Gary D. Stormo

According to our database, Gary D. Stormo authored at least 60 papers between 1984 and 2018.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2018

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

Shuxiang Ruan, Gary D. Stormo

BMC Bioinform., 2018

2017

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

Shuxiang Ruan, Gary D. Stormo

PLoS Comput. Biol., 2017

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

Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo

Bioinform., 2017

2015

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

Zheng Zuo, Yiming Chang, Gary D. Stormo

Quant. Biol., 2015

Determination of specificity influencing residues for key transcription factor families.

Ronak Y. Patel, Christian Garde, Gary D. Stormo

Quant. Biol., 2015

2014

Discriminative motif optimization based on perceptron training.

Ronak Y. Patel, Gary D. Stormo

Bioinform., 2014

2013

Modeling the specificity of protein-DNA interactions.

Gary D. Stormo

Quant. Biol., 2013

2012

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density.

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

PLoS Comput. Biol., 2012

ScerTF: a comprehensive database of benchmarked position weight matrices for <i>Saccharomyces</i> species.

Aaron T. Spivak, Gary D. Stormo

Nucleic Acids Res., 2012

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs.

Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler

J. Comput. Biol., 2012

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

Ryan G. Christensen, Metewo Selase Enuameh, Marcus B. Noyes, Michael H. Brodsky, Scot A. Wolfe, Gary D. Stormo

Bioinform., 2012

2010

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

Gurmukh Sahota, Gary D. Stormo

Bioinform., 2010

Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation.

Alan L. Kwan, Susan K. Dutcher, Gary D. Stormo

Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

2009

Inferring Binding Energies from Selected Binding Sites.

Yue Zhao, David Granas, Gary D. Stormo

PLoS Comput. Biol., 2009

Discovering <i>cis-</i>Regulatory RNAs in <i>Shewanella</i> Genomes by Support Vector Machines.

Xing Xu, Yongmei Ji, Gary D. Stormo

PLoS Comput. Biol., 2009

2008

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

Jiajian Liu, Gary D. Stormo

Bioinform., 2008

2007

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

Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, Rakesh Nagarajan

Nucleic Acids Res., 2007

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

Yiyong Zhou, Corentin Cras-Méneur, Mitsuru Ohsugi, Gary D. Stormo, M. Alan Permutt

Bioinform., 2007

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

Xing Xu, Yongmei Ji, Gary D. Stormo

Bioinform., 2007

Session Introduction.

Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo

Proceedings of the Biocomputing 2007, 2007

2006

An improved map of conserved regulatory sites for <i>Saccharomyces cerevisiae</i>.

Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel

BMC Bioinform., 2006

Using mRNAs lengths to accurately predict the alternatively spliced gene products in <i>Caenorhabditis elegans</i>.

Ritesh Agrawal, Gary D. Stormo

Bioinform., 2006

2005

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

Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos

Nucleic Acids Res., 2005

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

Jiajian Liu, Gary D. Stormo

BMC Bioinform., 2005

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

Jin Billy Li, Miao Zhang, Susan K. Dutcher, Gary D. Stormo

Bioinform., 2005

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

Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin

Bioinform., 2005

2004

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

Jianhua Ruan, Gary D. Stormo, Weixiong Zhang

Nucleic Acids Res., 2004

White Paper: Training the Next Generation of Informaticians: The Impact of "BISTI" and Bioinformatics - A Report from the American College of Medical Informatics.

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

J. Am. Medical Informatics Assoc., 2004

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

Jianhua Ruan, Gary D. Stormo, Weixiong Zhang

Bioinform., 2004

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

Yongmei Ji, Xing Xu, Gary D. Stormo

Bioinform., 2004

2003

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

Ting Wang, Gary D. Stormo

Bioinform., 2003

Selecting Degenerate Multiplex PCR Primers.

Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

An Iterative Loop Matching Approach to the Prediction of RNA Secondary Stru.

Jianhua Ruan, Gary D. Stormo, Weixiong Zhang

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002

Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans.

D. Guhathakurta, L. A. Schriefer, M. C. Hresko, R. H. Waterston, Gary D. Stormo

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Specificity of Protein-DNA Interactions.

Gary D. Stormo

Proceedings of the Gene Regulations and Metabolism - Postgenomic Computational Approaches, 2002

2001

Identifying target sites for cooperatively binding factors.

Debraj Guha Thakurta, Gary D. Stormo

Bioinform., 2001

Selection of optimal DNA oligos for gene expression arrays.

Fugen Li, Gary D. Stormo

Bioinform., 2001

The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA).

Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin

Bioinform., 2001

SAMIE: Statistical Algorithm for Modeling Interaction Energies.

Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

2000

DNA binding sites: representation and discovery.

Gary D. Stormo

Bioinform., 2000

Phylogenetically enhanced statistical tools for RNA structure prediction.

Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo

Bioinform., 2000

Selecting Optimum DNA Oligos for Microarrays.

Fugen Li, Gary D. Stormo

Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering, 2000

1999

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.

G. Z. Hertz, Gary D. Stormo

Bioinform., 1999

Modeling Regulatory Networks with Weight Matrices.

D. C. Weaver, Christopher T. Workman, Gary D. Stormo

Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

A Phylogenetic Approach to RNA Structure Prediction.

Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

1998

An RNA folding method capable of identifying pseudoknots and base triples.

Jack E. Tabaska, Robert B. Cary, Harold N. Gabow, Gary D. Stormo

Bioinform., 1998

Xlandscape: the graphical display of word frequencies in sequences.

Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo

Bioinform., 1998

1997

Displaying the information contents of structural RNA alignments: the structure logos.

Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo

Comput. Appl. Biosci., 1997

PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices.

Q. K. Chen, G. Z. Hertz, Gary D. Stormo

Comput. Appl. Biosci., 1997

Automated Alignment of RNA Sequences to Pseudoknotted Structures.

Jack E. Tabaska, Gary D. Stormo

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Finding Common Sequence and Structure Motifs in a Set of RNA Sequences.

Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

DNA Sequence Classification Using DAWGs.

Samuel Levy, Gary D. Stormo

Proceedings of the Structures in Logic and Computer Science, 1997

1995

MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.

Q. K. Chen, G. Z. Hertz, Gary D. Stormo

Comput. Appl. Biosci., 1995

Graph-Theoretic Approach to RNA Modeling Using Comparative Data.

Robert B. Cary, Gary D. Stormo

Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

1994

Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence.

Gary D. Stormo, David Haussler

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites.

John M. Heumann, Alan S. Lapedes, Gary D. Stormo

Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994

1993

SIGNAL SCAN 3.0: new database and program features.

Dan S. Prestridge, Gary D. Stormo

Comput. Appl. Biosci., 1993

1990

Identification of consensus patterns in unaligned DNA sequences known to be functionally related.

G. Z. Hertz, G. W. Hartzell III, Gary D. Stormo

Comput. Appl. Biosci., 1990

1986

Sequence landscapes.

B. Clift, David Haussler, Ross M. McConnell, Thomas D. Schneider, Gary D. Stormo

Nucleic Acids Res., 1986

1984

Delila system tools.

Thomas D. Schneider, Gary D. Stormo, Matthew A. Yarus, Larry Gold

Nucleic Acids Res., 1984