Google scholar profile
Preprints
Alexander Baryshev, Alyssa La Fleur, Benjamin Groves, Cirstyn Michel, David Baker, Ajasja Ljubetič and Georg Seelig, Massively parallel protein-protein interaction measurements by sequencing (MP3-seq) enables rapid screening of protein heterodimers, bioRxiv.
Yue Zhang, Shunfu Mao, Sumit Mukherjee, Sreeram Kannan and Georg Seelig, UNCURL-App: Interactive Database-Driven Analysis of Single Cell RNA Sequencing Data, biorxiv.
2022
Johannes Linder, Samantha E. Koplik, Anshul Kundaje and Georg Seelig, Deciphering the Impact of Genetic Variation on Human Polyadenylation using APARENT2, Genome Biology 23, 232 (2022). biorxiv.
Karen Zhang, Yuan-Jyue Chen, Kathryn Doroschak, Karin Strauss, Luis Ceze, Georg Seelig, Jeff Nivala, A nanopore interface for high-bandwidth DNA computing, Nature Communications 13, 4904 (2022). bioRxiv.
Alberto Carignano, Dai Hua Chen, Cannon Mallory, Clay Wright, Georg Seelig* and Eric Klavins*, Modular, robust and extendible multicellular circuit design in yeast, eLife 11 e74540 (2022).
Johannes Linder, Alyssa La Fleur, Zibo Chen, Ajasja Ljubetič, David Baker, Sreeram Kannan, Georg Seelig, Interpreting Neural Networks for Biological Sequences by Learning Stochastic Masks, Nature Machine Intelligence, 4, 41 (2022). bioRxiv
Shunfu Mao, Yue Zhang, Georg Seelig and Sreeram Kannan, CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature, Bioinformatics 38, 1393 (2022). bioRxiv
Sebastian M. Castillo-Hair and Georg Seelig, Machine Learning for Designing Next-Generation RNA Therapeutics (Review), Accounts of Chemical Research 55, 24 (2022).
2021
Johannes Linder and Georg Seelig, Fast activation maximization for molecular sequence design, BMC Bioinformatics 22, 510 (2021). arXiv.
Anna Kuchina*, Leandra M Brettner*, Luana Paleologu, Charles M Roco, Alexander B Rosenberg, Alberto Carignano, Ryan Kibler, Matthew Hirano, R. William DePaolo, Georg Seelig, Microbial single-cell RNA sequencing by split-pool barcoding, Science 371, eaba5257 (2021). bioRxiv, pdf.
Kimberly A Aldinger, Zachary Thomson, Parthiv Haldipur, Mei Deng, Andrew E Timms, Matthew Hirano, Gabriel Santpere, Charles Roco, Alexander B Rosenberg, Belen Lorente-Galdos, Forrest O Gulden, Diana O'Day, Lynne M Overman, Steven Lisgo, Paula Alexandre, Nenad Sestan, Dan Doherty, William B Dobyns, Georg Seelig, Ian A Glass, Kathleen J Millen, Spatial and single-cell transcriptional landscape of human cerebellar development, Nature Neuroscience 24, 1163 (2021). biorxiv.
Tanya Grancharova, Kaytlyn A Gerbin, Alexander B Rosenberg, Charles M Roco, Joy Arakaki, Colette DeLizzo, Stephanie Q Dinh, Rory Donovan-Maiye, Matthew Hirano, Angelique Nelson, Joyce Tang, Julie A Theriot, Calysta Yan, Vilas Menon, Sean P Palecek, Georg Seelig, Ruwanthi N Gunawardane, A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes, Scientific Reports 11, 15845 (2021). bioRxiv
Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis H Ceze, Molecular level similarity search brings computing to DNA Data Storage, Nature Communications 12, 4764 (2021). bioRxiv.
Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, Luis Ceze and Karin Strauss, Robust Digital Molecular Design of Binarized Neural Networks, In: Matthew R. Lakin, Peter Sulc. (eds), 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021).
2020
Johannes Linder, Nicholas Bogard, Alexander Rosenberg, Georg Seelig, A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences, Cell Systems 11, 49 (2020).
Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Kendall Stewart, Siena Dumas Ang, Patrick Weiss, Bill Peck,. Georg Seelig, Luis Ceze, Karin Strauss, Quantifying Molecular Bias in DNA Data Storage, Nature Communications 11, 3264 (2020).
Sifang Chen and Georg Seelig, Programmable patterns in a DNA-based reaction-diffusion system, Soft Matter 16, 3555 (2020).
2019
Nicholas Bogard*, Johannes Linder*, Alexander B. Rosenberg and Georg Seelig, A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation, Cell 178, 91 (2019); https:/doi.org/10.1016/j.cell.2019.04.046. Earlier version on bioRxiv.
Paul J. Sample, Ban Wang, David W. Reid, Vladimir Presnyak, Iain McFadyen, David R. Morris and Georg Seelig, Human 5'UTR design and variant effect prediction from a massively parallel translation assay, Nature Biotechnology 37, 803, (2019). Earlier version on bioRxiv.
Kimberly A. Aldinger, Andrew E. Timms, Zachary Thomson, Ghayda M. Mirzaa, James T. Bennett, Alexander B. Rosenberg, Charles M. Roco, Matthew Hirano, Fatima Abidi, Parthiv Haldipur, Chi V. Cheng, Sarah Collins, Kaylee Park, Jordan Zeiger, Lynne M. Overmann, Fowzan S. Alkuraya, Leslie G. Biesecker, Stephen R. Braddock, Sara Cathey, Megan T. Cho, Brian H.Y. Chung, David B. Everman, Yuri A. Zarate, Julie R. Jones, Charles E. Schwartz, Amy Goldstein, Robert J. Hopkin, Ian D. Krantz, Roger L. Ladda, Kathleen A. Leppig, Barbara C. McGillivray, Susan Sell, Katherine Wusik, Joseph G. Gleeson, Deborah A. Nickerson, Michael J. Bamshad, Dianne Gerrelli, Steven N. Lisgo, Georg Seelig, Gisele E. Ishak, A. James Barkovich, Cynthia J. Curry, Ian A. Glass, Kathleen J. Millen, Dan Doherty, and William B. Dobyns, Redefining the Etiologic Landscape of Cerebellar Malformations, Am. J. Human Genetics 105, 606 (2019).
Randolph Lopez, Yuan-Jyue Chen, Siena Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Georg Seelig, Karin Strauss and Luis Ceze, DNA Assembly for Nanopore Data Storage Readout, Nature Communications 10, 2933 (2019).
Gokul Gowri, Randolph Lopez and Georg Seelig, Combined Amplification and Molecular Classification for Gene Expression Diagnostics. In: Thachuk C., Liu Y. (eds) DNA Computing and Molecular Programming. DNA 2019 (DNA 25). Lecture Notes in Computer Science 11648.
Douglas Carmean, Luis Ceze, Georg Seelig, Karin Strauss, Kendall Stewart and Max Willsey, DNA Data Storage and Hybrid Molecular-Electronic Computing, Proceeding of the IEEE 107, 63 (2019); doi: 10.1109/JPROC.2018.2875386.
2018
Alexander B Rosenberg*, Charles Roco*, Richard A Muscat, Anna Kuchina, Paul Sample, Sumit Mukherjee, Wei Chen, David J Peeler, Zizhen Yao, Suzie H Pun, Drew L Sellers, Bosiljka Tasic, and Georg Seelig, Single cell profiling of the developing mouse brain and spinal cord with split-pool barcoding, Science 360, 176 (2018). pdf
Randolph Lopez Barrezueta , Ruofan Wang, and Georg Seelig, A molecular multi-gene classifier for disease diagnostics, Nature Chemistry 10, 746 (2018). (pdf, view only )
Gourab Chatterjee, Yuan-Jyue Chen and Georg Seelig, Nucleic acid strand displacement with synthetic mRNA inputs in mammalian cells, ACS Synthetic Biology 7, 2737 (2018); doi: 10.1021/acssynbio.8b00288.
Sumit Mukherjee, Yue Zhang, Joshua Fan, Sreeram Kannan and Georg Seelig, Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge, Bioinformatics 34, i124 (2018).
Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg Seelig, Luis Ceze and Karin Strauss, Scaling up DNA data storage and random access retrieval, Nature Biotechnology 36, 242 (2018).
Sumit Mukherjee, Alberto Carignano, Georg Seelig and Su-In Lee, Identifying progressive gene network perturbations from single-cell RNA-seq data, 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Honolulu, HI, USA, 2018, pp. 5034-5040, doi: 10.1109/EMBC.2018.8513444 (2018). (also on bioRxiv)
Abhishek K Gupta, Tushar Murthy, Kiran V. Paul, Oscar Ramirez, Joseph B Fisher, Sridhar Rao, Alexander B. Rosenberg, Georg Seelig, Alex C Minella and Manoj M. Pillai, Degenerate minigene library analysis enables identification of altered branch point utilization by mutant splicing factor 3B1 (SF3B1), Nucleic Acids Research 47, 970 (2018); https://doi.org/10.1093/nar/gky1161.
2017
Niranjan Srinivas, James Perkin, Georg Seelig, Erik Winfree and David Soloveichik, Enzyme-free nucleic acid dynamical systems, Science 358, eaal2052 (2017). An earlier version is on bioRxiv.
Josh T. Cuperus*, Benjamin Groves*, Anna Kuchina*, Alexander Rosenberg*, Nebojsa Jojic, Stanley Fields and Georg Seelig, Deep learning of the regulatory grammar of yeast 5' untranslated regions from 500,000 random sequences, Genome Research 27, 2015 (2017). An earlier version can be found on bioRxiv.
Gourab Chatterjee, Neil Dalchau, Richard A Muscat, Andrew Phillips and Georg Seelig, A spatially localized architecture for fast and modular DNA computing, Nature Nanotechnology 12, 920 (2017). An earlier version is on bioRxiv. See also News & Views by Estevez-Torres and Rondelez.
Pengfei Wang, Gourab Chatterjee, Hao Yan, Thomas H. LaBean, Andrew J. Turberfield, Carlos E. Castro, Georg Seelig and Yongang Ke, Practical aspects of structural and dynamic DNA nanotechnology (review), Materials Research Society Bulletin 42, 889 (2017).
Sherry Xi Chen and Georg Seelig, A DNA Neural Network Constructed from Molecular Variable Gain Amplifiers, In: Brijder R., Qian L. (eds) DNA Computing and Molecular Programming. DNA 2017 (DNA 23). Lecture Notes in Computer Science, vol 10467 (2017).
Lea Starita, Nadav Ahituv, Maitreya J Dunham, Jacob O Kitzman, Frederick Roth, Georg Seelig, Jay Shendure, Douglas Fowler, Variant interpretation: functional data to the rescue, The American Journal of Human Genetics 101, 315 (2017).
James Bornholt, Randolph Lopez, Douglas M. Carmean, Georg Seelig, Luiz Ceze and Karin Strauss, Toward a DNA-based Archival Storage System, IEEE Micro 37, 98 (2017).
2016
Benjamin Groves*, Arjun Khakhar*, Cory Nadel, Richard Gardner, and Georg Seelig, Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination, eLife 5, e15200 (2016). DOI: http://dx.doi.org/10.7554/eLife.15200
Benjamin Groves*, Yuan-Jyue Chen*, Chiara Zurla*, Sergii Pochekailov, Jonathan L. Kirschman, Philip Santangelo and Georg Seelig, Computing in mammalian cells with nucleic acid strand exchange, Nature Nanotechnology 11, 287 (2016). doi:10.1038/nnano.2015.278
Scott E. Boyken, Zibo Chen, Ben Groves, Robert A. Langan, Gustav Oberdorfer, Alex Ford, Jason Gilmore, Chunfu Xu, Frank DiMaio, Jose Henrique Pereira, Banumathi Sankaran, Georg Seelig, Peter H. Zwart, and David Baker, De novo design of protein homo-oligomers with modular hydrogen bond network mediated specificity, Science 352, 680 (2016).
Christoph Zechner, Georg Seelig, Marc Rullan, and Mustafa Khammash, Molecular circuits for dynamic noise filtering, Proc. Nat. Acad. Sci. 113, 4729 (2016). doi: 10.1073/pnas.1517109113
Sergii Pochekailov, Rebecca Black, Venkata Chavali, Arjun Khakhar, and Georg Seelig, A fluorescent readout for the oxidation state of electron transporting proteins in cell free settings, ACS Synthetic Biology 5, 662 (2016). doi: 10.1021/acssynbio.5b00274
Sherry Xi Chen and Georg Seelig, An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination, J. Am. Chem. Soc. 138, 5076 (2016). DOI: 10.1021/jacs.6b00277
James Bornholt, Randolph Lopez, Douglas M. Carmean, Luis Ceze, Georg Seelig, and Karin Strauss, A DNA-Based Archival Storage System, ASPLOS '16: Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems, Pages 637–649, (2016). https://doi.org/10.1145/2872362.2872397
2015
Alexander B. Rosenberg, Rupali Pathwardhan, Jay Shendure, and Georg Seelig, Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences, Cell 163, 698 (2015).
Yuan-Jyue Chen, Benjamin Groves, Richard Muscat and Georg Seelig, DNA nanotechnology from the test tube to the cell (review), Nature Nanotechnology 10, 748 (2015).
Yuan-Jyue Chen, Sundipta Rao and Georg Seelig, Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks, J. Vis. Exp. 105, e53087 (2015). doi:10.3791/53087
2014
Timothy J. Strovas, Alexander B. Rosenberg, Richard A. Muscat, Brianna E. Kuypers and Georg Seelig, A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations, ACS Synthetic Biology 3, 324 (2014).
Neil Dalchau, Georg Seelig and Andrew Phillips, Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks, In: Murata S., Kobayashi S. (eds) DNA Computing and Molecular Programming. DNA 2014 (DNA 20). Lecture Notes in Computer Science 8727 (2014). https://doi.org/10.1007/978-3-319-11295-4_6.
2013
Yuan-Jyue Chen, Neil Dalchau, Niranjan Srinivas, Andrew Phillips, Luca Cardelli, David Soloveichik and Georg Seelig, Programmable chemical controllers made from DNA, Nature Nanotechnology 8, 755 (2013).
Xi Sherry Chen, David Yu Zhang and Georg Seelig, Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA, Nature Chemistry 5, 782 (2013).
Richard A. Muscat, Karin Strauss, Luis Ceze and Georg Seelig, DNA-based Molecular Architecture with Spatially Localized Components, ISCA (2013): ACM SIGARCH Computer Architecture News 41, 177 (2013). https://doi.org/10.1145/2508148.2485938
2011
David Yu Zhang and Georg Seelig, Dynamic DNA nanotechnology using strand displacement reactions (review), Nature Chemistry 3, 103 (2011).
David Yu Zhang and Georg Seelig, DNA-based Fixed Gain Amplifiers and Linear Classifier Circuits, In: Sakakibara Y., Mi Y. (eds) DNA Computing and Molecular Programming. DNA 2010 (DNA 16) Lecture Notes in Computer Science 6518, 176 (2011).
2010
David Soloveichik, Georg Seelig, and Erik Winfree, DNA as a Universal Substrate for Chemical Kinetics, Proc. Nat. Acad. Sci. USA 107, 5393 (2010).
2009
Georg Seelig and David Soloveichik, Time-Complexity of Multilayered DNA Strand Displacement Circuits , In: Deaton R., Suyama A. (eds) DNA Computing and Molecular Programming. DNA 2009. (DNA 15) Lecture Notes in Computer Science 5877, 144 (2009). https://doi.org/10.1007/978-3-642-10604-0_15
David Soloveichik, Georg Seelig, and Erik Winfree, DNA as a Universal Substrate for Chemical Kinetics (Extended Abstract), DNA 14 In: Goel A., Simmel F.C., Sosík P. (eds) DNA Computing. DNA 2008. (DNA 14) Lecture Notes in Computer Science, vol 5347 (2009). https://doi.org/10.1007/978-3-642-03076-5_6
2006
Georg Seelig, David Soloveichik, David Yu Zhang and Erik Winfree, Enzyme-Free Nucleic Acid Logic Circuits, Science 324, 1585 (2006); also see W. Fontana, Pulling strings, p. 1552 of the same issue. (4 page pdf, 248KB)
Georg Seelig, Bernard Yurke and Erik Winfree, Catalyzed Relaxation of a Metastable DNA Fuel, J. Am Chem. Soc. 128, 12211 (2006). (10 page pdf, 1.4MB)
2005
Georg Seelig, Bernard Yurke and Erik Winfree, In: Ferretti C., Mauri G., Zandron C. (eds) DNA Computing. DNA 2004. (DNA 10)Lecture Notes in Computer Science, vol 3384 (2005). https://doi.org/10.1007/11493785_29
Previous work in condensed matter physics
Georg Seelig, A. V. Andreev, and K. A. Matveev, Phonon resistance of electron liquids in quantum wires, Phys. Rev. Lett. 94, 066802 (2005).
Georg Seelig, Sebastian Pilgram, and Markus Büttiker, Decoherence in ballistic mesoscopic interferometers, Turk. J. Phys. 27, 331 (2003).
G. Seelig, S. Pilgram, A. N. Jordan, and M. Büttiker, Probe configuration dependent de-phasing in a mesoscopic interferometer, Phys. Rev. B. 68, (R)161310 (2003).
Georg Seelig and K. A. Matveev, Electron-phonon scattering in quantum point contacts, Phys. Rev. Lett. 90, 176804, (2003).
Karyn Le Hur and Georg Seelig, Capacitance of a quantum dot from the channel-anisotropic two-channel Kondo model, Phys. Rev. B. 65, 165338 (2002).
Georg Seelig and Markus Büttiker, Charge-fluctuation-induced dephasing in a gated mesoscopic interferometer, Phys. Rev. B 64, 245313 (2001).
Guido Burkard, Georg Seelig and Daniel Loss, Spin interactions and switching in vertically tunnel-coupled quantum dots, Phys. Rev. B 62, 2581 (2000).
Preprints
Alexander Baryshev, Alyssa La Fleur, Benjamin Groves, Cirstyn Michel, David Baker, Ajasja Ljubetič and Georg Seelig, Massively parallel protein-protein interaction measurements by sequencing (MP3-seq) enables rapid screening of protein heterodimers, bioRxiv.
Yue Zhang, Shunfu Mao, Sumit Mukherjee, Sreeram Kannan and Georg Seelig, UNCURL-App: Interactive Database-Driven Analysis of Single Cell RNA Sequencing Data, biorxiv.
2022
Johannes Linder, Samantha E. Koplik, Anshul Kundaje and Georg Seelig, Deciphering the Impact of Genetic Variation on Human Polyadenylation using APARENT2, Genome Biology 23, 232 (2022). biorxiv.
Karen Zhang, Yuan-Jyue Chen, Kathryn Doroschak, Karin Strauss, Luis Ceze, Georg Seelig, Jeff Nivala, A nanopore interface for high-bandwidth DNA computing, Nature Communications 13, 4904 (2022). bioRxiv.
Alberto Carignano, Dai Hua Chen, Cannon Mallory, Clay Wright, Georg Seelig* and Eric Klavins*, Modular, robust and extendible multicellular circuit design in yeast, eLife 11 e74540 (2022).
Johannes Linder, Alyssa La Fleur, Zibo Chen, Ajasja Ljubetič, David Baker, Sreeram Kannan, Georg Seelig, Interpreting Neural Networks for Biological Sequences by Learning Stochastic Masks, Nature Machine Intelligence, 4, 41 (2022). bioRxiv
Shunfu Mao, Yue Zhang, Georg Seelig and Sreeram Kannan, CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature, Bioinformatics 38, 1393 (2022). bioRxiv
Sebastian M. Castillo-Hair and Georg Seelig, Machine Learning for Designing Next-Generation RNA Therapeutics (Review), Accounts of Chemical Research 55, 24 (2022).
2021
Johannes Linder and Georg Seelig, Fast activation maximization for molecular sequence design, BMC Bioinformatics 22, 510 (2021). arXiv.
Anna Kuchina*, Leandra M Brettner*, Luana Paleologu, Charles M Roco, Alexander B Rosenberg, Alberto Carignano, Ryan Kibler, Matthew Hirano, R. William DePaolo, Georg Seelig, Microbial single-cell RNA sequencing by split-pool barcoding, Science 371, eaba5257 (2021). bioRxiv, pdf.
Kimberly A Aldinger, Zachary Thomson, Parthiv Haldipur, Mei Deng, Andrew E Timms, Matthew Hirano, Gabriel Santpere, Charles Roco, Alexander B Rosenberg, Belen Lorente-Galdos, Forrest O Gulden, Diana O'Day, Lynne M Overman, Steven Lisgo, Paula Alexandre, Nenad Sestan, Dan Doherty, William B Dobyns, Georg Seelig, Ian A Glass, Kathleen J Millen, Spatial and single-cell transcriptional landscape of human cerebellar development, Nature Neuroscience 24, 1163 (2021). biorxiv.
Tanya Grancharova, Kaytlyn A Gerbin, Alexander B Rosenberg, Charles M Roco, Joy Arakaki, Colette DeLizzo, Stephanie Q Dinh, Rory Donovan-Maiye, Matthew Hirano, Angelique Nelson, Joyce Tang, Julie A Theriot, Calysta Yan, Vilas Menon, Sean P Palecek, Georg Seelig, Ruwanthi N Gunawardane, A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes, Scientific Reports 11, 15845 (2021). bioRxiv
Callista Bee, Yuan-Jyue Chen, David Ward, Xiaomeng Liu, Georg Seelig, Karin Strauss, Luis H Ceze, Molecular level similarity search brings computing to DNA Data Storage, Nature Communications 12, 4764 (2021). bioRxiv.
Johannes Linder, Yuan-Jyue Chen, David Wong, Georg Seelig, Luis Ceze and Karin Strauss, Robust Digital Molecular Design of Binarized Neural Networks, In: Matthew R. Lakin, Peter Sulc. (eds), 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021).
2020
Johannes Linder, Nicholas Bogard, Alexander Rosenberg, Georg Seelig, A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences, Cell Systems 11, 49 (2020).
Yuan-Jyue Chen, Christopher N. Takahashi, Lee Organick, Kendall Stewart, Siena Dumas Ang, Patrick Weiss, Bill Peck,. Georg Seelig, Luis Ceze, Karin Strauss, Quantifying Molecular Bias in DNA Data Storage, Nature Communications 11, 3264 (2020).
Sifang Chen and Georg Seelig, Programmable patterns in a DNA-based reaction-diffusion system, Soft Matter 16, 3555 (2020).
2019
Nicholas Bogard*, Johannes Linder*, Alexander B. Rosenberg and Georg Seelig, A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation, Cell 178, 91 (2019); https:/doi.org/10.1016/j.cell.2019.04.046. Earlier version on bioRxiv.
Paul J. Sample, Ban Wang, David W. Reid, Vladimir Presnyak, Iain McFadyen, David R. Morris and Georg Seelig, Human 5'UTR design and variant effect prediction from a massively parallel translation assay, Nature Biotechnology 37, 803, (2019). Earlier version on bioRxiv.
Kimberly A. Aldinger, Andrew E. Timms, Zachary Thomson, Ghayda M. Mirzaa, James T. Bennett, Alexander B. Rosenberg, Charles M. Roco, Matthew Hirano, Fatima Abidi, Parthiv Haldipur, Chi V. Cheng, Sarah Collins, Kaylee Park, Jordan Zeiger, Lynne M. Overmann, Fowzan S. Alkuraya, Leslie G. Biesecker, Stephen R. Braddock, Sara Cathey, Megan T. Cho, Brian H.Y. Chung, David B. Everman, Yuri A. Zarate, Julie R. Jones, Charles E. Schwartz, Amy Goldstein, Robert J. Hopkin, Ian D. Krantz, Roger L. Ladda, Kathleen A. Leppig, Barbara C. McGillivray, Susan Sell, Katherine Wusik, Joseph G. Gleeson, Deborah A. Nickerson, Michael J. Bamshad, Dianne Gerrelli, Steven N. Lisgo, Georg Seelig, Gisele E. Ishak, A. James Barkovich, Cynthia J. Curry, Ian A. Glass, Kathleen J. Millen, Dan Doherty, and William B. Dobyns, Redefining the Etiologic Landscape of Cerebellar Malformations, Am. J. Human Genetics 105, 606 (2019).
Randolph Lopez, Yuan-Jyue Chen, Siena Ang, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Georg Seelig, Karin Strauss and Luis Ceze, DNA Assembly for Nanopore Data Storage Readout, Nature Communications 10, 2933 (2019).
Gokul Gowri, Randolph Lopez and Georg Seelig, Combined Amplification and Molecular Classification for Gene Expression Diagnostics. In: Thachuk C., Liu Y. (eds) DNA Computing and Molecular Programming. DNA 2019 (DNA 25). Lecture Notes in Computer Science 11648.
Douglas Carmean, Luis Ceze, Georg Seelig, Karin Strauss, Kendall Stewart and Max Willsey, DNA Data Storage and Hybrid Molecular-Electronic Computing, Proceeding of the IEEE 107, 63 (2019); doi: 10.1109/JPROC.2018.2875386.
2018
Alexander B Rosenberg*, Charles Roco*, Richard A Muscat, Anna Kuchina, Paul Sample, Sumit Mukherjee, Wei Chen, David J Peeler, Zizhen Yao, Suzie H Pun, Drew L Sellers, Bosiljka Tasic, and Georg Seelig, Single cell profiling of the developing mouse brain and spinal cord with split-pool barcoding, Science 360, 176 (2018). pdf
Randolph Lopez Barrezueta , Ruofan Wang, and Georg Seelig, A molecular multi-gene classifier for disease diagnostics, Nature Chemistry 10, 746 (2018). (pdf, view only )
Gourab Chatterjee, Yuan-Jyue Chen and Georg Seelig, Nucleic acid strand displacement with synthetic mRNA inputs in mammalian cells, ACS Synthetic Biology 7, 2737 (2018); doi: 10.1021/acssynbio.8b00288.
Sumit Mukherjee, Yue Zhang, Joshua Fan, Sreeram Kannan and Georg Seelig, Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge, Bioinformatics 34, i124 (2018).
Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg Seelig, Luis Ceze and Karin Strauss, Scaling up DNA data storage and random access retrieval, Nature Biotechnology 36, 242 (2018).
Sumit Mukherjee, Alberto Carignano, Georg Seelig and Su-In Lee, Identifying progressive gene network perturbations from single-cell RNA-seq data, 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Honolulu, HI, USA, 2018, pp. 5034-5040, doi: 10.1109/EMBC.2018.8513444 (2018). (also on bioRxiv)
Abhishek K Gupta, Tushar Murthy, Kiran V. Paul, Oscar Ramirez, Joseph B Fisher, Sridhar Rao, Alexander B. Rosenberg, Georg Seelig, Alex C Minella and Manoj M. Pillai, Degenerate minigene library analysis enables identification of altered branch point utilization by mutant splicing factor 3B1 (SF3B1), Nucleic Acids Research 47, 970 (2018); https://doi.org/10.1093/nar/gky1161.
2017
Niranjan Srinivas, James Perkin, Georg Seelig, Erik Winfree and David Soloveichik, Enzyme-free nucleic acid dynamical systems, Science 358, eaal2052 (2017). An earlier version is on bioRxiv.
Josh T. Cuperus*, Benjamin Groves*, Anna Kuchina*, Alexander Rosenberg*, Nebojsa Jojic, Stanley Fields and Georg Seelig, Deep learning of the regulatory grammar of yeast 5' untranslated regions from 500,000 random sequences, Genome Research 27, 2015 (2017). An earlier version can be found on bioRxiv.
Gourab Chatterjee, Neil Dalchau, Richard A Muscat, Andrew Phillips and Georg Seelig, A spatially localized architecture for fast and modular DNA computing, Nature Nanotechnology 12, 920 (2017). An earlier version is on bioRxiv. See also News & Views by Estevez-Torres and Rondelez.
Pengfei Wang, Gourab Chatterjee, Hao Yan, Thomas H. LaBean, Andrew J. Turberfield, Carlos E. Castro, Georg Seelig and Yongang Ke, Practical aspects of structural and dynamic DNA nanotechnology (review), Materials Research Society Bulletin 42, 889 (2017).
Sherry Xi Chen and Georg Seelig, A DNA Neural Network Constructed from Molecular Variable Gain Amplifiers, In: Brijder R., Qian L. (eds) DNA Computing and Molecular Programming. DNA 2017 (DNA 23). Lecture Notes in Computer Science, vol 10467 (2017).
Lea Starita, Nadav Ahituv, Maitreya J Dunham, Jacob O Kitzman, Frederick Roth, Georg Seelig, Jay Shendure, Douglas Fowler, Variant interpretation: functional data to the rescue, The American Journal of Human Genetics 101, 315 (2017).
James Bornholt, Randolph Lopez, Douglas M. Carmean, Georg Seelig, Luiz Ceze and Karin Strauss, Toward a DNA-based Archival Storage System, IEEE Micro 37, 98 (2017).
2016
Benjamin Groves*, Arjun Khakhar*, Cory Nadel, Richard Gardner, and Georg Seelig, Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination, eLife 5, e15200 (2016). DOI: http://dx.doi.org/10.7554/eLife.15200
Benjamin Groves*, Yuan-Jyue Chen*, Chiara Zurla*, Sergii Pochekailov, Jonathan L. Kirschman, Philip Santangelo and Georg Seelig, Computing in mammalian cells with nucleic acid strand exchange, Nature Nanotechnology 11, 287 (2016). doi:10.1038/nnano.2015.278
Scott E. Boyken, Zibo Chen, Ben Groves, Robert A. Langan, Gustav Oberdorfer, Alex Ford, Jason Gilmore, Chunfu Xu, Frank DiMaio, Jose Henrique Pereira, Banumathi Sankaran, Georg Seelig, Peter H. Zwart, and David Baker, De novo design of protein homo-oligomers with modular hydrogen bond network mediated specificity, Science 352, 680 (2016).
Christoph Zechner, Georg Seelig, Marc Rullan, and Mustafa Khammash, Molecular circuits for dynamic noise filtering, Proc. Nat. Acad. Sci. 113, 4729 (2016). doi: 10.1073/pnas.1517109113
Sergii Pochekailov, Rebecca Black, Venkata Chavali, Arjun Khakhar, and Georg Seelig, A fluorescent readout for the oxidation state of electron transporting proteins in cell free settings, ACS Synthetic Biology 5, 662 (2016). doi: 10.1021/acssynbio.5b00274
Sherry Xi Chen and Georg Seelig, An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination, J. Am. Chem. Soc. 138, 5076 (2016). DOI: 10.1021/jacs.6b00277
James Bornholt, Randolph Lopez, Douglas M. Carmean, Luis Ceze, Georg Seelig, and Karin Strauss, A DNA-Based Archival Storage System, ASPLOS '16: Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems, Pages 637–649, (2016). https://doi.org/10.1145/2872362.2872397
2015
Alexander B. Rosenberg, Rupali Pathwardhan, Jay Shendure, and Georg Seelig, Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences, Cell 163, 698 (2015).
Yuan-Jyue Chen, Benjamin Groves, Richard Muscat and Georg Seelig, DNA nanotechnology from the test tube to the cell (review), Nature Nanotechnology 10, 748 (2015).
Yuan-Jyue Chen, Sundipta Rao and Georg Seelig, Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks, J. Vis. Exp. 105, e53087 (2015). doi:10.3791/53087
2014
Timothy J. Strovas, Alexander B. Rosenberg, Richard A. Muscat, Brianna E. Kuypers and Georg Seelig, A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations, ACS Synthetic Biology 3, 324 (2014).
Neil Dalchau, Georg Seelig and Andrew Phillips, Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks, In: Murata S., Kobayashi S. (eds) DNA Computing and Molecular Programming. DNA 2014 (DNA 20). Lecture Notes in Computer Science 8727 (2014). https://doi.org/10.1007/978-3-319-11295-4_6.
2013
Yuan-Jyue Chen, Neil Dalchau, Niranjan Srinivas, Andrew Phillips, Luca Cardelli, David Soloveichik and Georg Seelig, Programmable chemical controllers made from DNA, Nature Nanotechnology 8, 755 (2013).
Xi Sherry Chen, David Yu Zhang and Georg Seelig, Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA, Nature Chemistry 5, 782 (2013).
Richard A. Muscat, Karin Strauss, Luis Ceze and Georg Seelig, DNA-based Molecular Architecture with Spatially Localized Components, ISCA (2013): ACM SIGARCH Computer Architecture News 41, 177 (2013). https://doi.org/10.1145/2508148.2485938
2011
David Yu Zhang and Georg Seelig, Dynamic DNA nanotechnology using strand displacement reactions (review), Nature Chemistry 3, 103 (2011).
David Yu Zhang and Georg Seelig, DNA-based Fixed Gain Amplifiers and Linear Classifier Circuits, In: Sakakibara Y., Mi Y. (eds) DNA Computing and Molecular Programming. DNA 2010 (DNA 16) Lecture Notes in Computer Science 6518, 176 (2011).
2010
David Soloveichik, Georg Seelig, and Erik Winfree, DNA as a Universal Substrate for Chemical Kinetics, Proc. Nat. Acad. Sci. USA 107, 5393 (2010).
2009
Georg Seelig and David Soloveichik, Time-Complexity of Multilayered DNA Strand Displacement Circuits , In: Deaton R., Suyama A. (eds) DNA Computing and Molecular Programming. DNA 2009. (DNA 15) Lecture Notes in Computer Science 5877, 144 (2009). https://doi.org/10.1007/978-3-642-10604-0_15
David Soloveichik, Georg Seelig, and Erik Winfree, DNA as a Universal Substrate for Chemical Kinetics (Extended Abstract), DNA 14 In: Goel A., Simmel F.C., Sosík P. (eds) DNA Computing. DNA 2008. (DNA 14) Lecture Notes in Computer Science, vol 5347 (2009). https://doi.org/10.1007/978-3-642-03076-5_6
2006
Georg Seelig, David Soloveichik, David Yu Zhang and Erik Winfree, Enzyme-Free Nucleic Acid Logic Circuits, Science 324, 1585 (2006); also see W. Fontana, Pulling strings, p. 1552 of the same issue. (4 page pdf, 248KB)
Georg Seelig, Bernard Yurke and Erik Winfree, Catalyzed Relaxation of a Metastable DNA Fuel, J. Am Chem. Soc. 128, 12211 (2006). (10 page pdf, 1.4MB)
2005
Georg Seelig, Bernard Yurke and Erik Winfree, In: Ferretti C., Mauri G., Zandron C. (eds) DNA Computing. DNA 2004. (DNA 10)Lecture Notes in Computer Science, vol 3384 (2005). https://doi.org/10.1007/11493785_29
Previous work in condensed matter physics
Georg Seelig, A. V. Andreev, and K. A. Matveev, Phonon resistance of electron liquids in quantum wires, Phys. Rev. Lett. 94, 066802 (2005).
Georg Seelig, Sebastian Pilgram, and Markus Büttiker, Decoherence in ballistic mesoscopic interferometers, Turk. J. Phys. 27, 331 (2003).
G. Seelig, S. Pilgram, A. N. Jordan, and M. Büttiker, Probe configuration dependent de-phasing in a mesoscopic interferometer, Phys. Rev. B. 68, (R)161310 (2003).
Georg Seelig and K. A. Matveev, Electron-phonon scattering in quantum point contacts, Phys. Rev. Lett. 90, 176804, (2003).
Karyn Le Hur and Georg Seelig, Capacitance of a quantum dot from the channel-anisotropic two-channel Kondo model, Phys. Rev. B. 65, 165338 (2002).
Georg Seelig and Markus Büttiker, Charge-fluctuation-induced dephasing in a gated mesoscopic interferometer, Phys. Rev. B 64, 245313 (2001).
Guido Burkard, Georg Seelig and Daniel Loss, Spin interactions and switching in vertically tunnel-coupled quantum dots, Phys. Rev. B 62, 2581 (2000).