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DiffGR:Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps

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genomics, Proteomics & Bioinformatics 2024年第2期22卷 143-155页

作者： Huiling Liu Wenxiu Ma Department of statistics University of California RiversideRiversideCA 92521USA

Recent advances in high-throughput chromosome conformation capture(Hi-C)techniques have allowed us to map genome-wide chromatin interactions and uncover higher-order chromatin structures,thereby shedding light on the principles of genome architecture and ***,statistical methods for detecting changes in large-scale chromatin organization such as topologically associating domains(TADs)are still ***,we proposed a new statistical method,DiffGR,for detecting differentially interacting genomic regions at the TAD level between Hi-C contact *** utilized the stratum-adjusted correlation coefficient to measure similarity of local TAD *** then developed a nonparametric approach to identify statistically significant changes of genomic interacting *** simulation studies,we demonstrated that DiffGR can robustly and effectively discover differential genomic regions under various ***,we successfully revealed cell type-specific changes in genomic interacting regions in both human and mouse Hi-C datasets,and illustrated that DiffGR yielded consistent and advantageous results compared with state-of-the-art differential TAD detection *** DiffGR R package is published under the GNU General Public License(GPL)≥2 license and is publicly available at https://***/wmalab/DiffGR.

关键词： Hi-C Differential analysis Topologically associating domain Stratum-adjusted correlation coefficient Nonparametric method

Reconstruct recent multi-population migration history by using identical-by-descent sharing

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Journal of Genetics and genomics 2024年第6期51卷 642-651页

作者： Wenxiao Zhang Kai Yuan Ru Wen Haifang Li Xumin Ni School of Mathematics and statistics Beijing Jiaotong UniversityBeijing 100044China The Stanley Center for Psychiatric Research Broad Institute of MIT and HarvardCambridgeMA 02142USA Baidu Incorporated Beijing 100085China

Identical-by-descent(IBD)is a fundamental genomic characteristic in population genetics and has been widely used for population history ***,limited by the nature of IBD,which could only capture the relationship between two individuals/haplotypes,existing IBD-based history inference is constrained to two *** this study,we propose a framework by leveraging IBD sharing in multipopulation and develop a method,MatrixiBD,to reconstruct recent multi-population migration ***,we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple *** our model,we establish a theoretical connection between migration history and IBD *** method is rigorously evaluated through simulations,revealing its remarkable accuracy and ***,we apply MatrixiBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South *** taking into account the IBD sharing across multiple populations simultaneously,MatrixlBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics,providing a holistic perspective on intricate patterns embedded within the recent population migration history.

关键词： Population genetics IBD sharing Migration history Structured coalescent theory Gene flow

An approach to incorporate linkage disequilibrium structure into genomic association analysis

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Journal of Genetics and genomics 2008年第6期35卷 381-385页

作者： Diane Wagener statistics and Epidemiology unit Research Triangle Institute

In this study, we propose to use the principal component analysis （PCA） and regression model to incorporate linkage disequilibrium （LD） in genomic association data analysis. To accommodate LD in genomic data and reduce multiple testing, we suggest performing PCA and extracting the PCA score to capture the variation of genomic data, after which regression analysis is used to assess the association of the disease with the principal component score. An empirical analysis result shows that both genotype-based correlation matrix and haplotype-based LD matrix can produce similar results for PCA. Principal component score seems to be more powerful in detecting genetic association because the principal component score is quantitatively measured and may be able to capture the effect of multiple loci.

关键词： genetic association analysis principal component analysis linkage disequilibrium

Identification of Protein Coding Regions of Rice Genes Using Alternative Spectral Rotation Measure and Linear Discriminant Analysis

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genomics, Proteomics & Bioinformatics 2004年第3期2卷 167-173页

作者： Jiao Jin Department of statistics and Financial Mathematics School of Mathematical SciencesBeijing Normal Uni-versityBeijing 100875 Beijing genomics Institute Beijing 101300China

An improved method, called Alternative Spectral Rotation (ASR) measure, for predicting protein coding regions in rice DNA has been developed. The method is based on the Spectral Rotation (SR) measure proposed by Kotlar and Lavner, and its accuracy is higher than that of the SR measure and the Spectral Content (SC) measure proposed by Tiwari et al. In order to increase the identifying accuracy, we chose three di?erent coding characters, namely the asymmetric, purine, and stop-codon variables as parameters, and an approving result was presented by the method of Linear Discriminant Analysis (LDA).

关键词： Alternative Spectral Rotation measure DFT nonparametric fitting LDA

Estimating geographic variation of infection fatality ratios during epidemics

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Infectious Disease Modelling 2024年第2期9卷 634-643页

作者： Joshua Ladau Eoin L.Brodie Nicola Falco Ishan Bansal Elijah B.Hoffman Marcin P.Joachimiak Ana M.Mora Angelica M.Walker Haruko M.Wainwright Yulun Wu Mirko Pavicic Daniel Jacobson Matthias Hess James B.Brown Katrina Abuabara Departments of Computational Precision Health and Dermatology University of CaliforniaSan FranciscoCA94115USA Arva Intelligence Inc.Salt Lake CityUT84101USA Computational Biosciences Group Lawrence Berkeley National LaboratoryBerkeleyCA94720USA Earth and Environmental Sciences Area Lawrence Berkeley National LaboratoryBerkeleyCA94720USA Graduate Group in Biostatistics University of CaliforniaBerkeleyCA94720USA Biosystems Data Science Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCA94720USA Center for Environmental Research and Community Health(CERCH) School of Public HealthUniversity of CaliforniaBerkeleyCA94720USA Bredesen Center for Interdisciplinary Research and Graduate Education University of TennesseeKnoxvilleTN37996USA Department of Nuclear Science and Engineering Massachusetts Institute of TechnologyBostonMA02139USA Biosciences Oak Ridge National LaboratoryOak RidgeTN37830USA University of California DavisCA95616USA statistics Department University of CaliforniaBerkeleyCA94720USA Division of Epidemiology and Biostatistics University of California Berkeley School of Public Health2121 Berkeley WayBerkeleyCA94720USA

Objectives We aim to estimate geographic variability in total numbers of infections and infection fatality ratios(IFR;the number of deaths caused by an infection per 1,000 infected people)when the availability and quality of data on disease burden are limited during an *** We develop a noncentral hypergeometric framework that accounts for differential probabilities of positive tests and reflects the fact that symptomatic people are more likely to seek *** demonstrate the robustness,accuracy,and precision of this framework,and apply it to the united States(U.S.)COVID-19 pandemic to estimate county-level SARS-CoV-2 *** The estimators for the numbers of infections and IFRs showed high accuracy and precision;for instance,when applied to simulated validation data sets,across counties,Pearson correlation coefficients between estimator means and true values were 0.996 and 0.928,respectively,and they showed strong robustness to model *** the county-level estimators to the real,unsimulated COVID-19 data spanning April 1,2020 to September 30,2020 from across the U.S.,we found that IFRs varied from 0 to 44.69,with a standard deviation of 3.55 and a median of *** The proposed estimation framework can be used to identify geographic variation in IFRs across settings.

关键词： Infection fatality ratio Infection fatality rate Noncentral hypergeometric distribution COVID-19 SARS-CoV-2

Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion

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Molecular Plant 2014年第4期7卷 642-656页

作者： Julie Jacquemin Jetty S.S. Ammiraju Georg Haberer Dean D. Billheimer Yeisoo Yu Liana C. Liu Luis F. Rivera Klaus Mayer Mingsheng Chen Rod A. Wing Arizona genomics Institute School of Plant Sciences University of Arizona Tucson AZ 85721 USA MIPS/IBIS Helmholtz Center Munich Ingoistaedter Landstrasse 1 85764 Neuherberg Germany Arizona statistics Consulting Laboratory School of Plant Sciences University of Arizona Tucson AZ 85721 USA State Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences 8eijing 100101 China

In analyzing gene families in the whole-genome sequences available for O. sativa （AA）, O. glaberrima （AA）, and O. brachyantha （FF）, we observed large size expansions in the AA genomes compared to FF genomes for the superfamilies F-box and NB-ARC, and five additional families： the Aspartic proteases, BTB/POZ proteins （BTB）, Glutaredoxins, Trypsin a-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.

关键词： gene family expansion Oryza tandem duplication duplicated gene evolution.

Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq analysis

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Frontiers of Medicine 2024年第1期18卷 147-168页

作者： Weiwei Xian Mohammad Asad Shuai Wu Zhixin Bai Fengjiao Li Junfeng Lu Gaoyu Zu Erin Brintnell Hong Chen Ying Mao Guomin Zhou Bo Liao Jinsong Wu Edwin Wang Linya You Department of Human Anatomy&Histoembryology School of Basic Medical SciencesFudan UniversityShanghai200032China Cumming School of Medicine University of CalgaryCalgaryAlbertaT2N 4N1Canada Glioma Surgery Division Department of NeurosurgeryHuashan HospitalFudan UniversityShanghai200040China Department of Pathology Huashan HospitalFudan UniversityShanghai200040China Department of Neurosurgery Huashan HospitalFudan UniversityShanghai200040China Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention Fudan UniversityShanghai200040China School of Mathematics and statistics Hainan Normal UniversityHaikou570100China

The association of neurogenesis and gliogenesis with glioma remains *** conducting single-cell RNA-seq analyses on 26 gliomas,we reported their classification into primitive oligodendrocyte precursor cell(pri-OPC)-like and radial glia(RG)-like tumors and validated it in a public cohort and TCGA *** RG-like tumors exhibited wild-type isocitrate dehydrogenase and tended to carry EGFR mutations,and the pri-OPC-like ones were prone to carrying TP53 *** subclones only in pri-OPC-like tumors showed substantially down-regulated MHC-I genes,suggesting their distinct immune evasion ***,the two subgroups appeared to extensively modulate glioma-infiltrating lymphocytes in distinct *** specific genes not expressed in normal immune cells were found in glioma-infiltrating *** example,glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors IGLC2/IGKC were expressed in pri-OPC-like and RG-like glioma-infiltrating lymphocytes,*** expression was positively correlated with those of immune checkpoint genes(e.g.,LGALS33)and poor survivals as validated by the increased expression of LGALS3 upon IGKC overexpression in Jurkat *** finding indicated a potential inhibitory role in tumor-infiltrating lymphocytes and could provide a new way of cancer immune evasion.

关键词： single-cell RNA-seq glioma radial glia primitive oligodendrocyte precursor cell immune escape

Comparing the Time-Deformation Method with the Fractional Fourier Transform in Filtering Non-Stationary Processes

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Journal of Signal and Information Processing 2012年第4期3卷 491-501页

作者： Mengyuan Xu Wayne A. Woodward Henry L. Gray Department of Statistical Science Southern Methodist University Dallas USA statistics genomics unit NIH/NIMH (National Institutes of Health/National Institute of Mental Health) Bethesda USA

The classical linear filter is able to extract components from multi-component stochastic processes where the frequencies of components do not overlap over time, but fail for those processes where the frequencies overlap over time. In this paper, we discuss two filtering methods for non-stationary processes: the G-filtering method and the Fractional Fourier transform (FrFT) method. The FrFT method is mainly designed for linear chirp signals where the frequency is linearly changing with time. The G-filter can be used to filter signals with wide range of frequency behaviors such as linear chirps, quadratic chirps and other type of chirp signals with strong time-varying frequency behavior. If frequencies of the components can be approximated or separated by a straight line or a polynomial curve, the G-filter can successfully extract components from the original series. We show that the G-filter is applicable to a wider variety of filtering applications than methods such as the FrFT which require data of a specified frequency behavior.

关键词： Filtering Time-Frequency Time-Deformation Fractional Fourier Transform

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

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genomics, Proteomics & Bioinformatics 2020年第6期18卷 749-759页

作者： Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao China National Center for Bioinformation Beijing 100101China National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house *** particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global *** provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each *** change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes ***,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe ***,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with ***,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://***/ncov/.

关键词： 2019nCoVR SARS-CoV-2 Database Genomic variation Haplotype