Facciotti Lab

Photo Credits: BMC Bioinformatics, PLoS One, Cell Press, ACS Synthetic Biology

Microbial Genomics

DNA sequencing technologies are providing incredible opportunities for discovery and understanding in the biological sciences.  This is particularly true in the microbial sciences, where new tools now offer views into the genomes of many model and non-model microorganisms and into the metagenomic composition and dynamics of microbial communities. However, studies interpreting the functional expression of these genomes (what the genomes do and how they do it) are lagging far behind.  We are interested developing experimental and computational approaches to bridge this knowledge gap.

Systems Biology

One of the major goals of Systems Biology is to decipher the structures and understand the dynamics of cellular networks in a way that allows us to predicatively rewire these cellular circuits for our own purpose.  This ability will facilitate the rewiring of disease-perturbed networks back to health and the engineering of novel cellular factories.  We are interested in utilizing the tools and frameworks of Systems Biology to learn more about how structure and dynamics in gene regulatory networks lead to the emergence of complex phenotypes.

Synthetic Biology

Developing the means to efficiently engineer biological systems has broad application, from fighting disease to engineering microbial factories and beyond. We are interested in pursuing questions related to standards development, chassis/circuit interactions, and the interface between genomic systems and synthetic biology.

Molecular Biophysics

The chemical and biophysical properties of macromolecules are at the core of most biological phenotypes.  Developing a molecular-level understanding of key macromolecules is therefore critical to both understanding and engineering more complex biological systems.  When possible, we work with collaborators to develop a better biophysical understanding of macromolecules that may be of further scientific and/or biotechnological interest.  To date, studies have focused primarily on the haloarchaeal opsins and haloarchaeal lipid systems.

Lab News

6/11/2014 – Biomedical Engineering PhD Student Phil Seitzer successfully defended his thesis a couple of weeks ago and will officially graduate tomorrow. Congratulations to Phil!
9/03/2013 – UC Davis iGEM Presents Work on RiboTales at the 2013 iGEM World Championships at MIT
UC Davis iGEMers Aura Ferreiro, Amy Soon, Alex Neckelmann, and David Hwang presented their work on RiboTales and The Data Depot at MIT. Great presentation and very cool work! Congratulations to the group.
8/28/2013 – AmberCycle team selected as top 10 innovators
The AmberCycle team has been selected by LAUNCH as one of this year’s top 10 Innovators. See more about biocycling PET and the LAUNCH program at: LAUNCH Systems Challenge 2013. Check it out!
8/23/2013 – Mike Starr Completes Masters Thesis
Congratulations to Mike Starr for finishing his Masters thesis!
8/14/2013 – iGEM hosting NorCal gathering
UC Davis iGEM is getting ready to host other NorCal teams tomorrow for a mid-summer iGEM meet-up. Synbio, food, and fun!
8/5/2013 – JContextExplorer 2.0 User Manual and Web Tutorials Now Available!
Want to use JContextExplorer 2.0 but do not know how to use it? Wait no longer; graduate student Phil Seitzer has written a 130 page user manual as well as produced two 20 min tutorial videos. You can find both on our lab’s software page. Check it out!
7/30/2013 – Paper Published on Schiff-base Dynamics in Bacteriorhodopsin
Congratulations to Dr. Ting Wang on the publication of her manuscript “Schiff Base Switch II Precedes the Retinal Thermal Isomerization in the Photocycle of Bacteriorhodopsin.” Check it out here:
6/23/2013 – Two Group Projects Highlighted at 2013 Halophiles Conference
Facciotti highlighted two projects at the 2013 Halophiles Conference on the University of Connecticut campus. (1) The talk “High-resolution phylogenomics of halophilic archaea” described the group’s work on halophile genome sequencing and (2) the talk “Closing the Loop: X-ray Structure and Molecular Dynamics of the D96G/F171C/F219L Mutant of Bacteriorhodopsin” discussed our work on structure, dynamics and function of bacteriorhodopsin.
5/22/2013 – JContextExplorer 2.0 is now available!
Graduate student Phillip Seitzer has released JContextExplorer version 2.0. In this update, the user now has the ability to easily load genome sets from a drop down menu and many other analytical and user interface updates. To find out more about the changes and to download JCE 2.0 visit our software page.
5/17/2013 – Nick Csicery Awarded Ghausi Medal, the College of Engineering’s Highest Award for Graduating Senior
Lab member and two year UCD iGEMer Nick Csicery was officially awarded the Ghausi Medal. This reflects Nick’s academic achievements, leadership, and many contributions to the College. Congratulations Nick!
5/16/2013 – AmberCycle Team Presents at the 2013 Big Bang! Competition Finals
Undergraduate students Akshay Sethi, Matthew Remich, and managerial economics and MBA student Gerald Dion, presented their business plan for AmberCycle, a synthetic biology-based company that aims to biocycle PET plastic into high-quality products. This project was directly inspired by Akshay and Mattan’s success at the 2012 iGEM competition but evolved tremendously since then. The presentation was outstanding!! Congratulations to the team for making it to the final five!
4/29/2013 – MIT’s Dr. David Kong videos into BIM143 lecture
Dr. David Kong, from Lincoln Lab and MIT, and Facciotti have collaborated to create a short microfluidics/gene assembly wet lab in Facciotti’s Synthetic Biology elective course BIM143. Dr. Kong donated devices and videoed in, Invitrogen provided reagents, and our students brought their enthusiasm. Thank you to Dr. Kong and Invitrogen for the wonderful contributions!
2/14/2013 – Lizzy Wilbanks Receives Dissertation Year Fellowship from UC Davis
Graduate student Lizzy Wilbanks has received a dissertation year fellowship from UC Davis. This fellowship will run for the 2013-2014 academic year. As a part of the award, Lizzy will give two research talks, one at UC Davis, and a second at another UC or CSU campus. Congratulations Lizzy!
2/5/2013 – Another Paper Published!
The work of former undergraduate student Ayla Sessions (now attending graduate school at UCSD) along with a collaboration with Dr. Yong Duan and Dr. Ting Wang has resulted in the paper entitled, “Deprotonation of d96 in bacteriorhodopsin opens the proton uptake pathway.” Check it out on our publications page: Facciotti Lab Publications.
1/16/2013 – “JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison”
Graduate student Phil Seitzer has created a new and awesome bioinformatic tool for comparative genomics. Check out the paper in BMC Bioinformatics. And the Java based script on our Software page.
1/4/2013 – Paper Published in ACS – Synthetic Biology
The work of undergraduates, Keegan Owsley, Tim Fenton and the rest of the 2010 UC Davis iGEM Team has culminated in the publication entitled, “Promoter Element Arising from the Fusion of Standard BioBrick Parts” is now published! The work involved collaboration between the Facciotti Lab and the Tagkopoulos Lab.10/29/2012 – iGEM Team Prepares for World Championship JamboreeThe 2012 UC Davis iGEM team is making their final preparations for the World Championship Jamboree at MIT starting Nov. 2nd. This hardworking group of 10 undergraduates is excited to represent both UC Davis and their work to the rest of the world! You can find more information about their project through their wiki: Scientific Track and Entrepreneurship Track.
10/13/2012 – iGEM Team Invades Stanford
The 2012 iGEM team has traveled to Stanford, CA to attend the iGEM Americas-Western Regional Jamboree. Competing against 24 other deserving teams, this year’s iGEM team hopes to advance to the World Championship Jamboree held in Cambridge, MA in early November.
10/11/2012 – Lab Updates
We’ve been very busy at the Facciotti Lab! For the year, we have published 5 papers, with another in press. Keep an eye out for another two manuscripts which were just submitted and one more that is on the brink of submission! Find links and citations to these new manscripts on our Publications Page.
07/01/2012 – Facciotti Awarded a Hellman Fellowship
Dr. Facciotti was awarded a Hellman Fellowship for 2012-2013. The award will support new work on ChIP-seq.
03/24/2012 – Mike Starr Presents at UC Davis DEB Symposium
Graduate student Mike Starr presented his work on haloarchaeal bioplastic production at the annual DEB symposium at Christian Brothers Winery in Napa today. It was a great talk!
02/09/2012 – A workflow for genome-wide mapping of archaeal transcription factors with ChIP-Seq
The manuscript, “A workflow for genome-wide mapping of archaeal transcription factors with ChIP-Seq” has now been published! This effort was made possible by the collective work of graduate students, lab technicians, and undergraduate students, espeically Rachel Kjolby and Chia-Ying Wu (both now lab alumni). Check out a copy of the manuscript here.
01/12/2012 – New Article in Press
The Facciotti Lab is starting off 2012 strong – we have a new and exciting paper in press! The manuscript titled, “A workflow for genome-wide mapping of archaeal transcription factors with ChIP-Seq” has been officially accepted by Nucleic Acids Research and should be available to view in the coming weeks.
01/12/2012 – @FacciottiLabUCD
The Facciotti Lab wishes everyone a happy new year! Follow our new twitter account: @FacciottiLabUCD for instant updates on lab news and other interesting scientific tidbits. Here’s to a science filled 2012!
11/07/2011 – The Awards Keep Coming!
The 2011 UC Davis iGEM team has been recognized with the BEST FOUNDATIONAL ADVANCE award for their work developing a simple and effective workflow for expanding part families, their characterization, and their visualization in 3D on the web. To find out more about their project visit their wiki: http://2011.igem.org/Team:UC_Davis
11/07/2011 – The UC Davis 2011 iGEM Team Places in the Top Sixteen of the World Championship Jamboree!
The 2011 UC Davis team of Keegan Owsley, Tim Fenton, Aaron Heukroth and Nick Csicsery wrapped up their unbelievable run in this year’s iGEM competition by placing in the Sweet Sixteen at the World Championship Jamboree. The 2011 iGEM competition included hundreds of teams vying for 65 spots in the World Championship Jamboree that included traditional powerhouses of MIT, Berkeley, Imperial College London, a Brown – Stanford collaborative, and Yale among many others. To see a list of the top 16 teams in the WORLD follow this link: http://igemwatch.net/?attachment_id=1766
10/28/2011 – ARC Students Visit Genome Center
The Facciotti Lab and the Genome Center hosted 13 students from Prof. Ken Kubo’s American River College Biotechnology Club. Marc Facciotti and Erin Lynch led a tour of the Genome Center facilities and discussed trends in modern biology, strategies for successfully transferring to a research university, and what it takes to get a job doing work at the cutting edge. Prof. Oliver Fiehn graciously took time to talk with the students about metabolomic research while graduate student Russell Neches showed off his new 3D printer. It was a fun afternoon for all!

Prof. Facciotti shows students around a typical research lab.

Russell Neches shows off his new 3D printer.

Prof. Fiehn of the Genome Center talks metabolomics.

10/10/2011 – Another Gold Medal for iGEM!
The 2011 iGEM team has earned another GOLD medal at the iGEM Regional Jamboree in Indianapolis, Indiana. To learn more about their project visit the team wiki: http://2011.igem.org/Team:UC_Davis
10/8/2011 – Off to Indy!
Dr. Facciotti and the iGEM team have set off to Indianapolis, Indiana for the iGEM Regional Jamboree. Results from the competition and more information about iGEM can be found on the iGEM website: http://igem.org/Main_Page
8/9/2011 – New Article In Press!
Andrew Yao and Marc Facciotti’s newest paper, “Regulatory multidimensionality of gas vesicle biogenesis in Halobacterium salinarum NRC-1″ is now in press! A provisional copy of the manuscript can be found here.
8/6/2011 – Just published!
Aaron Darling, Andrew Tritt, Jonathan Eisen and Marc Facciotti just published the manuscript “Mauve assembly metrics” in Bioionformatics. To read the paper click here.
7/11/2011 – Facciotti Lab Welcomes GREAT Program Intern
The Facciotti Lab is happy to welcome Weiwei Yang visiting us from Zhejiang University in Hangzhou, China as part of the UC Davis GREAT program.More information about the GREAT Program can be found at: http://great.ucdavis.edu/
6/23/2011 – High School Interns Ready to Work
2011 Summer Interns Katie Shao and Kathryn Tutt with local high school teachers Ann Moriarty and Mylee Lam have joined the Facciotti Lab for the summer. They will be investigating the world of halophiles and working on developing experiments that will inspire high school students to pursue science. You can keep up to date with their work on their website.
6/20/2011 – Ready Set… iGEM!
The 2011 UC Davis iGEM Team of Tim Fenton, Keegan Owsley, Aaron Heuckroth and Nick Csicsery are now officially in lab, hard at work on their project. Watch out for progress reports and interesting happenings coming soon!
6/14/2011 – Phil Seitzer Presents at 12th Annual UC Systemwide Bioengineering Symposium
Phil Seitzer has presented his work titled “An Iterative Monte Carlo Simulation Algorithm Reveals Subtle Variations in Common Regulatory Motifs of Closely Related Transription Factors” at the 12th Annual UC Systemwide Bioengineering Symposium (http://engineering.ucsb.edu/biosymposium/) in Santa Barbara.
5/26/2011 – Two Facciotti Lab High School Interns Win $1000 Dollar Scholorship
2010 Davis Senior High intern Brooke Darah and current Davis Senior High intern Katie Shao have each won $1000 Monsanto Imagine Scholarships for their work in the lab. Congratulations Brooke and Katie! For more information about summer internships please visit our education page.
5/20/2011 – Facciotti Lab Heads To New Orleans For ASM Conference
Marc, Lizzy and Erin will be attending the ASM Conference this weekend in New Orleans. Marc and Lizzy will be talking, while Lizzy and Erin will be presenting posters. For more information about ASM or the conference please visit the ASM Conference Home Page.
3/21/2011 – Facciotti Lab Intern Katie Shao Wins at Sacramento Science Fair
Davis Senior High School student intern Katie Shao was awarded 1st Place for her project titled “Evolutionary Genetics: a Novel Means of Engineering Technologically Efficient Bacteriorhodopsins” in the Chemistry and Health Sciences Senior Division of the Sacramento Regional Science Fair. The competition was held March 18th at Rosemont High School in Sacramento. Congratulations to Katie!
3/12/2011 – 69th Genome AssembledThe hard work of Research Associate, Andrew Tritt, has resulted in the successful assembly of our 69th haloarchaeal genome!
2/8/2011 – Roche 454 Jr. SequencerThis new tool will be shared by the Genome Center and is ready to sequence some bugs. The first organism to be sequenced will be a halophilic organism that was isolated by Davis Senior High students from commercial salts.
2/3/2011 – Facciotti Lab Welcomes Erin LynchWe welcome the newest graduate student to our lab, Erin Lynch. Congratulations!
1/31/2011 – 50+ New Halophiles SequencedWe have just shotgun sequenced 50+ new halophilic archaea through the DNA Technologies Core at UC Davis. To find out which organisms were sequenced and other sequence information please visit the Haloarchaea Phylogenomics Database: here.

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