ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.


:We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at .


Genome Biol


Genome biology


Beeravolu CR,Hickerson MJ,Frantz LAF,Lohse K




Has Abstract


2018-09-25 00:00:00














  • Large-scale and high-confidence proteomic analysis of human seminal plasma.

    abstract:BACKGROUND:The development of mass spectrometric (MS) techniques now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Body fluids are also popular targets of proteomic analysis because of their potential for biomarker discovery. Seminal plasma has not yet receive...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Pilch B,Mann M

    更新日期:2006-01-01 00:00:00

  • Localizing the proteome.

    abstract::The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Simpson JC,Pepperkok R

    更新日期:2003-01-01 00:00:00

  • Identifying repeat domains in large genomes.

    abstract::We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Zhi D,Raphael BJ,Price AL,Tang H,Pevzner PA

    更新日期:2006-01-01 00:00:00

  • Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma.

    abstract:BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Kubicek CP,Herrera-Estrella A,Seidl-Seiboth V,Martinez DA,Druzhinina IS,Thon M,Zeilinger S,Casas-Flores S,Horwitz BA,Mukherjee PK,Mukherjee M,Kredics L,Alcaraz LD,Aerts A,Antal Z,Atanasova L,Cervantes-Badillo MG,Challac

    更新日期:2011-01-01 00:00:00

  • A prediction-based resampling method for estimating the number of clusters in a dataset.

    abstract:BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dudoit S,Fridlyand J

    更新日期:2002-06-25 00:00:00

  • Quantification of cell identity from single-cell gene expression profiles.

    abstract::The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Efroni I,Ip PL,Nawy T,Mello A,Birnbaum KD

    更新日期:2015-01-22 00:00:00

  • The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci.

    abstract:BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yang R,Zheng Z,Chen Q,Yang L,Huang H,Miki D,Wu W,Zeng L,Liu J,Zhou JX,Ogas J,Zhu JK,He XJ,Zhang H

    更新日期:2017-05-31 00:00:00

  • Systematic identification of genetic influences on methylation across the human life course.

    abstract:BACKGROUND:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gaunt TR,Shihab HA,Hemani G,Min JL,Woodward G,Lyttleton O,Zheng J,Duggirala A,McArdle WL,Ho K,Ring SM,Evans DM,Davey Smith G,Relton CL

    更新日期:2016-03-31 00:00:00

  • Personal genomes and precision medicine.

    abstract::A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...

    journal_title:Genome biology



    authors: Highnam G,Mittelman D

    更新日期:2012-12-19 00:00:00

  • Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging.

    abstract::A central goal of biogerontology is to identify robust gene-expression biomarkers of aging. Here we develop a method where the biomarkers are networks of genes selected based on age-dependent activity and a graph-theoretic property called modularity. Tested on Caenorhabditis elegans, our algorithm yields better biomar...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fortney K,Kotlyar M,Jurisica I

    更新日期:2010-01-01 00:00:00

  • The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication.

    abstract:BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Badouin H,Velt A,Gindraud F,Flutre T,Dumas V,Vautrin S,Marande W,Corbi J,Sallet E,Ganofsky J,Santoni S,Guyot D,Ricciardelli E,Jepsen K,Käfer J,Berges H,Duchêne E,Picard F,Hugueney P,Tavares R,Bacilieri R,Rustenh

    更新日期:2020-09-07 00:00:00

  • Copy number variation goes clinical.

    abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...

    journal_title:Genome biology



    authors: Le Caignec C,Redon R

    更新日期:2009-01-01 00:00:00

  • A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

    abstract::Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

    更新日期:2012-08-31 00:00:00

  • Identification of transcription factor binding sites using ATAC-seq.

    abstract::Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Li Z,Schulz MH,Look T,Begemann M,Zenke M,Costa IG

    更新日期:2019-02-26 00:00:00

  • 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.

    abstract:BACKGROUND:The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which t...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Uribe-Lewis S,Stark R,Carroll T,Dunning MJ,Bachman M,Ito Y,Stojic L,Halim S,Vowler SL,Lynch AG,Delatte B,de Bony EJ,Colin L,Defrance M,Krueger F,Silva AL,Ten Hoopen R,Ibrahim AE,Fuks F,Murrell A

    更新日期:2015-04-01 00:00:00

  • Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.

    abstract:BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FM

    更新日期:2006-01-01 00:00:00

  • Identification of cyanobacterial non-coding RNAs by comparative genome analysis.

    abstract:BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Axmann IM,Kensche P,Vogel J,Kohl S,Herzel H,Hess WR

    更新日期:2005-01-01 00:00:00

  • Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features.

    abstract:BACKGROUND:The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yu G,Gail MH,Consonni D,Carugno M,Humphrys M,Pesatori AC,Caporaso NE,Goedert JJ,Ravel J,Landi MT

    更新日期:2016-07-28 00:00:00

  • Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers.

    abstract:BACKGROUND:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sa JK,Hwang JR,Cho YJ,Ryu JY,Choi JJ,Jeong SY,Kim J,Kim MS,Paik ES,Lee YY,Choi CH,Kim TJ,Kim BG,Bae DS,Lee Y,Her NG,Shin YJ,Cho HJ,Kim JY,Seo YJ,Koo H,Oh JW,Lee T,Kim HS,Song SY,Bae JS,Park WY,Han HD

    更新日期:2019-11-26 00:00:00

  • Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells.

    abstract:BACKGROUND:While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS:We systematically compare five different...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Wang Y,Liu KI,Sutrisnoh NB,Srinivasan H,Zhang J,Li J,Zhang F,Lalith CRJ,Xing H,Shanmugam R,Foo JN,Yeo HT,Ooi KH,Bleckwehl T,Par YYR,Lee SM,Ismail NNB,Sanwari NAB,Lee STV,Lew J,Tan MH

    更新日期:2018-05-29 00:00:00

  • Concept recognition for extracting protein interaction relations from biomedical text.

    abstract:BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

    更新日期:2008-01-01 00:00:00

  • Escape from X inactivation in mice and humans.

    abstract::A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Berletch JB,Yang F,Disteche CM

    更新日期:2010-01-01 00:00:00

  • PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications.

    abstract::We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fang J,Ma Q,Chu C,Huang B,Li L,Cai P,Batista PJ,Tolentino KEM,Xu J,Li R,Du P,Qu K,Chang HY

    更新日期:2019-12-20 00:00:00

  • Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.

    abstract:BACKGROUND:Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental stud...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Coyne RS,Hannick L,Shanmugam D,Hostetler JB,Brami D,Joardar VS,Johnson J,Radune D,Singh I,Badger JH,Kumar U,Saier M,Wang Y,Cai H,Gu J,Mather MW,Vaidya AB,Wilkes DE,Rajagopalan V,Asai DJ,Pearson CG,Findly RC,Di

    更新日期:2011-10-17 00:00:00

  • ELXR: a resource for rapid exon-directed sequence analysis.

    abstract::ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (Ref...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Schageman JJ,Horton CJ,Niu S,Garner HR,Pertsemlidis A

    更新日期:2004-01-01 00:00:00

  • Large-scale assignment of orthology: back to phylogenetics?

    abstract::Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Gabaldón T

    更新日期:2008-10-30 00:00:00

  • Signaling netwErks get the global treatment.

    abstract::Two landmark studies of cell signaling, by RNA interference and phosphoproteomics, provide complementary global views of the pathways downstream of receptor kinases, including those regulated by Erks. ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Yaffe MB,White FM

    更新日期:2007-01-01 00:00:00

  • A computational investigation of kinetoplastid trans-splicing.

    abstract::Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gopal S,Awadalla S,Gaasterland T,Cross GA

    更新日期:2005-01-01 00:00:00

  • Consensus clustering and functional interpretation of gene-expression data.

    abstract::Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus cluste...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Swift S,Tucker A,Vinciotti V,Martin N,Orengo C,Liu X,Kellam P

    更新日期:2004-01-01 00:00:00

  • A comparison of automatic cell identification methods for single-cell RNA sequencing data.

    abstract:BACKGROUND:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Abdelaal T,Michielsen L,Cats D,Hoogduin D,Mei H,Reinders MJT,Mahfouz A

    更新日期:2019-09-09 00:00:00