Publications related to Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

Related publications (32)

The role of LRRK2 in lung adenocarcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

EPFL2024

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Dariia Gudkova, Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Hüseyin Baris Atakan, Daniel Alpern, Mustafa Demir

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Matteo Dal Peraro

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Publishing Group2024

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-typ ...

OXFORD UNIV PRESS2024

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Sebastian Martin Waszak

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

2023

A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy

Nicolas Jean Philippe Guex

GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, i ...

2023

Chromatin modules and their implication in genomic organization and gene regulation

Judith Franziska Kribelbauer, Bart Deplancke, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

2023

Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report

Andrea Cavalli

Breast carcinoma is the most prevalent cancer among women globally. It has variable clinical courses depending on the stage and clinical-biological features. This case report describes a 56-year-old female with invasive breast cancer without estrogen or pr ...

FRONTIERS MEDIA SA2023

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

NATURE PORTFOLIO2023

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Julien Léonard Duc, Evaristo Jose Planet Letschert, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard

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 ...

2023