David M. McCandlish

发表

MAVE-NN: Quantitative Modeling of Genotype-Phenotype Maps as Information Bottlenecks

Justin B. Kinney, Ammar Tareen, William T. Ireland, 2020 .

Contingency and entrenchment in protein evolution under purifying selection

Joshua B. Plotkin, David M. McCandlish, Premal Shah, 2014, Proceedings of the National Academy of Sciences.

Mutational Biases Influence Parallel Adaptation

Arlin Stoltzfus, David M. McCandlish, A. Stoltzfus, 2017, bioRxiv.

splice sites by noncanonical base-pairing to U1 snRNA involving

Sonya M. Hanson, David M. McCandlish, J. Kinney, 2022 .

Evolutionary paths that link orthogonal pairs of binding proteins

David M. McCandlish, D. McCandlish, S. Fleishman, 2023, Research square.

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

David M. McCandlish, J. Kinney, D. McCandlish, 2020, bioRxiv.

Genomic and experimental evidence that ALKATI does not predict single agent sensitivity to ALK inhibitors

David M. McCandlish, J. Pritchard, D. McCandlish, 2021, iScience.

Mutation and selection induce correlations between selection coefficients and mutation rates

Joshua L. Payne, David M. McCandlish, A. V. Cano, 2023, bioRxiv.

Mutation bias and the predictability of evolution

Joshua L. Payne, David M. McCandlish, A. V. Cano, 2023, Philosophical Transactions of the Royal Society B.

Epistasis and the Dynamics of Reversion in Molecular Evolution

Joshua B Plotkin, David M. McCandlish, Premal Shah, 2016, Genetics.

Mutation bias shapes the spectrum of adaptive substitutions

Joshua L. Payne, David M. McCandlish, A. V. Cano, 2021, Proceedings of the National Academy of Sciences.

Field-theoretic density estimation for biological sequence space with applications to 5′ splice site diversity and aneuploidy in cancer

David M. McCandlish, J. Kinney, Jason M. Sheltzer, 2021, Proceedings of the National Academy of Sciences.

Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer

David M. McCandlish, J. Kinney, Jason M. Sheltzer, 2020 .

Inferring the shape of global epistasis

David M. McCandlish, J. Plotkin, Jakub Otwinowski, 2018, Proceedings of the National Academy of Sciences.

Evolution of Epistasis: Small Populations Go Their Separate Ways

David M. McCandlish, D. McCandlish, G. I. Lang, 2020, Journal of Molecular Evolution.

Detecting epistasis from an ensemble of adapting populations

David M. McCandlish, J. Plotkin, D. McCandlish, 2015, Evolution; international journal of organic evolution.

The diversity of evolutionary dynamics on epistatic versus non-epistatic fitness landscapes

David M. McCandlish, J. Plotkin, D. McCandlish, 2014, 1410.2508.

On the role of epistasis in adaptation

David M. McCandlish, J. Plotkin, D. McCandlish, 2014 .

Modeling Evolution Using the Probability of Fixation: History and Implications

Arlin Stoltzfus, David M. McCandlish, A. Stoltzfus, 2014, The Quarterly Review of Biology.

Evolution on Arbitrary Fitness Landscapes when Mutation is Weak

David M. McCandlish, David Martin McCandlish, D. McCandlish, 2012 .

THE INEVITABILITY OF UNCONDITIONALLY DELETERIOUS SUBSTITUTIONS DURING ADAPTATION

David M. McCandlish, J. Plotkin, C. Epstein, 2013, Evolution; international journal of organic evolution.

ON THE FINDABILITY OF GENOTYPES

David M. McCandlish, D. McCandlish, 2013, Evolution; international journal of organic evolution.

Formal properties of the probability of fixation: identities, inequalities and approximations.

David M. McCandlish, J. Plotkin, C. Epstein, 2013, Theoretical population biology.

VISUALIZING FITNESS LANDSCAPES

David M. McCandlish, D. McCandlish, 2011, Evolution; international journal of organic evolution.

Minimum epistasis interpolation for sequence-function relationships

David M. McCandlish, D. McCandlish, Juannan Zhou, 2019, Nature Communications.

Selection for Protein Stability Enriches for Epistatic Interactions

David M. McCandlish, J. Kinney, J. Plotkin, 2018, bioRxiv.

The role of epistasis in protein evolution

David M. McCandlish, J. Plotkin, D. McCandlish, 2013, Nature.

The genealogical decomposition of a matrix population model with applications to the aggregation of stages

David M. McCandlish, Erol Akçay, D. McCandlish, 2016, bioRxiv.

A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning.

Andrew V. Colasanti, Michael Y Tolstorukov, Andrew V Colasanti, 2007, Journal of molecular biology.

Long-term evolution on complex fitness landscapes when mutation is weak

David M. McCandlish, D. McCandlish, 2018, Heredity.

Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals

Cory L. Strope, David M. McCandlish, A. Stoltzfus, 2015, bioRxiv.

Annual Review of Genomics and Human Genetics Massively Parallel Assays and Quantitative Sequence – Function Relationships

David M. McCandlish, J. Kinney, D. McCandlish, 2019 .

Assortative mating can impede or facilitate fixation of underdominant alleles

Mitchell G. Newberry, David M. McCandlish, J. Plotkin, 2016, bioRxiv.

Guidelines for releasing a variant effect predictor

David M. McCandlish, K. Lindorff-Larsen, M. Dias, 2024, ArXiv.

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

David M. McCandlish, J. Kinney, M. Kooshkbaghi, 2022, Genome Biology.

The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

David M. McCandlish, A. Stoltzfus, C. Witt, 2019, bioRxiv.