Junior Researcher Spotlight Yingnan Ju - HIVE MC-IU
Yingnan Ju is a Ph.D. student in Intelligent Systems Engineering at Indiana University, Bloomington, working with Professor Katy Börner. Yingnan received his master’s degree in software engineering from Peking University before working as a software engineer at Microsoft Research Asia, where he focused on augmented/mixed reality (AR/MR).
His research at IU is centered around data visualization, computer vision, and machine learning. For his Ph.D., he is developing different methods to visualize the structure, function, and results of CNN algorithms in support of algorithm optimization, validation, and teaching.
For HuBMAP, Yingnan has been working on single cell and glomeruli segmentation for kidney tissue and the computation of distances between different cell types in support of a vasculature based common coordinate framework.
While working from home, Yingnan enjoys his four monitors and is considering adding more. In his free time, he likes biking, hiking, and doing exercises with Nintendo Switch. He is also an avid pumpkin carver. Happy Autumn!
Have a junior researcher in your group who has been contributing to goals of HuBMAP? Please contact help@hubmapconsortium.org with the subject "Junior Researcher Spotlight" to arrange a feature.
Reminder: HIVE Quarterly Progress Reports Due October 1
September Demo Day
"Thank You!"
A special thank you to the HIVE - Indiana University Mapping Component for their coordination of our September Demo Day. The two-day meeting featured guest speakers, lessons learned/opportunities to improve from our inaugural data release, identifying priorities for the future, and connecting with one another virtually. Meeting proceedings and will be posted once the recordings are available.
NIH-HCA: CCF ASCT+B Tables Meeting
When: October 10, 2020 @ 1:30 PM ET.
Agenda:
Presentation and discussion of ASCT+B MASTER tables
Skin
Vasculature
Table Data Entry Standardization (Carol Goble's team, University of Manchester)
KPMP Ontologies (Oliver He, U Michigan)
If you would like to attend but don't see a Zoom invite in your calendar, please register and share more info on your expertisehere.
Upcoming Meetings
Wednesday, September 23 @ 10 AM -
DRT Portal
Thursday, September 24 @ 4 PM - Communications & Engagement
The National Human Genome Research Institute (NHGRI) and the Eunice Kennedy Shriver National Institute for Child Health and Human Development (NICHD) are co-collaborating on a new initiative, developmental Genotype-Tissue Expression (dGTEx), to catalog and analyze transcriptional profiles from a wide variety of tissues from the pediatric period, including neonates through adolescents, in a post-mortem setting.
UC San Diego Institute for Genomic Medicine Symposium on Spatial Omics
The UC San Diego Institute for Genomic Medicine is holding a virtual symposium on Monday, October 26, 2020. This meeting calls scientists from across the United States to come together and contribute their cutting-edge ideas on "Spatial Omics.” As a platform for researchers to discuss the latest advancements on spatial gene expression, this meeting strives to glean novel insights into the role cell-type specific regulatory mechanisms play in complex traits. It is in conjunction with the virtual American Society of Human Genetics meeting occurring on October 27th through October 30th, 2020.
HuBMAP PIs Long Cai and Katy Börner will be presenting.
The course opened Tuesday, September 1, 2020 in parallel with the 1st HuBMAP Portal Release. It will welcome students continuously until the 2nd HuBMAP Portal Release begin of January 2021.
The course aims to provide you with:
Theoretical and practical understanding of different single-cell tissue analysis techniques.
Expertise in single-cell data harmonization used to federate data from different individuals analyzed using different technologies in diverse labs.
Hands-on skills in the design and usage of semantic ontologies that describe human anatomy, cell types, and biomarkers (e.g., marker genes or proteins).
Knowledge on the design and usage of a semantically annotated three-dimensional reference system for the healthy human body.
An understanding of how the HuBMAP reference atlas might be used to understand human health but also to diagnose and treat disease.
NASA is requesting $28 billion to return to the moon and construct a small restaurant.
It may have great food, but no atmosphere.
HIVE Infrastructure
Developers in need of HIVE infrastructure may request access through the PSC web form, foundhere.
Instructions for using HIVE infrastructure can now be found in the "Quick Links" section of the Collaboration Portal. A direct link to this documentation can be found here. Please report any issues or direct any questions to help@hubmapconsortium.org.
Content Suggestions
The IEC is seeking to collect information of general interest from individual members and groups to share with the rest of the Consortium. Please submit content suggestions by emailing admin@hubmapconsortium.org.
Past Newsletters are available on the Collaboration Portal.
For comments, suggestions about how to improve the HuBMAP Happenings, or questions about the consortium, please contact: help@hubmapconsortium.org
