Alain Laederach

Large-scale structural analysis of pre-mRNA structure using RADIS

RADIS enables comprehensive pre-mRNA structural analysis across intronic and intergenic regions, revealing structural patterns and relationships with splice-site strength and variant effects.

Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR

The paper introduces hmSEEKR, a k-mer-based hidden Markov model that identifies non-linear sequence similarities in transcriptomes, revealing functional RNA domains with biological relevance.

Sequence and structure of protein binding sites in RNA impact biomolecular condensates

The paper investigates how RNA-protein binding site context, not just valence, affects biomolecular condensate properties in Ashbya gossypii.

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

The paper investigates the structural determinants of inverted Alu-mediated backsplicing in the HIPK3 gene using SHAPE-JuMP and finds that long-range Alu-mediated base pairs are required for circularization, but not full-length Alu elements.

An intricate balancing act: Upstream and downstream frameshift co-regulatory elements

The paper investigates the RNA structures and interactions of the 5' and 3' regions of the SARS-CoV-2 frameshifting element, revealing their co-regulatory roles and implications for therapeutic interventions.

Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses

The paper shows that predicted SARS-CoV-2 FSE mutants abolish frameshifting and suppress structural transitions, highlighting the role of alternative conformations in ribosomal transitions.

Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation

The paper shows that Orb2 regulates rare-codon-enriched mRNA expression in Drosophila neurons, impacting mGluR function and social behavior.

Structural conservation of MALAT1 long non-coding RNA in cells and in evolution

The paper investigates structural conservation of MALAT1 lncRNA across species and cell types using SHAPE chemical probing, finding uniform structural conservation despite sequence differences.

Quantitative prediction of variant effects on alternative splicing using endogenous pre-messenger RNA structure probing

The paper predicts variant effects on alternative splicing using structural probing data and a computational framework, achieving 90% accuracy for splice-altering variants.

Distinct responses to rare codons in select Drosophila tissues

The paper identifies tissue-specific responses to rare codons in Drosophila, showing unique expression capabilities in testis and brain and a role for rare codons in restricting protein expression in the testis.

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

ShapeJumper processes SHAPE-JuMP sequencing data to identify RNA molecule proximal interactions with high resolution.

Characterization of a Disease-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing

The paper identifies a genetic variant in NPNT associated with COPD risk and lung function through splicing analysis using long-read sequencing.