Model-Based Clustering with Measurement or Estimation Errors.


:Model-based clustering with finite mixture models has become a widely used clustering method. One of the recent implementations is MCLUST. When objects to be clustered are summary statistics, such as regression coefficient estimates, they are naturally associated with estimation errors, whose covariance matrices can often be calculated exactly or approximated using asymptotic theory. This article proposes an extension to Gaussian finite mixture modeling-called MCLUST-ME-that properly accounts for the estimation errors. More specifically, we assume that the distribution of each observation consists of an underlying true component distribution and an independent measurement error distribution. Under this assumption, each unique value of estimation error covariance corresponds to its own classification boundary, which consequently results in a different grouping from MCLUST. Through simulation and application to an RNA-Seq data set, we discovered that under certain circumstances, explicitly, modeling estimation errors, improves clustering performance or provides new insights into the data, compared with when errors are simply ignored, whereas the degree of improvement depends on factors such as the distribution of error covariance matrices.


Genes (Basel)




Zhang W,Di Y




Has Abstract


2020-02-10 00:00:00












  • The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

    abstract::The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of hi...


    pub_type: 杂志文章


    authors: Jones SJ,Haulena M,Taylor GA,Chan S,Bilobram S,Warren RL,Hammond SA,Mungall KL,Choo C,Kirk H,Pandoh P,Ally A,Dhalla N,Tam AKY,Troussard A,Paulino D,Coope RJN,Mungall AJ,Moore R,Zhao Y,Birol I,Ma Y,Marra M,Jo

    更新日期:2017-12-11 00:00:00

  • Comparative Genomics of the Transport Proteins of Ten Lactobacillus Strains.

    abstract::The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert negative effects on h...


    pub_type: 杂志文章


    authors: Zafar H,Saier MH Jr

    更新日期:2020-10-21 00:00:00

  • PPARGC1A rs8192678 and NRF1 rs6949152 Polymorphisms Are Associated with Muscle Fiber Composition in Women.

    abstract::PPARGC1A rs8192678 G/A (Gly482Ser) and NRF1 rs6949152 A/G polymorphisms have been associated with endurance athlete status, endurance performance phenotypes, and certain health-related markers of different pathologies such as metabolic syndrome, diabetes, and dyslipidemia. We hypothesized that they could be considered...


    pub_type: 杂志文章


    authors: Yvert T,Miyamoto-Mikami E,Tobina T,Shiose K,Kakigi R,Tsuzuki T,Takaragawa M,Ichinoseki-Sekine N,Pérez M,Kobayashi H,Tanaka H,Naito H,Fuku N

    更新日期:2020-08-27 00:00:00

  • A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity.

    abstract::Propionibacteria have been studied extensively since the early 1930s due to their relevance to industry and importance as human pathogens. Still, their unique metabolism is far from fully understood. This is partly due to their signature high GC content, which has previously hampered the acquisition of quality sequenc...


    pub_type: 杂志文章


    authors: McCubbin T,Gonzalez-Garcia RA,Palfreyman RW,Stowers C,Nielsen LK,Marcellin E

    更新日期:2020-09-23 00:00:00

  • Identification of Candidate Genes for Seed Glucosinolate Content Using Association Mapping in Brassica napus L.

    abstract::Rapeseed contains glucosinolates, a toxic group of sulfur-containing glucosides, which play critical roles in defense against herbivores and microbes. However, the presence of glucosinolates in rapeseed reduces the value of the meal as feed for livestock. We performed association mapping of seed glucosinolate (GS) con...


    pub_type: 杂志文章


    authors: Qu CM,Li SM,Duan XJ,Fan JH,Jia LD,Zhao HY,Lu K,Li JN,Xu XF,Wang R

    更新日期:2015-11-18 00:00:00

  • Genome Sequence of the Freshwater Yangtze Finless Porpoise.

    abstract::The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. Afte...


    pub_type: 杂志文章


    authors: Yuan Y,Zhang P,Wang K,Liu M,Li J,Zheng J,Wang D,Xu W,Lin M,Dong L,Zhu C,Qiu Q,Li S

    更新日期:2018-04-16 00:00:00

  • Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation).

    abstract::The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgressi...


    pub_type: 杂志文章


    authors: Chester M,Leitch AR,Soltis PS,Soltis DE

    更新日期:2010-07-02 00:00:00

  • Synthesis of Biomaterials Utilizing Microfluidic Technology.

    abstract::Recently, microfluidic technologies have attracted an enormous amount of interest as potential new tools for a large range of applications including materials synthesis, chemical and biological detection, drug delivery and screening, point-of-care diagnostics, and in-the-field analysis. Their ability to handle extreme...


    pub_type: 杂志文章,评审


    authors: Wang X,Liu J,Wang P,deMello A,Feng L,Zhu X,Wen W,Kodzius R,Gong X

    更新日期:2018-06-05 00:00:00

  • Characterization, Expression, and Interaction Analyses of OsMORF Gene Family in Rice.

    abstract::The multiple organellar RNA editing factors (MORF) gene family plays a key role in organelle RNA editing in flowering plants. MORF genes expressions are also affected by abiotic stress. Although seven OsMORF genes have been identified in rice, few reports have been published on their expression patterns in different t...


    pub_type: 杂志文章


    authors: Zhang Q,Shen L,Ren D,Hu J,Chen G,Zhu L,Gao Z,Zhang G,Guo L,Zeng D,Qian Q

    更新日期:2019-09-10 00:00:00

  • A Magnesium Transport Protein Related to Mammalian SLC41 and Bacterial MgtE Contributes to Circadian Timekeeping in a Unicellular Green Alga.

    abstract::Circadian clocks in eukaryotes involve both transcriptional-translational feedback loops, post-translational regulation, and metabolic, non-transcriptional oscillations. We recently identified the involvement of circadian oscillations in the intracellular concentrations of magnesium ions (Mg2+i) that were conserved in...


    pub_type: 杂志文章


    authors: Feord HK,Dear FEG,Obbard DJ,van Ooijen G

    更新日期:2019-02-19 00:00:00

  • DNA Replication Through Strand Displacement During Lagging Strand DNA Synthesis in Saccharomyces cerevisiae.

    abstract::This review discusses a set of experimental results that support the existence of extended strand displacement events during budding yeast lagging strand DNA synthesis. Starting from introducing the mechanisms and factors involved in leading and lagging strand DNA synthesis and some aspects of the architecture of the ...


    pub_type: 杂志文章,评审


    authors: Giannattasio M,Branzei D

    更新日期:2019-02-21 00:00:00

  • Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection.

    abstract::Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pin...


    pub_type: 杂志文章


    authors: Toffolatti SL,De Lorenzis G,Brilli M,Moser M,Shariati V,Tavakol E,Maddalena G,Passera A,Casati P,Pindo M,Cestaro A,Maghradze D,Failla O,Bianco PA,Quaglino F

    更新日期:2020-02-28 00:00:00

  • Identification of Long Non-Coding RNAs Deregulated in Multiple Myeloma Cells Resistant to Proteasome Inhibitors.

    abstract::While the clinical benefit of proteasome inhibitors (PIs) for multiple myeloma (MM) treatment remains unchallenged, dose-limiting toxicities and the inevitable emergence of drug resistance limit their long-term utility. Disease eradication is compromised by drug resistance that is either present de novo or therapy-ind...


    pub_type: 杂志文章


    authors: Malek E,Kim BG,Driscoll JJ

    更新日期:2016-10-06 00:00:00

  • X-Linked Duchenne-Type Muscular Dystrophy in Jack Russell Terrier Associated with a Partial Deletion of the Canine DMD Gene.

    abstract::A 9-month old male Jack Russell Terrier started showing paraparesis of the hindlimbs after a walk. Hospitalized, the dog went into cardiac arrest, and later died. Necroscopic examination revealed a severe thickness of the diaphragm, esophagus, and base of the tongue, leading to the diagnosis of muscular dystrophy. The...




    authors: Brunetti B,Muscatello LV,Letko A,Papa V,Cenacchi G,Grillini M,Murgiano L,Jagannathan V,Drögemüller C

    更新日期:2020-10-08 00:00:00

  • The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.

    abstract::The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was...


    pub_type: 杂志文章


    authors: Taylor GA,Kirk H,Coombe L,Jackman SD,Chu J,Tse K,Cheng D,Chuah E,Pandoh P,Carlsen R,Zhao Y,Mungall AJ,Moore R,Birol I,Franke M,Marra MA,Dutton C,Jones SJM

    更新日期:2018-11-30 00:00:00

  • Genomic Selection for Optimum Index with Dry Biomass Yield, Dry Mass Fraction of Fresh Material, and Plant Height in Biomass Sorghum.

    abstract::Sorghum is one of the world's major crops, expresses traits for resilience to climate change, and can be used for several purposes including food and clean fuels. Multiple-trait genomic prediction and selection models were implemented using genotyping-by-sequencing single nucleotide polymorphism markers and phenotypic...


    pub_type: 杂志文章


    authors: Habyarimana E,Lopez-Cruz M,Baloch FS

    更新日期:2020-01-05 00:00:00

  • Transcriptomic Analysis Reveals Involvement of the Macrophage Migration Inhibitory Factor Gene Network in Duchenne Muscular Dystrophy.

    abstract::Duchenne muscular dystrophy (DMD) is a progressive hereditary muscular disease with X-linked recessive inheritance, that leads patients to premature death. The loss of dystrophin determines membrane instability, causing cell damage and inflammatory response. Macrophage migration inhibitory factor (MIF) is a cytokine t...


    pub_type: 杂志文章,meta分析


    authors: Lombardo SD,Mazzon E,Mangano K,Basile MS,Cavalli E,Mammana S,Fagone P,Nicoletti F,Petralia MC

    更新日期:2019-11-18 00:00:00

  • Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland.

    abstract::Listeria monocytogenes is a major human foodborne pathogen that is prevalent in the natural environment and has a high case fatality rate. Whole genome sequencing (WGS) analysis has emerged as a valuable methodology for the classification of L. monocytogenes isolates and the identification of virulence islands that ma...


    pub_type: 杂志文章


    authors: Hilliard A,Leong D,O'Callaghan A,Culligan EP,Morgan CA,DeLappe N,Hill C,Jordan K,Cormican M,Gahan CGM

    更新日期:2018-03-20 00:00:00

  • Genetic Architecture Underpinning Yield Components and Seed Mineral-Nutrients in Sesame.

    abstract::Genetic dissection of yield components and seed mineral-nutrient is crucial for understanding plant physiological and biochemical processes and alleviate nutrient malnutrition. Sesame (Sesamum indicum L.) is an orphan crop that harbors rich allelic repertoire for seed mineral-nutrients. Here, we harness this wide dive...


    pub_type: 杂志文章


    authors: Teboul N,Gadri Y,Berkovich Z,Reifen R,Peleg Z

    更新日期:2020-10-18 00:00:00

  • Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis.

    abstract::The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal ...


    pub_type: 杂志文章


    authors: Baker Frost D,da Silveira W,Hazard ES,Atanelishvili I,Wilson RC,Flume J,Day KL,Oates JC,Bogatkevich GS,Feghali-Bostwick C,Hardiman G,Ramos PS

    更新日期:2021-01-20 00:00:00

  • Mutational Spectrum and Clinical Features of Patients with LOXHD1 Variants Identified in an 8074 Hearing Loss Patient Cohort.

    abstract::Variants of the LOXHD1 gene, which are expressed in hair cells of the cochlea and vestibule, have been reported to cause a progressive form of autosomal recessive non-syndromic hereditary hearing loss, DFNB77. In this study, genetic screening was conducted on 8074 Japanese hearing loss patients utilizing massively par...


    pub_type: 杂志文章


    authors: Maekawa K,Nishio SY,Abe S,Goto SI,Honkura Y,Iwasaki S,Kanda Y,Kobayashi Y,Oka SI,Okami M,Oshikawa C,Sakuma N,Sano H,Shirakura M,Uehara N,Usami SI

    更新日期:2019-09-23 00:00:00

  • The Puzzling Fate of a Lupin Chromosome Revealed by Reciprocal Oligo-FISH and BAC-FISH Mapping.

    abstract::Old World lupins constitute an interesting model for evolutionary research due to diversity in genome size and chromosome number, indicating evolutionary genome reorganization. It has been hypothesized that the polyploidization event which occurred in the common ancestor of the Fabaceae family was followed by a lineag...


    pub_type: 杂志文章


    authors: Bielski W,Książkiewicz M,Šimoníková D,Hřibová E,Susek K,Naganowska B

    更新日期:2020-12-10 00:00:00

  • Hair of the Dog: Identification of a Cis-Regulatory Module Predicted to Influence Canine Coat Composition.

    abstract::Each domestic dog breed is characterized by a strict set of physical and behavioral characteristics by which breed members are judged and rewarded in conformation shows. One defining feature of particular interest is the coat, which is comprised of either a double- or single-layer of hair. The top coat contains coarse...


    pub_type: 杂志文章


    authors: Whitaker DT,Ostrander EA

    更新日期:2019-04-26 00:00:00

  • Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection.

    abstract::Grouper is one of the favorite sea food resources in Southeast Asia. However, the outbreaks of the viral nervous necrosis (VNN) disease due to nervous necrosis virus (NNV) infection have caused mass mortality of grouper larvae. Many aqua-farms have suffered substantial financial loss due to the occurrence of VNN. To b...


    pub_type: 杂志文章


    authors: Kim JO,Kim JO,Kim WS,Oh MJ

    更新日期:2017-01-13 00:00:00

  • Delineation of Novel Compound Heterozygous Variants in LTBP2 Associated with Juvenile Open Angle Glaucoma.

    abstract::Juvenile open angle glaucoma (JOAG), which is an uncommon form of primary open angle glaucoma, is a clinically and genetically heterogeneous disorder. We report on a family with a recessively inherited form of JOAG. The proband has a superior and an inferior never fiber layer thinning in both the eyes and the nasal vi...




    authors: Saeedi O,Yousaf S,Tsai J,Palmer K,Riazuddin S,Ahmed ZM

    更新日期:2018-10-30 00:00:00

  • An Introduction to Systems Analytics and Integration of Big Omics Data.

    abstract::A major technological shift in the research community in the past decade has been the adoption of high throughput (HT) technologies to interrogate the genome, epigenome, transcriptome, and proteome in a massively parallel fashion [...]. ...


    pub_type: 社论


    authors: Hardiman G

    更新日期:2020-02-26 00:00:00

  • Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors.

    abstract::In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient editing of human i...


    pub_type: 杂志文章


    authors: Sürün D,Schneider A,Mircetic J,Neumann K,Lansing F,Paszkowski-Rogacz M,Hänchen V,Lee-Kirsch MA,Buchholz F

    更新日期:2020-05-06 00:00:00

  • Microfluidic Quantitative PCR Detection of 12 Transgenes from Horse Plasma for Gene Doping Control.

    abstract::Gene doping, an activity which abuses and misuses gene therapy, is a major concern in sports and horseracing industries. Effective methods capable of detecting and monitoring gene doping are urgently needed. Although several PCR-based methods that detect transgenes have been developed, many of them focus only on a sin...


    pub_type: 杂志文章


    authors: Tozaki T,Ohnuma A,Kikuchi M,Ishige T,Kakoi H,Hirota KI,Kusano K,Nagata SI

    更新日期:2020-04-23 00:00:00

  • Multi-Trait Genomic Prediction of Yield-Related Traits in US Soft Wheat under Variable Water Regimes.

    abstract::The performance of genomic prediction (GP) on genetically correlated traits can be improved through an interdependence multi-trait model under a multi-environment context. In this study, a panel of 237 soft facultative wheat (Triticumaestivum L.) lines was evaluated to compare single- and multi-trait models for predic...


    pub_type: 杂志文章


    authors: Guo J,Khan J,Pradhan S,Shahi D,Khan N,Avci M,Mcbreen J,Harrison S,Brown-Guedira G,Murphy JP,Johnson J,Mergoum M,Esten Mason R,Ibrahim AMH,Sutton R,Griffey C,Babar MA

    更新日期:2020-10-28 00:00:00

  • Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell.

    abstract::One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affe...


    pub_type: 杂志文章


    authors: Villarino GH,Hu Q,Scanlon MJ,Mueller L,Bombarely A,Mattson NS

    更新日期:2017-08-03 00:00:00