Single Cell Analysis Course

Visitor of the Week: Marek Svoboda

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Meet Marek Svoboda of Dartmouth College. Marek is a PhD Student in Quantitative Biomedical Sciences and a member of Dr. Giovanni Bosco’s lab. He is wrapping up his two-week training at our Single Cell Analysis course and is considering to attend our Single Cell Analyses meeting this fall.

What are your research interests? What are you working on?
I am using a mouse model of Autism Spectrum Disorder (ASD) with a mutation in a specific gene (PTEN) to characterize the molecular pathways responsible for the developmental abnormalities observed in humans. In my research, my goal is to move us closer to an effective treatment of ASD by combining medical knowledge with wet lab and computational techniques.

How did you decide to make this the focus of your research?
My main interests lie in neuroscience and genetics, both of which are essential for the study of Autism, an increasingly prevalent developmental disorder in children. In my future, I would like to become both a researcher discovering new ways to treat neurological diseases and a physician delivering those directly to patients.

How did your scientific journey begin?
I have always been interested in psychology and the inner workings of the human mind. At high school, I was inspired by my amazing Biology teacher and the more I learned about the human body, the more I wanted to understand the nervous system and the associated pathology. Later in college, I decided to become a physician-scientist with a focus on neuroscience.

Was there something specific about the Single Cell Analysis course that drew you to apply?
I am the only person doing single cell RNA sequencing (scRNA-seq) in my lab, and the only person doing scRNA-seq of neurons at my institution. Therefore, my primary motivation has been to acquire some of the more advanced wet lab and analytical skills for this technique. More generally, though, I personally believe that the ability to extract a wealth of information from individual cells bears an incredible potential for the future of personalized medicine. While I am using scRNA-seq in my own thesis research project, I hope to combine it with other single cell techniques in my future research and maybe even clinical practice.

What and/or how will you apply what you’ve learned from the course to your work?
I have already learnt some of the basic analytical processing steps for the data that I will obtain from my own experiments, which I am really excited about – though, I know more is yet to come! I really like the combination of wet lab and bioinformatics that this course offers. At Dartmouth, I am a member of the Single Cell Interest Group, and so I am also looking forward to sharing all the cool single cell techniques and other ideas with my colleagues back home.

What is your key takeaway from the Course?
There is so much more to single cell analysis than just RNA! Depending on the question, it may be a good idea to complement the transcriptomic data with the other ‘omics’ approaches, which are all fairly doable – with the right guidance and resources, of course.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Make sure to have as few outside commitments during the course as possible, as the course itself is relatively intense and at the same time absolutely worth it. Come here ready to work hard, learn a lot, but also socialize and meet new people. Be mindfully present every second of the course, as the time spent here is extremely valuable!

What do you like most about your time at CSHL?
I really appreciate the fact that during the course, the conditions are perfectly conducive to what we are meant to focus on here. The course is extremely well-organized: one day we show up to lab and it is ready for RNA extraction. The next day, as if by a miracle (in fact, by tireless work of TAs, often into the late night), the lab is ready for confocal microscopy. Everything we need is available to us here all the time, and the atmosphere at CSHL feels very welcoming overall. As a result, taking a course at CSHL is a worry-free experience that creates a wealth of lasting memories.

Marek received financial support from Regeneron to cover a portion of his course tuition and a Research Alumni Award from Dartmouth to specifically attend this course. On behalf of Marek, thank you to Regeneron and the alumni of Dartmouth’s graduate program for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Marek for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Claire Olingy

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Meet Claire Olingy of La Jolla Institute for Allergy and Immunology (LJI). Claire is a postdoctoral fellow in Catherine “Lynn” Hedrick’s lab in the Division of Inflammation Biology. She’s participating in her first course at CSHL: Single Cell Analysis

What are your research interests? What are you working on?
I am interested in the role myeloid immune cells play in anti-tumor immunity during cancer progression and metastasis. I’m currently working to understand whether we can leverage these cells as early diagnostics and to enhance patient responses to immunotherapies.

How did you decide to make this the focus of your research? 
Cancer is the second leading cause of death in the United States after heart disease, yet there is still so much we don’t understand about this diverse group of diseases. During my PhD in biomedical engineering, I became increasingly interested in the role that the immune system plays in health and disease. Our immune systems are really involved in everything! I closely followed the success stories of cancer immunotherapies and recognized the immense potential the field holds, both for treating cancer and many other diseases. This inspired me to pursue a postdoctoral fellowship at La Jolla Institute for Allergy and Immunology in the lab of Lynn Hedrick, who is a leader in myeloid cell biology. LJI is a great place to learn about and conduct immunology research because you are surrounded by experts and have access to the resources necessary to study important questions in immunology.

How did your scientific journey begin? 
I have always loved math and knew I wanted to study engineering in college. However while I was in high school and my grandfather was diagnosed with colon cancer, I realized I also wanted to work in a field where I could have an impact on human health. I majored in biomedical engineering at my grandfather’s alma mater, Washington University in St. Louis. I became involved in undergraduate research and recognized that research would give me the opportunity to better understand and contribute to unanswered questions in biology and medicine.

Was there something specific about the Single Cell Analysis course that drew you to apply?
I applied to the Single Cell Analysis course because of the diversity of techniques the course offered to study cells at the single cell level, including bioinformatics tools to analyze single cell data. Some of these techniques can be intimidating for a first-timer like myself so I was looking for exposure, as well as how to appropriately design experiments in my research. Initially, I was most interested in the single cell sequencing approaches this course covers, but many of the skills I’ve so far learned in the first week could be applied to my research. 

What and/or how will you apply what you've learned from the course to your work? 
The immune system is extremely heterogeneous so that it can respond to the wide range of pathogens and diseases our bodies face. The techniques I’ve learned in this course will enable me to study this diversity during the progression of cancer, which is really only possible with single cell approaches. And I’m looking forward to sharing what I’ve learned with my labmates and collaborators at my home institution.

What is your key takeaway from the course?
The instructors did a great job designing this course so that it highlights a lot of exciting technologies that are being used in a wide range of biological fields. My key takeaway is that it can be very valuable to look to other fields for inspiration that can be applied to my own work. I’ve also learned that understanding how new technologies work before applying them to my research is critical when it comes to designing experiments that will actually answer the scientific questions I’m interested in.
 
If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I think it’s important to come to this course with a willingness to learn new techniques outside your immediate field and to consider how you may be able to expand your own research. Many of my peers (including myself) came primarily to learn about a specific technique, but to me, one of the most valuable takeaways is the new ideas we’re bringing back to our home institution. Also, to ensure you get the most out of this course, spend time before the course learning some basic programming! 

What do you like most about your time at CSHL?
I have most enjoyed getting to know a really diverse group of scientists who are at different stages in their scientific journey, studying different fields, and from all over the world. Everyone is here to learn and the beautiful CSHL environment makes it a really enjoyable experience!

Claire received a fellowship from the Helmsley Charitable Trust to cover a portion of her course tuition. On behalf of Claire, thank you to the Helmsley Charitable Trust for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Claire for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Kenny Yu

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Meet Kenny Yu of the University of Manchester (United Kingdom). Kenny, a NIHR Academic Clinical Lecturer (which is the U.S. equivalent to a resident with a research component in his/her training) at his home institution, is currently at St. Michael's Hospital (Canada) to conduct his research at Peter Dirks' lab. The Single Cell Analysis course brought the CSHL first-timer onto our campus where he expanded his research technique repertoire and established lifelong connections.

What are your research interests? What are you working on? 
I am a neurosurgeon-in-training from the UK and did a PhD during my residency. My specific interest is in the tumor infiltrating immune cells in brain tumors. 

Was there something specific about the Single Cell Analysis course that drew you to apply?
Being a novice to the single cell analysis field, I was drawn to the combination of practical modules and the subsequent data analysis that this course offered.

Kenny Yu delivering his student presentation towards the end of the course.

Kenny Yu delivering his student presentation towards the end of the course.

What is your key takeaway from the Course?
Single cell technology is a powerful technique that is able to probe tissues in unprecedented detail, and this course has opened my eyes to a wide range of potential single cell technologies.

If someone curious in attending your course asked you for feedback or advice on it, what would you tell him/her? 
The emphasis on taking a single cell experiment from cell isolation to RNA extraction, sequencing and subsequent analysis is a fantastic learning experience, and to interact with world-class faculty and cutting edge technology is invaluable. I would recommend this course without hesitation. 

What do you like most about your time at CSHL? 
I have met a great group of people who, hopefully, will become both lifelong friends and collaborators!

Kenny received a stipend from the Howard Hughes Medical Institute (HHMI) to cover a portion of his course tuition. On behalf of Kenny, we want to thank HHMI for continuing to support and enable young scientists to attend a CSHL course to expand their skills, knowledge, and network. 

Thank you to Kenny for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course – go here.