We are interested in understanding how biological organisms process information using complex biochemical networks and how such networks can be engineered to program cellular behavior. The focus of our research is the identification of systematic design rules for the de novo construction of biological control circuits with DNA and RNA components. Our approach integrates the design of molecular circuitry in the test tube and in the cell with the investigation of existing biological pathways. Engineered circuits are being applied to problems in disease diagnostics and therapy.
We're in the Department of Electrical & Computer Engineering and the Paul G. Allen School of Computer Science & Engineering.
Lab news
7/25: Congratulations, Dr. Yin!
6/25: Congratulations, Dr. La Fleur!
6/25: Enhancer design paper by Chris, Sebastian, Gun and Wouter Meuleman now out at Cell Systems!
1/25: Collaborations with the Shi and Schier labs published in Molecular Cell and Developmental Cell, respectively. Good start to the year!
12/24: We're sorry to see Angela leave but excited for the Yu lab at Baylor!
12/24: Georg was appointed to the Chris and Heidi Stolte Endowed Professorship in Computer Science & Engineering
10/24: New preprint by Lukas and team explains how microRNA can be used to predictably regulate mRNA stability across cell types.
10/24: Alyssa's review on Decoding Biology with MPRAs + ML is published in Genes & Development!
8/24: New paper on gene regulation during Zebrafish embryogenesis led by Jialin Liu from the Schier lab. With a model by Sebastian and Chris!
8/24: MP3-seq paper by Alyssa, Cirstyn and former lab members Alex and Ben is now published at Nature Chemical biology!
6/24: Sebastian's paper on 5'UTR engineering is published in Nature Communications!
6/24: The microSPLiT protocol is published in Nature Protocols, congratulations Anna and team!
6/24: Congrats to Chris, Sebastian, Gun and our collaborators at Altius on submitting a paper describing how to design cell type-specific enhancers!
11/23: Paper on zebrafish 5'UTRs out on bioRxiv. Awesome collaboration with Madalena from the Schier lab!
6/23: Congratulations Lukas for winning an EMBO Postdoctoral fellowship!
6/23: Paper on engineering 5'UTRs for gene editing is on bioRxiv! Nice work by Sebastian, Ban, Johannes and collaborators at 2seventy bio.
4/23: Congratulations Gun for winning an IC Postdoctoral fellowship!
4/23: Paper on drug sensitivity of polyandenylation is on bioRxiv. Nice work Angela and Johannes! Great collaboration with the Shi lab.
2/23: Welcome to the lab, Lukas!
2/23: MP3 paper is out on bioRxiv! Fantastic work by Alex, Alyssa, Cirstyn, Ben and friends!
2/23: Good luck at Parse, Ian, and welcome Lukas!
11/22: APARENT2 paper is out at Genome Biology. Congratulations Johannes and Sam!
11/22: Welcome to the lab Madelyn!
8/22: Congratulations Dr. Baryshev!
6/22: Thank you Alex and Liz and good luck with your next steps!
5/22: Congratulations Dr. Zhang!
3/22: Alberto's paper on multicellular yeast consortia will be published by eLife!
1/22: Anna starting her own lab at the ISB. Excited to see all the cool work the Kuchina lab is going to do!
1/22: Scrambler paper is out at Nature Machine Intelligence. Congrats Johannes and Alyssa!
11/21: Congrats Yue and Shunfu for getting the CellMeSH paper accepted at Bioinformatics!
10/21: Alberto's paper on engineering yeast consortia is out on bioRxiv!
10/21: Welcome new lab members Cirstyn, Quoc and Nikolay!
7/21: Congrats to Arjun for getting an assistant professor position at CSU. Check out the Arjun Lab!
6/21: Paper on SPLiT-seq applied to the developing human cerebellum is out at Nature Neuro. Awesome collaboration with Kim Aldinger, Kathy Millen and others!
4/21: Congratulations Prof. Kuchina!
4/21: Congratulations Dr. Linder!
3/21: Welcome Gun!
3/21: Congratulations Sam on winning an NSF GRFP award!
3/21: Welcome Ian! And congratulations on your training grant!
1/21: Angela wins a WRF Postdoctoral Fellowship!
12/20 MicroSPLiT paper is out at Science!
12/20: Alyssa and Johannes present their work at MLCB.
11/20: Angela was awarded a WRF postdoctoral fellowship. Wonderful news!
10/20: Georg promoted to full professor. Thanks everyone for the awesome work that made this possible!
6/20: Congratulations Dr. Wang!
5/20: Paper by Yue and Shunfu on automated cell type annotation is out on bioRxiv! Fun collaboration with Sreeram Kannan.
5/20: Image search with DNA molecules, up on bioRxiv. Awesome work by the MISL team!
5/20: Manuscript from our collaboration with AICS on iPSC to cardio differentiation is now on bioRxiv.
5/20 Johannes's latest paper on fast protein and DNA sequence design is out on arXiv!
5/20: Fast and diverse sequence design paper by Johannes, Nick and Alex accepted at Cell Systems!
4/20: Yue's paper on interactive scRNA-seq data analysis is now on bioRxiv!
3/20: Sifang's paper got accepted at Soft Matter. Awesome work!
2/20: Congratulations to Max for winning an NIH postdoctoral fellowship!
1/20: Congratulations Dr. Brettner!
12/19: Congratulations Dr. Rao!
11/19: Johannes's paper was accepted for an oral presentation at MLCB2019 (10/118 acceptance rate for talks)!
8/19: Gokul presented his work on making better molecular classifiers at DNA25!
8/5: Excited to host DNA25 in Seattle this year!
7/19: Optimus 5' paper is online at Nature Biotechnology! Nice work, Paul and Ban! Great collaboration with folks at Moderna.
6/19: Our APA paper is out at Cell! Nice work, Nick and Johannes!
6/19: Georg gives presentations on MPRA work at UMass and NYU.
6/19: Congratulations Dr. Roco!
3/19: Congratulations Dr. Chen!
2/19: Programmed DNA pattern formation. Paper by Sifang is on bioRxiv!
11/18: Splicing paper by Manoj Pillai lab (with Alex and myself as co-authors) just came out!
11/18: Gourab's and Yuan's paper on strand displacement in cells accepted at ACS Synthetic Biology!
11/18: Georg gives a presentation on 5'UTR modeling at the mRNA Health Conference in Boston.
10/18: Ban and Nick give talks at ASHG. Nicely done!
8/18: Congratulations Dr. Lopez!!
5/18: Congratulations to Arjun and Sumit for graduating with their PhD!
5/18: Congratulations to Arjun and Sumit for graduating with their PhD!
4/18: Good luck to Paul for his new adventure at Bellwether Bio. Sad to see another great lab member move on!
4/18: Welcome to the lab, Max!
4/18: Predicting the impact of variants on APA. Paper by Nick, Johannes and Alex is on bioRxiv!
4/18: Inferring gene networks from scRNA-seq data. Paper by Sumit and Alberto (with Su-In Lee) accepted at EMBC!
3/18: The SPLiT-seq paper is out at Science! Make sure to check out the movie!
3/18: Congratulations, Dr. Mukherjee!!
2/18: Our paper describing UNCURL, a new approach to scRNA-seq data analysis, was accepted to ISMB. Congrats Sumit and Yue!
2/18: Our paper on SPLiT-seq was accepted at Science. Congrats to Alex, Charlie and the entire team!
2/18: Randolph's paper on DNA diagnostics accepted at Nature Chemistry!
2/18: Sad and excited that Ben got an offer from Amyris and will soon leave us.
2/18: The MISL paper on scaling up DNA data storage is out at Nature Biotechnology!
12/17: Sunny and Sifang pass their general exams with style. Nicely done!
12/17: Our review paper on DNA nanotechnology now out in MRS bulletin.
11/17: Johannes passes the quals, nice going!
11/17: Welcome to the lab Matt!
11/17: Congrats to Lee, Siena, Yuan-Jyue, Randolph and the entire MISL team! Their paper was accepted to Nature Biotechnology.
10/17: Charlie wins a fellowship from the Interdisciplinary Training Program in Cancer Research. Congratulations!
10/17: Yeast 5'UTR library paper by Anna. Ben, Alex and our friends Josh Cuperus, Stan Fields and Nebosja Jojic accepted at Genome Research. Nice work, everyone!
9/17: Sifang, Sunny and Georg all give talks at DNA23 in Austin. Great to see so many of our friends there!
9/17: Our position paper on variant interpretation using massively parallel reporter assays is out in AJHG!
7/17: Gourab's paper is now online at Nature Nano: A spatially localized architecture for fast and modular DNA computing. See also News & Views by Esteves-Torres and Rondelez.
6/17: NSF is funding our work on DNA diagnostics. Nice work Randolph!
6/17: Congratulations, Dr. Chatterjee!!
6/17: Gourab's paper on localized DNA circuits was accepted at Nature Nanotechnology (also on bioRxiv). Congratulations Gourab!
5/17: Sumit and Yue's paper on learning from scRNA-seq data is out on bioRxiv
5/17: Congratulations to Charlie for passing his quals! Awesome research proposal!
5/17: Congratulations to Sifang, Sunny and Sherry for getting their papers accepted at DNA23!
5/17: Yeast 5'UTR library paper by Anna. Ben, Alex and our friends Josh Cuperus, Stan Fields and Nebosja Jojic is is now on bioRxiv
5/17 Georg visited ETH in Zurich and Max Planck Institute for Molecular Cell Biology and Genetics in Dresden
4/17: Our lab was awarded an R01 from NHGRI (with Jay Shendure)!
4/17: Lab alumnus Richard Muscat runs Zurich Marathon in 3:17
3/17: Charlie wins a Translational Research Training Program graduate fellowship. Congratulations!
3/17: Georg gives a talk on localized DNA circuits and DNA diagnostics at the 1st European Congress on Cell-Free Synthetic Biology
2/17: Georg gives talks on SPLiT-seq and splicing at the Friedrich Miescher Institute and the ETH DBSSE in Basel
1/17: Gourab presents his work on DNA circuits at the RNA Nanotechnology Gordon Research Conference