Methods in molecular biology (Clifton, N.J.)

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Publications

volume 2856, 2024

Atsushi Okabe
Methods for Genome-Wide Chromatin Interaction Analysis. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Yuanlong Liu
Systematic Inference of Multi-scale Chromatin Sub-compartments Using Calder2. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Yoshito Hirata, Hiroki Sugishita, Yukiko Gotoh
Reconstruction of 3D Chromosome Structure from Single-Cell Hi-C Data via Recurrence Plots. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Dennis Hecker, Marcel H Schulz
Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Ryohei Nakamura
Acquisition and Analysis Methods for Hi-C Data from Medaka Early Embryos. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Soya Shinkai, Shuichi Onami
4D Genome Analysis Using PHi-C2. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Hideki Tanizawa, Claire Yik-Lok Chung, Shun-Ichiro Fuse, Tomomi Hayashi, Peter Weisel, Ken-Ichi Noma
Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Shin Fujishiro, Masaki Sasai
Three-Dimensional Simulation of Whole-Genome Structuring Through the Transition from Anaphase to Interphase. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Andrea J Kriz
HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosome. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Akinori Awazu, Tetsushi Komoto
Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Hisashi Miura, Rory T Cerbus, Izumi Noda, Ichiro Hiratani
CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Jiankang Wang, Haoping Chen
Extracting Chromosome Structural Information as One-Dimensional Metrics and Integrating Them with Epigenomics. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Hiroaki Ohishi, Hiroshi Ochiai
Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Giovanni B Brandani
Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Brydon P G Wall, My Nguyen, J Chuck Harrell, Mikhail G Dozmorov
Machine and Deep Learning Methods for Predicting 3D Genome Organization. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Aleksandra A Galitsyna
Single-Cell Hi-C Analysis Workflow with Pairtools. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Xiaotao Wang
Supervised Chromatin Loop Detection Using Peakachu Version 2. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Kristian Jeppsson
Structural Maintenance of Chromosomes Complexes. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Jiankang Wang
Exploring Cohesin-Related Multiomics Information in the Web Browser. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Ryuichiro Nakato
Exploring Contact Distance Distributions with Google Colaboratory. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Simon Thomas Kelly, Kugui Tanaka, Chiaki Hosaka, Satoshi Yuhara
Read Mapping for Hi-C Analysis. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Doris Chen, Martin Xaver, Franz Klein
Processing and Visualization of Protec-Seq Data for the Generation of Calibrated, Genome-Wide Double Double-Strand Break (dDSB) Maps. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Yuya Nagaoka, Ryuichiro Nakato
Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPy. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Toyonori Sakata
Micro-C Analysis Workflow Using Pairtools and Juicer. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Laura Rumpf, Marcel H Schulz
Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT. Methods in molecular biology (Clifton, N.J.) 2856 (2024)
Naomichi Takemata
Hi-C/3C-seq Data Analysis for Prokaryotic Genomes with HiC-Pro. Methods in molecular biology (Clifton, N.J.) 2856 (2024)

volume 2854, 2024

Renxia Zhang, Hui Zheng
Luciferase Reporter Assay for Determining the Signaling Activity of Interferons. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Chunfu Zheng, Liting Zhang
Identifying RNA Sensors in Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Huibin Yu, Dewi Megawati, Chunfu Zheng, Stefan Rothenberg
Protein Kinase R (PKR) as a Novel dsRNA Sensor in Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Hongjuan You, Chunfu Zheng
A Guideline Strategy for Identifying a Viral Gene/Protein Evading Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Yan Chen, Jingyu Wang, Chunfu Zheng, Zheng Liu
Cryo-Electron Microscopy in the Study of Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Chaoqun Li, Mutian Jia
Click Chemistry in Detecting Protein Modification. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Tao Yang, Yi Yuan, Feng Ma
Luciferase Reporter Systems in Investigating Interferon Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Yangkun Shen, Xiangqian Zhao, Chunfu Zheng, Qi Chen
CRISPR-Mediated Construction of Gene-Knockout Mice for Investigating Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Tao Yu, Dan Hou, Chunfu Zheng
Investigation of Protein Lysine Acetylation in Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Madhurima Bhattacharya, Debipreeta Bhowmik, Qian Yin
In Vitro Cleavage Assay to Characterize DENV NS2B3 Antagonism of cGAS. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Chenhe Su, Chenhao Su, Chunfu Zheng
Identifying an Abnormal Phosphorylated Adaptor by Viral Kinase Using Mass Spectrometry. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Chunfu Zheng, Liting Zhang
DNA PAMPs as Molecular Tools for the cGAS-STING Signaling Pathways. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Tong Wu, Chunfu Zheng, Xiaodong Zou
The Application of Organoids in the Study of Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Weizheng Liang, Zhenpeng Zhu, Chunfu Zheng
Application of Proteomics Technology Based on LC-MS Combined with Western Blotting and Co-IP in Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Lijuan Qiu, Xiaoli He, Chunfu Zheng, Li Li
Identifying a Gene Deficiency in the Antiviral Innate Immune Signaling Pathway. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Yangkun Shen, Zhihua Feng, Chunfu Zheng, Qi Chen
CRISPR-Mediated Library Screening of Gene-Knockout Cell Lines for Investigating Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Zhihua Feng, Yangkun Shen, Chunfu Zheng, Qi Chen
CRISPR-Mediated Viral Gene Knockout to Investigate Viral Evasion of Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Zhe Wang, Penghui Hu, Xiao Shan, Baochen Wang, Hui Xiong, Qiujing Yu
In Vitro and In Vivo Evaluation of Virus-Induced Innate Immunity in Mouse. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Chenhe Su, Chenhao Su, Chunfu Zheng
Identifying a Ubiquitinated Adaptor Protein by a Viral E3 Ligase Through Co-immunoprecipitation. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Sisi Xia, Xiaoping Huo, Chunfu Zheng, Jun Chen
Yeast Two-Hybrid Assay for Investigating Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Wei Liu, Bo Liu
Phagosome Isolation with Magnetic Beads and Purification of Toll-Like Receptor (TLR) Complexes in Phagosomes. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Xiao Man Wu, Si Yao Zheng, Ming Xian Chang
Zebrafish as a Model for Investigating Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Ting Li, Chunfu Zheng, Huifang Zhu
A Guideline Strategy for Identifying Genes/Proteins Regulating Antiviral Innate Immunity. Methods in molecular biology (Clifton, N.J.) 2854 (2024)
Chenhe Su, Chenhao Su, Chunfu Zheng
Identifying a Ubiquitinated Adaptor Protein by a Viral E3 Ligase Through Co-immunoprecipitation. Methods in molecular biology (Clifton, N.J.) 2854 (2024)