A new paper in Nature by Alexander Green et al. on “Cellular logic computation using ribocomputing devices” describes a 12-input logic gate that operates at the post-transcriptional level (i.e. as switchable RNA toeholds). IEEE Spectrum, the flagship magazine of the world’s largest professional engineering organization, reached out to Julius for his […]
The Lucks Lab is hiring a research technologist. If you, or someone you know, is interested in working with a great team of scientists unraveling the RNA sequence:structure:function relationship, this job may be for you! See the job listing here. Job Summary: The Research Technologist will perform duties in […]
Congratulations to one of the first postdocs of the Lucks Lab, Dr. James Chappell, on starting his lab at Rice University! James joins the BioSciences department at Rice as an assistant professor, where he’ll be focused on creating RNA regulators of gene expression, exploring the portability of these regulators in bacteria […]
The group’s paper on Cotranscriptional folding of a riboswitch at nucleotide resolution has been recommended by F1000Prime! F1000, or Faculty of 1000, is a post-publication peer review service which utilizes recommendations from thousands of experts to recommend the most important papers in the field. Our work on Cotrans SHAPE-Seq was recommended by F1000 […]
Luyi Cheng, a PhD student in the IBIS graduate program at Northwestern, has joined the Lucks Lab for her PhD research! Luyi completed her B.S. in Biochemistry at the University of Washington and did undergraduate research in structural biology. She brings her expertise and passion for structural biology to the […]
Phillip Clauer, who just wrapped up his sophomore year in the Biochemistry and Molecular Biology program at Penn State, has joined our lab for summer research! For the past 2 years Phillip has been working on genetic circuits in the Salis Lab at Penn State, and he’s hoping to expand his […]
The latest publication from the Voigt lab, published today in Nature Chemical Biology, describes the use of an elaborate optogenetic circuit in E. coli to create spatially and temporally resolved pattens of gene expression that respond to light. In this particular instance, expression of red, green or blue fluorescence proteins is triggered by exposure […]
Congratulations to Julius Lucks for being named a Camille Dreyfus Teacher-Scholar! This prestigious award of the Camille and Henry Dreyfus foundation is given annually to young faculty who have an outstanding body of scholarship and a commitment to education in the fields of chemistry, chemical engineering and related sciences. Click […]
Several Northwestern University Center for Synthetic Biology faculty, staff and students are featured in a Northwestern University video “At Northwestern, We March for Science Everyday.” Click the link to see our own, Julius Lucks, voicing his support for public funding of scientific research!
A new nucleic acid detection method promises attomolar detection of viral nucleic acids using the CRISPR-Cas13a/C2c2 system. The work, published last week in Science, hit the web during the same week as attorneys for UC Berkeley announced that they will appeal the USPTO’s decision that Berkeley’s CRISPR patents do not overlap with those […]
Eric and Kyle’s paper “Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding” is now online at Nucleic Acids Research! This work makes cotranscriptional SHAPE-Seq even easier and more accessible by developing a “one-pot” synthesis for roadblocking DNA templates and uncovers important details about how collision with different transcription roadblocks can […]
Alex’s paper “Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator” is online in Nucleic Acids Research. In this work we report a breakthrough in RNA engineering that allowed us to create some of the largest dynamic range RNA regulators we currently know of that […]
Adam Silverman has joined the Lucks lab as a PhD student in the Department of Chemical and Biological Engineering. Adam completed his undergraduate degree from Georgia Tech’s Department of Chemical and Biomolecular Engineering. As an undergrad, Adam worked in the Mark Styczynski lab on developing a clinically-relevant bacterial biosensor for […]
James and Julius were recently asked to write a preview on a new paper published in Cell Systems (“Design and Construction of Generalizable RNA-Protein Hybrid Controllers by Level-Matched Genetic Signal Amplification”). Read their preview, “Turning It Up to 11: Modular Proteins Amplify RNA Sensors for Sophisticated Circuitry,” on how ligand-sensing RNA […]
Congratulations to Dr. Loughrey on successfully defending his PhD work! David joined the Lucks lab after completing his B.S. in Chemical Engineering at University College Dublin and has been instrumental in helping the lab develop next generation techniques for RNA structure determination. Check out David’s publication on SHAPE-Seq 2.0 here! […]
We are seeking a creative and enthusiastic postdoctoral researcher to lead a project to map nascent RNA structure as part of multiple efforts sponsored by the NIH. Recently our laboratory created co- transcriptional SHAPE-Seq which uses chemical probing and next-generation sequencing to map the structure of nascent RNAs at single-nucleotide […]
Julius and James recently shared with Benchling, a life science data management and collaboration platform, the conceptual design and implementation of small transcription activating RNAs (STARs). The minisite details how terminator structures in biology are used to halt transcription and how they can be cleverly reconfigured to attenuate or activate […]
Julius and Khalid recently attended the inaugural retreat of the Engineering Biology Research Consortium (EBRC) held at Caltech. EBRC (https://www.ebrc.org) aims to be the leading organization in the field of synthetic biology, showcasing cutting-edge research, identifying and addressing global challenges in the field, and building an inclusive community of students, […]
Congratulations to the iGEM team at Imperial College who managed to win the Grand Prize at this years iGEM competition for their “ecolibrium” project that we recently featured on our website. @imperialigem wins the Grand Prize at #iGEM2016 #GiantJamboree! Congratulations! You guys are some real STARs! https://t.co/4i9ayYM3Nh — The Lucks […]
Kyle, Eric, and Angela’s paper “Cotranscriptional Folding of a Riboswitch at Nucleotide Resolution” is online in Nature Structural and Molecular Biology and a featured news story through Northwestern. With the development of cotranscriptional SHAPE-seq, this paper marks a milestone in RNA biology as the first strategy for the measurement of nascent RNA […]
In the weeks before officially moving to the Chicagoland area, the Lucks Lab attended the 2016 SEED (Synthetic Biology: Engineering, Evolution & Design) conference, held in the historic Hilton Chicago. As part of receiving the ACS Synthetic Biology Young Investigator Award, Julius presented a research seminar on the groups latest […]
Congratulations to the Imperial College London 2016 iGEM team for using Small Transcription Activating RNAs (STARs) regulators in their project – ecolibrium! Their project looks at developing a framework and new tools for engineering co-cultures of bacteria. We’re honored that they choose to use STARs and the power of RNA […]
Eric and Julius recently attended the 18th Annual Rustbelt RNA Meeting in Cleveland. Eric had the opportunity to present a short talk on his latest work on SHAPE-Seq technology and was later presented with the award for best talk! Congratulations Eric!
The entire Lucks Lab for RNA Engineering has recently moved to Northwestern University! The lab joins the Department of Chemical and Biological Engineering in the McCormick School of Engineering and joins Danielle Tullman Ercek’s group as the newest members of Northwestern’s Center for Synthetic Biology, which aims to program biological […]
The Lucks Lab for RNA Engineering is excited to announce that Khalid K. Alam has joined the lab as the newest postdoctoral fellow! Khalid recently completed his PhD work on aptamer evolution and engineering from the Burke Lab at the University of Missouri, and supplements the Lucks Lab’s expertise […]
Julius was named the recipient of the 2016 ACS Synthetic Biology Young Investigator Award. Established in 2014, the award recognizes the contribution of a scientist who has made a major impact on the field of synthetic biology, early in their career. Julius was presented with the award and gave a […]
Katherine and Matthew have joined the lab from the Biochemistry, Molecular and Cellular Biology program – welcome Katherine and Mathew!
Anyone that has spent any time with us knows how much we love Trello. If you haven’t heard of it, it is a lightweight team management tool that we use throughout the lab – from writing papers and grants, to managing lab orders and our lab safety system. We’ve even […]
Dr. Watters next heads to Jennifer Doudna’s lab – go Dr. Watters!
Kyle is the recipient of an Austin Hooey Graduate Award. The Hooey award is the highest honor that CBE bestows on graduate students, and recognizes those students who have demonstrated the highest research quality and productivity, and who have demonstrated a track record of service to their research group, department, and community. […]
Congratulations Alex for winning the CBE 2016 Outstanding Scholar Award! The award recognizes Alex’s outstanding research accomplishments as an undergraduate and his transition to industry where he will join Caribou Biosciences. Congratulations Alex!
Melissa, Kyle, Tim and Paul’s paper “Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators” is out in RNA! This paper marks an important milestone for us – its our first manuscript on using information gleaned from in-cell SHAPE-Seq experiments to inform the design of new […]
Spats v1.0.0 is an update to the Spats pipeline for processing Next-Generation Sequencing Reads as part of SHAPE-Seq experiments. The major difference between v0.8.0 and v1.0.0 is the migration to the cutadapt utility for removing adapter sequences from the fastxtoolkit. This release still relies on fastx_revcomp, but the code is structured […]
Kyle, Angela, Eric and Alex’s paper “Characterizing RNA structures in vitro and in vivo with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)” is out in Methods! This is a very comprehensive manuscript, outlining the necessary background for understanding chemical probing of RNA structure – from the experiments that can […]
Eric, Kyle and David’s review “RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs” is out in Current Opinion in Biotechnology! In this review, we outline the case that the time is right for a systems-level study of RNA structure and function – partly […]
Cameron’s review “Engineered Protein Machines: Emergent Tools for Synthetic Biology” is out in the inaugural edition of Cell Chemical Biology! This is a great summary of recent work in synthetic biology to make ‘orthogonal’ versions of core cellular protein machines – from polymerases all the way to ribosomes. By acting […]
Julius was recently invited to be a member of the Editorial Board of Nucleic Acids Research. Nucleic Acids Research is a preeminent journal featuring cutting edge research into the physical, chemical, biochemical and biological aspects of nucleic acids and the protein machinery that interacts with them in the cell. Its […]
Chelsea recently passed her A exam and Karl recently passed his masters exam – congratulations! Karl will be joining Merk back in Ireland soon – we’ll miss you Karl!
Julius was the recent recipient of the Mr. and Mrs. Richard F. Tucker `50 Excellence in Teaching Award, the highest award for teaching in the Cornell College of Engineering. The award recognizes Julius’ excellence and achievements in teaching Heat and Mass Transfer, and his co-creation of ChemE 7770 “Advanced Principles […]
We were recently delighted to host Professor Venkat Gopalan from Ohio State University in the lab! Professor Gopalan studies RNase P, an ancient RNA that catalyzes a key reaction required for all life. It’s discovery by Sidney Altman earned him a Nobel Prize in Chemistry 1989 for the discovery that RNA molecules can […]
Sarai’s paper was recently featured in a Biotechnology and Bioengineering spotlight Shining RNA STAR power on bacterial gene expression. Each issue of B&B features four spotlights highlighting the most exciting work in the journal. It’s quite an honor! Congratulations Sarai, James, Sitara and Rebecca!
The Lucks Lab now officially has an Addgene page! Addgene is a non-profit plasmid repository that promotes sharing of life sciences research materials through their distribution system. We have greatly benefited from easy access to the explosion of molecular tools out there which has really helped us accelerate our research! If […]
Sarai and Alex recently won best poster awards for their posters on engineering STARs and RNA circuits at the 2015 Fall SynBERC retreat! Congratulations team!
We recently helped out with a new public engagement activity called ‘Building with Biology’! Sponsored by the National Science Foundation and based at the Museum of Science in Boston, Building with Biology is a program designed to promote conversations between the public and scientists about synthetic biology. As part of […]
Our method for characterizing the cellular structure and function of RNA regulators is out in Nucleic Acids Research. The paper outlines our method for applying SHAPE-Seq to characterize RNA structures within E. coli cells by directly applying the 1M7 SHAPE reagent to cell culture. Since we are very interested in […]
Kyle has been selected as an inaugural Fleming Graduate Scholar in the School of Chemical and Biomolecular Engineering. The Fleming Scholarships are due to a generous gift from Sam and Nancy Fleming to support the most outstanding PhD students pursuing research in biomolecular engineering at Cornell. Congratulations Kyle!
We have an influx of new Lucks Lab members! Welcome Angela, Aron, Jane, Yan and Raashed!
We had another fantastic year at the Cold Spring Harbor Laboratory Synthetic Biology summer course! Led by James (universally voted a Rock STAR scientist by everyone at the course), we successfully delivered a thrilling module on characterizing genetic circuitry using cell-free TX-TL reactions. Actually I can’t thank James enough for all […]
A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future is out in Current Opinion in Chemical Biology! James, Kyle and Melissa did a fantastic job making our case for why we think we are in a renaissance in RNA synthetic biology right now. In the review, […]
Our paper on improving Small Transcription Activating RNAs with Rational RNA Engineering Strategies is out in Biotechnology and Bioengineering! In this paper, Sarai, James, Sitara and Rebecca outline several different strategies for improving the fold activation of weak STARs, including promoter tuning and RNA stabilization strategies. We hope this helps […]
Our paper on Generating effective models and parameters for RNA genetic circuits is out in ACS Synthetic Biology. In this paper, Chelsea developed a simplified ODE model to model the dynamics of RNA genetic circuits. These ‘effective’ models essentially course grain a lot of the biochemical details of gene expression […]
We were recently invited to prepare a paper for the journal Methods about using cell-free transcription-translation reactions (TX-TL) to characterize genetic circuits. We immediately joined forces with Vincent Noireaux’s and Richard Murray’s groups and had a lot of fun putting this together! What started out as a brief intro to the […]
Congratulations Rebecca, Melissa, Misha, Tim, Ray and Sitara (not pictured)! Melissa is our first Dr. from the group, and will be joining Jim Collin’s lab at MIT in the Fall as a post-doctoral researcher. Also staying on the East Coast, Misha will be headed to join a consulting firm in […]
This month, the issue of ACS Synthetic Biology is devoted to RNA Synthetic Biology. In addition check out our shout outs! Melissa and James are featured in Introducing Our Authors. Justin Gallivan has a very nice perspective called RNA Synthetic Biology: From the Test Tube and Back Again. It includes […]
Melissa -> Dr. Takahashi!
Melissa is the recipient of an Austin Hooey Graduate Award. The Hooey award is the highest honor that CBE bestows on graduate students, and recognizes those students who have demonstrated the highest research quality and productivity, and who have demonstrated a track record of service to their research group, department, and […]
The Division of Molecular and Cellular Biosciences (MCB) at the National Science Foundation (NSF) recently launched a blog to keep people up to date on the exciting science that they are funding. Today’s post actually featured the Lucks Lab, and talked about some of our exciting breakthroughs and outreach activities we […]
STARs are featured in the April issue of Nature Methods! In her Research Highlights article “RNA that activates transcription”, Nicole Rusk describes some of the behind the scenes of how we created STARs. She also does a great job of capturing the spirit and the mission of the Lucks Lab!
Cameron and Tim have been awarded the prestigious NSF Graduate Fellowship. The NSF graduate fellowship recognizes and supports outstanding graduate students in science and engineering, and is one of the most highly sought after awards at this stage of their careers. NSF fellows have gone on to become recognized leaders in their […]
Eric Strobel is the newest addition to the group! Eric comes to us from Jeff Robert’s lab at Cornell and is an expert on transcriptional pausing. For a bit of history, the Robert’s lab did pioneering work on deciphering the mechanism of intrinsic termination, making Eric’s addition to the group […]
We are doing the CSHL Summer Course again this year. Please apply!
And Trending #1!
James and Melissa’s Nature Chemical Biology paper on “Creating Small Transcription Activating RNAs” (STARs) is out! As we all know, RNA is an awesome molecule that does many things across the cell. It is particularly good at regulating gene expression. However, we noticed recently that of all the things RNA does […]
Julius is the recipient of a 2015 CAREER Award from the National Science Foundation. According to the NSF, “the Faculty Early Career Development (CAREER) Program is a Foundation-wide activity that offers the National Science Foundation’s most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through […]
According to Google Scholar, the original SHAPE-Seq experiment paper in PNAS has over 100 citations! For those unfamiliar with it, SHAPE-Seq uses chemical probing and next generation sequencing to characterize RNA structures in very high throughput and with nucleotide resolution. It is built off of the powerful SHAPE chemistry developed by […]
Rebecca was awarded another research grant as part of Cornell’s engineering learning initiatives (ELI) program. The ELI program enhances undergraduate learning by providing opportunities for students to engage in cooperative learning and undergraduate research. As part of this program, Rebecca will be working with Sarai on uncovering the design principles that […]
Elizabeth is our newest undergraduate in the lab, working with Paul on engineering RNA gene regulatory systems. Welcome Elizabeth!
Both Sarai and David successfully defended their A exams within the last week to officially become PhD Candidates! They both did an excellent job putting their research into context and describing their fantastic progress towards their thesis research. Everyone was very impressed! Congratulations Sarai and David!
In an effort to bring peace to the galaxy, the Lucks Lab held the first annual Light-Dark Star Wars Federation Conference. While this historic event did not garner the results the organizers had wanted, they still came in second place in the CBE Halloween Costume Party Contest. A behind the […]
Julius has been selected to be the US Chair of the Synthetic Biology Working Group that is part of the EU-US Task Force on Biotechnology Research. Founded in 1990 by the European Commission and the White House Office of Science and Technology Policy, the EU-US Task Force on Biotechnology Research […]
Karl is the latest addition to the Lucks Group. Karl is interested in engineering RNAs to control all aspects of gene expression, and how this can be linked to biotechnology applications. Welcome Karl!
David, Kyle and Alex just published their SHAPE-Seq 2.0 paper in Nucleic Acids Research. This paper was a monumental amount of work, and aimed to address two big issues in the SHAPE-Seq experiment – examining whether or not there were biases in the experiment due to the various steps of […]
Sarai and Melissa received AIChE Women’s Initiatives Committee Travel Awards to attend the AIChE national meeting in Atlanta in November. These are prestigious awards, based on their strong scholastic achievement combined with a demonstrated passion towards the mission of WIC – promoting the entry, development, and participation of women with AIChE […]
The Lucks Lab was recently admitted into the Cornell Field of Computational Biology. Cornell’s field system allows faculty members to create bridges between departments, and is one of the features of Cornell that fosters its highly collaborative environment. Joining the field of computational biology will allow the lab to push […]
Rebecca was awarded research funding as part of Cornell’s engineering learning initiatives (ELI) program. The ELI program enhances undergraduate learning by providing opportunities for students to engage in cooperative learning and undergraduate research. As part of this program, Rebecca will be working with Sarai on uncovering the design principles that underlie […]
Angela Yu is rotating in the lab from the Tri-Institutional computational biology and medicine program. Angela got her undergraduate degree in computational biology at UPenn. She’ll be working on some new computational RNA folding projects in her rotation. Welcome Angela!
Congratulations Chelsea, Alex, Paul and Cameron for passing their qualifying exam with flying colors! Now let’s do some science!
The Lucks Lab is featured in the recent Cornell Engineering Magazine. The article, entitled ‘Code Breaker’, delves into the lab’s quest to unlock the secrets of RNA molecules to both understand and engineer living systems. The article also dives into some of the twists and turns in Julius’ career trajectory, […]
Melissa and Julius are back teaching the CSHL SynBio summer course. Following off of last year’s success, we brought a ton of TX-TL to the course (thanks to Richard Murray!), a bunch of research questions, and some Trello organizational skills to enable the 2014 students to push the boundaries of […]
We traveled out to sunny LA to present some of the lab’s latest work at the inaugural Synthetic Biology, Engineering, Evolution and Design (SEED) meeting. Julius gave a talk on the latest results from the lab and James, Melissa and Chelsea presented posters on their work. We were pumped by […]
Congratulations to Kyle for passing his A exam and ascending to PhD candidacy! Kyle did a fantastic job telling us all about his SHAPE-Seq innovations. Congratulations Kyle!
Congratulations to Helen and Matt for graduating in the Cornell Class of 2014! Helen is off to apply her Chemical Engineering skills to the problems faced by wine production at the E. & J. Gallo Winery in Livingston, CA. In fact, her first job will be as a project […]
Julius gave a talk recently to the Harvard Widely Applied Math (WAM) seminar series on ‘Controlling Cells through RNA Folding’. It was great to be back for an official visit!
Sitara was recently honored with Best Poster in the Applied Research category at the Cornell Undergraduate Research Board’s Spring Forum. Her poster, entitled “Engineering Light-Activated RNA Gene Regulators,” covered her work over the past year. Together with Sarai and Rebecca, Sitara has characterized interactions between RNA aptamers and their […]
Tim is the recipient of the 2014 Cornell Engineering Alumni Association Undergraduate Research Award! Given to the most outstanding undergraduate researcher in the whole Engineering College, this award is one of the highest honors bestowed on undergraduate researchers. Tim received the award because of his extreme enthusiasm, hard […]
Melissa and James’ paper on characterizing the fast dynamics of RNA genetic circuitry is out! We have been hypothesizing for a while that RNA-only circuits would be fast compared to protein circuits because RNAs degrade faster than proteins. (To understand why the speed of genetic circuits is determined by […]
Tim was awarded research funding as part of Cornell’s engineering learning initiatives (ELI) program. The ELI program enhances undergraduate learning by providing opportunities for students to engage in cooperative learning and undergraduate research. As part of this program, Tim will be working with Kyle on continuing to use SHAPE experiments to […]
Who is the new super postdoc on the right? And what is she got up her sleeve?
This just speaks for itself …
Our review was recently featured in a Biotechnology Journal Editorial by Kristala Prather and Ali Khademhosseini – “Biomolecular Engineering – latest advances and applications.” In the editorial, Julius’s talk from the 2013 ICBE meeting – “A Family of Orthogonal Chimeric Antisense RNA Transcription Regulators” (based on Melissa’s NAR Paper) was highlighted along […]
Julius recently attended the NIH High-Risk High-Reward symposium in Bethesda, MD as part of our NIH New Innovator Award. It was truly an amazing group of people with talks from some of the most innovative researchers supported by the NIH!
Ray Zhuang, a junior CBE major in the Lucks Lab has been chosen by Genentech to win the Scheele Outstanding Junior Award. The award “recognizes a student who excels in scholarship, leadership, and campus activities, and is given to a student who “upon graduation will be a positive reflection of […]
Welcome to the four new CBE graduate students in the lab: Chelsea Hu, Paul Carlson, Alexandra Westbrook and Cameron Glasscock!
Julius was recently quoted in “What Are Genetically Recoded Organisms?” in Popular Science by Francie Diep. The article is a nice read about the Isaacs’ lab recent Science paper “Genomically Recoded Organisms Expand Biological Functions”. The paper describes the first complete milestone of the rEcoli project (see here for an […]
Sarai won the Best Poster Award at the 4th annual CBE Graduate Research Symposium for her poster “Engineering Light Activated RNA Transcriptional Switches”. Students and faculty from all of the broad research areas covered by CBE vote on the best poster awards, reflecting Sarai’s great job in communicating her research […]
Our review paper “The Centrality of RNA for Engineering Gene Expression” is out! The review covers the ethos of the lab, and has three main sections: an update of all the known natural and synthetic RNA-based regulatory mechanisms out there, an outline of computational RNA structure prediction tools and how they have […]
Julius was quoted in the recent article “DARPA Courts Biotech Researchers” on the benefits of the DARPA YFA program getting junior faculty into the DARPA system. It is an interesting read about the role DARPA can play alongside more traditional funders like the NIH to continue to propel biotech research. See the […]
Julius has been named a New Innovator by the Director of the National Institutes of Health, Dr. Francis Collins. The goal of the NIH Director’s New Innovator Award Program is to support exceptionally creative new investigators who propose highly innovative projects that have the potential for unusually high impact. The […]