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Gary D. Stormo
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2010 – 2019
- 2018
- [j44]Shuxiang Ruan
, Gary D. Stormo
Comparison of discriminative motif optimization using matrix and DNA shape-based models. BMC Bioinform. 19(1): 86:1-86:8 (2018) - 2017
- [j43]Shuxiang Ruan
BEESEM: estimation of binding energy models using HT-SELEX data. Bioinform. 33(15): 2288-2295 (2017) - [j42]Shuxiang Ruan
Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput. Biol. 13(7) (2017) - 2015
- [j41]Zheng Zuo, Yiming Chang, Gary D. Stormo:
A quantitative understanding of lac repressor's binding specificity and flexibility. Quant. Biol. 3(2): 69-80 (2015) - [j40]Ronak Y. Patel, Christian Garde, Gary D. Stormo:
Determination of specificity influencing residues for key transcription factor families. Quant. Biol. 3(3): 115-123 (2015) - 2014
- [j39]Ronak Y. Patel, Gary D. Stormo:
Discriminative motif optimization based on perceptron training. Bioinform. 30(7): 941-948 (2014) - 2013
- [j38]Gary D. Stormo:
Modeling the specificity of protein-DNA interactions. Quant. Biol. 1(2): 115-130 (2013) - 2012
- [j37]Ryan G. Christensen, Metewo Selase Enuameh, Marcus B. Noyes, Michael H. Brodsky
Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinform. 28(12): 84-89 (2012) - [j36]Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler
Fast, Sensitive Discovery of Conserved Genome-Wide Motifs. J. Comput. Biol. 19(2): 139-147 (2012) - [j35]Aaron T. Spivak, Gary D. Stormo:
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res. 40(Database-Issue): 162-168 (2012) - [j34]Claudia Coronnello
Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. PLoS Comput. Biol. 8(12) (2012) - 2010
- [j33]Gurmukh Sahota, Gary D. Stormo:
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinform. 26(21): 2672-2677 (2010) - [c16]Alan L. Kwan, Susan K. Dutcher, Gary D. Stormo:
Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation. BIBE 2010: 99-105
2000 – 2009
- 2009
- [j32]Xing Xu, Yongmei Ji, Gary D. Stormo:
Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines. PLoS Comput. Biol. 5(4) (2009) - [j31]Yue Zhao, David Granas, Gary D. Stormo:
Inferring Binding Energies from Selected Binding Sites. PLoS Comput. Biol. 5(12) (2009) - 2008
- [j30]Jiajian Liu, Gary D. Stormo:
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinform. 24(17): 1850-1857 (2008) - 2007
- [j29]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): 1883-1891 (2007) - [j28]Yiyong Zhou, Corentin Cras-Méneur
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinform. 23(16): 2073-2079 (2007) - [j27]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): 238-244 (2007) - [c15]Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo:
Session Introduction. Pacific Symposium on Biocomputing 2007: 470-471 - 2006
- [j26]Ritesh Agrawal, Gary D. Stormo:
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans. Bioinform. 22(10): 1239-1244 (2006) - [j25]Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinform. 7: 113 (2006) - 2005
- [j24]Jin Billy Li, Miao Zhang, Susan K. Dutcher, Gary D. Stormo:
Procom: a web-based tool to compare multiple eukaryotic proteomes. Bioinform. 21(8): 1693-1694 (2005) - [j23]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): 1815-1824 (2005) - [j22]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: 176 (2005) - [j21]Christopher T. Workman
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 33(Web-Server-Issue): 389-392 (2005) - 2004
- [j20]Jianhua Ruan
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinform. 20(1): 58-66 (2004) - [j19]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): 1603-1611 (2004) - [j18]Charles P. Friedman, Russ B. Altman, Isaac S. Kohane, Kathleen A. McCormick, Perry L. Miller, Judy G. Ozbolt, Edward H. Shortliffe
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): 167-172 (2004) - [j17]Jianhua Ruan
ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res. 32(Web-Server-Issue): 146-149 (2004) - 2003
- [j16]Ting Wang, Gary D. Stormo:
Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinform. 19(18): 2369-2380 (2003) - [c14]Jianhua Ruan
An Iterative Loop Matching Approach to the Prediction of RNA Secondary Stru. CSB 2003: 519-520 - [c13]Richard Souvenir, Jeremy Buhler
Selecting Degenerate Multiplex PCR Primers. WABI 2003: 512-526 - 2002
- [c12]Gary D. Stormo:
Specificity of Protein-DNA Interactions. Gene Regulations and Metabolism 2002: 87-101 - [c11]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: 425-436 - 2001
- [j15]Debraj Guha Thakurta, Gary D. Stormo:
Identifying target sites for cooperatively binding factors. Bioinform. 17(7): 608-621 (2001) - [j14]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): 859-861 (2001) - [j13]Fugen Li, Gary D. Stormo:
Selection of optimal DNA oligos for gene expression arrays. Bioinform. 17(11): 1067-1076 (2001) - [c10]Panayiotis V. Benos, Alan S. Lapedes, D. S. Fields, Gary D. Stormo:
SAMIE: Statistical Algorithm for Modeling Interaction Energies. Pacific Symposium on Biocomputing 2001: 115-126 - 2000
- [j12]Gary D. Stormo:
DNA binding sites: representation and discovery. Bioinform. 16(1): 16-23 (2000) - [j11]Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo:
Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinform. 16(6): 501-512 (2000) - [c9]Fugen Li, Gary D. Stormo:
Selecting Optimum DNA Oligos for Microarrays. BIBE 2000: 200-207
1990 – 1999
- 1999
- [j10]G. Z. Hertz, Gary D. Stormo:
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinform. 15(7): 563-577 (1999) - [c8]Viatcheslav R. Akmaev, Scott T. Kelley, Gary D. Stormo:
A Phylogenetic Approach to RNA Structure Prediction. ISMB 1999: 10-17 - [c7]D. C. Weaver, Christopher T. Workman, Gary D. Stormo:
Modeling Regulatory Networks with Weight Matrices. Pacific Symposium on Biocomputing 1999: 112-123 - 1998
- [j9]Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo:
Xlandscape: the graphical display of word frequencies in sequences. Bioinform. 14(1): 74-80 (1998) - [j8]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): 691-699 (1998) - 1997
- [j7]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): 29-35 (1997) - [j6]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): 583-586 (1997) - [c6]Samuel Levy, Gary D. Stormo:
DNA Sequence Classification Using DAWGs. Structures in Logic and Computer Science 1997: 339-352 - [c5]Jan Gorodkin, Laurie J. Heyer, Gary D. Stormo:
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences. ISMB 1997: 120-123 - [c4]Jack E. Tabaska, Gary D. Stormo:
Automated Alignment of RNA Sequences to Pseudoknotted Structures. ISMB 1997: 311-318 - 1995
- [j5]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): 563-566 (1995) - [c3]Robert B. Cary, Gary D. Stormo:
Graph-Theoretic Approach to RNA Modeling Using Comparative Data. ISMB 1995: 75-80 - 1994
- [c2]John M. Heumann, Alan S. Lapedes, Gary D. Stormo:
Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites. ISMB 1994: 188-194 - [c1]Gary D. Stormo, David Haussler:
Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence. ISMB 1994: 369-375 - 1993
- [j4]Dan S. Prestridge, Gary D. Stormo:
SIGNAL SCAN 3.0: new database and program features. Comput. Appl. Biosci. 9(1): 113-115 (1993) - 1990
- [j3]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): 81-92 (1990)
1980 – 1989
- 1986
- [j2]B. Clift, David Haussler, Ross M. McConnell, Thomas D. Schneider
Sequence landscapes. Nucleic Acids Res. 14(1): 141-158 (1986) - 1984
- [j1]Thomas D. Schneider
Delila system tools. Nucleic Acids Res. 12(1): 129-140 (1984)
Coauthor Index
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