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Prediction of sorghum miRNAs and their targets with computational methods

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Chinese Science Bulletin 2010年第13期55卷 1263-1270页

作者： DU JiangFeng WU YongJun FANG XiaoFeng CAO JunXia ZHAO Liang TAO ShiHeng bioinformatics center Northwest Agricultural & Forestry University Yangling 712100 China College of Life Sciences Northwest Agricultural & Forestry University Yangling 712100 China

microRNAs 是 21-nt 的一个班在 post-transcriptional 起关键作用的长、非编码、最新识别的 RNA 基因规定。他们的目标涉及各种各样的生物过程，包括开发，新陈代谢，和压力反应。尽管很多 miRNAs 在许多种类被报导了，在蜀黍的 miRNAs... 详细信息

microRNAs 是 21-nt 的一个班在 post-transcriptional 起关键作用的长、非编码、最新识别的 RNA 基因规定。他们的目标涉及各种各样的生物过程，包括开发，新陈代谢，和压力反应。尽管很多 miRNAs 在许多种类被报导了，在蜀黍的 miRNAs 的报告是有限的。基于 genomic 调查顺序(GSS ) 和 microRNA (miRNA ) 使用相同搜索第二等的结构， 17 新 miRNAs 的一个总数在这个工作被识别。他们被发现在 11 个 miRNA 家庭之中不均匀的分布式。一些 miRNA 基因在多重地点并且在超过一 genomic 上下文被发现。大多数 miRNAs 在一样的王国以内被保存，但是我们在蜀黍发现 sbi-miR127 和 sbi-miR466 与 H 显示出保存。现代人并且 M。musculus 分别地。经由联机软件 miRU 的那些 17 新 miRNAs 的分析证明他们可能调整 64 目标基因，其大多数涉及 RNA 处理，新陈代谢，房间周期，蛋白质降级，压力反应和交通。11 个 miRNA 家庭中的至少 7 个指向在新陈代谢和压力反应是必要的蛋白质，包括 NADPH 细胞色素 P450 reductase， nucleoside diphosphate kinase 和 superoxide dismutase，建议 miRNAs 起在生物过程的一个必要作用。

关键词： miRNA 高粱细胞色素P450 超氧化物歧化酶计算预测应激反应新陈代谢

Sarve:synthetic data and local differential privacy for private frequency estimation

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Cybersecurity 2022年第4期5卷 97-116页

作者： Gatha Varmal Ritu Chauhan Dhananjay Singh Amity Institute of Information Technology Amity UniversityNoidaIndia center for Computational Biology and bioinformatics Amity UniversityNoidaIndia Department of Electronics Engineering HUFSSeoulKorea

The collection of user attributes by service providers is a double-edged *** are instrumental in driving statistical analysis to train more accurate predictive models like *** analysis of the collected user data includes frequency estimation for categorical ***,the users deserve privacy guarantees against inadvertent identity *** algorithms called frequency oracles were developed to randomize or perturb user attributes and estimate the frequencies of their *** propose Sarve,a frequency oracle that used Randomized Aggregatable Privacy-Preserving Ordinal Response(RAPPOR)and Hadamard Response(HR)for randomization in combination with fake *** design of a service-oriented architecture must consider two types of complexities,namely computational and *** functions of such systems aim to minimize the two complexities and therefore,the choice of privacy-enhancing methods must be a calculated *** variant of RAPPOR we had used was realized through bloom flters.A bloom filter is a memory-efficient data structure that offers time complexity of O(1).On the other hand,HR has been proven to give the best communication costs of the order of log(b)for b-bits ***,Sarve is a step towards frequency oracles that exhibit how privacy provisions of existing methods can be combined with those of fake data to achieve statistical results comparable to the original *** also implemented an adaptive solution enhanced from the work of Arcolezi et *** use of RAPPOR was found to provide better privacy-utility tradeoffs for specific privacy budgets in both high and general privacyregimes.

关键词： Synthetic data Differential privacy Frequency estimation Frequency oracle Privacy

Monascus pilosus-fermented black soybean inhibits lipid accumulation in adipocytes and in high-fat diet-induced obese mice

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Asian Pacific Journal of Tropical Medicine 2015年第4期8卷 276-282页

作者： Young-Sil Lee Bong-Keun Choi Hae Jin Lee Dong-Ryung Lee Jinhua Cheng Won-Keun Lee Seung Hwan Yang Joo-Won Suh center for Nutraceutical and Pharmaceutical Materials Myongji University Interdisciplinary Program of Biomodulation Myongji University Division of Bioscience and bioinformatics College of Natural ScienceMyongji University

Objective:To explore the anti-obesity effects and the mechanism of action of Monascus pilosus(***)-fermented black soybean(MFBS)extracts(MFBSE)and MFBS powders(MFBSP)in adipocytes and high-fat diet(HFD)-induced obese mice,***:Black soybean was fermented with ***,and the main constituents in MFBS were analyzed by HPLC *** vitro,MFBSE were examined for anti-adipogenic effects using Oil-Red O *** vivo,mice were fed a normal-fat diet(NFD)control,HFD control or HFD containing 1 g/kg MFBSP for 12 weeks,and then body weight gain and tissues weight ***-time PCR and western blot assay were used to determine the mechanism of anti-adipogenic ***:MFBSE inhibited lipid accumulation in 3T3-L1 adipocytes without exerting cell *** treatment in HFD-fed mice significantly decreased the body weight gain compared with the HFD control *** and MFBSP treatment resulted in significantly lower mRNA levels of adipogenesis-related genes,such as peroxisome proliferator-activated receptorγ(PPARγ),fatty acid-binding protein 4(FABP4),and fatty acid synthase(FAS),in adipocytes and in white adipose tissue(WAT)of HFD-induced obese ***:These results suggest that the anti-obesity effects of MFBS are elicited by regulating the expression of adipogenesis-related genes in adipocytes and WAT of HFDinduced obese mice.

关键词： Monascus pilosus Black soybean Adipocytes High-fat diet-induced obese mice Anti-obesity Adipogenesis-related genes

Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform

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Journal of Integrative Plant Biology 2015年第11期57卷 980-991页

作者： Yang L Xiao Cui Rui Li Piaopiao Huang Jie Zong Danqing Yao Gang Li Dabing Zhang Zheng Yuan State Key Laboratory of Hybrid Rice School of Life Sciences and BiotechnologyShanghai Jiao Tong University Novel bioinformatics Company Shanghai Agricultural Technology Extension and Service center

DNA markers play important roles in plant breed- ing and genetics. The Insertion/Deletion （InDel） marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor- intensive. We developed an end-to-end computational solution （InDel Markers Development Platform, IMDP） to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequen- ces alignment pipeline （AGA-pipe） and next-generation re- sequencing data mapping pipeline （NGS-pipe）. With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA- pipe and NGS-pipe, we developed 2o5,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction （PCR） analysis of subgroup-specific markers indicated that the precision reached 90% （86 of 95）. Finally, to make them available to the public, we have integrated the InDels/markers information into a website （Rice InDel Marker Database, RIMD, http：I/2o2.12o.45.71/）. The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.

关键词： Genetic polymorphism genome alignment InDel marker molecular breeding next-generation sequencing

HCSGD：An integrated database of human cellular senescence genes

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Journal of Genetics and Genomics 2017年第5期44卷 227-234页

作者： Qiongye Dong Hongqing Han Xuehui Liu Lei Wei Wei Zhang Zhen Zhao Michael Q.Zhang Xiaowo Wang Ministry of Education Key Laboratory of bioinformatics Center for Synthetic and Systems Biology Department of Automation Tsinghua University Beijing100084 China bioinformatics Division Tsinghua National Laboratory for Information Science and Technology Beijing 100084 China Department of Basic Medical Sciences School of Medicine Tsinghua University Beijing 100084 China

Cellular senescence is an irreversible cell cycle arrest program in response to various exogenous and endogenous stimuli like telomere dysfunction and DNA *** has been widely accepted as an antitumor program and is also found closely related to embryo development,tissue repair,organismal aging and age-related degenerative *** the past decades,numerous efforts have been made to uncover the gene regulatory mechanisms of cellular *** is a strong demand to integrate these data from various resources into one open *** facilitate researchers on cellular senescence,we have developed Human Cellular Senescence Gene Database（HCSGD） by integrating multiple online published data sources into a comprehensive senescence gene annotation platform（http：//***/member/xwwang/HCSGD）.Potential Human Cellular Senescence Genes（HCSGS）were collected by combining information from published literatures,gene expression profiling data and Protein-Protein Interaction ***,genes are annotated with gene ontology annotation and microRNA/drug/compound target *** provides a valuable resource to visualize cellular senescence gene networks,browse annotated functional information,and retrieve senescenceassociated genes with a user-friendly web interface.

关键词： Cellular senescence Meta-analysis Text-mining

Bioinformatic and Experimental Analyses Reveal That KIF4A Is a Biomarker of Therapeutic Sensitivity and Predicts Prognosis in Cervical Cancer Patients

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Current Medical Science 2022年第6期42卷 1273-1284页

作者： Jie WU Lan LI Hao ZHONG Hao-han ZHANG Jing LI Hui-bo ZHANG Ya-qi ZHAO Bin XU Qi-bin SONG Cancer center Renmin Hospital of Wuhan UniversityWuhan430030China Department of bioinformatics Wissenschaftszentrum WeihenstephanTechnical University of MunichFreising85354Germany

Objective This study aims to investigate the expression,prognostic value,and function of kinesin superfamily 4A(KIF4A)in cervical *** Cervical cancer cell lines(Hela and SiHa)and TCGA data were used for experimental and bioinformatic *** survival(OS)and progression free survival(PFS)were compared between patients with high or low KIF4A *** number variation(CNV)and somatic mutations of patients were visualized and GISTIC 2.0 was used to identify significantly altered *** function of KIF4A was also explored based on transcriptome analysis and validated by experimental *** and immunotherapeutic benefits were inferred using multiple reference databases and *** Patients with high KIF4A expression had better OS and ***4A could inhibit proliferation and migration and induce G1 arrest of cervical cancer *** 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 *** analysis revealed that low KIF4A expression may indicate an immune escape phenotype,and patients in this group may benefit more from *** respect to chemotherapy,cisplatin and gemcitabine may respond better in patients with high KIF4A expression,while 5-fluorouracil *** 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.

关键词： kinesin superfamily 4A cervical cancer prognosis chemotherapy immunotherapy

Human cross-tissue cell atlases: unprecedented resources towards systematic understanding of physiology and diseases

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Signal Transduction and Targeted Therapy 2022年第11期7卷 3980-3981页

作者： Peng Zhang Shao Li Institute for TCM-X MOE Key Laboratory of BioinformaticsBioinformatics DivisionBNRISTDepartment of AutomationTsinghua University100084BeijingChina

Recently,three landmark cross-tissue single-cell atlases were published in Science,by the Tabula Sapiens Consortium,1 Eraslan et al.,2 and Domínguez Conde et al.,3 respectively,which collectively provided the comprehensive characterization of more than million cells across more than 30 human tissues,along with the deep interpretation of disease-associated genetic variations in the context of tissues and cell types.

关键词： al. diseases collective

Allosteric modulation of G protein-coupled receptors as a novel therapeutic strategy in neuropathic pain

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Acta Pharmaceutica Sinica B 2024年第1期14卷 67-86页

作者： Chunhao Zhu Xiaobing Lan Zhiqiang Wei Jianqiang Yu Jian Zhang School of Pharmacy Ningxia Medical UniversityYinchuan 750004China Medicinal Chemistry and bioinformatics center Shanghai Jiao Tong University School of MedicineShanghai 200025China School of Basic Medical Science Ningxia Medical UniversityYinchuan 750004China Medicinal Chemistry and bioinformatics center Ocean University of ChinaQingdao 266100China State Key Laboratory of Pharmaceutical Biotechnology Nanjing UniversityNanjing 210023China

Neuropathic pain is a debilitating pathological condition that presents significant therapeutic challenges in clinical ***,current pharmacological treatments for neuropathic pain lack clinical efficacy and often lead to harmful adverse *** G protein-coupled receptors(GPCRs)are widely distributed throughout the body,including the pain transmission pathway and descending inhibition pathway,the development of novel neuropathic pain treatments based on GPCRs allosteric modulation theory is gaining *** research has shown that allosteric modulators targeting GPCRs on the pain pathway can effectively alleviate symptoms of neuropathic pain while reducing or eliminating adverse *** review aims to provide a comprehensive summary of the progress made in GPCRs allosteric modulators in the treatment of neuropathic pain,and discuss the potential benefits and adverse factors of this *** will also concentrate on the development of biased agonists of GPCRs,and based on important examples of biased agonist development in recent years,we will describe universal strategies for designing structure-based biased *** is foreseeable that,with the continuous improvement of GPCRs allosteric modulation and biased agonist theory,effective GPCRs allosteric drugs will eventually be available for the treatment of neuropathic pain with acceptable safety.

关键词： Neuropathic pain Allosteric modulators G protein-coupled receptors Analgesia

Silencing of Transposable Elements by piRNAs in Drosophila:An Evolutionary Perspective

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Genomics, Proteomics & bioinformatics 2017年第3期15卷 164-176页

作者： Shiqi Luo Jian Lu State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsCollege of Life Sciences and Peking-Tsinghua Center for Life SciencesPeking University Beijing Advanced Innovation center for Food Nutrition and Human Health College of Food Science and Nutritional EngineeringChina Agricultural University

Transposable elements （TEs） are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated bio- logical processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level. Decades of theoretical and experimental studies have well established ＂transposition-selection＂ population genetics model, which assumes that the equilibrium between TE replication and purifying selection determines the copy number of TEs in the genome. In the last decade, P-element-induced wimpy testis （PIW1）- interacting RNAs （piRNAs） were demonstrated to be master repressors of TE activities in Droso- phila, The discovery of piRNAs revolutionized our understanding of TE repression, because it reveals that the host organisms have evolved an adaptive mechanism to defend against TE invasion. Tremendous progress has been made to understand the molecular mechanisms by which piRNAs repress active TEs, although many details in this process remain to be further explored. The inter- action between piRNAs and TEs well explains the molecular mechanisms underlying hybrid dysge- nesis for the IoR and P-M systems in Drosophila, which have puzzled evolutionary biologists for decades. The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms.

关键词： Transposable element piRNA Hybrid dysgenesis Evolution Drosophila