Gary D. Stormo

Publication Activity (10 Years)

Years Active: 1984-2018
Publications (10 Years): 3

Top Topics

Sequence Similarity

High Throughput

Probabilistic Model

Top Venues

PLoS Comput. Biol.

Publications

Shuxiang Ruan, Gary D. Stormo
Comparison of discriminative motif optimization using matrix and DNA shape-based models. BMC Bioinform. 19 (1) (2018)
Shuxiang Ruan, Gary D. Stormo
Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput. Biol. 13 (7) (2017)
Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo
BEESEM: estimation of binding energy models using HT-SELEX data. Bioinform. 33 (15) (2017)
Zheng Zuo, Yiming Chang, Gary D. Stormo
A quantitative understanding of lac repressor's binding specificity and flexibility. Quant. Biol. 3 (2) (2015)
Ronak Y. Patel, Christian Garde, Gary D. Stormo
Determination of specificity influencing residues for key transcription factor families. Quant. Biol. 3 (3) (2015)
Ronak Y. Patel, Gary D. Stormo
Discriminative motif optimization based on perceptron training. Bioinform. 30 (7) (2014)
Gary D. Stormo
Modeling the specificity of protein-DNA interactions. Quant. Biol. 1 (2) (2013)
Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler
Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. J. Comput. Biol. 19 (2) (2012)
Claudia Coronnello, Ryan J. Hartmaier, Arshi Arora, Luai Huleihel, Kusum V. Pandit, Abha S. Bais, Michael Butterworth, Naftali Kaminski, Gary D. Stormo, Steffi Oesterreich, Panayiotis V. Benos
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Comput. Biol. 8 (12) (2012)
Ryan G. Christensen, Metewo Selase Enuameh, Marcus B. Noyes, Michael H. Brodsky, Scot A. Wolfe, Gary D. Stormo
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinform. 28 (12) (2012)
Aaron T. Spivak, Gary D. Stormo
species. Nucleic Acids Res. 40 (Database-Issue) (2012)
Alan L. Kwan, Susan K. Dutcher, Gary D. Stormo
Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation. BIBE (2010)
Gurmukh Sahota, Gary D. Stormo
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinform. 26 (21) (2010)
Xing Xu, Yongmei Ji, Gary D. Stormo
Genomes by Support Vector Machines. PLoS Comput. Biol. 5 (4) (2009)
Yue Zhao, David Granas, Gary D. Stormo
Inferring Binding Energies from Selected Binding Sites. PLoS Comput. Biol. 5 (12) (2009)
Jiajian Liu, Gary D. Stormo
zinc-finger transcription factors. Bioinform. 24 (17) (2008)
Yiyong Zhou, Corentin Cras-Méneur, Mitsuru Ohsugi, Gary D. Stormo, M. Alan Permutt
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinform. 23 (16) (2007)
Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, Rakesh Nagarajan
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Xing Xu, Yongmei Ji, Gary D. Stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinform. 23 (15) (2007)
Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo
Session Introduction. Pacific Symposium on Biocomputing (2007)
Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
. BMC Bioinform. 7 (2006)
Ritesh Agrawal, Gary D. Stormo
. Bioinform. 22 (10) (2006)
Jiajian Liu, Gary D. Stormo
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinform. 6 (2005)
Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinform. 21 (9) (2005)
Jin Billy Li, Miao Zhang, Susan K. Dutcher, Gary D. Stormo
Procom: a web-based tool to compare multiple eukaryotic proteomes. Bioinform. 21 (8) (2005)
Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinform. 20 (1) (2004)
Charles P. Friedman, Russ B. Altman, Isaac S. Kohane, Kathleen A. McCormick, Perry L. Miller, Judy G. Ozbolt, Edward H. Shortliffe, Gary D. Stormo, M. Cleat Szczepaniak, David Tuck, Jeffrey J. Williamson
White Paper: Training the Next Generation of Informaticians: The Impact of "BISTI" and Bioinformatics - A Report from the American College of Medical Informatics. J. Am. Medical Informatics Assoc. 11 (3) (2004)
Yongmei Ji, Xing Xu, Gary D. Stormo
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinform. 20 (10) (2004)
Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang
Selecting Degenerate Multiplex PCR Primers. WABI (2003)
Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
An Iterative Loop Matching Approach to the Prediction of RNA Secondary Stru. CSB (2003)
Ting Wang, Gary D. Stormo
Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinform. 19 (18) (2003)
D. Guhathakurta, L. A. Schriefer, M. C. Hresko, R. H. Waterston, Gary D. Stormo
Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans. Pacific Symposium on Biocomputing (2002)
Gary D. Stormo
Specificity of Protein-DNA Interactions. Gene Regulations and Metabolism (2002)
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinform. 17 (10) (2001)
Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo
SAMIE: Statistical Algorithm for Modeling Interaction Energies. Pacific Symposium on Biocomputing (2001)
Fugen Li, Gary D. Stormo
Selection of optimal DNA oligos for gene expression arrays. Bioinform. 17 (11) (2001)
Debraj Guha Thakurta, Gary D. Stormo
Identifying target sites for cooperatively binding factors. Bioinform. 17 (7) (2001)
Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo
Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinform. 16 (6) (2000)
Gary D. Stormo
DNA binding sites: representation and discovery. Bioinform. 16 (1) (2000)
Fugen Li, Gary D. Stormo
Selecting Optimum DNA Oligos for Microarrays. BIBE (2000)
G. Z. Hertz, Gary D. Stormo
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinform. 15 (7) (1999)
D. C. Weaver, Christopher T. Workman, Gary D. Stormo
Modeling Regulatory Networks with Weight Matrices. Pacific Symposium on Biocomputing (1999)
Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo
A Phylogenetic Approach to RNA Structure Prediction. ISMB (1999)
Jack E. Tabaska, Robert B. Cary, Harold N. Gabow, Gary D. Stormo
An RNA folding method capable of identifying pseudoknots and base triples. Bioinform. 14 (8) (1998)
Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo
Xlandscape: the graphical display of word frequencies in sequences. Bioinform. 14 (1) (1998)
Samuel Levy, Gary D. Stormo
DNA Sequence Classification Using DAWGs. Structures in Logic and Computer Science (1997)
Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. ISMB (1997)
Q. K. Chen, G. Z. Hertz, Gary D. Stormo
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Appl. Biosci. 13 (1) (1997)
Jack E. Tabaska, Gary D. Stormo
Automated Alignment of RNA Sequences to Pseudoknotted Structures. ISMB (1997)
Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo
Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. 13 (6) (1997)
Q. K. Chen, G. Z. Hertz, Gary D. Stormo
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci. 11 (5) (1995)
Robert B. Cary, Gary D. Stormo
Graph-Theoretic Approach to RNA Modeling Using Comparative Data. ISMB (1995)
John M. Heumann, Alan S. Lapedes, Gary D. Stormo
Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites. ISMB (1994)
Gary D. Stormo, David Haussler
Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence. ISMB (1994)
Dan S. Prestridge, Gary D. Stormo
SIGNAL SCAN 3.0: new database and program features. Comput. Appl. Biosci. 9 (1) (1993)
G. Z. Hertz, G. W. Hartzell III, Gary D. Stormo
Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. 6 (2) (1990)
B. Clift, David Haussler, Ross M. McConnell, Thomas D. Schneider, Gary D. Stormo
Sequence landscapes. Nucleic Acids Res. 14 (1) (1986)
Thomas D. Schneider, Gary D. Stormo, Matthew A. Yarus, Larry Gold
Delila system tools. Nucleic Acids Res. 12 (1) (1984)