compbioZurich

2022-01-06

ZH Sem Bioinfo - Jacopo Marino

An ion channel that allows you to see at night: the cryo-EM structure of the rod CNG channel opens up the hypothesis of mRNA editing on the CNGB1 sequence

Jacopo Marino, Laboratory of Biomolecular Research, Paul Scherrer Institut

Thursday, 2022-01-06
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

ZH Sem Bioinfo - Hans-Joachim Ruschewey

Taxonomic profiling of metagenomes from diverse environments with mOTUs3

Thursday, 2021-12-16
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

ZH Sem Bioinfo - Mirjam Zünd

mVIRs: A tool to identify and locate inducible prophages in microbial genomes using NGS data

Thursday, 2021-12-09
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

ZH Sem Bioinfo - Tülay Karakulak

CanIsoNet beta-version: A Database to Study the Functional Impact of Isoform Switching Events in Cancer

Thursday, 2021-12-02
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

ZH Sem Bioinfo - Ziying Yang

Structured metadata for genomic correlations in the Progenetix database

Thursday, 2021-11-18
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

Zürich Seminars in Bioinformatics

Max Verbiest

Functional implications of Short tandem repeat (STR) variation in NGS data

Thursday, 2021-10-28
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

ZH Sem Bioinfo - Siyuan Luo

Identifying clones and quantifying diversity in repertoire sequencing data.

Thursday, 2021-10-21
12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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 ...

ZH Sem Bioinfo - David Wissel

Supervised Hierarchical Autoencoders for Multi-Omics Integration in Cancer Survival Models

Thursday, 2021-10-14
12:00 UZH Irchel Y55-l-06/08 and ZOOM Call (12:15)

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 ...

ZH Sem Bioinfo - Ahmad Al Ajami

Comparison of Probabilistic Cell Type Annotation Methods Applied to Immunological CITE-seq Data

Thursday, 2021-10-07
12:15 UZH Irchel Y34-K-01 and ZOOM Call

@mbaudis 2021-10-07: more ...

ZH Sem Bioinfo - Marija Dmitrijeva

A global exploration of factors contributing to rates of horizontal gene transfer

Thursday, 2021-09-30
12:15 UZH Irchel Y34-K-01 and ZOOM Call

@mbaudis 2021-09-30: more ...

ZH Sem Bioinfo - Rahel Paloots

Introducing Progenetix Cell Line Beacon

A comprehensive cancer cell line variant knowledge resource

Thursday, 2021-06-17
12:15 om ZOOM Call

@mbaudis 2021-06-17: more ...

ZH Sem Bioinfo - Adriano Martinelli

A computational framework to analyse phenotypic heterogeneity in spatial single cell data

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 ...

ZH Sem Bioinfo - Emanuel Sonder

Stratifying sources of heterogeneity in single-cell whole-genome bisulfite sequencing datasets

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 ...