We’d like to invite you to our annual Omicsoft User Group Meeting in Cambridge, MA, September 19-20, 2017, where you’ll learn more about enterprise data analysis and management.
There’s free registration and attendance for a limited time only.
In the past ten years, OmicSoft has helped numerous users from major pharma and biotech companies (as well as research institutions) accelerate their bioinformatics and genomics research. Last year, we successfully held our kick-off OmicSoft User Group Meeting. More than 30 leading pharmaceutical and biotech companies and more than 100 experts and scientists in the field of bioinformatics/genomics/genetics attended the meeting.
Last year, our action-packed one-day meeting provided an open platform for our users and industry peers to learn, to network, and to impact the development of OmicSoft products. This year OmicSoft has had several milestones and technology breakthroughs including: our acquisition by QIAGEN, Array Suite 10,0. release, Cloud-Based Lands, Single Cell RNA-Seq support, upcoming integration with QIAGEN's bioinformatics products, Web-based solutions and more. We are expanding the 2017 OmicSoft User Group Meeting into a two-day event with:
Learn, network, impact. Come join us and leading pharma, biotech companies and research institutions.
Please contact us for potential presentation and collaboration opportunities.
In addition to the traditional National Cherry Blossom Festival, this spring Washington, D.C. will welcome the AACR Annual Meeting 2017 on April 1-5!
We’ll be delighted to meet you at our booth (#1643) where you can learn more about our solutions dedicated to cancer research and biomarker discovery. We'll feature our complete portfolio of products dedicated to cancer research and biomarker testing.
Meet our experts and discuss sample prep, NGS kits and quality control, gene expression and miRNA regulation, pathway analysis and epigenetics, and solid tumor and blood cancer biomarkers.
We’re also hosting a Spotlight theater presentation and presenting several posters. Check out the following for details.
Topic: Achieving NGS insights using QIAGEN ‘Now Generation’ technologies
Date/time: 10:00 a.m., Tuesday, April 4
Location: Spotlight Theater A, Exhibit Hall A
Guest speaker: Monika Mehta, Ph.D., R&D Scientist, Sequencing Facility, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Advanced Technology Research Facility, Frederick, MD
Topic 1: Integrative approach to biomarker discovery by performing comparative analysis of two cancers, hepatocellular carcinoma and endometrioid endometrial carcinoma, using genetics and transcriptomics from RNA sequencing data
Date/time: Monday, April 3 – 1:00 p.m. - 5:00 p.m.
Location: Section 39, 2840 / 13
Topic 2: RNA profiles of circulating tumor cells and extracellular vesicles for therapy stratification of metastatic breast cancer patients
Date/time: Tuesday, April 4 – 8:00 a.m. - 12:00 p.m.
Location: Section 31, 3777 / 3
Topic 3: RNA fusion detection in thyroid nodules with a targeted RNA sequencing panel
Date/time: Wednesday, April 5 – 8:00 a.m. - 12:00 p.m.
Location: Section 17, 5408 / 19
We look forward to seeing you there.
Throughout SOT 2017 you can find us in booth #1812, Exhibit Hall E. You're also welcome to join our workshop and exhibitor presentation Tuesday, where our speaker, Dev Mistry, will present during lunch.
March 14th, 12:00 p.m. - 1:00 p.m.
Location: Room 340, Baltimore Convention Center
Investigating Nrf2’s protective role in kidney through transcriptomics and proteomics data interpretation using Ingenuity Pathway Analysis (IPA)
Transcription factor Nrf2 can play a protective role against oxidative stress and nephrotoxic insults. Nrf2’s protective role in kidney is investigated by comparing Nrf2 knockout mice to their wild-type counterparts. These mice are also treated with CDDO-me, an Nrf2 inducer. Here we analyze and interpret these published (Shelton LM et al., PMID 26422507) transcriptomics and proteomics datasets using IPA. IPA identifies Nrf2 as the key upstream regulator accompanying the activation of detoxification-related pathways and biological processes. Comparison analysis of transcriptomics and proteomics datasets shows enrichment of similar pathways and cellular processes, and highlights IPA as a powerful tool for multi-omics tox analysis.
We hope to see you March 12-16, 2017 in Baltimore Convention Center, MD (1 W Pratt St, Baltimore, MD 21201)
You can find informations about SOT 2017 in their official website here: http://www.toxicology.org/events/am/AM2017/index.asp
We'll be attending PAG XXV, the largest ag-genomics meeting in the world, January 14-18 in San Diego, CA, USA. PAG is one of our favorite events to meet researchers from all over the world within plant and animal genomics. As always, we've prepared scientific activities for you, which you can read more about below.
Monday, January 16. 12:50-3:00 pm
Royal Palm Salon 5-6
QIAGEN bioinformatics offers genome scientists continuity in their research. CLC Genomics Workbench and a series of specialized modules integrate all NGS data analysis capabilities required to power modern plant and animal research into a single platform – from DNA-seq and variant detection, advanced RNA-seq and epigenomics capabilities, to a comprehensive toolbox for metagenomics or plant pathogen analysis. The direct integration with Ingenuity Pathway Analysis (IPA) allows researchers to explore the biological consequences of the results of RNA-seq or epigenomics experiments.
For this workshop we have picked two NGS application areas that we will explore in greater depth: Dr. Jamie Hill (Product owner, CLC Genomics Workbench, QIAGEN) will focus on RNA-seq capabilities and best practices. And Dr. Mark Borodovski is presenting on gene finding and annotation of metagenomes or pathogen genomes.
Speaker: Jamie Hill, Senior Bioinformatics Scientist, QIAGEN Aarhus
For few areas of genomics, do best practices evolve as quickly and continuously as for RNA-seq applications. As a consequence of the rapid development within RNA-seq, researchers struggle to ensure that their analysis pipelines meet the latest standards. In the daily routine users often run a mix of different bioinformatics tools for the respective analysis step they perform best, from read mapping through isoform quantification to the detection of differential abundance. However, integrating and testing the best performers among a growing number of analysis solutions is complex and time consuming.
RNA-seq analysis is a declared focus area for QIAGEN bioinformatics. Users of CLC Genomics Workbench and Biomedical Genomics Workbench rely on us to constantly evaluate emerging bioinformatics approaches and integrate leading approaches into our solutions in a way that follows modern design control and quality assurance criteria. In our workshop we will share best practices as well as some of the recent improvements and underlying methods implemented into our RNA-seq solution.
Speaker: Mark Borodovsky, Georgia Institute of Technology, Atlanta, GA, USA, Gene Probe, Inc., Atlanta, GA, USA
Gene prediction and annotation plays central role in genomics. However, in spite of much attention, open problems still exist and stimulate development of new algorithmic solutions in all categories of gene finding. Particularly, gene prediction in short assemblies of NGS reads e.g. in short metagenomic sequences, is far from trivial.
The gene finder, MetaGeneMark, has been frequently used in individual labs for analysis of short sequences. It has also been used as a part of comprehensive pipelines, such as DOE JGI IMG/M pipeline for annotation of environmental metagenomes.
Implementation of MetaGeneMark in the CLC Genomic Workbench, its applications and the theory behind MetaGeneMark is the subject of this presentation.
Presenter: Marta Matvienko
Location: Grand Exhibit Hall
NGS assemblies of plant genomes often consist of thousands of contigs. Sequencing the segregating progenies is regularly used to anchor the de novo assembled contigs into chromosomescale assemblies. The analysis of sequencing data from segregating progenies usually involves custom scripting, and requires advanced bioinformatics skills. Here we present a userfriendly workflow that can be performed in CLC Genomics Workbench, enabling biologists to proceed with this type of data analysis.
We used the publicly available ddRADSeq data for sacred lotus, Nelumbo nucifera (Liu et al, 2016), and the corresponding genomic assembly consisting of 3,602 contigs. The alignments, as well as all variant calling and variant filtering were performed in CLC Genomics Workbench. The variants were called using the Fixed Ploidy Variant caller, filtered against control reads of the other parent, and selected for homozygosity and variant quality. This part of the workflow produced a known variants track, which was used to call variants in the progenies. We further filtered the variant tracks using the workbench's comparative tools, and ended up with 4K variants detected in at least 70% of F2 samples.
To assess the quality of variant calls, we exported the data from CLC Genomics Workbench and submitted them to the MadMapper program, which clustered contigs into chromosomes. Most of the genomic assembly (72.5%) was clustered into 9 lotus chromosomes; a similar number, 70.6% was anchored by Liu et al. This confirmed the quality of the marker data for chromosomescale assemblies outputted by the workbench using the user-friendly workflow.
