標(biāo)題: Titlebook: Computational Biology of Transcription Factor Binding; Istvan Ladunga Book 2010 Springer Science+Business Media, LLC 2010 Annotation.ChIP- [打印本頁] 作者: 詞源法 時間: 2025-3-21 20:03
書目名稱Computational Biology of Transcription Factor Binding影響因子(影響力)
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書目名稱Computational Biology of Transcription Factor Binding網(wǎng)絡(luò)公開度學(xué)科排名
書目名稱Computational Biology of Transcription Factor Binding被引頻次
書目名稱Computational Biology of Transcription Factor Binding被引頻次學(xué)科排名
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書目名稱Computational Biology of Transcription Factor Binding讀者反饋
書目名稱Computational Biology of Transcription Factor Binding讀者反饋學(xué)科排名
作者: 沐浴 時間: 2025-3-21 21:27
Components and Mechanisms of Regulation of Gene Expression, with specific DNA motifs in the control regions of the genes that they regulate. Upon binding to DNA, and through specific protein–protein interactions, these regulatory proteins convey signals to the basal transcriptional machinery, containing the respective RNA polymerases, resulting in particula作者: Initiative 時間: 2025-3-22 01:34 作者: 口音在加重 時間: 2025-3-22 05:40
Three-Dimensional Structures of DNA-Bound Transcriptional Regulators,rily based on three-dimensional structural studies using the methods of X-ray crystallography and NMR. Vast amount of accumulated experimental data have revealed the basic principles of protein–DNA complex formation paving the way for better modeling and prediction of DNA-binding properties of trans作者: 廣大 時間: 2025-3-22 10:42
Identification of Promoter Regions and Regulatory Sites, expression patterns, cell specificity and development. This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences.作者: BRINK 時間: 2025-3-22 13:31 作者: BRINK 時間: 2025-3-22 17:31 作者: Heresy 時間: 2025-3-23 00:33
The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Predf (semi-)automated computer-assisted prediction methods is needed to find TFBS over an entire genome, which is a first step in reconstructing mechanisms that control gene activity. Bioinformatics journals continue to publish diverse methods for predicting TFBS on a monthly basis. To help practitione作者: Anthem 時間: 2025-3-23 01:44
Computational Analysis of ChIP-seq Data,e genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics of ChIP-seq data and introduces a computational procedure to identify protein–DNA interactions 作者: 拍下盜公款 時間: 2025-3-23 06:46 作者: attenuate 時間: 2025-3-23 12:14
Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors,f the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we 作者: Dysarthria 時間: 2025-3-23 16:09
,Inferring Protein–DNA Interaction Parameters from SELEX Experiments,f oligonucleotides, of the oligomers with a high binding affinity for a given molecular target. The highest affinity binding sequences isolated through SELEX can have numerous research, diagnostic, and therapeutic applications. Recently, important new modifications of the SELEX protocol have been pr作者: labyrinth 時間: 2025-3-23 22:01 作者: PALMY 時間: 2025-3-23 23:30 作者: analogous 時間: 2025-3-24 04:29 作者: 毗鄰 時間: 2025-3-24 09:27
Computing Chromosome Conformation,n vivo. 3C studies indicate that genomes are likely organized into dynamic networks of physical contacts between genes and regulatory DNA elements. These interactions are mediated by proteins and are important for the regulation of genes. For these reasons, mapping physical connectivity networks wit作者: blackout 時間: 2025-3-24 14:29 作者: 一夫一妻制 時間: 2025-3-24 16:17
Evolution of ,-Regulatory Sequences in ,,r, we review probabilistic models of evolution of transcription factor binding sites, which provide the theoretical basis for a number of new bioinformatics tools for comparative sequence analysis. We illustrate how important functional and evolutionary insights on binding site gain and loss can be 作者: 茁壯成長 時間: 2025-3-24 20:18 作者: 相符 時間: 2025-3-25 00:15 作者: 過剩 時間: 2025-3-25 03:42 作者: Adornment 時間: 2025-3-25 07:31
X-Ray and Neutron InstrumentationHence, we developed Jstacs, an object-oriented Java framework for sequence analysis, which allows the user to combine different statistical models and different learning principles in a modular manner with little effort. In this chapter we explain how Jstacs can be used for the recognition of transcription factor binding sites.作者: gusher 時間: 2025-3-25 12:39 作者: 結(jié)束 時間: 2025-3-25 17:34
L. A. Feigin,D. I. Svergun,George W. Tayloror binding specificity, which allows accurate predictions of binding sites for any transcription factor of interest. In this chapter we discuss how to accurately determine protein–DNA interaction parameters from SELEX experiments. The chapter addresses experimental and computational procedure needed to generate and analyze appropriate data.作者: oncologist 時間: 2025-3-25 22:29 作者: botany 時間: 2025-3-26 03:11
Index of symbols and abbreviations,inding sites to a more holistic study of regulatory evolution. We point out common technical challenges, such as reliable sequence alignment and binding site prediction, when doing comparative regulatory sequence analysis and note some potential solutions thereof.作者: lipoatrophy 時間: 2025-3-26 06:23
Components and Mechanisms of Regulation of Gene Expression, players participating in these processes, the transcription factors and co-regulators, the .-regulatory elements that often function as transcription factor docking sites, and the emerging role of small RNAs in the regulation of gene expression.作者: 鬧劇 時間: 2025-3-26 12:22 作者: Incompetent 時間: 2025-3-26 12:56
The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Predr families. This chapter introduces the TFBS detection problem and reviews current strategies for evaluating algorithm effectiveness. In this chapter, a novel and robust assessment tool, the Motif Tool Assessment Platform (MTAP), is introduced and discussed.作者: avulsion 時間: 2025-3-26 19:32 作者: 朝圣者 時間: 2025-3-27 00:44
Computing Chromosome Conformation,out proper understanding and application of publicly available bioinformatics tools. This chapter explains how 5C studies are performed and describes stepwise how to use currently available bioinformatics tools for experimental design, data analysis, and interpretation.作者: 畏縮 時間: 2025-3-27 03:50 作者: 六邊形 時間: 2025-3-27 09:04
2.1.1.3.2 Symmetry of a surface layer,cription factors. In this review, our intent is to provide a general overview of the three-dimensional structures of DNA-bound transcriptional regulators starting from the basic principles of specific DNA recognition and ending with high-order multiprotein–DNA complexes.作者: Diskectomy 時間: 2025-3-27 11:26 作者: DEAF 時間: 2025-3-27 15:33 作者: obtuse 時間: 2025-3-27 20:21
L. A. Feigin,D. I. Svergun,George W. Taylorments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses and recommend strategies for effective motif discovery from these data.作者: 按等級 時間: 2025-3-27 22:13
Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors,ments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses and recommend strategies for effective motif discovery from these data.作者: 類人猿 時間: 2025-3-28 02:14
2.1.1.3.2 Symmetry of a surface layer,ription: in prokaryotic organisms operators are involved; in eukaryotic organisms, proximal promoter regions, enhancers, silencers, and insulators are present. This chapter will describe the various DNA regions involved in transcription and transcriptional regulation.作者: TSH582 時間: 2025-3-28 07:46 作者: Bereavement 時間: 2025-3-28 13:07
Index of symbols and abbreviations,nding sites (TFBS), and has been used to show that there are a large number of TE-derived TFBS. Many of these TE-derived TFBS show poor conservation and would go unnoticed using conservation screens. Here, we describe a simple pipeline method for using data generated through ChIP-seq to identify TE-derived TFBS.作者: 手銬 時間: 2025-3-28 16:12
Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators,ription: in prokaryotic organisms operators are involved; in eukaryotic organisms, proximal promoter regions, enhancers, silencers, and insulators are present. This chapter will describe the various DNA regions involved in transcription and transcriptional regulation.作者: bypass 時間: 2025-3-28 22:42
Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factorery in the peak environments. These methods have been implemented in, among others, Valouev et al.’s Quantitative Enrichment of Sequence Tags (QuEST) software tool. We demonstrate the prediction of the human growth-associated binding protein (GABPα) based on ChIP-seq observations.作者: Neuralgia 時間: 2025-3-28 23:06 作者: 上坡 時間: 2025-3-29 05:23
Three-Dimensional Structures of DNA-Bound Transcriptional Regulators,cription factors. In this review, our intent is to provide a general overview of the three-dimensional structures of DNA-bound transcriptional regulators starting from the basic principles of specific DNA recognition and ending with high-order multiprotein–DNA complexes.作者: 惡意 時間: 2025-3-29 08:45
,Motif Discovery Using Expectation Maximization and Gibbs’ Sampling,ple times from different initial parameters. Gibbs’ sampling is stochastic so that it may arrive at different solutions from the same initial parameters. In both cases multiple runs are advised because comparisons of the solutions after each run can indicate whether a global, optimum solution is likely to have been achieved.作者: enumaerate 時間: 2025-3-29 11:35
Istvan LadungaGuides scientists of all disciplines through the jungle of regulatory regions, ChIP-seq, about 200 motif discovery tools and others.Includes vital tricks-of-the-trade from experts well-versed in the t作者: 我悲傷 時間: 2025-3-29 16:05 作者: Irremediable 時間: 2025-3-29 21:47
https://doi.org/10.1007/978-1-60761-854-6Annotation; ChIP-seq; Genome browsers; Motif discovery tools; Promoter; Statistics; Transcriptional regula作者: 噱頭 時間: 2025-3-30 02:45
978-1-4939-6166-5Springer Science+Business Media, LLC 2010作者: inhibit 時間: 2025-3-30 07:02 作者: GUEER 時間: 2025-3-30 12:16
2.1.1.3.2 Symmetry of a surface layer, with specific DNA motifs in the control regions of the genes that they regulate. Upon binding to DNA, and through specific protein–protein interactions, these regulatory proteins convey signals to the basal transcriptional machinery, containing the respective RNA polymerases, resulting in particula作者: 鉆孔 時間: 2025-3-30 14:13
2.1.1.3.2 Symmetry of a surface layer,ory elements, on the DNA are footprints for the .-acting proteins involved in transcription, either for the positioning of the basic transcriptional machinery or for the regulation – in simple terms turn on or turn off – thereof. The basic transcriptional machinery is DNA-dependent RNA polymerase (R作者: 進取心 時間: 2025-3-30 17:18 作者: Interferons 時間: 2025-3-31 00:44
2.1.1.3.2 Symmetry of a surface layer, expression patterns, cell specificity and development. This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences.作者: Facilities 時間: 2025-3-31 04:11 作者: 面包屑 時間: 2025-3-31 08:56
X-Ray and Neutron Instrumentationffer from each other by pursuing different objectives and by taking into account different sources of information. For methods based on statistical approaches, these programs differ at an elementary level from each other by the statistical models used for individual binding sites and flanking sequen作者: FILLY 時間: 2025-3-31 10:31 作者: 有斑點 時間: 2025-3-31 15:50
https://doi.org/10.1007/978-1-4757-6624-0e genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics of ChIP-seq data and introduces a computational procedure to identify protein–DNA interactions 作者: 一加就噴出 時間: 2025-3-31 19:58
Structural Studies of Inorganic Materialsatin immunoprecipitation combined by next-generation sequencing (ChIP-seq) but also in advanced statistical analyses. A fundamental issue, however, is the alarming number of false positive predictions. This problem can be remedied by improved peak calling methods of twin peaks, one at each strand of作者: 易于 時間: 2025-3-31 21:43
L. A. Feigin,D. I. Svergun,George W. Taylorf the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we
