Correction to: The performance of coalescent-based species tree estimation methods under models of missing data.

Abstract:

:After publication of [1], the authors were informed by John A. Rhodes of a counterexample to Theorem 11 of [1].

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Nute M,Chou J,Molloy EK,Warnow T

doi

10.1186/s12864-020-6540-1

subject

Has Abstract

pub_date

2020-02-10 00:00:00

pages

133

issue

1

issn

1471-2164

pii

10.1186/s12864-020-6540-1

journal_volume

21

pub_type

杂志文章,已发布勘误
  • Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes.

    abstract:BACKGROUND:The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting inserti...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-516

    authors: Yeo ZX,Wong JC,Rozen SG,Lee AS

    更新日期:2014-06-24 00:00:00

  • Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins.

    abstract:BACKGROUND:Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced geno...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-369

    authors: Lilburn TG,Gu J,Cai H,Wang Y

    更新日期:2010-06-10 00:00:00

  • Correction to: RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes.

    abstract::An amendment to this paper has been published and can be accessed via the original article. ...

    journal_title:BMC genomics

    pub_type: 杂志文章,已发布勘误

    doi:10.1186/s12864-020-06939-7

    authors: Onizuka S,Yamazaki Y,Park SJ,Sugimoto T,Sone Y,Sjöqvist S,Usui M,Takeda A,Nakai K,Nakashima K,Iwata T

    更新日期:2020-08-11 00:00:00

  • Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach.

    abstract:BACKGROUND:The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and d...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-592

    authors: He D,Liu ZP,Chen L

    更新日期:2011-12-02 00:00:00

  • Lung transcriptomic clock predicts premature aging in cigarette smoke-exposed mice.

    abstract:BACKGROUND:Lung aging is characterized by a number of structural alterations including fibrosis, chronic inflammation and the alteration of inflammatory cell composition. Chronic exposure to cigarette smoke (CS) is known to induce similar alterations and may contribute to premature lung aging. Additionally, aging and C...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6712-z

    authors: Choukrallah MA,Hoeng J,Peitsch MC,Martin F

    更新日期:2020-04-09 00:00:00

  • Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.

    abstract:BACKGROUND:Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5484-9

    authors: Velie BD,Lillie M,Fegraeus KJ,Rosengren MK,Solé M,Wiklund M,Ihler CF,Strand E,Lindgren G

    更新日期:2019-02-04 00:00:00

  • Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum.

    abstract:BACKGROUND:Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1517-1

    authors: Guo Y,Tang K,Rowe LA,Li N,Roellig DM,Knipe K,Frace M,Yang C,Feng Y,Xiao L

    更新日期:2015-04-18 00:00:00

  • SMaSH: Sample matching using SNPs in humans.

    abstract:BACKGROUND:Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotide polymorphisms (SNPs), omics data types often only provide low to moderat...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6332-7

    authors: Westphal M,Frankhouser D,Sonzone C,Shields PG,Yan P,Bundschuh R

    更新日期:2019-12-30 00:00:00

  • Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers.

    abstract:BACKGROUND:Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species ar...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-S5-S5

    authors: Luo H,Sun C,Sun Y,Wu Q,Li Y,Song J,Niu Y,Cheng X,Xu H,Li C,Liu J,Steinmetz A,Chen S

    更新日期:2011-12-23 00:00:00

  • Semantic integration of gene expression analysis tools and data sources using software connectors.

    abstract:BACKGROUND:The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists exe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-S6-S2

    authors: Miyazaki FA,Guardia GD,Vêncio RZ,de Farias CR

    更新日期:2013-10-25 00:00:00

  • How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis.

    abstract:BACKGROUND:Prediction methods are increasingly used in biosciences to forecast diverse features and characteristics. Binary two-state classifiers are the most common applications. They are usually based on machine learning approaches. For the end user it is often problematic to evaluate the true performance and applica...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S4-S2

    authors: Vihinen M

    更新日期:2012-06-18 00:00:00

  • The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago.

    abstract:BACKGROUND:Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1769-9

    authors: Lautwein T,Lerch S,Schäfer D,Schmidt ER

    更新日期:2015-07-22 00:00:00

  • Expression of immune-response genes in lepidopteran host is suppressed by venom from an endoparasitoid, Pteromalus puparum.

    abstract:BACKGROUND:The relationships between parasitoids and their insect hosts have attracted attention at two levels. First, the basic biology of host-parasitoid interactions is of fundamental interest. Second, parasitoids are widely used as biological control agents in sustainable agricultural programs. Females of the grega...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-484

    authors: Fang Q,Wang L,Zhu J,Li Y,Song Q,Stanley DW,Akhtar ZR,Ye G

    更新日期:2010-09-02 00:00:00

  • Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium.

    abstract:BACKGROUND:Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3474-8

    authors: Zhu S,Tang S,Tan Z,Yu Y,Dai Q,Liu T

    更新日期:2017-01-10 00:00:00

  • Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content.

    abstract:BACKGROUND:Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in man...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-188

    authors: Abel J,Mrázek J

    更新日期:2012-05-15 00:00:00

  • Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs.

    abstract:BACKGROUND:MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRN...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-413

    authors: Zhu YP,Xue W,Wang JT,Wan YM,Wang SL,Xu P,Zhang Y,Li JT,Sun XW

    更新日期:2012-08-21 00:00:00

  • A transcript profiling approach reveals the zinc finger transcription factor ZNF191 is a pleiotropic factor.

    abstract:BACKGROUND:The human zinc finger protein 191 (ZNF191) is a member of the SCAN domain family of Krüppel-like zinc finger transcription factors. ZNF191 shows 94% identity to its mouse homologue zinc finger protein 191(Zfp191), which is the most highly conserved among the human-mouse SCAN family member orthologues pairs. ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-241

    authors: Li J,Chen X,Gong X,Liu Y,Feng H,Qiu L,Hu Z,Zhang J

    更新日期:2009-05-22 00:00:00

  • Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing.

    abstract:BACKGROUND:Glandular trichomes produce a wide variety of commercially important secondary metabolites in many plant species. The most prominent anti-malarial drug artemisinin, a sesquiterpene lactone, is produced in glandular trichomes of Artemisia annua. However, only limited genomic information is currently available...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-465

    authors: Wang W,Wang Y,Zhang Q,Qi Y,Guo D

    更新日期:2009-10-09 00:00:00

  • Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group.

    abstract:BACKGROUND:The Bacillus cereus sensu lato group currently includes seven species (B. cereus, B. anthracis, B. mycoides, B. pseudomycoides, B. thuringiensis, B. weihenstephanensis and B. cytotoxicus) that recent phylogenetic and phylogenomic analyses suggest are likely a single species, despite their varied phenotypes. ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-564

    authors: Scott E 2nd,Dyer DW

    更新日期:2012-10-22 00:00:00

  • Thrifty metabolic programming in rats is induced by both maternal undernutrition and postnatal leptin treatment, but masked in the presence of both: implications for models of developmental programming.

    abstract:BACKGROUND:Maternal undernutrition leads to an increased risk of metabolic disorders in offspring including obesity and insulin resistance, thought to be due to a programmed thrifty phenotype which is inappropriate for a subsequent richer nutritional environment. In a rat model, both male and female offspring of undern...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-49

    authors: Ellis PJ,Morris TJ,Skinner BM,Sargent CA,Vickers MH,Gluckman PD,Gilmour S,Affara NA

    更新日期:2014-01-21 00:00:00

  • Multiple actions of lysophosphatidic acid on fibroblasts revealed by transcriptional profiling.

    abstract:BACKGROUND:Lysophosphatidic acid (LPA) is a lipid mediator that acts through specific G protein-coupled receptors to stimulate the proliferation, migration and survival of many cell types. LPA signaling has been implicated in development, wound healing and cancer. While LPA signaling pathways have been studied extensiv...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-387

    authors: Stortelers C,Kerkhoven R,Moolenaar WH

    更新日期:2008-08-14 00:00:00

  • Genome-wide analysis of the WRKY gene family and their positive responses to phytoplasma invasion in Chinese jujube.

    abstract:BACKGROUND:The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production,...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5789-8

    authors: Xue C,Li H,Liu Z,Wang L,Zhao Y,Wei X,Fang H,Liu M,Zhao J

    更新日期:2019-06-07 00:00:00

  • Preferred and avoided codon pairs in three domains of life.

    abstract:BACKGROUND:Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserv...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-463

    authors: Tats A,Tenson T,Remm M

    更新日期:2008-10-08 00:00:00

  • High-throughput comparison of gene fitness among related bacteria.

    abstract:BACKGROUND:The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent a...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-212

    authors: Canals R,Xia XQ,Fronick C,Clifton SW,Ahmer BM,Andrews-Polymenis HL,Porwollik S,McClelland M

    更新日期:2012-05-30 00:00:00

  • Genome-wide analysis of the GH3 family in apple (Malus × domestica).

    abstract:BACKGROUND:Auxin plays important roles in hormone crosstalk and the plant's stress response. The auxin-responsive Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acids (JAs) to amino acids during hormone- and stress-rel...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-297

    authors: Yuan H,Zhao K,Lei H,Shen X,Liu Y,Liao X,Li T

    更新日期:2013-05-02 00:00:00

  • Transcriptional response to sulfide in the Echiuran Worm Urechis unicinctus by digital gene expression analysis.

    abstract:BACKGROUND:Urechis unicinctus, an echiuran worm inhabiting the U-shaped burrows in the coastal mud flats, is an important commercial and ecological invertebrate in Northeast Asian countries, which has potential applications in the study of animal evolution, coastal sediment improvement and marine drug development. Furt...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2094-z

    authors: Liu X,Zhang L,Zhang Z,Ma X,Liu J

    更新日期:2015-10-21 00:00:00

  • An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes.

    abstract:BACKGROUND:Alternative σ factors are important transcriptional regulators in bacteria. While σ(B) has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σ(H) has not yet been well defined in Listeria, even though σ(H) c...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2432-9

    authors: Liu Y,Orsi RH,Boor KJ,Wiedmann M,Guariglia-Oropeza V

    更新日期:2016-02-16 00:00:00

  • Genome-wide expression profiling of leaves and roots of watermelon in response to low nitrogen.

    abstract:BACKGROUND:Nitrogen (N) is a key macronutrient required for plant growth and development. In this study, watermelon plants were grown under hydroponic conditions at 0.2 mM N, 4.5 mM N, and 9 mM N for 14 days. RESULTS:Dry weight and photosynthetic assimilation at low N (0.2 mM) was reduced by 29 and 74% compared with h...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4856-x

    authors: Nawaz MA,Chen C,Shireen F,Zheng Z,Sohail H,Afzal M,Ali MA,Bie Z,Huang Y

    更新日期:2018-06-13 00:00:00

  • Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.

    abstract:BACKGROUND:Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of severa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1711-1

    authors: Boschiero C,Gheyas AA,Ralph HK,Eory L,Paton B,Kuo R,Fulton J,Preisinger R,Kaiser P,Burt DW

    更新日期:2015-07-31 00:00:00

  • Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization.

    abstract:BACKGROUND:Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-682

    authors: Lewis RA,Laing E,Allenby N,Bucca G,Brenner V,Harrison M,Kierzek AM,Smith CP

    更新日期:2010-12-01 00:00:00