4,407 results match your criteria Genome Biology [Journal]


Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data.

Genome Biol 2019 Apr 18;20(1):78. Epub 2019 Apr 18.

Bioinformatics, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, 3052, Australia.

The vast quantities of short-read sequencing data being generated are often exchanged and stored as aligned reads. However, aligned data becomes outdated as new reference genomes and alignment methods become available. Here we describe Bazam, a tool that efficiently extracts the original paired FASTQ from alignment files (BAM or CRAM format) in a format that directly allows efficient realignment. Read More

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http://dx.doi.org/10.1186/s13059-019-1688-1DOI Listing

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio.

Genome Biol 2019 Apr 18;20(1):79. Epub 2019 Apr 18.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.

Background: Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses.

Results: Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1686-3DOI Listing
April 2019
6 Reads

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.

Genome Biol 2019 Apr 19;20(1):71. Epub 2019 Apr 19.

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3' cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. Read More

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http://dx.doi.org/10.1186/s13059-019-1671-xDOI Listing

Machine learning and complex biological data.

Genome Biol 2019 Apr 16;20(1):76. Epub 2019 Apr 16.

Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics and Genomics, The University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA.

Machine learning has demonstrated potential in analyzing large, complex biological data. In practice, however, biological information is required in addition to machine learning for successful application. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1689-0DOI Listing
April 2019
1 Read

DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis.

Genome Biol 2019 Apr 16;20(1):75. Epub 2019 Apr 16.

Department of Statistics, Northwestern University, Evanston, IL, 60208, USA.

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias. Read More

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http://dx.doi.org/10.1186/s13059-019-1682-7DOI Listing

Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency.

Genome Biol 2019 Apr 15;20(1):69. Epub 2019 Apr 15.

Earlham Institute, Norwich, NR4 7UZ, UK.

Background: Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination limits breeding efforts in crops; therefore, increasing recombination rates can reduce linkage drag and generate new genetic combinations.

Results: We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). Read More

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http://dx.doi.org/10.1186/s13059-019-1675-6DOI Listing

Comparative analysis of sequencing technologies for single-cell transcriptomics.

Genome Biol 2019 04 9;20(1):70. Epub 2019 Apr 9.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We generate a resource of 468 single cells and 1297 matched single cDNA samples, performing SMARTer and Smart-seq2 protocols on two cell lines with RNA spike-ins. Read More

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http://dx.doi.org/10.1186/s13059-019-1676-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454680PMC

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.

Genome Biol 2019 04 5;20(1):72. Epub 2019 Apr 5.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.

Following publication of the original article [1], the authors would like to highlight the following two corrections. Read More

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http://dx.doi.org/10.1186/s13059-019-1687-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450011PMC
April 2019
1 Read

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

Genome Biol 2019 Apr 2;20(1):64. Epub 2019 Apr 2.

Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. Read More

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http://dx.doi.org/10.1186/s13059-019-1660-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444547PMC
April 2019
2 Reads

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing.

Genome Biol 2019 04 1;20(1):68. Epub 2019 Apr 1.

Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden.

Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Read More

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http://dx.doi.org/10.1186/s13059-019-1673-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444814PMC

Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list.

Genome Biol 2019 03 28;20(1):67. Epub 2019 Mar 28.

Stem Cell and Development Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.

Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. p values are frequently abused for this purpose. As an alternative, we propose a method of ranking by confidence bounds on the log fold change, based on the previously developed TREAT test. Read More

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http://dx.doi.org/10.1186/s13059-019-1674-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437914PMC

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.

Genome Biol 2019 03 27;20(1):65. Epub 2019 Mar 27.

Department of Computer Science, Stony Brook University, Stony Brook, USA.

We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin's approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Read More

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http://dx.doi.org/10.1186/s13059-019-1670-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437997PMC

All models are wrong, but some organoids may be useful.

Genome Biol 2019 03 27;20(1):66. Epub 2019 Mar 27.

Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1186/s13059-019-1677-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437983PMC

Interactive roles of chromatin regulation and circadian clock function in plants.

Genome Biol 2019 03 22;20(1):62. Epub 2019 Mar 22.

Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain.

Circadian rhythms in transcription ultimately result in oscillations of key biological processes. Understanding how transcriptional rhythms are generated in plants provides an opportunity for fine-tuning growth, development, and responses to the environment. Here, we present a succinct description of the plant circadian clock, briefly reviewing a number of recent studies but mostly emphasizing the components and mechanisms connecting chromatin remodeling with transcriptional regulation by the clock. Read More

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http://dx.doi.org/10.1186/s13059-019-1672-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429827PMC

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

Genome Biol 2019 03 22;20(1):63. Epub 2019 Mar 22.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK.

Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Here, we describe a new statistical method for calling cells from droplet-based data, based on detecting significant deviations from the expression profile of the ambient solution. Read More

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http://dx.doi.org/10.1186/s13059-019-1662-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431044PMC

TAD fusion score: discovery and ranking the contribution of deletions to genome structure.

Genome Biol 2019 03 21;20(1):60. Epub 2019 Mar 21.

Genome Center, UC Davis, Davis, USA.

Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Read More

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http://dx.doi.org/10.1186/s13059-019-1666-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427865PMC

Melissa: Bayesian clustering and imputation of single-cell methylomes.

Genome Biol 2019 03 21;20(1):61. Epub 2019 Mar 21.

School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK.

Measurements of single-cell methylation are revolutionizing our understanding of epigenetic control of gene expression, yet the intrinsic data sparsity limits the scope for quantitative analysis of such data. Here, we introduce Melissa (MEthyLation Inference for Single cell Analysis), a Bayesian hierarchical method to cluster cells based on local methylation patterns, discovering patterns of epigenetic variability between cells. The clustering also acts as an effective regularization for data imputation on unassayed CpG sites, enabling transfer of information between individual cells. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1665-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427844PMC
March 2019
9 Reads

Measuring the reproducibility and quality of Hi-C data.

Genome Biol 2019 03 19;20(1):57. Epub 2019 Mar 19.

Department of Genome Sciences, University of Washington, Seattle, USA.

Background: Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study.

Results: Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. Read More

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http://dx.doi.org/10.1186/s13059-019-1658-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423771PMC
March 2019
1 Read

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.

Genome Biol 2019 03 19;20(1):58. Epub 2019 Mar 19.

Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.

Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference genome. Our method is robust to systematic sequencing errors, inexact repeats with fuzzy boundaries, and low sequencing coverage. Read More

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http://dx.doi.org/10.1186/s13059-019-1667-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425644PMC

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.

Genome Biol 2019 03 19;20(1):59. Epub 2019 Mar 19.

Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany.

Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and continuous cell transitions. Partition-based graph abstraction (PAGA) provides an interpretable graph-like map of the arising data manifold, based on estimating connectivity of manifold partitions ( https://github.com/theislab/paga ). Read More

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http://dx.doi.org/10.1186/s13059-019-1663-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425583PMC

Exploring human host-microbiome interactions in health and disease-how to not get lost in translation.

Genome Biol 2019 03 15;20(1):56. Epub 2019 Mar 15.

Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.

A meeting report on the 7th Wellcome Trust conference on Exploring Human Host-Microbiome Interactions in Health and Disease, held at Hinxton, UK, 5-7 December 2018. Read More

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http://dx.doi.org/10.1186/s13059-019-1669-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419321PMC

RnBeads 2.0: comprehensive analysis of DNA methylation data.

Genome Biol 2019 03 14;20(1):55. Epub 2019 Mar 14.

Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany.

DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, we describe a new version of our RnBeads software - an R/Bioconductor package that implements start-to-finish analysis workflows for Infinium microarrays and various types of bisulfite sequencing. Read More

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http://dx.doi.org/10.1186/s13059-019-1664-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419383PMC

Analysis of error profiles in deep next-generation sequencing data.

Genome Biol 2019 03 14;20(1):50. Epub 2019 Mar 14.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.

Background: Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions. Read More

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http://dx.doi.org/10.1186/s13059-019-1659-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417284PMC
March 2019
3 Reads

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.

Genome Biol 2019 03 12;20(1):54. Epub 2019 Mar 12.

Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.

Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association. We present clonealign, which assigns gene expression states to cancer clones using single-cell RNA and DNA sequencing independently sampled from a heterogeneous population. Read More

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http://dx.doi.org/10.1186/s13059-019-1645-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417140PMC

Correction to: DNA copy number evolution in Drosophila cell lines.

Genome Biol 2019 03 11;20(1):53. Epub 2019 Mar 11.

Department of Pharmacology and Cancer Biology, Levine Science Research Center, Duke University Medical Center, 308 Research Drive, Durham, NC, 27708, USA.

Following publication of the original article [1], the authors reported the following errors. Read More

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http://dx.doi.org/10.1186/s13059-019-1668-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410492PMC

I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms.

Genome Biol 2019 03 7;20(1):52. Epub 2019 Mar 7.

Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, NC, USA.

We propose a statistical boosting method, termed I-Boost, to integrate multiple types of high-dimensional genomics data with clinical data for predicting survival time. I-Boost provides substantially higher prediction accuracy than existing methods. By applying I-Boost to The Cancer Genome Atlas, we show that the integration of multiple genomics platforms with clinical variables improves the prediction of survival time over the use of clinical variables alone; gene expression values are typically more prognostic of survival time than other genomics data types; and gene modules/signatures are at least as prognostic as the collection of individual gene expression data. Read More

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http://dx.doi.org/10.1186/s13059-019-1640-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404283PMC

Assessing taxonomic metagenome profilers with OPAL.

Genome Biol 2019 03 4;20(1):51. Epub 2019 Mar 4.

Mathematics Department, Oregon State University, Corvallis, OR, USA.

The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profilers on datasets of CAMI and the Human Microbiome Project. Read More

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http://dx.doi.org/10.1186/s13059-019-1646-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398228PMC
March 2019
1 Read

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing.

Genome Biol 2019 03 1;20(1):48. Epub 2019 Mar 1.

Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany.

Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI5 exon skipping prediction challenge. The MMSplice modules are neural networks scoring exon, intron, and splice sites, trained on distinct large-scale genomics datasets. Read More

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http://dx.doi.org/10.1186/s13059-019-1653-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396468PMC

Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors.

Genome Biol 2019 03 1;20(1):49. Epub 2019 Mar 1.

Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.

Histone acetylation plays a central role in gene regulation and is sensitive to the levels of metabolic intermediates. However, predicting the impact of metabolic alterations on acetylation in pathological conditions is a significant challenge. Here, we present a genome-scale network model that predicts the impact of nutritional environment and genetic alterations on histone acetylation. Read More

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http://dx.doi.org/10.1186/s13059-019-1661-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397465PMC
March 2019
2 Reads

Improving the usability and archival stability of bioinformatics software.

Genome Biol 2019 02 27;20(1):47. Epub 2019 Feb 27.

Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St SE, Minneapolis, MN, 55455, USA.

Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication. Read More

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http://dx.doi.org/10.1186/s13059-019-1649-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391762PMC
February 2019
1 Read

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes.

Genome Biol 2019 02 26;20(1):46. Epub 2019 Feb 26.

The ithree institute, University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia.

Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. Read More

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http://dx.doi.org/10.1186/s13059-019-1643-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391755PMC
February 2019

Identification of transcription factor binding sites using ATAC-seq.

Genome Biol 2019 02 26;20(1):45. Epub 2019 Feb 26.

Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, 52074, Germany.

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 considering ATAC-seq protocol artifacts. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1642-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391789PMC
February 2019
6 Reads

Correction to: Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

Genome Biol 2019 02 22;20(1):43. Epub 2019 Feb 22.

Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.

Following publication of the original article [1], it was reported that the incorrect "Additional file 3" was published. The correct additional file is given below. Read More

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http://dx.doi.org/10.1186/s13059-019-1656-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385436PMC
February 2019

Correction to: Rapid turnover of life-cycle-related genes in the brown algae.

Genome Biol 2019 02 22;20(1):44. Epub 2019 Feb 22.

CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.

Following publication of the original article [1], it was noticed that the author names were published with initials instead of full names. The article [1] has been updated. Read More

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http://dx.doi.org/10.1186/s13059-019-1657-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385437PMC
February 2019

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

Genome Biol 2019 02 21;20(1):38. Epub 2019 Feb 21.

Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA.

Background: The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.

Results: We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Read More

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http://dx.doi.org/10.1186/s13059-019-1650-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383267PMC
February 2019

Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells.

Genome Biol 2019 02 21;20(1):37. Epub 2019 Feb 21.

Department of Pathology and Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.

Background: Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes and macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear. Read More

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http://dx.doi.org/10.1186/s13059-019-1651-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383285PMC
February 2019
1 Read

dStruct: identifying differentially reactive regions from RNA structurome profiling data.

Genome Biol 2019 02 21;20(1):40. Epub 2019 Feb 21.

Department of Biomedical Engineering and Genome Center, University of California, Davis, One Shields Avenue, Davis, 95616, CA, USA.

RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling of molecular RNA structures. RNA structurome profiling data can be used to identify differentially structured regions between groups of samples. Existing methods are limited in scope to specific technologies and/or do not account for biological variation. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1641-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385470PMC
February 2019
2 Reads

Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history.

Genome Biol 2019 02 21;20(1):36. Epub 2019 Feb 21.

Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.

Background: Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood.

Results: Here, we report a comprehensive analysis of peach evolution based on genome sequences of 480 wild and cultivated accessions. Read More

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http://dx.doi.org/10.1186/s13059-019-1648-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383288PMC
February 2019
1 Read

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm.

Genome Biol 2019 02 21;20(1):41. Epub 2019 Feb 21.

Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.

Background: Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.

Results: In this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Read More

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http://dx.doi.org/10.1186/s13059-019-1652-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385439PMC
February 2019

Fragile DNA contributes to repeated evolution.

Genome Biol 2019 02 21;20(1):39. Epub 2019 Feb 21.

Department of Biology, University of Konstanz, Konstanz, Germany.

Sequence features that affect DNA fragility might facilitate fast, repeated evolution by elevating mutation rates at genomic hotspots. Read More

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http://dx.doi.org/10.1186/s13059-019-1655-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383211PMC
February 2019
1 Read

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.

Genome Biol 2019 02 21;20(1):42. Epub 2019 Feb 21.

Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany.

Background: DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. Read More

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http://dx.doi.org/10.1186/s13059-019-1654-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385462PMC
February 2019

Rapid turnover of life-cycle-related genes in the brown algae.

Genome Biol 2019 02 14;20(1):35. Epub 2019 Feb 14.

Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.

Background: Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. Read More

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http://dx.doi.org/10.1186/s13059-019-1630-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374913PMC
February 2019
2 Reads

Skmer: assembly-free and alignment-free sample identification using genome skims.

Genome Biol 2019 02 13;20(1):34. Epub 2019 Feb 13.

Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093, CA, USA.

The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. Read More

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http://dx.doi.org/10.1186/s13059-019-1632-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374904PMC
February 2019
1 Read

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma.

Genome Biol 2019 02 13;20(1):33. Epub 2019 Feb 13.

RNA Editing Lab., Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Viale San Paolo, 15 00146, Rome, Italy.

Background: Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer.

Results: Here, we characterize the inosinome signature in normal brain and de novo glioblastoma (GBM) using new metrics that re-stratify GBM patients according to their editing profiles and indicate this post-transcriptional event as a possible molecular mechanism for sexual dimorphism in GBM. We find that over 85% of de novo GBMs carry a deletion involving the genomic locus of ADAR3, which is specifically expressed in the brain. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13059-019-1647-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373152PMC
February 2019
6 Reads

NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans.

Genome Biol 2019 02 11;20(1):32. Epub 2019 Feb 11.

Clinical Bioinformatics Lab, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, 75015, Paris, France.

State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study, we curated 737 high-confidence pathogenic non-coding variants associated with monogenic Mendelian diseases. In addition to interspecies conservation, a comprehensive set of recent and ongoing purifying selection signals in humans is explored, accounting for lineage-specific regulatory elements. Read More

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http://dx.doi.org/10.1186/s13059-019-1634-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371618PMC
February 2019

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.

Genome Biol 2019 02 11;20(1):31. Epub 2019 Feb 11.

Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, 351-0198, Japan.

Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled massively parallel profiling of transcriptomes, thereby promoting large-scale studies encompassing a wide range of cell types of multicellular organisms. With this background, we propose CellFishing.jl, a new method for searching atlas-scale datasets for similar cells and detecting noteworthy genes of query cells with high accuracy and throughput. Read More

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http://dx.doi.org/10.1186/s13059-019-1639-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371477PMC
February 2019

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

Genome Biol 2019 02 11;20(1):30. Epub 2019 Feb 11.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

Background: Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across human tissues and in genetically diverse populations. This has identified disease-relevant splicing events, as well as associations between splicing and genomic features, including sequence composition and conservation. Read More

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http://dx.doi.org/10.1186/s13059-019-1644-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371455PMC
February 2019
1 Read

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.

Genome Biol 2019 02 11;20(1):29. Epub 2019 Feb 11.

INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.

How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Read More

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13059-019-1627-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369560PMC
February 2019
3 Reads

Modeling double strand break susceptibility to interrogate structural variation in cancer.

Genome Biol 2019 02 8;20(1):28. Epub 2019 Feb 8.

MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.

Background: Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs).

Results: We used experimentally quantified DSB frequencies in cell lines with matched chromatin and sequence features to derive the first quantitative genome-wide models of DSB susceptibility. Read More

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http://dx.doi.org/10.1186/s13059-019-1635-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368699PMC
February 2019

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

Genome Biol 2019 02 5;20(1):27. Epub 2019 Feb 5.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

Background: CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed.

Results: Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner. Read More

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http://dx.doi.org/10.1186/s13059-019-1637-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362594PMC
February 2019