Gary D. Stormo

61 papers A 6C 3Misc 4Journal 45Unranked 3

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Finding motifs using DNA images derived from sparse representations. Bioinform. Shane K. Chu, Gary D. Stormo
2018	J	`jnl`	Comparison of discriminative motif optimization using matrix and DNA shape-based models. BMC Bioinform. Shuxiang Ruan, Gary D. Stormo
2017	J	`jnl`	BEESEM: estimation of binding energy models using HT-SELEX data. Bioinform. Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo
2017	J	`jnl`	Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput. Biol. Shuxiang Ruan, Gary D. Stormo
2015	J	`jnl`	A quantitative understanding of lac repressor's binding specificity and flexibility. Quant. Biol. Zheng Zuo, Yiming Chang, Gary D. Stormo
2015	J	`jnl`	Determination of specificity influencing residues for key transcription factor families. Quant. Biol. Ronak Y. Patel, Christian Garde, Gary D. Stormo
2014	J	`jnl`	Discriminative motif optimization based on perceptron training. Bioinform. Ronak Y. Patel, Gary D. Stormo
2013	J	`jnl`	Modeling the specificity of protein-DNA interactions. Quant. Biol. Gary D. Stormo
2012	J	`jnl`	Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. J. Comput. Biol. Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler
2012	J	`jnl`	Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Comput. Biol. 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
2012	J	`jnl`	Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinform. Ryan G. Christensen, Metewo Selase Enuameh, Marcus B. Noyes, Michael H. Brodsky, Scot A. Wolfe, Gary D. Stormo
2012	J	`jnl`	ScerTF: a comprehensive database of benchmarked position weight matrices for Nucleic Acids Res. Aaron T. Spivak, Gary D. Stormo
2010	C	`conf`	Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation. BIBE Alan L. Kwan, Susan K. Dutcher, Gary D. Stormo
2010	J	`jnl`	Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinform. Gurmukh Sahota, Gary D. Stormo
2009	J	`jnl`	Discovering PLoS Comput. Biol. Xing Xu, Yongmei Ji, Gary D. Stormo
2009	J	`jnl`	Inferring Binding Energies from Selected Binding Sites. PLoS Comput. Biol. Yue Zhao, David Granas, Gary D. Stormo
2008	J	`jnl`	Context-dependent DNA recognition code for C Bioinform. Jiajian Liu, Gary D. Stormo
2007	J	`jnl`	A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinform. Yiyong Zhou, Corentin Cras-Méneur, Mitsuru Ohsugi, Gary D. Stormo, M. Alan Permutt
2007	J	`jnl`	PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. Nucleic Acids Res. Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, Rakesh Nagarajan
2007	J	`jnl`	RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinform. Xing Xu, Yongmei Ji, Gary D. Stormo
2007	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo
2006	J	`jnl`	An improved map of conserved regulatory sites for BMC Bioinform. Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
2006	J	`jnl`	Using mRNAs lengths to accurately predict the alternatively spliced gene products in Bioinform. Ritesh Agrawal, Gary D. Stormo
2005	J	`jnl`	Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinform. Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, Jan Gorodkin
2005	J	`jnl`	Procom: a web-based tool to compare multiple eukaryotic proteomes. Bioinform. Jin Billy Li, Miao Zhang, Susan K. Dutcher, Gary D. Stormo
2005	J	`jnl`	Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinform. Jiajian Liu, Gary D. Stormo
2005	J	`jnl`	enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos
2004	J	`jnl`	A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinform. Yongmei Ji, Xing Xu, Gary D. Stormo
2004	J	`jnl`	An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinform. Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
2004	J	`jnl`	ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res. Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
2004	J	`jnl`	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. 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
2003	—	`conf`	An Iterative Loop Matching Approach to the Prediction of RNA Secondary Stru. CSB Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
2003	J	`jnl`	Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinform. Ting Wang, Gary D. Stormo
2003	C	`conf`	Selecting Degenerate Multiplex PCR Primers. WABI Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang
2002	Misc	`conf`	Identifying Muscle Regulatory Elements and Genes in the Nematode Caenorhabditis Elegans. Pacific Symposium on Biocomputing D. Guhathakurta, L. A. Schriefer, M. C. Hresko, R. H. Waterston, Gary D. Stormo
2002	—	`conf`	Specificity of Protein-DNA Interactions. Gene Regulations and Metabolism Gary D. Stormo
2001	J	`jnl`	Identifying target sites for cooperatively binding factors. Bioinform. Debraj Guha Thakurta, Gary D. Stormo
2001	Misc	`conf`	SAMIE: Statistical Algorithm for Modeling Interaction Energies. Pacific Symposium on Biocomputing Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo
2001	J	`jnl`	Selection of optimal DNA oligos for gene expression arrays. Bioinform. Fugen Li, Gary D. Stormo
2001	J	`jnl`	The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinform. Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
2000	J	`jnl`	DNA binding sites: representation and discovery. Bioinform. Gary D. Stormo
2000	J	`jnl`	Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinform. Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo
2000	C	`conf`	Selecting Optimum DNA Oligos for Microarrays. BIBE Fugen Li, Gary D. Stormo
1999	A	`conf`	A Phylogenetic Approach to RNA Structure Prediction. ISMB Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo
1999	J	`jnl`	Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinform. G. Z. Hertz, Gary D. Stormo
1999	Misc	`conf`	Modeling Regulatory Networks with Weight Matrices. Pacific Symposium on Biocomputing D. C. Weaver, Christopher T. Workman, Gary D. Stormo
1998	J	`jnl`	An RNA folding method capable of identifying pseudoknots and base triples. Bioinform. Jack E. Tabaska, Robert B. Cary, Harold N. Gabow, Gary D. Stormo
1998	J	`jnl`	Xlandscape: the graphical display of word frequencies in sequences. Bioinform. Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo
1997	A	`conf`	Automated Alignment of RNA Sequences to Pseudoknotted Structures. ISMB Jack E. Tabaska, Gary D. Stormo
1997	—	`conf`	DNA Sequence Classification Using DAWGs. Structures in Logic and Computer Science Samuel Levy, Gary D. Stormo
1997	J	`jnl`	Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo
1997	A	`conf`	Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. ISMB Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo
1997	J	`jnl`	PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. Comput. Appl. Biosci. Q. K. Chen, G. Z. Hertz, Gary D. Stormo
1995	A	`conf`	Graph-Theoretic Approach to RNA Modeling Using Comparative Data. ISMB Robert B. Cary, Gary D. Stormo
1995	J	`jnl`	MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci. Q. K. Chen, G. Z. Hertz, Gary D. Stormo
1994	A	`conf`	Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites. ISMB John M. Heumann, Alan S. Lapedes, Gary D. Stormo
1994	A	`conf`	Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence. ISMB Gary D. Stormo, David Haussler
1993	J	`jnl`	SIGNAL SCAN 3.0: new database and program features. Comput. Appl. Biosci. Dan S. Prestridge, Gary D. Stormo
1990	J	`jnl`	Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. G. Z. Hertz, G. W. Hartzell III, Gary D. Stormo
1986	J	`jnl`	Sequence landscapes. Nucleic Acids Res. B. Clift, David Haussler, Ross M. McConnell, Thomas D. Schneider, Gary D. Stormo
1984	J	`jnl`	Delila system tools. Nucleic Acids Res. Thomas D. Schneider, Gary D. Stormo, Matthew A. Yarus, Larry Gold