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


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


BMC Genomics


BMC genomics


Nute M,Chou J,Molloy EK,Warnow T




Has Abstract


2020-02-10 00:00:00












  • Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

    abstract:BACKGROUND:HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen B,Zhong D,Monteiro A

    更新日期:2006-06-17 00:00:00

  • Fluorescent amplification for next generation sequencing (FA-NGS) library preparation.

    abstract:BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chiniquy J,Garber ME,Mukhopadhyay A,Hillson NJ

    更新日期:2020-01-28 00:00:00

  • The human olfactory transcriptome.

    abstract:BACKGROUND:Olfaction is a versatile sensory mechanism for detecting thousands of volatile odorants. Although molecular basis of odorant signaling is relatively well understood considerable gaps remain in the complete charting of all relevant gene products. To address this challenge, we applied RNAseq to four well-chara...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Olender T,Keydar I,Pinto JM,Tatarskyy P,Alkelai A,Chien MS,Fishilevich S,Restrepo D,Matsunami H,Gilad Y,Lancet D

    更新日期:2016-08-11 00:00:00

  • Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle.

    abstract:BACKGROUND:Variation in environment, management practices, nutrition or selection objectives has led to a variety of different choices being made in the use of genetic material between countries. Differences in genome-level homozygosity between countries may give rise to regions that result in inbreeding depression to ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Howard JT,Haile-Mariam M,Pryce JE,Maltecca C

    更新日期:2015-10-19 00:00:00

  • The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids.

    abstract:BACKGROUND:The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and on centromeric chromatin in meiotic prophase. We studied the relationship between these chromatin m...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mulugeta Achame E,Wassenaar E,Hoogerbrugge JW,Sleddens-Linkels E,Ooms M,Sun ZW,van IJcken WF,Grootegoed JA,Baarends WM

    更新日期:2010-06-10 00:00:00

  • Transcriptional analysis of the mammalian heart with special reference to its endocrine function.

    abstract:BACKGROUND:Pharmacological and gene ablation studies have demonstrated the crucial role of the endocrine function of the heart as mediated by the polypeptide hormones ANF and BNP in the maintenance of cardiovascular homeostasis. The importance of these studies lies on the fact that hypertension and chronic congestive h...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McGrath MF,de Bold AJ

    更新日期:2009-06-01 00:00:00

  • Integrative genomic and functional profiling of the pancreatic cancer genome.

    abstract:BACKGROUND:Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candid...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Shain AH,Salari K,Giacomini CP,Pollack JR

    更新日期:2013-09-16 00:00:00

  • Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean.

    abstract:BACKGROUND:Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the me...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li S,Darwish O,Alkharouf NW,Musungu B,Matthews BF

    更新日期:2017-09-05 00:00:00

  • Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

    abstract:BACKGROUND:Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) w...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bera BC,Virmani N,Kumar N,Anand T,Pavulraj S,Rash A,Elton D,Rash N,Bhatia S,Sood R,Singh RK,Tripathi BN

    更新日期:2017-08-23 00:00:00

  • Re-evaluation of the role of Indian germplasm as center of melon diversification based on genotyping-by-sequencing analysis.

    abstract:BACKGROUND:The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gonzalo MJ,Díaz A,Dhillon NPS,Reddy UK,Picó B,Monforte AJ

    更新日期:2019-06-03 00:00:00

  • A genomics-based systems approach towards drug repositioning for rheumatoid arthritis.

    abstract:BACKGROUND:Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by inflammation and destruction of synovial joints. RA affects up to 1 % of the population worldwide. Currently, there are no drugs that can cure RA or achieve sustained remission. The unknown cause of the disease represents a significan...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Xu R,Wang Q

    更新日期:2016-08-22 00:00:00

  • Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish.

    abstract:BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Lie KK,Tørresen OK,Solbakken MH,Rønnestad I,Tooming-Klunderud A,Nederbragt AJ,Jentoft S,Sæle Ø

    更新日期:2018-03-06 00:00:00

  • The transcriptional landscape of mouse beta cells compared to human beta cells reveals notable species differences in long non-coding RNA and protein-coding gene expression.

    abstract:BACKGROUND:Insulin producing beta cell and glucagon producing alpha cells are colocalized in pancreatic islets in an arrangement that facilitates the coordinated release of the two principal hormones that regulate glucose homeostasis and prevent both hypoglycemia and diabetes. However, this intricate organization has a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Benner C,van der Meulen T,Cacéres E,Tigyi K,Donaldson CJ,Huising MO

    更新日期:2014-07-22 00:00:00

  • Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies.

    abstract:BACKGROUND:The ability to identify regions of the genome inherited with a dominant trait in one or more families has become increasingly valuable with the wide availability of high throughput sequencing technology. While a number of methods exist for mapping of homozygous variants segregating with recessive traits in c...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Levine AP,Connor TM,Oygar DD,Neild GH,Segal AW,Maxwell PH,Gale DP

    更新日期:2015-03-10 00:00:00

  • Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine.

    abstract:BACKGROUND:Genome-scale functional genomic screens across large cell line panels provide a rich resource for discovering tumor vulnerabilities that can lead to the next generation of targeted therapies. Their data analysis typically has focused on identifying genes whose knockdown enhances response in various pre-defin...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhu Z,Ihle NT,Rejto PA,Zarrinkar PP

    更新日期:2016-06-13 00:00:00

  • Selective constraint, background selection, and mutation accumulation variability within and between human populations.

    abstract:BACKGROUND:Regions of the genome that are under evolutionary constraint across multiple species have previously been used to identify functional sequences in the human genome. Furthermore, it is known that there is an inverse relationship between evolutionary constraint and the allele frequency of a mutation segregatin...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hodgkinson A,Casals F,Idaghdour Y,Grenier JC,Hernandez RD,Awadalla P

    更新日期:2013-07-23 00:00:00

  • End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries.

    abstract:BACKGROUND:We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an EcoRI- and a BamHI-digested library) and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori). RESUL...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Suetsugu Y,Minami H,Shimomura M,Sasanuma S,Narukawa J,Mita K,Yamamoto K

    更新日期:2007-09-07 00:00:00

  • Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca).

    abstract:BACKGROUND:The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda w...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu W,Zhao Y,Liu Z,Zhang Y,Lian Z,Li N

    更新日期:2006-11-17 00:00:00

  • PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

    abstract:BACKGROUND:Equally important and challenging as genome annotation, is the subsequent classification of predicted genes into their respective pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) represents a database consisting of known genes and their respective biochemical functionalities. Although accessible ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Altermann E,Klaenhammer TR

    更新日期:2005-05-03 00:00:00

  • Differentially expressed genes for aggressive pecking behaviour in laying hens.

    abstract:BACKGROUND:Aggressive behaviour is an important aspect in the daily lives of animals living in groups. Aggressive animals have advantages, such as better access to food or territories, and they produce more offspring than low ranking animals. The social hierarchy in chickens is measured using the 'pecking order' concep...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Buitenhuis B,Hedegaard J,Janss L,Sørensen P

    更新日期:2009-11-19 00:00:00

  • Core genome components and lineage specific expansions in malaria parasites plasmodium.

    abstract:BACKGROUND:The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, wh...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cai H,Gu J,Wang Y

    更新日期:2010-12-01 00:00:00

  • OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.

    abstract:BACKGROUND:Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Thybert D,Avner S,Lucchetti-Miganeh C,Chéron A,Barloy-Hubler F

    更新日期:2008-12-31 00:00:00

  • Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears.

    abstract:BACKGROUND:The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri ('Dangshansuli', an Asian pear) and Pyrus communis ('Bartlett', a European pear) genomes, but the patterns of ge...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sun M,Zhang M,Singh J,Song B,Tang Z,Liu Y,Wang R,Qin M,Li J,Khan A,Wu J

    更新日期:2020-11-19 00:00:00

  • Cell population-specific expression analysis of human cerebellum.

    abstract:BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

    更新日期:2012-11-12 00:00:00

  • Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters.

    abstract:BACKGROUND:Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by f...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Miao Z,Li D,Zhang Z,Dong J,Su Z,Wang T

    更新日期:2012-02-06 00:00:00

  • Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.

    abstract:BACKGROUND:The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is significantly hindering data interpretation and analysis of researchers. Effective navigation approaches...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Praneenararat T,Takagi T,Iwasaki W

    更新日期:2012-01-01 00:00:00

  • Treatment-independent miRNA signature in blood of Wilms tumor patients.

    abstract:BACKGROUND:Blood-born miRNA signatures have recently been reported for various tumor diseases. Here, we compared the miRNA signature in Wilms tumor patients prior and after preoperative chemotherapy according to SIOP protocol 2001. RESULTS:We did not find a significant difference between miRNA signature of both groups...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Schmitt J,Backes C,Nourkami-Tutdibi N,Leidinger P,Deutscher S,Beier M,Gessler M,Graf N,Lenhof HP,Keller A,Meese E

    更新日期:2012-08-07 00:00:00

  • Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides.

    abstract:BACKGROUND:Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McMurdie PJ,Hug LA,Edwards EA,Holmes S,Spormann AM

    更新日期:2011-06-02 00:00:00

  • Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells.

    abstract:BACKGROUND:The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome of Itk-deficient CD3+ T-cells, including CD4+ and CD8+ subsets, using Affymetrix microarrays. RESULTS:The lar...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Blomberg KE,Boucheron N,Lindvall JM,Yu L,Raberger J,Berglöf A,Ellmeier W,Smith CE

    更新日期:2009-05-18 00:00:00

  • Transposon libraries identify novel Mycobacterium bovis BCG genes involved in the dynamic interactions required for BCG to persist during in vivo passage in cattle.

    abstract:BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Mendum TA,Chandran A,Williams K,Vordermeier HM,Villarreal-Ramos B,Wu H,Singh A,Smith AA,Butler RE,Prasad A,Bharti N,Banerjee R,Kasibhatla SM,Bhatt A,Stewart GR,McFadden J

    更新日期:2019-05-28 00:00:00