Bioinformatics Software | QIAGEN Digital Insights

Accelerating Drug Discovery with Comprehensive Curated Knowledge
2024-06-13 13:00 - 14:00 (America/Halifax) | Virtual - Americas - EST, United States
In the rapidly evolving landscape of drug discovery, the ability to integrate high-quality research findings into knowledge graphs is paramount. For over twenty years, the Ingenuity team with QIAGEN has curated these nodes and relationships. Our QIAGEN Biomedical KB-HD make these data available for consumption outside of Ingenuity Pathway Analysis.
In this talk, we will:
• Explore how to query and leverage this curated data resource to accelerate the drug discovery process.
• Provide live demonstration of the underlying database Biomedical-HD
• Show how the Biomedical KB-HD can be rapidly deployed
• Show how the underlying schema and ontologies could serve as a scaffold for integrating your own research
Overall, this demonstration will show the critical role of knowledge graphs in predicting adverse outcomes and toxicity, highlighting their transformative potential in steering pharmaceutical research and development.
Learn more about Biomedical KB: https://qiagen.showpad.com/share/GmpIJaN5kRfsHRD5WPwgc

HGMD Pro in action: Search, curate and classify genetic variants - Session 2
2024-06-18 13:00 - 14:00 | Virtual - Americas - EST, United States
In this live, interactive training session, our technical expert will show you how the Human Gene Mutation Database (HGMD) Professional can help you get better variant data faster.

You will learn how to:
• Differentiate between clinically significant variants and variants of unknown significance (VUS)
• Use batch search vs. advanced search, including their differences
• Curate genes using HGMD Pro’s accurate, up-to-date information
• Determine the predominant type of genetic variant that occurs in a specific gene to understand the genetic mechanisms underlying associated diseases
• Additional topics of interest based on registration feedback

HGMD Pro in action: Search, curate and classify genetic variants - Session 2
2024-06-18 13:00 - 14:00 | HSMD-screen-grab-2

Leveraging the QIAGEN Knowledge Graph and causal embeddings for insights into drug repurposing
2024-06-18 13:00 - 14:30 | Virtual - Americas - EST, United States
By connecting diverse entities and relationships, biomedical knowledge graphs hold the potential to uncover new insights from existing data. This webinar introduces a machine learning-based approach that utilizes causal interactions from the QIAGEN Knowledge Graph to predict novel drug-disease relationships and construct networks that capture relevant supporting evidence. We will present examples that showcase the application of this approach in the context of drug repurposing.

Leveraging the QIAGEN Knowledge Graph and causal embeddings for insights into drug repurposing
2024-06-18 13:00 - 14:30 | HSMD-screen-grab-2

QIAGEN Ingenuity Pathway Analysis (IPA) for grant writing and publications with new features
2024-06-20 13:00 - 15:00 | Virtual - Americas - EST, United States
QIAGEN Ingenuity Pathway Analysis (IPA) is more than just an analysis program; it can also help you write grants and publications. IPA provides biological insights backed by expert-curated findings and thousands of pre-analyzed multiomics datasets. You can search for existing knowledge on molecules of interest, build networks and review results from public studies. Or you can identify key pathways, regulatory molecules and functional changes in your results and see how your data relates to published studies.
Join us to learn how to:
• Search IPA’s vast collection of curated literature and omics data
• Relate molecules to phenotypes and functions
• Build your own networks and predict activity changes
• Explore a library of over 90,000 precomputed IPA analyses pulled from publicly available studies
• Format your dataset and set up an analysis
• Deeply interrogate key Canonical Pathways
• Predict regulators causing your observed expression changes
• Contextualize your results by comparing them to internal and public data
• Generate the necessary tables and figures for your manuscript
Do you already have an IPA license? Install IPA and start using it now: https://qiagen.showpad.com/share/CBv30blCPKFDUYHRWtAvI
Learn more about IPA or request a free trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/

RNA-seq data analysis and interpretation with sankey plot update
2024-06-25 13:00 - 14:30 | Virtual - Americas - EST, United States
For RNA-seq data, you 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, Venn diagrams, sankey plot and others
• Easily customize RNA-seq workflows
• Export publication-quality graphics, tables and reports
• Send differential expression tables to QIAGEN Ingenuity Pathway Analysis directly from QIAGEN CLC Genomics Workbench to analyze and interpret relevant pathways
Learn more about CLC or request a free trial: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-workbench-premium/

Benefits of integrating targeted next-generation sequencing (NGS) panels into molecular diagnostics of solid tumors
2024-06-27 13:00 - 14:00 | Virtual - Americas - EST, United States
Variant detection of multiple genes from a single tumor sample requires high-throughput molecular testing. To meet this demand, targeted next-generation sequencing (NGS) panels are useful in clinical settings for accurate tumor profiling and the identification of essential molecular aberrations for personalized therapies. By focusing only on a subset of genes, targeted NGS is not only a cost-effective solution, but can rapidly deliver insights into a tumor molecular profile.
To address this challenge, a clinical research team led by Dr. Michela Bulfoni at the Istituto di Anatomia Patologica designed custom NGS panels, named “Glioma” and “Routine Diagnostics”, targeting single nucleotide variations, insertions/deletions, fusions, and copy number variations of tumor-associated essential genes.
In this webinar, attendees will:
Understand the clinical utility of custom-designed NGS panels for accurate tumour diagnosis
Learn about the design and application of these NGS panels
Gain insights into the cost-effectiveness and high sensitivity of NGS panels in improving sample throughput

Benefits of integrating targeted next-generation sequencing (NGS) panels into molecular diagnostics of solid tumors
2024-06-27 13:00 - 14:00 | HSMD-screen-grab-2

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp - Session#1
2024-07-09 13:00 - 14:00 | Virtual - Americas - EST, United States
Join us for three 60-minute training sessions for QIAGEN Ingenuity Pathway Analysis (IPA).

In this training, you’ll learn how to:

Tuesday July 9 – Session#1: 1pm ET/10am PT

IPA general overview
Upload your dataset (RNA-seq, scRNA-seq, proteomics, metabolomics and more)
Set up core/pathway analysis in IPA

Wednesday July 10 – Session#2: 1pm ET/10am PT

Understand the different result types produced (pathways, key regulators, and more)
Customize chart outputs using filters and different chart types like a volcano plot like bubble chart

Thursday July 11 – Session#3: 1pm ET/10am PT

Compare different experimental conditions (different ‘omics data, treatments, time points, 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

If you are able to attend, then we will have additional scientists on the call for Q&A. If you are unable to attend, registering will still allow you to view the recordings.

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp - Session#1
2024-07-09 13:00 - 14:00 | HSMD-screen-grab-2

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp - Session#2
2024-07-10 13:00 - 14:00 | Virtual - Americas - EST, United States

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp - Session#2
2024-07-10 13:00 - 14:00 | HSMD-screen-grab-2

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp - Session#3
2024-07-11 13:00 - 14:00 | Virtual - Americas - EST, United States

QIAGEN Ingenuity Pathway Analysis (IPA) summer camp - Session#3
2024-07-11 13:00 - 14:00 | HSMD-screen-grab-2

De novo assembly, BLAST and genome finishing with QIAGEN CLC Genomics Workbench
2024-07-17 13:00 - 14:30 | Virtual - Americas - EST, United States
Description
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.

De novo assembly, BLAST and genome finishing with QIAGEN CLC Genomics Workbench
2024-07-17 13:00 - 14:30 | HSMD-screen-grab-2

Antimicrobial resistance (AMR) and multi-locus sequence typing (MLST) with QIAGEN CLC Genomics Workbench
2024-07-18 13:00 - 14:30 | Virtual - Americas - EST, United States
You asked for it by popular demand, and we’re here to deliver. In this training, we’ll cover how antimicrobial resistance (AMR) is used for isolation or can be easily integrated with other functionalities such as multi-locus sequence typing (MLST).
In this training, we’ll cover:

Introduction to AMR, MLST and relevant databases
QIAGEN Microbial Insight - Antimicrobial Resistance database (QMI-AR)
Importing data and downloading needed databases
Finding resistance with nucleotide DB, PointFinder and ShortBRED
Integrating AMR with MLST
Exporting high-resolution graphics and result tables.

Antimicrobial resistance (AMR) and multi-locus sequence typing (MLST) with QIAGEN CLC Genomics Workbench
2024-07-18 13:00 - 14:30 | HSMD-screen-grab-2

Assessing drug safety with QIAGEN Biomedical KB-AI
2024-07-23 13:00 - 14:00 | Virtual - Americas - EST, United States
Are you a healthcare professional, clinical researcher or data scientist interested in drug safety research? If so, you know how vital understanding a drug’s adverse effects is to maximize its effect while minimizing its risks. This webinar will show how the QIAGEN Biomedical KB-AI knowledge graph can be used to explore scientific and pharmacovigilance data. Focusing on immune checkpoint inhibitors (ICIs), we will also demonstrate how Neo4j and Python can be combined to query, visualize and analyze this data effectively.
We’ll cover the following:

Drug safety profiling in Biomedical KB-AI
Pharmacovigilance case study of ICIs: Pembrolizumab
Comparative analysis of ICIs for comprehensive safety monitoring

Assessing drug safety with QIAGEN Biomedical KB-AI
2024-07-23 13:00 - 14:00 | HSMD-screen-grab-2

Checkpoint inhibitor and immuno-oncology investigation through OmicSoft Lands APIs
2024-07-24 13:00 - 14:30 | Virtual - Americas - EST, United States
While there is great interest in the scientific community to investigate drug targets and biomarkers from public immune-oncology data, such investigation is hindered by the difficulty in finding and combining related datasets to perform large-scale meta-analyses. This webinar will focus on how high quality curated genomic repositories such as the QIAGEN OmicSoft Lands database immediately allows in-depth investigations across diverse data-sources (GEO, CPTAC, TCGA, GTEx and many more) to discover and validate candidate checkpoint inhibitor drug targets and biomarker investigation.
In this webinar you will learn how to

Easily identify relevant samples using extensive manually curated clinical metadata
Visualize and identify checkpoint inhibition biology related drug target and biomarkers expression patterns in bulk and single cell RNA-seq studies.
Reveal how the expression of a group of biomarkers (or genes/proteins of interest) correlates in normal and disease tissue

IPA deep dive: miRNA investigation using QIAGEN Ingenuity Pathway Analysis (IPA)
2024-07-24 13:00 - 14:30 | Virtual - Americas - EST, United States
In this 90-minute training session, you will learn how to identify target mRNAs for your miRNAs of interest and associate them with pathways, diseases, biological functions, tissues and cell types.
Topics that will be covered include:

How to analyze miRNA-seq datasets alone or both miRNA and corresponding mRNA datasets together
How to use QIAGEN IPA without a dataset, using miRNA IDs
Introduction to databases and curated content specific to miRNA
How to effectively apply various filters and functionalities to identify biomarkers, key targets and biological mechanisms

Learn more about IPA or request for a trial.

Checkpoint inhibitor and immuno-oncology investigation through OmicSoft Lands APIs
2024-07-24 13:00 - 14:30 | HSMD-screen-grab-2

Probing OncoLand using OmicSoft Studio
2024-07-30 13:00 - 14:00 | Virtual - Americas - EST, United States
There's more than one way to probe our OncoLand data. With the OmicSoft Studio graphical user interface (GUI), you won't need a script to fetch the data you want. This training will show how high-quality curated genomic repositories, such as the QIAGEN OmicSoft Lands, immediately allow in-depth investigations across diverse oncology and normal tissues/cells data sources (GEO, CPTAC, TCGA, GTEx and many more) to discover and validate candidate checkpoint inhibitor drug targets and biomarker investigation.
You will learn to generate data for questions such as:

How is a gene (or a set of genes) expressed across different conditions (e.g., diseases, treatments, cell types)?
How is the expression of a gene correlated with the expression of other genes?
For a list of genes, can we generate a heatmap studying their expression across different conditions?
How do you get a list of biomarkers specific to a condition from public studies?

Probing OncoLand using OmicSoft Studio
2024-07-30 13:00 - 14:00 | HSMD-screen-grab-2

Discovery from sample-level public data (GEO, SRA and more) using IPA Land Explorer
2024-08-01 13:00 - 14:00 | Virtual - Americas - EST, United States
Within QIAGEN Ingenuity Pathway Analysis (IPA), public data sourced from OmicSoft is already processed and standardized, making it easy to jump to the actual research. In this training, we'll show how to effectively use sample-level public data and metadata from sources like GEO, SRA, TCGA, GTEx, Blueprint, CCLE and other sources using the IPA Analysis Match and Land Explorer features. We will walk through various use cases, such as biomarker discovery, drug target investigation, studying survival in custom patient cohorts, multi-gene correlation and more.
You will learn to answer questions such as:

How is a gene of interest expressed across different conditions (e.g. diseases, treatments, cell lines)?
Is there correlation in the expression for two genes or biomarkers of user interest for a given condition?
For a given condition of interest, can we derive a list of genes (e.g., genes specific to a disease, treatment or cell type)?
Can we generate custom cohorts of patients (e.g., example TP53 wt vs mutant or PDCD1 high vs low expression) and then, generate survival curves representing those cohorts? Can we generate p-values to see if there is significant difference?
Can we detect expression of a gene in different cell types from single cell data?

Discovery from sample-level public data (GEO, SRA and more) using IPA Land Explorer
2024-08-01 13:00 - 14:00 | HSMD-screen-grab-2

QIAGEN Ingenuity Pathway Analysis (IPA) new user training
2024-08-06 13:00 - 15:00 | Virtual - Americas - EST, United States
Are you new to QIAGEN IPA or interested in expanding your skill set? Join us as we learn more on large dataset analysis and knowledge base queries using QIAGEN IPA.
You’ll learn how to:

Upload multiple dataset types (e.g., RNA-seq, proteomics, metabolomics) and perform interactive core/pathway analysis in IPA
Learn how to interpret different results, including pathways, key regulators, impact on biological functions/diseases and more
Compare different experimental conditions (e.g., single-cell clusters, disease types) and identify similarities and contrasts
Generate a network for hypothesis generation, even without a dataset or experimental design

Do you already have an IPA license? Install IPA and start using it now.
Don't have a license? Learn more about IPA or request a free trial.

Sharing your analysis results with others in Ingenuity Pathway Analysis
2024-08-08 13:00 - 14:00 | Virtual - Americas - EST, United States
QIAGEN’s Ingenuity Pathway Analysis (IPA) is a powerful tool that allows you to upload your omics data and analyze it to identify key biological pathways and mechanisms and regulatory molecules. But did you know you can share your analysis results with others? In this 60-minute webinar, we’ll explore the Share Manager and the Collaboration Workspace in IPA and go over the many ways you can share your analysis results with other or how they can share their results with you.
Attendees will learn how to:

Share datasets and analysis with other IPA users
Use the Share with me feature
Email interactive pathways to other IPA users
Use a Collaboration Workspace (CWS)
