Genome-to-genome analysis of Epstein-Barr virus infection

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Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopi ...

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention an ...

Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. De ...

Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. Howev ...

NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape du ...

The temporal coordination of events at cellular and tissue scales is essential for the proper development of organisms, and involves cell-intrinsic processes that can be coupled by local cellular signalling and instructed by global signalling, thereby crea ...

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag"variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit ge ...

Mouse models have been instrumental in understanding human disease biology and proposing possible new treatments. The precise control of the environment and genetic composition of mice allows more rigorous observations, but limits the generalizability and ...

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understan ...

Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict ...

Human transforming growth factor beta-induced (TGFBI), is a gene responsible for various corneal dystrophies. TGFBI produces a protein called TGFBI, which is involved in cell adhesion and serves as a recognition sequence for integrins. An alteration in cel ...

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transf ...

Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteri ...

Epigenetics plays an important role in cancer development and progression. Cancer cells hijack the epigenome by modifying the histone protein units responsible for packaging DNA, or by modifying the DNA itself, resulting in changes to chromatin topology an ...

Hearing Loss (HL) is the most prevalent sensorineural disorder, affecting 360 million people worldwide. As genetic causes lead to 50% of pre-lingual deafness, gene therapy is considered as a potential therapeutic strategy. Mutations in the TMC1 gene are li ...

Genome-to-genome analysis of Epstein-Barr virus infection

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Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Antagonism as a Foraging Strategy in Microbial Communities

DNA methylation enables recurrent endogenization of giant viruses in an animal relative

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Host genomics of SARS-CoV-2 infection

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL

Towards a physical understanding of developmental patterning

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Mouse Systems Genetics as a Prelude to Precision Medicine

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

Rare variants in antiviral response genes drive severe viral respiratory infections in children

Allele-specific gene disruption through discrimination of a single base change by S. aureus Cas9-KKH prevents progressive hearing loss after AAV-mediated gene delivery

Mutation update: TGFBI pathogenic and likely pathogenic variants in corneal dystrophies

Scaling Out Bioinformatics in the Data Center

Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells

A Tale of Two Tumors: Unraveling the Complexities of Epigenetic Dysregulation in Cancer

Delivery of CRISPR/Cas9 using AAV-PHP.B in the inner ear leads to allele-specific inactivation of the mutated Tmc1 allele and protects auditory function in Beethoven mice