The mid-developmental transition



Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, Yanai I. The mid-developmental transition and the evolution of animal body plans. Nature. 2016



A nice blog about our paper by Susanna Pilny


Group of pets sitting, white background.

05/05/2016: Kelly Rae Chi also wrote a great piece on this project for Biotechniques, called “Phyla for Thought”:




CEL-Seq2: Single-cell RNA-Seq

In 2012, our lab published CEL-Seq,  a method for single-cell RNA-Seq. The method is highly-multiplexed, uses in vitro transcription (IVT) to amplify, and has become one of the best methods for single-cell RNA-Seq. We believe it is actually THE best method!


Here is the CEL-Seq protocol. This is how we freeze individual cells, though we also use a plate version, and the C1. Here is a link to the bioinformatic scripts for the initial analysis.

We have recently developed CEL-Seq2 which has three times better sensitivity than the original, and is also cheaper and faster. Our recent paper in Genome Biology contains the full protocol.

Kelly Rae Chi also mentions CEL-Seq in her review for The Scientist on single-cell RNA-Seq methods.





The Society of Genes

Here’s the website for the book:


Nearly four decades ago Richard Dawkins published The Selfish Gene, famously reducing humans to “survival machines” whose sole purpose was to preserve “the selfish molecules known as genes.” How these selfish genes work together to construct the organism, however, remained a mystery. Standing atop a wealth of new research, The Society of Genes now provides a vision of how genes cooperate and compete in the struggle for life.

Pioneers in the nascent field of systems biology, Itai Yanai and Martin Lercher present a compelling new framework to understand how the human genome evolved and why understanding the interactions among our genes shifts the basic paradigm of modern biology. Contrary to what Dawkins’s popular metaphor seems to imply, the genome is not made of individual genes that focus solely on their own survival. Instead, our genomes comprise a society of genes which, like human societies, is composed of members that form alliances and rivalries.

In language accessible to lay readers, The Society of Genes uncovers genetic strategies of cooperation and competition at biological scales ranging from individual cells to entire species. It captures the way the genome works in cancer cells and Neanderthals, in sexual reproduction and the origin of life, always underscoring one critical point: that only by putting the interactions among genes at center stage can we appreciate the logic of life.