Author

Timothy P. Riley

Amgen (United States)

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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Biochemistry· 1 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:protein design· 2 Assay:protein sequence· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Approach:machine learning (classical)· 1 Research Focus:sequence-to-function modeling· 1 Research Focus:software / tool· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Kathy Y. WeiiD· 2 shared Ameya HarmalkariD· 1 shared Anja Hoenig· 1 shared Austin J. RiceiD· 1 shared Christine Elaine TinbergiD· 1 shared Danqing LiiD· 1 shared Devika Prabhakaran· 1 shared Doris Rau· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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2 shared papersBiochemistry

Kathy Y. WeiORCID

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Author profile →

2 papers

Recent·Most cited

An Artificial Intelligence Model for Translating Natural Language into Functional de Novo Proteins

Timothy P. Riley, Mohammad S. Parsa, Pourya Kalantari, Ismail Naderi, Kiana Azimian, Nemya Begloo, Oleg S. Matusovsky, Eliot Osher, Devika Prabhakaran, Rahul Yadav, Klem Simelis, Indran Mathavan, Jeeven Singh, Kooshiar Azimian, Kathy Y. Wei

This paper introduces MP4, a transformer-based model that translates natural language into functional de novo proteins, achieving high performance in sequence realism, fold quality, and function alignment.

ACS Synthetic Biology · Aug 10, 2026Peer-reviewedBiochemistry

Towards generalizable prediction of antibody thermostability using machine learning on sequence and structure features

Ameya Harmalkar, Roshan Rao, Yuxuan Richard Xie, Jonas Honer, Wibke Deisting, Jonas Anlahr, Anja Hoenig, Julia Czwikla, Eva Sienz-Widmann, Doris Rau, Austin J. Rice, Timothy P. Riley, Danqing Li, Hannah B. Catterall, Christine Elaine Tinberg, , Kathy Y. Wei

This paper develops machine learning models to predict antibody thermostability using sequence and structure features, showing better generalization with a CNN over pre-trained language models.

mAbs · Jan 22, 2023Peer-reviewedBioinformatics