2016 Single Cell Genomics Conference

Last week I attended the 2016 Single Cell Genomics (SCG) Conference at the Wellcome Genome Campus in Hinxton, Cambridge, UK. This conference started in 2013 at the Weizmann Institute of Science, moved to the Karolina Institute in 2014, and was most recently held in the Hubrecht Institute in 2015. A PDF of the program is located here and my notes on the talks including links to various methods, publications and twitter accounts for the speakers are on GitHub. You could follow the tweets online using the twitter hashtag of #SCGen16.

John Marioni kicking off #scgen16 pic.twitter.com/bD7H7rhsBN

— Martin Hemberg (@m_hemberg) September 14, 2016

This was a fantastic conference that I would highly suggest to anyone working in the single cell genomics world. Some random take aways of things I noticed compared to other conferences I recently attended were:

1. I was bummed that many of the speakers did not have their talks streamed. As I attended in person, I was fortunate enough to see all the talks, but apparently there was a pretty big waitlist for this conference. The organizers decided to offer a stream for a reduced registration fee with the caveat that not all talks may be streamed.  I assume this was primarily driven by the fact that many presenters discussed unpublished work, but still I'm sure this was frustrating for the waitlisted individuals who were not able to attend in person.

Deeply dissapointed that all speakers in the last session have requested their talks NOT be streamed #SCGen16

— Tal Shay (@tal_shay) September 15, 2016

Hope immunologists are more open to streaming for the less fortunate people who were left out due to lack of space #SCGen16

— Tal Shay (@tal_shay) September 15, 2016

2. Similar to #1, almost none of the speakers made their slides available online (even the ones that agreed to have their talk streamed). I recently attend the Joint Statistical Meetings in Chicago, IL July 31-Aug 3 this year where Karl Broman kept a great list of links to talks from speakers at JSM 2016 (I also kept my own notes). I was really hoping to be able to go back and review slides after the conference ended, but to my knowledge, I was the only one to post slides. To be fair, JSM is significantly larger than the single-cell genomics conference, but I was expecting at least some speakers to post their slides online. I gave a talk on progress in deal with batch effects and biases in single-cell RNA-seq data.

.@stephaniehicks on progress in batch effect & biases in SC RNA-seq data #SCGen16 pic.twitter.com/NaWL6xQV7M

— Ankur Sharma (@asharmaiisc) September 16, 2016

3. The power of the pre-print! Much of the work discussed was either published or in pre-prints.  Sarah Teichmann presented work on the sensitivity, specificity and accuracy of different scRNA-seq protocols using ERCC spike-ins and has a pre-print available on bioRxiv. She humorously pointed out a sense of relief after Lior Pachter sounding positive about the paper by tweeting it.

Power of @biorxivpreprint ;-) #SCGen16 #ASAPbio pic.twitter.com/ZZF1kuvXnt

— Ankur Sharma (@asharmaiisc) September 15, 2016

4. As someone who's very much interested in promoting women in STEM, I was interested to see the ratio of female to male speakers and attendees at the conference.  Though there were fewer women, I was excited to see such prominent women showcasing their work, but as always, there is room for improvement. Sean Davis from NCI has a single cell GitHub repository, which contains list of people (males and females) working in this field. It would be great place to start for looking for additional female speakers.

Breakdown of speakers (by my count) at #SCGen16: 28 men and 12 women (30%). Room for improvement.

— Davis McCarthy (@davisjmcc) September 16, 2016

5. Finally, there were many fantastic biological talks and a lesser number of equally wonderful methods talks, but a few of my favorite methods talks included:

Allon Klein's talk on visualisation and cell fate prediction by far the most engaging of the conference #SCGen16

— Larry Bird, PhD (@Bird_leahry) September 16, 2016

David van Dijk: "MAGIC" method for diffusion-based imputation of expression values in scRNA-seq data. Promising results, lots of Qs #SCGen16

— Davis McCarthy (@davisjmcc) September 16, 2016

John Marioni of the EBI gets computational. How to quantify technical noise? #SCGen16

— Tal Nawy (@nawy_t) September 16, 2016

6. Lack of twitter presence. I don't believe having a twitter presence is relevant to having good research in genomics, but I have noticed a large community of people who work in genomics on twitter.  Therefore, it was interesting to me that so few of the speakers at this conference had a presence on twitter. Just for my own curiosity, I did a quick analysis of the tweets from there conference [code in RMarkdown] to find out the top 50 most tweeted words at the conference (after removing the #scgen16 hashtag).

If you want to know more about some of the talks, I have some notes here on GitHub.