Browse by CSHL Author

Paper

Chen, Wei-Chia, Zhou, Juannan, McCandlish, David M (October 2024) Density estimation for ordinal biological sequences and its applications. Physical Review E, 110 (4). ISSN 2470-0045

Sun, Mengyi, Stoltzfus, Arlin, McCandlish, David M (October 2024) A fitness distribution law for amino-acid replacements. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Sokirniy, Ivan, Inam, Haider, Tomaszkiewicz, Marta, Reynolds, Joshua, McCandlish, David, Pritchard, Justin (September 2024) A side-by-side comparison of variant function measurements using deep mutational scanning and base editing. bioRxiv. ISSN 2692-8205 (Submitted)

Gitschlag, Bryan L, Pereira, Claudia V, Held, James P, McCandlish, David M, Patel, Maulik R (September 2024) Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans. Nature Communications, 15 (1). p. 8237. ISSN 2041-1723 (Public Dataset)

Seitz, EE, McCandlish, DM, Kinney, JB, Koo, PK (June 2024) Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. Nature Machine Intelligence, 6 (6). pp. 701-713. ISSN 2522-5839 (Public Dataset)

Rozhoňová, Hana, Martí-Gómez, Carlos, McCandlish, David M, Payne, Joshua L (May 2024) Robust genetic codes enhance protein evolvability. PLoS Biology, 22 (5). e3002594. ISSN 1545-7885 (Public Dataset)

Posfai, Anna, Zhou, Juannan, McCandlish, David M, Kinney, Justin B (May 2024) Gauge fixing for sequence-function relationships. bioRxiv.

Posfai, Anna, McCandlish, David M, Kinney, Justin B (May 2024) Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. bioRxiv. (Submitted)

Livesey, Benjamin J, Badonyi, Mihaly, Dias, Mafalda, Frazer, Jonathan, Kumar, Sushant, Lindorff-Larsen, Kresten, McCandlish, David M, Orenbuch, Rose, Shearer, Courtney A, Muffley, Lara, Foreman, Julia, Glazer, Andrew M, Lehner, Ben, Marks, Debora S, Roth, Frederick P, Rubin, Alan F, Starita, Lea M, Marsh, Joseph A (April 2024) Guidelines for releasing a variant effect predictor. ArXiv. ISSN 2331-8422 (Submitted)

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya M, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (February 2024) Specificity, synergy, and mechanisms of splice-modifying drugs. Nature Communications, 15 (1). p. 1880. ISSN 2041-1723 (Public Dataset)

Seitz, Evan E, McCandlish, David M, Kinney, Justin B, Koo, Peter K (November 2023) Interpreting cis -regulatory mechanisms from genomic deep neural networks using surrogate models. bioRxiv. (Submitted)

Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel F, McCandlish, David M, Lippman, Zachary B (October 2023) Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size. Science, 382 (6668). pp. 315-320. ISSN 0036-8075

Gitschlag, Bryan L, Cano, Alejandro V, Payne, Joshua L, McCandlish, David M, Stoltzfus, Arlin (October 2023) Mutation and Selection Induce Correlations between Selection Coefficients and Mutation Rates. The American Naturalist, 202 (4). pp. 534-557. ISSN 0003-0147

Rozhoňová, Hana, Martí-Gómez, Carlos, McCandlish, David M, Payne, Joshua L (June 2023) Protein evolvability under rewired genetic codes. bioRxiv. (Submitted)

Cano, Alejandro V, Gitschlag, Bryan L, Rozhoňová, Hana, Stoltzfus, Arlin, McCandlish, David M, Payne, Joshua L (May 2023) Mutation bias and the predictability of evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 378 (1877). p. 20220055. ISSN 0962-8436

Weinstein, Jonathan Yaacov, Martí-Gómez, Carlos, Lipsh-Sokolik, Rosalie, Hoch, Shlomo Yakir, Liebermann, Demian, Nevo, Reinat, Weissman, Haim, Petrovich-Kopitman, Ekaterina, Margulies, David, Ivankov, Dmitry, McCandlish, David M, Fleishman, Sarel J (May 2023) Designed active-site library reveals thousands of functional GFP variants. Nature Communications, 14 (1). p. 2890. ISSN 2041-1723

Ferrer, Miriam, Anthony, Tracy G, Ayres, Janelle S, Biffi, Giulia, Brown, Justin C, Caan, Bette J, Cespedes Feliciano, Elizabeth M, Coll, Anthony P, Dunne, Richard F, Goncalves, Marcus D, Grethlein, Jonas, Heymsfield, Steven B, Hui, Sheng, Jamal-Hanjani, Mariam, Lam, Jie Min, Lewis, David Y, McCandlish, David, Mustian, Karen M, O'Rahilly, Stephen, Perrimon, Norbert, White, Eileen P, Janowitz, Tobias (April 2023) Cachexia: A systemic consequence of progressive, unresolved disease. Cell, 186 (9). pp. 1824-1845. ISSN 0092-8674

Avizemer, Ziv, Martí-Gómez, Carlos, Hoch, Shlomo Yakir, McCandlish, David M, Fleishman, Sarel J (April 2023) Evolutionary paths that link orthogonal pairs of binding proteins. Research Square. (Submitted)

Ishigami, Yuma, Wong, Mandy S, Martí-Gómez, Carlos, Ayaz, Andalus, Kooshkbaghi, Mahdi, Hanson, Sonya, McCandlish, David M, Krainer, Adrian R, Kinney, Justin B (December 2022) Specificity, synergy, and mechanisms of splice-modifying drugs. (Public Dataset) (Submitted)

Zhou, Juannan, Wong, Mandy S, Chen, Wei-Chia, Krainer, Adrian R, Kinney, Justin B, McCandlish, David M (September 2022) Higher-order epistasis and phenotypic prediction. Proceedings of the National Academy of Sciences of USA, 119 (39). e2204233119. ISSN 0027-8424

Tareen, Ammar, Kooshkbaghi, Mahdi, Posfai, Anna, Ireland, William T, McCandlish, David M, Kinney, Justin B (April 2022) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biology, 23 (1). p. 98. ISSN 1474-7596

Cano, Alejandro V, Rozhoňová, Hana, Stoltzfus, Arlin, McCandlish, David M, Payne, Joshua L (February 2022) Mutation bias shapes the spectrum of adaptive substitutions. Proceedings of the National Academy of Sciences of USA, 119 (7). e2119720119-e2119720119. ISSN 0027-8424

Inam, H, Sokirniy, I, Rao, Y, Shah, A, Naeemikia, F, O'Brien, E, Dong, C, McCandlish, DM, Pritchard, JR (November 2021) Genomic and experimental evidence that ALK^ATI does not predict single agent sensitivity to ALK inhibitors. iScience, 24 (11). p. 103343. ISSN 2589-0042

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason M, Kinney, Justin B, McCandlish, David M (October 2021) Field-theoretic density estimation for biological sequence space with applications to 5' splice site diversity and aneuploidy in cancer. Proceedings of the National Academy of Sciences of USA, 118 (40). ISSN 1091-6490

McCandlish, DM (September 2021) System-specificity of genotype-phenotype map structure: Comment on “From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics” by Susanna Manrubia et al. Physics of Life Reviews. ISSN 1571-0645

Chen, Wei-Chia, Zhou, Juannan, Sheltzer, Jason, Kinney, Justin, McCandlish, David (December 2020) Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer. BioRxiv. (Unpublished)

Zhou, Juannan, Wong, Mandy, Chen, Wei-Chia, Krainer, Adrian, Kinney, Justin, McCandlish, David (October 2020) Empirical variance component regression for sequence-function relationships. BioRxiv. (Unpublished)

Tareen, Ammar, Posfai, Anna, Ireland, William, McCandlish, David, Kinney, Justin (July 2020) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. BioRxiv. (Unpublished)

McCandlish, D. M., Lang, G.I. (July 2020) Evolution of Epistasis: Small Populations Go Their Separate Ways. Journal of Molecular Evolution, 88 (5). pp. 418-420.

Zhou, J., McCandlish, D. M. (April 2020) Minimum Epistasis Interpolation for Sequence-Function Relationships. Nature Communication, 11 (1782). pp. 1-11. ISSN 2041-1723 (Public Dataset)

Storz, J. F., Natarajan, C., Signore, A. V., Witt, C. C., McCandlish, D. M., Stoltzfus, A. (July 2019) The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function. Philos Trans R Soc Lond B Biol Sci, 374 (1777). p. 20180238. ISSN 0962-8436 (Public Dataset)

Kinney, J. B., McCandlish, D. M. (May 2019) Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet, 20. pp. 99-127. ISSN 1527-8204

McCandlish, D. M. (September 2018) Long-term evolution on complex fitness landscapes when mutation is weak. Heredity (Edinb). ISSN 0018-067x

Posfai, A., Zhou, J., Plotkin, J. B., Kinney, J. B., McCandlish, D. M. (August 2018) Selection for Protein Stability Enriches for Epistatic Interactions. Genes (Basel), 9 (9). ISSN 2073-4425 (Print)2073-4425

Otwinowski, J., McCandlish, D. M., Plotkin, J. B. (July 2018) Inferring the shape of global epistasis. Proc Natl Acad Sci U S A. ISSN 0027-8424

Stoltzfus, A., McCandlish, D. M. (September 2017) Mutational biases influence parallel adaptation. Mol Biol Evol, 34 (9). pp. 2163-2172. ISSN 0737-4038

Bienvenu, François, Akcay, Erol, Legendre, Stéphane, McCandlish, David (June 2017) The genealogical decomposition of a matrix population model with applications to the aggregation of stages. Theoretical Population Biology, 115. pp. 69-80.

Newberry, M. G., McCandlish, D. M., Plotkin, J. B. (December 2016) Assortative mating can impede or facilitate fixation of underdominant alleles. Theor Popul Biol, 112. pp. 14-21. ISSN 1096-0325 (Electronic)0040-5809 (Linking)

McCandlish, D. M., Shah, P., Plotkin, J. B. (July 2016) Epistasis and the Dynamics of Reversion in Molecular Evolution. Genetics, 203 (3). pp. 1335-51. ISSN 1943-2631 (Electronic)0016-6731 (Linking)

McCandlish, D. M., Plotkin, J. B. (March 2016) Transcriptional errors and the drift barrier. Proc Natl Acad Sci U S A, 113 (12). pp. 3136-8. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

Stoltzfus, A., McCandlish, D. M. (November 2015) Mutation-biased adaptation in Andean house wrens. Proc Natl Acad Sci U S A, 112 (45). pp. 13753-4. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

McCandlish, D. M., Otwinowski, J., Plotkin, J. B. (September 2015) Detecting epistasis from an ensemble of adapting populations. Evolution, 69 (9). pp. 2359-70. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

Shah, P., McCandlish, D. M., Plotkin, J. B. (June 2015) Contingency and entrenchment in protein evolution under purifying selection. Proc Natl Acad Sci U S A, 112 (25). E3226-35. ISSN 1091-6490 (Electronic)0027-8424 (Linking)

McCandlish, D. M., Epstein, C. L., Plotkin, J. B. (February 2015) Formal properties of the probability of fixation: identities, inequalities and approximations. Theor Popul Biol, 99. pp. 98-113. ISSN 1096-0325 (Electronic)0040-5809 (Linking)

Norris, Ryan W., Strope, Cory L., McCandlish, David M., Stoltzfus, Arlin (2015) Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals. bioRxiv.

McCandlish, D. M., Epstein, C. L., Plotkin, J. B. (May 2014) The inevitability of unconditionally deleterious substitutions during adaptation. Evolution, 68 (5). pp. 1351-64. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

McCandlish, David M., Stoltzfus, Arlin (2014) Modeling evolution using the probability of fixation: history and implications. The Quarterly Review of Biology, 89 (3). pp. 225-252. ISSN 0033-57701539-7718

McCandlish, D. M. (September 2013) On the findability of genotypes. Evolution, 67 (9). pp. 2592-603. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

McCandlish, D. M., Rajon, E., Shah, P., Ding, Y., Plotkin, J. B. (May 2013) The role of epistasis in protein evolution. Nature, 497 (7451). E1-2; discussion E2. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

McCandlish, D. M. (June 2011) Visualizing fitness landscapes. Evolution, 65 (6). pp. 1544-58. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

Tolstorukov, M. Y., Colasanti, A. V., McCandlish, D. M., Olson, W. K., Zhurkin, V. B. (August 2007) A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol, 371 (3). pp. 725-38. ISSN 0022-2836 (Print)0022-2836 (Linking)