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TBA

Zurich Seminars in Bioinformatics - Santiago Castro

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract

TBA

Zurich Seminars in Bioinformatics - Gregor Rot

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract

Previous ¶

Microbiome Signatures in Host - Spatial and Single Cell Transcriptomics

Zurich Seminars in Bioinformatics - Stine Anzböck

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract The tumor-associated microbiome is an integral part of the tumor microenvironment and holds great promise for a better understanding of carcinogenesis, response to therapy and early diagnosis of cancer. However, current methods limit the understanding of the spatial distribution of the microbiome in the tumor and their interaction with host cells. To this end, we have developed SpaceMicrobe, a novel computational framework to detect and profile the microbiome in 10X Visium Spatial Gene Expression data, a widely used commercially-available spatial transcriptomics technology. Continue reading

Variational Autoencoders Supporting Conditioning in Single Cell Transcriptomics and Their Consistency

Zurich Seminars in Bioinformatics - Eljas Röllin

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract Prediction of cell response to perturbation is a key goal in computational biology. To this end, different Variational Autencoder (VAE) based models have been suggested in the past. We are interested in such models and their ability to recognize their own output. We argue that this is a desirable model property, and phrase it in the context of cycle consistency. Continue reading

Analysis of copy number variant heterogeneity in the hierarchical NCIt cancer classification system

Zurich Seminars in Bioinformatics - Ziying Yang

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract Cancers are heterogeneous diseases with unifying features of abnormal and consuming cell growth, where the deregulation of normal cellular functions is caused by accumulative mutations. Due to these mutations, malignant tumors present with patterns of somatic genome variants on diverse levels of heterogeneity. Among the different mutation types, genomic copy number aberrations(CNA) have emerged as one of the most distinct classes. Continue reading

Detecting Single Cell Blasts in Acute Myeloid Leukaemia using an Auto-Encoder

Zurich Seminars in Bioinformatics - Alice Driessen

12:15 UZH Irchel Y13-K-05 and ZOOM Call

Abstract Acute myeloid leukaemia (AML) is a haematological cancer in the bone marrow, with accumulation and expansion of immature cells of the myeloid lineage. Unfortunately, almost half of paediatric AML patients relapse after standard treatment with chemotherapy or stem cell transplantation. Personalised medicine including immunotherapies have the potential to target chemotherapy resistant cells and achieve long-term remission. However, identifying suitable targets for AML therapy is hampered by high patient heterogeneity, complex disease evolution and challenging discrimination between aberrant and developing cells. Therefore, we aimed to build a single-cell cytometry AML map to identify malignant cells and place them along the developmental trajectory using data from 20 patients and three time points over the course of the disease. Continue reading

Multi-omics studies of cancer signalling and immune infiltration

Zurich Seminars in Bioinformatics - Pedro Beltrao

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract Genetic alterations in cancer cells trigger oncogenic transformation, a process largely mediated by the dysregulation of kinase and transcription factor (TF) activities. While the mutational profiles of thousands of tumours have been extensively characterised, the measurements of protein activities have been technically limited until recently. We compiled public data of matched genomics and (phospho)proteomics measurements for 1,110 tumours that we used to estimate activity changes in 218 kinases and 292 TFs. Continue reading

Inflammatory bowel disease at single-cell and sub-cellular spatial resolution

Zurich Seminars in Bioinformatics - Helena L. Cromwell

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract CosMx Spatially Molecular Imaging (SMI) (NanoString) is a recently developed technology that enables spatially resolved profiling of tissue at molecule-level resolution at an unprecedented scale (up to 1,000 RNA analytes). We applied scRNA-seq and CosMx SMI to investigate the molecular basis of Ulcerative colitis and Crohn’s disease: chronic inflammatory bowel diseases (IBD) that show a perplexing heterogeneity in manifestations and response to treatment. Continue reading

Searching in nucleotide archives at Petabase scale with MetaGraph

Zurich Seminars in Bioinformatics - Mikhail Karasikov

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract High-throughput sequencing data is continuously accumulating in massive archives such as the NCBI Sequence Read Archive (SRA), which currently contains over 50 Petabytes of sequences. However, despite recent advances, even such a basic operation as sequence search effectively remains intractable due to the lack of cost-efficient solutions. To address this problem and enable aggregated data analysis at Petabase scale, we developed MetaGraph, a tool for indexing very large collections of sequences in de Bruijn graphs. Continue reading

Nucleosome footprints in the cell-free DNA of cancer patients

Zurich Seminars in Bioinformatics - Zsolt Balázs

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract Cell-free DNA (cfDNA) is free floating DNA released from cells into bodily fluids like blood. cfDNA sequencing is being increasingly utilized in cancer diagnosis and monitoring. While many applications focus on detecting cancer-specific mutations, cfDNA can potentially tell us much more about the disease. Nucleosome-protected regions are slow to degrade in the bloodstream, therefore, nucleosome occupancy in the cell of origin can be inferred from cfDNA fragmentation. Continue reading

Genome-wide study of variations in Plasmodium falciparum and their association with different malaria interventions in Tanzania

Zurich Seminars in Bioinformatics - Catherine Bakari Mvaa (Christian Nsanzabana group @ TPH)

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract Malaria affects millions of people globally, and it remains one of the major public health problems occurring in most parts of Tanzania, causing thousands of deaths each year, especially among vulnerable persons in rural settings with poor health systems. Even though the burden has decreased due to the deployment of different interventions in recent years, all those gains are threatened by biological threats that largely affect the success of different control strategies. The parasite uses different mechanisms to escape diagnostic tools and drug treatment, challenging one of the key control strategies, based on prompt detection and case management. Sequencing technologies, especially Next Generation Sequencing (NGS) have played a major role in understanding parasite genomic variation including drug resistance, diagnostic resistance, and population structure. Continue reading

A journey into the nucleus: Lnc-ing paraspeckles, lncRNA, RNA processing and phase separation

NCCR RNA and Disease seminar

Archa Fox, The University of Western Australia

Host: Prof. Dr. Magdalini Polymenidou

The seminar will be preceded by a short presentation:

Unraveling genetic modifiers and cellular pathways of physiological TDP-43 oligomerization.”

Laura de Vos (Polymenidou group, UZH)

Comprehensive network prediction for any fully sequence genome in STRING database

Zurich Seminars in Bioinformatics - Damian Szklarczyk

Abstract Every day new genomes are sequenced and existing genomes are re-sequenced and re-annotated. In the new version of STRING the user can submit any fully sequenced genome for complete network and functional annotation. To do so. will require only minimal input from the user in a form of the proteome in a FASTA format and, if known, a taxonomical clade of the given genome. Continue reading

Towards a quantitative understanding of long-range transcriptional regulation

ETHZ seminar - Luca Giorgetti, FMI Basel

recently published Nature paper on “Nonlinear control of transcription through enhancer–promoter interactions”

CompbioZurich Website Redesign

Re-implementing the Site with Mkdocs

The compbiozurich.org website has been redesigned based on the Mkdocs framework & using the Material template system. Continue reading

Novel Minimal HDV-like Ribozymes

Zurich Seminars in Bioinformatics - Lukas Malfertheiner

Abstract The hepatitis delta virus (HDV) ribozyme catalyzes site-specific self-cleavage and was first discovered in the single-stranded circular RNA virus HDV. HDV-like ribozymes (DRZ) share the conserved nested double-pseudoknot structure motif. Through a bioinformatic search using an adapted minimal active DRZ motif, we discovered hundreds of novel minimal DRZ sequences in bacteriophage genomes associated with the human microbiome. A subclass of these hits was identified to occur in direct conjunction with viral tRNA genes, indicating that we have found a solely RNA-based factor that can site-specifically cleave tRNA 3'-trailers, thus making large protein enzymes redundant for this task.

12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Supervised spatial inference of dissociated single-cell data with _SageNet_

Zurich Seminars in Bioinformatics - Elyas Heidari

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. Continue reading

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

Zurich Seminars in Bioinformatics - Rahel Paloots

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. Continue reading

Copy number variation data calibration towards intgerative analysis in cancer

Zurich Seminars in Bioinformatics - Hangjia Zhao

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.

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

Zurich Seminars in Bioinformatics - Maciek Bak | Biozentrum, University of Basel | Swiss Institute of Bioinformatics

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.

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

Zurich Seminars in Bioinformatics - Jacopo Marino, Laboratory of Biomolecular Research, Paul Scherrer Institut

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).

Taxonomic profiling of metagenomes from diverse environments with mOTUs3

Zurich Seminars in Bioinformatics - Hans-Joachim Ruschewey

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.

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

Zurich Seminars in Bioinformatics - Mirjam Zünd

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.

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

Zurich Seminars in Bioinformatics - Tülay Karakulak

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.

Structured metadata for genomic correlations in the Progenetix database

Zurich Seminars in Bioinformatics - Ziying Yang

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.

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

Zurich Seminars in Bioinformatics - Max Verbiest

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.

Identifying clones and quantifying diversity in repertoire sequencing data.

Zurich Seminars in Bioinformatics - Siyuan Luo

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.

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

Zurich Seminars in Bioinformatics - David Wissel

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.

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

Zurich Seminars in Bioinformatics - Ahmad Al Ajami

12:15 UZH Irchel Y34-K-01 and ZOOM Call

Abstract: A fundamental task in the analysis of single-cell RNA-sequencing data is cell type annotation. Current cell type annotation methods rely on either prior biological knowledge, which is not always available in a comprehensive and consistent manner, or well-annotated reference datasets, which are not always complete, i.e., not all cell types present in the target are represented in the reference data. We propose conducting cell type annotation in a probabilistic framework to fill the gap incomplete references create. Continue reading

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

Zurich Seminars in Bioinformatics - Marija Dmitrijeva

12:15 UZH Irchel Y34-K-01 and ZOOM Call

Horizontal gene transfer - the exchange of genetic material between organisms through mechanisms other than reproduction, has been shown to play an important role in prokaryotic genome evolution. Previous studies have predominantly focused on recent horizontal gene transfer events, often limiting investigation to human-associated microorganisms. In this study, we aim to conduct a more global survey of the factors contributing to horizontal gene transfer. Continue reading

Introducing Progenetix Cell Line Beacon - A comprehensive cancer cell line variant knowledge resource

Zurich Seminars in Bioinformatics - Rahel Paloots

12:15 om ZOOM Call

Cancer cell lines are good models for studying the disease mechanisms and testing for possible drugs. For the cell lines to be accurate representations of the disease, they would need to be genetically highly similar to their primary neoplasias. Another issue when working with cell lines is the possible contamination or misidentification of the cell lines. To address both of these concerns, the genetics of both cancer cell lines and their origins will need to be evaluated. Cancers as well as cancer cell lines exhibit copy number variation (CNV) profiles that show regions in the chromosomes that have been deleted or amplified. Continue reading

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

Zurich Seminars in Bioinformatics - Adriano Martinelli

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.

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

Zurich Seminars in Bioinformatics - Emanuel Sonder

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.

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

Zurich Seminars in Bioinformatics - Max Brambach

12:15 om ZOOM Call

Discovering copy number variation across multiple cancer types

Zurich Seminars in Bioinformatics - Qingyao Huang

12:15 om ZOOM Call

Abstract Genomic variations are direct cause of tumor formation and accomplice in its continuous evolution. While point mutations can be pinpointed to a targeted genetic element, copy number variations (CNVs) involve copy number gain or loss of a large DNA segment which often covers hundreds of genetic elements in one event. Although the vast majority of variations are not directly fucntionally cancer promoting, we observe consistency in CNV landscape within the same cancer types and corresponding increase in heterogeneity along with increased distinction in physiology and morphology. This implies that particular CNV may promote cancer type-specific progression. Continue reading

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

Zurich Seminars in Bioinformatics - Stephany Orjuela

12:15 om ZOOM Call

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

Zurich Seminars in Bioinformatics - Giancarlo Russo

12:15 om ZOOM Call

Abstract Knowledge about the age of a stain or rather the time since deposition (TsD) would provide law enforcing authorities with valuable information for the prosecution of criminal offences. There is no reliable method for estimation of TsD available yet. The aim of this study is to gain further insight into the RNA degradation pattern of forensically relevant body fluids, and to find markers that allow to estimate the TsD interval. Stain samples from several body fluids were exposed to indoora nd outdoor conditions for up to 1.5 years. We were able to identify degradation as well as body fluid specific signatures in both indoor and outdoor samples. Continue reading

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

Zurich Seminars in Bioinformatics - Anthony Sonrel

12:15 om ZOOM Call

Recently, the ability to profile gene expression at the single-cell level has been expanded to include the measure of both RNA and protein levels from the same cells (Stoeckius et al., 2017). While RNA-based data has broadly proven sufficient for cell type detection and classification, its usage for determining drug target is still limiting: we still often rely on the assumption that RNA expression levels are representative of protein expression levels. Continue reading

Protein-protein interaction prediction using co-evolution based method

Zurich Seminars in Bioinformatics - Tao Fang

12:15 om ZOOM Call

It has been found that protein families consisting of orthologous proteins usually show divergent sequence similarities due to amino acid mutations in evolutionary history while structures of protein families are usually much more conserved. This phenomenon can be explained by two types of mutant positions in the protein sequence. One is conserved regions across the protein family and even a slight change in this region could result in critical loss of protein structure or function. Another is the so-called compensated mutation or coevolution region in protein. Continue reading

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

Zurich Seminars in Bioinformatics - Annika Gable

12:15 om ZOOM Call

Functional enrichment analysis (also called gene set enrichment analysis or pathway analysis) is a widely-used method to interpret genome-wide experiments, especially in transcriptomics and proteomics. The method relies on previously annotated gene sets, such as pathways, cellular locations, protein families, disease genes, or other annotation terms. Continue reading

Phylogeny and Metabolic Potential of SAR324

Zurich Seminars in Bioinformatics - Lukas Malfertheiner

12:15 om ZOOM Call

The bacterial SAR324 cluster is ubiquitous in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 20% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes instead of the previously used 16s rRNA single gene marker, the former Deltaproteobacteria cluster SAR324 is since 2018 classified as its own phylum. Yet, very little is known about the phylogeny, metabolic potential and the influence of SAR324 on the different environments where they live. We downloaded all publicly available SAR324 genomes (65) from the genome taxonomy database, and also constructed 18 new genomes out of different oceanic metagenomic samples, including from under the Ross Ice Shelf in the Antarctica. Continue reading

Doublet identification and characterization in single-cell data

Zurich Seminars in Bioinformatics - Pierre-Luc Germain

12:15 om ZOOM Call

Doublets (i.e. two cells captured as a single cell) can form at a high frequency in single-cell sequencing studies (often 10-20%). They can appear as spurious 'new cell types' or distort trajectory and co-expression analyses. While experimental strategies can be used to mitigate this effect, they are insufficient and need to be complemented with doublet identification methods. Continue reading

2020 11 05 zh seminars in bioinformatics

Zurich Seminars in Bioinformatics - João Rodrigues

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

12:15 om ZOOM Call

ReSeq simulates realistic Illumina high-throughput sequencing data

Zurich Seminars in Bioinformatics - Stephan Schmeing

12:00 in Y-55L-06, UZH Irchel Campus and 12:15 om ZOOM Call

Abstract In high-throughput sequencing data, performance comparisons between computational tools are essential for making informed decisions in the data processing from raw data to the scientific result. Simulations are a critical part of method comparisons, but for standard Illumina sequencing of genomic DNA, they are often oversimplified, which leads to optimistic results for most tools. Continue reading

2020 07 09 zh seminars in bioinformatics

Zurich Seminars in Bioinformatics - Lennart Opitz

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

12:00 in Y-55L-06, UZH Irchel Campus and 12:15 om ZOOM Call

Flanking sequence preference modulates _de novo_ DNA methylation in the mouse genome

Zurich Seminars in Bioinformatics - Izaskun Mallona

12:15 (ZOOM Call)

Abstract Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. Continue reading

Progenetix data acquisition & processing pipeline

ZH Seminars Bioinformatics - Qingyao Huang

12:15 (ZOOM Call)

Abstract Over the years we maintain and update the Progenetix database, which provides an overview of copy number abnormalities in human cancer from currently 113322 array and chromosomal Comparative Genomic Hybridization (CGH) experiments, as well as Whole Genome or Whole Exome Sequencing (WGS, WES) studies. The cancer profile data in Progenetix was curated from 1600 articles and represents 420 and 542 different cancer types, according to the International classification of Diseases in Oncology (ICD-O) and NCIt "neoplasm" classification, respectively. In this seminar, I will give an overview of our current pipeline from data retrieval, metadata extraction/curation, data processing and evaluation to the inclusion/exlusion in the database. Continue reading

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

Zurich Seminars in Bioinformatics - Simone Tiberi

12:15 (ZOOM Call)

aGOtool.org web-tool for protein-centric functional enrichment

ZH Seminars Bioinformatics - David Lyon

12:15 (ZOOM Call)

Setting up a pipeline for horizontal gene transfer detection

ZH Seminars Bioinformatics - Marija Dmitrijeva

12:15 (Skype Call)

Abstract In addition to vertically transferring genes to their descendants, bacteria can horizontally transfer genes to other members in their community. These horizontally transferred genes frequently confer various selective advantages to the recipient such as antibiotic resistance and the ability to scavenge rare nutrients. Thus, gaining insight into the principles behind horizontal gene transfer is important for understanding the evolution of prokaryotic genomes. Continue reading

Censored predictors in single cell regression models

ZH Seminars Bioinformatics - Reto Gerber

12:15 (Skype Call)

Abstract Flow and mass cytometry enable the classification of a large number of cells into cell populations. Furthermore, the abundance of cell populations can have an association with a covariate that has additional information about the sample, such as treatment group, age, sex, survival time, etc. In differential abundance analysis, the goal is then to find cell populations whose abundance changes according to a covariate. Continue reading

The Microbe Atlas Project

ZH Seminars Bioinformatics - Joao Rodrigues

12:15 (Skye call)

HackyHour Zurich - data analysis made social

ZH Seminars Bioinformatics - Nils Eling

12:15, Y34-J-01, UZH Irchel campus

Abstract HackyHour is an internationally recognized effort to form local communities of students and researchers and offer a space to discuss ideas, problems and new tools related to scientific data analysis. Key features of such a recurring event are the social and informal setting, an inclusive environment inviting beginners and experts and an interactive exchange of computational knowledge. Continue reading

Knowledge standards drive clinical interpretation of genomic variants in cancers

ZH Seminars Bioinformatics - Alex H. Wagner

Washington University School of Medicine, St. Louis

12:15 in Y-55L-12, UZH Irchel campus (room subject to change)

Abstract The use of diagnostic gene sequencing in the clinical setting is increasingly common. Established sequencing panels targeting genes involved in cancer predisposition, tumor growth, and chemoresistance are widely available, and numerous efforts to validate whole-exome and whole-genome clinical sequencing assays are underway. As a result, genome analysts and molecular pathologists are increasingly tasked to the labor-intensive process of interpreting the clinical significance of tumor variants. Building these clinical reports entails reviewing the literature, population frequency databases, and predicted functional impact of each observed variant. Continue reading

Interval statistics reveal frequently altered gene copies across cancers

ZH Seminars Bioinformatics - Qingyao Huang

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

Abstract Various types of genomic aberration are observed in malignant tumours, including single nucleotide mutation and copy number variations (CNV). While the former are focal changes, the effects of which can be localised to individual genetic elements, the latter often contain megabases of genomic regions, covering hundreds of genetic elements. CNV has been successfully used on a coarse scale (cytoband level) as molecular features to define subtypes in many cancer entities. However, a systematic understanding of the CNV patterns in cancers is not established. Continue reading

2019 11 27 zh seminars in bioinformatics

ZH Seminars Bioinformatics - Joao Rodrigues

12:15 in Y-55L-12, UZH Irchel campus

Functional enrichment in the STRING protein-protein interaction database

ZH Seminars Bioinformatics - Annika Gable

Abstract I will talk about the extended enrichment functionality in STRING, which accepts whole genomes or proteomes with values, including RNASeq, microarrays, ranked genomes, protein abundances, etc. A high-powered enrichment of various annotation databases such as GO-terms is computed within a minute.

Also, I will talk about what we can learn from analyzing the users’ inputs in an aggregated fashion, as well as providing a preliminary comparison of enrichment results between our new enrichment and a similar tool, GSEA.

2019 10 09 zh seminars in bioinformatics

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

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

ZH Seminars Bioinformatics - Tom Ashhurst | Sydney Cytometry Facility, The University of Sydney and Centenary Institute

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

Abstract West Nile virus (WNV) and Zika virus (ZIKV) are responsible for central nervous system (CNS) diseases including encephalitis, Guillian-Barré syndrome and congenital neurological abnormalities in the developing fetus. A successful immune response must carefully balance pathogen elimination against destruction of the host’s CNS. To study these diseases in detail, we analyzed the cellular composition of virally infected mice tissue by high-dimensional flow (30-parameter) and mass (47-parameter) cytometry along with Imaging Mass Cytometry™ and characterized and contrasted the evolving immune response over time. Continue reading

ISMB - ECCB 2019

ISMB/ECCB 2019 is the largest and most high profile annual meeting of scientists working in computational biology. This year's conference will be on July 21-25 in Basel.

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

ZH Seminars Bioinformatics - Helena L. Crowell

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

Abstract Single-cell RNA-sequencing (scRNA-seq) has quickly become an empowering technology to profile the transcriptomes of individual cells on a large scale. Many early analyses of differential expression have aimed at identifying differences between cell types (or clusters), and thus are focused on finding markers for cell populations (experimental units are cells). Continue reading

Wrangling of copy number data in cancer genomic analysis

Seminar in Interdisciplinary Life Science (SILS)

Michael Baudis & Bo Gao

Tuesday, 2019-06-04
17:30 in Y03-G85, UZH Irchel campus

2019 04 17 zh seminars in bioinformatics

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

Novel in silico methods to unveil DNA methylation heterogeneity in cohorts, tissues and cells

UZH DMMD Seminar

Izaskun Mallon

Tuesday, 2019-04-16
14:00 in Y15-G-40, UZH Irchel campus

Abstract Epigenomics modulates cell development and function, and its alterations capture and mediate functional properties of cells, tissues and states, including differentiation and disease. From all epigenomics marks, DNA methylation can be measured reliably in almost any sample type, including clinical specimens. Continue reading

2019 04 10 zh seminars in bioinformatics

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

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

ZH Seminars Bioinformatics - Masaomi Hatakeyama

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

Abstract I will show the latest update of Finger millet genome assembly scaffolded by Bionano Saphyr at chromosomal length scale. I will introduce yet another polyploid analysing tool called EAGLE-RC and show some results on the resequencing data.

Relaunch - compbiozurich.org with Github Based Hosting

As of 2019-03-25, the compbiozurich.org webste is being hosted as a Github project. This move will allow an "open contributions" structure, in which members of Zurich's Bioinformatics & Computational Biology community can participate in content creation. Typical examples of such user-driven updates could be:

seminar announcements
links to resources - software, databases, teaching materials - maintained by members of the CompbioZurich community
job postings
information about teaching events and programs

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

ZH Seminars Bioinformatics - Ge Tan

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

Abstract Illumina’s technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Sequencing runs typically generate millions of reads in which the vast majority of the reads has an average error rate below 1/1000. However, some paired-end sequencing data show the presence of a subpopulation of reads where the second read (R2) has lower average qualities. We show that the fragment length is a major driver of increased error rates in the R2 reads. Continue reading

Brupbacher Meeting 2019

The 14th Charles Rodolphe Brupbacher Symposium "Breakthroughs in Cancer Research and Therapy" will take place on January 29 - February 1, 2019. The event is co-organised with the University of Zurich.

Berners-Lee proposes the Web

Tim Berners-Lee makes a proposal for linking documents across servers.