Foundations of Computational Genomics Course

Visitor of the Week: Oscar Perez


Meet Oscar Perez, director of the Developmental Biology Laboratory 113 in the Pontificia Universidad Católica del Ecuador’s School of Biological Sciences, a graduate student in Dr. Federico Brown’s lab at the University of Sao Paulo, and the Ecuadorian representative in the Latin American Society for Development Biology Board. Oscar was on campus for two courses this year – Scientific Writing Retreat followed by Computational Genomics – but his history with CSHL started twelve years ago when he took his first CSHL course. We caught up with him to ask what keeps him coming back.

What are your research interests? What are you working on?
I am interested in the evolutionary comparison of reproductive strategies and early development of Ecuadorian chordates. My research is currently focused in the plasticity of oocyte organization and how this can modify the embryological events. I apply the comparative method in order to find molecular variations in oogenesis and embryogenesis of the Ecuadorian megadiverse fauna.

How did you decide to make this the focus of your research?
Since an early age, I was always interested in nature and I was fortunate to have a childhood surrounded by forests and open fields. I clearly remember hearing the Quito frogs singing in the cold nights and looking for bugs under the stones in the morning. I have to thank my mother for showing me a marvelous chicken birth and what I consider my very first exposure to embryology. Every child should have a similar opportunity.

How did your scientific journey begin?
I had the great fortune of working with great mentors with Dr. Eugenia del Pino, Dr. Richard Elinson, and Dr. Luis Coloma being the most influential to my scientific formation. I became extremely interested in embryological events while working with the outstanding Ecuadorian embryologist Dr. Eugenia del Pino. In her lab, I had the opportunity to be involved – for the first time – in the diverse and fascinating area of embryology by studying the embryos of Ecuadorian frogs which began my fascination for this almost unknown field of biology. My love for molecular techniques, evolution, and direct development came from Dr. Elinson’s expertise, and my passion for reproductive biology and ecology came from scientific interaction with the brilliant herpetologist Dr. Luis Coloma.

Was there something specific about the Computational Genomics course that drew you to apply?
There were three main reasons I applied for the Computational Genomics course in CSHL: 1) My previous experience in the CSHL Xenopus and live imaging training courses were brilliant; 2) The outstanding instructors listed for the genomics course; and 3) CSHL is considered one of the most prestigious scientific institutes in the world.

What and/or how will you apply what you've learned from the course to your work?
Undoubtedly, all the information I acquired from the course will be of great help in my research and institution. I have to say that my research in the non-model science world. Ecuadorian alternative models such as frogs, ascidians, and sea slugs do not have standardized molecular tools as in mice, Xenopus, or the human. Fortunately, in this course I learned of alternative ways to take advantage of modern computational tools to analyze transcriptomic data from my non-model species and still get informative results despite the absence of reference genomes and other existing tools that are easily obtained in human and mouse. Institutionally, my Computational Genomics training is very important because these skills can be shared with other laboratories and groups in collaborative investigations.

What is your key takeaway from the course?
The take-home message from the Computational Genomics course is that genomics is a flexible tool that can offer several alternative strategies to solve one single question. The experience of the genomics experts and mentors were extremely useful to learn how to effectively extract many hidden results from your data.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
My answer would say to complete all the homework sent by the instructors before the course. Even when you are not required to be an expert in the field, you must have a certain level of knowledge in order to get in the fast lane of learning. Also, bring data. If you have an unsolved problem in this regard, the Computational Genomics course is the right place to solve it.

How many CSHL courses have you attended?
Computational Genomics, 2018
Scientific Writing Retreat, 2018
Immunocytochemistry, In Situ Hybridization & Live Cell Imaging, 2009
Cell & Developmental Biology of Xenopus, 2006

Thinking back on your course at CSHL (Cell & Developmental Biology of Xenopus in 2006), did you notice differences or similarities between that course and Computational Genomics?
I still clearly remember how intense and diverse the training was at the Xenopus course in 2006 and, even after 12 years, that same level intensity and high quality of the courses in CSHL has remained the same. Although, considering the tasks sent weeks before the course started, preparation of a poster, and the mid-term test, I could even say that Computational Genomics might be more demanding than the 2006 course.

Since your first two CSHL courses, your career stage has changed. Given your present position, did your experience in the course change in any way?
Course features such as intensity and quality of the knowledge offered are contrastable; however, it is without doubt that CSHL offers first-rate courses instructed by leaders in the field of science. Over the years, my capacity of appreciating this knowledge has evolved. When I was a younger researcher, I did not fully appreciate how great an opportunity it was to train and be trained in one the most prestigious scientific institutes in the world. But, as my experience has expanded, I have become more aware of the magnitude of having opportunities to learn and to learn from such a source.

What do you like most about your time at CSHL?
The confidence that you acquire by mastering specific techniques. The rate of learning in CSHL is very high as is the demand and complexity of the courses. It is great to have the opportunity to ask your questions to pioneers, leaders, and scientific experts that collaborate with CSHL to teach and share their knowledge. 

Oscar received a fellowship from Pontificia Universidad Catolica del Ecuador (PUCE). On behalf of Oscar, thank you to the PUCE for supporting and enabling our scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Oscar 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.

Repeat Visitor: Sumangala Shetty


Every so often, we host a course trainee multiple times in a year. One such trainee from 2017 is Sumangala “Suma” Shetty, a research and teaching specialist at Paul Copeland’s lab in Robert Wood Johnson Medical School – Rutgers University. 

Suma made her debut at CSHL Meetings & Courses six years ago when she attended the 2012 Translational Control meeting. She still clearly remembers being surprised by the “talks [going] past 10 PM” and that “attendance was still at its peak during the evenings”. Last year, Suma returned to CSHL to attend three courses – The Genome Access Course, Scientific Writing Retreat, and Computational Genomics – and from our conversation it doesn’t seem like we’ve seen the last of her. 

Tell us about your research interests and what you’re working on. 
My research focuses on understanding the mechanism of synthesis for a specialized group of proteins referred to as selenoproteins. Selenoproteins play a crucial role in cellular homeostasis, thyroid hormone metabolism, redox regulation, storage and transport of selenium, protein folding, and signaling skeletal muscle regeneration.

The Genome Access Course, Fall Session, 2017

The Genome Access Course, Fall Session, 2017

We offer roughly 30 courses per year and you participated in three of those courses last year. How did you decide which courses to apply for?
In concert with my want to transition into an independent scientist, I have been focusing on developing new skill sets to keep pace with emerging data mining techniques and high-throughput screening methods for genomic data analysis. Since independent research relies on grant funding, I was interested in a workshop that focused on grant writing. Similarly, I surveyed for courses on bioinformatics and data analysis tools. There are several online tools and resources, and I have acquired several online certificates for data analysis as well as developed programming skills using Python. But I was longing for face-to-face interaction with fellow beginners to discuss pitfalls and potentials, and, most importantly, get feedback. 

Keeping in mind my two goals and learning environment criteria, I consulted my mentors for advice. In addition, in December 2016, I attended a CRISPR workshop by NIH where I met Dr. Vielka Selezar. At that point in time she had just joined Cape Breton University (Canada) as a new faculty member and was in a similar situation as me so I asked her for advice. She shared with me her learning experience at CSHL’s Computational Genomics course and highly recommended it. Interestingly, when I visited the CSHL website, I found several other courses that suited my needs and I narrowed down the list to the three most relevant for my career. 

What is your key takeaway from each of the three courses?
I totally enjoyed each of the courses, especially given their highly-interactive setups. The Genome Access Course exposed me to a rich collection of databases and tools. It was so engrossing and involved that I didn’t even need my second shot of caffeine in the afternoon! Totally loved it and, in fact, I think The Genome Access Course should be made mandatory for all graduate students.

Scientific Writing Retreat, 2017

Scientific Writing Retreat, 2017

My second course was the Scientific Writing Retreat. This workshop was an eye opener for several reasons: 1) It taught me how to overcome writer’s block and clean a draft for clarity; 2) I learned inside information on how a manuscript submitted to a journal is reviewed and how to improve the chances of it being accepted; 3) I chatted with a grant writing expert; and 4) The one-on-one review of my manuscript draft was, in my opinion, the best feature of this course. At the end, I felt like my fellow participants, the mentors, and I had become a tight-knit network that I could always approach with any of my tough writing issues. Charla and Steve thank you very, very much. 

And finally, Computational Genomics was the most intense and most exciting seven-day course I have ever attended. We were in class almost all day till midnight and still every one of us showed up at 9:00 the next morning. It was highly informative and full of new tools to explore. My favorite part was working in teams on our take-home midterm exam and also on our final project, because I learnt a lot from my course mates. Also, through an online course on genomic data analysis by Johns Hopkins University, I had heard lectures from James Taylor and Jeff Leek but it was cool and an honor to meet and hear them in person at the course. They were extremely helpful, very humble, and the course was much more fun than an online course. 

One similarity I noticed that was consistent in the three courses is that all of the course mentors were highly motivated and inspiring. They were extremely helpful, always available, and their enthusiasm was infectious.

Have you already applied what you learned from each course to your work?
I am using the data analysis tools on our pre-existing RNA-seq and proteomics data, and currently, we are storyboarding some new applications for our project using genome analysis tools. Also, tips from the Scientific Writing Retreat enabled me to finish my manuscript. 

Computational Genomics, 2017

Computational Genomics, 2017

If someone interested in a CSHL course asked you for advice, what would that be?
After my experience, I strongly believe that CSHL courses are a crucial resource for learning current techniques under the direct supervision of the experts. I think a stronger awareness about CSHL courses should be raised among graduate students and postdocs; and therefore, I would strongly encourage those interested in a CSHL course to apply. A number of the courses post their past lectures online so it’s easy to browse the content and analyze if the course will suit your needs.

Our readers are curious about how course tuitions are funded. Would you like to share how you were able to pay for three courses in one year? 
I am fortunate in that my PI, Paul Copeland, strongly supports my career growth. We both agreed that expanding my skill set will add new insights to our current projects and, therefore, I received financial support for my courses from Paul.

What did you like most about your time at CSHL? 
The intensity and enthusiasm of everyone I met. More importantly, the one-on-one interaction and personalized discussion with experts on our individual projects.

Do you have any future plans to attend another course or, perhaps, a meeting at CSHL?
Absolutely yes. The CSHL Meetings & Courses website is in my browser favorite list, and I am already planning to apply for the Statistical Methods for Functional Genomics course. 

Thank you to Suma for sharing with us her experience. We look forward to having her back at the Laboratory soon. 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: Seda Arat


Meet Seda Arat of The Jackson Laboratory in Farmington, CT. Seda is a postdoctoral associate in the field of Computational Genetics and Systems Biology, and is a part of Greg Carter's lab. She made her first trip to CSHL for the 2017 Foundations of Computational Genomics course. 

What are your research interests? What are you working on?
My long-term research interests involve analyzing high-throughput sequencing data and computational modeling of biological systems. I am currently working on understanding the molecular regulation of mammalian meiosis from a computational analysis perspective.

Was there something specific about the Foundations of Computational Genomics course that drew you to apply?
My current projects require deeper understanding of analysis of protein-DNA binding and histone modifications. And since I am a mathematician by training, I wanted to have a fundamental and comprehensive understanding of sequencing techniques and computational methods in genomics.

What is your key takeaway from the Course?
It was something Jeff Leek, one of our instructors, said: “Look at your data." And to do so in each and every step of the analysis. 

Seda with fellow course trainees finalizing their end-of-course group project.

Seda with fellow course trainees finalizing their end-of-course group project.

How many CSHL courses have you attended? Any plans to attend a near future CSHL course and/or meeting? 
This was my first CSHL course, and I plan to attend Statistical Methods for Functional Genomics and/or Advanced Sequencing Technologies & Applications next year.

If someone curious in attending a future iteration of this course asked you for feedback or advice on it, what would you tell him/her?
It is a fast-paced and intense course, which consists of a very nice blend of lectures, hands-on workshops, and group projects. I would definitely recommend bringing your own data and biological questions so you're able to conduct more investigations and learn different perspectives and approaches from others. 

What do you like most about your time at CSHL?
My time at the course was, I think, one of the most productive periods of my life! I love being able to focus on nothing but learning, applying, and collaborating and, since I didn't have to worry about commuting or cooking, I was able to do just that during my time here - that was great!

Thank you to Seda 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.