Inferring transcript phylogenies

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Scarless genome editing in budding yeast with elimination of the selection marker has many advantages. Some markers such as URA3 and TRP1 can be recycled through counterselection. This permits seamless genome modification with pop-in/pop-out, in which a DN ...

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs condi ...

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We a ...

Establishing with precision the quantity and identity of the cell types of the brain is a prerequisite for a detailed compendium of gene and protein expression in the central nervous system (CNS). Currently, however, strict quantitation of cell numbers has ...

Background: Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction ...

Computing the edit distance between two genomes is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ) model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under t ...

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs h ...

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...

Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes, yet its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few co ...

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

Transposable elements (TEs), also called jumping genes, are genetic elements capable of changing their position within the genome of their host. They make up large fractions of genomes, including 45% of human DNA content, according to current estimates. S ...

Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to ...

Background: Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individual ...

Spiroplasma poulsonii is a vertically transmitted endosymbiont of Drosophila melanogaster that causes male-killing, that is the death of infected male embryos during embryogenesis. Here, we report a natural variant of S. poulsonii that is efficiently verti ...

Blood flukes or schistosomes are the causative agents of human schistosomiasis, one of the major neglected tropical diseases. Draft genome sequences have been reported for schistosomes, but functional genomics tools are needed to investigate the role and e ...

BACKGROUND: Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arr ...

Almost half of the human genome is derived from exogenous genetic invaders, most of them related to retroviruses. This is the consequence of longstanding interactions between retroelements and higher organisms, governed by a delicate equilibrium between vi ...

Inferring transcript phylogenies

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Automated plasmid design for marker-free genome editing in budding yeast

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Statistical learning quantifies transposable element-mediated cis-regulation

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Intact Drosophila central nervous system cellular quantitation reveals sexual dimorphism

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

A transcript perspective on evolution

Computational identification and experimental characterization of preferred downstream positions in human core promoters

KRAB zinc finger protein-mediated control of transposon-embedded regulatory sequences from human germline to early embryos

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

Personal receptor repertoires: olfaction as a model

Blind killing of both male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

Human U6 promoter drives stronger shRNA activity than its schistosome orthologue in Schistosoma mansoni and human fibrosarcoma cells

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

Innate immunity against retroviral pathogens: from an ambiguous genetic self to novel therapeutic approaches