Bioinformatics

Visitor of the Week: Maggie McCoy

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Meet Maggie McCoy of Syracuse University. The first year graduate student is a member of Dr. Melissa Pepling’s lab and is about to embark on a new lab project that will require the analysis of large genomic data sets. She came down to Cold Spring Harbor for her first CSHL course – The Genome Access Course – where she participated in an intensive two-day introduction to bioinformatics and the various tools available to her and her work.

What are your research interests? What are you working on?
I am interested in reproductive biology, specifically how female eggs (oocytes) develop. Women have about 6-7 million eggs while they are in-utero, but before birth women will lose about 2/3 of their eggs and this decline continues throughout development. Our lab studies this phenomenon in mice. Female mouse germ cells undergo a series of incomplete cell divisions resulting in clusters called cysts. Soon after birth, mouse germ cell cysts break down into individual oocytes to form primordial follicles. During cyst breakdown, a subset of oocytes in each cyst dies by programmed cell death with only a third of the initial number of oocytes surviving. The long-term goal of our work is to understand the mechanisms that regulate cyst breakdown, and why this early oocyte loss occurs.

How did you decide to make this the focus of your research?
My mother had children at an older age, and now that I’m studying reproductive biology, I realize how fortunate my mother was to be able to have children when she was ready. Sometimes I think women feel biological pressures to have kids while they are younger because reproduction can become much harder later in life and egg loss increases with age. Males, on the other hand, can constantly produce sperm throughout their lives. This biological dilemma was what drew me to reproductive biology research.

How did your scientific journey begin?
I was always interested in science; constantly begging my mom to let me mix cornstarch and water because it made such a cool dynamic mixture. In high school I took AP chemistry with an awesome teacher who really pushed us to understand the material at a broader level, and how we would apply this. For my final project in that class I synthesized polymer strings from two different chemicals and was able to collect these “strings” and braid them. Watching something physical and 3D be made from solutions was incredible.

Was there something specific about The Genome Access Course that drew you to apply?
I am starting a new project in the lab that will look into how anesthesia administered to a pregnant subject may affect the germ cells of the offspring. I will need to analyze genomic data with bioinformatic tools. Our lab doesn’t often work with large genomic data sets, so I thought this course would be a good introduction into genomic work.

What and/or how will you apply what you’ve learned from the course to your work?
I learned a lot about available bioinformatic tools that will help me with my work; such as ENSEMBL, Encode and galaxy that can used to analyze data. Before this course I didn’t know many of these sites existed or how to access them.

What is your key takeaway from the course?
There is so much research that can be done from genomics work, and there are so many tools to help you analyze your data. One of my biggest takeaways was that because there are so many tools available, it can be hard to know which genome browser you should use, or what filter to set. While this is true, the instructors emphasized that I shouldn’t be afraid to play around with different data sets and see how different analysis tools work because the only way to become comfortable with bioinformatics work is to practice.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
Definitely take it! Even if you have never worked with genomic data before, don’t be scared. This course will introduce you to so many bioinformatic tools and allow your research to grow.   

What do you like most about your time at CSHL?
The campus was breathtaking. I had never been to Long Island before, and the Cold Spring Harbor Laboratory did not disappoint. It was a great opportunity to connect with other people from different backgrounds and see how we are all using genomics and bioinformatics in very different ways.

Thank you to Maggie 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: Paola Silveira

Photo provided by Paola Silveira

Photo provided by Paola Silveira

Meet Paola Silveira of the Federal University of Rio de Janeiro (Brazil). Paola is a member of Amilcar Tanuri's molecular biology lab in the Department of Genetics and in March 2018 will be defending her thesis. Paola is on campus to attend her first CSHL course, 2017 Advanced Sequencing Technologies & Applications.

What are your research interests? What are you working on?
I'm interested in HIV and other endemic viruses affecting Brazil. Currently, I’m working on the next generation sequencing technologies to elucidate the origins and epidemiology of Zika virus, and determining whether there is a viral genetic basis of adverse fetal outcomes resulting from in utero ZIKV infection. 

Was there something specific about the Advanced Sequencing Technologies & Applications course that drew you to apply?
I wanted to gain more knowledge on new sequencing platforms and applications; particularly learn data processing and master bioinformatic tools that are available to me but I wasn't familiar with. The course met these needs and has since broadened my view of the genomics field. I have acquired data analysis know-how, and will confidently apply these new skills when I return to my home institution.

What is your key takeaway from the Course?
I’m looking forward to the next years of the genomic era. The advancements in DNA sequencing technologies and in the bioinformatics field are expanding our knowledge, and turning previously-unimaginable scientific and novel biological applications into achievements.

If someone curious in attending a future iteration of Advanced Sequencing Technologies & Applications course asked you for feedback or advice on it, what would you tell him/her?
For those interested in this course, I would strongly recommend this amazing opportunity. You will learn and you will be learning from the best who are each enthusiastic, supportive, and vested in your learning.  

What do you like most about your time at CSHL?
I’m delighted with the landscape of CSHL campus. Here you're surrounded by green and always be surprised by science sculpture. Additionally, I have met a great group of people here.

Paola received a stipend from the Howard Hughes Medical Institute (HHMI) to cover a portion of her course tuition. On behalf of Paola, 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 Paola 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: Mario Banuelos

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Meet Mario Banuelos of the University of California, Merced. Mario, a fifth year PhD Candidate, is part of Suzanne Sindi's lab in the Applied Mathematics Department. On campus for the Genome Informatics meeting, the registration for which he won via our raffle at the 2015 SACNAS conference, he presented a poster entitled “Genetic variants over generations: Sparsity-constrained optimization tools for structural variant detection.”

What are your research interests? What are you working on?
I primarily work on developing statistical and mathematical methods for modeling and inference of genomic variants (e.g. transposable elements and structural variants).

Was there something specific about the Genome Informatics meeting that drew you to attend?
The opportunity to share and receive feedback on my work was a big motivation, and I also wanted the chance to meet and potentially collaborate with others who are doing amazing work.

Mario Banuelos presenting his work at one of the poster sessions at the 2017 Genome Informatics meeting.

Mario Banuelos presenting his work at one of the poster sessions at the 2017 Genome Informatics meeting.

What is your key takeaway from the Meeting?
The science presented at this meeting covers a wide array of topics in genome informatics, but leaders from throughout those fields present novel work that definitely encourages interdisciplinary approaches to solve some of these problems. As an applied mathematician, I love seeing that type of environment fostered by these meetings.

How many CSHL meetings have you attended?
Genome Informatics is my first CSHL meeting and I plan to attend Biological Data Science next year.

If someone curious in attending a future iteration of  Genome Informatics meeting asked you for feedback or advice on it, what would you tell him/her?
I would tell them to make an effort to meet new people, expand their comfort zone, and learn about the different science people are doing (even if it does not directly relate to what they study).

What do you like most about your time at CSHL?
It’s amazing to walk around the beautiful campus and through the buildings named after pioneers of molecular biology. I also appreciated that CSHL Meetings & Courses understands the social aspect of growing as a scientist and the value of talking to colleagues over a cup of coffee. 

Thank you to Mario 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: Adam Blanchard

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Meet Adam Blanchard of the University of Nottingham (United Kingdom). Adam is a postdoctoral research fellow in the School of Veterinary Medicine and Science - Cellular Microbiology with Sabine Totemeyer as his mentor. He is on campus for the Programming for Biology course. 

What are your research interests? What are you working on?
Most of my research interests are based around host/pathogen interactions, focusing on bacteria with an impact on animal welfare. I enjoy implementing novel methods, such as metatranscriptomics, to investigate the host response to complex bacterial communities and which genetic factors play a role in disease.

Was there something specific about the Programming for Biology course that drew you to apply?
Knowing a scripting language is becoming increasingly important in biology, so attending a course like this will enable me to gain a head start that will undoubtedly benefit my career. The delivery style of the Programming for Biology course material seemed very concise. I have taken similar online courses which I felt lacked the personal interaction needed when troubleshooting and gaining a deeper understanding of the topics.

What is your key takeaway from the Course?
The Programming for Biology course is very well organized. There is a good balance of "need to know" information and other bits which have allowed for an effective learning experience; as you do not get bogged down with unnecessary detail.

How many CSHL courses have you attended? Do you have any near future plans to attend another course at CSHL?
This is my first one and, if I get the opportunity, I would love to participate in the Immersive Approaches to Biological Data Visualization course as it looks very interesting and is showcasing novel ideas. I really enjoy science outreach and an important aspect of this is data visualization. I feel being able to convey complex results in an easy-to-understand image is a powerful tool in helping people understand what you do and are trying to achieve.

If someone curious in attending a future iteration of Programming for Biology course asked you for feedback or advice on it, what would you tell him/her?
The environment at Cold Spring Harbor Laboratory is very positive. The instructors and teaching assistants are there to help at every step which is helpful because the course is tough. Also since all of the course participants begin the course at a similar level of understanding, there are plenty of opportunity for team work.

What do you like most about your time at CSHL?
The course instructors, teaching assistants and members of staff have been fantastic and have provided a really enjoyable two weeks. They balanced the course schedule well with lectures, practical sessions, sports and field trips. They also make sure you do not forget to go for meals when you are engrossed in the problem sets.

Adam received a scholarship from the Helmsley Charitable Trust to cover a portion of his course tuition. On behalf of Adam, 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 Yvanka 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: Saleh Tamim

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Meet Saleh Tamim of the University of Delaware. The bioinformatics and systems biology PhD student is a member of Blake Meyer's lab in the Donald Danforth Plant Science Center. Saleh is on campus for the Frontiers and Techniques in Plant Science course. Read on for what the CSHL first-timer has to say about the annual course and his experience so far. 

What are your research interests? What are you working on?
My research interests generally involve the application of bioinformatics and computational techniques to address biological problems. I am currently investigating a class of small RNAs (phasiRNAs) that are highly abundant in grass reproductive tissues.  

Was there something specific about the Frontiers and Techniques in Plant Science course that drew you to apply? 
Coming from a computational background, I applied for this course to learn more about different plant research work and respective techniques used to answer biological questions.

What is your key takeaway form the Course? 
My key takeaway from the course is that plant biology is diverse, and that there are still a lot of unanswered questions. I learned that it is important to focus and specialize on a particular area of interest, and to embrace collaboration when a research problem requires skills outside your main area of research. 

If someone curious in attending your course asked you for feedback or advice on it, what would you tell him/her? 
I will definitely encourage him/her to apply. I think the acquired knowledge as well as interaction (with both speakers and fellow participants) throughout the course is unique and very valuable to someone interested in plant biology.  

What do you like most about your time at CSHL?
I love the campus, it is beautiful. I also enjoyed meeting different people from different parts of the world.

Saleh received financial aid from the Helmsley Charitable Trust. On behalf of Saleh, 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 Saleh 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.