Analysis of multi-omics data using the Cancer Genomics Cloud

This October, the CGC Webinar Series features a talk by Dr. Min Zhang from Purdue University.

Dr. Min Zhang is a professor in the Department of Statistics and the Associate Director of Data Science at Purdue University Center for Cancer Research. By incorporating biological knowledge in statistical modeling, her research focuses on developing new statistical methods to analyze high-dimensional clinical and omics data that often occurs in biomedical research.  

In this presentation, Dr. Zhang will share her experience organizing a workshop on using CGC to access, share, and analyze multi-omics datasets with RNA-seq data as a case study. Dr. Zhang worked with the CGC Seven Bridges team to design a 4 part lecture that taught undergraduate and graduate students how to run a RNA-seq analysis, bulk and single-cell using the CGC. She will also share how she is using the CGC to implement SIGNET for genome-wide gene regulatory network construction.

References

1. Chen C, Zhang D*, Hazbun T*, Zhang M*. (*co-corresponding authors, 2019). Inferring gene regulatory networks from a population of yeast segregants. Scientific Reports. 9(1):1197. <https://www.nature.com/articles/s41598-018-37667-4>

2. Chen C, Ren M, Zhang M, and Zhang D. (2018). A two-stage penalized least squares method for constructing large systems of structural equations. Journal of Machine Learning Research. 19. <https://www.jmlr.org/papers/volume19/16-225/16-225.pdf>.

MORE ABOUT THE SPEAKER

Dr. Min Zhang is a professor in the Department of Statistics and the Associate Director of Data Science at Purdue University Center for Cancer Research. After obtaining an MD with a residency in cancer and a PhD in Neuroscience, she received another PhD from the Department of Biological Statistics and Computational Biology at Cornell University. By incorporating biological knowledge in statistical modeling, she has focused on developing new statistical methods to analyze high-dimensional clinical and omics data that often occurs in biomedical research.

LinkedIn: https://www.linkedin.com/in/min-zhang-80844a97

FragPipe enables one-stop proteomics data analysis

This August, the CGC Webinar Series features a talk by Dr. Fengchao Yu from University of Michigan and Dr. Rowan Beck from Seven Bridges.

In this upcoming webinar, Dr. Yu will present talk about FragPipe, a one-stop proteomics data analysis suite. Dr. Yu developed Fragpipe with other members of his lab. FragPipe supports both DDA and DIA data. MSFragger in FragPipe can perform closed, open, and mass-offset searches. FragPipe also supports label-free, isotopic- labeling, and isobaric labeling quantifications. Following his presentation, Dr. Beck will demonstrate how to run Fragpipe on the Cancer Genomics Cloud using publicly available data.

MORE ABOUT THE SPEAKER

Fengchao is a research investigator from Alexey Nesvizhskii's lab at University of Michigan. His research interests include Proteomics and Bioinformatics. Currently, Fengchao is the leading developer and maintainer of FragPipe, MSFragger, and IonQuant.

A Comparative Analysis of the Molecular Characteristics of Canine and Human Glioma

This July, the CGC Webinar Series features a talk by Dr. Nadia Lanman from Purdue University.

In this upcoming webinar, Dr. Lanman will present her research studying human gliomas using dog as a model organism. Spontaneous gliomas in dogs are being used as a translational model for human glioma, but molecular characterization is not yet complete.  This work utilizes publicly available datasets to characterize the molecular characteristics of canine gliomas. Dr. Lanman shows how key canonical pathways altered in human gliomas are likewise altered in canine gliomas, and how the canine tumor microenvironment (TME), like that in humans, appears to be immunosuppressive. Gene expression profiles of astrocytomas and oligodendrogliomas show alterations in a number of signaling pathways, including several immune-related and TME-specific pathways.  Dr. Lanman and her team will show how they developed a Naïve Bayes classifier that accurately classifies canine glioma pathologies based on gene expression profiles alone. 

MORE ABOUT THE SPEAKER

Dr. Lanman is a research assistant professor in the Department of Comparative Pathobiology at Purdue University. In 2015, Dr. Lanman took a position with the Purdue University Center for Cancer Research, directing the Computational Genomics Shared Resource (CG-SR) and managing the Purdue side of the Collaborative Core for Cancer Bioinformatics (C3B), a joint bioinformatics core shared between IU and Purdue. Dr. Lanman’s work at the cancer center focuses on managing the bioinformatics core, training, and data analysis. Dr. Lanman’s research is focused on utilizing large genomics datasets to expand our knowledge of the molecular basis of cancer as well as immune and inflammatory diseases. Dr. Lanman is particularly interested in data integration and in developing methods for datasets that leverage temporal or spatial resolution.

Mapping the genome of chemoresistant ovarian cancer with multi-Omic profiling

This June, the CGC Webinar Series features a talk by Dr. Michelle R. Jones from Cedars-Sinai Medical Center.

In this upcoming webinar, Dr. Jones will present her research on ovarian cancer and how she has used the CGC to map the genome of chemoresistant ovarian cancer with multi-omic profiling. Ovarian cancer is the most lethal gynecologic cancer, with most patients diagnosed at late stage and succumbing to disease due to relapse and the development of chemo-resistance. Paired primary (chemo-naive) and relapse ovarian cancer tumors were profiled for the first time in this study, and revealed large scale conservation of gene regulation and expression throughout disease progression. Insights into the differences in Homologous recombination deficient and proficient tumors implicate differing immune evasion pathways and novel candidates for further study.

MORE ABOUT THE SPEAKER

Dr. Jones is a research scientist in the Center for Bioinformatics & Functional Genomics at Cedars-Sinai Medical Center. Her lab works on projects that apply genomics methods to improve our understanding of inherited risk for ovarian cancer, and mapping the somatic genome of ovarian cancer to improve our understanding of this lethal gynecological cancer.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Applications and workflows on the CGC: an update on available pipelines and how to run a GWAS on the cloud

This May, the CGC Webinar Series features a talk by Drs. Zélia Worman and Rowan Beck from Seven Bridges. Zelia is a Program Manager and Rowan is a Community Engagement Manager, both working on the Cancer Genomics Cloud.

In this upcoming webinar, they will talk about the new tools and datasets that are available on the Cancer Genomics Cloud (CGC), and will demonstrate how to run a Genome-wide association study (GWAS) on the CGC. With the growth of large-scale genomics, it’s hard to keep track of all the different tools and gold standards to analyze a particular dataset. The CGC not only hosts petabytes of public data integrated with the Cancer Research Data Commons ecosystem, but also provides the tools and pipelines to analyze it. As more data is added to the CGC, the public apps gallery has been updated to meet our users’ needs. In this webinar, we will highlight the new and updated applications and workflows to run variant calling, epigenetic studies, and long sequence reads, among others. We will also demonstrate how to perform a GWAS using the power of cloud computing.

Using the CGC, users have access to public genome cancer data without any requirement of software installation or system configuration. This setup  provides access to comprehensive pan-cancer genome analyses and facilitates data mining in wide research areas, such as therapeutic discovery process. As GWAS are fairly computationally intensive, using the cloud can provide an accessible platform for all researchers, particularly ones that do not have access to a high performance computing platform.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Bridging the gap between data scientist, clinicians and biologists using CRDC and CGC cloud resources

This April, the CGC Webinar Series features a talk by Dr. Daoud Meerzaman, Branch Chief of the Computational Genomics and Bioinformatics Branch (CGBB) at the Center for Biomedical Informatics & Information Technology (CBIIT), National Cancer Institute (NCI).

In this upcoming webinar, Dr. Meerzaman will talk about the Cancer Genomics Cloud (CGC) and the Cancer Research Data Commons (CRDC), and how these resources work together to bridge the gap between data scientists, clinicians and biologists. The recent explosion and ease of access to large-scale omics data provides a complex and vast framework for discovery. However, there are obstacles to optimal data management and analysis as the current bioinformatics tools require strong programming skills, but many scientists and clinicians do not have the expertise or the resources to go from data production, through bioinformatic and statistical analysis and ultimately clinical interpretation.

On April 28th, 2pm ET Dr. Meerzaman will highlight how the CGC can provide various approaches to mitigate these challenges. The CGC is a cloud based infrastructure that hosts data from different publicly available projects (such as the TCGA) and connects them with analytical tools to allow users to easily share, integrate, visualize and analyze these data. 

Dr. Meerzaman has published over 50 articles and served as an invited reviewer for multiple peer-reviewed scientific journals. You can find some of his work in the following review in the AACR Cancer Research Journal and research paper in Nature Biotechnology.

More about the speaker

MORE ABOUT US AND THE CGC

Seven Bridges is the leading biomedical data company, specializing in software and data analytics to drive public and private healthcare research. We deliver end-to-end bioinformatic solutions — including access to datasets, analytic workflows and algorithms, cloud-computing infrastructure, and scientific support — that speed the path from raw experimental data to new treatments and diagnostics.

The Cancer Genomics Cloud (CGC), powered by Seven Bridges and funded by the National Cancer Institute, is a flexible cloud resource platform that enables storage, analysis, and computation of large cancer datasets in the cloud. Since its launch in 2016, the platform has been continuously iterated with new applications and features to address the exponential growth and diversity of complex datasets. With the CGC, any user with an account can easily access petabytes of data, share it, analyze and use the computational power of the cloud without having to learn how to program and get familiar with several different data portals.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Genomic Alterations in Extraskeletal Myxoid Chondrosarcoma

The CGC webinar series is back in March, featuring a talk by Ms. Trudy Zou from the University of Pittsburgh School of Medicine, in Pittsburgh, PA, USA. Trudy conducts research primarily studying chondrosarcoma with Drs. Rebecca Watters and Kurt Weiss at the Musculoskeletal Oncology Laboratory (MOL). 

The Musculoskeletal Oncology Laboratory focuses on studying Extra skeletal myxoid chondrosarcoma (EMC), a rare sarcoma subtype with an indolent course and high rates of recurrence and metastasis to the lungs. In 70% of cases, it is characterized by the translocation of the NR4A3 gene on chromosome 9 to the EWSR1 N-terminal transactivation domain on chromosome 22.

In this webinar, Trudy will present an extremely rare primary EMC sample collected from a patient with matching lung metastasis, pelvic metastasis, normal lung, and blood available at the MOL lab. They used whole genome sequencing to identify structural variants that contribute to metastasis to the lungs and progression to pelvic metastases and that can be targeted for therapy. Trudy started using the Cancer Genomics Cloud in November 2021, and will be presenting the results of her and the lab’s work.

Trudy Zou is a medical student in the Physician Scientist Training Program at the University of Pittsburgh School of Medicine. She is primarily studying chondrosarcoma with Drs. Rebecca Watters and Kurt Weiss at the Musculoskeletal Oncology Laboratory (MOL). She earned her Bachelor of Science in cellular and molecular biology at Duke University, where she also studied drivers of metastasis and therapeutics for chondrosarcoma under Dr. Julia Visgauss. 

MORE ABOUT US AND THE CGC

Seven Bridges is the leading biomedical data company, specializing in software and data analytics to drive public and private healthcare research. We deliver end-to-end bioinformatic solutions — including access to datasets, analytic workflows and algorithms, cloud-computing infrastructure, and scientific support — that speed the path from raw experimental data to new treatments and diagnostics.

The Cancer Genomics Cloud (CGC), powered by Seven Bridges and funded by the National Cancer Institute, is a flexible cloud resource platform that enables storage, analysis, and computation of large cancer datasets in the cloud. Since its launch in 2016, the platform has been continuously iterated with new applications and features to address the exponential growth and diversity of complex datasets. With the CGC, any user with an account can easily access petabytes of data, share it, analyze and use the computational power of the cloud without having to learn how to program and get familiar with several different data portals.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.

Join us at our virtual Office Hours and ask any questions you may have and get help directly from Seven Bridges experts. We hold Office Hours on Tuesdays and Thursdays every week. All are welcome and encouraged to attend with any questions they may have. Click here to join the 10:00 am ET Tuesday and 2:00 pm ET Thursday office hours hosted by Dave Roberson.