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

Abrahams L, Hurst LD.

Mol Biol Evol. 2020 Apr 1;37(4):1148-1164. doi: 10.1093/molbev/msz299.


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

Ho AT, Hurst LD.

PLoS Genet. 2019 Sep 17;15(9):e1008386. doi: 10.1371/journal.pgen.1008386. eCollection 2019 Sep.


Conditional expression explains molecular evolution of social genes in a microbe.

de Oliveira JL, Morales AC, Stewart B, Gruenheit N, Engelmoer J, Brown SB, de Brito RA, Hurst LD, Urrutia AO, Thompson CRL, Wolf JB.

Nat Commun. 2019 Jul 23;10(1):3284. doi: 10.1038/s41467-019-11237-2.


A century of bias in genetics and evolution.

Hurst LD.

Heredity (Edinb). 2019 Jul;123(1):33-43. doi: 10.1038/s41437-019-0194-2. Epub 2019 Jun 12. Review.


The architecture of intra-organism mutation rate variation in plants.

Wang L, Ji Y, Hu Y, Hu H, Jia X, Jiang M, Zhang X, Zhao L, Zhang Y, Jia Y, Qin C, Yu L, Huang J, Yang S, Hurst LD, Tian D.

PLoS Biol. 2019 Apr 9;17(4):e3000191. doi: 10.1371/journal.pbio.3000191. eCollection 2019 Apr.


Author Correction: Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression.

Wang J, Singh M, Sun C, Besser D, Prigione A, Ivics Z, Hurst LD, Izsvák Z.

Nat Protoc. 2019 Aug;14(8):2596. doi: 10.1038/s41596-018-0086-6.


Exonic splice regulation imposes strong selection at synonymous sites.

Savisaar R, Hurst LD.

Genome Res. 2018 Oct;28(10):1442-1454. doi: 10.1101/gr.233999.117. Epub 2018 Aug 24.


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

Huang J, Li J, Zhou J, Wang L, Yang S, Hurst LD, Li WH, Tian D.

Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):E7559-E7567. doi: 10.1073/pnas.1806110115. Epub 2018 Jul 23.


Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA.

Yokoyama M, Stevens E, Laabei M, Bacon L, Heesom K, Bayliss S, Ooi N, O'Neill AJ, Murray E, Williams P, Lubben A, Reeksting S, Meric G, Pascoe B, Sheppard SK, Recker M, Hurst LD, Massey RC.

Genome Biol. 2018 Jul 18;19(1):94. doi: 10.1186/s13059-018-1469-2.


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

Mühlhausen S, Schmitt HD, Pan KT, Plessmann U, Urlaub H, Hurst LD, Kollmar M.

Curr Biol. 2018 Jul 9;28(13):2046-2057.e5. doi: 10.1016/j.cub.2018.04.085. Epub 2018 Jun 18.


Refining the Ambush Hypothesis: Evidence That GC- and AT-Rich Bacteria Employ Different Frameshift Defence Strategies.

Abrahams L, Hurst LD.

Genome Biol Evol. 2018 Apr 1;10(4):1153-1173. doi: 10.1093/gbe/evy075.


Scientific aptitude better explains poor responses to teaching of evolution than psychological conflicts.

Mead R, Hejmadi M, Hurst LD.

Nat Ecol Evol. 2018 Feb;2(2):388-394. doi: 10.1038/s41559-017-0442-x. Epub 2018 Jan 8.


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

Liu H, Huang J, Sun X, Li J, Hu Y, Yu L, Liti G, Tian D, Hurst LD, Yang S.

Nat Ecol Evol. 2018 Jan;2(1):164-173. doi: 10.1038/s41559-017-0372-7. Epub 2017 Nov 20.


Faster Evolving Primate Genes Are More Likely to Duplicate.

O'Toole ÁN, Hurst LD, McLysaght A.

Mol Biol Evol. 2018 Jan 1;35(1):107-118. doi: 10.1093/molbev/msx270.


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

Hurst LD, Batada NN.

Genome Biol. 2017 Nov 7;18(1):213. doi: 10.1186/s13059-017-1337-5.


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

Abrahams L, Hurst LD.

Mol Biol Evol. 2017 Dec 1;34(12):3064-3080. doi: 10.1093/molbev/msx223.


It's easier to get along with the quiet neighbours.

Hurst LD.

Mol Syst Biol. 2017 Sep 26;13(9):943. doi: 10.15252/msb.20177961. No abstract available.


Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals.

Link V, Aguilar-Gómez D, Ramírez-Suástegui C, Hurst LD, Cortez D.

Genome Biol Evol. 2017 Sep 1;9(9):2198-2210. doi: 10.1093/gbe/evx155.


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

Zadora J, Singh M, Herse F, Przybyl L, Haase N, Golic M, Yung HW, Huppertz B, Cartwright JE, Whitley G, Johnsen GM, Levi G, Isbruch A, Schulz H, Luft FC, Müller DN, Staff AC, Hurst LD, Dechend R, Izsvák Z.

Circulation. 2017 Nov 7;136(19):1824-1839. doi: 10.1161/CIRCULATIONAHA.117.028110. Epub 2017 Sep 13. Erratum in: Circulation. 2018 Oct 9;138(15):e423.


How to tame an endogenous retrovirus: HERVH and the evolution of human pluripotency.

Römer C, Singh M, Hurst LD, Izsvák Z.

Curr Opin Virol. 2017 Aug;25:49-58. doi: 10.1016/j.coviro.2017.07.001. Epub 2017 Jul 24. Review.


SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity.

Casey RT, Ascher DB, Rattenberry E, Izatt L, Andrews KA, Simpson HL, Challis B, Park SM, Bulusu VR, Lalloo F, Pires DEV, West H, Clark GR, Smith PS, Whitworth J, Papathomas TG, Taniere P, Savisaar R, Hurst LD, Woodward ER, Maher ER.

Mol Genet Genomic Med. 2017 Mar 2;5(3):237-250. doi: 10.1002/mgg3.279. eCollection 2017 May.


Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance.

Mead R, Hejmadi M, Hurst LD.

PLoS Biol. 2017 May 23;15(5):e2002255. doi: 10.1371/journal.pbio.2002255. eCollection 2017 May.


Estimating the prevalence of functional exonic splice regulatory information.

Savisaar R, Hurst LD.

Hum Genet. 2017 Sep;136(9):1059-1078. doi: 10.1007/s00439-017-1798-3. Epub 2017 Apr 12. Review.


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

Thumann G, Harmening N, Prat-Souteyrand C, Marie C, Pastor M, Sebe A, Miskey C, Hurst LD, Diarra S, Kropp M, Walter P, Scherman D, Ivics Z, Izsvák Z, Johnen S.

Mol Ther Nucleic Acids. 2017 Mar 17;6:302-314. doi: 10.1016/j.omtn.2017.02.002. Epub 2017 Feb 10.


Comparative Analyses of Selection Operating on Nontranslated Intergenic Regions of Diverse Bacterial Species.

Thorpe HA, Bayliss SC, Hurst LD, Feil EJ.

Genetics. 2017 May;206(1):363-376. doi: 10.1534/genetics.116.195784. Epub 2017 Mar 9.


Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution.

Savisaar R, Hurst LD.

Mol Biol Evol. 2017 May 1;34(5):1110-1126. doi: 10.1093/molbev/msx061.


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

Liu H, Jia Y, Sun X, Tian D, Hurst LD, Yang S.

Mol Biol Evol. 2017 Jan;34(1):119-130. doi: 10.1093/molbev/msw226. Epub 2016 Oct 20.


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

Wang L, Zhang Y, Qin C, Tian D, Yang S, Hurst LD.

Proc Biol Sci. 2016 Oct 26;283(1841). pii: 20161785.


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

Xie Z, Wang L, Wang L, Wang Z, Lu Z, Tian D, Yang S, Hurst LD.

Proc Biol Sci. 2016 Oct 26;283(1841). pii: 20161016.


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

McLysaght A, Hurst LD.

Nat Rev Genet. 2016 Sep;17(9):567-78. doi: 10.1038/nrg.2016.78. Epub 2016 Jul 25. Review.


Purifying Selection on Exonic Splice Enhancers in Intronless Genes.

Savisaar R, Hurst LD.

Mol Biol Evol. 2016 Jun;33(6):1396-418. doi: 10.1093/molbev/msw018. Epub 2016 Jan 23.


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

Wang J, Singh M, Sun C, Besser D, Prigione A, Ivics Z, Hurst LD, Izsvák Z.

Nat Protoc. 2016 Feb;11(2):327-46. doi: 10.1038/nprot.2016.016. Epub 2016 Jan 21. Erratum in: Nat Protoc. 2019 Aug;14(8):2596.


Pluripotency and the endogenous retrovirus HERVH: Conflict or serendipity?

Izsvák Z, Wang J, Singh M, Mager DL, Hurst LD.

Bioessays. 2016 Jan;38(1):109-17. doi: 10.1002/bies.201500096. Review.


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

Hurst LD, Ghanbarian AT, Forrest AR; FANTOM consortium, Huminiecki L.

PLoS Biol. 2015 Dec 18;13(12):e1002315. doi: 10.1371/journal.pbio.1002315. eCollection 2015 Dec.


Genes that Escape X-Inactivation in Humans Have High Intraspecific Variability in Expression, Are Associated with Mental Impairment but Are Not Slow Evolving.

Zhang Y, Castillo-Morales A, Jiang M, Zhu Y, Hu L, Urrutia AO, Kong X, Hurst LD.

Mol Biol Evol. 2016 Jan;33(1):302. doi: 10.1093/molbev/msv180. Epub 2015 Nov 13. No abstract available.


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

Wu X, Hurst LD.

Mol Biol Evol. 2016 Feb;33(2):518-29. doi: 10.1093/molbev/msv251. Epub 2015 Nov 5.


Parent-progeny sequencing indicates higher mutation rates in heterozygotes.

Yang S, Wang L, Huang J, Zhang X, Yuan Y, Chen JQ, Hurst LD, Tian D.

Nature. 2015 Jul 23;523(7561):463-7. doi: 10.1038/nature14649. Epub 2015 Jul 15.


Neighboring Genes Show Correlated Evolution in Gene Expression.

Ghanbarian AT, Hurst LD.

Mol Biol Evol. 2015 Jul;32(7):1748-66. doi: 10.1093/molbev/msv053. Epub 2015 Mar 4.


Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee.

Liu H, Zhang X, Huang J, Chen JQ, Tian D, Hurst LD, Yang S.

Genome Biol. 2015 Jan 2;16:15. doi: 10.1186/s13059-014-0566-0.


Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.

Sealey KL, Harris SR, Fry NK, Hurst LD, Gorringe AR, Parkhill J, Preston A.

J Infect Dis. 2015 Jul 15;212(2):294-301. doi: 10.1093/infdis/jiu665. Epub 2014 Dec 8.


Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.

Wang J, Xie G, Singh M, Ghanbarian AT, Raskó T, Szvetnik A, Cai H, Besser D, Prigione A, Fuchs NV, Schumann GG, Chen W, Lorincz MC, Ivics Z, Hurst LD, Izsvák Z.

Nature. 2014 Dec 18;516(7531):405-9. doi: 10.1038/nature13804. Epub 2014 Oct 15.


Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations.

Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD, Harberd NP.

Genome Res. 2014 Nov;24(11):1821-9. doi: 10.1101/gr.177659.114. Epub 2014 Oct 14.


Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs.

Schüler A, Ghanbarian AT, Hurst LD.

Mol Biol Evol. 2014 Dec;31(12):3164-83. doi: 10.1093/molbev/msu249. Epub 2014 Aug 25.


Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients.

Yin S, Yang J, Lin B, Deng W, Zhang Y, Yi X, Shi Y, Tao Y, Cai J, Wu CI, Zhao G, Hurst LD, Zhang J, Hu L, Kong X.

Sci Rep. 2014 Aug 12;4:6036. doi: 10.1038/srep06036.


A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators.

Hurst LD, Sachenkova O, Daub C, Forrest AR, Huminiecki L; FANTOM consortium.

Genome Biol. 2014 Jul 31;15(7):413. doi: 10.1186/s13059-014-0413-3.


Predicting the virulence of MRSA from its genome sequence.

Laabei M, Recker M, Rudkin JK, Aldeljawi M, Gulay Z, Sloan TJ, Williams P, Endres JL, Bayles KW, Fey PD, Yajjala VK, Widhelm T, Hawkins E, Lewis K, Parfett S, Scowen L, Peacock SJ, Holden M, Wilson D, Read TD, van den Elsen J, Priest NK, Feil EJ, Hurst LD, Josefsson E, Massey RC.

Genome Res. 2014 May;24(5):839-49. doi: 10.1101/gr.165415.113. Epub 2014 Apr 9.


The evolution, impact and properties of exonic splice enhancers.

Cáceres EF, Hurst LD.

Genome Biol. 2013 Dec 20;14(12):R143. doi: 10.1186/gb-2013-14-12-r143.


Positive charge loading at protein termini is due to membrane protein topology, not a translational ramp.

Charneski CA, Hurst LD.

Mol Biol Evol. 2014 Jan;31(1):70-84. doi: 10.1093/molbev/mst169. Epub 2013 Sep 28.


Genes that escape X-inactivation in humans have high intraspecific variability in expression, are associated with mental impairment but are not slow evolving.

Zhang Y, Castillo-Morales A, Jiang M, Zhu Y, Hu L, Urrutia AO, Kong X, Hurst LD.

Mol Biol Evol. 2013 Dec;30(12):2588-601. doi: 10.1093/molbev/mst148. Epub 2013 Sep 10. Erratum in: Mol Biol Evol. 2016 Jan;33(1):302.

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