TY - JOUR AU - Weirauch, M. T. AU - Cote, A. AU - Norel, R. AU - Annala, M. AU - Zhao, Y. AU - Riley, T. R. AU - Saez-Rodriguez, J. AU - Cokelaer, T. AU - Vedenko, A. AU - Talukder, S. AU - Bussemaker, H. J. AU - Morris, Q. D. AU - Bulyk, M. L. AU - Stolovitzky, G. AU - Hughes, T. R. PY - 2013 DA - 2013// TI - Evaluation of methods for modeling transcription factor sequence specificity JO - Nat Biotechnol VL - 31 UR - https://doi.org/10.1038/nbt.2486 DO - 10.1038/nbt.2486 ID - Weirauch2013 ER - TY - JOUR AU - Yang, Y. H. AU - Dudoit, S. AU - Luu, P. AU - Lin, D. M. AU - Peng, V. AU - Ngai, J. AU - Speed, T. P. PY - 2002 DA - 2002// TI - Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.4.e15 DO - 10.1093/nar/30.4.e15 ID - Yang2002 ER - TY - JOUR AU - Wang, J. PY - 2008 DA - 2008// TI - Computational biology of genome expression and regulation–a review of microarray bioinformatics JO - J Environ Pathol Toxicol Oncol VL - 27 UR - https://doi.org/10.1615/JEnvironPatholToxicolOncol.v27.i3.10 DO - 10.1615/JEnvironPatholToxicolOncol.v27.i3.10 ID - Wang2008 ER - TY - JOUR AU - Wang, J. AU - Nygaard, V. AU - Smith-Sorensen, B. AU - Hovig, E. AU - Myklebost, O. PY - 2002 DA - 2002// TI - MArray: analysing single, replicated or reversed microarray experiments JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.8.1139 DO - 10.1093/bioinformatics/18.8.1139 ID - Wang2002 ER - TY - JOUR AU - Djordjevic, M. AU - Sengupta, A. M. AU - Shraiman, B. I. PY - 2003 DA - 2003// TI - A biophysical approach to transcription factor binding site discovery JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1271603 DO - 10.1101/gr.1271603 ID - Djordjevic2003 ER - TY - JOUR AU - Gerland, U. AU - Moroz, J. D. AU - Hwa, T. PY - 2002 DA - 2002// TI - Physical constraints and functional characteristics of transcription factor-DNA interaction JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.192693599 DO - 10.1073/pnas.192693599 ID - Gerland2002 ER - TY - JOUR AU - Berg, O. G. AU - von Hippel, P. H. PY - 1987 DA - 1987// TI - Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters JO - J Mol Biol VL - 193 UR - https://doi.org/10.1016/0022-2836(87)90354-8 DO - 10.1016/0022-2836(87)90354-8 ID - Berg1987 ER - TY - JOUR AU - Granek, J. A. AU - Clarke, N. D. PY - 2005 DA - 2005// TI - Explicit equilibrium modeling of transcription-factor binding and gene regulation JO - Genome Biol VL - 6 UR - https://doi.org/10.1186/gb-2005-6-10-r87 DO - 10.1186/gb-2005-6-10-r87 ID - Granek2005 ER - TY - JOUR AU - Kinney, J. B. AU - Murugan, A. AU - Callan, C. G. AU - Cox, E. C. PY - 2010 DA - 2010// TI - Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.1004290107 DO - 10.1073/pnas.1004290107 ID - Kinney2010 ER - TY - JOUR AU - Roider, H. G. AU - Kanhere, A. AU - Manke, T. AU - Vingron, M. PY - 2007 DA - 2007// TI - Predicting transcription factor affinities to DNA from a biophysical model JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl565 DO - 10.1093/bioinformatics/btl565 ID - Roider2007 ER - TY - JOUR AU - Foat, B. C. AU - Morozov, A. V. AU - Bussemaker, H. J. PY - 2006 DA - 2006// TI - Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl223 DO - 10.1093/bioinformatics/btl223 ID - Foat2006 ER - TY - JOUR AU - Wang, J. AU - Morigen PY - 2009 DA - 2009// TI - BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-345 DO - 10.1186/1471-2105-10-345 ID - Wang2009 ER - TY - JOUR AU - Zhao, Y. AU - Granas, D. AU - Stormo, G. D. PY - 2009 DA - 2009// TI - Inferring binding energies from selected binding sites JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000590 DO - 10.1371/journal.pcbi.1000590 ID - Zhao2009 ER - TY - JOUR AU - Sun, W. AU - Hu, X. AU - Lim, M. H. AU - Ng, C. K. AU - Choo, S. H. AU - Castro, D. S. AU - Drechsel, D. AU - Guillemot, F. AU - Kolatkar, P. R. AU - Jauch, R. AU - Prabhakar, S. PY - 2013 DA - 2013// TI - TherMos: Estimating protein-DNA binding energies from in vivo binding profiles JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt250 DO - 10.1093/nar/gkt250 ID - Sun2013 ER - TY - JOUR AU - Tomovic, A. AU - Oakeley, E. J. PY - 2007 DA - 2007// TI - Position dependencies in transcription factor binding sites JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm055 DO - 10.1093/bioinformatics/btm055 ID - Tomovic2007 ER - TY - JOUR AU - Benos, P. V. AU - Bulyk, M. L. AU - Stormo, G. D. PY - 2002 DA - 2002// TI - Additivity in protein-DNA interactions: how good an approximation is it? JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/gkf578 DO - 10.1093/nar/gkf578 ID - Benos2002 ER - TY - JOUR AU - Bulyk, M. L. AU - Johnson, P. L. AU - Church, G. M. PY - 2002 DA - 2002// TI - Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.5.1255 DO - 10.1093/nar/30.5.1255 ID - Bulyk2002 ER - TY - JOUR AU - Man, T. K. AU - Stormo, G. D. PY - 2001 DA - 2001// TI - Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.12.2471 DO - 10.1093/nar/29.12.2471 ID - Man2001 ER - TY - JOUR AU - Tipping, M. PY - 2001 DA - 2001// TI - Sparse Bayesian learning and the relevance vector machine JO - J Mach Learn Res VL - 1 ID - Tipping2001 ER - TY - JOUR AU - Bland, J. M. AU - Altman, D. G. PY - 1986 DA - 1986// TI - Statistical methods for assessing agreement between two methods of clinical measurement JO - Lancet VL - 1 UR - https://doi.org/10.1016/S0140-6736(86)90837-8 DO - 10.1016/S0140-6736(86)90837-8 ID - Bland1986 ER - TY - JOUR AU - Jolma, A. AU - Yan, J. AU - Whitington, T. AU - Toivonen, J. AU - Nitta, K. R. AU - Rastas, P. AU - Morgunova, E. AU - Enge, M. AU - Taipale, M. AU - Wei, G. AU - Palin, K. AU - Vaquerizas, J. M. AU - Vincentelli, R. AU - Luscombe, N. M. AU - Hughes, T. R. AU - Lemaire, P. AU - Ukkonen, E. AU - Kivioja, T. AU - Taipale, J. PY - 2013 DA - 2013// TI - DNA-binding specificities of human transcription factors JO - Cell VL - 152 UR - https://doi.org/10.1016/j.cell.2012.12.009 DO - 10.1016/j.cell.2012.12.009 ID - Jolma2013 ER - TY - JOUR AU - Zhao, Y. AU - Ruan, S. AU - Pandey, M. AU - Stormo, G. D. PY - 2012 DA - 2012// TI - Improved models for transcription factor binding site identification using nonindependent interactions JO - Genetics VL - 191 UR - https://doi.org/10.1534/genetics.112.138685 DO - 10.1534/genetics.112.138685 ID - Zhao2012 ER - TY - JOUR AU - Chen, X. AU - Hughes, T. R. AU - Morris, Q. PY - 2007 DA - 2007// TI - RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm224 DO - 10.1093/bioinformatics/btm224 ID - Chen2007 ER - TY - JOUR AU - Park, P. J. PY - 2009 DA - 2009// TI - ChIP-seq: advantages and challenges of a maturing technology JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2641 DO - 10.1038/nrg2641 ID - Park2009 ER - TY - JOUR AU - Stennard, F. A. AU - Costa, M. W. AU - Elliott, D. A. AU - Rankin, S. AU - Haast, S. J. AU - Lai, D. AU - McDonald, L. P. AU - Niederreither, K. AU - Dolle, P. AU - Bruneau, B. G. AU - Zorn, A. M. AU - Harvey, R. P. PY - 2003 DA - 2003// TI - Cardiac T-box factor Tbx20 directly interacts with Nkx2-5, GATA4, and GATA5 in regulation of gene expression in the developing heart JO - Dev Biol VL - 262 UR - https://doi.org/10.1016/S0012-1606(03)00385-3 DO - 10.1016/S0012-1606(03)00385-3 ID - Stennard2003 ER - TY - JOUR AU - Yang, Y. H. AU - Speed, T. PY - 2002 DA - 2002// TI - Design issues for cDNA microarray experiments JO - Nat Rev Genet VL - 3 ID - Yang2002 ER - TY - BOOK AU - Jackson, J. E. PY - 1991 DA - 1991// TI - A User's Guids to Principal Components PB - Sons, Inc CY - New York UR - https://doi.org/10.1002/0471725331 DO - 10.1002/0471725331 ID - Jackson1991 ER - TY - JOUR AU - Jackson, J. E. PY - 1980 DA - 1980// TI - Principal components and factor analysis: part I- principal components JO - J Qual Technol VL - 12 ID - Jackson1980 ER - TY - JOUR AU - Wang, J. PY - 2010 DA - 2010// TI - The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-412 DO - 10.1186/1471-2105-11-412 ID - Wang2010 ER - TY - JOUR AU - Stormo, G. D. AU - Fields, D. S. PY - 1998 DA - 1998// TI - Specificity, free energy and information content in protein-DNA interactions JO - Trends Biochem Sci VL - 23 UR - https://doi.org/10.1016/S0968-0004(98)01187-6 DO - 10.1016/S0968-0004(98)01187-6 ID - Stormo1998 ER - TY - JOUR AU - Wang, J. PY - 2007 DA - 2007// TI - A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle JO - J Biomed Inform VL - 40 UR - https://doi.org/10.1016/j.jbi.2007.02.003 DO - 10.1016/j.jbi.2007.02.003 ID - Wang2007 ER - TY - JOUR AU - Newburger, D. E. AU - Bulyk, M. L. PY - 2009 DA - 2009// TI - UniPROBE: an online database of protein binding microarray data on protein-DNA interactions JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn660 DO - 10.1093/nar/gkn660 ID - Newburger2009 ER - TY - JOUR AU - Ward, L. D. AU - Bussemaker, H. J. PY - 2008 DA - 2008// TI - Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn154 DO - 10.1093/bioinformatics/btn154 ID - Ward2008 ER -