Haicheng Li's repositories
1kg-list
千人基因组样本表，2024.1.18
alibi
Algorithms for monitoring and explaining machine learning models
Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome-cheatsheets
👩💻👨💻 Awesome cheatsheets for popular programming languages, frameworks and development tools. They include everything you should know in one single file.
awesome-spider
爬虫集合
bilibili-helper-o
哔哩哔哩 (bilibili.com) 辅助工具，可以替换播放器、推送通知并进行一些快捷操作
caj2pdf-qt
CAJ 转 PDF 转换器（GUI 版本）
Clone-Wars
100+ open-source clones of popular sites like Airbnb, Amazon, Instagram, Netflix, Tiktok, Spotify, Whatsapp, Youtube etc. See source code, demo links, tech stack, github stars.
EpiAnno
Single-cell epigenomic data annotation via supervised non-linear embedding
Graph2MDA
Graph2MDA is an architecture based on the multi-mode attributed graph for identifing new microbe-drug association.
lihaicheng7003
profile
mBodymap
A comprehensive database for microbes across human body sites
mmvec
Neural networks for microbe-metabolite interaction analysis
mrmr
Python implementation of mRMR (minimum-Redundancy-Maximum-Relevance) for feature selection.
NetMoss
学习一下工作
PDFPatcher
PDF补丁丁
PHAT
Explainable deep hypergraph learning modeling the peptide secondary structure prediction
python3-cookbook
《Python Cookbook》 3rd Edition Translation
scib
Benchmarking analysis of data integration tools
ScienceDecrypting
破解CAJViewer带有效期的文档，支持破解科学文库、标准全文数据库下载的文档。无损破解，保留文字和目录，解除有效期限制。
scikit-feature
open-source feature selection repository in python
scorecardpy
Scorecard Development in python, 评分卡
threadpool_executor_shrink_able
pip install threadpool_executor_shrink_able 最好的python线程池，可以实现线程池自动缩小，实现java keepAliveTime参数的功能。，shap threadpoolexecutor, realize java keepAliveTime,bounded work queue,direct display of thread errors
tome_code
The scripts used for the analyses in TOME project
winsw
A wrapper executable that can run any executable as a Windows service, in a permissive license.