Honorary Staff - Dr Lars Jermiin

Lars Jermiin Photo
Position: Honorary Associate Professor - University of Sydney and OCE Science Leader - CSIRO Entomology
Phone: +61 2 6246 4043 (CSIRO Entomology)
Fax: +61 2 6246 4094 (CSIRO Entomology)
Mobile Phone: +61 431 172 425
Email: lars.jermiin@csiro.au
Location: CSIRO Entomology, Black Mountain Laboratories, Clunies Ross Street, Canberra, ACT 2601, Australia
Address: CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
Links: CSIRO
CSIRO Staff Home


Services

Reviewer: (since 1994)
Antarctic Science, Australian Journal of Zoology, Gene, Genetics, Insectes Sociaux, International Journal of Biochemistry and Cell Biology, Journal of Molecular Evolution, Marine Ecology-Progress Series, Molecular Biology and Evolution, Naturwissenschaften.

Assessor: (since 1995)
Member of the Australian Research Council (ARC) Panel of Assessors.

Associate Supervisor: (since 1995)

  • TD Andrews (Australian National University - PhD awarded 1998).

    KE Sloper (Australian National University - PhD awarded 1998).
  • SA Murray (University of Sydney - PhD awarded 2003).
  • GIA Herbert (Australian National University - PhD awarded 2004).
  • SK Kummerfeld (University of Sydney - BSc Adv. Hons. awarded 2001).
  • S Carrizo (University of Sydney - BSc Hons. awarded 2003).
  • S Wickham (University of Sydney - BSc Hons. awarded 2004).

Supervisor: (since 2001)

  • IT Hyman (University of Sydney - PhD ongoing).
  • Y Zhang (University of Sydney - PhD ongoing).
  • KW "Rex" Lau (University of Sydney - PhD ongoing).
  • SYW Ho (University of Sydney - MSc awarded 2004).
  • M Peate (University of Sydney - BSc Grad. Dip. awarded 2001).
  • SYW Ho (University of Sydney - BSc Adv. Hons. awarded 2002).
  • L Childs (University of Sydney - BSc Hons. awarded 2003).
  • A Shaw (University of Sydney - BSc Hons. ongoing).

Current and Past Professional Associations

  • The International Society for Computational Biology (2003 - ) (ISCB)
  • The Australian Association for Bioinformatics (2003 - 2004) (AAB)
  • The Society of Systematic Biologists (2000 - 2004) (SSB)
  • The Society of Australian Systematic Biologists (1997 - 2004) (SASB)
  • The Genetic Society of Australia (1993 - 2004) (GSA)
  • The Society of Molecular Biology and Evolution (1995 - 2001)
  • The Society for the Study of Evolution (1990 - 2000)
  • The European Society for Evolutionary Biology (1988 - 1993)

Areas of Interest

My research focuses on developing and using statistical and computational tools to estimate and understand evolutionary patterns and processes at the molecular level. It also covers the more classical biological disciplines (e.g., genetics, ecology, taxonomy, systematics, etc) and is moving towards addressing important biotechnological problems. The raison d’être behind my research is given below.

Recent advances in DNA sequencing techniques have produced a wealth of genomic data, and the challenge now is to analyse this increasingly large and complex body of data. When the research entails comparing data obtained from more than two genomes, it is important that these comparisons are done in the context of underlying evolutionary history; from a statistical point of view, this is the only sound approach to comparing data from more than two genomes.

Comparisons of genomes and genomic data can be done using a variety of phylogenetic and tree-dependent comparative methods. The methods rest on assumptions, and when these are violated by the data, there is an increased change that conclusions drawn from analyses of such data may be invalid; hence, it is important that the data are surveyed using methods that can detect violation of these assumptions. Until recently, however, such methods were either available (but then rarely used), or unavailable (because nobody had realised that there was a problem and then developed the solution), or prone to give biased results (due to poor design).

When the assumptions of phylogenetic and tree-dependent comparative methods are violated, which is unknown in most cases, we are left with only a few options, that is to:

  • Abandon the data set and choose another one; or
  • Assume that the violation will not confound the ensuing analysis; or
  • Use methods that are confounded to a lesser extent by the complexity
    of the data.

None of these options is attractive if the study entails comparing
genomes or genomic data from more than two related organisms.

My research focuses on the development and use of bioinformatics tools
to mine the ever-increasing body of complex genomic data in a computationally efficient and statistically sound manner. Currently, the thrust is on inventing and using (i) methods to detect violation of phylogenetic assumptions; (ii) computational implementations of the general Markov model of substitutions; and (iii) time-reversible Markov models for analysis of genomic data after transformation of the data has occurred. The new methods, several of which have been published since 2005, allow me to address fundamental scientific questions pertaining to our understanding of:

  • The origin and evolution of life;
  • The mechanisms that govern the evolution of genomes;
  • The genetic basis of diversity among organisms, including microbes,
    crinoids, butterflies, yeasts and angiosperms;
  • The evolution of complex systems, including gene products involved
    in photosynthesis, gene products involved in oxidative
    phosphorylation, and the function and evolution of optical
    microstructures.

In the future, I intend to use phylogenetic know-how as a platform for developing molecules of potential importance to the biotechnology and pharmaceutical industries. Enzymes are of particular interest.


Research Output

Book Chapters
Papers Published in Peer-reviewed Journals
Papers Published in Peer-reviewed Conference Proceedings
Papers in Conference Proceedings
Software from the Bioinformatics Lab

Book Chapters

  • 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)
  • 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

  • Jayaswal, V, Jermiin LS, Poladian L, Robinson J.Two stationary, non-homogeneous Markov models of nucleotide sequence evolution. Systematic Biology (In press)
  • Zhang Y, Chen M, Church WB, Lau KW, Larkum AWD, Jermiin LS. The molecular structure of the IsiA-Photosystem I supercomplex, modelled from high-resolution, crystal structures of Photosystem I and the CP43 protein. Biochimica et Biophysica Acta – Bioenergetics 1797, 457-465 [2010].
  • 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].
  • Sumner JG, Charleston MA, Jermiin LS, Jarvis PD. Markov invariants, plethysms, and phylogenetics. Journal of Theoretical Biology 253, 601-615 [2008].
  • 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].
  • 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).
  • 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).
  • 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).
  • 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].
  • 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).
  • 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].
  • 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).
  • Holland BR, Jermiin LS, Moulton V. Improved consensus network techniques for ge-nome-scale phylogeny. Molecular Biology and Evolution 23, 848-855 [2006].
  • 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].
  • 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].
  • Poladian L, Jermiin LS. Multi-objective evolutionary algorithms and phylogenetic inference with multiple data sets. Soft Computing 10, 358-368 [2006].
  • Jayaswal V, Jermiin LS, Robinson J. Estimation of phylogeny using a general Markov model. Evolutionary Bioinformatics Online 1, 62-80 [2005]. (Code Link).
  • Jermiin LS, Poladian L, Charleston MA. Is the 'Big Bang' in animal evolution real? Science 310, 1910-1911 [2005].
  • 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].
  • 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].
  • 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]
  • 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].
  • Ho SYW, Jermiin LS. Tracing the decay of the historical signal in biological sequence data. Systematic Biology 53, 623-637 [2004] (Data link).
  • 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).
  • Wroe S, Field J, Fullagar R, Jermiin LS. Megafaunal extinction in the Late Quatenary and the global overkill hypothesis. Alcheringa 28, 291-333 [2004].
  • Kummerfeld SK, Weiss AS, Fekete A, Jermiin LS. AMID: Autonomous modeler of intragenic duplication. Applied Bioinformatics 2, 169-176 [2003].
  • 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).
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • Crozier RH, Jermiin LS, Chiotis M. Molecular evidence for a Jurassic origin of ants. Naturwissenschaften 84, 22-23 [1997].
  • 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]).
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • 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].
  • Tomiuk J, Jermiin LS. Changes in relative mobility of pancreatic amylase variants in isoelectric focusing. Primates 32, 124-129 [1991].

Papers Published in Peer-reviewed Conference Proceedings

  • 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)
  • 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).
  • Wickham S, Poladian L, Large M, Jermiin LS. 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).
  • Poladian L, Wickham S, Large M, Jermiin LS. 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).
  • 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).
  • 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].

Papers in Conference Proceedings

  • 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)
  • 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).
  • 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).
  • 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).
  • 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).

Software from the Bioinformatics Lab

  • Jermiin LS, Anpilogova O (1997) TreeCons: a program to generate a majority-rule consensus from trees obtained by maximum likelihood analysis of DNA and protein sequences (ANSI C Code)
  • Jermiin LS (2003) Hetero: a program to simulate the evolution of DNA on a four-taxon tree (ANSI C Code) (Code link)
  • Jayaswal V (2005). BH: a maximum-likelihood program to infer phylogeny under a general Markov model (Java code) (Code link)
  • Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS (2006) SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides (Java Code) (Code link)
  • Ababneh F (2006) Symtest: a set of statistical programs designed to test the symmetry, marginal symmetry and internal symmetry of divergence matrices obtained by comparing matching (homologous) nucleotide sequences (R Code) (Code link)
  • Jermiin LS (2006) DMP: a program to estimate the symmetrical directional mutation pressure that is excreted upon protein-coding genes (ANSI C Code)
  • Jayaswal V (2007). BH+I: a maximum-likelihood program to infer phylogeny under a general Markov model with invariant sites (Java code) (Code link)
  • Jermiin LS (2007) Homo: a program to assess stationarity in nucleotide and amino acid sequences (ANSI C Code)