Evolutionary genomics: new perspectives and novel medical applications

Publikacje

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

Autorzy: Xianqing Jia, Qijun Zhang, Mengmeng Jiang, Ju Huang, Luyao Yu, Milton Brian Traw, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Opublikowane w: PLOS Biology, Numer 19/3, 2021, Strona(/y) e3001164, ISSN 1545-7885
Wydawca: 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

Autorzy: Alan M Rice, Atahualpa Castillo Morales, Alexander T Ho, Christine Mordstein, Stefanie Mühlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 38/1, 2020, Strona(/y) 67-83, ISSN 1537-1719
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msaa188

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

Autorzy: Atahualpa Castillo Morales, Alan M Rice, Alexander T Ho, Christine Mordstein, Stefanie Mühlhausen, Samir Watson, Laura Cano, Bethan Young, Grzegorz Kudla, Laurence D Hurst
Opublikowane w: Genome Biology and Evolution, 2021, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evab196

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

Autorzy: Alexander T Ho, Laurence D Hurst
Opublikowane w: Molecular Biology and Evolution, 2021, ISSN 0737-4038
Wydawca: 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

Autorzy: Liam Abrahams, Laurence D Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 37/4, 2019, Strona(/y) 1148-1164, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msz299

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

Autorzy: Alexander T Ho, Laurence D Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 38/1, 2020, Strona(/y) 244-262, ISSN 1537-1719
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msaa210

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

Autorzy: Christine Mordstein, Laura Cano, Atahualpa Castillo Morales, Bethan Young, Alexander T Ho, Alan M Rice, Michael Liss, Laurence D Hurst, Grzegorz Kudla
Opublikowane w: Genome Biology and Evolution, 2021, ISSN 1759-6653
Wydawca: Oxford University Press
DOI: 10.1093/gbe/evab106

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

Autorzy: Laurence D. Hurst, Nizar N. Batada
Opublikowane w: Genome Biology, Numer 18/1, 2017, ISSN 1474-760X
Wydawca: BMC
DOI: 10.1186/s13059-017-1337-5

Faster Evolving Primate Genes Are More Likely to Duplicate

Autorzy: Áine N O’Toole, Laurence D Hurst, Aoife McLysaght
Opublikowane w: Molecular Biology and Evolution, Numer 35/1, 2017, Strona(/y) 107-118, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msx270

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

Autorzy: Liam Abrahams, Laurence D Hurst
Opublikowane w: Genome Biology and Evolution, 2018, ISSN 1759-6653
Wydawca: 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

Autorzy: 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
Opublikowane w: Circulation, Numer 136/19, 2017, Strona(/y) 1824-1839, ISSN 0009-7322
Wydawca: 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

Autorzy: Liam Abrahams, Laurence D Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 34/12, 2017, Strona(/y) 3064-3080, ISSN 0737-4038
Wydawca: 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

Autorzy: Haoxuan Liu, Ju Huang, Xiaoguang Sun, Jing Li, Yingwen Hu, Luyao Yu, Gianni Liti, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Opublikowane w: Nature Ecology & Evolution, Numer 2/1, 2018, Strona(/y) 164-173, ISSN 2397-334X
Wydawca: 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

Autorzy: Ju Huang, Jing Li, Jun Zhou, Long Wang, Sihai Yang, Laurence D. Hurst, Wen-Hsiung Li, Dacheng Tian
Opublikowane w: Proceedings of the National Academy of Sciences, 2018, Strona(/y) 201806110, ISSN 0027-8424
Wydawca: 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

Autorzy: Stefanie Mühlhausen, Hans Dieter Schmitt, Kuan-Ting Pan, Uwe Plessmann, Henning Urlaub, Laurence D. Hurst, Martin Kollmar
Opublikowane w: Current Biology, Numer 28/13, 2018, Strona(/y) 2046-2057.e5, ISSN 0960-9822
Wydawca: Cell Press
DOI: 10.1016/j.cub.2018.04.085

Exonic splice regulation imposes strong selection at synonymous sites

Autorzy: Rosina Savisaar, Laurence D. Hurst
Opublikowane w: Genome Research, 2018, ISSN 1088-9051
Wydawca: 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

Autorzy: XianMing Wu, Laurence D. Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 33/2, 2016, Strona(/y) 518-529, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msv251

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

Autorzy: Laurence D. Hurst, Avazeh T. Ghanbarian, Alistair R. R. Forrest, Lukasz Huminiecki
Opublikowane w: PLOS Biology, Numer 13/12, 2015, Strona(/y) e1002315, ISSN 1545-7885
Wydawca: Public Library of Science
DOI: 10.1371/journal.pbio.1002315

Purifying Selection on Exonic Splice Enhancers in Intronless Genes

Autorzy: Rosina Savisaar, Laurence D. Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 33/6, 2016, Strona(/y) 1396-1418, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msw018

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

Autorzy: Jichang Wang, Manvendra Singh, Chuanbo Sun, Daniel Besser, Alessandro Prigione, Zoltán Ivics, Laurence D Hurst, Zsuzsanna Izsvák
Opublikowane w: Nature Protocols, Numer 11/2, 2016, Strona(/y) 327-346, ISSN 1754-2189
Wydawca: 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

Autorzy: Haoxuan Liu, Yanxiao Jia, Xiaoguang Sun, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Opublikowane w: Molecular Biology and Evolution, Numer 34/1, 2017, Strona(/y) 119-130, ISSN 0737-4038
Wydawca: 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

Autorzy: Long Wang, Yanchun Zhang, Chao Qin, Dacheng Tian, Sihai Yang, Laurence D. Hurst
Opublikowane w: Proceedings of the Royal Society B: Biological Sciences, Numer 283/1841, 2016, Strona(/y) 20161785, ISSN 0962-8452
Wydawca: 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

Autorzy: Zhengqing Xie, Long Wang, Lirong Wang, Zhiqiang Wang, Zhenhua Lu, Dacheng Tian, Sihai Yang, Laurence D. Hurst
Opublikowane w: Proceedings of the Royal Society B: Biological Sciences, Numer 283/1841, 2016, Strona(/y) 20161016, ISSN 0962-8452
Wydawca: Royal Society of London
DOI: 10.1098/rspb.2016.1016

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

Autorzy: Aoife McLysaght, Laurence D. Hurst
Opublikowane w: Nature Reviews Genetics, Numer 17/9, 2016, Strona(/y) 567-578, ISSN 1471-0056
Wydawca: Nature Publishing Group
DOI: 10.1038/nrg.2016.78

The architecture of intra-organism mutation rate variation in plants

Autorzy: 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
Opublikowane w: PLOS Biology, Numer 17/4, 2019, Strona(/y) e3000191, ISSN 1545-7885
Wydawca: 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

Autorzy: Alexander T. Ho, Laurence D. Hurst
Opublikowane w: PLOS Genetics, Numer 15/9, 2019, Strona(/y) e1008386, ISSN 1553-7404
Wydawca: Public Library of Science
DOI: 10.1371/journal.pgen.1008386

Codon Usage and Splicing Jointly Influence mRNA Localization

Autorzy: Christine Mordstein, Rosina Savisaar, Robert S. Young, Jeanne Bazile, Lana Talmane, Juliet Luft, Michael Liss, Martin S. Taylor, Laurence D. Hurst, Grzegorz Kudla
Opublikowane w: Cell Systems, 2020, ISSN 2405-4712
Wydawca: Cell Press
DOI: 10.1016/j.cels.2020.03.001

Estimating the prevalence of functional exonic splice regulatory information

Autorzy: Rosina Savisaar, Laurence D. Hurst
Opublikowane w: Human Genetics, 2017, ISSN 0340-6717
Wydawca: 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

Autorzy: 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
Opublikowane w: Molecular Therapy - Nucleic Acids, Numer 6, 2017, Strona(/y) 302-314, ISSN 2162-2531
Wydawca: Nature Publishing Group
DOI: 10.1016/j.omtn.2017.02.002

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

Autorzy: Savisaar Rosina, Laurence D. Hurst
Opublikowane w: Molecular Biology and Evolution, Numer 34, 2017, Strona(/y) msx061, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msx061

Autorzy: 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
Opublikowane w: Molecular Genetics & Genomic Medicine, Numer 5/3, 2017, Strona(/y) 237-250, ISSN 2324-9269
Wydawca: 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

Autorzy: Long Wang, Yingying Sun, Xiaoguang Sun, Luyao Yu, Lan Xue, Zhen He, Ju Huang, Dacheng Tian, Laurence D. Hurst, Sihai Yang
Opublikowane w: Genome Biology, Numer 21/1, 2020, ISSN 1474-760X
Wydawca: SpringerNature
DOI: 10.1186/s13059-020-02060-w

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

Autorzy: Liam Abrahams, Rosina Savisaar, Christine Mordstein, Bethan Young, Grzegorz Kudla, Laurence D Hurst
Opublikowane w: Nucleic Acids Research, 2021, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab750

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