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Author

  • Michael Lynch
2015

Background mutational features of the radiation-resistant bacterium deinococcus radiodurans

Long, H., Kucukyildirim, S., Sung, W., Williams, E., Lee, H., Ackerman, M., Doak, T. G., Tang, H. & Lynch, M., Jan 1 2015, In : Molecular biology and evolution. 32, 9, p. 2383-2392 10 p.

Research output: Contribution to journalArticle

28 Scopus citations
2014

Editorial expression of concern: Non-adaptive origins of interactome complexity

Fernández, A. & Lynch, M., Dec 18 2014, In : Nature. 516, 7531, 1 p.

Research output: Contribution to journalEditorial

Open Access

Erratum: Editorial expression of concern: Non-adaptive origins of interactome complexity (Nature (2011) 474 (502-505) DOI: 10.1038/nature09992)

Fernández, A. & Lynch, M., Dec 18 2014, In : Nature. 516, 7531, 1 p.

Research output: Contribution to journalComment/debate

Open Access
2015

Genetics: Feedforward loop for diversity

Lynch, M., Jul 23 2015, In : Nature. 523, 7561, p. 414-416 3 p.

Research output: Contribution to journalArticle

6 Scopus citations
2012

High mutation rates in the mitochondrial genomes of Daphnia pulex

Xu, S., Schaack, S., Seyfert, A., Choi, E., Lynch, M. & Cristescu, M. E., Feb 1 2012, In : Molecular biology and evolution. 29, 2, p. 763-769 7 p.

Research output: Contribution to journalArticle

33 Scopus citations
2017

Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in vibrio cholerae and vibrio fischeri

Dillon, M. M., Sung, W., Sebra, R., Lynch, M. & Cooper, V. S., Jan 1 2017, In : Molecular Biology and Evolution. 34, 1, p. 93-109 17 p.

Research output: Contribution to journalArticle

29 Scopus citations
2011

The ecoresponsive genome of Daphnia pulex

Colbourne, J. K., Pfrender, M. E., Gilbert, D., Thomas, W. K., Tucker, A., Oakley, T. H., Tokishita, S., Aerts, A., Arnold, G. J., Basu, M. K., Bauer, D. J., Cáceres, C. E., Carmel, L., Casola, C., Choi, J. H., Detter, J. C., Dong, Q., Dusheyko, S., Eads, B. D., Fröhlich, T. & 49 others, Geiler-Samerotte, K. A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E. V., Kültz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J. R., Muller, J., Pangilinan, J., Patwardhan, R. P., Pitluck, S., Pritham, E. J., Rechtsteiner, A., Rho, M., Rogozin, I. B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y. I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J. R., Andrews, J., Crease, T. J., Tang, H., Lucas, S. M., Robertson, H. M., Bork, P., Koonin, E. V., Zdobnov, E. M., Grigoriev, I. V., Lynch, M. & Boore, J. L., Feb 4 2011, In : Science. 331, 6017, p. 555-561 7 p.

Research output: Contribution to journalArticle

785 Scopus citations
2015
39 Scopus citations
2013

Large-scale detection of in vivo transcription errors

Gout, J. F., Thomas, W. K., Smith, Z., Okamoto, K. & Lynch, M., Nov 12 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 46, p. 18584-18589 6 p.

Research output: Contribution to journalArticle

59 Scopus citations
2012

Drift-barrier hypothesis and mutation-rate evolution

Sung, W., Ackerman, M. S., Miller, S. F., Doak, T. G. & Lynch, M., Nov 6 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 45, p. 18488-18492 5 p.

Research output: Contribution to journalArticle

171 Scopus citations
2014

Evolutionary cell biology: Two origins, one objective

Lynch, M., Field, M. C., Goodson, H. V., Malik, H. S., Pereira-Leal, J. B., Roos, D. S., Turkewitz, A. P. & Sazer, S., Dec 2 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 48, p. 16990-16994 5 p.

Research output: Contribution to journalReview article

54 Scopus citations
2016

Evolution of the insertion-deletion mutation rate across the tree of life

Sung, W., Ackerman, M. S., Dillon, M. M., Platt, T. G., Fuqua, C., Cooper, V. S. & Lynch, M., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 8, p. 2583-2591 9 p.

Research output: Contribution to journalArticle

26 Scopus citations
2012

Extraordinary genome stability in the ciliate Paramecium tetraurelia

Sung, W., Tucker, A. E., Doak, T. G., Choi, E., Thomas, W. K. & Lynch, M., Nov 20 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 47, p. 19339-19344 6 p.

Research output: Contribution to journalArticle

60 Scopus citations
2018

Limited mutation-rate variation within the Paramecium aurelia species complex

Long, H., Doak, T. G. & Lynch, M., Jul 1 2018, In : G3: Genes, Genomes, Genetics. 8, 7, p. 2523-2526 4 p.

Research output: Contribution to journalArticle

4 Scopus citations
2020
2014

Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data

Maruki, T. & Lynch, M., 2014, In : Genetics. 197, 4, p. 1303-1313 11 p.

Research output: Contribution to journalArticle

14 Scopus citations
2017

Estimating seven coefficients of pairwise relatedness using population-genomic data

Ackerman, M. S., Johri, P., Spitze, K., Xu, S., Doak, T. G., Young, K. & Lynch, M., May 2017, In : Genetics. 206, 1, p. 105-118 14 p.

Research output: Contribution to journalArticle

10 Scopus citations
2015

Genotype-frequency estimation from high-throughput sequencing data

Maruki, T. & Lynch, M., Oct 2015, In : Genetics. 201, 2, p. 473-486 14 p.

Research output: Contribution to journalArticle

13 Scopus citations

A male-specific genetic map of the microcrustacean Daphnia pulex based on single-sperm whole-genome sequencing

Xu, S., Ackerman, M. S., Long, H., Bright, L., Spitze, K., Ramsdell, J. S., Thomas, W. K. & Lynch, M., Sep 1 2015, In : Genetics. 201, 1, p. 31-38 8 p.

Research output: Contribution to journalArticle

20 Scopus citations
2014

Genome-wide linkage-disequilibrium profiles from single individuals

Lynch, M., Xu, S., Maruki, T., Jiang, X., Pfaffelhuber, P. & Haubold, B., Apr 11 2014, In : Genetics. 198, 1, p. 269-281 13 p.

Research output: Contribution to journalArticle

12 Scopus citations

Deciphering the evolutionary history of open and closed mitosis

Sazer, S., Lynch, M. & Needleman, D., Jan 1 2014, In : Current Biology. 24, 22, p. R1099-R1103

Research output: Contribution to journalReview article

30 Scopus citations
2016

Mutation and human exceptionalism: Our future genetic load

Lynch, M., Mar 2016, In : Genetics. 202, 3, p. 869-875 7 p.

Research output: Contribution to journalArticle

34 Scopus citations

Promoter architecture and sex-specific gene expression in Daphnia pulex

Raborn, R. T., Spitze, K., Brendel, V. P. & Lynch, M., Oct 2016, In : Genetics. 204, 2, p. 593-612 20 p.

Research output: Contribution to journalArticle

10 Scopus citations

High mutational rates of large-scale duplication and deletion in Daphnia pulex

Keith, N., Tucker, A. E., Jackson, C. E., Sung, W., Lledó, J. I. L., Schrider, D. R., Schaack, S., Dudycha, J. L., Ackerman, M., Younge, A. J., Shaw, J. R. & Lynch, M., Jan 2016, In : Genome research. 26, 1, p. 60-69 10 p.

Research output: Contribution to journalArticle

28 Scopus citations
2017

Catalytic properties of RNA polymerases IV and V: Accuracy, nucleotide incorporation and rNTP/dNTP discrimination

Marasco, M., Li, W., Lynch, M. & Pikaard, C. S., Jan 1 2017, In : Nucleic Acids Research. 45, 19, p. 11315-11326 12 p.

Research output: Contribution to journalArticle

4 Scopus citations
2013

Spliced DNA sequences in the Paramecium germline: Their properties and evolutionary potential

Catania, F., McGrath, C. L., Doak, T. G. & Lynch, M., 2013, In : Genome biology and evolution. 5, 6, p. 1200-1211 12 p.

Research output: Contribution to journalArticle

9 Scopus citations
2016

Low base-substitution mutation rate in the germline genome of the ciliate tetrahymena thermophila

Long, H., Winter, D. J., Chang, A. Y. C., Sung, W., Wu, S. H., Balboa, M., Azevedo, R. B. R., Cartwright, R., Lynch, M. & Zufall, R. A., 2016, In : Genome Biology and Evolution. 8, 12, p. 3629-3639 11 p.

Research output: Contribution to journalArticle

10 Scopus citations
2011

Statistical inference on the mechanisms of genome evolution

Lynch, M., Jun 2011, In : PLoS genetics. 7, 6, e1001389.

Research output: Contribution to journalArticle

20 Scopus citations
2018

Periodic variation of mutation rates in bacterial genomes associated with replication timing

Dillon, M. M., Sung, W., Lynch, M. & Cooper, V. S., Jul 1 2018, In : mBio. 9, 4, e01371-18.

Research output: Contribution to journalArticle

8 Scopus citations
2014

Population-genetic inference from pooled-sequencing data

Lynch, M., Bost, D., Wilson, S., Maruki, T. & Harrison, S., May 2014, In : Genome biology and evolution. 6, 5, p. 1210-1218 9 p.

Research output: Contribution to journalArticle

43 Scopus citations
2020

The Limits to Estimating Population-Genetic Parameters with Temporal Data

Lynch, M. & Ho, W. C., Apr 1 2020, In : Genome biology and evolution. 12, 4, p. 443-455 13 p.

Research output: Contribution to journalArticle

Open Access
2013

The role of hybridization in the origin and spread of asexuality in Daphnia

Xu, S., Innes, D. J., Lynch, M. & Cristescu, M. E., Sep 1 2013, In : Molecular Ecology. 22, 17, p. 4549-4561 13 p.

Research output: Contribution to journalArticle

27 Scopus citations
2017

Genome-wide mutation rate response to pH change in the coral reef pathogen vibrio shilonii AK1

Strauss, C., Long, H., Patterson, C. E., Te, R. & Lynch, M., Jul 1 2017, In : mBio. 8, 4, e01021-17.

Research output: Contribution to journalArticle

6 Scopus citations
2014

Characterization of newly gained introns in Daphnia populations

Li, W., Kuzoff, R., Wong, C. K., Tucker, A. & Lynch, M., Jan 1 2014, In : Genome biology and evolution. 6, 9, p. 2218-2234 17 p.

Research output: Contribution to journalArticle

12 Scopus citations
2016

Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a Consensus Symposium

Bréchignac, F., Oughton, D., Mays, C., Barnthouse, L., Beasley, J. C., Bonisoli-Alquati, A., Bradshaw, C., Brown, J., Dray, S., Geras'kin, S., Glenn, T., Higley, K., Ishida, K., Kapustka, L., Kautsky, U., Kuhne, W., Lynch, M., Mappes, T., Mihok, S., Møller, A. P. & 8 others, Mothersill, C., Mousseau, T. A., Otaki, J., Pryakhin, E., Rhodes, O. E., Salbu, B., Strand, P. & Tsukada, H., Jul 1 2016, In : Journal of Environmental Radioactivity. 158-159, p. 21-29 9 p.

Research output: Contribution to journalReview article

38 Scopus citations
2017

The landscape of transcription errors in eukaryotic cells

Gout, J. F., Li, W., Fritsch, C., Li, A., Haroon, S., Singh, L., Hua, D., Fazelinia, H., Smith, Z., Seeholzer, S., Thomas, K., Lynch, M. & Vermulst, M., Oct 1 2017, In : Science advances. 3, 10, e1701484.

Research output: Contribution to journalArticle

24 Scopus citations
2019

The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018

Jensen, J., Payseur, B. A., Stephan, W., Aquadro, C. F., Lynch, M., Charlesworth, D. & Charlesworth, B., Jan 2019, In : Evolution. 73, 1, p. 111-114 4 p.

Research output: Contribution to journalComment/debate

15 Scopus citations

Genetic control of male production in Daphnia pulex

Ye, Z., Molinier, C., Zhao, C., Haag, C. R. & Lynch, M., Jul 30 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 31, p. 15602-15609 8 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
2012

Evolutionary significance of whole-genome duplication

McGrath, C. L. & Lynch, M., Nov 1 2012, Polyploidy and Genome Evolution. Springer-Verlag Berlin Heidelberg, Vol. 9783642314421. p. 1-20 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

27 Scopus citations

The evolution of multimeric protein assemblages

Lynch, M., May 2012, In : Molecular biology and evolution. 29, 5, p. 1353-1366 14 p.

Research output: Contribution to journalArticle

44 Scopus citations
2018

A maximum-likelihood approach to estimating the insertion frequencies of transposable elements from population sequencing data

Jiang, X., Tang, H., Mohammed Ismail, W. & Lynch, M., Jan 1 2018, In : Molecular biology and evolution. 35, 10, p. 2560-2571 12 p.

Research output: Contribution to journalArticle

Specificity of the DNA Mismatch Repair System (MMR) and Mutagenesis Bias in Bacteria

Long, H., Miller, S. F., Williams, E. & Lynch, M., Oct 1 2018, In : Molecular Biology and Evolution. 35, 10, p. 2414-2421 8 p.

Research output: Contribution to journalArticle

7 Scopus citations
2012

The effect of variable frequency of sexual reproduction on the genetic structure of natural populations of a cyclical parthenogen

Allen, D. E. & Lynch, M., Mar 1 2012, In : Evolution. 66, 3, p. 919-926 8 p.

Research output: Contribution to journalArticle

14 Scopus citations
2017

Genotype calling from population-genomic sequencing data

Maruki, T. & Lynch, M., May 1 2017, In : G3: Genes, Genomes, Genetics. 7, 5, p. 1393-1404 12 p.

Research output: Contribution to journalArticle

19 Scopus citations
2012

The spread of a transposon insertion in Rec8 is associated with obligate asexuality in Daphnia

Eads, B. D., Tsuchiya, D., Andrews, J., Lynch, M. & Zolan, M. E., Jan 17 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 3, p. 858-863 6 p.

Research output: Contribution to journalArticle

26 Scopus citations
2013

A genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria

Raymann, K., Bobay, L. M., Doak, T. G., Lynch, M. & Gribaldo, S., Mar 2013, In : G3: Genes, Genomes, Genetics. 3, 3, p. 505-516 12 p.

Research output: Contribution to journalArticle

9 Scopus citations
2018

Escherichia coli cultures maintain stable subpopulation structure during long-term evolution

Behringer, M. G., Choi, B. I., Miller, S. F., Doak, T. G., Karty, J. A., Guo, W. & Lynch, M., May 15 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 20, p. E4642-E4650

Research output: Contribution to journalArticle

10 Scopus citations
2019

Evolution of protein interfaces in multimers and fibrils

Zabel, W. J., Hagner, K. P., Livesey, B. J., Marsh, J. A., Setayeshgar, S., Lynch, M. & Higgs, P. G., Jun 14 2019, In : Journal of Chemical Physics. 150, 22, 225102.

Research output: Contribution to journalArticle

Open Access
2017

Population Genomics of Paramecium Species

Johri, P., Krenek, S., Marinov, G. K., Doak, T. G., Berendonk, T. U. & Lynch, M., May 1 2017, In : Molecular Biology and Evolution. 34, 5, p. 1194-1216 23 p.

Research output: Contribution to journalArticle

9 Scopus citations

The glyphosate-based herbicide roundup does not elevate genome-wide mutagenesis of Escherichia coli

Tincher, C., Long, H., Behringer, M., Walker, N. & Lynch, M., Oct 1 2017, In : G3: Genes, Genomes, Genetics. 7, 10, p. 3331-3335 5 p.

Research output: Contribution to journalArticle

1 Scopus citations