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April 29, 2026
We're honored to be recognized with the 2026 Open Science Champion award by the Center for Open and REproducible Science, with special shout out to Eterna! Check out Stanford Data Science's CORES symposium!
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March 19, 2026
Our lab had a retreat at the Marconi Lodge to discuss the future of RNA modeling and design, organized by Ann Kladwang. We're really grateful to recent alumni in California — David Cox, Kalli Kappel, and Rachael Kretsch — for joining us. Join them as they kick off their independent research careers at Stanford, UCLA, and Harvard!
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February 25, 2026
Stanford Medicine magazine explains how the Greenleaf lab and our lab worked with the Eterna gaming platform to create tiny RNA computers. These RNA's can sense ratiometric gene signatures and may enable low cost diagnostics and therapeutics for active tuberculosis and other complex diseases.
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February 18, 2026
Welcome to Chaitanya Joshi, our newest postdoctoral fellow! Chaitanya is joining our lab after developing the first RNA deep learning design methods at the University of Cambridge! He's both an A*STAR fellow and Stanford Data Sciences Fellow.
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February 1, 2026
We've been selected to lead a big project on RNA Structure Prediction as part of the first wave of the new AI@HHMI initiative! The project integrates AI with gigascale biochemical datasets and internet-scale crowdsourcing to advance RNA 3D structure prediction. If you're interested in joining the team as an AI and Data engineers, our close collaborators at Janelia Research Center are hiring!
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January 7, 2026
We've launched Part 2 of the Stanford RNA 3D Folding Challenge on Kaggle! Deadline is March, 2026. Hidden leaderboard targets now include cryo-EM structures of new-to-Nature RNA folds, RNA complexes with small molecules and proteins, and assemblies up to 6000 nts, solved in collaboration with the AI@HHMI initiative at Janelia Research Center and experimental groups around the world.
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January 2, 2026
A great way to kick off the new year – PDB's first 2026 "Molecule of the Month" are natural RNA-only assemblies discovered by Rachael Kretsch in our lab!
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November 7, 2025
CASP16 special issue papers led by Rachael Kretsch assess the quantitative 3D accuracy and biological relevance of blind RNA structure predictions from ~60 groups and, for the first time, water ensembles around an RNA. Our lab also contributed to assessment of protein complexes. The overall picture: deep learning has fueled limited progress in modeling RNA and its complexes, with much progress required. In 2026, we'll be returning to CASP not as assessors but as predictors – reach out if you're interested in helping us close the gap!
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September 24, 2025
We closed the Stanford RNA 3D Folding competition on Kaggle! Congratulations to Kagglers john, odat, and team Eigen for producing the first automated solutions to RNA structure prediction problems that are human-competitive in a blind prediction challenge. Read more at our summary post and the solution summaries on the leaderboard. And here's the Preprint!
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April 30, 2025
Christian Choe, joint between the Das and Huang labs, defended his Ph.D. thesis on "RNA Calculators and Protein Sculpting" successfully. Congratulations, Christian!
Previous news
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April 29, 2025
Congratulations to Rachael Kretsch, joint student between the Das and Chiu labs, for defending her thesis "Dissecting the unnoticed: how cryo-EM led to conceptual shifts and structural discovery in RNA"!
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April 3, 2025
Congratulations to lab postdoctoral fellow Alissa Hummer for being selected as a Schmidt Science Fellow! Alissa make a pivot from machine learning to biochemistry, with a focus on RNA's biological interactions.
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February 27, 2025
We've launched the Stanford RNA 3D Folding challenge on Kaggle! Come see if your codes for 3D structure prediction can beat the top experts in the world and get to biologically meaningful accuracies. Along with collaborators from CASP, RNA-Puzzles, and the Institute of Protein Design, we'll be releasing Easter eggs throughout the challenge up until the final submission deadline of 29 May, 2025. Let’s get to superhuman performance for RNA structure prediction! See you in the Kaggle discussions!
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February 15, 2025
Welcome to Hazel Yang and Jigyasa Verma! Hazel is joining the lab after her Ph.D. research in cryo-EM technology development with Hongwei Wang at Tsinghua University. Jigyasa is coming to us from her Ph.D. work at U. British Columbia with Christopher Lowen.
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February 1, 2025
A paper summarizing results of the RNA-Puzzles blind competitions over many years is now out in Nature Methods! Due to conflicts (involvement in experimental structure determination), we had to sit out a few of these targets, but we're stoked that our methods, based on Rosetta modeling with human input, still top out rankings based on best-RMSD structures.
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January 5, 2025
Rhiju will chair the first session "Structure-Based Elucidation of RNA Function" at the 2025 Gordon Conference in RNA Nanotechnology. See you in Ventura, CA!
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December 10, 2024
Rhiju will be in Stockholm to celebrate the recent Nobel Prizes in RNA, molecular structure prediction and design, and deep learning, along with many other trainees of the amazing David Baker! See you there, and congratulations to this year's Nobel laureates!
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December 1, 2024
This year's Critical Assessment of Structure Prediction (CASP16) involved a beautiful array of RNA, RNA-protein, RNA-DNA-protein, and RNA-small-molecule targets. There's even a challenge to predict water and ions around a ribozyme, evaluated by direct comparison to cryo-EM maps. Rachael Kretsch, Shujun He, and Rhiju will present the assessment of these targets at the CASP16 conference in Punta Cana on Dec. 1-4, 2024!
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April 29, 2024
Congrats to Ved Topkar for succesfully defending his thesis on "Determinants of mRNA Localization in Oligodendrocytes"!
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February 27, 2024
We've released chemical mapping data on 2.1M RNA sequences as well as a deep learning model RibonanzaNet, distilled from an 800-team Kaggle competition and the Eterna OpenKnot challenge. All data and models are publicly available -- check out our preprint: Ribonanza: deep learning of RNA structure through dual crowdsourcing.
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December 30, 2023
We've launched an online Stanford Coursera course: RNA Biology with Eterna. Learn the basics of RNA biology from the point of view of the molecules' folding and biochemistry. It's a totally free course, targeting students at college level, with interactive components based on the Eterna videogame.
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December 17, 2023
Call to action to RNA and ML folks everywhere: We are getting ready to scale up our chemical mapping data protocol, initially to 8M sequences, and then onwards to 100 M and, hopefully 1B, sequences. For this Ribonanza 2 initiative, we're looking for diverse sets of RNA molecules from as many different groups as possible! Do you have a list of natural or designed RNA sequences that you're curious to visualize? We collected the first round in January 15, 2024, and if you're interested in joining the next round, e-mail us at ribonanza [at] stanford.edu.
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December 15, 2023
Rhiju spoke at the MLSB workshop at NeurIPS on Dec. 15, 2023, in New Orleans. We announced results of the Ribonanza competition. Impressive models came in from many teams demonstrating the deep learning of RNA structure from a data set involving 2.1M RNA sequences. But it's not over yet -- different models predict different answers for new RNAs -- stay tuned for Ribonanza 2!
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November 12, 2023
It was exciting to meet the next generation of scientists at ABRCMS in Phoenix! Congrats to lab postbacc Josh Johnson, who won a poster award for his work on Coronavirus Frameshift Stimulating Element Structure Determination and Therapeutic Design. Josh is pictured here with Rhiju and Gloria Regisford, Josh's undergraduate mentor at Prairie View A&M. Also wonderful to coordinate with Jill Townley from Eterna, who demo-ed research and education on Eterna at the ABRCMS RNA Society booth!
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October 29, 2023
The version of record of our CASP15 RNA assessment paper is out in the Proteins special issue. Read about it here. Also in the same issue: a perspective from groups (including ours) who experimentally solved the CASP15 3D RNA structures, as well as papers from the four top predictor groups, AIchemy_RNA2, Chen, RNAPolis, and GeneSilico. None used deep learning!
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September 7, 2023
We’ve teamed up with Kaggle to accelerate progress in RNA structure prediction through a new machine learning competition. Check out the new Ribonanza challenge! Register by Nov. 30, 2023, deadline for model submission is Dec. 7, 2023. Winning models to be open sourced and presented at NeurIPS MLSB workshop. Visit the competition webpage.
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August 9, 2023
Congrats to Ana Espeleta, RosettaCommons REU, for presenting her work on "Training an RNA sequence designer using deep learning neural networks" at RosettaCon 20!
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July 22, 2023
Rhiju and many lab members attended EternaCon 9! Congrats to all players and presenters on scientific and educational achievements over the last year! The schedule is here.
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May 24, 2023
Rhiju was honored to join many of his heroes in RNA science at the RNA Worlds symposium at U. Colorado, Boulder. Talks from his session, The Future World of RNA are now available on YouTube!
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April 29, 2023
Ramya Rangan presented her work on the RNA structure landscape of yeast introns at the RNA society 2023 meeting in Singapore!
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March 30, 2023
Congratulations to Jose Chacon, Ph.D. student at UCSD who worked with the Das lab in 2020-21 as a SSRP student-turned-research-affiliate -- Jose has just been awarded the NSF Graduate Research Fellowship!
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March 9, 2023
Congratulations to Ramya Rangan for successfully defending her Ph.D. thesis in Biophysics! Ramya's thesis has focused on RNA structures in non-coding RNA, from the SARS-CoV-2 genome to yeast introns!
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March 8, 2023
Ernst Pulido, current lab rotation student, spoke at the UCSF Gladstone Institute on his career pathway as a first-generation scholar, at an event announcing Gladstone's expansion with a visit from San Francisco Mayor London Breed!
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January 31, 2023
Rhiju spoke at the The RNA World session as part of the 67th Biophysical Society annual meeting on Feb. 19, 2023.
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December 13, 2022
Rachael Kretsch, Phillip Pham, Ramya Ranga, and Rhiju assessed the RNA category at CASP15! It was a lot of fun to co-assess with the RNA-puzzles team and to work with the CASP organizers. This picture is from the conference in Antalya, Turkey and shows Rachael, Rhiju, John Moult (CASP), and Eric Westhof (RNA-Puzzles). Learn more about the assessment at the CASP15 website and our presentation. And the talk recording is now up on YouTube too.
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October 17, 2022
Welcome Vivian Wu and Rui Huang to the Das lab! Vivian is joining as the Das lab manager and Rui is joining as a lab tech.
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June 5, 2022
We were thrilled that the majority of the lab was able to attend the RNA 2022 conferencein Boulder, Colorado! Congrats to Ved Topkar for winning a Poster Award for his poster deciphering RNA Transport in oligodendrocytes!
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May 18, 2022
We're proud to be part of one of 12 centers selected as an Antiviral Drug Discovery (AViDD) Center for Pathogens of Pandemic Concern. We look forward to continuing the work we did in collaboration with the labs of Jeff Glenn, Wah Chiu, Ralph Baric, and other colleagues in SARS-CoV-2 to develop Outpatient Antiviral Cocktails against SARS-CoV-2 and other Potential Pandemic RNA Viruses! Read more at the NIH website.
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April 7, 2022
Rachael Kretsch presented the SLAC Public Lecture on Thursday, April 7, 2022 on a very exciting topic: "Revolutionary 3-D Views of Viral RNA Using Cryogenic Electron Microscopy". Come join us by Zoom!
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February 11, 2022
Congratulations to Alexis Van Zandt for being named an HBCU STEM queen! She's on the cover of Ebony magazine! Alexis, a recent graduate of Prairie View A&M University, worked with the Das laboratory and the Center for Genetically Engineered Materials to develop a better design-oriented understanding of the ribosome in 2021.
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February 10, 2022
Ramya Rangan presented her work on The RNA structure landscape of S. cerevisiae introns at the RNA Club of the Center for Molecular Biology of RNA at U.C. Santa Cruz. Congrats on a great talk and wonderful interactions!
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September 24, 2021
We’re tremendously excited and honored at Rhiju's selection in the most recent cohort of amazing HHMI Investigators. Big thanks to current lab members, lab alumni, the Eterna project and many wonderful collaborators in the RNA world for making this possible!
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September 1, 2021
Rosetta REU researcher Philip Pham joined our lab to test the ARES neural network for cryo-EM — we’re delighted that Philip will continue with us through the next academic year.
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September 1, 2021
Congrats to Grace Nye, Brenda Garibay, and Kailee Yoshimura for their awesome research on viral RNA structure, 3' UTR isoforms, and smiFISH probes in our lab, as part of the SSRP program. Special congratulations to Brenda and Kailee who took home awards for best presentations at the SSRP symposium!
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September 1, 2021
We’ve been delighted to host Alexis Van Zandt and Dina Tekle, both from Prairie View A&M, for the CGEM REU program this summer. Both Alexis and Dina were part of ‘Team ribosome’ and worked to develop a database of ribosome mutations and their functions.
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August 26, 2021
Out today in Science - our work in collaboration with Ron Dror's Lab on ARES, a geometric deep learning algorithm that improves identification of accurate 3D RNA structures.
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August 23, 2021
We’re excited to publish our cryo-EM structure of the frameshift stimulation element of the SARS-CoV-2 RNA genome in Nature Structure and Molecular Biology. This work appeared on bioRxiv in 2020, and the new paper includes improved antisense oligonucleotide that target this intricate RNA fold. Thanks to many labs, including those of Jeff Glenn, Wah Chiu, Tim Sheahan, Ralph Baric, and Victoria D'Souza, for this collaboration! You can read more about our work to rapidly solve RNA structures with Wah Chiu at this SLAC piece that also includes the Tetrahymena ribozyme.
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August 12, 2021
We’ve reported high resolution cryo-EM structures of the full-length Tetrahymena ribozyme in a paper out today. Wonderful to start getting a close look at this paradigmatic RNA-only enzyme, discovered by Tom Cech and colleagues four decades ago! You can read more about our work to rapidly solve RNA structures with Wah Chiu at this SLAC piece.
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August 1, 2021
We're delighted that Rachael Kretsch will present on RNA cryo-EM at the American Crystallographic Association meeting this week! Rachael's talk will be on Tuesday, August 3, 2021, as part of the session "2.2.5 What Can & Can't We See Reliably at Resolution X?", 12-3pm ET. We are also very happy to celebrate the presentation of the Buerger Award to our wonderful collaborator Wah Chiu. Congratulations!
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July 25, 2021
We were pleased to help host EternaCon 2021, a virtual celebration of Eterna's efforts in inclusion, ribosome engineering, and mRNA vaccine research, with previews of upcoming developments. Check out what happened, including video of talks, at the EternaCon 2021 page .
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May 20, 2021
Congratulations to Hannah for successfully defending her Ph.D. in Chemistry! PhD student Hannah Wayment-Steele has been awarded the Chemical Computing Group excellence award from the American Chemical Society! You can read more about the award here. She will present her work at the ACS national meeting later in 2021. Hannah also spoke recently on work developing computational methods for mRNA stabilization at Schrodinger's Multiscale Modelling for Biotherapeutics symposium.
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May 17, 2021
Congratulations to Rachael Kretsch for being awarded a Bio-X Bowes Stanford Interdisciplinary Graduate Fellowship! The award will support her thesis research on advancing RNA structure determination with cryo-EM and computer modeling, with close collaboration from Wah Chiu.
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May 16, 2021
Congratulations to Ramya Rangan for being awarded a 2021 Gerald J. Lieberman Fellowship! This Stanford-wide fellowship supports PhD students intending to pursue careers in academia who have demonstrated potential for leadership roles through their research accomplishments, teaching and university service.
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May 10, 2021
India is entering into lockdown and there's hope of developing new mRNA vaccines against emerging regional variants of SARS-CoV-2 like B.1.617. Eterna has launched a design lab to create a superfolder mRNA encoding the "S-2P" spike protein for the B.1.617 variant and raising funds to experimentally test the stability and potency of the top-ranked solutions here at Stanford. Come join us at Eterna.
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May 10, 2021
We’re proud to help celebrate the PDB’s 50th anniversary and the future of structural biology in a new Comment on RNA structure in Nature Methods. Read more about it here!
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March 30, 2021
Our year-long collaboration with Maria Barna's group and Eterna, which started at the onset of the COVID-19 pandemic, has resulted in a variety of novel methods and principles for designing stabilized mRNA therapeutics. Our first preprint describing our experimental results is up! Check out this Q&A with Maria Barna and Rhiju Das explaining why and how we did this research.
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March 23, 2021
Congratulations to Lexy Strom, senior biology major at San Diego State university and Das lab SSRP student-turned-research-affiliate, who was awarded the NSF Graduate Research Fellowship!
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October 29, 2020
Rhiju spoke on our recent SARS-CoV-2 RNA structural biology research at an upcoming Biophysical Society symposium entitled "Biophysicists Address COVID-19 Challenges” on Thursday, Oct. 29, 2020. See you there! Register for free at the biophysical society website.
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October 24, 2020
Rhiju spoke about our recent work on SARS-CoV-2 RNA structural biology at the (virtual) Rustbelt RNA Meeting 2020 on Oct. 24, 2020. Register at the meeting site.
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October 23, 2020
Congrats to David Cox, who has been selected to speak at the Stanford.Berkeley.UCSF Next Generation Faculty symposium highlighting exceptional early career scientists! Register for the symposium, which will be on Oct. 23, 2020
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August 24, 2020
Improving the stability of RNA vaccines will be important for worldwide vaccine distribution. We present a biophysical model for predicting RNA degradation in a new preprint led by Hannah Wayment-Steele. Through a variety of mRNA design challenges launched through the OpenVaccine challenge on Eterna by Do Soon Kim, we predict that the stability of any RNA vaccine can be increased at least two-fold either through rational design, as demonstrated by Eterna participants, or algorithmically, through the algorithms RiboTree (developed by Christian Choe) and LinearDesign.
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July 25, 2020
EternaCon 2020 is happening on Saturday-Sunday, July 25-26, 2020! Starts at 9am PDT, 12pm EDT, 4pm UTC. Come (virtually) and hear about the latest Eterna innovations in OpenVaccine and super-folder ribosomes, including talks from Eterna players, world-leading researchers, and Eterna's latest allies at HBCU Prairie View A&M. Checkout the <href="https: 2020"="" eternacon="" eternagame.org="">schedule and register to attend virtually. </href="https:>
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July 21, 2020
Welcome to our new summer students Jose Chacon and Alexandra “Lexy” Strom!
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July 20, 2020
We've resolved the SARS-CoV-2 frameshift stimulation element with our hybrid structure determination pipeline Ribosolve, and we report effects of antisense oligonucleotides on this RNA's function and on virus replication in cell culture. Read more in our bioRxiv preprint. Many thanks to our colleagues in Glenn, Chiu, d'Souza, and Baric labs and SLAC for this fruitful collaboration, much of which occurred in the midst of.our university shutdowns.
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May 31, 2020
Which RNA secondary structure package best predicts experimental data? Hannah Wayment-Steele used high-throughput structural data from Eterna to answer this question, and found a suprising result: lesser-known packages developed by statistical learning performed notably better than more widely-used packages. Motivated by these results, she developed a multi-task learning algorithm trained on Eterna data, named EternaFold, which showed the best predictions on Eterna data as well as completely independent datasets of viral RNAs and synthetic mRNAs important for vaccine design. We hope that the EternaFold algorithm will be useful for improving RNA design, and that the EternaBench database will provide an independent platform to benchmark more improvements in secondary structure prediction.
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May 18, 2020
Congratulations to Roger Wellington-Oguri, Eli Fisker, Mathew Zada, Michelle Wiley, Jill Townley, and Eterna Players for the first peer-reviewed scientific publication written entirely by videogame players. The paper "Evidence of an Unusual Poly(A) RNA Signature Detected by High-throughput Chemical Mapping" was just accepted in the journal Biochemistry. The paper is coming out back to back with a companion paper from our lab that validates the players' discovery of an unusual polyadenosine signature in RNA structure mapping experiments. These same player authors are leading scientific discussions in Eterna's OpenVaccine mRNA vaccine stabilization efforts.
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May 14, 2020
Das lab's COVID-19 mRNA vaccine stabilization efforts, along with Eterna OpenVaccine, are featured in PBS Nova's recent Decoding COVID-19 TV special. More about our efforts in the Stanford School of Medicine Scope blog. Rhiju also presented the efforts at the Stanford School of Medicine's COVID-19 Town Hall. Come play the Eterna game to help us stabilize RNA vaccines at eternagame.org. If you're interested in a more detailed science seminar given in Stanford's Frontiers in Biosciences series, please contact Rhiju directly.
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April 18, 2020
There are many conserved and likely structured elements of the SARS-CoV-2 genome, such as those identified in a previous preprint, with no known 3D structure, which nonetheless may be useful targets for small molecule therapeutics. Ramya Rangan and Andy Watkins have performed studies with our latest structure prediction code, FARFAR2, to make publicly available collections of de novo 3D models of these elements. Their linked preprint has been made available in bioRxiv.
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March 28, 2020
To aid in the design of nucleic acid-based therapeutics for the raging COVID-19 pandemic, Ramya Rangan and Ivan (Vanya) Zheludev have worked quickly to conduct a comprehensive conservation analysis of the SARS-CoV-2 genome. Their preprint, published today in bioRxiv, identifies in this RNA virus many highly conserved sequences and secondary structure. A follow-up analysis confirms the conservation of many of these regions in the 739 SARS-CoV-2 genomes published during the current outbreak. The regions they have identified provide promising targets for the development of antiviral anti-sense oligonucleotide treatments as we continue to fight the COVID-19 pandemic.
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March 22, 2020
We are proud to launch Eterna's OpenVaccine challenge. These puzzle seeks improved mRNA sequences for COVID-19 vaccines, with a special focus to stabilizing these molecules against degradation to help enable their deployment for mass immunization. Experimental tests are being carried out in collaboration with Maria Barna's lab in Stanford Genetics. Come join us!
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December 12, 2019
Our laboratory won the overall prize in the Kornberg memorial Biochemistry department baking contest , for the second year in a row! In addition, Ramya Rangan won first place in the pie category for her blueberry pie, rotation student Jon Doenier took the cake with his chocolate mousse cake, Vanya Zheludhev directed this year's skit video, and Matt Adrianowycz MC-ed the winning ceremonies. Happy holidays to all and to the entire department!
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December 3, 2019
In collaboration with Wah Chiu's lab, we're pushing the limits of cryo-EM single-particle analysis to solve structures. An article in Nature Communications describes our results on a 40 kDa RNA, the SAM-IV riboswitch aptamer. The paper includes analyses confirming that the ligand-binding site can be detected in the RNA. Come play the Eterna puzzle celebrating this beautiful molecule (worth 500 points).
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December 2, 2019
After a successful pilot experiments in early 2019, Eterna is releasing Ribosome Challenge Round 1. The goal of this challenge is to create a superfolder variant of the E. coli ribosome whose assembly might be less fragile to mutations or changed solution conditions. If achieved, such a molecule could help worldwide efforts to repurpose the ribosome to make alternative polymers and more. Our initial challenge is making use of algorithmic innovations from Liang Huang (Oregon State University) and rapid in vitro assembly measurements by the lab of Mike Jewett (Northwestern University), as well as new hand-designed layouts of the ribosome RNA in two dimensions that match its three-dimensional structure. This lab round collects solutions on Feb. 1, 2020 -- and remember that you need to play the incoming puzzle progression to enter the lab and take part in the discussion and solving.
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August 27, 2019
Congratulations to Kalli Kappel for winning the American Chemical Society’s 2019 Chemical Computing Group excellence award for graduate students. She will be presenting at the ACS meeting in San Diego in late August, on a hybrid method for rapid experimental RNA structure determination called Ribosolve.
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July 20, 2019
The fifth annual EternaCon was held at Stanford University on July 20-21 2019! Much of our lab was there as we discuss the next ambitious moonshots for this exciting project. Check out the schedule of events at http://eternawiki.org/wiki/index.php5/Eternacon.
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July 14, 2019
Rhiju spoke about "Computational Design of RNA Structure/Function" at the Gordon Research Conference on Computer-aided Drug Design, describing our latest studies and inventions on new design principles for RNA therapeutics.
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June 23, 2019
Rhiju spoke at the 2019 Synthetic Biology: Engineering, Evolution & Design (SEED) in the "Cell Free Synthetic Biology" session on June 23-27, 2019. The topic: a new kind of molecular calculator developed to enable inexpensive diagnostics for active tuberculosis, sepsis, and other diseases tied to ratiometric gene signatures.
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June 11, 2019
Rhiju spoke at the RNA society conference in Krakow, Poland on June 11-16, 2019. He presented a new Ribosolve method to solve RNA 3D structures rapidly.
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April 8, 2019
The latest paper by Kalli Kappel, on a Rosetta computational infrastructure for modeling energetics of RNA-protein complexes, has been published in PNAS. Check out Kalli's other recent papers on RNA-protein structure modeling with Rosetta in Structure and Nature Methods!
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April 6, 2019
Ann Kladwang celebrates her 10th anniversary as a research associate in the Das laboratory. Congratulations and thanks, Ann, from everyone who has learned RNA experiments from you!
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December 12, 2018
Kalli Kappel gave a talk titled 'Structure determination of RNA and RNA-protein complexes through cryo-EM and computational modeling' at the Bay Area RNA Club's yearly meeting at the University of California, San Francisco.
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December 9, 2018
Congratulations to Das laboratory for winning two categories in the annual Biochemistry department holiday baking championship as well as the grand prize! Not bad for a bunch of mostly theorists. Dr. Michael Gotrik won for an ollallieberry cheesecake, and Dr. Feriel Melaine won for an apple pie with a French twist.
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August 11, 2018
The fourth annual EternaCon is happening on Saturday, August 11, and Sunday, August 12, 2018 at Stanford University. Come join us at Li Ka Shing Center (Room 120) or tune in online. As in prior years, the event is fully organized by Eterna players, and most speakers and panels are by players. We also welcome Liang Huang, Dave Hendrix, and Ingmar Riedel-Kruse as scientist guest speakers. More information and late registrations available through Eterna, and a draft schedule is available here.
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May 20, 2018
Congratulations to Matt Adrianowycz for winning a Stanford Centennial Teaching Award! Remarkably, Matt has won the award as a first-year Ph.D. student, for his teaching in Chemistry 141: The Chemical Principles of Life.
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April 19, 2018
Rhiju spoke at Tsinghua University at the 2018 Tsinghua International Symposium of Computational Structural Biology and Biophysics, on Eterna's recent progress in RNA design of on-demand molecular calculators. More information about the event can be found here.
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April 13, 2018
Kate Coppess has won a 2018 NSF graduate research fellowship award! Kate is also a Stanford EDGE-STEM fellow and co-president of Graduate Students of Applied Physics and Physics Congratulations, Kate!
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April 5, 2018
Our lab and Eterna are piloting a new form of peer review for scientific publications. Because so many of our upcoming papers will involve players as co-authors, we wanted to find a way for anyone to leave & respond to comments on papers before and during paper review, in the nearly frictionless way that Google docs allow. So that's what we're doing. We are making papers available on preprint servers like arXiv and bioRxiv and we are including a Google doc link in the abstract that players (or other members of the public) can follow. We can all leave comments -- and comments on comments -- in that Google doc. These comments will show up as notifications to the paper's lead author, who can join those threads and quickly make edits to the paper. As a pilot, Rhiju is putting up a paper on a data analysis method for quantifying thermodynamics in RNA structure mapping experiments. Check it out on the LIFFT BioRxiv preprint and the LIFFT community review Google doc . An Eterna blog post is here.
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December 4, 2017
Kalli Kappel spoke at the 4th International Conference on Protein and RNA Structure Prediction! She presented her latest work on Computational modeling of missing RNA coordinates into density maps of ribonucleoprotein machines.
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December 3, 2017
We're pleased to report our latest methods in 3D RNA modeling and Eterna design. Three preprints on BioRxiv highlight Blind prediction of noncanonical RNA structure at atomic accuracy, Computational design of asymmetric three-dimensional RNA structures and machines, and Prospects for recurrent neural network models to learn RNA biophysics from high-throughput data. Check out preprints through our publications page.
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November 15, 2017
Congratulations to collaborators Tosan Omabegho & Zev Bryant for reporting their design of a fast molecular machine whose direction can be reversed back and forth by RNA. The paper "Controllable molecular motors engineered from myosin and RNA" and a commentary are now out in Nature Nanotechnology.
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October 21, 2017
A rousing EternaCon happened on 2017 Saturday and Sunday October 21-22, 2017. Nearly 50 Eterna players and experts in CRISPR technologies and inexpensive diagnostics came together to consider the possibility of citizen scientists inventing medicine.
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July 30, 2017
Our latest papers take us closer to multidimensional chemical mapping of RNA in vivo and in complex structural ensembles. You can read about these methods before publication through preprints on bioRxiv: RNA structure inference through chemical mapping after accidental or intentional mutations and Allosteric logic of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping. Update: the M2-seq paper is out in PNAS.
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July 22, 2017
Michelle Wu spoke at the ISMB RNA-SIG meeting in Prague, Czech Republic. She presented work from our lab and Eterna on "Recurrent neural network models of RNA interactions".
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May 30, 2017
Johan Andreasson presented a talk from the Eterna project reporting the discovery of "Thermodynamically optimal riboswitches through massively parallel design" at the RNA 2017 conference in Prague, Czech republic. Collaborators Marcin Magnus (Bujnicki lab) and Brant Gracia (Russell lab) will also be giving talks on work involving computational and experimental methods from the Das lab.
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April 11, 2017
Joe Yesselman reported his work on "Automated Design of Three-Dimensional Asymmetric RNA Structures at Near-Atomic Accuracy" in an invited talk at FNANO 2017 (Foundation of Nanoscience)!
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March 30, 2017
Rhiju presented recent progress in 'RNA puzzles' at a Cell Press webinar "Predicting and Observing RNA Folding: A Progress Report" along with Kathleen Hall, Sarah Woodon, and Rob Batey. The web cast is available at the Cell website.
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February 15, 2017
Congratulations to Kalli Kappel for winning a travel award to the 2017 Biophysical Society annual meeting, in New Orleans, LA. She presented her work on "Blind predictions of RNA/protein relative binding affinities", and won a best poster prize!
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October 15, 2016
Congratulations to Andy Watkins for receiving a Dean's Fellowship to support his early postdoctoral work in the Das lab! Andy joins us after completing his Ph.D. from the Arora and Bonneau labs at NYU.
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September 19, 2016
Siqi Tian successfully defended his Ph.D. thesis on "Robust Validation of RNA Secondary Structure & Ensembles through Multidimensional Chemical Mapping" on September 19, 2016.
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August 15, 2016
Congratulations to Clarence Yu Cheng for successfully defending his Ph.D. thesis on "Advancing multidimensional chemical mapping of RNA structure through next-generation sequencing".
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July 1, 2016
Get ready for Eternacon 2016! This year's meeting will take place at Stanford University on Saturday and Sunday, July 16-17. For more information, please visit the Eternacon 2016 wiki.
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June 3, 2016
Congratulations to Kalli Kappel for receiving a Grace Hopper Celebration Scholarship! She will represent our lab at the GHC on October 16, 2016.
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June 1, 2016
We are launching a beta version of a new site describing workflows through all the RNA software and experimental resources that we've developed. Do you want to learn an RNA's secondary structure? Model its tertiary structure? Come check out RiboKit and send us feedback.
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May 28, 2016
Upcoming: Dr. Joe Yesselman will represent our lab at the international RNA 2016 conference in Kyoto, Japan, which starts on July 28, 2016. He will present collaborative work with the Greenleaf and Herschlag labs showing that "Surprisingly Accurate Energetic Modeling Deconvolves Big Data on RNA 3D Folding".
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May 5, 2016
Stanford magazine writes about our lab and recent developments in Eterna, including the player-created Eterna100 benchmark and the OpenTB challenge.
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May 4, 2016
Eterna has launched the OpenTB challenge, a collaboration with Purvesh Khatri's bioinformatics lab and Will Greenleaf's genetics lab to develop new molecules for tuberculosis diagnostics. Come play eterna to take part in the game. Press accounts are at Wall Street Journal, including multimedia, and NPR .
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February 17, 2016
Eterna citizen scientists are lead authors on peer-reviewed paper "Principles for Predicting RNA Secondary Structure Design Difficulty". Press coverage includes Science Magazine, Washington Post, Reuters.
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February 15, 2016
elNando888 and Ben Keep presented Eterna at the AAAS 2016 annual meeting, in the session on "Massively-Collaborative Global Research in Mathematics and Science".
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October 27, 2015
Vineet Kosaraju was awarded the 2015 Davidson fellowship for his "3D RNA Engineering in a Massive Open Laboratory" project on Eterna. Congratulations, Vineet!
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July 25, 2015
RNA lab (a joint collaboration of Eterna and NOVA) is a marquee banner app in the Chrome Web store. And RNA lab is now part of NOVA's partner collection in Khan Academy.
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July 11, 2015
The first ever EternaCon happened at Stanford University on July 11-12! Video and proceedings are being collected at the Eterna site.
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June 5, 2015
Rhiju speaks at Interactive Media & Games seminar about 'massive open laboratory’, which is an expansion of the conventional video game and computer-assisted design of RNA molecules.
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June 2, 2015
Pablo Cordero gave his final thesis talk on "Using factorization methods to find structure in RNA molecules and networks". Congratulations, Pablo!
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May 25, 2015
Want to make an RNA domain fast? Use Primerize to design primers that you can use to assemble templates for in vitro transcription.
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May 21, 2015
Fang-Chieh Chou defended his thesis on "Advancing high resolution predictions of RNA structure and energetics". Congratulations, Fang!
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January 5, 2015
Rhiju to receive 2015 OpenEye Outstanding Junior Faculty Award in Computational Chemistry!
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September 23, 2014
Rhiju will give a keynote at DNA20, the 20th international conference on DNA computing and molecular programming, in Kyoto, Japan.
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July 30, 2014
Rhiju & Fang recognized with the CLASHBUSTERS! award from the lab of Jane & Dave Richardson at the RNA/protein session of RosettaCon 2014. And Joe Yesselman won best poster of the conference for "Towards Automated Design of 3D RNA Structure"!
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June 3, 2014
Clarence Cheng presented a new technology for solving RNA 3D folds through multiplexed hydroxyl radical cleavage analysis (MOHCA-seq) at the international RNA society meeting on June 3-8, 2014 in Quebec City, Canada. Congratulations to Clarence for being selected to give a talk in the High Throughput methods session. Rhiju also presented on EteRNA at the Bioinformatics Workshop at the meeting.
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May 15, 2014
Newly discovered mushroom named after lab member! Congratulations to Wipapat (Ann) Kladwang for co-discovering Pseudobaeospora wipapatiae, described in "A ruby-colored Pseudobaeospora species is described as new from material collected on the island of Hawaii", in the newest issue of Mycologia.
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April 24, 2014
Congratulations to the PBS NovaLab/EteRNA team for creating NOVA's RNA VirtuaLab, interactive content on RNA and molecular biology for US schools.
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February 4, 2014
First scientific paper from EteRNA, "RNA Design Rules from a Massive Open Laboratory", published in PNAS. A nice highlight in Science magazine was also published here: Online Video Game Plugs Players Into Remote-Controlled Biochemistry Lab.
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December 6, 2013
Das Lab initiates our monthly 'open group meeting', focused on science happening on EteRNA. See our first meeting here, and join us interactively at our next meetings, happening monthly. Stay tuned to news on EteRNA for more information.
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November 26, 2013
Presenting our new fixed backbone design server for RNA. Want to know what sequence best fits a given phosphate backbone? Come try our server and submit any RNA in PDB format.
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November 18, 2013
Parin Sripakdeevong, Ph.D. student in biophysics, will be defending his thesis on Modeling noncanonical RNA 3D structures at atomic resolution under the Rosetta framework on Monday, Nov 18th, 2013: 3:00 PM - 4:00 PM in Clark S360.
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November 8, 2013
A NOVA feature on our colleague Adrien Treuille and the EteRNA project has won a Kavli award for scientific reporting. Congratulations to Adrien and to director Joshua Seftel!
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October 8, 2013
Rhiju gave a keynote at the Design Research Conference in Chicago on Oct. 8, 2013. The 12th annual Design Research Conference hosted by IIT Institute of Design will explore design’s role in mediating these forces: Are they opposable? Synthesized? Unified? Practicing designers, artists, scientists, engineers, educators, and entrepreneurs will present a variety of perspectives on balancing multiple creative forces amidst complex systems and issues.
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August 15, 2013
Das lab new website is going up!
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July 1, 2013
Kyle Beauchamp, joint student with Vijay Pande, defended his Ph.D. thesis in Biophysics, entitled Inferring protein structure and dynamics from simulation and experiment. Congratulations, Kyle!