Visitor of the Week: Deeptiman "Deep" Chatterjee

Meet Deeptiman “Deep” Chatterjee of Tulane University School of Medicine. Deep is a fifth-year Ph.D. candidate in Dr. Wu-Min Deng’s lab taking part in Single Cell Analyses. This is his first meeting at CSHL and he came into it with a bang: Deep presented a flash talk introducing his poster entitled “Constructing a Comprehensive Transcriptomic Atlas of Developing Adult Drosophila Ovary and Oogenesis”. His approach from a biological perspective without much computational made his poster different than that of the other presenters. But as they “all are working towards the same goal, [Deep was still able to have] a great experience to learn from others and get fresh feedback and good comments!”

What are your research interests? What are you working on?
My research interests lie in bridging developmental biology with that of tumor biology. I generally use classical genetics, confocal microscopy and single cell sequencing techniques in the fruit fly model system to address specific questions. In my current research, I’m trying to understand what makes specific groups of cells to consistently be more susceptible to tumor formation than their neighbors in the ovarian epithelial tissue.

How did you decide to make this the focus of your research?
My mother was a cancer survivor, and she died from cancer-related complications 11 years later. Experiencing this debilitating disease from such proximity made me appreciate this disease and I wanted to study its fundamentals at its earliest stages. Fruit flies have been extensively used to study some of these basic steps, and so when I got the opportunity to work in Dr. Wu-Min Deng’s lab, I knew I had to take it.

How did your scientific journey begin?
We had a retired biology teacher in middle school back in India, who would still teach us because he simply loved teaching. He told us to break down every complex concept into its simplest parts. I still use that logic. I also was inspired by my biology teacher in high school, who singlehandedly had set up a simple biotechnology lab for only 6 students, teaching us to standardize some of the most common protocols used in biological labs. That hands-on experience set me up for an early career in science. I went on to do an MS in yeast genetics, and I switched fields for my Ph.D.

Was there something specific about the Single Cell Analyses meeting that drew you to attend?
The methodologies used in our lab have always been wet-lab benchwork. But we have never shied away pursuing new approaches. We have recently been involved in a lot of single cell transcriptomic data generation to answer relevant questions raised in many projects in the lab. I have learnt to process and analyze these datasets in the last year by myself but was limited by my limited knowledge of the field. This being my first single cell analysis meeting of any kind, I wanted to gauge the current state of the field, to learn from it and to apply my biologically-relevant perspective to it. The opportunity to present my work as a poster allowed me better participation in a field that I’m not so familiar with.

What is your key takeaway from the Meeting?
Single cell analysis is a rapidly evolving field, and to come to meetings such as these, even for participants out of this field, is a massive learning opportunity. It also makes one appreciate the importance of interdisciplinary sciences, connecting distant fields.

What and/or how will you apply what you’ve picked up from the Meeting to your work?
I particularly liked the entire session on spatial transcriptomics, which seems most relevant to my field of research and is also really cool! I also really enjoyed the talks on RNA velocity and vector fields and would love to integrate them into my research if it applies.

If someone curious in attending this meeting asked you for feedback or advice on it, what would you tell him/her?
Definitely attend! Even if it seems irrelevant to your field, it showcases really cool science and due to the structural and functional nature of the applications of single cell techniques, it can always be applied somewhere. It’s also a great learning opportunity from some of the pioneers in the field!

Also, definitely go to the bar at the end of the day. Some of the best scientific discussions transpired there.

What do you like most about your time at CSHL?
CSHL definitely loves to feed you. Thanks for having me!

Thank you to Deep 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. 

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: Yvanka de Soysa

Meet Yvanka de Soysa of the University of California, San Francisco. Yvanka, a Sri Lankan national and graduate student in Deepak Srivastava's lab at the J. David Gladstone Institutes, is on campus for the 2017 Single Cell Analyses meeting where she presented a poster titled "Single Cell Transcriptome Analysis of Early Cardiogenesis and its Perturbation Upon Hand2 Loss".

What are your research interests? What are you working on?
I am interested in the molecular mechanisms of embryonic heart development with my main question being: What are the important genes and cell types that form the embryonic heart, and how does incorrect activity/behavior of these genes/cell types lead to babies being born with heart defects? 

Was there something specific about the Single Cell Analyses meeting that drew you to attend?
Being that I am new to computational biology and have only been working with single cell transcriptome data for less than a year, this meeting presented a great opportunity to learn more about single cell analysis and technical methods. Also, my abstract was chosen for a poster presentation and I was eager to share and discuss my work in the poster session to get feedback from the experts in this field. The response I received and and the conversations around my poster from the other meeting attendees were very encouraging and exciting.

What is your key takeaway from the Meeting?
I am really excited by the diversity of methods for probing molecular features of single cells. I am primarily working with single cell transcriptomics, and this meeting has taught me a lot about the different types single cell proteomics and epigenomics methods as well as single cell imaging modalities. 

How many CSHL meetings have you attended and any plans to participate in a future CSHL meeting or course?
This is my very first meeting at CSHL, and I am interested in applying to attend the course on Chromatin, Epigenetics and Gene Expression.

If someone curious in attending a future iteration of Single Cell Analyses meeting asked you for feedback or advice on it, what would you tell him/her?
I would definitely recommend that they attend the next Single Cell Analyses meeting and make sure to spend time at the bar at the end of each day because my most insightful and valuable scientific discussions came from chatting and brainstorming with other attendees over drinks. 

What do you like most about your time at CSHL?
During the breaks between sessions, I've been taking short walks to explore the campus. It is truly a beautiful space and the views across the water from the campus are breathtaking. I am also a huge fan of the Waltz of the Polypeptides piece that is on campus. 

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.