David M McCandlish
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Explore the profile of David M McCandlish including associated specialties, affiliations and a list of published articles.
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43
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791
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Recent Articles
1.
Zebell S, Marti-Gomez C, Fitzgerald B, Pinto Da Cunha C, Lach M, Seman B, et al.
bioRxiv
. 2025 Mar;
PMID: 40060596
Cryptic genetic variants exert minimal or no phenotypic effects alone but have long been hypothesized to form a vast, hidden reservoir of genetic diversity that drives trait evolvability through epistatic...
2.
Seitz E, McCandlish D, Kinney J, Koo P
Nat Mach Intell
. 2025 Feb;
6(6):701-713.
PMID: 39950082
Deep neural networks (DNNs) have greatly advanced the ability to predict genome function from sequence. However, elucidating underlying biological mechanisms from genomic DNNs remains challenging. Existing interpretability methods, such as...
3.
Chen W, Zhou J, McCandlish D
Phys Rev E
. 2024 Nov;
110(4-1):044408.
PMID: 39562961
Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence...
4.
Sun M, Stoltzfus A, McCandlish D
bioRxiv
. 2024 Oct;
PMID: 39464166
The effect of replacing the amino acid at a given site in a protein is difficult to predict. Yet, evolutionary comparisons have revealed highly regular patterns of interchangeability between pairs...
5.
Gitschlag B, Pereira C, Held J, McCandlish D, Patel M
Nat Commun
. 2024 Sep;
15(1):8237.
PMID: 39300074
Cells possess multiple mitochondrial DNA (mtDNA) copies, which undergo semi-autonomous replication and stochastic inheritance. This enables mutant mtDNA variants to arise and selfishly compete with cooperative (wildtype) mtDNA. Selfish mitochondrial...
6.
Posfai A, Zhou J, McCandlish D, Kinney J
bioRxiv
. 2024 May;
PMID: 38798671
Quantitative models of sequence-function relationships are ubiquitous in computational biology, e.g., for modeling the DNA binding of transcription factors or the fitness landscapes of proteins. Interpreting these models, however, is...
7.
Posfai A, McCandlish D, Kinney J
bioRxiv
. 2024 May;
PMID: 38798625
Quantitative models that describe how biological sequences encode functional activities are ubiquitous in modern biology. One important aspect of these models is that they commonly exhibit gauge freedoms, i.e., directions...
8.
Rozhonova H, Marti-Gomez C, McCandlish D, Payne J
PLoS Biol
. 2024 May;
22(5):e3002594.
PMID: 38754362
The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein...
9.
Chen W, Zhou J, McCandlish D
ArXiv
. 2024 May;
PMID: 38699164
Biological sequences do not come at random. Instead, they appear with particular frequencies that reflect properties of the associated system or phenomenon. Knowing how biological sequences are distributed in sequence...
10.
Livesey B, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, et al.
ArXiv
. 2024 May;
PMID: 38699161
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as...