Author

T. Clark

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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Scientific Communication & Education· 2 Bioengineering· 1 Cancer Biology· 1 Immunology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Research Focus:host-pathogen & immune response· 2 Organism:human· 2 Approach:statistical model· 2 Assay:structural biology· 2 Organism:virus· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

R. Raman· 3 shared R. Sasisekharan· 3 shared M. Martone· 2 shared N. L. Miller· 2 shared A. Jayaraman· 1 shared A. Kenall· 1 shared A. Mohammed· 1 shared A. Viglione· 1 shared

Activity by Year

2017-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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Curved chords = mutual co-authorship

3 shared papersBioengineering

R. Raman

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Machine Learning-Guided Antibody Engineering That Leverages Domain Knowledge To Overcome The Small Data Problem

T. Clark, V. Subramanian, A. Jayaraman, E. Fitzpatrick, R. Gopal, N. Pentakota, T. Rurak, S. Anand, A. Viglione, K. Tharakaraman, R. Raman, R. Sasisekharan

This paper presents a machine learning platform that enhances antibody affinity and neutralizing potency using domain knowledge and limited experimental data.

bioRxiv · Jun 2, 2023 · PreprintBioengineering

A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F

N. L. Miller, T. Clark, R. Raman, R. Sasisekharan

The paper explains the broad immune escape of SARS-CoV-2 BA.2 variant mutations S371L/F through structural analysis of spike trimer conformational dynamics.

bioRxiv · Feb 25, 2022 · PreprintMicrobiology

Pancreatic cancer ductal cell of origin drives CD73-dependent generation of immunosuppressive adenosine

K. Singh, E. Y. Faraoni, Y. Dai, V. Chandra, E. Vucic, T. Mills, M. Pruski, T. Clark, G. Van Buren, N. C. Thosani, J. S. Bynon, C. J. Wray, D. Bar-Sagi, K. L. Poulsen, L. A. Vornik, , J. Bailey Lundberg

This study identifies CD73 as a key driver of immunosuppression in pancreatic ductal adenocarcinoma, showing its role in adenosine generation and tumor progression.

bioRxiv · Nov 29, 2021 · PreprintCancer Biology

Mapping Potential Antigenic Drift Sites (PADS) on SARS-CoV-2 Spike in Continuous Epitope-Paratope Space

N. L. Miller, T. Clark, R. Raman, R. Sasisekharan

The paper identifies potential antigenic drift sites on SARS-CoV-2 spike protein and projects them into epitope-paratope space to assess mutation synergy across variants of concern.

bioRxiv · Jun 7, 2021 · PreprintImmunology

A Data Citation Roadmap for Scientific Publishers

H. Cousijn, A. Kenall, E. Ganley, M. Harrison, D. Kernohan, T. Lemberger, F. Murphy, P. Polischuk, S. Taylor, M. Martone, T. Clark

This paper provides a roadmap for scientific publishers to implement data citation following the JDDCP principles, guiding authors and publishers through the lifecycle of a paper.

bioRxiv · Mar 7, 2018Scientific Communication & Education

A Data Citation Roadmap for Scholarly Data Repositories

M. Fenner, M. Crosas, J. Grethe, D. Kennedy, H. Hermjakob, P. Rocca-Serra, G. Durand, R. Berjon, S. Karcher, M. Martone, T. Clark

This paper provides a roadmap for scholarly data repositories to implement data citation following the Joint Declaration of Data Citation Principles, with 11 recommendations divided into three phases.

bioRxiv · Oct 9, 2017Scientific Communication & Education