Lars Jermiin - Research Output

Book Chapters

1. Jermiin LS, Ho JWK, Lau KW, Jayaswal V. SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences. Pp 65-91. In Bioinformatics for DNA sequence analysis (Ed. Posada D), Humana Press, Totowa, NJ. [2009] (Invited)

2. Jermiin LS, Jayaswal V, Ababneh F, Robinson J. Phylogenetic model evaluation. Pp 331-363. In Bioinformatics: Vol. I: Data, Sequences Analysis and Evolution (Ed. Keith J), Humana Press, Totowa, NJ. [2008] (Invited)

Papers Published in Peer-reviewed Journals

55. Yuasa HJ, Ball HJ, Fern Ho Y, Austin CJD, Whittington CM, Belov K, Maghzal GJ, Jermiin LS, Hunt LS. Characterization and evolution of vertebrate indolamine 2, 3-dioxygenases. IDOs from monotremes and marsupials. Comparative Biochemistry and Physiology B 153, 137-144 [2009] .

54. Sumner JG, Charleston MA, Jermiin LS, Jarvis PD. Markov invariants, plethysms, and phylogenetics. Journal of Theoretical Biology 253, 601-615 [2008].

53. Hyman IT, Ho SYW, Jermiin LS. Molecular phylogeny of Australian Helicarionidae, Microsystidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA. Molecular Phylogenetics and Evolution 24, 792-812 [2007].

52. Golubchik T, Wise MJ, Easteal S, Jermiin LS. Mind the gaps: Evidence of bias in estimates of multiple sequence alignments. Molecular Biology and Evolution 24, 2433-2442 [2007]. (Data link).

51. Ball HJ, Weiser S, Sanchez-Perez A, Austin JDC, Austerbauer F, Miu J, McQuillan J, Stocker R, Jermiin LS, Hunt NH. Characterization of an indoleamine 2,3-dioxygenase-like gene found in humans and mice. Gene 396, 203-213 [2007] (Data link).

50. Jayaswal V, Robinson J, Jermiin LS. Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution. Systematic Biology 56, 155-162 [2007] (Code Link).

49. Zhang Y, Chen M, Zhou BB, Jermiin LS, Larkum AWD. Evolution of inner antennas of Cyanobacteria, algae and plants. Journal of Molecular Evolution 64, 321-331 [2007].

48. Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS. SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides. Bioinformatics 22, 2162-2163 [2006] (Code link).

47. Ababneh F, Jermiin LS, Robinson J. Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree. Journal of Mathematical Modelling and Algorithms 5, 291-308 [2006].

46. Ababneh F, Jermiin LS, Ma C, Robinson J. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics 22, 1225-1231 [2006] (Code link).

45. Holland BR, Jermiin LS, Moulton V. Improved consensus network techniques for ge-nome-scale phylogeny. Molecular Biology and Evolution 23, 848-855 [2006].

44. Messing CG, Mayer DL, Siebeck UE, Jermiin LS, Vaney DI, Rouse GW. A modern, soft-bottom, shallow-water, tropical crinoid fauna (Echinodermata) from the Great Barrier Reef. Coral Reefs 25, 164-168 [2006].

43. Wickham S, Large MCL, Poladian L, Jermiin LS. Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours. Journal of the Royal Society Interface 3, 99-108 [2006].

42. Poladian L, Jermiin LS. Multi-objective evolutionary algorithms and phylogenetic inference with multiple data sets. Soft Computing 10, 358-368 [2006].

41. Jayaswal V, Jermiin LS, Robinson J. Estimation of phylogeny using a general Markov model. Evolutionary Bioinformatics Online 1, 62-80 [2005].

40. Jermiin LS, Poladian L, Charleston MA. Is the 'Big Bang' in animal evolution real? Science 310, 1910-1911 [2005].

39. Murray S, Flø Jørgensen M, Ho SYH, Patterson DJ, Jermiin LS. Improving the analysis of Dinoflagellate phylogeny based on rDNA. Protist 156, 269-286 [2005].

38. Till M, Zhou BB, Zomaya A, Jermiin LS. Phylogenetic analysis using maximum likelihood methods in homogeneous parallel environments. Lecture Notes in Computer Science 3320, 274-279 [2004].

37. Premzl M, Gready JE, Jermiin LS, Simonic T, Marshall Graves JA. Evolution of vertebrate genes related to Prion and Shadoo proteins - clues from comparative genomic analysis - Molecular Biology and Evolution 21, 2210-2231 [2004].

36. Jermiin LS, Ho SYW, Ababneh F, Robinson J, AWD Larkum. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Systematic Biology 53, 638-643 [2004].

35. Ho SYW, Jermiin LS. Tracing the decay of the historical signal in biological sequence data. Systematic Biology 53, 623-637 [2004] (Data link).

34. Hardy MP, Owczarek CM, Jermiin LS, Ejdebäck M, Hertzog PJ. Characterization of the type I interferon locus and identification of novel genes. Genomics 84, 331-345 [2004] (Data link).

33. Wroe S, Field J, Fullagar R, Jermiin LS. Megafaunal extinction in the Late Quatenary and the global overkill hypothesis. Alcheringa 28, 291-333 [2004].

32. Kummerfeld SK, Weiss AS, Fekete A, Jermiin LS. AMID: Autonomous modeler of intragenic duplication. Applied Bioinformatics 2, 169-176 [2003] (Code link).

31. Jermiin LS, Ho SYW, Ababneh F, Robinson J, AWD Larkum. Hetero: A program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics 2, 159-163 [2003] (Code link) (Paper link).

30. Angelats C, Wang X-W, Jermiin LS, Copeland N, Jenkins N, Baker RT. Characterization of the mouse Usp15 ubiquitin specific protease. Mammalian Genome 14, 31-46 [2003].

29. Simpson AGB, Roger AJ, Silberman JD, Leipe D, Edgcomb VP, Jermiin LS, Patterson DJ, Sogin ML. Evolutionary history of "early diverging" eukaryotes: the excavate taxon Carpediomonas is a close relative of Giardia. Molecular Biology and Evolution 19, 1782-1791 [2002].

28. Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, Peacock WJ, Thorne A. Lake Mungo 3: A response to recent critique. Archaeology of Oceania 36, 170-174 [2001].

27. Lahoud MH, Ristevski S, Venter DJ, Jermiin LS, Bertoncello I, Zavarsek S, Hasthorpe S, Dargo J, de Kretzer D, Hertzog PJ, Kola I. Gene targeting of Desrt, a novel ARID class DNA binding protein, causes growth retardation and abnormal development of reproductive organs. Genome Research 11, 1327-1334 [2001].

26. Adcock GJ, Dennis ES, Easteal S, Huttley GA, Jermiin LS, Peacock WJ, Thorne A. Human origins and ancient human DNA - Response. Science 292, 1656 [2001].

25. Board PG, Coggan M, Chelvanayagam G, Easteal S, Jermiin LS, Schulte KG, Danley DE, Hoth LR, Griffor MC, Kamath AV, Rosner MH, Chrunyk BA, Perregaux DE, Gabel CA, Geoghegan KF, and Pandit J. Characterization of the Omega class of glutathione transferases. Chemico-Biological Interactions 133, 204-206 [2001].

24. Millen RS, Olmstead RG, Adams KL, Palmer JD, Kavanagh TA, Lao NT, Heggie L, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS, Wolfe KH. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645-658 [2001].

23. Board PG, Chelvanayagam G, Jermiin LS, Tetlow N, Tzeng H-F, Anders NW, Blackburn AC. Identification of novel glutathione transferases and polymorphic variants by expressed sequence tag data base analysis. Drug Metabolism and Disposition 29, 544-547 [2001].

22. Adcock GJ, Dennis ES, Easteal S, Huttley G, Jermiin LS, Peacock WJ, Thorne AG. Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins. Proceedings of the National Academy of Science USA 98: 537-542 [2001] (Erratum in Proceedings of the National Academy of Science USA 99, 541 [2002].

21. Chiotis M, Jermiin LS, Crozier RH. A molecular framework for the phylogeny of the ant subfamily Dolichoderinae. Molecular Phylogeny and Evolution 17, 108-116 [2000].

20. Board PG, Coggan M, Chelvanayagam G, Easteal S, Jermiin LS, Schulte KG, Danley DE, Hoth LR, Griffor MC, Kamath AV, Rosner MH, Chrunyk BA, Perregaux DE, Gabel CA, Geoghegan KF, and Pandit J. Identification, characterization and crystal structure of the Omega class of glutathione transferases. Journal of Biological Chemistry 275, 24798-24806 [2000].

19. Wolf MJ, Easteal S, Kahn M, McKay BD, Jermiin LJ. TrExML: a maximum likelihood approach for extensive tree-space exploration. Bioinformatics 16, 383-394 [2000].

18. Board PG, Chelvanayagam G, Jermiin LS, Blackburn AC. Identification and characterization of the Zeta class of glutathione transferases. Clinical Chemistry and Enzymology 16, 379-384 [2000].

17. Jones RA, Jermiin LS, Easteal S, Patel B, Beacham IR. Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium. Journal of Applied Microbiology 86, 93-107 [1999].

16. Board PG, Blackburn AC, Jermiin LS, Chelvanayagam G. Polymorphism of Phase II enzymes: Identification of new enzymes and polymorphic variants by database analysis. Toxicology Letters 102-103, 149-154 [1998].

15. Zhou J, Ng AYN, Tymms, MJ, Jermiin LS, Seth AK, Thomas RS and Kola I. A novel transcription factor, ELF15, belongs to the ELF subfamily of ETS genes and maps to human chromosome 11p13-15, a region subject to LOH and rearrangement in human carcinoma cell lines. Oncogene 17, 2719-2732 [1998].

14. Andrews TD, Jermiin LS, Easteal S. Accelerated evolution of the cytochrome b gene of simian primates: adaptive evolution in concert with other mitochondrial proteins? Journal of Molecular Evolution 47, 249-257 [1998].

13. Board PG, Baker RT, Chelvanayagam G, Jermiin LS. Zeta, a novel class of glutathione transferases in a range of species from plants to humans. Journal of Chemistry 328, 929-935 [1997].

12. Jermiin, LS, Olsen G, Mengersen KL, Easteal S. Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis. Molecular Biology and Evolution 14, 1296-1302 [1997].

11. Foster, PG, Jermiin LS, Hickey, DA. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. Journal of Molecular Evolution 44, 282-288 [1997].

10. Crozier RH, Jermiin LS, Chiotis M. Molecular evidence for a Jurassic origin of ants. Naturwissenschaften 84, 22-23 [1997].

9. Jermiin LS, Foster PG, Graur D, Lowe RM, Crozier RH. Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA. Journal of Molecular Evolution 42, 476-480 [1996] (Erratum in Journal of Molecular Evolution 44, 478 [1997]).

8. Jermiin LS, Graur D, Crozier RH. Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA. Molecular Biology and Evolution 12, 558-563 [1995].

7. Poiani A, Jermiin LS. A comparative analysis of some life-history traits between cooperatively and non-cooperatively breeding Australian passerines. Evolutionary Ecology 8, 471-488 [1994].

6. Jermiin LS, Graur D, Lowe RM, Crozier RH. Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes. Journal of Molecular Evolution 39, 160-173 [1994].

5. Jermiin LS, Crozier RH. The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: amino acid sequence divergence in Hymenoptera may be associated with nucleotide content. Journal of Molecular Evolution 38, 282-294 [1994].

4. Dod B, Jermiin LS, Boursot P, Chapman VH, Tønnes Nielsen J, Bonhomme F. Counterselection on sex chromosomes in the Mus musculus European hybrid zone. Journal of Evolutionary Biology 6, 529-546 [1993].

3. Jermiin LS, Mahler V. Revised descriptions of the morphology of Trachyphloeus bifoveolatus, T. angustisetulus, T. spinimanus, and T. digitalis. (Coleoptera: Curculionidae). Entomologist's Gazette 44, 139-153 [1993].

2. Jermiin LS, Loeschcke V, Simonsen V, Mahler V. Electrophoretic and morphometric analysis of two sibling species pairs in Trachyphloeus (Coleoptera: Curculionidae). Entomologica Scandinavica 22, 159-170 [1991].

1. Tomiuk J, Jermiin LS. Changes in relative mobility of pancreatic amylase variants in isoelectric focusing. Primates 32, 124-129 [1991].

6. Jayaswal V, Poladian L, Jermiin LS. Single- and multi-objective phylogenetic analysis of primate evolution using a genetic algorithm. Proceedings of the IEEE Congress on Evolutionary Computation 4146 - 4153 (Singapore; September 25 - 28, 2007)

5. Till M, Zhou BB, Zomaya A, Jermiin LS. Phylogenetic analysis using maximum likelihood methods in homogeneous parallel environments. Proceedings of the 5th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT-2004, Singapore; December 2004).

4. Wickham S, Poladian L, Large M, Jermiin L. Evolution of two-dimensional optical microstructures in butterfly scales. Proceedings of the 8th International Conference on Optics Within Life Sciences (OWLS8-2004, Melbourne, Australia; November 2004).

3. Poladian L, Wickham S, Large M, Jermiin L. Biological strategies to suppress iridescence in low-contrast 3D photonic crystals. Proceedings of the 8th International Conference on Optics Within Life Sciences (OWLS8-2004, Melbourne, Australia; November 2004).

2. Zhou BB, Till M, Zomaya A, Jermiin LS. Parallel implementation of maximum likelihood methods for phylogenetic analysis. Proceedings of the Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC'04): In the Proceedings of the International Parallel and Distributed Processing Symposium (Santa Fe, New Mexico, USA, April 26-30, 2004).

1. Nicholas FW, Cothran EG, Jermiin LS, Nesbitt B. A phylogenetic analysis of Brumbies. Proceedings for the Association for the Advancement of Animal Breeding and Genetics 15: 160-165 [2003].

5. Large M, Wickham S, Poladian L, Jermiin LS. Iridescence control in low contrast biological microstructures. In International Quantum Electronics Conference 2005: 579-359 (Nippon Toshi Center Hotel, Tokyo, Japan, July 11-15, 2005)

4. Poladian L, Jermiin LS. What might evolutionary algorithms (EA) and multi-objective optimisation (MOO) contribute to phylogenetics and the Total Evidence debate? Biological Applications of Genetic and Evolutionary Computing: In the Proceedings of the Genetic and Evolutionary Computing Conference (GECCO-2004, Seattle, USA, June 27-30, 2004).

3. Poladian L, Jermiin LS. Phylogenetic inference using evolutionary multi-objective optimisation. Post-deadline paper: In the Proceedings of the Genetic and Evolutionary Computing Conference (GECCO-2004, Seattle, USA, June 27-30, 2004).

2. Jermiin LS, Blankenship RE, Lockhart PJ, Larkum AWD. Phylogenetic reconstruction of ancient photosynthetic lineages using chlorophyll and bacteriochlorophyll biosynthetic genes. S9-012 [2001]. In: PS2001 Proceedings: 12th International Congress on Photosynthesis. CSIRO Publishing, Melbourne, Australia (ISBN 0643 067 116).

1. Blankenship RE, Reymond J, Lince M, Larkum AWD, Jermiin LS, Lockhart PJ, Zhaxybayeva O, Gogarten JP. Evolution of photosynthetic antennas and reaction centers. PL13 [2001]. In: PS2001 Proceedings: 12th International Congress on Photosynthesis. CSIRO Publishing, Melbourne, Australia (ISBN 0643 067 116).