Author

P. D. Hsu

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioengineering· 3 Biochemistry· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:deep learning· 3 Assay:CRISPR screen· 2 Research Focus:gene regulatory network inference· 2 Assay:DNA methylation· 1 Approach:experimental assay· 1 Approach:genetic perturbation / CRISPR· 1 Research Focus:host-pathogen & immune response· 1

Frequent Co-Authors

P. Lotfy· 3 shared S. Konermann· 3 shared J. Tycko· 2 shared J. Wei· 2 shared M. G. Durrant· 2 shared A. E. Friedland· 1 shared A. Fanton· 1 shared A. Patil· 1 shared

Activity by Year

2018-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersBioengineering

P. Lotfy

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Kinase-independent activity of DYRK1A promotes viral entry of highly pathogenic human coronaviruses

M. S. Strine, W. L. Cai, J. Wei, M. M. Alfajaro, R. B. Filler, S. B. Biering, S. Sarnik, A. Patil, K. S. Cervantes, C. K. Collings, P. C. DeWeirdt, R. E. Hanna, K. Schofield, C. Hulme, S. Konermann, , C. B. Wilen

This study shows DYRK1A promotes viral entry of SARS-CoV, SARS-CoV-2, and MERS-CoV by regulating ACE2 and DPP4 transcription without its kinase activity.

bioRxiv · Sep 13, 2022 · PreprintMicrobiology

Large-scale discovery of recombinases for integrating DNA into the human genome

M. G. Durrant, A. Fanton, J. Tycko, M. Hinks, S. S. Chandrasekaran, N. T. Perry, J. Schaepe, P. P. Du, P. Lotfy, M. C. Bassik, L. Bintu, A. S. Bhatt, P. D. Hsu

This paper identifies and validates new large serine recombinases (LSRs) for efficient DNA integration into human genomes, achieving higher efficiency than existing tools.

bioRxiv · Nov 5, 2021Bioengineering

Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting

J. Wei, P. Lotfy, K. Faizi, S. Baungaard, E. Gibson, E. Wang, H. Slabodkin, E. Kinnaman, S. Chandrasekaran, H. Kitano, M. G. Durrant, C. V. Duffy, P. D. Hsu, S. Konermann

The paper develops a deep learning model to predict CRISPR-Cas13d guide RNA efficiency and identifies novel orthologs with improved specificity and reduced toxicity for RNA targeting.

bioRxiv · Sep 14, 2021Bioengineering

Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d

C. Zhang, S. Konermann, N. J. Brideau, P. Lotfy, S. J. Novick, T. Strutzenberg, P. R. Griffin, P. D. Hsu, D. Lyumkis

The paper determines the structural basis of CRISPR-Cas13d's RNA-guided ribonuclease activity through cryo-EM and biochemical analysis, revealing its molecular architecture and activation mechanisms.

bioRxiv · May 4, 2018Biochemistry

Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells

J. Tycko, L. A. Barrera, N. Huston, A. E. Friedland, X. Wu, J. S. Gootenberg, O. O. Abudayyeh, V. E. Myer, C. J. Wilson, P. D. Hsu

The paper screens SaCas9 specificity using a barcoded pairwise library of sgRNAs and identifies optimal spacer lengths for off-target activity.

bioRxiv · Feb 22, 2018Bioengineering