BioTreasury:a community-based repository enabling indexing and rating of bioinformatics tools

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis assignments.Therefore,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently needed.In this study,we introduce Bio Treasury(http://biotreasury.rjmart.cn),an integrated communitybased repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics tools.Bio Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 entries.In the past two years,we have continuously improved and maintained Bio Treasury,adding several exciting features,including creating structured homepages for every tool and user,a hierarchical category of bioinformatics tools and classifying tools using large language model(LLM).Bio Treasury streamlines the tool submission process with intelligent auto-completion.Additionally,Bio Treasury provides a wide range of social features,for example,enabling users to participate in interactive discussions,rate tools,build and share tool collections for the public.We believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical community.It empowers researchers to effectively discover and evaluate bioinformatics tools,fostering collaboration and advancing bioinformatics research.

Bioinformatic approaches of liquid-liquid phase separation in human disease

Biomolecular aggregation within cellular environments via liquid-liquid phase separation(LLPS)spontaneously forms droplet-like structures,which play pivotal roles in diverse biological processes.These structures are closely associated with a range of diseases,including neurodegenerative disorders,cancer and infectious diseases,highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis,and exploring potential therapeutic interventions.In this review,we delineate recent advancements in LLPS research,emphasizing its pathological relevance,therapeutic considerations,and the pivotal role of bioinformatic tools and databases in facilitating LLPS investigations.Additionally,we undertook a comprehensive analysis of bioinformatic resources dedicated to LLPS research in order to elucidate their functionality and applicability.By providing comprehensive insights into current LLPS-related bioinformatics resources,this review highlights its implications for human health and disease.

Integration of association and computational methods reveals functional variants of LEPR gene for abdominal fat content in chickens

Leptin receptor(LEPR)plays a vital role in obesity in humans and animals.The objective of this study is to assess LEPR functional variants for chicken adipose deposition by integration of association and in-silico analysis using a unique chicken population,the Northeast Agricultural University broiler lines divergently selected for abdominal fat content(NEAUHLF).Five online bioinformatics tools were used to predict the functionality of the single nucleotide polymorphisms(SNPs)in coding region.Further,the possible structure–function relationship of high confidence SNPs was determined by bioinformatics analyses,including the conservation and stability analysis based on amino acid residues,prediction of protein ligand-binding sites,and the superposition of protein tertiary structure.Meanwhile,we analyzed the association between abdominal fat traits and 20 polymorphisms of chicken LEPR gene.The integrated results showed that rs731962924(N867I)and rs13684622(C1002R)could lead to striking changes in the structure and function of proteins,of which rs13684622(C1002R)was significantly associated with abdominal fat weight(AFW,P=0.0413)and abdominal fat percentage(AFP,P=0.0260)in chickens.Therefore,we are of the opinion that rs13684622(C1002R)may be an essential functional SNP affecting chicken abdominal fat deposition,and potentially applied to improvement of broiler abdominal fat in molecular marker-assisted selection(MAS)program.Additionally,the coupling of association with computer electronic predictive analysis provides a new avenue to identify important molecular markers for breeders.

CRISPR-Cas9 sgRNA design and outcome assessment: Bioinformatics tools and aquaculture applications

The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture.Single-guide RNA(sgRNA)design is presumably the most crucial task in a typical CRISPR-Cas9 experiment;an understanding of algorithms behind sgRNA design programs is thus essential for improved efficacy and specificity.We focus this review on the bioinformatics aspects in genome editing experiments and describe commonly used computational approaches and tools of sgRNA design and outcome assessment.We show an example of sgRNA design with optimal parameter settings and appropriate interpretation of results and present a brief overview of CRISPR-Cas9 applications,such as genetic improvement and sustainability in aquaculture.We discuss challenging issues,particularly in the context of computational biology,in the use of computational tools in CRISPR-based genome editing.This review provides a synthesis of bioinformatics tools used for CRISPR-Cas9 sgRNA design and outcome assessment and offers a general view of CRISPR-based applications in farmed fish,which are expected to facilitate genome editing programs and hence improve aquaculture breeding,production,and sustainability.

An integrative database and its application for plant synthetic biology research

Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants.Limited by few well-characterized bioparts for plant chassis,the development of plant synthetic biology lags behind that of its microbial counterpart.Here,we constructed a web-based Plant Synthetic BioDatabase(PSBD),which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals.Online bioinformatics tools including local BLAST,chem similarity,phylogenetic analysis,and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta.We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quan-titative regulation in tobacco leaves.More powerful synthetic devices were then assembled to amplify the transcriptional signals,enabling enhanced expression offlavivirus non-structure 1 proteins in plants.The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.

Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented resolution.Most recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human diseases.In this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT applications.With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.

Fundamental and practical approaches for single-cell ATAC-seq analysis

Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility landscapes.With the rapid development of single-cell technology,open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches.The application of scATAC-seq has become as popular as that of scRNA-seq.However,owing to the nature of scATAC-seq data,which are sparse and noisy,processing the data requires different methodologies and empirical experience.This review presents a practical guide for processing scATAC-seq data,from quality evaluation to downstream analysis,for various applications.In addition to the epigenomic profiling from scATAC-seq,we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage.We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.

Web Resources for Microbial Data

There are multitudes of web resources that are quite useful for the microbial scientific research community. Here, we provide a brief introduction on some of the most notable microbial web resources and an evaluation of them based upon our own user experience.