A Request to Cold Spring Harbor Lab Regarding 'Genome' Conferences

Cold Spring Harbor lab has been the premier research center in biological sciences. Sadly, it is making mistakes in recent years, and those mistakes will hurt the organization, if not started to hurt already.

Thankfully the research center still has intelligent people. For example, three years back, I wrote a letter to the editor of Genome Research requesting to allow arxiv preprint submission, and my letter was supported by a number of other bioinformaticians. CSHL not only understood the point and changed its previous position on Genome Research, but also spearheaded the effort to start biorxiv preprint server for biology. Hopefully this letter will reach some of those cool heads.

We are sad to find that the Cold Spring Harbor lab conferences have been taken over by clowns. Such conferences usually have the name ‘genome’, but rarely acknowledge any leading discoveries related to genomes, informatics or biology of genomes. We previously wrote about the ‘Biology of Genomes’ conferences, where only those connected to ENCODE project got to speak. Afterward a number of leading researchers sent us private emails agreeing with what we said. They were not undergrads or grad students, but directors of labs or higher. More importantly, they published papers with major discoveries. Fast forward by 2-3 years, they all moved on to different conferences and told us that they see no value in going to ‘Biology of Genomes’ at CSHL. Another collaborator of us (a graduate student), went to one of the CSHL conferences organized by ENCODE clown John Stamatoyannopoulos and was very disappointed.

We are currently monitoring the ‘Genome Informatics’ 2015 conference, and are sad to find that CSHL is damaging itself in the same manner. We made some of those points in our previous commentary, and Dr. Gholson Lyon from CSHL commented about our post in twitter.

The most important point from our post, that he did not mention, is that the talks are not based on merit any more. For example, the biggest contribution to informatics last year was the algorithmic idea of minimizer. It has been adopted in KMC making it the fastest k-mer counter. It has been adopted in genome assembly by Rayan Chikhi to build an ultra-low RAM assembler (~1GB for human genome). It was used by Derrick Wood and Steven Salzberg to create Kraken, an ultrafast metagenome search program. Minimizer is now being used by Heng Li to build an extremely efficient aligner - minimap. The concept of minimizer has been revolutionary to anyone, who is seriously doing informatics.

The idea originated from James Yorke in 2004, and therefore we expected him to give a keynote speech at this informatics conference. After all, 2014 had been the year, when his concept got recognized by the scientific community. Instead, we find the same boring Mark Gerstein as keynote speaker. Gerstein was an ENCODE leader, who blew up big time and had been unapologetic about it.

Let’s go to the biology and medicine side. Where are the people like Bill Martin, who are using informatics to answer real biological questions? In contrast “Personal and Medical Genomics” has very little to report apart from hype. Yet the conference has “Discussion leaders” in the later category, but not in former (biochemistry/biology).

On the technology side, what is the explanation of having three talks on Oxford Nanopore apart from connections? Not only the technology is immature, no new informatics discovery came from this community. Most ideas were borrowed from those working on Pacbio.

We understand that these conferences have become big business for CSHL, but promoting clowns has not made many businesses successful. CSHL should get rid of the current organizers, and rethink its strategy about these conferences with more serious researchers on board.