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Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective

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Science China(Life Sciences) 2014年第11期57卷 1121-1130页

作者： MA Qin CHEN Xin LIU Chao MAO XiZeng ZHANG HanYuan JI Fei WU ChunGuo XU Ying computational systems biology Laboratory Department of Biochemistry and Molecular Biology and Institute of Bioinformatics University of Georgia BioEnergy Science Center Oak Ridge National Laboratory College of Computer Science and Technology Jilin University Provincial Hospital Affiliated to Shandong University

The availability of a large number of sequenced bacterial genomes facilitates in-depth studies about why genes(operons)in a bacterial genome are globally organized the way they *** have previously discovered that(the relative)transcription-activation frequencies among different biological pathways encoded in a genome have a dominating role in the global arrangement of *** complicating factor in such a study is that some operons may be involved in multiple pathways with different activation frequencies.A quantitative model has been developed that captures this information,which tends to be minimized by the current global arrangement of operons in a bacterial(and archaeal)genome compared to possible alternative arrangements.A study is carried out here using this model on a collection of 52 closely related Escherichia coli genomes,which revealed interesting new insights about how bacterial genomes evolve to optimally adapt to their environments through adjusting the(relative)genomic locations of the encoding operons of biological pathways once their utilization and hence transcription activation frequencies change,to maintain the above energy-efficiency *** specifically we observed that it is the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies of a specific pathway across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes(and operons)encoding specific pathways across different genomes.

关键词：细菌基因组组织大肠杆菌基因组转录激活频率变化能源定量模型操纵子

Towards efficiency in rare disease research： what is distinctive and important？

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Science China(Life Sciences) 2017年第7期60卷 686-691页

作者： Jinmeng Jia Tieliu Shi The Center for Bioinformatics and computational biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University Shanghai 200241 China

Characterized by their low prevalence, rare diseases are often chronically debilitating or life threatening. Despite their low prevalence, the aggregate number of individuals suffering from a rare disease is estimated to be nearly 400 million *** the past decades, efforts from researchers, clinicians, and pharmaceutical industries have been focused on both the diagnosis and therapy of rare diseases. However, because of the lack of data and medical records for individual rare diseases and the high cost of orphan drug development, only limited progress has been achieved. In recent years, the rapid development of next-generation sequencing(NGS)-based technologies, as well as the popularity of precision medicine has facilitated a better understanding of rare diseases and their molecular etiology. As a result, molecular subclassification can be identified within each disease more clearly, significantly improving diagnostic accuracy. However, providing appropriate care for patients with rare diseases is still an enormous challenge. In this review, we provide a brief introduction to the challenges of rare disease research and make suggestions on where and how our efforts should be focused.

关键词：疾病研究人员制药行业临床医生开发费用患病率患者诊断

Three Lemmas on Dynamic Cavity Method

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Communications in Theoretical Physics 2011年第7期56卷 157-162页

作者： Erik Aurell Hamed Mahmoudi Department of computational biology AlbaNova University Centre Department of Information and Computer Science Aalto UniversityFinland

We study the dynamic cavity method for dilute kinetic Ising models with synchronous update rules. For the parallel update rule we find for fully asymmetric models that the dynamic cavity equations reduce to a Markovian dynamics of the (time-dependent) marginal probabilities. For the random sequential update rule, also an instantiation of a synchronous update rule, we find on the other hand that the dynamic cavity equations do not reduce to a Markovian dynamics, unless an additional assumption of time factorization is introduced. For symmetric models we show that a fixed point of ordinary Belief propagation is also a fixed point of the dynamic cavity equations in the time factorized approximation. For clarity, the conclusions of the paper are formulated as three lemmas.

关键词：引理时间变化对称模型马尔可夫方程工厂化固定点同步

Competition of RNA splicing: line in or circle up

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Science China(Life Sciences) 2014年第12期57卷 1232-1233页

作者： YANG Li CHEN Ling-Ling Key Laboratory of computational biology CAS-MPG Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences State Key Laboratory of Molecular biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences

The advent of high throughput technologies has revealed that mammalian genomes are pervasively transcribed,most for long noncoding RNAs(lnc RNAs,at least 200 nt long).Thousands of lnc RNAs from intergenic regions(large intergenic noncoding RNA,linc RNA)have been uncovered by massive deep sequencing from the repertoire of polyadenylated(poly(A)+)RNAs,together with multiple chromatin land-

关键词： RNA剪接非编码RNA 竞争哺乳动物动物基因组信使RNA mRNA poly

Fenton reactions drive nucleotide and ATP syntheses in cancer

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Journal of Molecular Cell biology 2018年第5期10卷 448-459页

作者： Huiyan Sun Chi Zhang Sha Cao Tao Sheng Ning Dong Ying Xu College of Computer Science and Technology Jilin University Changchun China computational systems biology Lab Department of Biochemistry and Molecular Biology and institute of Bioinformatics University of Georgia GA USA School of Public Health Jilin University Changchun China The First Hospital of Jilin University Changchun China

我们在场 14 癌症的织物 transcriptomic 数据的计算研究打字到地址：什么可以驾驶癌症房间分割？我们到由 Fenton 反应的细胞内部的 pH 的那坚持的混乱的分析点可能在癌症开发的根。明确地，我们统计上证明了 Fenton 反应发生在癌症 cy... 详细信息

我们在场 14 癌症的织物 transcriptomic 数据的计算研究打字到地址：什么可以驾驶癌症房间分割？我们到由 Fenton 反应的细胞内部的 pH 的那坚持的混乱的分析点可能在癌症开发的根。明确地，我们统计上证明了 Fenton 反应发生在癌症 cytosol，越过所有 14 癌症的线粒体打字，基于经由 Michaelis-Menten 方程综合的癌症组织基因表示数据。另外，我们证明了在疾病房间的 cytosol 的(i) Fenton 反应将连续地房间由产生网质子通过综合的联合使 pH 稳定，对哪个作出回应增加他们的 pH 对哪个 glycolytic ATP 并且由核苷酸综合体消费他们，它可以驱使房间分割连续地综合的核苷酸根除；并且(ii ) 在线粒体的 Fenton 反应与最终来自 H 2 O 2, 大部分从有免疫力的房间发源。一个模型被开发连接这些到癌症开发，在一些变化可以被选择以 Fenton 反应支配的率便于房间分割的地方。

关键词： Fenton 核苷酸 ATP 综合体癌症反应驾驶 H2O2

Enzyme annotation for orphan reactions and its applications in biomanufacturing

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Green Chemical Engineering 2023年第2期4卷 137-145页

作者： Zhen Zhang Chun Li Key Lab for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China Center for Synthetic&systems biology Department of Chemical EngineeringTsinghua UniversityBeijing100084China

There are lots of biochemical reactions in the biosynthetic pathway without associated *** predicted by retro-biosynthetic tools are not assigned gene ***,non-natural reactions designed with novel functions also lack suitable *** these reactions can be categorized as orphan *** absence of protein-encoding genes in these orphan reactions limits their direct experimental *** tools have been developed to find candidate enzymes for these orphan ***,we discuss recent advances in these computational tools,including reaction similarity-based methods for calculating the substructural similarity between orphan reactions and known enzymatic reactions;sequence-based tools combine metabolic knowledge base and phenotypic information with genomic,transcriptomic,and metabolomic data to mine appropriate enzymes for orphan reactions;and approaches based on the creation of enzyme variants for orphan reactions as enzyme engineering modifications and de novo design of *** believe that our review will greatly facilitate the design of microbial cell factories and contribute to the development of the biomanufacturing field.

关键词： Enzyme annotation Orphan reactions Reaction similarity Gene mining computational enzyme design

APOBEC deaminases-mutases with defensive roles for immunity

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Science China(Life Sciences) 2009年第10期52卷 893-902页

作者： Courtney PROCHNOW Ronda BRANSTEITTER Molecular and computational biology University of Southern CaliforniaLos Angeles CA 90089 USA

In recent years, tremendous progress has been made in the elucidation of the biological roles and molecular mechanisms of the apolioprotein B mRNA-editing enzyme catalytic polypeptide (APOBEC) family of enzymes. The APOBEC family of cytidine deaminases has important functional roles within the adaptive and innate immune system. Activation induced cytidine deaminase (AID) plays a central role in the biochemical steps of somatic hypermutation and class switch recombination during antibody maturation, and the APOBEC 3 enzymes are able to inhibit the mobility of retroelements and the replication of retroviruses and DNA viruses, such as the human immunodeficiency virus type-1 and hepatitis B virus. Recent advances in structural and functional studies of the APOBEC enzymes provide new biochemical insights for how these enzymes carry out their biological roles. In this review, we provide an overview of these recent advances in the APOBEC field with a special emphasis on AID and APOBEC3G.

关键词： APOBEC cytidine deaminase activation induced cytidine deamination somatic hypermutation class switch recombination HyperIgM 2 syndrome human immunodeficiency virus (HIV) DNA deamination

Level spacing statistics for two-dimensional massless Dirac billiards

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Chinese Physics B 2014年第7期23卷 41-52页

作者：黄亮徐洪亚来颖诚 Celso Grebogid Institute of computational Physics and Complex systems and Key Laboratory for Magnetism and Magnetic Materials of MOE Lanzhou University School of Electrical Computerand Energy EngineeringArizona State University Department of Physics Arizona State University Institute for Complex systems and Mathematical biology School of Natural and Computing SciencesKing's CollegeUniversity of Aberdeen

Classical-quantum correspondence has been an intriguing issue ever since quantum theory was proposed. The search- ing for signatures of classically nonintegrable dynamics in quantum systems comprises the interesting field of quantum chaos. In this short review, we shall go over recent efforts of extending the understanding of quantum chaos to relativistic cases. We shall focus on the level spacing statistics for two-dimensional massless Dirac billiards, i.e., particles confined in a closed region. We shall discuss the works for both the particle described by the massless Dirac equation （or Weyl equation） and the quasiparticle from graphene. Although the equations are the same, the boundary conditions are typically different, rendering distinct level spacing statistics.

关键词： quantum chaos level spacing statistics Dirac billiards graphene billiards

Smart Breeding Platform:A web-based tool for high-throughput population genetics,phenomics,and genomic selection

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Molecular Plant 2024年第5期17卷 677-681页

作者： Huihui Li Xin Li Peng Zhang Yingwei Feng Junri Mi Shang Gao Lele Sheng Mohsin Ali Zikun Yang Liang Li Wei Fang Wensheng Wang Qian Qian Fei Gu Wenbin Zhou State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Nanfan Research Institute CAASSanyaHainan 572024China DAMO Academy Alibaba GroupHangzhou 310023China Hupan Lab Hangzhou 310023China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key Laboratory of Rice biology China National Rice Research InstituteHangzhouZhejiang 310006China

Dear Editor,In the era of big data and artificial intelligence,"smart breeding"has become a broad conceptual framework encompassing the paradigm shift of crop breeding to relying on analysis of high-throughput population genetics and phenomics data to conduct genomic selection,allowing identification and optimal use of the genetic potential in crop species(Xiao et al.,2022;Xu et al.,2022;Wang et al.,2023).Most existing tools for analyzing high-throughput breeding data require extensive computational power,complex installation processes,and command-line expertise and are therefore challenging and inconvenient for the majority of researchers and breeders(Brandies and Hogg,2021).

关键词： breeding artificial breed