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Engineering at the limits of complexity with molecular-scale parts

Creative Commons

Attribution 4.0 International

Soumya Tripathy

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Publication

Structural bioinformatics studies of six human ABC transporters and their AlphaFold2- predicted water-soluble QTY variants

QRB Discov. 2024 Jan 19;5:e1. doi: 10.1017/qrd.2024.2. PMID: 38577032; PMCID: PMC10988169.

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Study of glutamate transporters and their AF2 predicted water-soluble QTY variants and uncovering the natural mutations L->Q, I->T, F->Y,

Karago ̈l A, Karago ̈l T, Smorodina E, Zhang S (2024) Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F- >Y and Q->L, T->I and Y->F. PLoS ONE 19(4): e0289644.

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Study of serotonin, dopamine, norepinephrine transporters and their AF2 predicted water-soluble QTY variants and uncovering natural mutation

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Design of a water-soluble transmembrane receptor kinase with intact molecular function by QTY code

Li, M., Tang, H., Qing, R. et al. Design of a water-soluble transmembrane receptor kinase with intact molecular function by QTY code. Nat Commun 15, 4293 (2024). https://doi.org/10.1038/s41467-024-48513-9

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Scalable biomimetic sensing system with membrane receptor dual-monolayer probe and graphene transistor arrays

Rui Qing, et al. "Scalable biomimetic sensing system with membrane receptor dual-monolayer probe and graphene transistor arrays." Science Advances. DOI: 10.1126/sciadv.adf1402

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How to Grow (Almost) Anything: a Hybrid Distance Learning Model for Global Laboratory-Based Synthetic Biology Education

Perry, Eyal, et al. "How to grow (almost) anything: a hybrid distance learning model for global laboratory-based synthetic biology education." Nature Biotechnology (2022): 1-6.

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Distillation of Language Model Semantics to Folded Three-Dimensional Protein Structures

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Learning on knowledge graph dynamics provides an early warning of impactful research

Weis, J.W., Jacobson, J.M. Learning on knowledge graph dynamics provides an early warning of impactful research. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-00907-6

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Non-full-length Water-Soluble CXCR4QTY and CCR5QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Recepto

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Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions

Chatterjee, P., Ponnapati, M., Kramme, C. et al. Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions. Commun Biol 3, 715 (2020). https://doi.org/10.1038/s42003-020-01470-7

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A Cas9 with PAM recognition for adenine dinucleotides

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An engineered ScCas9 with broad PAM range and high specificity and activity

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QTY code designed thermostable and water-soluble chimeric chemokine receptors with tunable ligand affinity

Rui Qing, Qiuyi Han, Michael Skuhersky, Haeyoon Chung, Myriam Badr, View ORCID ProfileThomas Schubert, and Shuguang Zhang. PNAS first published November 27, 2019 (https://doi.org/10.1073/pnas.1909026116). Edited by Alan R. Fersht, University of Cambridge, Cambridge, United Kingdom, and approved October 30, 2019 (received for review May 24, 2019).

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Minimal PAM specificity of a highly similar SpCas9 ortholog

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Minimal PAM specificity of a highly similar SpCas9 ortholog

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Chimeric CRISPR guides enhance Cas9 target specificity

Noah Jakimo, Pranam Chatterjee, Joseph M. Jacobson. Chimeric CRISPR guides enhance Cas9 target specificity, doi: https://doi.org/10.1101/147686

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Genomic nucleic acid memory storage with directed endonucleases

Jakimo, N. "Genomic nucleic acid memory storage with directed endonuclease"

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Language & tools for context-aware biology

Fracchia, C. "Language & tools for context-aware biology"

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Exploration of Methods for Many-Site Genome Editing with MAGE

Sterling, B. "Exploration of Methods for Many-Site Genome Editing with MAGE"

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Photoelectrochemical Synthesis of Low-Cost DNA Microarrays

Chow, B. "Photoelectrochemical Synthesis of Low-Cost DNA Microarrays"

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Growing Machines

Griffith, S. "Growing Machines"

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Nanostructure Fabrication by Electron and Ion Beam Patterning of Nanoparticles

Kong, D. "Nanostructure Fabrication by Electron and Ion Beam Patterning of Nanoparticles"

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Printed Inorganic Transistors

Ridley, B. "Printed Inorganic Transistors"

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The Design of a Molecular Assembly Line Based on Biological Molecules

Chow, B. "The Design of a Molecular Assembly Line Based on Biological Molecules"

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Reverse-QTY code design of active human serum albumin self-assembled amphiphilic nanoparticles for effective anti-tumor drug doxorubicin...

Run Meng, Shilei Hao, Changfa Sun, Zongkun Hou, Yao Hou, Lili Wang, Peiying Deng, Jia Deng, Yaying Yang, Haijian Xia, Bochu Wang, Rui Qing, Shuguang Zhang. "Reverse-QTY code design of active human serum albumin self-assembled amphiphilic nanoparticles for effective anti-tumor drug doxorubicin release in mice." PNAS.