ZH Sem Bioinfo - Mirjam Zünd

TBD

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

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