A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

Its out on the Molecular Systems Biology website. Yay!

This paper summarizes quite a bit of work by Naomi and Ilan. It started with "here is a short 2-week project" and ended as big part of Naomi's PHD and a massive paper.

Highlights (from our synopsis):

By tracing the evolutionary history of transcriptional networks across 23 fungi, two seemingly contradictory trends are observed: rapid target turnover and conserved function. This is reconciled by a model that invokes strong selection to conserve the overall function of a motif, but not its individual targets.

• The vast majority of cis-regulatory elements in genes’ promoters are rapidly gained and lost across species.
• Despite this rapid turnover, most transcription factors are associated with a conserved function even at great evolutionary distances.
• A functional selection turnover model reconciles these two phenomena by invoking a preference to conserve the overall function of the motif but not the individual target genes.
• Our model fits the variation in measured transcription factor binding profiles across species in both yeasts and mammals.

Farewell to Naomi

The last week was marked with farewell events to Naomi. 

It started on Tuesday with a trip and picnic. Since Naomi is (was) a joint student of both Hanah Margalit and myself, we had a trip with the two groups.

On the road

Noa and Daniela

After the trip we had a nice lunch in a forest. Daniela was the star of the event, sitting in the middle and checking the choice of food.

Then came the more official part of the ceremony where we said our farewell wishes and exchanged cards and presents :-)

On Thursday afternoon we had the dissertation exam. Unlike the custom in many universities, in the Hebrew University the exam is a private event - the judges and the student without any audience.  Naomi surveyed the results from her dissertation and the judges asked questions.

Naomi at the start of the presentation

After the presentation and Q&A, the judges convened, and after a short discussion decided this was a great presentation and wonderful dissertation. We called Naomi to tell her the news.

Celebratory fresh PhD

Yesterday Hanah and I took Naomi for a lunch to have a chance for a more intimiate farewell. 

Today Naomi came to finish the TODO list on an ongoing project with Avital and Mor (from Hanah's lab). And at 3:30, she left, after tearful hugs with everyone. 

We wish Naomi easy move to Cambridge, MA, and much fun and success in her postdoctoral fellowship!

Evolution of Transcription Factors Binding paper is accepted!

Yay!

Just got email that a paper by Naomi, Ilan Wapinski, Aviv Regev, Hanah Margalit and me was accepted to Molecular Systems Biology. This paper represents almost two years of work by Naomi and Ilan, and undergone several dramatic ups & down during this time. So it is great to hear that it is officially accepted.

It made just in time for Naomi to print her dissertation listing this paper as "accepted for publication" instead of "in review".

We celebrated by an impromptu toast in the lab.

More details once the paper appears....

This is also a good chance to add a picture of Naomi & Ilan from a trip to CSHL at the time we started talking about this project.

CSLS Yearly Retreat

One of our local sources of excellence is the undergraduate program in "Computer Science and Computational Biology" which is often nicknamed CSLS. This elite program accepts relatively few students (~20/year) with very high entry grades. The students study both Computer Science and Life Sciences as well as specialized courses. To meet these requirements the program has a very high courseload.

Overcoming the challenges of such a program is often dependent on team spirit. Classes that formed a supporting social group usually had better success and the students felt they learned more and were happier. To help form such interactions we employ various activities, including specialized classes and study sessions for this group. One of the most important activities is the yearly retreat.

In the retreat, which takes place toward the end of the academic term, we take students in all stages of the program together with the teachers and TAs of the program.

The location of the retreat is Hof Dor, a beautiful beach that borders a large nature reserve along on of the most unique shorelines in Israel.

Although we spent two days next to the beach, most of the day was in the lecture hall.

The packed program had talks by senior year students who presented their final project. These projects involve working with researchers at the Hebrew University on a range of topics.

The talks in the retreat serve as a milestone in the project, as they provide a chance to present the research question, methods and results to a supportive audience. For the younger students these talk open a window to current research questions and how computational analysis plays a role in a range of biological studies.

Many credits go to Naomi for mentoring the projects throughout the year and working with the students on the presentations.

In addition we had a a keynote talk by Nathalie Balaban on non-genetic variability in bacteria and it's evolutionary importance.

However, sitting in a hot room listing to talks can be tiring.

To fight the sleepiness, Naomi arranged for an impromptu streach session, and later a musical interlude.

In spite of the heat, many of the talks inspired interesting discussions.

To top things off we ended the meeting with a guided trip in the nature reserve.

Alon and me took advantage of the flat sea to do two quick dives (one in the evening and the other early in the morning) at the local beach.

Three minutes about science

Our training as Scientist is aimed at giving clear, precise and scholarly presentations. Public presentations are often different, as they need to hide many details and fine points, and instead focus on why this is interesting and exciting.

Recently there was a call for a national competition for students to give 3 minute public talks about science. This is the Israeli branch of the FameLab competition.

Our very own Naomi participated in one of the two preliminary competitions. She disappeared from the lab for half a day. When we next met her we learned that she one of finalists that were vote to participate in the national competition.

We immediately asked for a repeat performance. I recorded it with my iPhone. Our version was 3:11, a bit over the target time. It's in Hebrew, so my apologies to non-Hebrew speakers.

Naomi's talk was about the epigenetic inheritance research we published with Ollie Rando's a bit more than a year ago.

Unfortunately, the final competition took place when Naomi was traveling, and so we did not get to see her advance to the international competition.