Abstract TBD
@mbaudis 2022-06-16: more ...
Abstract Spatially-resolved transcriptomics uncovers patterns of gene expression at supercellular, cellular, or subcellular resolution, providing insights into spatially variable cellular functions, diffusible morphogens, and cell-cell interactions. However, for practical reasons, multiplexed single cell RNA-sequencing remains the most widely used technology for profiling transcriptomes of single cells, especially in the context of large-scale anatomical atlassing.
@mbaudis 2022-05-19: more ...
Cancer cell lines are good and inexpensive models to study disease mechanisms and identify possible new drugs, However, many times cancer cell lines have been found to be either misidentified or contaminated. Additionally, cancer cell lines only represent a small clonal population of the origin as well as accumulate some additional mutations during in vitro handling.
@mbaudis 2022-05-12: more ...
Abstract Genomic instability is common in human cancer. As a form of genomic instability, copy number variations (CNV) play an important role in cancer development. Elucidating the relationship between CNV and cancer evolvement can improve the understanding of the pathogenetic mechanism of cancer.
@mbaudis 2022-05-05: more ...
The processing of nascent pre-mRNA consists of many steps, where splicing and primary transcript polyadenylation play key roles in determining transcriptome and subsequently, proteome diversity. Several studies indicate that many RNA-binding proteins (RBPs) act both on splicing as well as 3’ end processing but the context of this multi-level regulation and the full spectrum of RBPs involved are yet to be discovered. To facilitate answering these questions we have developed a novel computational method to identify RBPs that could shape the pre-mRNA maturation.
@mbaudis 2022-03-24: more ...
Abstract I will present the latest advances in cryo-electron microscopy and how this technique allows to solve protein structures at fast pace also of difficult protein targets, thus revolutionizing the field of structural biology and biomedicine. I will then focus on the recent developments on solving the structure of a ion channel that is located in rod photoreceptors of the retina, a protein complex that was discovered nearly 35 years ago and its structure has finally being revealed (article).
@mbaudis 2022-01-06: more ...
Abstract Taxonomic profiling is a crucial task in microbiome research that aims at detecting and quantifying the relative abundance of microbes in biological samples. However, in many environments, varying fractions of microbial species still lack a sequenced genome and remain unaccounted for during taxonomic profiling based on shotgun metagenomic data.
@mbaudis 2021-12-16: more ...
Abstract An estimated 40 - 50% of mammalian gut bacteria carry a prophage in their genome. Prophages can be induced upon stress and produce phage particles to infect and kill bacterial populations and thereby directly modulate the composition of the gut microbiota. Despite advances in studying prophages using whole-genome sequencing, challenges in identifying and locating inducible prophages within their host have limited our understanding of phage-bacterial interactions.
@mbaudis 2021-12-09: more ...
Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer. Switches in the expression of alternative isoforms can alter protein interaction networks of associated genes giving rise to cancer progression and metastases. We have recently analyzed the pathogenic impact of switching events in 1209 cancer samples covering 27 different cancer types.
@KarakulakTulay 2021-12-02: more ...
Abstract Enormous amounts of biomedical data have been and are being produced at an unprecedented rate by researchers all over the world. However, in order to enable reuse, there is an urgent need to understand the structure of datasets, the experimental conditions under which they were produced and the information that other investigators may need to make sense of the data.
@mbaudis 2021-11-18: more ...
Short tandem repeats (STRs) are genomic elements that consist of consecutive repetitions of a 1-6 nucleotide motif. They are abundant in the human genome and are known to be mutational hotspots. Several cancer types are known to have a microsatellite instability high (MSI-H) subtype wherein the DNA mismatch repair system is defective, leading to hypermutation of STRs.
@mbaudis 2021-10-28: more ...
The adaptive immune system is remarkable for its ability to produce immunoglobulins that can specifically bind to a wide variety of antigens. During adaptive immune responses, activated B cells expand and undergo accelerated mutation of their B cell receptor (BCR), forming a clone of diversified cells that can be related back to a common ancestor.
@mbaudis 2021-10-21: more ...
Abstract With the increasing amount of high-throughput sequencing data becoming available, the proper integration of differently sized and heterogeneous molecular and clinical groups of variables has become crucial in cancer survival models.
@mbaudis 2021-10-14: more ...
@mbaudis 2021-10-07: more ...
@mbaudis 2021-09-30: more ...
@mbaudis 2021-06-17: more ...
Highly-multiplexed imaging technologies with single-cell resolution, such as imaging mass cytometry or multiplexed ion beam imaging, are revolutionising the field of biomedical research.
2021-05-27: more ...
DNA methylation is on the base level a binary mark. However, when calculating average methylation rates across cells in bulk samples, certain regions of the genome exhibit intermediate methylation values, indicating heterogeneous methylation patterns.
2021-05-20: more ...
2021-05-06: more ...
2021-03-25: more ...
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2021-03-04: more ...
@mbaudis 2021-02-04: more ...
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@mbaudis 2019-12-11: more ...
@qingyao 2019-12-04: more ...
@mbaudis 2019-11-27: more ...
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Helena L. Crowell 2019-06-05: more ...
Damian 2019-05-22: more ...
@KyleGao 2019-04-17: more ...
@mbaudis 2019-04-10: more ...
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@mbaudis 2019-03-20: more ...