Welcome Dr. Li Song to the CQB
Dr. Li Song joined the CQB as a Project Leader in May of 2023. His project “Predicting TCR and BCR specificity to microbiomes by massively mining RNA-seq samples”, seeks to develop novel computational methods to more efficiently process huge amounts of raw sequencing data in order to extract microbiome and immune repertoire information and, ultimately, associate T-Cell and B-Cell receptors with their microbiome binding targets.
Congratulations to our Latest Pilot Awardee
We have awarded Dr. Duncan Morhardt, Assistant Professor of Surgery with a pilot grant for his project “Spatial transcriptomic dissection of the vertebrate urinary development program using zebrafish” in which he will catalogue the expression landscape of urethral development in zebrafish in order to increase our understanding of genitourinary development and of its congenital malformations. Read more about Dr. Morhardt’s project.
Team Science Supplements Awarded
We are excited to announce that two Team Science Supplements have been awarded to CQB Project leaders! These supplements support the development of team science projects that bring together two or more investigators from IDeA (Institutional Development Award) states with different perspectives and expertise to address complex basic, behavioral, clinical and/or translational research questions with complementary approaches.
“Multi-omics modeling of bacterial metabolism and effects on immune physiology”
Dr. Anne Hoen, Associate Professor, Epidemiology
Dr. Benjamin Ross, Assistant Professor, Micro Immunology
Dr. Li Song, Assistant Professor, Biomedical Data Science
Dr. Mark Sundrud, Professor of Medicine; Professor of Immunology and Microbiology
Using a novel multi-omic approach to investigate the impact of key microbiota-derived metabolites on host gene expression, and leveraging the diverse expertise of the awardees, this project will provide comprehensive datasets and new models which will facilitate a greater understanding of host-microbe-metabolite interactions in the gut.
“Defining the pathogenic role of myeloid cell populations in glomerulonephritis using Spatial Transcriptomics and DNA Methylation”
Dr. Sladjana Skopelja-Gardner, Assistant Professor, Medicine
Dr. Lucas Salas Diaz, Assistant Professor, Epidemiology
Studying how myeloid cells mediate glomerulonephritis, this project will help identify potential targetable pathways to prevent lupus nephritis flares and develop a non-invasive approach to define myeloid cell contributions to kidney disease through novel urine DNA methylation approaches.
Cloud Computing Supplement Awarded
Dr. Shannon Soucy and Mr. Timothy Sullivan of the CQB Data Analytics Core* have been awarded a cloud computing supplement to evaluate and optimize cloud compute systems for genomic data science. They will disseminate their findings through training documentation and pass on new advances to users through decreased cost and shorter turnaround times.
Data Analytics Core Summer Interns
This summer three interns are working with the CQB DAC, assisting the core and gaining valuable experience in Data analytics.
Andrew Huang – A rising Junior at Berkley College in California focusing on pipeline development and optimization of computational resources.
Yuxuan Peng – A QBS (Quantitative Biomedical Sciences) master’s student with a BSc in Biology from the University of Washington in Seattle. This summer she is researching cutting edge analytic methods, performing data analysis, interpreting results, and authoring analytic reports.
Anton Hung – A QBS master’s student with a BSc in Health Informatics from Western University in Toronto. This summer he is researching cutting edge analytic methods, performing data analysis, and developing code to improve results reporting.
“Data analytics is one of the most in-demand skills in the workforce. The collaboration between the Genomic Data Analytics Core Summer Internship program and the Quantitative Biomedical Sciences program at Dartmouth helps train future leaders in the field — and fill critical research needs within our community.”
– E. Chandlee Bryan, M.Ed.
Career Services Manager, Geisel School of Medicine at Dartmouth
Workshops and Seminars
UPCOMING! Spatial Transcriptomics on the Visium CytAssist Platform Seminar
Please join Thursday, September 21st, 12:00pm-1:30pm at DHMC, Auditorium E for a joint seminar between 10x Genomics and Illumina showcasing the latest developments in spatial transcriptomics using the Visium CytAssist platform. Learn more and register by September 18th!
RNA-seq Data Analysis Workshop
The Data Analytics Core ran a four-day RNA-seq Data Analysis Workshop in June which introduced bulk RNA-seq data analysis, with an emphasis on differential expression analysis.
40 Attendees
- 19 Dartmouth
- 21 External
“I have tried a few RNA seq workshops and this one has by far been the most helpful. I really appreciated being able to understand what each line of code means.”
-Workshop Participant
Grant Program
10x Genomics and the Center for Quantitative Biology are teaming up for a grant program to support an innovative research project at Dartmouth. The winner will receive a Visium CytAssist slide, library prep and sequencing at no cost. Applications can be submitted HERE, through October 27th, 2023.
Self-Guided Data Science Training Modules
The NIGMS has supported the creation of a series of self-guided data science training modules that leverage cloud compute resources to analyze a multitude of data types and analytic procedures. The NIGMS and NH-INBRE are providing cloud credits to 10 people per cohort which will provide access to all NIGMS data science training modules for 6 weeks at a time. If you are interested, please contact Shannon Soucy (Shannon.Soucy@dartmouth.edu) by September 29th to be part of the 3rd cohort! The cohort will start September 30th and credits will expire on November 13th. Training modules include Fundamentals of Bioinformatics created by our own CQB DAC! For more information and a full list of modules visit: https://sites.dartmouth.edu/cqb/2023/09/12/self-guided-data-science-training-modules/
https://sites.dartmouth.edu/cqb/
Please CITE US! CQB COBRE grant from NIGMS (P20GM130454) For more information on citing the grant, https://sites.dartmouth.edu/cqb/cite-cqb-support/