Evolutionary genomics: new perspectives and novel medical applications

Publications

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

Author(s): Xianqing Jia, Qijun Zhang, Mengmeng Jiang, Ju Huang, Luyao Yu, Milton Brian Traw, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Published in: PLOS Biology, Issue 19/3, 2021, Page(s) e3001164, ISSN 1545-7885
Publisher: PLOS
DOI: 10.1371/journal.pbio.3001164

Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design

Author(s): Alan M Rice, Atahualpa Castillo Morales, Alexander T Ho, Christine Mordstein, Stefanie Mühlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D Hurst
Published in: Molecular Biology and Evolution, Issue 38/1, 2020, Page(s) 67-83, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa188

Causes and consequences of purifying selection on SARS-CoV-2

Author(s): Atahualpa Castillo Morales, Alan M Rice, Alexander T Ho, Christine Mordstein, Stefanie Mühlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D Hurst
Published in: Genome Biology and Evolution, 2021, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evab196

Variation in release factor abundance is not needed to explain trends in bacterial stop codon usage

Author(s): Alexander T Ho, Laurence D Hurst
Published in: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab326

A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences

Author(s): Liam Abrahams, Laurence D Hurst
Published in: Molecular Biology and Evolution, Issue 37/4, 2019, Page(s) 1148-1164, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz299

Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors

Author(s): Alexander T Ho, Laurence D Hurst
Published in: Molecular Biology and Evolution, Issue 38/1, 2020, Page(s) 244-262, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa210

Transcription, mRNA export and immune evasion shape the codon usage of viruses

Author(s): Christine Mordstein, Laura Cano, Atahualpa Castillo Morales, Bethan Young, Alexander T Ho, Alan M Rice, Michael Liss, Laurence D Hurst, Grzegorz Kudla
Published in: Genome Biology and Evolution, 2021, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evab106

Depletion of somatic mutations in splicing-associated sequences in cancer genomes

Author(s): Laurence D. Hurst, Nizar N. Batada
Published in: Genome Biology, Issue 18/1, 2017, ISSN 1474-760X
Publisher: BMC
DOI: 10.1186/s13059-017-1337-5

Faster Evolving Primate Genes Are More Likely to Duplicate

Author(s): Áine N O’Toole, Laurence D Hurst, Aoife McLysaght
Published in: Molecular Biology and Evolution, Issue 35/1, 2017, Page(s) 107-118, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msx270

Refining the ambush hypothesis: evidence that GC and AT rich bacteria employ different frameshift defence strategies

Author(s): Liam Abrahams, Laurence D Hurst
Published in: Genome Biology and Evolution, 2018, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evy075

Disturbed Placental Imprinting in Preeclampsia Leads to Altered Expression of DLX5, a Human-Specific Early Trophoblast Marker

Author(s): Julianna Zadora, Manvendra Singh, Florian Herse, Lukasz Przybyl, Nadine Haase, Michaela Golic, Hong Wa Yung, Berthold Huppertz, Judith E. Cartwright, Guy Whitley, Guro M. Johnsen, Giovanni Levi, Annette Isbruch, Herbert Schulz, Friedrich C. Luft, Dominik N. Müller, Anne Cathrine Staff, Laurence D. Hurst, Ralf Dechend, Zsuzsanna Izsvák
Published in: Circulation, Issue 136/19, 2017, Page(s) 1824-1839, ISSN 0009-7322
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circulationaha.117.028110

Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts

Author(s): Liam Abrahams, Laurence D Hurst
Published in: Molecular Biology and Evolution, Issue 34/12, 2017, Page(s) 3064-3080, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msx223

Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias

Author(s): Haoxuan Liu, Ju Huang, Xiaoguang Sun, Jing Li, Yingwen Hu, Luyao Yu, Gianni Liti, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Published in: Nature Ecology & Evolution, Issue 2/1, 2018, Page(s) 164-173, ISSN 2397-334X
Publisher: Nature publishing group
DOI: 10.1038/s41559-017-0372-7

Identifying a large number of high-yield genes in rice by pedigree analysis, whole-genome sequencing, and CRISPR-Cas9 gene knockout

Author(s): Ju Huang, Jing Li, Jun Zhou, Long Wang, Sihai Yang, Laurence D. Hurst, Wen-Hsiung Li, Dacheng Tian
Published in: Proceedings of the National Academy of Sciences, 2018, Page(s) 201806110, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1806110115

Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica

Author(s): Stefanie Mühlhausen, Hans Dieter Schmitt, Kuan-Ting Pan, Uwe Plessmann, Henning Urlaub, Laurence D. Hurst, Martin Kollmar
Published in: Current Biology, Issue 28/13, 2018, Page(s) 2046-2057.e5, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2018.04.085

Exonic splice regulation imposes strong selection at synonymous sites

Author(s): Rosina Savisaar, Laurence D. Hurst
Published in: Genome Research, 2018, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.233999.117

Determinants of the Usage of Splice-Associated cis -Motifs Predict the Distribution of Human Pathogenic SNPs

Author(s): XianMing Wu, Laurence D. Hurst
Published in: Molecular Biology and Evolution, Issue 33/2, 2016, Page(s) 518-529, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msv251

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Author(s): Laurence D. Hurst, Avazeh T. Ghanbarian, Alistair R. R. Forrest, Lukasz Huminiecki
Published in: PLOS Biology, Issue 13/12, 2015, Page(s) e1002315, ISSN 1545-7885
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.1002315

Purifying Selection on Exonic Splice Enhancers in Intronless Genes

Author(s): Rosina Savisaar, Laurence D. Hurst
Published in: Molecular Biology and Evolution, Issue 33/6, 2016, Page(s) 1396-1418, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw018

Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression

Author(s): Jichang Wang, Manvendra Singh, Chuanbo Sun, Daniel Besser, Alessandro Prigione, Zoltán Ivics, Laurence D Hurst, Zsuzsanna Izsvák
Published in: Nature Protocols, Issue 11/2, 2016, Page(s) 327-346, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/nprot.2016.016

Direct Determination of the Mutation Rate in the Bumblebee Reveals Evidence for Weak Recombination-Associated Mutation and an Approximate Rate Constancy in Insects

Author(s): Haoxuan Liu, Yanxiao Jia, Xiaoguang Sun, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Published in: Molecular Biology and Evolution, Issue 34/1, 2017, Page(s) 119-130, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw226

Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

Author(s): Long Wang, Yanchun Zhang, Chao Qin, Dacheng Tian, Sihai Yang, Laurence D. Hurst
Published in: Proceedings of the Royal Society B: Biological Sciences, Issue 283/1841, 2016, Page(s) 20161785, ISSN 0962-8452
Publisher: Royal Society of London
DOI: 10.1098/rspb.2016.1785

Mutation rate analysis via parent–progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids

Author(s): Zhengqing Xie, Long Wang, Lirong Wang, Zhiqiang Wang, Zhenhua Lu, Dacheng Tian, Sihai Yang, Laurence D. Hurst
Published in: Proceedings of the Royal Society B: Biological Sciences, Issue 283/1841, 2016, Page(s) 20161016, ISSN 0962-8452
Publisher: Royal Society of London
DOI: 10.1098/rspb.2016.1016

Open questions in the study of de novo genes: what, how and why

Author(s): Aoife McLysaght, Laurence D. Hurst
Published in: Nature Reviews Genetics, Issue 17/9, 2016, Page(s) 567-578, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/nrg.2016.78

The architecture of intra-organism mutation rate variation in plants

Author(s): Long Wang, Yilun Ji, Yingwen Hu, Huaying Hu, Xianqin Jia, Mengmeng Jiang, Xiaohui Zhang, Lina Zhao, Yanchun Zhang, Yanxiao Jia, Chao Qin, Luyao Yu, Ju Huang, Sihai Yang, Laurence D. Hurst, Dacheng Tian
Published in: PLOS Biology, Issue 17/4, 2019, Page(s) e3000191, ISSN 1545-7885
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3000191

In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3’ additional stop codons

Author(s): Alexander T. Ho, Laurence D. Hurst
Published in: PLOS Genetics, Issue 15/9, 2019, Page(s) e1008386, ISSN 1553-7404
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1008386

Codon Usage and Splicing Jointly Influence mRNA Localization

Author(s): Christine Mordstein, Rosina Savisaar, Robert S. Young, Jeanne Bazile, Lana Talmane, Juliet Luft, Michael Liss, Martin S. Taylor, Laurence D. Hurst, Grzegorz Kudla
Published in: Cell Systems, 2020, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2020.03.001

Estimating the prevalence of functional exonic splice regulatory information

Author(s): Rosina Savisaar, Laurence D. Hurst
Published in: Human Genetics, 2017, ISSN 0340-6717
Publisher: Springer Verlag
DOI: 10.1007/s00439-017-1798-3

Engineering of PEDF-Expressing Primary Pigment Epithelial Cells by the SB Transposon System Delivered by pFAR4 Plasmids

Author(s): Gabriele Thumann, Nina Harmening, Cécile Prat-Souteyrand, Corinne Marie, Marie Pastor, Attila Sebe, Csaba Miskey, Laurence D. Hurst, Sabine Diarra, Martina Kropp, Peter Walter, Daniel Scherman, Zoltán Ivics, Zsuzsanna Izsvák, Sandra Johnen
Published in: Molecular Therapy - Nucleic Acids, Issue 6, 2017, Page(s) 302-314, ISSN 2162-2531
Publisher: Nature Publishing Group
DOI: 10.1016/j.omtn.2017.02.002

Both maintenance and avoidance of RNA-binding protein interactions constrain coding sequence evolution

Author(s): Savisaar Rosina, Laurence D. Hurst
Published in: Molecular Biology and Evolution, Issue 34, 2017, Page(s) msx061, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msx061

Author(s): Ruth T. Casey, David B. Ascher, Eleanor Rattenberry, Louise Izatt, Katrina A. Andrews, Helen L. Simpson, Benjamen Challis, Soo-Mi Park, Venkata R. Bulusu, Fiona Lalloo, Douglas E. V. Pires, Hannah West, Graeme R. Clark, Philip S. Smith, James Whitworth, Thomas G. Papathomas, Phillipe Taniere, Rosina Savisaar, Laurence D. Hurst, Emma R. Woodward, Eamonn R. Maher
Published in: Molecular Genetics & Genomic Medicine, Issue 5/3, 2017, Page(s) 237-250, ISSN 2324-9269
Publisher: Wiley Periodicals, Inc.
DOI: 10.1002/mgg3.279

Repeat-induced point mutation in Neurospora crassa causes the highest known mutation rate and mutational burden of any cellular life

Author(s): Long Wang, Yingying Sun, Xiaoguang Sun, Luyao Yu, Lan Xue, Zhen He, Ju Huang, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Published in: Genome Biology, Issue 21/1, 2020, ISSN 1474-760X
Publisher: SpringerNature
DOI: 10.1186/s13059-020-02060-w

Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption

Author(s): Liam Abrahams, Rosina Savisaar, Christine Mordstein, Bethan Young, Grzegorz Kudla, Laurence D Hurst
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab750

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