Welcome to the Ecker lab

Epigenetic Processes in Plants and Mammals

The Ecker lab studies plant, mouse, and human cells to decipher epigenetic processes during development and disease. Combining newly developed methods with genome- and methylome-sequencing, Ecker’s lab group examines changes in the epigenome, exploring, for example, how adding molecules such as methyl or hydroxy-methyl groups to the backbone of DNA can help cells fine-tune gene expression. Much of the team’s work on mouse and human epigenomics is focused on the brain. By understanding how the genome and epigenome communicate with one another, they aim to untangle the complexity of regulatory processes that underlie both normal development and disease.

Lab News

Dr. Hanqing Liu was selected as a prestigious Harvard Society of Fellows Junior Scholar. Congrats to Hanqing! We are all very proud of you!
Swift was awarded the Australian-American fellowship. Congrats Joseph!
Congratulations to Hanqing Liu on winning the Pioneer Fund Postdoctoral Scholar Award from the Salk Faculty Fellowship Committee
Congratulations to Zhuzhu Zhang. She has been awarded a Bridge to Independence Fellowship.
Congratulations to Natanella Illouz Eliaz. She has been awarded a Hewitt Fellowship and an Award of Excellence.
Congratulations to Hanqing Liu on being awarded the UCSD Biological Sciences Founding Faculty Award for Graduate Excellence
Peter Berube has been selected to become a Trainee in the NIH funded Pathways in Biological Science (PiBS) Graduate Training Program. Congratulations Peter!
Hanqing Liu receives David V. Goeddel Endowed Graduate Fellowship
Peter Berube, UCSD Division of Biological Sciences PhD graduate student joins the lab. Welcome Peter!
Tatsuya Nobori received a prestigious Human Frontier of Science Program (HSFP) Long Term Fellowship.
Learn more about Human Frontier Science Program here: https://www.hfsp.org/
Joseph Swift receives a prestigious Life Science Research Foundation (LSRF) Fellowship sponsored by Open Philanthropy
Learn more about the Life Sciences Research Foundation here: http://www.lsrf.org/
Natanella Illouz-Eliaz receives a prestigious US-Israel Binational Agricultural Research and Development Fund (BARD) fellowship
Mapping the Cellular Social Network of Proteins
To understand how cellular machinery functions, scientists have looked to an organism’s DNA. But genome sequence has not proven to be the complete instruction manual that researchers had hoped for. (more…)
Congrats Shelly!
Shelly submitted her thesis on August 31! Congrats Shelly – moving on to postdoc at UW!
Chongyuan Luo in Nature Communications
Congratulations Chongyuan Luo on Nature Communications publication describing snmC-seq2 – terrific improvements to single cell methylome profiling method!
Congrats Bobby!
Bobby Henley received an BRAIN Initiative Fellows: Ruth L. Kirschstein National Research Service Award (NRSA) Individual Postdoctoral Fellowship.
Ecker Lab featured in Science News
*From sciencenews.org In a landmark event more than a decade ago, geneticists unveiled the human genetic instruction book. This year, the book was turned into a movie adaptation in 3-D: Researchers cataloged how chemical (more…)
Ecker Lab featured in Popular Science
*From popsci.com June marked the release of the first map of the human epigenome: the chemical markers that tell your DNA what to express when. “Think of the genome as the hardware in your computer and the epigenome as the software,” says Joseph Ecker, director of the (more…)
Ecker Lab featured in Discover Magazine
*From discovermagazine.com In the 12 years since the Human Genome Project was completed, biologists have linked more than a thousand regions of the genome to disease. “But in most cases, we don’t actually know how they function,” says Manolis Kellis, a computational biologist at Massachusetts Institute of Technology. Enter the epigenome. (more…)
Systemic silencing: Mobile sRNA stabilizes genomes
Transcriptional gene silencing is a pivotal mechanism for regulating gene expression and genome stability. In Arabidopsis, combined analyses of small RNAs (sRNAs) and DNA methylation reveals that mobile 24-nt sRNAs are involved in reinforcing genome-wide silencing of transposons through DNA methylation. (more…)
Arabidopsis Research Roundup: January 29th
This weeks Arabidopsis Research Roundup features a paper from David Baulcombe and Joe Ecker that further deciphers mechanisms of RNA silencing and is kindly discussed by postdoc Mat Lewsey in a short audio description. Elsewhere there are three studies that include researchers from CPIB in Nottingham. (more…)
Grafted plants’ genomes can communicate with each other
Agricultural grafting dates back nearly 3,000 years. By trial and error, people from ancient China to ancient Greece realized that joining a cut branch from one plant onto the stalk of another could improve the quality of crops. (more…)
Salk researchers chart landscape of genetic and epigenetic regulation in plants
LA JOLLA—A new technique developed by Salk Institute scientists for rapidly mapping regions of DNA targeted by regulatory proteins could give scientists insight into what makes some plants drought tolerant or disease resistant, among other traits. (more…)
Congratulations Ecker lab alumni Mat Lewsey on launching his new group down under!

First day @latrobe AgriBio! Incredible modern building and acres of growth space. My office needs some plants tho. pic.twitter.com/kb1AcR14lw

The Salk Institute hosted the 2016 ENCODE Consortium Meeting from June 14-17, 2016
Gauging stem cells for regenerative medicine
Salk scientists and colleagues have proposed new molecular criteria for judging just how close any line of laboratory-generated stem cells comes to mimicking embryonic cells seen in the very earliest stages of human development, known as naïve stem cells. The tests found that no current protocols lead to truly naïve stem cells, (more…)
Extensive Variation Revealed in 1001 Genomes and Epigenomes of Arabidopsis
An international team of scientists has sequenced the whole genomes and epigenomes of more than 1,000 Arabidopsis thaliana plants, sampled from geographically diverse locations. The collection of 1,001 genomes and 1,001 epigenomes not only illuminates new aspects of the plant’s evolutionary history (more…)
Fertility success may get boost from new research
Infertile couples might be able to greatly boost their chances of having a baby by using the genetic discards of egg cells, researchers from the Salk Institute and Oregon Health and Science University said in a new study. (more…)
Salk Researchers Say Plant May Hold Key To Drought Resistance
The small green trays of plants in this Salk Institute greenhouse are far more captivating to these researchers than the ocean view. Carol Huang reaches out for a tray. (more…)
Mapping genome-wide transcription-factor binding sites using DAP-seq
DAP-seq is fast, inexpensive, easily scaled method enabling high-throughput generation of cistrome and epicistrome maps for any organism. (more…)
New kinds of brain cells discovered by Salk, UCSD scientists
Scientists from the Salk Institute and University of California San Diego report identifying a number of previously unknown types of human brain cells. They’ve also discovered genetic switches that make these neurons. (more…)
Shelly Trigg’s work lands on the cover of Nature Methods
Shelly Trigg’s work lands on the cover of Nature Methods. Congrats Shelly et al! (more…)
Congratulations Taiji on recent seed methylome paper in Genome Biology!
Read the paper here: http://rdcu.be/vR5K