ZH Sem Bioinfo - Lukas Malfertheiner

TBD

• Thursday, 2022-06-16
• 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract TBD

ZH Sem Bioinfo - Elyas Heidari

Supervised spatial inference of dissociated single-cell data with SageNet

• Thursday, 2022-05-19
• 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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.

ZH Sem Bioinfo - Rahel Paloots

The resemblance is uncanny a.k.a how similar are cancer cell lines really to their origins?

• Thursday, 2022-05-12
• 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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.

ZH Sem Bioinfo - Hangjia Zhao

Copy number variation data calibration towards intgerative analysis in cancer

• Thursday, 2022-05-05
• 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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.

ZH Sem Bioinfo - Maciek Bak

Biozentrum, University of Basel | Swiss Institute of Bioinformatics

Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP

• Thursday, 2022-03-24
• 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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

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

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.

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.

ZH Sem Bioinfo - Max Brambach

A morphometric framework for the embryo-wide quantification of tissue organisation at single cell resolution

• Thursday, 2021-05-06
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Qingyao Huang

Discovering copy number variation across multiple cancer types

• Thursday, 2021-03-25
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Stephany Orjuela

Analysis and Method development for High-Throughput DNA Methylation and Gene Expression with Applications to Colorectal Tumors

• Thursday, 2021-03-18
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Giancarlo Russo

Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces

• Thursday, 2021-03-11
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Anthony Sonrel

Leveraging single-cell RNA-seq with CITE-seq data

• Thursday, 2021-03-04
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Tao Fang

Protein-protein interaction prediction using co-evolution based method

• Thursday, 2021-02-04
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Annika Gable

From Biomolecular Networks to Pathways: Tools for the Interpretation of Genome-Wide Experiments

• Thursday, 2021-01-21
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Lukas Malfertheiner

Phylogeny and Metabolic Potential of SAR324

• Thursday, 2020-12-10
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Pierre-Luc Germain

Doublet identification and characterization in single-cell data

• Thursday, 2020-11-19
• 12:15 om ZOOM Call

ZH Sem Bioinfo - João Rodrigues

Modelling and estimating interactions from time-series observations of synthetic microbial community experiments

• Thursday, 2020-11-05
• 12:15 om ZOOM Call

ZH Sem Bioinfo - Stephan Schmeing

ReSeq simulates realistic Illumina high-throughput sequencing data

• Thursday, 2020-09-03
• 12:00 in Y-55L-06, UZH Irchel Campus and 12:15 om ZOOM Call

ZH Sem Bioinfo - Lennart Opitz

HiDRA-seq: High-Throughput SARS-CoV-2 Detection by RNA Barcoding and Amplicon Sequencing

• Thursday, 2020-07-09
• 12:00 in Y-55L-06, UZH Irchel Campus and 12:15 om ZOOM Call

ZH Sem Bioinfo - Moritz Schäfer

Deciphering the contribution of mechanisms involved in the regulation of gene expression in mESCs

• Thursday, 2020-07-02
• 12:00 in Y-55L-06, UZH Irchel Campus and 12:15 om ZOOM Call

ZH Sem Bioinfo - Izaskun Mallona

[Flanking sequence preference modulates de novo DNA methylation in the mouse genome

• Thursday, 2020-06-25
• 12:15 (ZOOM Call)

ZH Seminars Bioinformatics - Qingyao Huang

ZH Sem Bioinfo - Simone Tiberi

distinct: a method for differential analyses via hierarchical permutation tests, with applications to single-cell data

• Thursday, 2020-06-04
• 12:15 (ZOOM Call)

ZH Seminars Bioinformatics - David Lyon

ZH Seminars Bioinformatics - Marija Dmitrijeva

Setting up a pipeline for horizontal gene transfer detection

• Thursday, 2020-04-16
• 12:15 (Skype Call)

ZH Seminars Bioinformatics - Reto Gerber

Censored predictors in single cell regression models

• Thursday, 2020-04-09
• 12:15 (Skype Call)

ZH Seminars Bioinformatics - Joao Rodrigues

The Microbe Atlas Project

• Thursday, 2020-03-19
• 12:15 (Skye call)

ZH Seminars Bioinformatics - Nils Eling

HackyHour Zurich - data analysis made social

• Thursday, 2020-03-12
• 12:15, Y34-J-01, UZH Irchel campus

ZH Seminars Bioinformatics - Alex H. Wagner

Washington University School of Medicine, St. Louis

ZH Seminars Bioinformatics

Interval statistics reveal frequently altered gene copies across cancers

Qingyao Huang

• Wednesday, 2019-12-04
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Joao Rodrigues

• Wednesday, 2019-11-27
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics

Functional enrichment in the STRING protein-protein interaction database

Annika Gable

• Wednesday, 2019-11-13
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Anna Quaglieri

Walter and Eliza Hall Institute of Medical Research, Melbourne

Using the transcriptome to study therapy response in leukaemia

• Wednesday, 2019-10-09
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Tom Ashhurst

Sydney Cytometry Facility, The University of Sydney and Centenary Institute

High-dimensional flow mass cytometry with Imaging Mass Cytometry in WNV and ZIKV encephalitis

• Wednesday, 2019-10-02
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - David Lyon

“aGOtool” protein centric functional enrichment

• Wednesday, 2019-06-12
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Helena L. Crowell

On the discovery of population-specific state transitions from single-cell RNA sequencing data

• Wednesday, 2019-06-05
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Damian Szklarczyk

Analysis of date-tagged protein-protein associations derived from scientific literature.

• Wednesday, 2019-05-22
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Bo Gao

Minimum Error Normalization for Copy Number Analysis

• Wednesday, 2019-04-17
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Marija Dmitrijeva

Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

• Wednesday, 2019-04-10
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Masaomi Hatakeyama

Polyploid crop genome assembly by optical genome mapping and homeolog specific genomics analysis

• Wednesday, 2019-04-03
• 12:15 in Y-55L-12, UZH Irchel campus

ZH Seminars Bioinformatics - Ge Tan

Long fragments achieve lower base quality in Illumina paired-end sequencing

• Wednesday, 2019-03-20
• 12:15 in Y-55L-12, UZH Irchel campus

BIO612: Haoyang Cai: Focal Copy Number Changes in Cancer and Genome Structure