Determining the specificity of protein–DNA interactions von Stormo, Gary D, Zhao, Yue

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Quantitative analysis demonstrates most transcription factors require only simple models of specificity von Stormo, Gary D, Zhao, Yue

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Inherent limitations of probabilistic models for protein-DNA binding specificity von Ruan, Shuxiang, Stormo, Gary D

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An improved map of conserved regulatory sites for Saccharomyces cerevisiae von MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest

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Modeling the specificity of protein-DNA interactions von Stormo, Gary D.

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Redefining fundamental concepts of transcription initiation in bacteria von Mejía-Almonte, Citlalli, Busby, Stephen J. W., Wade, Joseph T., van Helden, Jacques, Arkin, Adam P., Stormo, Gary D., Eilbeck, Karen, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio

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Finding motifs using DNA images derived from sparse representations von Chu, Shane K, Stormo, Gary D

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Comparison of discriminative motif optimization using matrix and DNA shape-based models von Ruan, Shuxiang, Stormo, Gary D

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Improved models for transcription factor binding site identification using nonindependent interactions von Zhao, Yue, Ruan, Shuxiang, Pandey, Manishi, Stormo, Gary D

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High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding von Zuo, Zheng, Stormo, Gary D

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Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites von Noyes, Marcus B., Christensen, Ryan G., Wakabayashi, Atsuya, Stormo, Gary D., Brodsky, Michael H., Wolfe, Scot A.

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BEESEM: estimation of binding energy models using HT-SELEX data von Ruan, Shuxiang, Swamidass, S Joshua, Stormo, Gary D

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Quantitative specificity of STAT1 and several variants von Roy, Basab, Zuo, Zheng, Stormo, Gary D

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A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach von Wang, Peng, Sidney, John, Dow, Courtney, Mothé, Bianca, Sette, Alessandro, Peters, Bjoern

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An optimized two-finger archive for ZFN-mediated gene targeting von Gupta, Ankit, Christensen, Ryan G, Rayla, Amy L, Lakshmanan, Abirami, Stormo, Gary D, Wolfe, Scot A

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On the dependent recognition of some long zinc finger proteins von Zuo, Zheng, Billings, Timothy, Walker, Michael, Petkov, Petko M, Fordyce, Polly M, Stormo, Gary D

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The AP-1 transcription factor Batf controls T(H)17 differentiation von Schraml, Barbara U, Hildner, Kai, Ise, Wataru, Lee, Wan-Ling, Smith, Whitney A-E, Solomon, Ben, Sahota, Gurmukh, Sim, Julia, Mukasa, Ryuta, Cemerski, Saso, Hatton, Robin D, Stormo, Gary D, Weaver, Casey T, Russell, John H, Murphy, Theresa L, Murphy, Kenneth M

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Global and local architecture of the mammalian microRNA-transcription factor regulatory network von Shalgi, Reut, Lieber, Daniel, Oren, Moshe, Pilpel, Yitzhak

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Innate Host Defense Requires TFEB-Mediated Transcription of Cytoprotective and Antimicrobial Genes von Visvikis, Orane, Ihuegbu, Nnamdi, Labed, Sid A., Luhachack, Lyly G., Alves, Anna-Maria F., Wollenberg, Amanda C., Stuart, Lynda M., Stormo, Gary D., Irazoqui, Javier E.

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Inferring binding energies from selected binding sites von Zhao, Yue, Granas, David, Stormo, Gary D

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