Jason Ernst Lab News | Jason Ernst Research Lab

News

2024

July 2024: Emily receives a best talk award at ISMB Regulatory Systems Genomics
June 2024: Luke wins a dissertation year fellowship.

2023

October 2023: Tev defends his PhD thesis.
September 2023: Artur's paper on ChromGene is published.
August 2023: The Mammalian Methylation Consortium papers (including Ha, Adriana, Soo Bin, and Jason as co-authors) are published in Nature Aging and Science. The work is covered in the New York Times, El País, a Science perspective, and a UCLA news release.
July 2023: Jason will be co-organizing the RECOMB/ISCB Conference on Regulatory and Systems Genomics to be held at UCLA in November 2023.
July 2023: Jason will be a faculty at the UCLA Computational Genomics Summer Institue (CGSI).
June 2023: Our lab is hosting two students participating in the Bruins in Genomics summer program.
June 2023: Ha's paper Universal chromatin state annotation of the mouse genome is published.
February 2023: Ha defends her PhD thesis.
February 2023: Jason will be co-teaching Algorithms in Bioinformatics (CM122/CM222) with Eleazar Eskin in Spring 2023.

2022

November 2022: Paper led by Ha on A framework for group-wise summarization and comparison of chromatin state annotations is published.
November 2022: Ha gives an oral presentation at the ISCB/RECOMB Regulatory and System Genomics meeting.
October 2022: Ha gives an oral presentation at the American Society of Human Genetics.
September 2022: We are part of a BRAIN Initiative Cell Atlas Network (BICAN) grant to study the developing brain.
August 2022: Aahna, Elijah, and Saiyang receive research excellence awards for BIG summer.
July 2022: Jason is promoted to a full professor.
June 2022: We are hosting three students participating in the Bruins in Genomics summer program.
May 2022: Emily receives a Society of Women in Engineering scholarship.
April 2022: Emily is selected for the GATP training program.
February 2022: The paper on the mammalian methylation array is published in Nature Communications.
January 2022: Ha's paper on universal chromatin state annotations is published in Genome Biology.

2021

December 2021: Soo Bin defends her PhD.
September 2021: We receive with several other UCLA labs a grant to study the role of genomic variation influence on reprogramming part of the Impact of Genomic Variation on Function (IGVF) consortium.
August 2021: Soo Bin gives a highlight presentation at RECOMB on LECIF.
August 2021: Jeremy and Chris receive BIG Summer Research Excellence awards.
July 2021: Jennifer defends her PhD.
June 2021: Soo Bin receives a Dissertation Year Fellowship.
June 2021: We will be virtually hosting two students participating in the Bruins in Genomics summer program.
June 2021: Soo Bin's paper on conservation state annotation of the SARS-CoV-2 genome is now published.
May 2021: Emily receives a Society of Women in Engineering scholarship.
May 2021: Soo Bin's paper on LECIF is published at Nature Communications.
April 2021: We receive an NSF grant with Sriram Sankararaman and Noah Zaitlen.
March 2021: Jason will be co-teaching COM SCI M225/BIOINFO M225/HUM GEN M265 'Computational Methods in Genomics' with Bogdan Pasaniuc in Spring 2021.

2020

December 2020: Paper on the ConsHMM Atlas by Adriana and her former BIG summer students Brooke and Jennifer is published.
December 2020: Paper on CNEP is published at Nature Communications.
June 2020: Jason is selected to receive a JCCC-BSCRC Ablon Scholars Award.
June 2020: Shan Sabri defends his PhD.
June 2020: We are virtually hosting five students participating in the Bruins in Genomics summer program.
June 2020: Luke Li becomes a PhD student in the group.
May 2020: We receive funding from the David Geffen School of Medicine/Broad Stem Cell Research Center for comparative genomic analysis of the SARS-CoV-2 genome.
February 2020: Adriana defends her PhD thesis.

2019

November 2019: Artur's paper on χ-CNN for fine-mapping chromatin interactions is now published.
November 2019: Jason will be co-teaching COM SCI M225/BIOINFO M225/HUM GEN M265 'Computational Methods in Genomics' with Bogdan Pasaniuc in Winter 2020.
November 2019: Ha and Soo Bin present posters at the International Human Epigenome Consortium (IHEC) meeting.
October 2019: The Computational Medicine Department at UCLA, which Jason has a joint appointment with, opens.
August 2019: Grace, Jeremy, Rebecca, and Trevor win Bruins in Genomics best poster awards.
July 2019: Adriana's paper on ConsHMM and a single-nucleotide annotation of the human genome into conservation states is now published.
June 2019: Our lab is hosting four Bruin in Genomics (B.I.G.) summer students.
June 2019: Jason will be a faculty at the UCLA Computational Genomics Summer Institue (CGSI).
June 2019: Our lab now has a twitter account.
May 2019: Artur defends his PhD thesis.
May 2019: Shan is selected to receive a Dissertation Year Fellowship.
April 2019: Jason delivers a John H. Walsh Young Investigator Research Prize lecture.

2018

December 2018: Jason is selected to be the co-recipient of the John H. Walsh Young Investigator Research Prize.
November 2018: Jason will be co-teaching COM SCI M225/BIOINFO M225/HUM GEN M265 'Computational Methods in Genomics' with Bogdan Pasaniuc in Winter 2019.
September 2018: Aaron Zhou becomes a PhD student in the lab.
August 2018: Soo Bin and Jason write a research highlight that is published in Genome Biology.
August 2018: Pete's paper on ChromTime is published in Genome Biology and was selected as a 'Featured article'.
July 2018: Soo Bin receives a best poster award at ISMB.
July 2018: Jason is promoted to an Associate Professor and receives tenure.
July 2018: Our lab is hosting two Bruin in Genomics (B.I.G.) summer students.
June 2018: Jason receives a Rose Hills Foundation Innovator Award.
June 2018: Ha Vu joins the lab.
April 2018: Jason is a co-organizer of the Regulatory & Systems Genomics (RegSys) Community of Special Interest Meeting at ISMB to be held July 9-10th in Chicago.
March 2018: Pete defends his PhD thesis.

2017

November 2017: Ernst et al, Nature Biotech 2016 is selected to the annual regulatory and systems genomics top 10 papers reading list.
November 2017: Nature Protocols publishes a protocols paper on ChromHMM.
October 2017: Shan is selected to give an oral presentation at CSHL Single Cell Analyses meeting and Artur at the NIPS Machine Learning in Computational Biology Workshop.
October 2017: Jason will be co-teaching COM SCI M225/BIOINFO M225/HUM GEN M265 'Computational Methods in Genomics' with Bogdan Pasaniuc in Winter 2018.
October 2017: A new set of enhancer-gene link predictions extending the expression correlation approach in Ernst et al, 2011 to the Roadmap Epigenomics data is published as a part of this paper.
September 2017: Jason receives a NIH-NIDA Avenir award.
August 2017: We receive a grant from Kure It.
August 2017: Heather wins a Bruins in Genomics poster award.
July 2017: Our lab is hosting two Bruin in Genomics (B.I.G.) summer students.
June 2017: Soo Bin Kwon joins the lab.
April 2017: A new paper Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression is published in Cell Reports. This has been a collaboration with researchers at MD Anderson and Pete is a first author on the paper.
March 2017: Jennifer Zou is selected to receive a NSF Graduate Research Fellowship.
February 2017: A new paper Cooperative Binding of Transcription Factors Orchestrates Reprogramming is published in Cell. See the UCLA press release.This has been a collaboration with the Plath lab and Pete is a co-first author.
February 2017: Jason will be one of the organizers of the Regulatory Genomics Special Interest Group Meeting at ISMB 2017, which will now be integrated with the main ISMB meeting.

2016

November 2016: Jason will be co-teaching COM SCI M225/BIOINFO M265/HUM GEN M265 'Computational Methods in Genomics' with Bogdan Pasaniuc in Winter 2017.
October 2016: A new paper Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions is published online in Nature Biotechnology. The paper describes Sharpr-MPRA which combines dense Massively Parallel Reporter Assay (MPRA) tiling with computational inference, and enabled high-resolution mapping of activating and repressive nucleotides within more than 15,000 predicted regulatory regions in two human cell types. The maps can be visualized here.
October 2016: The associated SHARPR software (Systematic High-resolution Activation and Repression Profiling with Reporter-tiling) with the Nature Biotechnology paper is publicly released.
August 2016: Ashish and Scott win Bruins in Genomics poster awards.
August 2016: Two abstracts from the lab are selected for platform presentations at ASHG 2016.
July/August 2016: Jason and Adriana will be speaking in the UCLA Computational Genomics Summer Institute
July 2016: Our lab is hosting two Bruins in Genomics (B.I.G.) summer students
June 2016: Olivera defends her PhD thesis.
June 2016: Tevfik Dincer joins the lab.
April 2016: Pasquale Laise joins the lab as a visiting postdoc funded by a fellowship from Fondazione Umberto Veronesi.
April 2016: Jason will be a program co-chair for the Regulatory Genomics Special Interest Group meeting at ISMB 2016. Abstracts for oral presentation are due April 18th and poster presentation only May 9th.

2015

December 2015: Jason will be co-teaching COM SCI M225/BIOINFO M265/HUM GEN M265 'Computational Methods in Genomics' with Bogdan Pasaniuc in Winter 2016.
December 2015: The Roadmap Epigenomics project, which Jason was involved in, was selected as one of the Top 25 Science Stories of 2015 by Science News and one of the Top 100 stories by Discover Magazine.
November 2015: Jason's epigenome imputation paper is selected as one of the top papers in regulatory and systems genomics published in 2015.
October 2015: Jason will be a program co-chair for the Regulatory Genomics Special Interest Group meeting at ISMB 2016
September 2015: Pete wins a poster prize at the Academy of Computational Life Sciences summer school at Oxford.
August 2015: Earle and Hana win poster prizes at the Bruin in Genomics poster session.
August 2015: Jennifer Zou joins the lab (co-advised by Eleazar Eskin).
July 2015: Adriana is selected for the Biomedical Big Data Training Grant.
July 2015: Pete wins a poster prize at ISMB.
June 2015: Adriana Sperlea joins the lab.
June 2015: Shan Sabri joins the lab (co-advised by Kathrin Plath).
April 2015: Jason's work on epigenome imputation is featured on the cover of Nature Biotechnology.
March 2015: Jason will be a program co-chair for the Regulatory Genomics Special Interest Group (RegGenSIG) meeting at ISMB 2015.
February 2015: Jason's work on large-scale epigenomic imputation is now published online at the journal Nature Biotechnology and the associated ChromImpute software is publicly released. See the press release: UCLA, MIT computational biologists fill in knowledge gap for epigenomics maps.
February 2015: The Roadmap Epigenomics Consortium publishes the Integrative analysis of 111 reference human epigenomes in the journal Nature. Jason is one of the co-first authors on the paper. The Roadmap Epigenomics project receives extensive media coverage (e.g. NY Times, Washington Post).
January 2015: We are part of a Genomics of Gene Regulation grant (PIs Alex Hoffmann and Doug Black) that receives funding (see UCLA and NIH press releases).

2014

December 2014: UCLA launches the Institute for Quantitative and Computational Biosciences (see the Los Angeles Times article). Jason is a core member of the institute.
November 2014: Jason will be co-teaching with Bogdan Pasaniuc the seminar Current Topics in Bioinformatics (COM SCI/BIOL CH/HUM GEN M229S) in Winter 2015.
October 2014: We are part of a NIH U01 grant Genomic Strategies to Identify High-Impact Psychiatric Risk Variants (PIs: Nelson Freimer and Dan Geschwind) that receives funding.
September 2014: We are part of a NIH Roadmap Epigenomics R01 grant Epigenomic Control of RNA Splicing (PIs: Yi Xing and Alex Hoffmann) that receives funding.
August 2014: We receive with Kathrin Plath and Sri Kosuri a Broad Stem Cell Research Center Innovation Award for Understanding the combinatorial logic of gene regulation in pluripotent cells.
June 2014: Artur joins the lab and was selected to participate in Genomic Analysis & Interpretation Training Program.
June 2014: Pete is selected for the CIRM Training Grant.
May 2014: Jason joins the Editorial Board at Genome Research.
February 2014: Jason will be a program co-chair for the ISMB Regulatory Genomics Special Interest Group (RegGenSIG) meeting to be held July 12, 2014 in Boston.

2013

June 2013: Jason will be co-teaching with Bogdan Pasaniuc the seminar Current Topics in Bioinformatics (COM SCI/BIOL CH/HUM GEN M229S) in Fall 2013.
June 2013: Pete is selected for a Broad Stem Cell Research Center Pre-Doctoral Fellowship.
May 2013: Jason receives a NSF CAREER Award. See the UCLA Today article.
April 2013: Genome Research publishes online Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types by Ernst and Kellis. The paper takes the #1 position on the journal's list of 'Top 10 Most Read Articles.'
April 2013: ScienceWatch ranks the Ernst et al, Nature 2011 paper #6 for 'What's Hot In Biology' based on recent citation counts.
February 2013: Jason is selected as a 2013 Sloan Research Fellow. See press releases from UCLA, the University of California, the Sloan Foundation, and the New York Times ad.
January 2013: Nucleic Acids Research publishes Integrative annotation of chromatin elements from ENCODE data and selects it as a 'Featured Article' representing the top 5% of papers it publishes in terms of originality, significance and scientific excellence. Jason is a co-first author on the paper.

2012

November 2012: The Ernst et al, Nature 2011 and the Lindblad-Toh et al, Nature 2011 papers were selected as two of the top 10 most influential papers published in the year 2011 in the fields of regulatory genomics and systems biology.
September 2012: The ENCODE Project Consortium publishes An integrated encyclopedia of DNA elements in the human genome in the journal Nature. Jason contributes to the analysis presented in the paper. The ENCODE project receives extensive media coverage. See the Los Angeles Times story on the project.
September 2012: Jason receives a joint appointment in the UCLA Computer Science Department.
May 2012: Jason gives an invited talk at a symposium at the National Institute of Environmental Health Sciences.
May 2012: Jason becomes a member of the UCLA Molecular Biology Institute.
April 2012: The study Mapping and analysis of chromatin state dynamics in nine human cell types (Ernst et al, Nature 2011) receives the Massachusetts General Hospital 2012 Martin Prize for Excellence in Basic Research.
April 2012: PLoS Genetics publishes Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma by Wiggs et al and co-authored by Ernst, which uses ENCODE chromatin data to analyze novel Glaucoma GWAS hits.
March 2012: Nature Methods publishes ChromHMM: automating chromatin-state discovery and characterization by Ernst and Kellis.
February 2012: Research on chromatin states to interpret disease variants highlighted in the Nature technology feature Functional genomics: The changes that count.
February 2012: ChromHMM - software for chromatin state discovery and characterization is publicly released under an open source license.
January 2012: Jason Ernst Lab begins. Positions are available.

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Press, Commentaries, and Blog Coverage

Chromatin States Dynamics in Human (Ernst et al, Nature 2011)

Chromatin States (Ernst and Kellis, Nature Biotech 2010)

29 mammals

modENCODE

Dynamic Regulatory Events Miner (DREM)

Short Time-series Expression Miner (STEM)