受2020疫情影响，我们大三的科研训练从原来的做实验变成了读paper写综述。
我的科研训练主题是表观测序技术的发展及其在发育生物学中的应用，内容很多，但是时间有限（大三小学期最后一周就要答辩），所以综述的撰写可能还会根据实际进度调整。我先简单罗列了一些文献，接下来的时间里每天坚持打卡做记录。
感兴趣的朋友可以选看一些
PS：有的题目太长，没有打完整（QAQ）

Mypaper

Project

Transcriptome analysis

标粗为重点的应用：发育
一共42篇，19篇未读，23篇

• ChIP–seq: advantages and challenges of a maturing technology

• CUT&Tag for efficient epigenomic profiling of small samples and single cells 参考onenote笔记和idea

• Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

• Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data

• Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

• Profiling of Pluripotency Factors in Single Cells and
  Early Embryos CUT-RUN参考onenote笔记和idea

• Profiling chromatin states using single-cell itChIP-seq

• Single-cell RNA-sequencing: The future of genome biology is now

• MorphoSeq: Full Single-Cell Transcriptome Dynamics Up to Gastrulation in a Chordate

• Decoding the development of the human hippocampus

• Single-cell multimodal omics: the power of many

• The landscape of accessible chromatin in mammalian preimplantation embryos

• Resetting histone modifications during human parental-to-zygotic transition

• Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency

• A compendium of promoter-centered long-range chromatin interactions in the human genome

• Chromatin modifications and their function

• Integrative analysis of 111 reference human epigenomes

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

• Integrative analysis of haplotype-resolved epigenomes across human tissues

• Enhancers: five essential questions

• RNA sequencing: the teenage years

• RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis

• High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

• ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

• An improved ATAC-seq protocol reduces background and enables interrogation of frozen

• The cis-regulatory dynamics of embryonic development at single-cell resolution

• Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

• Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene

• Massively parallel single-cell chromatin landscapes of human immune cell development

• CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

• HiChIP: efficient and sensitive analysis of protein-directed genome architecture

• Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

• Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

• Principles of Chromosome Architecture Revealed by Hi-C

• Understanding Spatial Genome Organization: Methods and Insights

• Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early

My reading

• Chromatin accessibility dynamics in a model of human forebrain development
• Epigenetics: core misconcept
• Computational methods for single-cell omics across modalities
• Identifying gene expression programs of cell-type identity and cellular activity with single-cell
• RFECS: a random-forest based algorithm for enhancer identification from chromatin state
• Comprehensive Integration of Single-Cell Data
• Machine learning and complex biological data