The Genome Access Course

Visitor of the Week: Maggie McCoy


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.

Repeat Visitor: Tatiana Schnieder


Among the ~9,000 scientists we hosted this year, a number of them participated in multiple meetings and/or courses. Kicking off the 2018 edition of our Repeat Visitor series is Tatiana Schnieder, an assistant professor of clinical neurobiology at Columbia University and an adjunct assistant professor at Hunter College. Tatiana divides her work between two research labs – the neuropathology laboratory of Dr. Andrew Dwork at Columbia University Irvin Medical Center and epigenetics laboratory of Dr. Fatemeh G. Haghighi at Mount Sinai School of Medicine. This year, Tatiana took part in the 83rd CSHL Symposium on Quantitative Biology and joined the ranks of both the CSHL Protein course (Expression, Purification, & Analysis of Proteins & Protein Complexes) and The Genome Access Course (TGAC). Previously, she presented a poster during the Glia in Health & Disease meeting in 2016 as well as attended Blood Brain Barrier that same year. We reached out to Tatiana to chat with her about her experiences in CSHL meetings and courses, and to learn more about what keeps her coming back to campus.

Tell us about your research interests.

My research is focused on the question of brain-periphery interactions in psychiatric disorders. To be more specific, I am currently investigating whether or not the reported relationship between suicide and central and peripheral inflammation is mediated by changes in blood-brain barrier (BBB) permeability.

How did you decide to make this the focus of your research?

During my doctoral training, I investigated prefrontal white matter microglia in individuals who died by suicide; and although I did not find any significant differences in microglial activation between suicides and non-suicides, suicide decedents had significantly higher densities of juxtavascular phagocytic cells in dorsal white matter than diagnostically-matched non-suicide decedents. Interestingly, however, studies of animal models of psychiatric symptoms have attributed maladaptive behavior in rodents to peripheral inflammation and to the influx of peripheral immune cells into the brain parenchyma. These findings and my own findings in postmortem human brains prompted me to investigate the involvement of peripheral immune cells in pathology associated with completed suicide. Further research revealed that non-parenchymal immune cells do not contribute to the increase in perivascular cell density that we observed in suicide; which suggests that resident microglial cells -- rather than non-parenchymal immune cells -- cross-communicate immune responses between the periphery and central nervous system in suicide. Moreover, those who died by suicide had a lower surface area density of microvessels in dorsal white matter -- the same brain region where I found increased densities of perivascular phagocytes. Cumulatively, these findings indicated that changes in the properties of the neurovascular unit could be contributing to pathological changes that lead to suicide. This piqued my interest in the role of BBB in psychiatric disorders. The goal of my current project is to determine if completed suicide is associated with transcriptional, epigenetic, or protein changes in the neurovascular unit.

Expression, Purification & Analysis of Protein & Protein Complexes Class of 2018

Expression, Purification & Analysis of Protein & Protein Complexes Class of 2018

What led you to apply for the Protein course and how has it contributed to your work?

I applied to the Protein course to find answers to the challenges I faced during the preparation of my samples for HPLC/mass spectrometry. To assess changes in the expression level of key proteins crucial for BBB function and identify novel differentially expressed proteins, I use HPLC/mass spectrometry proteomics to interrogate protein expression profiles in isolated microvessels. To investigate BBB changes in psychiatric disorders and suicide specifically, I wanted to optimize a microvessel isolation protocol from postmortem frozen human tissue. It was important for me to develop the best method for the extraction of cytosolic, membrane, and transmembrane proteins that seal a gap between the brain endothelial cells. The two-week course gave me a lot of hands-on practice in protein isolation and, through extensive communication with the Instructors and use of the course materials, I was able to come up with the optimal protocol for my project. My main takeaway from the course is that it is imperative to learn as much as possible about your protein/s of interest before you start your experiments. Know your target well because what may work for one protein can be detrimental to another.

How about TGAC? Why did you register for it and what is your key takeaway?

My BBB project involves data that will require knowledge of bioinformatics, and I want to understand what goes into the analyses of the data I produce at the bench. I took TGAC to start learning how to analyze high-throughput data obtained using next-generation sequencing methods and mass spectrometry. As for my key takeaway: Apply what you learn in the course without delay. To acquire a new skill, one needs to practice often – if not daily – therefore it is important to “play” with your data so as to avoid forgetting what you pick up from the course.

The two courses have very different formats: the Protein course consists of hands-on training in a laboratory setting while The Genome Access Course is purely computational. What can you share about the differences or similarities between your experiences in the two courses?

The Genome Access Course Class of 2018 (Spring)

The Genome Access Course Class of 2018 (Spring)

The two courses I took were indeed very different: TGAC was a short two-day course, whereas Protein course was two weeks long and so requires a completely different level of commitment. What is expected of you is also different: TGAC course is mostly lecture-based with some hands-on computer work, and the Protein course is mostly lab-based with lectures sprinkled throughout the day and evening. You cannot really choose to opt out, and by the end of the first week you already feel like you are a part of a team. In fact, working in a team and as a team will be the main mode of learning in a longer course. Irrespective of which course you decide to take, you will be taught by the top experts in the field within a friendly and supportive learning environment, where you will always have the ability to discuss and clarify concepts that may be confusing. It was an amazing experience: I was challenged to step out of my comfort zone, which is how personal and professional growth happens.

The focus of the CSHL Symposium changes annually. This year its topic was “Brains & Behavior: Order & Disorder in the Nervous System,” with an emphasis on neuroscience and related technologies. Besides the overall topic, what attracted you to participate in it?

Once you graduate, it is easy to focus on your specific area of research and, sometimes, you lose sight of the bigger picture. I strive to prevent this from happening to me. As a college professor, I need to stay abreast of the new discoveries in the field of brain research, and attending the Symposium was a perfect way to catch up with the latest findings. It provided a diverse range of topics and speakers from top-notch brain research labs. When this Symposium hones in on this topic again, I would recommend aspiring neuroscientists to attend. If you haven’t yet decided what you want to dedicate your research to or are looking to expand your network, this is a great conference.

Since you’ve now experienced both meeting and course life at CSHL, what differences or similarities did you notice about the two program types?

The courses had a much more focused agenda and required a few prerequisites so you are more likely to meet people who share similar professional or academic experiences as you. The meetings, on the other hand, were eclectic and brought together people from very diverse backgrounds. But in both instances, expect to be surrounded by like-minded people enthusiastic about science and the discoveries it brings.

What did you like most about your meeting and courses this year?

I am very lucky to live a short train ride away from CSHL. Since the first CSHL meeting I attended in 2016 on Glia in Health and Disease, I keep coming back because the quality of the meetings and courses have always been stellar, and the content and organization of the events always meet my expectations. In fact, I am looking forward to attending the Blood Brain Barrier meeting in 2019.

Both the Protein course and TGAC will return to the Laboratory in 2019; and applications are already being accepted. Apply to the Protein course by January 31, 2019 here.

Thank you to Tatiana for sharing with us her experience, and we look forward to having her back at the Laboratory again. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here and here.

Visitor of the Week: Mike Tramantano


Meet Mike Tramantano of Cold Spring Harbor Laboratory (CSHL). Prior to joining CSHL President and Chief Executive Officer Bruce Stillman’s lab in February 2017 as a postdoctoral fellow, Mike earned his Ph.D. in Molecular and Cellular Biology from Stony Brook University (SBU). Since 2012, Mike has participated in six meetings at CSHL plus The Genome Access Course (TGAC) which kicks off later this afternoon.

What are your research interests? What are you working on?
In mammalian cells, stepwise assembly of large multi-protein complexes occurs at specific sites in the genome and is required to initiate DNA replication prior to cell division. My research focuses on understanding the recruitment mechanism that occurs upstream of this assembly and answering the question: How do cells recognize the correct sites in the genome for assembly to begin and what factors are involved in this process?

How did you decide to make this the focus of your research?
How human cells select sites for DNA replication is not well understood. If we can better understand this selection process, it can have broader implications to diseases where normal cell division is disrupted, such as cancer.

How did your scientific journey begin?
My passion for science began in high school Biology when I was first exposed to the topic of genetics. I was struck by the fact that all the information needed to make a human being was encoded in our DNA.

The Genome Access Course is your first CSHL course – was there something about this course in particular that drew you to register for it?
There is an increasing amount of data and tools publicly accessible to scientists online. TGAC appealed to me because it is an intensive instructional course teaching about these resources and how they can be best utilized in your research.

Your course kicks off later today - what do you hope to get out of the two-day course and how will it help with your work?
I hope to learn the fundamentals of analyzing deep sequencing data and the proper way to present this data. My research is beginning to enter a period where genome wide data and analyses will be necessary in order for me to continue my project.

If you can take part in another course or two, which one(s) would you register for and why?
I would like to register for either the Computational Genomics or Chromatin, Epigenetics and Gene Expression course, as the in-depth training in working with next generation sequencing technologies and chromatin biology present in those courses would be helpful in planning future experiments for my project.

Since you’re well-integrated in campus and have participated in a good number of meetings, what tips or insider-knowledge can you share with those attending their first CSHL meeting or course?
Don’t miss the wine and cheese! It is a Cold Spring Harbor tradition where many great ideas are shared and discussed in a casual atmosphere. I also suggest taking a walk up to Hillside (by the Quick building) to get the best views of the Harbor.

What, in your opinion, are the best features of a CSHL meeting that make it unique and worthwhile to participate in?
What I enjoy most about the meetings at CSHL is that they are relatively casual compared to other conferences at which I have participated. The interaction between visiting scientists always seems very constructive and positive. In addition, established faculty are very willing to share their knowledge with younger researchers – especially over a beer at the bar after the talks.

Thank you to Mike 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.