Bernd Timmermann

Aging and viral evolution impair immunity against dominant pan-coronavirus-reactive T cell epitope

The paper investigates how aging and viral mutations affect pan-coronavirus immunity, finding reduced T cell responses in older individuals and mutation-driven impact on humoral immunity.

Mesenchymal Osr1+ cells regulate embryonic lymphatic vessel formation

This study identifies mesenchymal Osr1+ cells as regulators of embryonic lymphatic vessel formation by controlling LEC proliferation and migration.

Odd skipped-related 1 controls the pro-regenerative response of Fibro-Adipogenic Progenitors

This study identifies Osr1 as essential for FAPs to support muscle regeneration by regulating communication with MuSCs and macrophages, and its loss leads to impaired regeneration and fibrosis.

Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3

The paper investigates how genomic rearrangements at the Lbx1/Fgf8 locus cause SHFM3 by altering chromatin structure and gene expression in mice.

Long-read transcriptome sequencing analysis with IsoTools

The paper introduces IsoTools, a Python package for analyzing long-read transcriptome data, showing it improves alternative and differential splicing analysis compared to short-read RNA-Seq.

A CRISPR-Cas9-engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions

This paper introduces a CRISPR-Cas9-engineered mouse model for GPI-anchor deficiency that mirrors human phenotypes, including cognitive impairments and epilepsy, and identifies synaptic transmission deficits.

Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites

The paper describes a method to generate trunk-like structures from mouse embryonic stem cells that mimic embryonic development features.

Alternative splicing coupled nonsense-mediated decay shapes the temperature-dependent transcriptome

The paper shows that temperature-dependent alternative splicing couples with nonsense-mediated decay to control rhythmic gene expression in mammals and plants.

Cell autonomous requirement of Neurofibromin (Nf1) for postnatal muscle hypertrophic growth and metabolic homeostasis

This study shows that Nf1 is required for postnatal muscle growth and metabolic homeostasis, with loss of Nf1 causing muscle atrophy and metabolic changes.

Integrated analysis of Xist upregulation and gene silencing at the onset of random X-chromosome inactivation at high temporal and allelic resolution

The paper uses allele-specific single-cell RNA-sequencing to study Xist upregulation and gene silencing during X-chromosome inactivation in mouse embryonic stem cells, identifying Nanog downregulation as a trigger and genetic variation's role in XCI.

The Developmental Transcriptome for Lytechinus variegatus Exhibits Temporally Punctuated Gene Expression Changes

This study analyzes the transcriptome of Lytechinus variegatus during embryonic and larval development, identifying four temporally distinct phases of gene expression.

Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development

The paper shows that preformed chromatin topology supports robust Shh transcription during limb development, with CTCF and ZRS alleles influencing enhancer-promoter communication.

Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression

The paper investigates TAD function in mice by editing TAD organization, finding that TADs provide robustness but are not essential for gene regulation, and that disease phenotypes arise from re-direction of regulatory contacts.

Crowdfunded whole-genome sequencing of the celebrity cat Lil BUB identifies causal mutations for her osteopetrosis and polydactyly

The paper uses crowdfunding to sequence a celebrity cat's genome, identifying mutations causing osteopetrosis and polydactyly, and highlights crowdfunding as a funding and communication tool.

Genome-wide strategies identify molecular niches regulated by connective tissue-associated transcription factors

The paper identifies molecular niches regulated by connective tissue-associated transcription factors through RNA-seq and ChIP-seq in chick limb cells.

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

This study sequenced wild tobacco genomes to uncover how nicotine biosynthesis evolved through gene duplications and transposable elements.

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

The paper improves gene feature delimitation from RNA-seq data in chickens by combining genome-guided gene prediction and de novo transcriptome assembly, increasing assignment rates by 20%.

The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history

This paper presents a half haplotype-resolved genome of hexaploid Ipomoea batatas, revealing two ancient whole genome duplication events and specialized compound biosynthesis gene clusters.