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Clinical applications of next-generation sequencing in colorectal cancers

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World Journal of Gastroenterology 2013年第40期19卷 6784-6793页

作者： Tae-Min Kim Sug-Hyung Lee Yeun-Jun Chung MRC Cancer Evolution research center College of MedicineThe Catholic University of KoreaSeoul 137-701South Korea integrated research center for genome polymorphism Department of MicrobiologyCollege of MedicineThe Catholic University of KoreaSeoul 137-701South Korea Department of Pathology College of MedicineThe Catholic University of KoreaSeoul 137-701South Korea

Like other solid tumors,colorectal cancer(CRC) is a genomic disorder in which various types of genomic alterations,such as point mutations,genomic rearrangements,gene fusions,or chromosomal copy number alterations,can contribute to the initiation and progression of the disease. The advent of a new DNA sequencing technology known as next-generation sequencing(NGS) has revolutionized the speed and throughput of cataloguing such cancer-related genomic alterations. Now the challenge is how to exploit this advanced technology to better understand the underlying molecular mechanism of colorectal carcinogenesis and to identify clinically relevant genetic biomarkers for diagnosis and personalized therapeutics. In this review,we will introduce NGS-based cancer genomics studies focusing on those of CRC,including a recent large-scale report from the Cancer genome Atlas. We will mainly discuss how NGS-based exome-,whole genome- and methylome-sequencing have extended our understanding of colorectal carcinogenesis. We will also introduce the unique genomic features of CRC discovered by NGS technologies,such as the relationship with bacterial pathogens and the massive genomic rearrangements of chromothripsis. Finally,we will discuss the necessary steps prior to development of a clinical application of NGS-related findings for the advanced management of patients with CRC.

关键词： Next-generation sequencing Cancer genomics Colorectal cancers Personalized medicine The cancer genome atlas

Two paths, one goal: mechanism of calcium homeostasis to balance plant growth and immunity

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Science China Life Sciences 2025年第1期 306-308页

作者： Aziz Ul Ikram Yanping Jing Huan Chen Jian Chen International genome center Jiangsu University Joint center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong University

Calcium(Ca2+) is an essential nutrient and a cellular signal in plants. The level of free Ca2+in the apoplast is ～10,000-fold higher than that in the cytoplasm at the resting state. This large Ca2+level gradient across the membrane between the interior and exterior can cause Ca2+overload and toxicity. Plants have evolved mechanisms to export Ca2+out of the cytoplasm or store it in intracellular organelles, such as endoplasmic reticulum（ER）, mitochondria, and vacuole.

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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University research Institute of Intelligent Computing Zhejiang Lab Shanghai research Institute for Intelligent Autonomous Systems center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

research status and prospects of the fractal analysis of metal material surfaces and interfaces

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International Journal of Minerals,Metallurgy and Materials 2025年第1期32卷 20-38页

作者： Qinjin Dai Xuefeng Liu Xin Ma Shaojie Tian Qinghe Cui Beijing Advanced Innovation center for Materials genome Engineering University of Science and Technology BeijingBeijing 100083China Beijing Laboratory of Metallic Materials and Processing for Modern Transportation University of Science and Technology BeijingBeijing 100083China Laboratory for Advanced Materials Processing of Ministry of Education University of Science and Technology BeijingBeijing 100083China School of Mechanical and Electrical Engineering Xinjiang Institute of EngineeringUrumqi 830023China

As a mathematical analysis method,fractal analysis can be used to quantitatively describe irregular shapes with self-similar or self-affine *** analysis has been used to characterize the shapes of metal materials at various scales and *** methods make it difficult to quantitatively describe the relationship between the regular characteristics and properties of metal material surfaces and ***,fractal analysis can be used to quantitatively describe the shape characteristics of metal materials and to establish the quantitative relationships between the shape characteristics and various properties of metal *** the perspective of two-dimensional planes and three-dimensional curved surfaces,this paper reviews the current research status of the fractal analysis of metal precipitate interfaces,metal grain boundary interfaces,metal-deposited film surfaces,metal fracture surfaces,metal machined surfaces,and metal wear *** relationship between the fractal dimensions and properties of metal material surfaces and interfaces is *** from three perspectives of fractal analysis,namely,research scope,image acquisition methods,and calculation methods,this paper identifies the direction of research on fractal analysis of metal material surfaces and interfaces that need to be *** is believed that revealing the deep influence mechanism between the fractal dimensions and properties of metal material surfaces and interfaces will be the key research direction of the fractal analysis of metal materials in the future.

关键词： metal material surfaces and interfaces fractal analysis fractal dimension homogeneity

A first-principles investigation on mechanical and metallic properties of titanium carbides under pressure

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Journal of Materials Science & Technology 2018年第10期34卷 1953-1958页

作者： Xiaojing Sha Namin Xiao Yongjun Guan Xiaosu Yi Materials genome center Beijing Institute of Aeronautical Materials

The titanium carbides are potential candidates to achieve both high hardness and refractory property. We carried out a structural search for titanium carbides at three pressures of 0 GPa, 30 GPa and 50 GPa. A phase diagram of the Ti-C system at 0 K was obtained by elucidating formation enthalpies as a function of compositions, and their mechanical and metallic properties of titanium carbides were investigated sys- tematically. We also discussed the relation of titanium concentration to the both mechanical and metallic properties of titanium carbides. It has been found that the average valence electron density and tractil-ity improved at higher concentrations of titanium, while the degree of covalent bonding directionality decreased. To this effect, the hardness of titanium carbide decreases as the content of titanium increases. Our results indicated that the titanium content significantly affected the metallic properties of the Ti-C system.

关键词： First-principles calculation Transition metal carbides Mechanical property and hardness High pressure phase stability

An inducible constitutive expression system in Bombyx mori mediated by phiC31 integrase

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Insect Science 2021年第5期28卷 1277-1289页

作者： Feng Wang Yan-Ting Ji Chi Tian Yuan-Cheng Wang Shen Xu Ri-Yuan Wang Qian-Qian Yang Ping Zhao Qing-You Xia State Key Laboratory of Silkworm genome Biology Chongqing Engineering and Technology Research Center for Novel Silk MaterialsBiological Science Research CenterSouthwest UniversityChongqingChina

Inducible gene-expression systems play important roles in gene functional assays in the post-genome *** phage-derived phiC31 integrase,which mediates an irreversible site-specific cassette exchange between the phage attachment site(attP)and the bacterial attachment site(attB),provides a promising option for the construction of a controllable gene-expression ***,we report a phiC3I integrase-mediated promoter flip system(FLIP)for the inducible expression of target genes in silk-worm(Bombyx mori).First,we constructed a FLIP reporter system,in which a BmAct4 promoter with enhanced translational efficiency was flanked by the attB and attP sites in a head-to-head orientation and further linked in a reverse orientation to a DsRed reporter *** coexpression of a C-terminal modified phiC3 I-NLS integrase carrying a simian virus 40(SV40)nuclear localization signal(NLS)effectively flipped the BmAct4 promoter through an attBlattP exchange,thereby activating the downstream expression of DsRed in a silkworm embryo-derived cell line,***,the FLIP system,together with a system continuously expressing the phiC3 I-NLS integrase,was used to construct binary transgenic silkworm *** between FLIP and phiC31-NLS transgenic silkworm lines resulted in the successful flipping of the BmAct4 promoter,with an approximately 39%heritable transformation efficiency in silkworm offispring,leading to the constitutive and high-level expression of DsRed in silkworms,which accounted for approximately 0.81%of the silkworm pupal *** successful development of the FLIP system offers an effective alternative for manipulating gene expression in silkworms and other lepidopteran species.

关键词： inducible gene expression PhiC31 integrase promoter flipping silkworm

Analysis of Transcriptome Changes Induced by Ptr ToxA in Wheat Provides Insights into the Mechanisms of Plant Susceptibility

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Molecular Plant 2009年第5期2卷 1067-1083页

作者： Iovanna Pandelova Melania F. Betts Viola A. Manning Larry J. Wilhelm Todd C. Mockler Lynda M. Ciuffetti Department of Botany and Plant Pathology and center for genome research and Biocomputing Oregon State University Corvallis OR 97331 USA

To obtain greater insight into the molecular events underlying plant disease susceptibility, we studied transcriptome changes induced by a host-selective toxin of Pyrenophora tritici-repentis, Ptr ToxA （ToxA）, on its host plant, wheat. Transcriptional profiling of ToxA-treated leaves of a ToxA-sensitive wheat cultivar was performed using the GeneChip Wheat genome Array. An improved and up-to-date annotation of the wheat microarray was generated and a new tool for array data analysis （BRAT） was developed, and both are available for public use via a web-based interface. Our data indicate that massive transcriptional reprogramming occurs due to ToxA treatment, including cellular responses typically associated with defense. In addition, this study supports previous results indicating that ToxA-induced cell death is triggered by impairment of the photosynthetic machinery and accumulation of reactive oxygen species. Based on results of this study, we propose that ToxA acts as both an elicitor and a virulence factor.

关键词： Gene expression transcriptome analysis defense responses fungal pathogenesis plant-microbe interactions host-selective toxin.

Network-Based Predictions and Simulations by Biological State Space Models: Search for Drug Mode of Action

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Journal of Computer Science & Technology 2010年第1期25卷 131-153页

作者： Rui Yamaguchi Seiya Imoto Satoru Miyano Human genome center Institute of Medical Science University of Tokyo

Since time-course microarrav data are short but contain a large number of genes, most of statistical models should be extended so that they can handle such statistically irregular situations. We introduce biological state space models that are established as suitable computational models for constructing gene networks from microarray gene expression data. This chapter elucidates theory and methodology of our biological state space models together with some representative analyses including discovery of drug mode of action. Through the applications we show the whole strategy of biological state space model analysis involving experimental design of time-course data, model building and analysis of the estimated networks.

关键词： gene networks state space models time-course gene expression data

Stacking fault,dislocation dissociation,and twinning in Pt_(3) Hf compounds:a DFT study

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Rare Metals 2021年第4期40卷 1020-1030页

作者： Shun-Meng Zhang Kai Xiong Cheng-Chen Jin Zong-Bo Li Jun-Jie He Yong Mao National center for International research on Photoelectric and Energy Materials School of Materials and EnergyMaterials Genome InstituteYunnan UniversityKunming 650091China

The Pt3Hf compound plays a decisive role in strengthening Pt-Hf alloy *** the stacking fault,dislocation dissociation,and twinning mechanisms in Pt3Hf is the first step in understanding its plastic *** this work,the generalized stacking fault energies(GSFE),including the complex stacking fault(CSF),the superlattice intrinsic stacking fault(SISF),and the antiphase boundary(APB) energies,are calculated using firstprinciples *** dislocation dissociation,deformation twinning,and yield behavior of Pt3Hf are discussed based on GSFE after their incorporation into the Peierls-Nabarro *** found that the unstable stacking fault energy(γus) of(111)APB is lower than that of SISF and(010) APB,implying that the energy barrier and critical stress required for(111)APB generation are lower than those required for(010)APB *** result indicates that the a superdislocation will dissociate into two collinear a/2 superpartial *** a/2 dislocation could further dissociate into a a/6 Shockley dislocation and a a/3 superShockley dislocation connected by a SISF,which results in an APB→SISF *** study also discovered that Pt3 Hf exhibits normal yield behavior,although the cross-slip of a a/2 dislocation is not forbidden,and the anomalous yield criterion is ***,it is observed that the energy barrier and critical stress for APB formation increases with increasing pressure and decreases as the temperature is *** the temperature rises above 1400 K,the a/2 dislocation slipping may change from the {111} planes to the {100} planes.

关键词： Platinum alloys Stacking fault energy Dislocation dissociation Twinning First-principles