Author

D. Farrell

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· 4 Microbiology· 1

Signature Assays, Organisms & Methods

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Assay:cryo-EM· 4 Approach:deep learning· 2 Approach:experimental assay· 2 Research Focus:protein structure prediction· 2 Organism:Arabidopsis· 1 Organism:bacteria (other)· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

F. DiMaio· 4 shared A. Kryshtafovych· 1 shared A. Lauko· 1 shared A. Muenks· 1 shared A. P. Joseph· 1 shared A. Patwardhan· 1 shared A. Perez· 1 shared A. Singharoy· 1 shared

Activity by Year

2019-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

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4 shared papersBiochemistry

F. DiMaio

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Author profile →

5 papers

Recent·Most cited

Robust residue-level error detection in cryo-electron microscopy models

G. Reggiano, D. Farrell, F. DiMaio

The paper develops MEDIC, a model to detect residue-level errors in cryo-EM structures, achieving 68% precision and 60% recall on validated structures and fixing multiple errors in rebuilt models.

bioRxiv · Sep 12, 2022 · PreprintBiochemistry

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

C. L. Lawson, A. Kryshtafovych, P. D. Adams, P. Afonine, M. L. Baker, B. A. Barad, P. Bond, T. Burnley, R. Cao, J. Cheng, G. Chojnowski, K. Cowtan, K. A. Dill, F. DiMaio, D. Farrell, , Wan

The paper evaluates cryo-EM model quality using benchmark maps, showing high accuracy and reproducibility across 13 teams and recommending multiple metrics for model assessment.

bioRxiv · Jun 12, 2020Biochemistry

Structure and lipid dynamics in the A. baumannii maintenance of lipid asymmetry (MLA) inner membrane complex

D. Mann, J. Fan, D. Farrell, K. Somboon, A. Muenks, S. Tzokov, S. Khalid, F. DiMaio, S. Miller, J. Bergeron

This study reports cryo-EM structures of the A. baumannii MLA complex in different states and proposes a molecular mechanism for lipid transport.

bioRxiv · May 30, 2020Biochemistry

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM

D. Farrell, I. Anishchanka, S. Shakeel, A. Lauko, L. A. Passmore, D. Baker, F. DiMaio

This paper uses deep learning and computational methods to determine an almost-complete atomic model of the Fanconi Anemia core complex from a low-resolution cryoEM map.

bioRxiv · May 1, 2020Biochemistry

Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome.

D. Farrell, J. Crispell, S. V. Gordon

The paper updates the functional annotation of the Mycobacterium bovis AF2122/97 genome by adding 616 new protein identifications and 69 new gene names based on orthologous information from M. tuberculosis H37Rv.

bioRxiv · Sep 14, 2019Microbiology