Visitor of the Week: Rafael Campos Martin

Meet Rafael "Rafa" Campos Martin of the Max Planck Institute of Plant Breeding. Rafa is a PhD student and member of Achim Tresch’s lab which is affiliated with the Max Planck Institute and the Medical Statistics and Computational Biology Department of Uniklinik Koln (Germany). The Spanish national is a CSHL first-timer and is on campus for the 2018 Systems Biology: Global Regulation of Gene Expression meeting where he presented a poster title “Linking chromatin states to gene expression with bidrectional Hidden Markov Models” during the first poster session. 

What are your research interests? What are you working on?
My main project is related to finding new candidate proteins that can bind to histone marks in highly transcribed genes. Our lab developed new machine learning models that we apply to different kinds of ‘omics data.

How did you decide to make this the focus of your research?
As an undergrad, I majored in chemistry and biochemistry and have always been amazed by how cells are able to organize molecules and repair themselves. From a chemist’s point-of–view, the reactions happening inside the cells are really fascinating. In order to better understand these connections, I decided to pursue a PhD in ‘omics data analysis where the cross-talks - or connections - can be explained via mathematical models.

How did your scientific journey begin? 
I have been fortunate to have had great teachers during my studies but my first, and most important, teacher would have to be my sister, Samantha. I credit her for sparking my curiosity because growing up she took me for walks in the forests and taught me about plants, insects, and how everything is connected.

Was there something specific about the Systems Biology: Global Regulation of Gene Expression meeting that drew you to attend?
I came because the topic of the meeting compliments my main project. Also, since I will soon be finishing my PhD, this meeting is a great opportunity to meet scientists from other labs and develop my next steps.

What is your key takeaway from the meeting?
From the talks to the people you will meet, there is always something interesting so pay attention and meet as many people as you can. For instance, I had fruitful discussions with people working with Neural Networks and learned of different ways they apply it, and the pros and cons of such modelling. In the process, I have become interested in Neural Networks and would like to incorporate it into my career. 

Did you pick up or learn something new from the meeting that you plan to apply to your work?  
Definitely! This meeting was attended by great scientists and it was really easy to engage them in a conversation. A few interesting ideas worth a try came up during these discussions; including finding a different application for an algorithm our lab has been working on. I spoke with people working to find new putative TF-binding and there is a strong possibility that our algorithm can be applied to their work to help answer their questions.

If someone curious in attending a future iteration of this meeting asked you for feedback or advice on it, what would you tell him/her?
Go for it. The location is great, the people are really interesting, and the food is tasty. But, if possible, try to come during a warmer month or you may experience a snowstorm.

What do you like most about your time at CSHL?
I experienced a nor’easter and the snow made CSHL even more beautiful.

Thank you to Rafa 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.

A Word From: Nancy Allbritton, Scott Fraser & Junhyong Kim

During November of last year, Cold Spring Harbor Laboratory hosted the fifth U.S. meeting of Single Cell Analyses. We met with meeting organizers Nancy Allbritton, Scott Fraser, and Junhyong Kim to chat about the biennial meeting. Their chemistry as an organizing team would have easily been picked up by those around us but, as our conversation quickly revealed, their chemistry extends beyond their jovial banter. 

Hailing from different subfields within single cell biology, they each contribute a unique “vantage point” to continually refine and refresh the meeting. Since its CSHL debut in 2009, the Single Cell Analyses meeting has quadrupled in size and now leaves the organizers at a crossroad: Allow the meeting to continue growing, or maintain it in its current “sweet spot?” 

But before we contemplated that great question, we examined the overall structure of the meeting and recent changes made to it.  

Junhyong: Every year, we think of something special to do. In 2015, we incorporated Nancy’s idea for technology discussion bites and had a session with NIH about future planning. Actually, a part of the Human Cell Atlas discussion started at that meeting.

Scott: Another thing we’ve changed is how we embrace the contributed abstracts in the oral sessions. When this meeting started out and was smaller, there was a need to draw in a larger set of invited speakers. Over the years, we’ve reduced the number of invited speakers and made space for more contributed talks, and they’ve been amazing. 

Nancy: I like the way we have a lot of people speaking now who submitted abstracts; I think that has kind of bookended the invited talks. The lightning talks were another big change we made this year that was an amazing success. 

Junhyong: Even with that change, I was glad that we didn’t pack the schedule. We had a lot of time to have good discussions and questions this year. 

Nancy: That central framework of not getting overly busy works for this community. It was laid down by Jim Eberwine and Xiaoliang Sunney Xie for the first meeting in 2009, and we’ve carried it over since then. 

Scott: Also, we have one poster session but we keep the posters up throughout the meeting. They were pretty well attended this year and the exchange has been great. I actually went back to see more of the posters after the session, and I know a number of people made appointments with poster presenters so they could have one-on-one discussions.

Junhyong: Every year, we make a point to reach out to a new community. In 2017, we introduced a session on evolution in cell biology.

Scott: We’ve even discussed how to formalize the community that session represents to really set the agenda for that field. It’s one that’s just emerging and over the years, we’ve been good at identifying emerging fields. Some of the quantitative ‘omics, like proteomics, started as parts of sessions here too. A benefit of having three of us from three different areas on the organizing team is it opens the door for seeing new areas that any one of us might have ignored. 

Junhyong: Yeah, it’s really fun to talk to first-time participants – like many of our invited speakers. They always remark how this meeting is a unique experience because of the diversity in the science.

Scott: In both the science and the participants, who are heterogeneous in origin, age, and the sorts of positions they’re in. And the audience diversity is maintained during the sessions. In some meetings when it becomes DNA, all the DNA people stay and everybody else leaves. But at this meeting, the different communities hang in there and, as a result, the questions and discussions are really good. The meeting is in a sweet spot: it’s big enough that it has great diversity but small enough that you actually feel like you can meet people randomly.

Over the last few years, the number of meetings catering to single cell biology has grown. Below is how the organizers see the CSHL meeting as filling a distinct niche.

Scott: Well, one of this year’s speakers said this was the first single cell meeting they've been to that wasn't essentially a DNA sequencing meeting.

Nancy: THAT’s what I really like about it. You hit the nail on the head. There are beginning to be a lot of single cell meetings now. Ours has a good mix of applications and technology, and of younger and older participants too. We three have very, very different backgrounds, so we end up with a nice mix of speakers that none of us - if we acted alone - could come up with.  

Scott: Or convince to attend.

Nancy: Exactly!

Scott: And we keep the DNA sequencing in because we feel sorry for one of the organizers. 

Nancy: There were a lot of great questions, discussion, and interactions this year; particularly between technology people and applications people.

Scott: And the discussions weren’t the converted preaching to one another, but people sharing ideas or vantage points, and arguing about the relative benefits of different approaches. In fact, the biggest problem for some of the speakers was the ability to go out and grab a cup of coffee during the breaks because they received so many questions, even after the Q&A sessions. One of the nice things about Cold Spring Harbor meetings is that the space and surrounds are really conducive to people spending time talking to one another. It makes it very easy to come up with the next killer experiment.

Junhyong: Absolutely. During this meeting’s almost ten-year history, we’ve emphasized pushing the boundaries of measurements and analysis, so that everybody can come here and learn. I think that’s a unique feature of this meeting compared to some of the other single cell meetings.

We switched gears to ask who they thought would benefit the most from attending and had a group brainstorming session about how the growth of the field is impacting clinical research:  

Junhyong: We need some Starbucks up here.

Scott: A barista would be really good, at least for the core organizers. And a sushi chef.

Scott: But seriously, one of the few groups that I think is under-represented at our meeting are those from teaching colleges. With the meeting taking place during term, it's difficult for them to get away. 

Nancy: There are some schools where a lot of good, undergraduate-powered research is being done, and that’s who we’re missing; they would benefit from attending this meeting.

Junhyong: The single cell field itself can be a little expensive. People from teaching colleges can certainly come here for the science, but it’d be hard to take the science back to their institutions. 

Scott: It’s an expensive technology but you don’t have to do just the Cadillac. Some biostat people I’ve met have been very good at teaching the underlying math and graphics.

Nancy: Also the protein stuff can be done, like the degradation work we saw this year. Even Amy Herr’s single cell western blots are pretty inexpensive relative to RNA-Seq.

Scott: Now that this meeting has grown, it would be nice to make it known that there is financial aid for groups like those from teaching colleges or grad students.

Junhyong: At Penn, Jim [Eberwine] and I run an annual single cell biology symposium. It was initially attended by a very small number of people but every year more and more people doing disease, translational, or clinical research come to it.

Scott: Yeah, that may be another community we’re under-serving right now. 

Nancy: I’d almost target that community before the predominantly undergrad institutions, since clinicians are sort of the end-result users of single cell technologies, with patients as the beneficiaries. The Single Cell Analysis course in the summer actually trains a lot of clinicians.  

Scott: The translational aspect of single cell analyses is exciting, one that’s just really exploded. Bringing more clinicians to the meeting would help us foster translation of the technologies. In the predominately undergrad campuses, we’d foster education which, I would argue, is pretty important too, given the number of students who started at schools where there’s a real research culture but not the huge research funding. 

Our chat finished off with each organizer sharing the development s/he is most excited about: 

Nancy: Seeing the technologies beyond RNA and DNA begin to mature.

Junhyong: Seeing the field grow to the extent where we now have hundreds of international projects has been very exciting. Also, the molecular biology and cell biology fields have become more quantitative overall. So now people take it for granted when you put up a PCA plot but ten years ago, people were like, “What is that? What are those axes?”

Scott: One important development is that we’re moving single cell analysis into cells and their normal contexts. Previously, many single cell biologists were trying to isolate single cells and study them without controlling their contexts. At the 2017 meeting, most of the talks brought in the interactions between individual cells, the things that must be going on in your body and mine right now because we aren’t just a clump of single cells.

The Single Cell Analyses meeting returns to the Laboratory in 2019; and during the summer, we offer the Single Cell Analysis course. For an introduction into the course, be sure to read our Q&A with 2017 Single Cell Analysis Alumnus Kenny Yu and watch this video from the 2017 instructors, TAs, and trainees. And for fun, below are three photographs that perfectly depict the chemistry between Nancy, Scott, and Junhyong.

Lastly, for more conversation with other meeting organizers, check out the rest of our A Word From series. 

Visitor of the Week: Alison Parisian

Meet Alison Parisian, a graduate student in the Biomedical Sciences program at the University of California San Diego. Alison is a member of Frank Furnari's lab, which is also a part of the Ludwig Institute for Cancer Research, and returned to the Lab to train at the 2018 Bioinformatics for Cancer Genomics course. 

What are your research interests? What are you working on?
I am interested in cancer genetics and epigenetics. My project involves developing and analyzing a stem cell-based model of a type of pediatric brain tumor called ATRT, in order to learn more about the mechanisms underlying these tumors and potentially identify novel therapeutic strategies. I am interested in cancer research because it is an important topic of research with major health implications, and I find the complexity of the underlying mechanisms interesting.

How did you decide to make this the focus of your research? 
I had hoped to pursue translational research in graduate school and studying cancer at UC San Diego was perfect for this goal.

How did your scientific journey begin? 
I first became interested in science and biology as a child, growing up in the country and learning from my father who has degrees in botany and entomology. I was always interested in how living things worked and that interest stayed with me through college, where I chose to major in Biology.

Was there something specific about the Bioinformatics for Cancer Genomics course that drew you to apply?
I applied to this course because I've been trying to learn how to analyze genomics data, and this course will teach me many of the methods I hoped to learn. Bioinformatics is becoming increasingly important in Biology and I believe it is an important skill to learn. I plan to use the bioinformatics techniques I learn here in my project, as well as help with other projects in the lab.

What is your key takeaway from the course?
I feel like I can apply what I've learned in the course to analyze whole genome sequencing data myself once I return to San Diego. I've learned a lot of helpful information on which tools to apply to different types of bioinformatic analysis, as well as what sorts of analysis are possible with different types of data. Overall, the course has helped make many types of bioinformatic analyses, which had seemed incredibly difficult, more accessible.

What and/or how will you apply what you've learned from the course to your work? 
I plan to apply what we learn about gene expression and pathway analysis to my own project once I return to San Diego, and will likely apply what I've learned about analyzing whole genome sequencing data to other projects later on.

How many CSHL courses have you attended?
This is my second course at CSHL. I previously attended the Brain Tumors course in 2016.

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?
This is an excellent course in teaching introductory bioinformatics skills for cancer research on a variety of topics. I would recommend the course for those interested in learning cancer bioinformatics skills, even if they have little prior experience. A wide range of topics are covered, but each is addressed in great enough depth and with enough hands-on practical applications that participants should be able to perform the different types of analyses independently after the course.

What do you like most about your time at CSHL?
Interacting with the other trainees in the course, who come from a variety of different universities and backgrounds, has been a wonderful experience. In addition, the Cold Spring Harbor campus is beautiful and it was amazing witnessing a beach sunset one day and experiencing snow the next. Coming from California it's not often I get to experience snow, and it was lovely watching the snow fall over the campus. 

Alison received a scholarship from the Helmsley Charitable Trust to cover a portion of her course tuition. On behalf of Alison, 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 Alison 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: Dan Kober

Meet Dan Kober of the UT Southwestern Medical Branch in Dallas, TX. Dan is a postdoc with a joint fellowship with Dan Rosenbaum and Arun Radhakrishnan. He made his debut visit to the Lab to train at the first-ever Cryoelectron Microscopy course, which coincided with not one but two late winter nor'easters. 

What are your research interests? What are you working on?
I’m interested in understanding how proteins sense and respond to changes in membrane cholesterol and lipid composition. I want to use structural and functional methods to understand the protein-membrane and protein-protein interactions that accomplish this. 

How did you decide to make this the focus of your research? 
The interest grew out of my thesis work studying protein-ligand interactions of immune receptors. A portion of that project looked at protein-phospholipid interactions, which this led to my current interest.

How did your scientific journey begin? 
As an undergraduate, I started as a chemistry major but became very interested in structural biology when I took a biochemistry and an immunology course and gained exposure to protein structures. I was really enamored with seeing how chemistry and biology intersect in protein structures. 

Was there something specific about the Cryoelectron Microscopy course that drew you to apply?
I had a background in structural biology and wanted to get a formal, comprehensive training in cryo-EM methods while I'm still relatively early in my postdoc training. 

What is your key takeaway from the Course?
Have a plan for power outages! But seriously, my main lesson from this course is that there are a lot of different options and methods to try with cryo-EM. But none of these options and methods will be a "magic bullet" because the most important thing is the biochemistry of your protein. 

What and/or how will you apply what you've learned from the course to your work? 
I am in the initial stages of my project and this course will help me improve how I'll approach my experiments. I think (and hope) that what I've learned will help me avoid a lot of pitfalls. Also, I'm hopeful that these ideas and tools will be useful to my lab and institution as well!

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?
I would definitely recommend this course to anyone! It covers a wide range of information that would be useful to someone at any level. We discussed everything from the basics to aspects of physics that are still not understood. We also got exposed to tools and ideas that are in development. 

What do you like most about your time at CSHL?
I’ve really enjoyed interacting with the other trainees and instructors. By just talking with people about their experiences in cryo-EM and science in general, I think I already learned a lot. 

Dan received a scholarship from the Helmsley Charitable Trust to cover a portion of his course tuition. On behalf of Dan, 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 Dan 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. Also, in relation to the nor'easter storms and power outage mentioned above, here is a great picture (and thread) of how the Lab handles surprise power outages.