標(biāo)題: Titlebook: Computational Methods for 3D Genome Analysis; Ryuichiro Nakato Book 2025 The Editor(s) (if applicable) and The Author(s), under exclusive [打印本頁] 作者: 恰當(dāng) 時(shí)間: 2025-3-21 17:57
書目名稱Computational Methods for 3D Genome Analysis影響因子(影響力)
書目名稱Computational Methods for 3D Genome Analysis影響因子(影響力)學(xué)科排名
書目名稱Computational Methods for 3D Genome Analysis網(wǎng)絡(luò)公開度
書目名稱Computational Methods for 3D Genome Analysis網(wǎng)絡(luò)公開度學(xué)科排名
書目名稱Computational Methods for 3D Genome Analysis被引頻次
書目名稱Computational Methods for 3D Genome Analysis被引頻次學(xué)科排名
書目名稱Computational Methods for 3D Genome Analysis年度引用
書目名稱Computational Methods for 3D Genome Analysis年度引用學(xué)科排名
書目名稱Computational Methods for 3D Genome Analysis讀者反饋
書目名稱Computational Methods for 3D Genome Analysis讀者反饋學(xué)科排名
作者: colostrum 時(shí)間: 2025-3-21 23:11
CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matricestation of the common workflow language (CWL)-based Hi-C analysis pipeline adopted by the 4DN Data Portal ecosystem. This reproducible and portable pipeline generates standard Hi-C contact matrices in formats such as .hic or .mcool from FASTQ files. It enables users to output their own Hi-C data in t作者: 和音 時(shí)間: 2025-3-22 01:35
Systematic Inference of Multi-scale Chromatin Sub-compartments Using Calder2rate chromatin compartment detection, and extended support for input and output formats. Calder2 thus stands as a refined analysis tool, significantly advancing genome-wide studies of 3D chromatin architecture and its functional implications.作者: 頌揚(yáng)本人 時(shí)間: 2025-3-22 06:51
1064-3745 uccessful .Methods in Molecular Biology. series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readil978-1-0716-4138-5978-1-0716-4136-1Series ISSN 1064-3745 Series E-ISSN 1940-6029 作者: Rheumatologist 時(shí)間: 2025-3-22 10:01
Internistische extraabdominelle Ursachenformance. This enables users to generate high-resolution datasets with fast turnaround and fewer unmapped reads. Finally, we discuss recent innovations in experimental techniques, bioinformatics techniques, and their applications in clinical testing for diagnostics.作者: gait-cycle 時(shí)間: 2025-3-22 13:03 作者: gait-cycle 時(shí)間: 2025-3-22 18:37 作者: hysterectomy 時(shí)間: 2025-3-23 00:20 作者: 搜集 時(shí)間: 2025-3-23 01:22 作者: AROMA 時(shí)間: 2025-3-23 08:13
https://doi.org/10.1007/978-3-658-08361-8This educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.作者: 壯麗的去 時(shí)間: 2025-3-23 13:27
Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPyentire workflow from FASTQ mapping to visualization. In this chapter, we demonstrate how to analyze and visualize Hi-C data using CustardPy and introduce several 3D genome features observed in Hi-C data.作者: 停止償付 時(shí)間: 2025-3-23 17:35
Single-Cell Hi-C Analysis Workflow with PairtoolsThis educational chapter aims to guide researchers in using open-source tools for scHi-C analysis, emphasizing critical steps of contact pair extraction, detection of ligation junctions, filtration, and deduplication.作者: hangdog 時(shí)間: 2025-3-23 19:18 作者: Prophylaxis 時(shí)間: 2025-3-24 00:49 作者: inflame 時(shí)間: 2025-3-24 04:10
Radiologische Notfalldiagnostik des Abdomensave been developed to comprehensively reveal 3D chromosome structures. Micro-C is one such method that can detect the structures at nucleosome resolution. In this chapter, I provide a basic method for Micro-C analysis. I present and discuss a series of data analyses ranging from mapping to basic downstream analyses, including loop detection.作者: Accommodation 時(shí)間: 2025-3-24 08:59
https://doi.org/10.1007/978-3-662-61508-9t and interaction matrix format for visualization with Juicebox. The method is demonstrated for the mouse composite X chromosome in which reads from the active and inactive X chromosomes are combined after mock DMSO treatment or targeted degradation of cohesin.作者: contradict 時(shí)間: 2025-3-24 11:35
Gespr?ch mit Angelika Freifrau von Fritschd comparing structures effectively depending on the characteristics of the genome or cell type. Here, we describe a method for acquiring Hi-C data from medaka early embryos and quantifying the structural changes during the developmental process.作者: tenuous 時(shí)間: 2025-3-24 15:11 作者: Meditate 時(shí)間: 2025-3-24 20:54
Erstversorgung durch den Krankenhausarztnd prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop?extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.作者: 帽子 時(shí)間: 2025-3-24 23:29 作者: AMBI 時(shí)間: 2025-3-25 06:35 作者: 群居男女 時(shí)間: 2025-3-25 07:50
Structural Maintenance of Chromosomes Complexesnd prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop?extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.作者: ADOPT 時(shí)間: 2025-3-25 12:57 作者: 錯(cuò) 時(shí)間: 2025-3-25 19:18 作者: 書法 時(shí)間: 2025-3-25 23:19
Methods for Genome-Wide Chromatin Interaction Analysisomatin structures such as a loop structure, a domain structure called topologically associating domains (TADs), and compartments. In this chapter, I introduce chromatin interaction techniques using NGS and outline the principles and features of each method.作者: strain 時(shí)間: 2025-3-26 01:59
Micro-C Analysis Workflow Using Pairtools and Juicerave been developed to comprehensively reveal 3D chromosome structures. Micro-C is one such method that can detect the structures at nucleosome resolution. In this chapter, I provide a basic method for Micro-C analysis. I present and discuss a series of data analyses ranging from mapping to basic downstream analyses, including loop detection.作者: 喪失 時(shí)間: 2025-3-26 06:16
HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosomet and interaction matrix format for visualization with Juicebox. The method is demonstrated for the mouse composite X chromosome in which reads from the active and inactive X chromosomes are combined after mock DMSO treatment or targeted degradation of cohesin.作者: 吹牛大王 時(shí)間: 2025-3-26 08:42
Acquisition and Analysis Methods for Hi-C Data from Medaka Early Embryosd comparing structures effectively depending on the characteristics of the genome or cell type. Here, we describe a method for acquiring Hi-C data from medaka early embryos and quantifying the structural changes during the developmental process.作者: extinct 時(shí)間: 2025-3-26 15:47 作者: 痛苦一生 時(shí)間: 2025-3-26 17:08
Erstversorgung durch den Krankenhausarztomatin structures such as a loop structure, a domain structure called topologically associating domains (TADs), and compartments. In this chapter, I introduce chromatin interaction techniques using NGS and outline the principles and features of each method.作者: ALIAS 時(shí)間: 2025-3-26 22:28
Methods for Genome-Wide Chromatin Interaction Analysisnuclear structure observation techniques, and the development of methods utilizing next-generation sequencers (NGSs) have significantly progressed these discoveries. Methods utilizing NGS enable genome-wide analysis, which is challenging with microscopy, and have elucidated concepts of important chr作者: FIR 時(shí)間: 2025-3-27 04:20 作者: 破譯密碼 時(shí)間: 2025-3-27 06:06 作者: CBC471 時(shí)間: 2025-3-27 12:55 作者: 一大群 時(shí)間: 2025-3-27 14:39 作者: Glycogen 時(shí)間: 2025-3-27 21:14 作者: 整潔 時(shí)間: 2025-3-27 21:55 作者: 惡名聲 時(shí)間: 2025-3-28 05:44
Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipelineutilized in chromatin research. To effectively leverage 3D genomics data obtained through advanced technologies, it is crucial to understand what processes are undertaken and what aspects require special attention within the bioinformatics pipeline. This protocol aims to demystify the Hi-C data anal作者: Liberate 時(shí)間: 2025-3-28 08:50 作者: Albinism 時(shí)間: 2025-3-28 11:36 作者: 容易生皺紋 時(shí)間: 2025-3-28 17:20
Supervised Chromatin Loop Detection Using Peakachu Version 2updated version that significantly improves extensibility, usability, and computational efficiency compared to its predecessor. It features pretrained models tailored for a wide range of experimental platforms, such as Hi-C, Micro-C, ChIA-PET, HiChIP, HiCAR, and TrAC-loop. This chapter offers a step作者: 一致性 時(shí)間: 2025-3-28 19:33
Systematic Inference of Multi-scale Chromatin Sub-compartments Using Calder2d by data resolution constraints. Consequently, comprehensive characterizations of sub-compartments have been limited to a select number of Hi-C experiments, with systematic comparisons across a wide range of tissues and conditions still lacking. Our original Calder algorithm marked a significant ad作者: 煩躁的女人 時(shí)間: 2025-3-29 00:19 作者: narcissism 時(shí)間: 2025-3-29 04:01 作者: lobster 時(shí)間: 2025-3-29 09:50
Computational Methods for 3D Genome Analysis978-1-0716-4136-1Series ISSN 1064-3745 Series E-ISSN 1940-6029 作者: Fermentation 時(shí)間: 2025-3-29 13:17 作者: prostate-gland 時(shí)間: 2025-3-29 19:24
Erstversorgung durch den Krankenhausarztnuclear structure observation techniques, and the development of methods utilizing next-generation sequencers (NGSs) have significantly progressed these discoveries. Methods utilizing NGS enable genome-wide analysis, which is challenging with microscopy, and have elucidated concepts of important chr作者: palpitate 時(shí)間: 2025-3-29 20:34
Erstversorgung durch den Krankenhausarztts and to safeguard the genome through cell division. These ring-shaped multi-subunit protein complexes, which are present in all kingdoms of life, achieve this by organizing chromosomes in three-dimensional space. Mechanistically, the SMC complexes hydrolyze ATP to either stably entrap DNA molecule作者: Entropion 時(shí)間: 2025-3-30 03:34
Internistische extraabdominelle Ursachenncing. As an unbiased genome-wide assay based on chromosome conformation capture, it provides rich insights into chromosome structure, dynamic chromosome folding and interactions, and the regulatory state of a cell. Bioinformatics analyses of Hi-C data require dedicated protocols as most genome alig作者: osculate 時(shí)間: 2025-3-30 07:32
Radiologische Notfalldiagnostik des Abdomensthe elucidation of the functions. In recent years, chromosome conformation capture (3C) techniques combined with next-generation sequencing analysis have been developed to comprehensively reveal 3D chromosome structures. Micro-C is one such method that can detect the structures at nucleosome resolut作者: 螢火蟲 時(shí)間: 2025-3-30 10:06 作者: 小卷發(fā) 時(shí)間: 2025-3-30 12:36 作者: Aerate 時(shí)間: 2025-3-30 19:37 作者: adroit 時(shí)間: 2025-3-30 20:51 作者: 品牌 時(shí)間: 2025-3-31 03:17
Feedback im Kontext von Potenzialanalysen, to detailed microscopic analysis. However, the circularity of prokaryotic genomes requires a number of tricks for Hi-C/3C-seq data analysis. Here, I provide a practical guide to use the HiC-Pro pipeline for Hi-C/3C-seq data obtained from prokaryotes.作者: Reservation 時(shí)間: 2025-3-31 06:01
https://doi.org/10.1007/978-3-658-24760-7 mapped to a reference genome to generate a two-dimensional contact matrix for identifying topologically associating domains (TADs), chromatin loops, and chromosomal compartments. On the other hand, the distance distribution of the paired-end mapped reads also provides insight into the 3D genome str作者: Prophylaxis 時(shí)間: 2025-3-31 09:32
https://doi.org/10.1007/978-3-658-24760-7updated version that significantly improves extensibility, usability, and computational efficiency compared to its predecessor. It features pretrained models tailored for a wide range of experimental platforms, such as Hi-C, Micro-C, ChIA-PET, HiChIP, HiCAR, and TrAC-loop. This chapter offers a step作者: BIAS 時(shí)間: 2025-3-31 15:44
https://doi.org/10.1007/978-3-658-24760-7d by data resolution constraints. Consequently, comprehensive characterizations of sub-compartments have been limited to a select number of Hi-C experiments, with systematic comparisons across a wide range of tissues and conditions still lacking. Our original Calder algorithm marked a significant ad作者: infarct 時(shí)間: 2025-3-31 21:16 作者: 奇思怪想 時(shí)間: 2025-3-31 21:54
https://doi.org/10.1007/978-3-658-08361-8sembles data analysis for bulk Hi-C, the unique challenges of scHi-C, such as high noise and protocol-specific biases, require specialized data processing strategies. In this tutorial chapter, we focus on using pairtools, a suite of tools optimized for scHi-C data, demonstrating its application on a作者: 寬容 時(shí)間: 2025-4-1 02:37
Ergebnisse der empirischen Untersuchung,We describe an approach for reconstructing three-dimensional (3D) structures from single-cell Hi-C data. This approach has been inspired by a method of recurrence plots and visualization tools for nonlinear time series data. Some examples are also presented.
