Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data
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Neil D. Lawrence | Antti Honkela | Magnus Rattray | Korbinian Grote | Ciira Wa Maina | Hendrik G. Stunnenberg | Filomena Matarese | George Reid | Neil D. Lawrence | M. Rattray | A. Honkela | H. Stunnenberg | C. Maina | F. Matarese | K. Grote | G. Reid
[1] John Shawe-Taylor,et al. Introduction to the Special Topic on Grammar Induction, Representation of Language and Language Learning , 2011, J. Mach. Learn. Res..
[2] David Higdon,et al. A process-convolution approach to modelling temperatures in the North Atlantic Ocean , 1998, Environmental and Ecological Statistics.
[3] A. Mortazavi,et al. Computation for ChIP-seq and RNA-seq studies , 2009, Nature Methods.
[4] Carl E. Rasmussen,et al. Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.
[5] Vidhya Jagannathan,et al. Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair , 2011, BMC Systems Biology.
[6] D. Komura,et al. A wave of nascent transcription on activated human genes , 2009, Proceedings of the National Academy of Sciences.
[7] Markus Harva,et al. Bayesian Estimation of Time Delays Between Unevenly Sampled Signals , 2008, 2006 16th IEEE Signal Processing Society Workshop on Machine Learning for Signal Processing.
[8] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[9] Neil D. Lawrence,et al. Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities , 2008, ECCB.
[10] Graziano Pesole,et al. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes , 2009, Nucleic Acids Res..
[11] Noel A Cressie,et al. Some topics in convolution-based spatial modeling , 2007 .
[12] Neil D. Lawrence,et al. Sparse Convolved Gaussian Processes for Multi-output Regression , 2008, NIPS.
[13] X. Darzacq,et al. In vivo dynamics of RNA polymerase II transcription , 2007, Nature Structural &Molecular Biology.
[14] Clifford A. Meyer,et al. Genome-wide analysis of estrogen receptor binding sites , 2006, Nature Genetics.
[15] E. Liu,et al. An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.
[16] Neil D. Lawrence,et al. Kernels for Vector-Valued Functions: a Review , 2011, Found. Trends Mach. Learn..
[17] Deborah B. Haarsma,et al. The Radio Wavelength Time Delay of Gravitational Lens 0957+561 , 1999 .
[18] H. Stunnenberg,et al. Identifying estrogen receptor target genes , 2007, Molecular oncology.
[19] Wyeth W. Wasserman,et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..
[20] Radford M. Neal. MCMC Using Hamiltonian Dynamics , 2011, 1206.1901.
[21] K. White,et al. Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer , 2009, Cell.
[22] Peter Tiño,et al. How accurate are the time delay estimates in gravitational lensing? , 2006, ArXiv.
[23] J. McNally,et al. Fast transcription rates of RNA polymerase II in human cells , 2011, EMBO reports.
[24] S. Kasif,et al. Immediate-Early and Delayed Primary Response Genes Are Distinct in Function and Genomic Architecture* , 2007, Journal of Biological Chemistry.
[25] Gil Ast,et al. Alternative splicing and disease , 2008, RNA biology.
[26] Neil D. Lawrence,et al. Computationally Efficient Convolved Multiple Output Gaussian Processes , 2011, J. Mach. Learn. Res..
[27] Quantitative Methods for Current Environmental Issues , 2005 .
[28] R. Sandberg,et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing , 2011, Nature.
[29] Andrew Gelman,et al. Handbook of Markov Chain Monte Carlo , 2011 .
[30] Neil D. Lawrence,et al. A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression , 2011, BMC Bioinformatics.
[31] D. Patel,et al. TRIM24 links a noncanonical histone signature to breast cancer , 2010, Nature.
[32] Brad T. Sherman,et al. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.
[33] H. Stunnenberg,et al. ChIP‐Seq of ERα and RNA polymerase II defines genes differentially responding to ligands , 2009, The EMBO journal.
[34] N. D. Clarke,et al. Integrative model of genomic factors for determining binding site selection by estrogen receptor-α , 2010, Molecular systems biology.
[35] D. Higdon. Space and Space-Time Modeling using Process Convolutions , 2002 .
[36] Clifford A. Meyer,et al. FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription , 2008, Cell.
[37] Ronald P. Barry,et al. Constructing and fitting models for cokriging and multivariable spatial prediction , 1998 .
[38] R. Padgett,et al. Rates of in situ transcription and splicing in large human genes , 2009, Nature Structural &Molecular Biology.
[39] Brent S. Pedersen,et al. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations , 2011, Bioinform..
[40] Wei Liu,et al. Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile , 2012, Bioinform..
[41] Jeffrey S. Rosenthal,et al. Optimal Proposal Distributions and Adaptive MCMC , 2011 .
[42] A. Malovannaya,et al. Global characterization of transcriptional impact of the SRC-3 coregulator. , 2010, Molecular endocrinology.
[43] Steven J. M. Jones,et al. Comprehensive molecular portraits of human breast tumours , 2013 .
[44] T. Misteli,et al. Transcription dynamics. , 2009, Molecular cell.
[45] G. Carter,et al. The generalized correlation method for estimation of time delay , 1976 .
[46] Petra C. Schwalie,et al. A CTCF-independent role for cohesin in tissue-specific transcription. , 2010, Genome research.
[47] R Edelson,et al. The Discrete Correlation Function: a New Method for Analyzing Unevenly Sampled Variability Data , 1988 .
[48] Antti Honkela,et al. Model-based method for transcription factor target identification with limited data , 2010, Proceedings of the National Academy of Sciences.
[49] Leighton J. Core,et al. A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells , 2011, Cell.
[50] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[51] Neil D. Lawrence,et al. puma: a Bioconductor package for propagating uncertainty in microarray analysis , 2009, BMC Bioinformatics.
[52] Marcus R. Frean,et al. Dependent Gaussian Processes , 2004, NIPS.
[53] C. Klinge. Estrogen receptor interaction with estrogen response elements. , 2001, Nucleic acids research.