiss
Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays.
Critical care medicine 2002;30(12):2711-21.
2002: Panayiotis V Benos; Alan S Lapedes; Gary stormo
Probabilistic code for DNA recognition by proteins of the EGR family.
Journal of molecular biology 2002;323(4):701-27.
2002: Panayiotis V Benos; Martha L Bulyk; Gary stormo
Additivity in protein-DNA interactions: how good an approximation is it?
Nucleic acids research 2002;30(20):4442-51.
2002: Yiing Lin; Mei Han; Brian Shimada; Lin Wang; Therese M Gibler; Aloka Amarakone; Tarif A Awad; Gary stormo; Russell N Van Gelder; Paul H Taghert
Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(14):9562-7.
2002: C Charles Gu; Dabeeru C Rao; Gary stormo; Chindo Hicks; Michael A Province
Role of gene expression microarray analysis in finding complex disease genes.
Genetic epidemiology 2002;23(1):37-56.
2002: Panayiotis V Benos; Alan S Lapedes; Gary stormo
Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .
BioEssays : news and reviews in molecular, cellular and developmental biology 2002;24(5):466-75.
2002: Debraj GuhaThakurta; Lisanne Palomar; Gary stormo; Pat Tedesco; Thomas Johnson; David W Walker; Gordon Lithgow; Stuart Kim; Christopher D Link
Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods.
Genome research 2002;12(5):701-12.
2002: Gary stormo; Kai Tan
Mining genome databases to identify and understand new gene regulatory systems.
Current opinion in microbiology 2002;5(2):149-53.
2002: Stephen M Beverley; Natalia S Akopyants; Sophie Goyard; Robin S Matlib; Jennifer L Gordon; Bernard H Brownstein; Gary stormo; Elena N Bukanova; Christian T Hott; Fugen Li; Sandra MacMillan; James N Muo; Libbey A Schwertman; Matthew R Smeds; Yujia Wang
Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2002;357(1417):47-53.
2002: Debraj GuhaThakurta; Lawrence A Schriefer; Michelle Coutu Hresko; Robert H Waterston; Gary stormo
Identifying muscle regulatory elements and genes in the nematode Caenorhabditis elegans.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():425-36.
2001: F Li; Gary stormo
Selection of optimal DNA oligos for gene expression arrays.
Bioinformatics (Oxford, England) 2001;17(11):1067-76.
2001: Gary stormo; Y Ji
Do mRNAs act as direct sensors of small molecules to control their expression?
Proceedings of the National Academy of Sciences of the United States of America 2001;98(17):9465-7.
2001: Debraj GuhaThakurta; Gary stormo
Identifying target sites for cooperatively binding factors.
Bioinformatics (Oxford, England) 2001;17(7):608-21.
2001: Tsz-Kwong Man; Gary stormo
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.
2001: Jan Gorodkin; S L Stricklin; Gary stormo
Discovering common stem-loop motifs in unaligned RNA sequences.
Nucleic acids research 2001;29(10):2135-44.
2001: Kai Tan; Gabriel Moreno-Hagelsieb; Julio Collado-Vides; Gary stormo
A comparative genomics approach to prediction of new members of regulons.
Genome research 2001;11(4):566-84.
2001: J Perren Cobb; Bernard H Brownstein; M A Watson; W D Shannon; Jason M Laramie; Yuyu Qiu; Gary stormo; J J Morrissey; Timothy G Buchman; Irene E Karl; Richard S Hotchkiss
Injury in the era of genomics.
Shock (Augusta, Ga.) 2001;15(3):165-70.
2001: Jan Gorodkin; R B Lyngso; Gary stormo
A mini-greedy algorithm for faster structural RNA stem-loop search.
Genome informatics. International Conference on Genome Informatics 2001;12():184-93.
2001: Panayiotis V Benos; Alan S Lapedes; DS Fields; Gary stormo
SAMIE: statistical algorithm for modeling interaction energies.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():115-26.
2000: Scott T Kelley; VR Akmaev; Gary stormo
Improved statistical methods reveal direct interactions between 16S and 23S rRNA.
Nucleic acids research 2000;28(24):4938-43.
2000: VR Akmaev; Scott T Kelley; Gary stormo
Phylogenetically enhanced statistical tools for RNA structure prediction.
Bioinformatics (Oxford, England) 2000;16(6):501-12.
2000: Gary stormo
Gene-finding approaches for eukaryotes.
Genome research 2000;10(4):394-7.
2000: C T Workman; Gary stormo
ANN-Spec: a method for discovering transcription factor binding sites with improved specificity.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000;():467-78.
2000: Gary stormo
DNA binding sites: representation and discovery.
Bioinformatics (Oxford, England) 2000;16(1):16-23.
1999: G Z Hertz; Gary stormo
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
Bioinformatics (Oxford, England) 1999;15(7-8):563-77.
1999: VR Akmaev; Scott T Kelley; Gary stormo
A phylogenetic approach to RNA structure prediction.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():10-7.
1999: D C Weaver; C T Workman; Gary stormo
Modeling regulatory networks with weight matrices.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1999;():112-23.
1998: Gary stormo
Information content and free energy in DNA--protein interactions.
Journal of theoretical biology 1998;195(1):135-7.
1998: Gary stormo; DS Fields
Specificity, free energy and information content in protein-DNA interactions.
Trends in biochemical sciences 1998;23(3):109-13.
1998: J E Tabaska; R B Cary; H N Gabow; Gary stormo
An RNA folding method capable of identifying pseudoknots and base triples.
Bioinformatics (Oxford, England) 1998;14(8):691-9.
1998: S Levy; L Compagnoni; E W Myers; Gary stormo
Xlandscape: the graphical display of word frequencies in sequences.
Bioinformatics (Oxford, England) 1998;14(1):74-80.
1997: Jan Gorodkin; LJ Heyer; S Brunak; Gary stormo
Displaying the information contents of structural RNA alignments: the structure logos.
Computer applications in the biosciences : CABIOS 1997;13(6):583-6.
1997: Jan Gorodkin; LJ Heyer; Gary stormo
Finding the most significant common sequence and structure motifs in a set of RNA sequences.
Nucleic acids research 1997;25(18):3724-32.
1997: DS Fields; Y He; A Y Al-Uzri; Gary stormo
Quantitative specificity of the Mnt repressor.
Journal of molecular biology 1997;271(2):178-94.
1997: Q K Chen; G Z Hertz; Gary stormo
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices.
Computer applications in the biosciences : CABIOS 1997;13(1):29-35.
1997: J E Tabaska; Gary stormo
Automated alignment of RNA sequences to pseudoknotted structures.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():311-8.
1997: Jan Gorodkin; LJ Heyer; Gary stormo
Finding common sequence and structure motifs in a set of RNA sequences.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():120-3.
1996: G Z Hertz; Gary stormo
Escherichia coli promoter sequences: analysis and prediction.
Methods in enzymology 1996;273():30-42.
1995: Q K Chen; G Z Hertz; Gary stormo
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.
Computer applications in the biosciences : CABIOS 1995;11(5):563-6.
1995: P Chen; Michael Ailion; Thomas A Bobik; Gary stormo; J Roth
Five promoters integrate control of the cob/pdu regulon in Salmonella typhimurium.
Journal of bacteriology 1995;177(19):5401-10.
1995: Y Cui; Q Wang; Gary stormo; J M Calvo
A consensus sequence for binding of Lrp to DNA.
Journal of bacteriology 1995;177(17):4872-80.
1995: A V Ulyanov; Gary stormo
Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions.
Nucleic acids research 1995;23(8):1434-40.
1995: Eric Snyder; Gary stormo
Identification of protein coding regions in genomic DNA.
Journal of molecular biology 1995;248(1):1-18.
1995: R B Cary; Gary stormo
Graph-theoretic approach to RNA modeling using comparative data.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():75-80.
1994: D S Fields; Gary stormo
Quantitative DNA sequencing to determine the relative protein-DNA binding constants to multiple DNA sequences.
Analytical biochemistry 1994;219(2):230-9.
1994: D Barrick; K Villanueba; J Childs; R Kalil; T D Schneider; C E Lawrence; L Gold; Gary stormo
Quantitative analysis of ribosome binding sites in E.coli.
Nucleic acids research 1994;22(7):1287-95.
1994: S Melov; G Z Hertz; Gary stormo; Thomas Johnson
Detection of deletions in the mitochondrial genome of Caenorhabditis elegans.
Nucleic acids research 1994;22(6):1075-8.
1994: Gary stormo; David Haussler
Optimally parsing a sequence into different classes based on multiple types of evidence.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():369-75.
1994: J M Heumann; A S Lapedes; Gary stormo
Neural networks for determining protein specificity and multiple alignment of binding sites.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():188-94.
1993: H E Selick; Gary stormo; R L Dyson; Bruce Alberts
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):2305-16.
1993: Gary stormo; S Strobl; Makoto Yoshioka; J S Lee
Specificity of the Mnt protein. Independent effects of mutations at different positions in the operator.
Journal of molecular biology 1993;229(4):821-6.
1993: Eric Snyder; Gary stormo
Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks.
Nucleic acids research 1993;21(3):607-13.
1993: D S Prestridge; Gary stormo
SIGNAL SCAN 3.0: new database and program features.
Computer applications in the biosciences : CABIOS 1993;9(1):113-5.
1992: robin gutell; A Power; G Z Hertz; E J Putz; Gary stormo
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.
1992: Steve Mount; C Burks; G Hertz; Gary stormo; Owen R White; C Fields
Splicing signals in Drosophila: intron size, information content, and consensus sequences.
Nucleic acids research 1992;20(16):4255-62.
1992: S Ringquist; S Shinedling; D Barrick; L Green; J Binkley; Gary stormo; L Gold
Translation initiation in Escherichia coli: sequences within the ribosome-binding site.
Molecular microbiology 1992;6(9):1219-29.
1992: L R Cardon; Gary stormo
Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments.
Journal of molecular biology 1992;223(1):159-70.
1991: D N Arvidson; Philip Youderian; T D Schneider; Gary stormo
Automated kinetic assay of beta-galactosidase activity.
BioTechniques 1991;11(6):733-4, 736, 738.
1991: Gary stormo; Makoto Yoshioka
Specificity of the Mnt protein determined by binding to randomized operators.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(13):5699-703.
1991: Gary stormo
Probing information content of DNA-binding sites.
Methods in enzymology 1991;208():458-68.
1990: D E Ruffner; Gary stormo; Olke C Uhlenbeck
Sequence requirements of the hammerhead RNA self-cleavage reaction.
Biochemistry 1990;29(47):10695-702.
1990: G Z Hertz; G W Hartzell; Gary stormo
Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
Computer applications in the biosciences : CABIOS 1990;6(2):81-92.
1990: L Gold; Gary stormo
High-level translation initiation.
Methods in enzymology 1990;185():89-93.
1990: Gary stormo
Consensus patterns in DNA.
Methods in enzymology 1990;183():211-21.
1989: Gary stormo; G W Hartzell
Identifying protein-binding sites from unaligned DNA fragments.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(4):1183-7.
1989: T D Schneider; Gary stormo
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique.
Nucleic acids research 1989;17(2):659-74.
1988: D S McPheeters; Gary stormo; L Gold
Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA.
Journal of molecular biology 1988;201(3):517-35.
1988: C Tuerk; P Gauss; Claude Thermes; D R Groebe; M Gayle; N Guild; Gary stormo; Yves d'Aubenton-Carafa; O C Uhlenbeck; Ignacio Tinoco
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.
Proceedings of the National Academy of Sciences of the United States of America 1988;85(5):1364-8.
1988: Gary stormo
Computer methods for analyzing sequence recognition of nucleic acids.
Annual review of biophysics and biophysical chemistry 1988;17():241-63.
1987: P J Romaniuk; P Lowary; H N Wu; Gary stormo; O C Uhlenbeck
RNA binding site of R17 coat protein.
Biochemistry 1987;26(6):1563-8.
1986: Gary stormo; T D Schneider; L Gold
Quantitative analysis of the relationship between nucleotide sequence and functional activity.
Nucleic acids research 1986;14(16):6661-79.
1986: D S McPheeters; A Christensen; E T Young; Gary stormo; L Gold
Translational regulation of expression of the bacteriophage T4 lysozyme gene.
Nucleic acids research 1986;14(14):5813-26.
1986: T D Schneider; Gary stormo; L Gold; A Ehrenfeucht
Information content of binding sites on nucleotide sequences.
Journal of molecular biology 1986;188(3):415-31.
1986: B Clift; David Haussler; R McConnell; T D Schneider; Gary stormo
Sequence landscapes.
Nucleic acids research 1986;14(1):141-58.
1984: L Gold; Gary stormo; R Saunders
Escherichia coli translational initiation factor IF3: a unique case of translational regulation.
Proceedings of the National Academy of Sciences of the United States of America 1984;81(22):7061-5.
1984: L M Munson; Gary stormo; Ronald Niece; W S Reznikoff
lacZ translation initiation mutations.
Journal of molecular biology 1984;177(4):663-83.
1984: Maria Trojanowska; E S Miller; J Karam; Gary stormo; L Gold
The bacteriophage T4 regA gene: primary sequence of a translational repressor.
Nucleic acids research 1984;12(15):5979-93.
1984: T D Schneider; Gary stormo; M A Yarus; L Gold
Delila system tools.
Nucleic acids research 1984;12(1 Pt 1):129-40.
1982: Peter H von Hippel; S C Kowalczykowski; N Lonberg; J W Newport; L S Paul; Gary stormo; L Gold
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.
1982: T D Schneider; Gary stormo; J S Haemer; L Gold
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation.
Nucleic acids research 1982;10(9):3013-24.
1982: Gary stormo; T D Schneider; L Gold; A Ehrenfeucht
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
Nucleic acids research 1982;10(9):2997-3011.
1982: Gary stormo; T D Schneider; L M Gold
Characterization of translational initiation sites in E. coli.
Nucleic acids research 1982;10(9):2971-96.
1981: L Gold; D Pribnow; T Schneider; S Shinedling; B S Singer; Gary stormo
Translational initiation in prokaryotes.
Annual review of microbiology 1981;35():365-403.