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Items: 1 to 50 of 62

1.

Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization.

Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R.

New Phytol. 2019 Aug 16. doi: 10.1111/nph.16122. [Epub ahead of print]

PMID:
31418861
2.

GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments.

Crotty SM, Minh BQ, Bean NG, Holland BR, Tuke J, Jermiin LS, von Haeseler A.

Syst Biol. 2019 Jul 31. pii: syz051. doi: 10.1093/sysbio/syz051. [Epub ahead of print]

PMID:
31364711
3.

Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in Triticum aestivum.

Benbow HR, Jermiin LS, Doohan FM.

G3 (Bethesda). 2019 Aug 8;9(8):2709-2722. doi: 10.1534/g3.119.400444.

4.

Sensitivity and specificity of information criteria.

Dziak JJ, Coffman DL, Lanza ST, Li R, Jermiin LS.

Brief Bioinform. 2019 Mar 20. pii: bbz016. doi: 10.1093/bib/bbz016. [Epub ahead of print]

PMID:
30895308
5.

Erratum to: Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species.

Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, McGaughran A, Oakeshott JG, Papanicolaou A, Perera OP, Rane RV, Richards S, Tay WT, Walsh TK, Anderson A, Anderson CJ, Asgari S, Board PG, Bretschneider A, Campbell PM, Chertemps T, Christeller JT, Coppin CW, Downes SJ, Duan G, Farnsworth CA, Good RT, Han LB, Han YC, Hatje K, Horne I, Huang YP, Hughes DST, Jacquin-Joly E, James W, Jhangiani S, Kollmar M, Kuwar SS, Li S, Liu NY, Maibeche MT, Miller JR, Montagne N, Perry T, Qu J, Song SV, Sutton GG, Vogel H, Walenz BP, Xu W, Zhang HJ, Zou Z, Batterham P, Edwards OR, Feyereisen R, Gibbs RA, Heckel DG, McGrath A, Robin C, Scherer SE, Worley KC, Wu YD.

BMC Biol. 2017 Aug 15;15(1):69. doi: 10.1186/s12915-017-0413-3. No abstract available.

6.

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species.

Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, McGaughran A, Oakeshott JG, Papanicolaou A, Perera OP, Rane RV, Richards S, Tay WT, Walsh TK, Anderson A, Anderson CJ, Asgari S, Board PG, Bretschneider A, Campbell PM, Chertemps T, Christeller JT, Coppin CW, Downes SJ, Duan G, Farnsworth CA, Good RT, Han LB, Han YC, Hatje K, Horne I, Huang YP, Hughes DST, Jacquin-Joly E, James W, Jhangiani S, Kollmar M, Kuwar SS, Li S, Liu NY, Maibeche MT, Miller JR, Montagne N, Perry T, Qu J, Song SV, Sutton GG, Vogel H, Walenz BP, Xu W, Zhang HJ, Zou Z, Batterham P, Edwards OR, Feyereisen R, Gibbs RA, Heckel DG, McGrath A, Robin C, Scherer SE, Worley KC, Wu YD.

BMC Biol. 2017 Jul 31;15(1):63. doi: 10.1186/s12915-017-0402-6. Erratum in: BMC Biol. 2017 Aug 15;15(1):69.

7.

Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini).

Escalona HE, Zwick A, Li HS, Li J, Wang X, Pang H, Hartley D, Jermiin LS, Nedvěd O, Misof B, Niehuis O, Ślipiński A, Tomaszewska W.

BMC Evol Biol. 2017 Jun 26;17(1):151. doi: 10.1186/s12862-017-1002-3.

8.

ModelFinder: fast model selection for accurate phylogenetic estimates.

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS.

Nat Methods. 2017 Jun;14(6):587-589. doi: 10.1038/nmeth.4285. Epub 2017 May 8.

9.

Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil.

Tay WT, Walsh TK, Downes S, Anderson C, Jermiin LS, Wong TK, Piper MC, Chang ES, Macedo IB, Czepak C, Behere GT, Silvie P, Soria MF, Frayssinet M, Gordon KH.

Sci Rep. 2017 Mar 28;7:45302. doi: 10.1038/srep45302.

10.

Identifying Optimal Models of Evolution.

Jermiin LS, Jayaswal V, Ababneh FM, Robinson J.

Methods Mol Biol. 2017;1525:379-420.

PMID:
27896729
11.

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

Kanost MR, Arrese EL, Cao X, Chen YR, Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N, Jiang H, Papanicolaou A, Qu J, Soulages JL, Vogel H, Walters J, Waterhouse RM, Ahn SJ, Almeida FC, An C, Aqrawi P, Bretschneider A, Bryant WB, Bucks S, Chao H, Chevignon G, Christen JM, Clarke DF, Dittmer NT, Ferguson LCF, Garavelou S, Gordon KHJ, Gunaratna RT, Han Y, Hauser F, He Y, Heidel-Fischer H, Hirsh A, Hu Y, Jiang H, Kalra D, Klinner C, König C, Kovar C, Kroll AR, Kuwar SS, Lee SL, Lehman R, Li K, Li Z, Liang H, Lovelace S, Lu Z, Mansfield JH, McCulloch KJ, Mathew T, Morton B, Muzny DM, Neunemann D, Ongeri F, Pauchet Y, Pu LL, Pyrousis I, Rao XJ, Redding A, Roesel C, Sanchez-Gracia A, Schaack S, Shukla A, Tetreau G, Wang Y, Xiong GH, Traut W, Walsh TK, Worley KC, Wu D, Wu W, Wu YQ, Zhang X, Zou Z, Zucker H, Briscoe AD, Burmester T, Clem RJ, Feyereisen R, Grimmelikhuijzen CJP, Hamodrakas SJ, Hansson BS, Huguet E, Jermiin LS, Lan Q, Lehman HK, Lorenzen M, Merzendorfer H, Michalopoulos I, Morton DB, Muthukrishnan S, Oakeshott JG, Palmer W, Park Y, Passarelli AL, Rozas J, Schwartz LM, Smith W, Southgate A, Vilcinskas A, Vogt R, Wang P, Werren J, Yu XQ, Zhou JJ, Brown SJ, Scherer SE, Richards S, Blissard GW.

Insect Biochem Mol Biol. 2016 Sep;76:118-147. doi: 10.1016/j.ibmb.2016.07.005. Epub 2016 Aug 12.

12.

Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?

Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KH, Richards S, Oakeshott JG.

Curr Opin Insect Sci. 2016 Feb;13:70-76. doi: 10.1016/j.cois.2015.12.001. Epub 2015 Dec 29. Review.

PMID:
27436555
13.

Population Genetic Structure and Potential Incursion Pathways of the Bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) in Australia.

Tay WT, Kerr PJ, Jermiin LS.

PLoS One. 2016 Jan 15;11(1):e0146699. doi: 10.1371/journal.pone.0146699. eCollection 2016.

14.

INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B.

Science. 2015 Jul 31;349(6247):487. doi: 10.1126/science.aaa7136.

15.

The genomes of two key bumblebee species with primitive eusocial organization.

Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC.

Genome Biol. 2015 Apr 24;16:76. doi: 10.1186/s13059-015-0623-3.

16.

Phylogenomics resolves the timing and pattern of insect evolution.

Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TK, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X.

Science. 2014 Nov 7;346(6210):763-7. doi: 10.1126/science.1257570. Epub 2014 Nov 6.

17.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages.

Jayaswal V, Wong TK, Robinson J, Poladian L, Jermiin LS.

Syst Biol. 2014 Sep;63(5):726-42. doi: 10.1093/sysbio/syu036. Epub 2014 Jun 12.

PMID:
24927722
18.

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics.

Vera-Ruiz VA, Lau KW, Robinson J, Jermiin LS.

BMC Bioinformatics. 2014;15 Suppl 2:S8. doi: 10.1186/1471-2105-15-S2-S8. Epub 2014 Jan 31.

19.

Fixed, free, and fixed: the fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin.

Rouse GW, Jermiin LS, Wilson NG, Eeckhaut I, Lanterbecq D, Oji T, Young CM, Browning T, Cisternas P, Helgen LE, Stuckey M, Messing CG.

Mol Phylogenet Evol. 2013 Jan;66(1):161-81. doi: 10.1016/j.ympev.2012.09.018. Epub 2012 Oct 11.

PMID:
23063883
20.

Intramolecular epistasis and the evolution of a new enzymatic function.

Noor S, Taylor MC, Russell RJ, Jermiin LS, Jackson CJ, Oakeshott JG, Scott C.

PLoS One. 2012;7(6):e39822. doi: 10.1371/journal.pone.0039822. Epub 2012 Jun 29.

21.

Reducing model complexity of the general Markov model of evolution.

Jayaswal V, Ababneh F, Jermiin LS, Robinson J.

Mol Biol Evol. 2011 Nov;28(11):3045-59. doi: 10.1093/molbev/msr128. Epub 2011 May 18.

PMID:
21593046
22.

Two stationary nonhomogeneous Markov models of nucleotide sequence evolution.

Jayaswal V, Jermiin LS, Poladian L, Robinson J.

Syst Biol. 2011 Jan;60(1):74-86. doi: 10.1093/sysbio/syq076. Epub 2010 Nov 16.

PMID:
21081482
23.

The molecular structure of the IsiA-Photosystem I supercomplex, modelled from high-resolution, crystal structures of Photosystem I and the CP43 protein.

Zhang Y, Chen M, Church WB, Lau KW, Larkum AW, Jermiin LS.

Biochim Biophys Acta. 2010 Apr;1797(4):457-65. doi: 10.1016/j.bbabio.2010.01.002. Epub 2010 Jan 11.

24.

Characterization and evolution of vertebrate indoleamine 2, 3-dioxygenases IDOs from monotremes and marsupials.

Yuasa HJ, Ball HJ, Ho YF, Austin CJ, Whittington CM, Belov K, Maghzal GJ, Jermiin LS, Hunt NH.

Comp Biochem Physiol B Biochem Mol Biol. 2009 Jun;153(2):137-144. Epub 2009 Feb 7.

PMID:
19416693
25.

Characterization and evolution of vertebrate indoleamine 2, 3-dioxygenases IDOs from monotremes and marsupials.

Yuasa HJ, Ball HJ, Ho YF, Austin CJ, Whittington CM, Belov K, Maghzal GJ, Jermiin LS, Hunt NH.

Comp Biochem Physiol B Biochem Mol Biol. 2009 Jun;153(2):137-44.

PMID:
19402226
26.

SeqVis: a tool for detecting compositional heterogeneity among aligned nucleotide sequences.

Jermiin LS, Ho JW, Lau KW, Jayaswal V.

Methods Mol Biol. 2009;537:65-91. doi: 10.1007/978-1-59745-251-9_4.

PMID:
19378140
27.

Phylogenetic model evaluation.

Jermiin LS, Jayaswal V, Ababneh F, Robinson J.

Methods Mol Biol. 2008;452:331-64. doi: 10.1007/978-1-60327-159-2_16. Review.

PMID:
18566772
28.

Markov invariants, plethysms, and phylogenetics.

Sumner JG, Charleston MA, Jermiin LS, Jarvis PD.

J Theor Biol. 2008 Aug 7;253(3):601-15. doi: 10.1016/j.jtbi.2008.04.001. Epub 2008 Apr 7.

PMID:
18513747
29.
30.

Mind the gaps: evidence of bias in estimates of multiple sequence alignments.

Golubchik T, Wise MJ, Easteal S, Jermiin LS.

Mol Biol Evol. 2007 Nov;24(11):2433-42. Epub 2007 Aug 20.

PMID:
17709332
31.

Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice.

Ball HJ, Sanchez-Perez A, Weiser S, Austin CJ, Astelbauer F, Miu J, McQuillan JA, Stocker R, Jermiin LS, Hunt NH.

Gene. 2007 Jul 1;396(1):203-13. Epub 2007 Apr 18. Erratum in: Gene. 2010 Oct 1;465(1-2):66.

PMID:
17499941
32.

Evolution of the inner light-harvesting antenna protein family of cyanobacteria, algae, and plants.

Zhang Y, Chen M, Zhou BB, Jermiin LS, Larkum AW.

J Mol Evol. 2007 Mar;64(3):321-31. Epub 2007 Feb 1.

PMID:
17273917
33.

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours.

Wickham S, Large MC, Poladian L, Jermiin LS.

J R Soc Interface. 2006 Feb 22;3(6):99-108. Erratum in: J R Soc Interface. 2006 Dec 22;3(11):851.

34.

SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.

Ho JW, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS.

Bioinformatics. 2006 Sep 1;22(17):2162-3. Epub 2006 Jun 9.

PMID:
16766557
35.

Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences.

Ababneh F, Jermiin LS, Ma C, Robinson J.

Bioinformatics. 2006 May 15;22(10):1225-31. Epub 2006 Feb 21.

PMID:
16492684
36.

Evolution. Is the "Big Bang" in animal evolution real?

Jermiin LS, Poladian L, Charleston MA.

Science. 2005 Dec 23;310(5756):1910-1. No abstract available.

PMID:
16373562
37.

Improving the analysis of dinoflagellate phylogeny based on rDNA.

Murray S, Flø Jørgensen M, Ho SY, Patterson DJ, Jermiin LS.

Protist. 2005 Nov;156(3):269-86. Epub 2005 Aug 1.

PMID:
16325541
38.

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny.

Holland BR, Jermiin LS, Moulton V; SMBE Tri-National Young Investigators.

Mol Biol Evol. 2006 May;23(5):848-55. Epub 2005 Nov 9.

PMID:
16280536
39.

Estimation of phylogeny using a general Markov model.

Jayaswal V, Jermiin LS, Robinson J.

Evol Bioinform Online. 2007 Feb 25;1:62-80.

40.

Evolution of vertebrate genes related to prion and Shadoo proteins--clues from comparative genomic analysis.

Premzl M, Gready JE, Jermiin LS, Simonic T, Marshall Graves JA.

Mol Biol Evol. 2004 Dec;21(12):2210-31. Epub 2004 Sep 1.

PMID:
15342797
41.

Characterization of the type I interferon locus and identification of novel genes.

Hardy MP, Owczarek CM, Jermiin LS, Ejdebäck M, Hertzog PJ.

Genomics. 2004 Aug;84(2):331-45.

PMID:
15233997
42.

AMID: autonomous modeler of intragenic duplication.

Kummerfeld SK, Weiss AS, Fekete A, Jermiin LS.

Appl Bioinformatics. 2003;2(3):169-76.

PMID:
15130804
43.

Hetero: a program to simulate the evolution of DNA on a four-taxon tree.

Jermiin LS, Ho SY, Ababneh F, Robinson J, Larkum AW.

Appl Bioinformatics. 2003;2(3):159-63.

PMID:
15130802
44.

Isolation and characterization of the mouse ubiquitin-specific protease Usp15.

Angelats C, Wang XW, Jermiin LS, Copeland NG, Jenkins NA, Baker RT.

Mamm Genome. 2003 Jan;14(1):31-46.

PMID:
12532266
45.

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

Simpson AG, Roger AJ, Silberman JD, Leipe DD, Edgcomb VP, Jermiin LS, Patterson DJ, Sogin ML.

Mol Biol Evol. 2002 Oct;19(10):1782-91.

PMID:
12270904
46.

Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs.

Lahoud MH, Ristevski S, Venter DJ, Jermiin LS, Bertoncello I, Zavarsek S, Hasthorpe S, Drago J, de Kretser D, Hertzog PJ, Kola I.

Genome Res. 2001 Aug;11(8):1327-34.

47.

Identification of novel glutathione transferases and polymorphic variants by expressed sequence tag database analysis.

Board PG, Chelvanayagam G, Jermiin LS, Tetlow N, Tzeng HF, Anders MW, Blackburn AC.

Drug Metab Dispos. 2001 Apr;29(4 Pt 2):544-7.

PMID:
11259348
48.

Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus.

Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS, Wolfe KH.

Plant Cell. 2001 Mar;13(3):645-58.

49.

Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins.

Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, Peacock WJ, Thorne A.

Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):537-42. Erratum in: Proc Natl Acad Sci U S A 2002 Jan 8;99(1):541.

50.

A molecular framework for the phylogeny of the ant subfamily dolichoderinae.

Chiotis M, Jermiin LS, Crozier RH.

Mol Phylogenet Evol. 2000 Oct;17(1):108-16.

PMID:
11020309

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