Visitor of the Week: Natasha Pacheco

Meet Natasha Pacheco of the Inova Translational Medicine Institute where she is a postdoctoral research fellow. Natasha is on campus for this summer’s Statistical Methods for Functional Genomics course which makes this her fourth time at the Laboratory. Her CSHL course and meeting history includes the 2015 Biology of Genomes, 2016 Programming for Biology course, and 2017 meeting of Genome Informatics.

What are your research interests? What are you working on?
I’m broadly interested in using bioinformatics applications to understand how genetic variants contribute to different diseases. My current research project focuses on characterizing noncoding DNA regulatory elements in congenital heart disease (CHD), with the ultimate goal of identifying genetic variants within noncoding DNA elements in CHD patients.

How did you decide to make this the focus of your research?
The need to understand the functional roles of noncoding DNA elements has long been recognized, yet it’s fascinating to me how little we know about basic concepts like what defines a noncoding DNA element. Before we can begin to address how different genetic variants could affect a noncoding DNA element’s functional role, we need better definitions of what noncoding DNA elements are and what their targets are under normal biological conditions.

How did your scientific journey begin?
I first got inspired in 8th grade when my science teacher played the movie Lorenzo’s Oil. This movie is based on a true story about a young boy diagnosed with the genetic disorder Adrenoleukodystrophy (ALD). I was so amazed by how such a seemingly small change in a single gene could cause such a devastating disorder like ALD. I knew then that I wanted to understand how genetics influences health and disease.

Was there something specific about the Statistical Methods in Functional Genomics course that drew you to apply?
My research project requires the integration of different types of bioinformatics tools and large “omics” data sets. I quickly realized that I needed a more solid foundation of the underlying statistics for many of the bioinformatics tools I need to use, and how to pick and use the best bioinformatics tools for my research needs.

What and/or how will you apply what you’ve learned from the course to your work?
So far I’ve learned how important it is to understand your data set and the question(s) you’re trying to ask, as well as great tools in R and Bioconductor to analyze and visualize different types of data.

What is your key takeaway from the course?
Really spend time to understand the statistics behind different bioinformatics tools, as different statistics can address different questions and affect how you interpret your results.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
I would say ask lots of questions, take advantage of all the great instructors’ expertise, and get plenty of rest before arriving for the course!

What do you like most about your time at CSHL?
I love walking around the campus and taking in the beautiful landscape, it’s a great way to clear my mind and come back to class refreshed and ready to learn.

Thank you to Natasha 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: Jonathan Diedrich

Meet Jonathan Diedrich of the St. Jude Children’s Research Hospital (SJCRH) in Memphis, TN. Jonathan is a postdoctoral fellow in Dr. Daniel Savic in the Pharmaceutical Sciences Department. He is on campus for the Statistical Methods for Functional Genomics course and we’re hoping to have him back for The Biology of Genomes meeting next year. 

What are your research interests? What are you working on?
My project employs functional genomic techniques to identify non-coding regulatory elements involved in chemotherapeutic drug resistance in childhood acute lymphoblastic leukemia.  

How did you decide to make this the focus of your research? 
I have always wanted to transition into the functional genomic field because I thoroughly believe that functional genomics and large-scale data analysis is the future of cancer research and precision medicine. As a postdoc in an extremely collaborative and supportive environment, I am in an excellent position to learn cutting edge functional genomic techniques and hone my analytical skills. 

How did your scientific journey begin? 
I actually started my research “career” in zoology! I studied comparative anatomy of carnivore skulls at Michigan State University where I fell in love with the research aspect of science and quickly knew I wanted to transition into the cancer field. I completed my PhD in Cancer Biology at Wayne State University with Dr. Izabela Podgorski as my mentor. My thesis project was to interrogate the effects of bone marrow adipocytes on metastatic prostate tumor progression. Dr. Podgorski’s exceptional mentoring and support during my PhD inspired me to pursue a career in academia; I am now in the first year of my postdoc and very excited for a career in science!

What and/or how will you apply what you've learned from the course to your work? 
Being competent in statistical analysis in the field of functional genomics is extremely crucial and this course has helped me develop my skills to become the expert in Dr. Savic’s laboratory regarding various statistical analyses for large-scale RNA-seq, ATAC-seq, ChIP-seq, and 3-dimensional profiling datasets. My participation in this course will benefit my data analysis as well as the members of my laboratory and department at SJCRH. I will be able to assist in the analysis and scientific discussions of my team and become an integral asset in functional genomic analyses.  

What is your key takeaway from the course?
The most important takeaway from this course is to understand the conceptual reasoning behind the complex analyses performed to evaluate large-scale genomic datasets, and to efficiently utilize the programs to visualize and interpret your data in a reproducible and reliable manner.  

How many CSHL courses have you attended?
This is my first course at CSHL and I am planning on hopefully attending next year’s Biology of Genomes meeting. I am very excited about the possibility of going!

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Be prepared to learn a lot! This is an amazing opportunity for anyone interested in functional genomics to learn directly from the experts in the field, so take full advantage of the course while you are here! To keep pace, practice maneuvering through R and get familiar with basic R syntax ahead of time. Also, don’t be afraid to ask as many questions as possible! The instructors are amazing, very eager to help, and want you to get as much as you can out of this course. 

What do you like most about your time at CSHL?
The best (non-science related) aspect of this course is the ability to meet and network with people from all over the world and who have similar interests and experiences. I have met so many great people within the first (of two) weeks I have been here and hopefully will have lasting friendships and future collaborations!

Thank you to Jonathan 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: Elitsa Stoyanova

Meet Elitsa Stoyanova of The Rockefeller University! The Nathaniel Heintz lab member and graduate student makes her first visit to campus for the Statistical Methods for Functional Genomics course. Elitsa shares with us the reasons that attracted her to apply to and attend the annual course, and advice useful for future trainees.

What are your research interests? What are you working on? 
My research interests are in neuroscience and epitranscriptomics. I currently study the epigenetic regulation of gene expression in the mouse cerebellum during development.

Was there something specific about the Statistical Methods for Functional Genomics course that drew you to apply? 
The main reason I wanted to attend this course was to establish and expand my network of peers. Having a support system that also doubles as a resource for collaborations and inspiration is a tremendous asset for every scientist. Furthermore, I wanted to strengthen my statistics and genomics skill set and to gain exposure to the newest techniques in the field. I am happy to share that I accomplished both of my goals through the course.

What is your key takeaway from the Course?
My key takeaway from this course is that there is always more to learn and there is always room for improvement. Now, I feel confident to share and discuss genomic analysis and I am looking forward to apply all the skills I acquired to my graduate thesis.

How many CSHL courses have you attended? How about CSHL meetings? 
So far I have only attended the Statistical Methods for Functional Genomics course, but I would love to take another one! And I have not planned to attend a meeting yet, but I’d be thrilled to come back and present my research.

If someone curious in attending your course asked you for feedback or advice on it, what would you tell him/her?
I would tell them to refresh their statistics and get ready for two intense weeks of learning!

What do you like most about your time at CSHL?
I absolutely loved our sailing trip in Oyster Bay and talking about the rich history of the area. 

Thank you to Elitsa 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.