Visitor of the Week: Sam Nicholls

Meet Sam Nicholls of the University of Birmingham (United Kingdom). The postdoctoral fellow in Nick Loman’s group is currently at CSHL participating in his first meeting: Genome Informatics. In addition to giving a talk, titled "Detecting microbial transmission and engraftment after faecal microbiota transplants with long-read metagenomics and reticulatus" during the Microbial and Metagenomics session, Sam’s work was featured as the front cover of the meeting’s abstract book. He has also been taking advantage of the chance to “meet in person a bunch of familiar Twitter avatars that [he’s] been messaging over the past year or so.”

What are your research interests? What are you working on?
I'm currently working on computational methods to analyse clinical microbiome samples. We're interested in determining whether we can identify and characterise species and strains that are transferred from donors to recipients in faecal microbiota transplants.

How did you decided to make this to focus of your research? 
This project is a natural follow-on from my PhD, which I finished a little over a year ago. My PhD was concerned with recovering haplotypes for particular genes of interest from the rumen (stomach) of a cow. We were interested in cataloguing the haplotypes of different hydrolases used to break down natural grasses in the stomach, with a view to investigate these for their potential use in the manufacture of biofuels. Now, I'm applying these skills and my experience to catalogue the genomes (and their haplotypes) that are transplanted from the gut of a healthy donor to the gut of an unwell recipient via faecal microbiota transplant, to characterise what it is about the procedure that makes it work as a successful therapy.

As part of my PhD, I created a data structure (called Hansel) for holding all possible pairwise observations of SNP variants on a set of short sequencing reads; and an algorithm (called Gretel) to use this matrix as crumbs for navigating a graph-like structure representing all possible ordered combinations of SNPs that make up the haplotypes for a region of interest. Although we didn't get so far as to test the recovered haplotypes for biofuel capabilities, as part of my final year I was able to put on a white coat and get in the lab to gain some wet lab experience of my own. I think it's important for bioinformaticians to know where their data comes from!

How did your scientific journey begin?
In the second year of my Computer Science and Statistics undergraduate degree with no plans for summer, I recall an e-mail being sent around the Computer Science Department at Aberystwyth University (United Kingdom) looking for someone who had knowledge of Perl, tree algorithms, and proteins for a placement at the Wellcome Trust Sanger Institute. Undeterred by ticking none of those boxes, I applied. The trip to Cambridge was awfully long from Aberystwyth and I didn't feel like the interview had gone particularly well. Good practice at least, I thought, but a few days later I was surprised to find that I'd been offered the summer job! On my first day, I remember someone dropping off a bunch of genetics textbooks to my desk and saying that I'd have to pick up a lot of new concepts quickly, which was a little intimidating, but I was keen to learn something completely new.

 Ultimately that short placement had more of an effect on me than I had expected. I was not really aware that my skills in computing could be applied to interesting, difficult real-world problems like those we find in biology. It was nice to be writing code that wasn't just a website, or an app, or something to sell. I liked that I could tell people about my work and even post it online as it was being written, something that was definitely not part of the ethos of my previous experience in industry.

 That placement led me to change my modules in my final year and to go on and pursue a PhD in bioinformatics, rather than returning to industry.

Was there something specific about the Genome Informatics meeting that drew you to attend?
As a bioinformatician, I always find myself a little lost at conferences that focus heavily on biology. I'm excited to be at Genome Informatics as this finally feels like a conference where everything makes sense to me! I was also happy at the prospect of finally meeting a bioinformatics hero of mine: Heng Li.

What is your key takeaway from the Meeting?

A takeaway in the literal sense: I'll be flying home this weekend with one of the Genome Informatics 2019 meeting posters, which features artwork that I submitted! The picture is an assembly graph from one of our complex clinical samples. It's a wonder to look at, but actually a rather terrible assembly...

What and/or how will you apply what you’ve picked up from the Meeting to your work?
Yesterday's morning session on sequencing algorithms, variant calling and genome assembly was a highlight for me so far. I'm quite interested in exploring some of the techniques for genome sketching that were discussed, and how we can apply these to our own clinical metagenomic data sets. 

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
I'm not sure how I feel about coffee at 9 in the evening, but this meeting has been full of excellent presentations that I'm going to have to go and read up more about. I'd definitely recommend Genome Informatics if you want to know what the cutting edge techniques and hot topics of bioinformatics are right now.

What do you like most about your time at CSHL?
I grew up in Swansea, Wales and moved to Aberystwyth for eight years to study my undergraduate and PhD; so I've spent most of my life near the sea. I enjoy the hustle and bustle of the city of Birmingham but I do miss the seaside. I've been enjoying walks around the campus and the views of the water. It's very calm and picturesque here. Thanks for having me!

Thank you to Sam 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: Luke Zappia

Last month, we launched the Repeat Visitor Series to celebrate - and show appreciation to - the scientists who participate in multiple meetings and/or courses in a short period of time. Suma Shetty debuted the Series and the next participant to be featured is Luke Zappia, who attended back-to-back meetings on Genome Informatics (November 1-4) and Single Cell Analyses (November 8-11). Luke had never been to Cold Spring Harbor Laboratory but made the most of his inaugural trip. 

Luke is a graduate student at The University of Melbourne (Australia) and is based in Alicia Oshlack's lab in the Murdoch Children's Research Institute (MCRI). The PhD candidate is working on methods for analyzing single-cell RNA sequencing data, which is a technology that measures the activity of genes in individual cells. We chatted with him on why - besides great timing - he attended both Genome Informatics and Single Cell Analyses, and what his experience was like at the two meetings. 

Was there something specific about the Genome Informatics meeting that compelled you to attend? 
Members of my lab have attended past Genome Informatics meetings and we believe it to be one of the premier bioinformatics conferences. We have found it to be a great opportunity to see excellent talks and interact with people from around the world who are in the field.

How about for the Single Cell Analyses meeting?
I work with single-cell data and since the Single Cell Analyses meeting took place the week after Genome Informatics, it was a good opportunity to make the most of my trip from Australia.

Let's talk key takeaways: what was your key takeaway from Genome Informatics? 
Bioinformatics is still a young field and we continue to push the boundaries of what is possible. And whenever I attend a bioinformatics meeting, I am always impressed by the wide range of problems people are tackling and the level of detail they put into their work.

What was your key takeaway from Single Cell Analyses?
People have developed a range of ways for measuring different things in individual cells beyond the common technologies I work with.

Do you have a takeaway that’s applicable to both meetings? 
We are lucky to be working at a time when we are seeing a revolution in how biology is studied, leading to many exciting new discoveries and developments.

How about similarities - did you notice any between the two meetings? 
Outside of both meetings having a range of interesting topics, there weren't too many similarities between them because they covered different content. As a result, each meeting attracted a distinct audience. 

Did you present at either meeting? 
I presented a talk at Genome Informatics during the Transcriptomics, Alternative Splicing, Gene Predictions Session, and a poster at Single Cell Analyses titled "Simulation and analysis tools for single-cell RNA sequencing data."

Thinking back on the scientific meetings and conferences you have attended, what do you like most about CSHL meetings? 
The set-up of a CSHL meeting is helpful in generating opportunities for discussions. Everything is located on campus so I was able to just focus on the meeting and speak with other attendees. And the days are long at a CSHL meeting! 

We noticed that you sketch your notes. What got you started in sketching talks? 
I have been doing it for the last four years or so. I saw some examples somewhere and thought it looked like an interesting idea. Mike Rohde is generally considered responsible for populating the idea. 

Can you walk us through your process of transcribing a talk into a drawing? 
I usually only sketch for the longer talks (> 30 mins) as I find it hard to pick out enough things to fill a page from a shorter talk. There are lots of different ways of doing it and some people do a really good job of shorter talks such as Alex Cagan. Personally, I try to prepare before the talk by adding the speakers name, title etc. Once the talk starts I watch out for key points they make or interesting figures, which usually form the main part of the sketch. Also, I draw on paper, although it would be interesting to try a tablet at some stage. 

Thank you to Luke for taking the time to chat with us at the 2017 Genome Informatics and 2017 Single Cell Analyses meetings and his sketch note process. Both meetings will return to the Laboratory in 2019. If you’re looking for a meeting in the years that Genome Informatics is not at CSHL, the Biological Data Science meeting is a great alternative. Also, we offer an annual Single Cell Analysis course during the summer. 

Visitor of the Week: Mario Banuelos

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.

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.