News


Adam joins the lab!

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 […]

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James and Julius preview a new article in Cell Systems!

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. David Loughrey on passing his defense!

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! […]

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Benchling minisite details the use of STARs for transcriptional control.

  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 […]

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The Lucks Lab and Northwestern featured prominently at the EBRC fall retreat!

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, […]


STARs Win Best New Basic Part Award at iGEM 2016 Competition!

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 […]


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Our paper on Cotranscriptional SHAPE-Seq is published!

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 […]


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Imperial iGEM team uses STARs!

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 […]


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The Lucks Lab moves to Northwestern University

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 […]


Khalid K. Alam joins as a postdoctoral fellow!

  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 […]

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Our 11th Paper is Published with Trello!

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 […]


Kyle Wins Austin Hooey Graduate Award

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. […]


Spats v1.0 is released!

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 […]


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Our methods paper on SHAPE-Seq v2.1 is out!

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 […]


Our review on RNA Systems Biology is out!

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 […]

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Cameron’s review on engineered protein machines is out!

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 joins Nucleic Acids Research Editorial Board!

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 […]

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Julius receives College Teaching Award

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 […]


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Professor Venkat Gopalan Visits the Lab!

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 Featured in B&B Spotlight!

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!

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Get our plasmids from the Lucks Lab AddGene Page!

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 […]


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Lucks Lab helps ‘Build with Biology’

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 in-cell SHAPE-Seq paper is out!

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 […]

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Kyle Becomes an Inaugural Fleming Fellow!

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!


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Another Great Year at CSHL SynBio

  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

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, […]

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Improving STARs with Rational RNA Engineering Strategies

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 RNA Circuitry Modeling Paper is Out!

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 […]

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Our TX-TL Methods Paper is Out!

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 to our Graduates!

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 […]

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Melissa wins Austin Hooey Graduate Award

  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 […]

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Lucks Lab Featured on NSF MCB Blog!

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 Featured in Nature Methods

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!

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Cameron and Tim Win NSF Graduate Fellowships!

  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 joins the group!

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 […]


STARs are born in Nature Chemical Biology!

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 […]

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Julius wins NSF CAREER award

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 […]


SHAPE-Seq turns 100!

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 […]


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Rebecca wins ELI funding again!

  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 […]


Sarai and David pass their A exams!

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!


Karl Brennan joins the lab!

  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!

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Our SHAPE-Seq v2.0 Paper is Out!

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 […]


Julius joins Computational Biology Field

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 wins an ELI Scholarship!

  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 […]

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Angela Yu Rotates in the Lab!

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!


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Lucks Lab Featured in Engineering College Magazine

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, […]


Kyle Passes his A Exam!

    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!

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Helen and Matt Graduate!

  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 […]


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Sitara wins Best Poster in Applied Research at CURB Spring Forum

  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 Wins Cornell Engineering Undergraduate Research Award

    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 […]

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Our ACS SynBio Paper on Fast RNA Circuitry is Out!

  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 wins an ELI scholarship!

  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 […]

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“Centrality of RNA for Engineering Gene Expression” featured in Biotechnology Journal Editorial

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 […]


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Ray Wins Genentech Scheele Outstanding Junior Award

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 […]


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Julius Quoted in Popular Science

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 Wins Best Poster Award

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 […]

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The Centrality of RNA for Engineering Gene Expression

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 Quoted in the Chronicle of Higher Education

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 […]

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Julius Named NIH Director’s New Innovator

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 […]


Lucks Lab helps create first CSHL Synthetic Biology Course

Julius and Melissa have helped create the first Cold Spring Harbor Laboratory (CSHL) summer course on synthetic biology. Cold Spring Harbor Laboratory has hosted summer courses and conferences on important topics of biology for over 65 years. Notable past courses include Max Delbruck’s original phage course, which helped crystallize the […]

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Rebecca Chew Joins the Group

Rebecca is our newest undergraduate in the lab, working with Sarai on engineering RNA switches. She is also part of Cornell’s 2013 iGem team which is off to a great start. Welcome Rebecca!

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Julius named James C. and Rebecca Q. Morgan Sesquicentennial Fellow

Julius has been named a James C. and Rebecca Q. Morgan Sesquicentennial Faculty Fellow in honor of the generous gift of the Morgans for recruiting emerging “stars” to the Cornell Faculty as part of the Faculty Renewal Sesquicentennial Challenge (http://as.cornell.edu/alumni/sesqui-challenge.cfm). More information at http://www.cheme.cornell.edu/news/index.cfm?news_id=62848 .


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Our First Paper is Published!

Melissa’s paper has been published in Nucleic Acids Research! A modular strategy for engineering orthogonal chimeric RNA transcription regulators outlines our new approach to creating basic RNA transcriptional regulators that can be used to build genetic networks. The background of the approach can be found here, where we showed how RNA-based transcription attenuators […]


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Sitara and Tim Win ELI Scholarships!

Sitara and Tim were awarded summer 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, Sitara and Tim will be working with Sarai and Kyle on […]


Julius awarded ONR Young Investigator Award!

Julius has been named a 2013 Office of Naval Research Young Investigator Award recipient. The ONR Young Investigator Program (YIP) seeks to identify and support academic scientists and engineers who show exceptional promise for doing creative research. The program aims to attract these rising stars to the Department of Navy’s […]

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Ray wins Amgen Research Scholarship!

Ray has been awarded a prestigious Amgen Research Scholarship to perform research at UC Berkeley this summer. The Amgen scholars program provides support for the country’s best and brightest undergraduate researchers to expand their research experiences. It is a highly competitive process and a great honor. Good work Ray!


Julius Wins Sloan Research Fellowship!

Since 1955, the Sloan Research Fellowships have sought to stimulate fundamental research by early-career scientists and scholars of outstanding promise.  These two-year fellowships are awarded yearly to 126 researchers in 8 fields in recognition of distinguished performance and a unique potential to make substantial contributions to their field. Previous Sloan […]

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Misha Baheti and Alex Settle join the group!

Misha and Alex are the two newest undergraduates in the group. Misha will be working with Melissa on engineering RNA circuitry, and Alex will be working with Kyle to dissect RNA structures in the cucumber mosaic virus genome as part of our Gates grant. Welcome to the lab!