As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,w...As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.展开更多
Rice is one of cereal crops and a model species for monocots.Since the release of the first draft rice genome sequences in 2002,considerable progress has been achieved in rice genomic researches,thanks to rapid develo...Rice is one of cereal crops and a model species for monocots.Since the release of the first draft rice genome sequences in 2002,considerable progress has been achieved in rice genomic researches,thanks to rapid development and efficient utilization of bioinformatics methods and tools.In this review,we summarize the progress of studies of rice genome sequencing and other omics and introduce the wellmaintained bioinformatics databases and tools developed for rice genome resources and breeding.After reviewing the history of rice bioinformatics,we use single-cell sequencing and machine learning as examples showing how bioinformatics integrates emerging technologies and how it continues to develop for future rice research.展开更多
Polyploidy is common among agriculturally important crops. Popular genetic methods and their implementations cannot always be applied to polyploid genetic data. We give an overview about available tools and their limi...Polyploidy is common among agriculturally important crops. Popular genetic methods and their implementations cannot always be applied to polyploid genetic data. We give an overview about available tools and their limitations in terms of levels of ploidy, auto- and allo-ploidy. The main classes of tools are genotype calling, linkage mapping and haplotyping. The usability of the tools is discussed with a focus on their applicability to data sets produced by state of the art technologies. We show that many challenges remain until the toolset for polyploidy provides similar functionalities as those which are already available for diploids. Some tools have been developed over a decade ago and are now outdated. In addition, we discuss necessary steps to overcome this shortage in the future.展开更多
The massive extension in biological data induced a need for user-friendly bioinformatics tools could be used for routine biological data manipulation. Bioanalyzer is a simple analytical software implements a variety o...The massive extension in biological data induced a need for user-friendly bioinformatics tools could be used for routine biological data manipulation. Bioanalyzer is a simple analytical software implements a variety of tools to perform common data analysis on different biological data types and databases. Bioanalyzer provides general aspects of data analysis such as handling nucleotide data, fetching different data formats information, NGS quality control, data visualization, performing multiple sequence alignment and sequence BLAST. These tools accept common biological data formats and produce human-readable output files could be stored on local computer machines. Bioanalyzer has a user-friendly graphical user interface to simplify massive biological data analysis and consume less memory and processing power. Bioanalyzer source code was written through Python programming language which provides less memory usage and initial startup time. Bioanalyzer is a free and open source software, where its code could be modified, extended or integrated in different bioinformatics pipelines. Bioinformatics Produce huge data in FASTA and Genbank format which can be used to produce a lot of annotation information which can be done with Python programming language that open the door form bioinformatics tool due to their elasticity in data analysis and simplicity which inspire us to develop new multiple tool software able to manipulate FASTA and Genbank files. The goal Develop new software uses Genomic data files to produce annotated data. Software was written using python programming language and biopython packages.展开更多
In this editorial preface, I briefly r eview cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SN...In this editorial preface, I briefly r eview cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP- containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.展开更多
Objective This study aims to investigate the expression,prognostic value,and function of kinesin superfamily 4A(KIF4A)in cervical cancer.Methods Cervical cancer cell lines(Hela and SiHa)and TCGA data were used for exp...Objective This study aims to investigate the expression,prognostic value,and function of kinesin superfamily 4A(KIF4A)in cervical cancer.Methods Cervical cancer cell lines(Hela and SiHa)and TCGA data were used for experimental and bioinformatic analyses.Overall survival(OS)and progression free survival(PFS)were compared between patients with high or low KIF4A expression.Copy number variation(CNV)and somatic mutations of patients were visualized and GISTIC 2.0 was used to identify significantly altered sites.The function of KIF4A was also explored based on transcriptome analysis and validated by experimental methods.Chemotherapeutic and immunotherapeutic benefits were inferred using multiple reference databases and algorithms.Results Patients with high KIF4A expression had better OS and PFS.KIF4A could inhibit proliferation and migration and induce G1 arrest of cervical cancer cells.Higher CNV load was observed in patients with low KIF4A expression,while the group with low KIF4A expression displayed more significantly altered sites.A total of 13 genes were found to mutate more in the low KIF4A expression group,including NOTCH1 and PUM1.The analysis revealed that low KIF4A expression may indicate an immune escape phenotype,and patients in this group may benefit more from immunotherapy.With respect to chemotherapy,cisplatin and gemcitabine may respond better in patients with high KIF4A expression,while 5-fluorouracil etc.may be responded better in patients with low KIF4A expression Conclusion KIF4A is a tumor suppressor gene in cervical cancer,and it can be used as a prognostic and therapeutic biomarker in cervical cancer.展开更多
Severe acute respiratory syndrome coronavirus(SARS-CoV)and SARS-CoV-2 are thought to transmit to humans via wild mammals,especially bats.However,evidence for direct bat-to-human transmission is lacking.Involvement of ...Severe acute respiratory syndrome coronavirus(SARS-CoV)and SARS-CoV-2 are thought to transmit to humans via wild mammals,especially bats.However,evidence for direct bat-to-human transmission is lacking.Involvement of intermediate hosts is considered a reason for SARS-CoV-2 transmission to humans and emergence of outbreak.Large biodiversity is found in tropical territories,such as Brazil.On the similar line,this study aimed to predict potential coronavirus hosts among Brazilian wild mammals based on angiotensin-converting enzyme 2(ACE2)sequences using evolutionary bioinformatics.Cougar,maned wolf,and bush dogs were predicted as potential hosts for coronavirus.These indigenous carnivores are philogenetically closer to the known SARS-CoV/SARS-CoV-2 hosts and presented low ACE2 divergence.A new coronavirus transmission chain was developed in which white-tailed deer,a susceptible SARS-CoV-2 host,have the central position.Cougar play an important role because of its low divergent ACE2 level in deer and humans.The discovery of these potential coronavirus hosts will be useful for epidemiological surveillance and discovery of interventions that can contribute to break the transmission chain.展开更多
Bioinformatics analysis often requires the filtering of multi-datasets,based on frequency or frequency of occurrence,for decisions on retention or deletion.Existing tools for this purpose often present a challenge wit...Bioinformatics analysis often requires the filtering of multi-datasets,based on frequency or frequency of occurrence,for decisions on retention or deletion.Existing tools for this purpose often present a challenge with complex installation,which necessitate custom coding,thereby impeding efficient data processing activities.To address this issue,Filterx,a user-friendly command line tool that written in C language,was developed that supports multi-condition filtering,based on frequency or occurrence.This tool enables users to complete the data processing tasks through a simple command line,greatly reducing both workload and data processing time.In addition,future development of this tool could facilitate its integration into various bioinformatics data analysis pipelines.展开更多
Though a relatively young discipline, translational bioinformatics （TBI） has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic...Though a relatively young discipline, translational bioinformatics （TBI） has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex- tualization of the term TBI, describes the discipline＇s brief history and past accomplishments, as well as current loci, and concludes with predictions of future directions in the field.展开更多
Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologi...Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at present.The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data.The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike.Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine.We review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers.展开更多
Natural products are among the most important sources of lead molecules for drug discovery.With the development of affordable whole-genome sequencing technologies and other‘omics tools,the field of natural products r...Natural products are among the most important sources of lead molecules for drug discovery.With the development of affordable whole-genome sequencing technologies and other‘omics tools,the field of natural products research is currently undergoing a shift in paradigms.While,for decades,mainly analytical and chemical methods gave access to this group of compounds,nowadays genomics-based methods offer complementary approaches to find,identify and characterize such molecules.This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work.In this context,this review gives a summary of tools and databases that currently are available to mine,identify and characterize natural product biosynthesis pathways and their producers based on‘omics data.A web portal called Secondary Metabolite Bioinformatics Portal(SMBP at http://www.secondarymetabolites.org)is introduced to provide a one-stop catalog and links to these bioinformatics resources.In addition,an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.展开更多
In the 2017 first issue of this Journal - Genomes, Proteomes and Bioinformatics - a special database article entitled ＂GSA： Gen- ome Sequence Archive＂ is published. This article provides a brief introduction to th...In the 2017 first issue of this Journal - Genomes, Proteomes and Bioinformatics - a special database article entitled ＂GSA： Gen- ome Sequence Archive＂ is published. This article provides a brief introduction to the platform developed by the authors from the BIG Data Center （BIGD） of Beijing Institute of Genomics （BIG）, Chinese Academy of Sciences （CAS）. The aim of the GSA project is to collect, integrate, and archive raw sequence data submitted by domestic and international users. It is one of the major activities being carried on by a team of around 50 young bioinformaticians at BIGD. In addition to the GSA system, they are also working on several bioinformatics service-orientated projects as described in one of their recent publications .展开更多
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED ...We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.展开更多
Bioinformatics, an interdisciplinary field that combines biology, mathematics, computer science, medicine, and health science, to integrate, analyze, and interpret biological data, is now becoming increasingly data-in...Bioinformatics, an interdisciplinary field that combines biology, mathematics, computer science, medicine, and health science, to integrate, analyze, and interpret biological data, is now becoming increasingly data-intensive. To dig out the treasure from big data powered by high-throughput sequencing technologies, it is highly dependent on Bioinformaties Commons that involves a variety of fundamental resources, includ- ing databases, web servers, algorithms, methods, software tools, ontologies, and standards. To be short, Bioinformatics Commons has become the cornerstone of life and health sciences, facilitating and accelerating the translation of big data into big discoveries.展开更多
Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two t...Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications： （1） immediate short-term training workshops and （2） long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute （NHLBI）-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health （NJH） and the University of Colorado School of Medicine （UCD）. The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national vip faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consis- tently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.展开更多
microRNAs (miRNAs) have been reported to be associated with the pathogenesis and progression of breast cancer.However,little is known about the pathways through which miRNAs regulate these processes,e.g.,the interacti...microRNAs (miRNAs) have been reported to be associated with the pathogenesis and progression of breast cancer.However,little is known about the pathways through which miRNAs regulate these processes,e.g.,the interaction between miRNAs and their target genes with regard to different pathological status of breast cancer,such as histological grades.This study investigated the possible roles of miRNAs in the differentiation of histological grades of breast cancer with a computational approach.Based on a microarray dataset,15 candidate miRNAs were identified,whose predicted target genes are enriched as differentially expressed between grade I and grade III breast tumors.Among them,9 key miRNAs focalize their target genes on 6 central signaling pathways.The SMAD7 protein,the main inhibitory protein in the TGF-β pathway,is predicted as a target of several miRNAs and is also regulated by several other pathways that are possibly targeted by miRNAs.It was hypothesized that miRNAs participate in the differentiation of breast cancer and the TGF-β pathway acts as a major implementary pathway on which several miRNAs take effect through multiple channels.The prediction power of the predicted miRNA target genes was validated on three independent datasets.The differential expression of three miRNAs was validated by real-time PCR on breast carcinoma samples of 10 patients.展开更多
A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome(SARS). For all the SARS-CoV associated proteins derivatedfrom the SARS-CoV genome, the physiochemical propertiess...A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome(SARS). For all the SARS-CoV associated proteins derivatedfrom the SARS-CoV genome, the physiochemical propertiessuch as the molecular weight, isoelectric point and extinction coefficient of each protein were calculated. Thetransmembrane segments and subcellular localization(SubLocation) prediction and conserved protein motifssearch against database were employed to analyze thefunction of SARS-CoV proteins. Also, the homology protein sequence alignment and evolutionary distance matrixcalculation between SARS-CoV associated proteins and the corresponding proteins of other coronaviruses wereemployed to identify the classification and phylogeneticrelationship between SARS-CoV and other coronaviruses.The results showed that SARS-CoV is a novel coronavirus which is different from any of the three previously knowngroups of coronviruses, but it is closer to BoCoV and MHV than to other coronaviruses. This study is in aid ofexperimental determination of SARS-CoV proteomics andthe development of antiviral vaccine.展开更多
We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-l-phospha...We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-l-phosphate uridyltransferase （GALT） involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http：//bioinformatica.isa.cnr.it/GALT/.展开更多
Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Proj...Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database （RAP-DB） （Ohyanagi et al., 2006） and Michigan State University Rice Genome Annotation Project （MSU-RGAP） （Ouyang et al., 2007） are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare （International Rice Genome Sequencing Project, 2005）. Beijing Genomics Institute Rice Information System （BGI-RIS） （Zhao et ai., 2004） is an available resource for indica rice cultivar 93-11;展开更多
It is our great honor to vip-edit this Thematic Issue on Bioinformatics in Science China Life Sciences. In recent years, a strong cohort of Chinese scientists has emerged as leading scholars in the exciting fields o...It is our great honor to vip-edit this Thematic Issue on Bioinformatics in Science China Life Sciences. In recent years, a strong cohort of Chinese scientists has emerged as leading scholars in the exciting fields of bioinforrnatics and computational biology. In this issue, we are pleased to pre- sent outstanding research work produced from 10 world renowned researchers.展开更多
基金supported by the National Natural Science Foundation of China(32470676 and 32170236)Central Guidance on Local Science and Technology Development Fund of Hebei Province(246Z2508G)+2 种基金Hebei Natural Science Foundation(C2020209064)Tangshan Science and Technology Program Project(21130217C)Key research project of North China University of Science and Technology(ZD-YG-202313-23).
文摘As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.
基金supported by the National Natural Science Foundation of China(31971865)Zhejiang Natural Science Foundation(LZ17C130001)+1 种基金the Innovation Method Project of China(2018IM0301002)the Jiangsu Collaborative Innovation Center for Modern Crop Production。
文摘Rice is one of cereal crops and a model species for monocots.Since the release of the first draft rice genome sequences in 2002,considerable progress has been achieved in rice genomic researches,thanks to rapid development and efficient utilization of bioinformatics methods and tools.In this review,we summarize the progress of studies of rice genome sequencing and other omics and introduce the wellmaintained bioinformatics databases and tools developed for rice genome resources and breeding.After reviewing the history of rice bioinformatics,we use single-cell sequencing and machine learning as examples showing how bioinformatics integrates emerging technologies and how it continues to develop for future rice research.
文摘Polyploidy is common among agriculturally important crops. Popular genetic methods and their implementations cannot always be applied to polyploid genetic data. We give an overview about available tools and their limitations in terms of levels of ploidy, auto- and allo-ploidy. The main classes of tools are genotype calling, linkage mapping and haplotyping. The usability of the tools is discussed with a focus on their applicability to data sets produced by state of the art technologies. We show that many challenges remain until the toolset for polyploidy provides similar functionalities as those which are already available for diploids. Some tools have been developed over a decade ago and are now outdated. In addition, we discuss necessary steps to overcome this shortage in the future.
文摘The massive extension in biological data induced a need for user-friendly bioinformatics tools could be used for routine biological data manipulation. Bioanalyzer is a simple analytical software implements a variety of tools to perform common data analysis on different biological data types and databases. Bioanalyzer provides general aspects of data analysis such as handling nucleotide data, fetching different data formats information, NGS quality control, data visualization, performing multiple sequence alignment and sequence BLAST. These tools accept common biological data formats and produce human-readable output files could be stored on local computer machines. Bioanalyzer has a user-friendly graphical user interface to simplify massive biological data analysis and consume less memory and processing power. Bioanalyzer source code was written through Python programming language which provides less memory usage and initial startup time. Bioanalyzer is a free and open source software, where its code could be modified, extended or integrated in different bioinformatics pipelines. Bioinformatics Produce huge data in FASTA and Genbank format which can be used to produce a lot of annotation information which can be done with Python programming language that open the door form bioinformatics tool due to their elasticity in data analysis and simplicity which inspire us to develop new multiple tool software able to manipulate FASTA and Genbank files. The goal Develop new software uses Genomic data files to produce annotated data. Software was written using python programming language and biopython packages.
文摘In this editorial preface, I briefly r eview cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP- containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.
基金supported by grants from Wuhan University Medical Faculty Innovation Seed Fund Cultivation Project(No.TFZZ2018025)Xiao-ping CHEN Foundation for the Development of Science and Technology of Hubei Province(No.CXPJJH12000001-2020313)the National Natural Science Foundation of China(No.81670123 and No.81670144).
文摘Objective This study aims to investigate the expression,prognostic value,and function of kinesin superfamily 4A(KIF4A)in cervical cancer.Methods Cervical cancer cell lines(Hela and SiHa)and TCGA data were used for experimental and bioinformatic analyses.Overall survival(OS)and progression free survival(PFS)were compared between patients with high or low KIF4A expression.Copy number variation(CNV)and somatic mutations of patients were visualized and GISTIC 2.0 was used to identify significantly altered sites.The function of KIF4A was also explored based on transcriptome analysis and validated by experimental methods.Chemotherapeutic and immunotherapeutic benefits were inferred using multiple reference databases and algorithms.Results Patients with high KIF4A expression had better OS and PFS.KIF4A could inhibit proliferation and migration and induce G1 arrest of cervical cancer cells.Higher CNV load was observed in patients with low KIF4A expression,while the group with low KIF4A expression displayed more significantly altered sites.A total of 13 genes were found to mutate more in the low KIF4A expression group,including NOTCH1 and PUM1.The analysis revealed that low KIF4A expression may indicate an immune escape phenotype,and patients in this group may benefit more from immunotherapy.With respect to chemotherapy,cisplatin and gemcitabine may respond better in patients with high KIF4A expression,while 5-fluorouracil etc.may be responded better in patients with low KIF4A expression Conclusion KIF4A is a tumor suppressor gene in cervical cancer,and it can be used as a prognostic and therapeutic biomarker in cervical cancer.
文摘Severe acute respiratory syndrome coronavirus(SARS-CoV)and SARS-CoV-2 are thought to transmit to humans via wild mammals,especially bats.However,evidence for direct bat-to-human transmission is lacking.Involvement of intermediate hosts is considered a reason for SARS-CoV-2 transmission to humans and emergence of outbreak.Large biodiversity is found in tropical territories,such as Brazil.On the similar line,this study aimed to predict potential coronavirus hosts among Brazilian wild mammals based on angiotensin-converting enzyme 2(ACE2)sequences using evolutionary bioinformatics.Cougar,maned wolf,and bush dogs were predicted as potential hosts for coronavirus.These indigenous carnivores are philogenetically closer to the known SARS-CoV/SARS-CoV-2 hosts and presented low ACE2 divergence.A new coronavirus transmission chain was developed in which white-tailed deer,a susceptible SARS-CoV-2 host,have the central position.Cougar play an important role because of its low divergent ACE2 level in deer and humans.The discovery of these potential coronavirus hosts will be useful for epidemiological surveillance and discovery of interventions that can contribute to break the transmission chain.
基金supported by grant CNTC-110202101039(JY-16)and YNTC-2022530000241008.
文摘Bioinformatics analysis often requires the filtering of multi-datasets,based on frequency or frequency of occurrence,for decisions on retention or deletion.Existing tools for this purpose often present a challenge with complex installation,which necessitate custom coding,thereby impeding efficient data processing activities.To address this issue,Filterx,a user-friendly command line tool that written in C language,was developed that supports multi-condition filtering,based on frequency or occurrence.This tool enables users to complete the data processing tasks through a simple command line,greatly reducing both workload and data processing time.In addition,future development of this tool could facilitate its integration into various bioinformatics data analysis pipelines.
基金supported in part by the Clinical and Translational Science Award(Grant No.UL1TR001117)to Duke University from the National Institutes of Health(NIH),United States
文摘Though a relatively young discipline, translational bioinformatics （TBI） has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex- tualization of the term TBI, describes the discipline＇s brief history and past accomplishments, as well as current loci, and concludes with predictions of future directions in the field.
文摘Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at present.The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data.The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike.Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine.We review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers.
文摘Natural products are among the most important sources of lead molecules for drug discovery.With the development of affordable whole-genome sequencing technologies and other‘omics tools,the field of natural products research is currently undergoing a shift in paradigms.While,for decades,mainly analytical and chemical methods gave access to this group of compounds,nowadays genomics-based methods offer complementary approaches to find,identify and characterize such molecules.This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work.In this context,this review gives a summary of tools and databases that currently are available to mine,identify and characterize natural product biosynthesis pathways and their producers based on‘omics data.A web portal called Secondary Metabolite Bioinformatics Portal(SMBP at http://www.secondarymetabolites.org)is introduced to provide a one-stop catalog and links to these bioinformatics resources.In addition,an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.
文摘In the 2017 first issue of this Journal - Genomes, Proteomes and Bioinformatics - a special database article entitled ＂GSA： Gen- ome Sequence Archive＂ is published. This article provides a brief introduction to the platform developed by the authors from the BIG Data Center （BIGD） of Beijing Institute of Genomics （BIG）, Chinese Academy of Sciences （CAS）. The aim of the GSA project is to collect, integrate, and archive raw sequence data submitted by domestic and international users. It is one of the major activities being carried on by a team of around 50 young bioinformaticians at BIGD. In addition to the GSA system, they are also working on several bioinformatics service-orientated projects as described in one of their recent publications .
基金supported in part by the National Institutes of Health of the United States(Grant Nos.UL1 RR024139 to Yale Clinical and Translational Science Award,1S10OD018034-01 to 6500 QTrap Mass Spectrometer for Yale University,1S10RR026707-01 to 5500QTrap Mass Spectrometer for Yale University,P30DA018343 to Yale/NIDA Neuroproteomics Center and NIDDK-K01DK089006 awarded to JR)
文摘We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
文摘Bioinformatics, an interdisciplinary field that combines biology, mathematics, computer science, medicine, and health science, to integrate, analyze, and interpret biological data, is now becoming increasingly data-intensive. To dig out the treasure from big data powered by high-throughput sequencing technologies, it is highly dependent on Bioinformaties Commons that involves a variety of fundamental resources, includ- ing databases, web servers, algorithms, methods, software tools, ontologies, and standards. To be short, Bioinformatics Commons has become the cornerstone of life and health sciences, facilitating and accelerating the translation of big data into big discoveries.
基金supported by a grant through the National Institutes of Health,National Heart,Lung,and Blood Institute to Dr.Nichole Reisdorph(Grant No.T15HL086386)
文摘Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications： （1） immediate short-term training workshops and （2） long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute （NHLBI）-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health （NJH） and the University of Colorado School of Medicine （UCD）. The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national vip faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consis- tently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.
基金supported by the National Natural Science Foundation of China (Grant Nos.30625012,30625019 and 60721003)National Key Basic Research and Development Program of China (Grant No.2004CB518605)National Hi-Tech Research and Development Program of China (Grant No.2006AA02Z325)
文摘microRNAs (miRNAs) have been reported to be associated with the pathogenesis and progression of breast cancer.However,little is known about the pathways through which miRNAs regulate these processes,e.g.,the interaction between miRNAs and their target genes with regard to different pathological status of breast cancer,such as histological grades.This study investigated the possible roles of miRNAs in the differentiation of histological grades of breast cancer with a computational approach.Based on a microarray dataset,15 candidate miRNAs were identified,whose predicted target genes are enriched as differentially expressed between grade I and grade III breast tumors.Among them,9 key miRNAs focalize their target genes on 6 central signaling pathways.The SMAD7 protein,the main inhibitory protein in the TGF-β pathway,is predicted as a target of several miRNAs and is also regulated by several other pathways that are possibly targeted by miRNAs.It was hypothesized that miRNAs participate in the differentiation of breast cancer and the TGF-β pathway acts as a major implementary pathway on which several miRNAs take effect through multiple channels.The prediction power of the predicted miRNA target genes was validated on three independent datasets.The differential expression of three miRNAs was validated by real-time PCR on breast carcinoma samples of 10 patients.
文摘A novel coronavirus has been identified as the causative agent of the severe acute respiratory syndrome(SARS). For all the SARS-CoV associated proteins derivatedfrom the SARS-CoV genome, the physiochemical propertiessuch as the molecular weight, isoelectric point and extinction coefficient of each protein were calculated. Thetransmembrane segments and subcellular localization(SubLocation) prediction and conserved protein motifssearch against database were employed to analyze thefunction of SARS-CoV proteins. Also, the homology protein sequence alignment and evolutionary distance matrixcalculation between SARS-CoV associated proteins and the corresponding proteins of other coronaviruses wereemployed to identify the classification and phylogeneticrelationship between SARS-CoV and other coronaviruses.The results showed that SARS-CoV is a novel coronavirus which is different from any of the three previously knowngroups of coronviruses, but it is closer to BoCoV and MHV than to other coronaviruses. This study is in aid ofexperimental determination of SARS-CoV proteomics andthe development of antiviral vaccine.
基金This work has been devel-oped in the frame of the CNR-Bioinformatics Project
文摘We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-l-phosphate uridyltransferase （GALT） involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http：//bioinformatica.isa.cnr.it/GALT/.
文摘Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database （RAP-DB） （Ohyanagi et al., 2006） and Michigan State University Rice Genome Annotation Project （MSU-RGAP） （Ouyang et al., 2007） are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare （International Rice Genome Sequencing Project, 2005）. Beijing Genomics Institute Rice Information System （BGI-RIS） （Zhao et ai., 2004） is an available resource for indica rice cultivar 93-11;
文摘It is our great honor to vip-edit this Thematic Issue on Bioinformatics in Science China Life Sciences. In recent years, a strong cohort of Chinese scientists has emerged as leading scholars in the exciting fields of bioinforrnatics and computational biology. In this issue, we are pleased to pre- sent outstanding research work produced from 10 world renowned researchers.
