Search Results - "McCandlish DM"

Inference and Visualization of Complex Genotype-Phenotype Maps.

Authors: Martí-Gómez C Zhou J Chen WC et al.

Source: Molecular biology and evolution [Mol Biol Evol] 2026 Feb 02; Vol. 43 (2).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE

GaugeFixer: overcoming parameter non-identifiability in models of sequence-function relationships.

Authors: Martí-Gómez C McCandlish DM Kinney JB

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 May 11. Date of Electronic Publication: 2026 May 11.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing.

Authors: Petti S Martí-Gómez C Kinney JB et al.

Source: Journal of mathematical biology [J Math Biol] 2026 Apr 29; Vol. 92 (5). Date of Electronic Publication: 2026 Apr 29.

Publication Type: Journal Article

Journal Info: Publisher: Springer Verlag Country of Publication: Germany NLM ID: 7502105 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-1416 (Electronic) Linking ISSN: 03036812 NLM ISO Abbreviation: J Math Biol Subsets: MEDLINE

Genetic background shapes AI-predicted variant effects.

Authors: Schilder BM Liu Z Desmarais JJ et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Apr 07. Date of Electronic Publication: 2026 Apr 07.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Guidelines for releasing a variant effect predictor.

Authors: Livesey BJ Badonyi M Dias M et al.

Source: Genome biology [Genome Biol] 2025 Apr 15; Vol. 26 (1), pp. 97. Date of Electronic Publication: 2025 Apr 15.

Publication Type: Journal Article

Journal Info: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE

Weakest link epistasis and the geometry of genetic load.

Authors: Labourel FJF Bansept F McCandlish DM

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Jan 27. Date of Electronic Publication: 2026 Jan 27.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Gauge fixing for sequence-function relationships.

Authors: Posfai A Zhou J McCandlish DM et al.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Mar 20; Vol. 21 (3), pp. e1012818. Date of Electronic Publication: 2025 Mar 20 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Meta-Research: Positive genetic interactions have greater scientific impact but are under-represented in the literature.

Authors: Sun M McCandlish DM

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Oct 27. Date of Electronic Publication: 2025 Oct 27.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning.

Authors: Seitz EE McCandlish DM Kinney JB et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Oct 08. Date of Electronic Publication: 2025 Oct 08.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans.

Authors: Gitschlag BL Pereira CV Held JP et al.

Source: Nature communications [Nat Commun] 2024 Sep 19; Vol. 15 (1), pp. 8237. Date of Electronic Publication: 2024 Sep 19.

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

Robust genetic codes enhance protein evolvability.

Authors: Rozhoňová H Martí-Gómez C McCandlish DM et al.

Source: PLoS biology [PLoS Biol] 2024 May 16; Vol. 22 (5), pp. e3002594. Date of Electronic Publication: 2024 May 16 (Print Publication: 2024).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101183755 Publication Model: eCollection Cited Medium: Internet ISSN: 1545-7885 (Electronic) Linking ISSN: 15449173 NLM ISO Abbreviation: PLoS Biol Subsets: MEDLINE

Inference and visualization of complex genotype-phenotype maps with gpmap-tools.

Authors: Martí-Gómez C Zhou J Chen WC et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Aug 26. Date of Electronic Publication: 2025 Aug 26.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Learning sequence-function relationships with scalable, interpretable Gaussian processes.

Authors: Zhou J Martí-Gómez C Petti S et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Aug 19. Date of Electronic Publication: 2025 Aug 19.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing.

Authors: Petti S Martí-Gómez C Kinney JB et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Aug 02. Date of Electronic Publication: 2025 Aug 02.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing.

Authors: Petti S Martí-Gómez C Kinney JB et al.

Source: ArXiv [ArXiv] 2025 Aug 01. Date of Electronic Publication: 2025 Aug 01.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101759493 Publication Model: Electronic Cited Medium: Internet ISSN: 2331-8422 (Electronic) Linking ISSN: 23318422 NLM ISO Abbreviation: ArXiv Subsets: PubMed not MEDLINE

Cryptic variation fuels plant phenotypic change through hierarchical epistasis.

Authors: Zebell SG Martí-Gómez C Fitzgerald B et al.

Source: Nature [Nature] 2025 Aug; Vol. 644 (8078), pp. 984-992. Date of Electronic Publication: 2025 Jul 09.

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE

Specificity, synergy, and mechanisms of splice-modifying drugs.

Authors: Ishigami Y Wong MS Martí-Gómez C et al.

Source: Nature communications [Nat Commun] 2024 Feb 29; Vol. 15 (1), pp. 1880. Date of Electronic Publication: 2024 Feb 29.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size.

Authors: Aguirre L Hendelman A Hutton SF et al.

Source: Science (New York, N.Y.) [Science] 2023 Oct 20; Vol. 382 (6668), pp. 315-320. Date of Electronic Publication: 2023 Oct 19.

Publication Type: Journal Article

Journal Info: Publisher: American Association for the Advancement of Science Country of Publication: United States NLM ID: 0404511 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9203 (Electronic) Linking ISSN: 00368075 NLM ISO Abbreviation: Science Subsets: MEDLINE

Mutation and Selection Induce Correlations between Selection Coefficients and Mutation Rates.

Authors: Gitschlag BL Cano AV Payne JL et al.

Source: The American naturalist [Am Nat] 2023 Oct; Vol. 202 (4), pp. 534-557. Date of Electronic Publication: 2023 Aug 25.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: University of Chicago Press Country of Publication: United States NLM ID: 2984688R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1537-5323 (Electronic) Linking ISSN: 00030147 NLM ISO Abbreviation: Am Nat Subsets: MEDLINE

Evolutionary paths that link orthogonal pairs of binding proteins.

Authors: Avizemer Z Martí-Gómez C Hoch SY et al.

Source: Cell systems [Cell Syst] 2025 May 21; Vol. 16 (5), pp. 101262. Date of Electronic Publication: 2025 Apr 10.

Publication Type: Journal Article

Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 101656080 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2405-4720 (Electronic) Linking ISSN: 24054712 NLM ISO Abbreviation: Cell Syst Subsets: MEDLINE