tv.qiagenbioinformatics.com

Checkpoint inhibitors investigation in context of biomarkers, drug targets...

Mon, 25 Aug 2025 10:42:38 GMT

This training will focus on how QIAGEN Omicsoft Studio and IPA can be used to discover new biomarkers, validate (or study) drug targets and identify novel mechanisms of action with user and/or public checkpoint inhibitor datasets from resources like GEO, SRA, TCGA and more.

In this training, you will learn how to:
· Investigate the expression of a gene/biomarker/drug target across different treatments and diseases
· Derive a biomarker/gene signature from a specific condition (for example, non-responders of a drug, a specific disease/disease subtype and more)
· Correlate expression of multiple genes and biomarkers
· Compare different experimental groups (user and/or public data) at both gene expression and pathways/regulatory networks activity levels

Public single cell RNA-seq data investigation using Omicsoft and Ingenuity...

Mon, 25 Aug 2025 10:42:08 GMT

Slides from this training:
https://qiagen.showpad.com/share/qm9IZA718x6x5h6pfsiTa

Single cell lands tutorials: https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/SingleCellLand/Gene_Views/

Single cell RNA-sequencing (scRNA-seq) has been widely used to investigate tissue heterogeneity, identify novel cell types, study pathogenic mechanisms, development of targeted therapy (including immunotherapy) and more. Accordingly tremendous amount of scRNA-seq data has been deposited to public domains like GEO.

In this training, attendees will learn how to

· Locate public single cell studies of their interest using Omicsoft Single Cell Lands

· Study different cell types by dimension reduction plots (example t-SNE, UMAP)

· Investigate expression of genes of interest across different cell types (Violin plots, overlay expression on cluster)

· Identify key pathways and regulators from scRNA-seq data using Ingenuity Pathway Analysis

Investigating public scRNA data using OmicSoft and QIAGEN IPA

Mon, 25 Aug 2025 10:41:38 GMT

In this training, attendees will learn how to

· Locate public single cell studies of their interest using Omicsoft Single Cell Lands

· Study different cell types by dimension reduction plots (example t-SNE, UMAP)

· Investigate expression of genes of interest across different cell types (Violin plots, overlay expression on cluster)

· Identify key pathways and regulators from scRNA-seq data using Ingenuity Pathway Analysis

Drug treatment, toxicology and target safety assessment using QIAGEN IPA and...

Mon, 25 Aug 2025 10:40:29 GMT

In this 90-minute training, you’ll learn how to do drug treatment, toxicology and target safety assessment-related discoveries using QIAGEN Ingenuity Pathway Analysis (IPA) and QIAGEN Omicsoft Lands.
Using public data from GTEx (normal tissue), GEO, cancer collections and more, you’ll learn how to use Omicsoft Lands to:
• Investigate a drug target or biomarker expression across different normal tissues, disease conditions, treatments and more
• Correlate expression of two or more genes
• Identify a list of genes or biomarkers specific to treatment, disease, normal tissue, cell type and more

Using findings from peer-reviewed publications and other sources, attendees we’ll explore with you how to use QIAGEN IPA to:
• Study the impact of targeting a gene/protein on different toxicological and biological functions
• Derive tox findings for a gene of interest from QIAGEN IPA’s knowledgebase
• Identify and study toxicity-related pathways, regulators and functions for an internal dataset or a public dataset
• Compare different drug treatments, other conditions or multi-omics data for novel discoveries

New user training: QIAGEN Ingenuity Pathway Analysis (IPA)

Mon, 30 Jun 2025 13:31:46 GMT

New user training: Large dataset analysis and knowledge base queries using QIAGEN Ingenuity Pathway Analysis (IPA)

Users will learn how to:
• Upload their dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more) and perform interactive core/pathway analysis in IPA
• Understand the different result types produced (pathways, key regulators, impact on biological functions/diseases and more)
• Compare different experimental conditions (treatments, timepoints, single-cell clusters, disease types and more) and identify similarities and contrasts
• Generate a network even without a dataset or experimental design for hypothesis generation

De novo assembly, BLAST and genome finishing using QIAGEN CLC Genomics Workbench

Tue, 27 Jun 2023 15:39:00 GMT

This webinar will introduce users to the tools available for short reads (Illumina) as well as long reads (Oxford Nanopore, Pac Bio) de novo assembly in CLC Genomics Workbench. It will also go over other useful functionalities such as BLAST and genome finishing.

Participants will learn the following:

o Download and install needed plugins.

o Import data required for the analysis.

o Run the de novo assembly workflow.

o For long reads, improve a de novo assembly by polishing with short, high-quality reads.

o Map reads to a reference and visualize an assembly.

o For long reads, correct raw long reads for further analysis.

o Use BLAST to investigate the contigs.

o Analyze and assemble contigs through Genome Finishing tools.

Discoveries from public immuno-oncology studies using Omicsoft and Ingenuity...

Thu, 12 Jan 2023 17:24:47 GMT

This training will focus on how QIAGEN Omicsoft Studio and Ingenuity Pathway Analysis (IPA) can be used to discover new biomarkers, validate (or study) drug targets and identify novel mechanism of action with user and/or public Immuno-Oncology studies from resources like GEO, SRA, TCGA and more.
Attendees will learn how to
• Investigate expression of a gene/biomarker/drug target across different treatments and diseases
• Derive a biomarker/gene signature from specific condition (example non-responders of a drug, a specific disease/disease subtype and more)
• Correlate expression of multiple genes and biomarkers
• Compare different experimental groups (user and/or public data) at both gene expression and pathways/regulatory networks activity levels

Transforming biological discovery and data science – How direct access to...

Wed, 12 Oct 2022 14:44:47 GMT

In this 90-minute webinar, you will learn more about the range of content offerings from QIAGEN Digital Insights that can empower and transform your in-house discovery and data science projects.

· Discover the virtual biobank of transcriptomic and non-transcriptomic data that is available in QIAGEN OmicSoft DiseaseLand and QIAGEN OmicSoft OncoLand

· Understand the rigorous curation process that ensures data fidelity and the ability to use rich, descriptive metadata to identify samples and comparisons

· Learn how over 600,000 samples of curated experimental data can be accessed via web-based and desktop applications and are available in a complete downloadable form for local integration and mining

· Discover more about QIAGEN Biomedical Knowledge Base (BKB), our knowledge base of biological relationships that provides the foundation for QIAGEN Ingenuity Pathway Analysis (IPA), but which is now available for construction of biomedical knowledge graphs, AI-driven target identification and local knowledge integration

Exploring drug response in low-grade glioma

Wed, 31 Aug 2022 02:58:16 GMT

This webinar introduces the Tumor Microenvironment (TME) Pathway in QIAGEN’s Ingenuity Pathway Analysis (IPA), demonstrating how users can explore immune and tumor interactions by constructing networks around targets like IL1B and predicting downstream effects on functions such as tumor proliferation. Using tools like Molecule Activity Predictor and Path Explorer, we show how curated literature-derived relationships can model cytokine activity and TME behavior. Additional features like BioProfiler, Land Explorer, and Activity Plot allow users to analyze public datasets (e.g., TCGA) for expression trends and regulatory roles, with use cases including PD-1–positive and –negative CD8+ T cells in lung cancer. IPA’s upstream regulator analysis further enabled prediction of key drivers influencing immune and tumor cell dynamics.

Somatic variants investigation in critical regulatory pathways

Thu, 25 Aug 2022 15:10:11 GMT

This training will focus on using QIAGEN Ingenuity Pathway analysis (IPA) and Human Somatic Mutation Database (HSMD) to identify key somatic variants associated with regulatory genes in ‘omic data and study the genomic characteristics of both target and disease to better understand the clinical relevance. Identifying and studying the genomic characteristics of drug targets and important genes are of great interest to many researchers as it can offer new insights into improving drug discovery and precision medicine. In this 90-minute training, the Human Somatic Mutation Database (HSMD) will be introduced for genomic investigation. HSMD is a web-based database containing data for hundreds of thousands of variants within the context of solid tumors and hematological malignancies. Specifically, HSMD provides gene-level, alteration-level, and disease-level information including clinically observed gene and variant frequencies across cancer types.

Attendees will learn how to:

· Use IPA to identify key regulators within a dataset of interest

· Use HSMD to investigate variants for target genes and cancer type of interest

· Synthesize key findings from drug labels, clinical trials, and PubMed articles for specific alterations and cancer types

Click here to learn more about HSMD and IPA.

Drug repurposing: from large-scale biological data to therapeutics

Fri, 08 Jul 2022 14:34:00 GMT

One of the challenges we are facing today is the high cost and slow pace of drug development for many disease areas such as cancer, CNS, rare diseases etc. Repurposing drugs for new indications will have a shorter developmental time, lower cost, and less safety risk than the traditional drug development process.

Join us for this 60-minute Webinar on Drug repurposing: from large-scale biological data to therapeutics. This one-hour event will show how our platform enables biologists to leverage transcriptomics and literature-curated biological data for in-silico drug repositioning and repurposing.

Through a series of short demonstrations, we will explore:
• A systems biology approach to discover new uses of existing FDA-approved drugs
• Accelerate drug discovery process and generate novel hypotheses from high-quality omics and literature curated data
• Estimate network of genes potentially perturbed by drugs and integrate it with drug and disease gene expression signatures
• Study how targets of interest are expressed across different diseases and tissues

Our system uses millions of curated literature findings in the QIAGEN/ IPA knowledgebase and the OmicSoft digital warehouse. The presentation is intended for both those familiar with Ingenuity Pathway and newcomers interested in learning more.

RNA-seq and single-cell RNA-seq data analysis

Mon, 09 May 2022 16:24:58 GMT

In this 90-minute training, users will learn how to easily analyze RNA-seq and single-cell RNA-seq (scRNA-seq) data using QIAGEN CLC Genomics Workbench software.

For RNA-seq and scRNA-seq data, users will learn how to:
• Import fastq files, cell matrix files and metadata and how to download references
• Map reads to a reference genome and generate gene and transcript counts and QC reports displaying % mapped reads, knee plots, etc.
• Generate visualizations of results, such as heatmaps, differential expression tables, PCA/PCOA plots, t-SNE plots, UMAP plots, dot plots, Venn diagrams and others
• Annotate single-cell clusters overlain with gene expression
• Easily customize RNA-seq and scRNA-seq workflows
• Export publication-quality graphics, tables and reports
• Send differential expression table to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench

Identifying antimicrobial resistance from Sample to Insight

Thu, 07 Apr 2022 18:26:52 GMT

Antimicrobial resistance (AMR) detection and surveillance is a high priority in healthcare and environmental settings for the safety of both patients and the general public. However, working with samples used for this type of monitoring, such as stool or wastewater, can be challenging, from the sample preparation to the sequencing to the bioinformatics.

In this 60-minute online summit, we will take you through a series of biological samples, including stool, wastewater and others. We'll demonstrate the workflows and characteristics of each, together with the answers and insights you can expect. There will also be a live Q&A session, giving you a chance to discuss your questions and use cases with our experts.

At this online virtual AMR summit, you will learn about:

Our kits for nucleic acid extraction from various sample types such as stool, sludge and wastewater
The importance of inhibitor removal during sample preparation
Sequencing workflows for AMR
Benefits of using hybrid capture versus shotgun sequencing
How to generate ShortBRED AMR marker abundance tables
How to associate and compare different metadata, such as sample type (stool, wastewater, etc.)
AMR alpha and beta diversity across sample types and how to determine the depth of coverage

Long-read sequencing analysis in the QIAGEN CLC Genomics Workbench

Thu, 24 Mar 2022 07:45:16 GMT

This tutorial is an introduction to working with the tools in the Long Read Support (beta) plugin. The Long Read Support (beta) plugin is a collection of tools developed for working with long, error-prone reads such as those produced by the single-molecule sequencing technologies of Pacific Biosciences or Oxford Nanopore Technologies.

Participants will take away how to:

• Download Plugin for Long read support
• Import data required for the analysis
• De novo assembly of a microbial sized genome using long, error-prone reads
• Improve a de novo assembly from long reads by polishing with short, high-quality reads
• Map long reads to a reference and visualizing an assembly
• Correct raw long reads for further analysis