Author

J. Phillips

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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Biophysics· 3 Microbiology· 1 Pathology· 1 Physiology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Approach:experimental assay· 3 Organism:human· 3 Approach:simulation· 2 Organism:virus· 2 Assay:bulk RNA-seq· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

A. Brace· 3 shared A. Trifan· 3 shared D. Hardy· 3 shared H. Ma· 3 shared L. Huang· 3 shared T. Gibbs· 3 shared A. Anandkumar· 2 shared A. Bogetti· 2 shared

Activity by Year

2018-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersBiophysics

A. Brace

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

A. Sreedasyam, C. Plott, M. S. Hossain, J. T. Lovell, J. Grimwood, J. W. Jenkins, C. Daum, K. Barry, J. Carlson, S. Shu, J. Phillips, M. Amirebrahimi, M. Zane, M. Wang, D. Goodstein, , E Cooper

The paper introduces the JGI Plant Gene Atlas, a resource that improves gene function annotations by analyzing transcript abundance across 18 species and 604 tissues, identifying 64,620 genes with unknown functions.

bioRxiv · Sep 30, 2022 · PreprintPlant Biology

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

A. Dommer, L. Casalino, F. Kearns, M. Rosenfeld, N. Wauer, S.-H. Ahn, J. Russo, S. Oliveira, C. Morris, A. Bogetti, A. Trifan, A. Brace, T. Sztain, A. Clyde, H. Ma, , Muholland

This paper uses AI-enabled multiscale computational microscopy to study SARS-CoV-2 Delta variant in respiratory aerosols, revealing atomic-level insights into airborne transmission.

bioRxiv · Nov 12, 2021Biophysics

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

A. Trifan, D. Gorgun, Z. Li, A. Brace, M. Zvyagin, H. Ma, A. R. Clyde, D. A. Clark, M. Salim, D. Hardy, T. Burnley, L. Huang, J. McCalpin, M. Emani, H. Yoo, , A. Ramanathan

This study develops an AI-driven multi-resolution simulation workflow to study SARS-CoV-2 RTC dynamics, combining cryo-EM with mesoscale simulations and AI methods.

bioRxiv · Oct 9, 2021 · PreprintBiophysics

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

L. Casalino, A. C. Dommer, Z. Gaieb, E. P. Barros, T. Sztain, S.-H. Ahn, A. Trifan, A. Brace, H. Ma, H. Lee, M. Turilli, A. Bogetti, S. Khalid, L. Chong, C. Simmerling, , R. E. Amaro

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

bioRxiv · Nov 19, 2020Biophysics

Hemozoin produced by mammals confers heme tolerance

R. Pek, X. Yuan, N. Rietzschel, J. Zhang, L. Jackson, E. Nishibori, A. Ribeiro, W. Simmons, J. Jagadeesh, H. Sugimoto, M. Z. Alam, L. Garrett, M. Haldar, M. Ralle, J. Phillips, , I. Hamza

The paper shows that mice lacking HRG1 accumulate excess heme in macrophages, which they tolerate by forming hemozoin, a process previously only observed in blood-feeding parasites.

bioRxiv · May 16, 2019Pathology

Data from an electronic health informatics pipeline to describe clearance dynamics of Hepatitis B surface antigen (HBsAg) and e-Antigen (HBeAg) in chronic HBV infection

L. O. Downs, D. Smith, S. F. Lumley, M. Patel, A. L. McNaughton, J. Mokaya, A. Ansari, H. Salih, K. A. Varnai, O. Freeman, S. Cripps, J. Phillips, J. Collier, K. Woods, K. Channon, , P. C. Matthews

The paper describes an electronic health informatics pipeline that collects longitudinal clinical data on HBsAg and HBeAg clearance in chronic HBV infection, revealing demographic and treatment-related factors associated with clearance.

bioRxiv · Mar 26, 2019Microbiology

Drug Repurposing: The Anthelmintics Niclosamide and Nitazoxanide are Potent TMEM16A Antagonists that Fully Bronchodilate Airways

K. Miner, K. Labitzke, B. Liu, P. Wang, K. Henckels, K. Gaida, R. Elliott, J. J. Chen, L. Liu, A. Leith, E. Trueblood, K. Hensley, X.-Z. Xia, O. Homann, B. Bennett, , J. K. Sullivan

This paper identifies niclosamide and nitazoxanide as potent TMEM16A antagonists that fully bronchodilate airways, offering new treatment options for severe asthma and COPD.

bioRxiv · Nov 14, 2018Physiology