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Dr Lars Jermiin

PhD

Contact Details

Lecturer Above The Bar
E: Lars.Jermiin@universityofgalway.ie
 
researcher
 

Biography

Lars Jermiin is Assistant Professor in Evolutionary Bioinformatics at School of Mathematical and Statistical Sciences, University of Galway, and Honorary Professor at Research School of Biology, Australian National University.

He holds an MSc (Population Genetics) from the University of Aarhus (1989) and a PhD (Molecular Evolution) from La Trobe University (1994). He conducted postdoctoral research at La Trobe University (1994-1995), Université d'Ottawa (1995), the Australian National University (1995-1998), and the University of Sydney (1998-2001).

In 2001, he was appointed Lecturer at the University of Sydney and later promoted to Senior Lecturer (2004), and Associate Professor (2008). In 2002, he co-founded the Sydney University Bioinformatics and Technology Centre (SUBIT) and later became Director of SUBIT (2003-7). In 2009, the Australian Commonwealth Scientific Industrial and Research Organisation (CSIRO) appointed him as Science Leader, to establish and lead a research team focusing on genome bioinformatics at CSIRO's Division of Entomology. Later, he served as Senior Principle Research Leader at CSIRO's Division of Land and Water (2014-17). In 2016, he was appointed Honorary Professor at the Australian National University and later served as Visiting Professor at the University College Dublin (2018-22). In 2022, he was appointed Data Stewardship Manager at Elixir - Ireland, and early in 2023 he was appointed Assistant Professor at University College Dublin's School of Biology and Environmental Sciences before taking up his current position.

Research Interests

Lars Jermiin is an expert in evolutionary biology and bioinformatics, with particular strengths in molecular phylogenetics and comparative genomics. His interests spans the ways in which genes and proteins, populations, and species diverge and adapt to changing environments. He has applied his knowledge and methodologies in a variety of research areas, including genome annotation, evolution, biosecurity, and the engineering of novel enzymes.

Much of his research focuses on developing methods to extract information from genomic data in a statistically sound and computationally efficient manner. His current focus is on promoting a new phylogenetic protocol (NAR Genomics and Bioinformatics 2, lqaa041) -- designed to mitigate model misspecification and confirmation bias -- and on developing methods and tools to support this protocol. Among these are methods and tools to: (i) detect violations of phylogenetic assumptions; (ii) find optimal models of sequence evolution for data that evolved under clocklike conditions; (iii) obtain phylogenetic estimates from data that evolved under non-clocklike conditions; and (iv) assess whether phylogenetic estimates are affected by ascertainment bias.

In addition, he is doing, or has done, applied research with multiple foci, including:

  • Insect Genome Projects -- He co-led the annotation and comparison of detoxification genes in the cotton bollworm and the corn earworm (BMC Biology 15, 63), the tobacco hornworm (Insect Biochemistry and Molecular Biology 76, 118-147), and two species of bumblebee (Genome Biology 16, 76).
  • Bat1K Genome Project -- He co-led the phylogenetic research in this project (Nature 583, 578-584) and co-leads further phylogenetic research of these data.
  • Plant Chloroplast Genomes -- He leads phylogenetic research aimed at uncovering the complexity of evolutionary processes underpinning the diversity of chloroplast genomes.
  • 1KITE Project -- He contributed to this project, with novel strategies and methods for analysing the phylogenomic data (Science 346, 763-767; Science 349, 487).
  • Biosecurity -- He contributed to research identifying the origins and incursion pathways of pests affecting agriculture and livestock (PLoS One 11, e0146699; Scientific Reports 7, 45302).
  • Design of Novel Enzymes ---He co-led the project aimed at engineering novel ¿-transaminases for use in a biotechnological setting (Green Chemistry 19, 5375-5380; International Patent Application PCT/AU2014/000617).




Peer Reviewed Journals

  Year Publication
(2023) 'The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity'
Waterhouse, R and Adam-Blondon, A-F and Balech, B and Barta, E and Heil, K and Hughes, G and Jermiin, L and Kalaš, M and Lanfear, J and Pafilis, E and Papageorgiou, A and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T (2023) 'The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity'. F1000Research, [DOI] [Details]
(2022) 'Corrigendum to: A likelihood-ratio test for lumpability of phylogenetic data: Is the Markovian property of an evolutionary process retained in recoded DNA?'
Vera-Ruiz, VA and Robinson, J and Jermiin, LS (2022) 'Corrigendum to: A likelihood-ratio test for lumpability of phylogenetic data: Is the Markovian property of an evolutionary process retained in recoded DNA?'. Systematic Biology, 71 (3) [DOI] [Details]
(2022) 'Contradictory phylogenetic signals in the Laurasiatheria anomaly zone'
Doronina, L and Hughes, GM and Moreno-Santillan, D and Lawless, C and Lonergan, T and Ryan, L and Jebb, D and Kirilenko, BM and Korstian, JM and Dávalos, LM and Vernes, SC and Myers, EW and Teeling, EC and Hiller, M and Jermiin, LS and Schmitz, J and Springer, MS and Ray, DA (2022) 'Contradictory phylogenetic signals in the Laurasiatheria anomaly zone'. Genes, 13 (5) [DOI] [Details]
(2022) 'A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family'
Salzberg, IL and Martos, AAR and Lombardi, L and Jermiin, LS and Blanco, A and Byrne, KP and Wolfe, KH (2022) 'A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family'. PLoS Genetics, 18 (11) [DOI] [Details]
(2022) 'A likelihood-ratio test for lumpability of phylogenetic data: Is the Markovian property of an evolutionary process retained in recoded DNA?'
Vera-Ruiz, VA and Robinson, J and Jermiin, LS (2022) 'A likelihood-ratio test for lumpability of phylogenetic data: Is the Markovian property of an evolutionary process retained in recoded DNA?'. Systematic Biology, 71 (3):660-675 [DOI] [Details]
(2022) 'Genetic and lipidomic analyses suggest that Nostoc punctiforme, a plant-symbiotic cyanobacterium, does not produce sphingolipids'
Belton, S and Lamari, N and Jermiin, LS and Mariscal, V and Flores, E and McCabe, PF and Ng, CKY (2022) 'Genetic and lipidomic analyses suggest that Nostoc punctiforme, a plant-symbiotic cyanobacterium, does not produce sphingolipids'. Access Microbiology, 4 (1) [DOI] [Details]
(2021) 'A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants'
McInerney, TW and Fulton-Howard, B and Patterson, C and Paliwal, D and Jermiin, LS and Patel, HR and Pa, J and Swerdlow, RH and Goate, A and Easteal, S and Andrews, SJ (2021) 'A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants'. BMC Bioinformatics, 22 (1) [DOI] [Details]
(2020) 'Six reference-quality genomes reveal evolution of bat adaptations'
Jebb, D and Huang, Z and Pippel, M and Hughes, GM and Lavrichenko, K and Devanna, P and Winkler, S and Jermiin, LS and Skirmuntt, EC and Katzourakis, A and Burkitt-Gray, L and Ray, DA and Sullivan, KAM and Roscito, JG and Kirilenko, BM and Dávalos, LM and Corthals, AP and Power, ML and Jones, G and Ransome, RD and Dechmann, DKN and Locatelli, AG and Puechmaille, SJ and Fedrigo, O and Jarvis, ED and Hiller, M and Vernes, SC and Myers, EW and Teeling, EC (2020) 'Six reference-quality genomes reveal evolution of bat adaptations'. Nature, 583 (7817):578-584 [DOI] [Details]
(2020) 'A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics'
Jermiin, LS and Catullo, RA and Holland, BR (2020) 'A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics'. NAR Genomics and Bioinformatics, 2 (2) [DOI] [Details]
(2020) 'A minimum reporting standard for multiple sequence alignments'
Wong, TKF and Kalyaanamoorthy, S and Meusemann, K and Yeates, DK and Misof, B and Jermiin, LS (2020) 'A minimum reporting standard for multiple sequence alignments'. NAR Genomics and Bioinformatics, 2 (2) [DOI] [Details]
(2020) 'Sensitivity and specificity of information criteria'
Dziak, JJ and Coffman, DL and Lanza, ST and Li, R and Jermiin, LS (2020) 'Sensitivity and specificity of information criteria'. Briefings in Bioinformatics, 21 (2):553-565 [DOI] [Details]
(2020) 'GHOST: Recovering historical signal from heterotachously evolved sequence alignments'
Crotty, SM and Minh, BQ and Bean, NG and Holland, BR and Tuke, J and Jermiin, LS and Haeseler, AV (2020) 'GHOST: Recovering historical signal from heterotachously evolved sequence alignments'. Systematic Biology, 69 (2):249-264 [DOI] [Details]
(2020) 'Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization'
Schilling, S and Kennedy, A and Pan, S and Jermiin, LS and Melzer, R (2020) 'Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization'. New Phytologist, 225 (1):511-529 [DOI] [Details]
(2020) 'Analysis of genomic sequence data reveals the origin and evolutionary separation of hawaiian hoary bat populations'
Pinzari, CA and Kang, L and Michalak, P and Jermiin, LS and Price, DK and Bonaccorso, FJ (2020) 'Analysis of genomic sequence data reveals the origin and evolutionary separation of hawaiian hoary bat populations'. Genome Biology and Evolution, 12 (9):1504-1514 [DOI] [Details]
(2019) 'Serpins: Genome-wide characterisation and expression analysis of the serine protease inhibitor family in Triticum aestivum'
Benbow, HR and Jermiin, LS and Doohan, FM (2019) 'Serpins: Genome-wide characterisation and expression analysis of the serine protease inhibitor family in Triticum aestivum'. G3: Genes, Genomes, Genetics, 9 (8):2709-2722 [DOI] [Details]
(2017) 'ModelFinder: Fast model selection for accurate phylogenetic estimates'
Kalyaanamoorthy, S and Minh, BQ and Wong, TKF and Von Haeseler, A and Jermiin, LS (2017) 'ModelFinder: Fast model selection for accurate phylogenetic estimates'. Nature Methods, 14 (6):587-589 [DOI] [Details]
(2017) 'Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini)'
Escalona, HE and Zwick, A and Li, HS and Li, J and Wang, X and Pang, H and Hartley, D and Jermiin, LS and Nedvěd, O and Misof, B and Niehuis, O and Ślipiński, A and Tomaszewska, W (2017) 'Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini)'. BMC Evolutionary Biology, 17 (1) [DOI] [Details]
(2017) 'Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species'
Pearce, SL and Clarke, DF and East, PD and Elfekih, S and Gordon, KHJ and Jermiin, LS and McGaughran, A and Oakeshott, JG and Papanikolaou, A and Perera, OP and Rane, RV and Richards, S and Tay, WT and Walsh, TK and Anderson, A and Anderson, CJ and Asgari, S and Board, PG and Bretschneider, A and Campbell, PM and Chertemps, T and Christeller, JT and Coppin, CW and Downes, SJ and Duan, G and Farnsworth, CA and Good, RT and Han, LB and Han, YC and Hatje, K and Horne, I and Huang, YP and Hughes, DST and Jacquin-Joly, E and James, W and Jhangiani, S and Kollmar, M and Kuwar, SS and Li, S and Liu, NY and Maibeche, MT and Miller, JR and Montagne, N and Perry, T and Qu, J and Song, SV and Sutton, GG and Vogel, H and Walenz, BP and Xu, W and Zhang, HJ and Zou, Z and Batterham, P and Edwards, OR an (2017) 'Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species'. BMC Biology, 15 (1) [DOI] [Details]
(2017) 'Erratum: Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species [BMC Biology., 15, (2017) (69)] DOI: 10.1186/s12915-017-0402-6'
Pearce, SL and Clarke, DF and East, PD and Elfekih, S and Gordon, KHJ and Jermiin, LS and McGaughran, A and Oakeshott, JG and Papanicolaou, A and Perera, OP and Rane, RV and Richards, S and Tay, WT and Walsh, TK and Anderson, A and Anderson, CJ and Asgari, S and Board, PG and Bretschneider, A and Campbell, PM and Chertemps, T and Christeller, JT and Coppin, CW and Downes, SJ and Duan, G and Farnsworth, CA and Good, RT and Han, LB and Han, YC and Hatje, K and Horne, I and Huang, YP and Hughes, DST and Jacquin-Joly, E and James, W and Jhangiani, S and Kollmar, M and Kuwar, SS and Li, S and Liu, NY and Maibeche, MT and Miller, JR and Montagne, N and Perry, T and Qu, J and Song, SV and Sutton, GG and Vogel, H and Walenz, BP and Xu, W and Zhang, HJ and Zou, Z and Batterham, P and Edwards, OR an (2017) 'Erratum: Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species [BMC Biology., 15, (2017) (69)] DOI: 10.1186/s12915-017-0402-6'. BMC Biology, 15 (1) [DOI] [Details]
(2017) 'Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil'
Tay, WT and Walsh, TK and Downes, S and Anderson, C and Jermiin, LS and Wong, TKF and Piper, MC and Chang, ES and Macedo, IB and Czepak, C and Behere, GT and Silvie, P and Soria, MF and Frayssinet, M and Gordon, KHJ (2017) 'Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil'. Scientific Reports, 7 [DOI] [Details]
(2017) 'Reverse engineering: Transaminase biocatalyst development using ancestral sequence reconstruction'
Wilding, M and Peat, TS and Kalyaanamoorthy, S and Newman, J and Scott, C and Jermiin, LS (2017) 'Reverse engineering: Transaminase biocatalyst development using ancestral sequence reconstruction'. Green Chemistry, 19 (22):5375-5380 [DOI] [Details]
(2016) 'Population Genetic structure and potential incursion pathways of the bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) In Australia'
Tay, WT and Kerr, PJ and Jermiin, LS (2016) 'Population Genetic structure and potential incursion pathways of the bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) In Australia'. PLoS ONE, 11 (1) [DOI] [Details]
(2016) 'Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta'
Kanost, MR and Arrese, EL and Cao, X and Chen, YR and Chellapilla, S and Goldsmith, MR and Grosse-Wilde, E and Heckel, DG and Herndon, N and Jiang, H and Papanicolaou, A and Qu, J and Soulages, JL and Vogel, H and Walters, J and Waterhouse, RM and Ahn, SJ and Almeida, FC and An, C and Aqrawi, P and Bretschneider, A and Bryant, WB and Bucks, S and Chao, H and Chevignon, G and Christen, JM and Clarke, DF and Dittmer, NT and Ferguson, LCF and Garavelou, S and Gordon, KHJ and Gunaratna, RT and Han, Y and Hauser, F and He, Y and Heidel-Fischer, H and Hirsh, A and Hu, Y and Jiang, H and Kalra, D and Klinner, C and König, C and Kovar, C and Kroll, AR and Kuwar, SS and Lee, SL and Lehman, R and Li, K and Li, Z and Liang, H and Lovelace, S and Lu, Z and Mansfield, JH and McCulloch, KJ and Mathew, (2016) 'Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta'. Insect Biochemistry and Molecular Biology, 76 :118-147 [DOI] [Details]
(2016) 'Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?'
Rane, RV and Walsh, TK and Pearce, SL and Jermiin, LS and Gordon, KH and Richards, S and Oakeshott, JG (2016) 'Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?'. Current Opinion in Insect Science, 13 :70-76 [DOI] [Details]
(2015) 'Response to Comment on Phylogenomics resolves the timing and pattern of insect evolution'
Kjer, KM and Ware, JL and Rust, J and Wappler, T and Lanfear, R and Jermiin, LS and Zhou, X and Aspöck, H and Aspöck, U and Beutel, RG and Blanke, A and Donath, A and Flouri, T and Frandsen, PB and Kapli, P and Kawahara, AY and Letsch, H and Mayer, C and McKenna, DD and Meusemann, K and Niehuis, O and Peters, RS and Wiegmann, BM and Yeates, DK and Von Reumont, BM and Stamatakis, A and Misof, B (2015) 'Response to Comment on Phylogenomics resolves the timing and pattern of insect evolution'. Science, 349 (6247) [DOI] [Details]
(2015) 'The genomes of two key bumblebee species with primitive eusocial organization'
Sadd, BM and Barribeau, SM and Bloch, G and de Graaf, DC and Dearden, P and Elsik, CG and Gadau, J and Grimmelikhuijzen, CJP and Hasselmann, M and Lozier, JD and Robertson, HM and Smagghe, G and Stolle, E and Van Vaerenbergh, M and Waterhouse, RM and Bornberg-Bauer, E and Klasberg, S and Bennett, AK and Câmara, F and Guigó, R and Hoff, K and Mariotti, M and Munoz-Torres, M and Murphy, T and Santesmasses, D and Amdam, GV and Beckers, M and Beye, M and Biewer, M and Bitondi, MMG and Blaxter, ML and Bourke, AFG and Brown, MJF and Buechel, SD and Cameron, R and Cappelle, K and Carolan, JC and Christiaens, O and Ciborowski, KL and Clarke, DF and Colgan, TJ and Collins, DH and Cridge, AG and Dalmay, T and Dreier, S and du Plessis, L and Duncan, E and Erler, S and Evans, J and Falcon, T and Flo (2015) 'The genomes of two key bumblebee species with primitive eusocial organization'. Genome Biology, 16 (1) [DOI] [Details]
(2014) 'Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics'
Vera-Ruiz, VA and Lau, KW and Robinson, J and Jermiin, LS (2014) 'Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics'. BMC Bioinformatics, 15 (Suppl. 2) [DOI] [Details]
(2014) 'Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages'
Jayaswal, V and Wong, TKF and Robinson, J and Poladian, L and Jermiin, LS (2014) 'Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages'. Systematic Biology, 63 (5):726-742 [DOI] [Details]
(2014) 'Phylogenomics resolves the timing and pattern of insect evolution'
Misof, B and Liu, S and Meusemann, K and Peters, RS and Donath, A and Mayer, C and Frandsen, PB and Ware, J and Flouri, T and Beutel, RG and Niehuis, O and Petersen, M and Izquierdo-Carrasco, F and Wappler, T and Rust, J and Aberer, AJ and Aspöck, U and Aspöck, H and Bartel, D and Blanke, A and Berger, S and Böhm, A and Buckley, TR and Calcott, B and Chen, J and Friedrich, F and Fukui, M and Fujita, M and Greve, C and Grobe, P and Gu, S and Huang, Y and Jermiin, LS and Kawahara, AY and Krogmann, L and Kubiak, M and Lanfear, R and Letsch, H and Li, Y and Li, Z and Li, J and Lu, H and Machida, R and Mashimo, Y and Kapli, P and McKenna, DD and Meng, G and Nakagaki, Y and Navarrete-Heredia, JL and Ott, M and Ou, Y and Pass, G and Podsiadlowski, L and Pohl, H and Von Reumont, BM and Schütte (2014) 'Phylogenomics resolves the timing and pattern of insect evolution'. Science, 346 (6210):763-767 [DOI] [Details]
(2013) 'Fixed, free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin'
Rouse, GW and Jermiin, LS and Wilson, NG and Eeckhaut, I and Lanterbecq, D and Oji, T and Young, CM and Browning, T and Cisternas, P and Helgen, LE and Stuckey, M and Messing, CG (2013) 'Fixed, free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin'. Molecular Phylogenetics and Evolution, 66 (1):161-181 [DOI] [Details]
(2012) 'Intramolecular epistasis and the evolution of a new enzymatic function'
Noor, S and Taylor, MC and Russell, RJ and Jermiin, LS and Jackson, CJ and Oakeshott, JG and Scott, C (2012) 'Intramolecular epistasis and the evolution of a new enzymatic function'. PLoS ONE, 7 (6) [DOI] [Details]
(2011) 'Reducing model complexity of the general Markov model of evolution'
Jayaswal, V and Ababneh, F and Jermiin, LS and Robinson, J (2011) 'Reducing model complexity of the general Markov model of evolution'. Molecular Biology and Evolution, 28 (11):3045-3059 [DOI] [Details]
(2011) 'Two stationary nonhomogeneous Markov models of nucleotide sequence evolution'
Jayaswal, V and Jermiin, LS and Poladian, L and Robinson, J (2011) 'Two stationary nonhomogeneous Markov models of nucleotide sequence evolution'. Systematic Biology, 60 (1):74-86 [DOI] [Details]
(2010) 'The molecular structure of the IsiA-Photosystem I supercomplex, modelled from high-resolution, crystal structures of Photosystem I and the CP43 protein'
Zhang, Y and Chen, M and Church, WB and Lau, KW and Larkum, AWD and Jermiin, LS (2010) '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 (4):457-465 [DOI] [Details]
(2010) 'Erratum to Characterization of an indoliamine 2,3-dioxygenase-like protein found in humans and mice [Gene, (2007), 203-213]'
Ball, HJ and Sanchez-Perez, A and Wieser, S and Austin, CJD and Astelbauer, F and Miu, J and McQuillan, JA and Stocker, R and Jermiin, LS and Hunt, NH (2010) 'Erratum to Characterization of an indoliamine 2,3-dioxygenase-like protein found in humans and mice [Gene, (2007), 203-213]'. Gene, 465 (1-2) [DOI] [Details]
(2009) 'Characterization and evolution of vertebrate indoleamine 2, 3-dioxygenases. IDOs from monotremes and marsupials'
Yuasa, HJ and Ball, HJ and Ho, YF and Austin, CJD and Whittington, CM and Belov, K and Maghzal, GJ and Jermiin, LS and Hunt, NH (2009) 'Characterization and evolution of vertebrate indoleamine 2, 3-dioxygenases. IDOs from monotremes and marsupials'. Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology, 153 (2):137-144 [DOI] [Details]
(2008) 'Markov invariants, plethysms, and phylogenetics'
Sumner, JG and Charleston, MA and Jermiin, LS and Jarvis, PD (2008) 'Markov invariants, plethysms, and phylogenetics'. Journal of Theoretical Biology, 253 (3):601-615 [DOI] [Details]
(2007) 'Evolution of the inner light-harvesting antenna protein family of cyanobacteria, algae, and plants'
Zhang, Y and Chen, M and Zhou, BB and Jermiin, LS and Larkum, AWD (2007) 'Evolution of the inner light-harvesting antenna protein family of cyanobacteria, algae, and plants'. Journal of Molecular Evolution, 64 (3):321-331 [DOI] [Details]
(2007) 'Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice'
Ball, HJ and Sanchez-Perez, A and Weiser, S and Austin, CJD and Astelbauer, F and Miu, J and McQuillan, JA and Stocker, R and Jermiin, LS and Hunt, NH (2007) 'Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice'. Gene, 396 (1):203-213 [DOI] [Details]
(2007) 'Mind the gaps: Evidence of bias in estimates of multiple sequence alignments'
Golubchik, T and Wise, MJ and Easteal, S and Jermiin, LS (2007) 'Mind the gaps: Evidence of bias in estimates of multiple sequence alignments'. Molecular Biology and Evolution, 24 (11):2433-2442 [DOI] [Details]
(2007) 'Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution'
Jayaswal, V and Robinson, J and Jermiin, L (2007) 'Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution'. Systematic Biology, 56 (2):155-162 [DOI] [Details]
(2007) 'Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA'
Hyman, IT and Ho, SYW and Jermiin, LS (2007) 'Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA'. Molecular Phylogenetics and Evolution, 45 (3):792-812 [DOI] [Details]
(2006) 'SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides'
Ho, JWK and Adams, CE and Lew, JB and Matthews, TJ and Ng, CC and Shahabi-Sirjani, A and Tan, LH and Zhao, Y and Easteal, S and Wilson, SR and Jermiin, LS (2006) 'SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides'. Bioinformatics, 22 (17):2162-2163 [DOI] [Details]
(2006) 'Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree'
Ababneh, F and Jermiin, LS and Robinson, J (2006) 'Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree'. Journal of Mathematical Modelling and Algorithms, 5 (3):291-308 [DOI] [Details]
(2006) 'Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences'
Ababneh, F and Jermiin, LS and Ma, C and Robinson, J (2006) 'Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences'. Bioinformatics, 22 (10):1225-1231 [DOI] [Details]
(2006) 'Improved consensus network techniques for genome-scale phylogeny'
Holland, BR and Jermiin, LS and Moulton, V (2006) 'Improved consensus network techniques for genome-scale phylogeny'. Molecular Biology and Evolution, 23 (5):848-855 [DOI] [Details]
(2006) 'A modern soft-bottom, shallow-water crinoid fauna (Echinodermata) from the Great Barrier Reef, Australia'
Messing, CG and Meyer, DL and Siebeck, UE and Jermiin, LS and Vaney, DI and Rouse, GW (2006) 'A modern soft-bottom, shallow-water crinoid fauna (Echinodermata) from the Great Barrier Reef, Australia'. Coral Reefs, 25 (1):164-168 [DOI] [Details]
(2006) 'Erratum: Exaggeration and suppression of iridescence: The evolution of two-dimensional butterfly structural colours (Journal of the Royal Society Interface (2005) 3(99-108) DOI: 10.1098/rsif.2005.0071)'
Wickham, S and Large, MCJ and Poladian, L and Jermiin, LS (2006) 'Erratum: Exaggeration and suppression of iridescence: The evolution of two-dimensional butterfly structural colours (Journal of the Royal Society Interface (2005) 3(99-108) DOI: 10.1098/rsif.2005.0071)'. Journal of the Royal Society Interface, 3 (11) [DOI] [Details]
(2006) 'Exaggeration and suppression of iridescence: The evolution of two-dimensional butterfly structural colours'
Wickham, S and Large, MCJ and Poladian, L and Jermiin, LS (2006) 'Exaggeration and suppression of iridescence: The evolution of two-dimensional butterfly structural colours'. Journal of the Royal Society Interface, 3 (6):99-109 [DOI] [Details]
(2006) 'Multi-objective evolutionary algorithms and phylogenetic inference with multiple data sets'
Poladian, L and Jermiin, LS (2006) 'Multi-objective evolutionary algorithms and phylogenetic inference with multiple data sets'. Soft Computing, 10 (4):359-368 [DOI] [Details]
(2005) 'Estimation of phylogeny using a general Markov model'
Jayaswal, V and Jermiin, LS and Robinson, J (2005) 'Estimation of phylogeny using a general Markov model'. Evolutionary Bioinformatics, 1 :62-80 [Details]
(2005) 'Is the big bang in animal evolution real?'
Jermiin, LS and Poladian, L and Charleston, MA (2005) 'Is the big bang in animal evolution real?'. Science, 310 (5756):1910-1911 [DOI] [Details]
(2005) 'Improving the analysis of dinoflagellate phylogeny based on rDNA'
Murray, S and Flø Jørgensen, M and Ho, SYW and Patterson, DJ and Jermiin, LS (2005) 'Improving the analysis of dinoflagellate phylogeny based on rDNA'. Protist, 156 (3):269-286 [DOI] [Details]
(2004) 'The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated'
Jermiin, LS and Ho, SYW and Ababneh, F and Robinson, J and Larkum, AWD (2004) 'The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated'. Systematic Biology, 53 (4):638-643 [DOI] [Details]
(2004) 'Tracing the decay of the historical signal in biological sequence data'
Ho, SYW and Jermiin, LS (2004) 'Tracing the decay of the historical signal in biological sequence data'. Systematic Biology, 53 (4):623-637 [DOI] [Details]
(2004) 'Evolution of vertebrate genes related to prion and shadoo proteins - Clues from comparative genomic analysis'
Premzl, M and Gready, JE and Jermiin, LS and Simonic, T and Marshall Graves, JA (2004) 'Evolution of vertebrate genes related to prion and shadoo proteins - Clues from comparative genomic analysis'. Molecular Biology and Evolution, 21 (12):2210-2231 [DOI] [Details]
(2004) 'Characterization of the type I interferon locus and identification of novel genes'
Hardy, MP and Owczarek, CM and Jermiin, LS and Ejdebäck, M and Hertzog, PJ (2004) 'Characterization of the type I interferon locus and identification of novel genes'. Genomics, 84 (2):331-345 [DOI] [Details]
(2004) 'Megafaunal extinction in the late Quaternary and the global overkill hypothesis'
Wroe, S and Field, J and Fullagar, R and Jermin, LS (2004) 'Megafaunal extinction in the late Quaternary and the global overkill hypothesis'. Alcheringa: An Australasian Journal of Palaeontology, 28 (1):291-331 [DOI] [Details]
(2004) 'Phylogenetic analysis using maximum likelihood methods in homogeneous parallel environments'
Till, M and Zhou, BB and Zomaya, A and Jermiin, LS (2004) 'Phylogenetic analysis using maximum likelihood methods in homogeneous parallel environments'. Lecture Notes in Computer Science, 3320 :274-279 [DOI] [Details]
(2003) 'Hetero: a program to simulate the evolution of DNA on a four-taxon tree'
Jermiin, LS and Ho, SYW and Ababneh, F and Robinson, J and Larkum, AWD (2003) 'Hetero: a program to simulate the evolution of DNA on a four-taxon tree'. Applied bioinformatics, 2 (3):159-163 [Details]
(2003) 'AMID: autonomous modeler of intragenic duplication'
Kummerfeld, SK and Weiss, AS and Fekete, A and Jermiin, LS (2003) 'AMID: autonomous modeler of intragenic duplication'. Applied bioinformatics, 2 (3):169-176 [Details]
(2003) 'Isolation and characterization of the mouse ubiquitin-specific protease Usp15'
Angelats, C and Wang, XW and Jermiin, LS and Copeland, NG and Jenkins, NA and Baker, RT (2003) 'Isolation and characterization of the mouse ubiquitin-specific protease Usp15'. Mammalian Genome, 14 (1):31-46 [DOI] [Details]
(2002) 'Evolutionary history of early-diverging eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia'
Simpson, AGB and Roger, AJ and Silberman, JD and Leipe, DD and Edgcomb, VP and Jermiin, LS and Patterson, DJ and Sogin, ML (2002) 'Evolutionary history of early-diverging eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia'. Molecular Biology and Evolution, 19 (10):1782-1791 [DOI] [Details]
(2002) 'Erratum: Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins, (Proceedings of the National Academy of Sciences of the United States of America (2001) 98:2 (537-542))'
Adcock, GJ and Dennis, ES and Easteal, S and Huttley, GA and Jermiin, LS and Peacock, WJ and Thorne, A (2002) 'Erratum: Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins, (Proceedings of the National Academy of Sciences of the United States of America (2001) 98:2 (537-542))'. Proceedings of the National Academy of Sciences of the United States of America, 99 (1) [Details]
(2001) 'Human origins and ancient human DNA - Response'
Adcock, GJ and Dennis, ES and Easteal, S and Huttley, GA and Jermiin, LS and Peacock, WJ and Thorne, A (2001) 'Human origins and ancient human DNA - Response'. Science, 292 (5522):1656-1656 [Details]
(2001) 'Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs'
Lahoud, MH and Ristevski, S and Venter, DJ and Jermiin, LS and Bertoncello, I and Zavarsek, S and Hasthorpe, S and Drago, J and De Kretser, D and Hertzog, PJ and Kola, I (2001) 'Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs'. Genome Research, 11 (8):1327-1334 [DOI] [Details]
(2001) 'Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins'
Adcock, GJ and Dennis, ES and Easteal, S and Huttley, GA and Jermiin, LS and Peacock, WJ and Thorne, A (2001) 'Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins'. Proceedings of the National Academy of Sciences of the United States of America, 98 (2):537-542 [DOI] [Details]
(2001) 'Characterization of the omega class glutathione transferases'
Board, PG and Coggan, M and Chelvanayagam, G and Easteal, S and Jermiin, LS and Schulte, GK and Danley, DE and Hoth, LR and Griffor, MC and Kamath, AV and Rosner, MH and Chrunyk, BA and Perregaux, DE and Gabel, CA and Geoghegan, KF and Pandit, J (2001) 'Characterization of the omega class glutathione transferases'. Chemico-Biological Interactions, 133 (1-3):204-206 [Details]
(2001) 'Many parallel losses of infa from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus'
Millen, RS and Olmstead, RG and Adams, KL and Palmer, JD and Lao, NT and Heggie, L and Kavanagh, TA and Hibberd, JM and Gray, JC and Morden, CW and Calie, PJ and Jermiin, LS and Wolfe, KH (2001) 'Many parallel losses of infa from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus'. The Plant Cell, 13 (3):645-658 [DOI] [Details]
(2001) 'Identification of novel glutathione transferases and polymorphic variants by expressed sequence tag database analysis'
Board, PG and Chelvanayagam, G and Jermiin, LS and Tetlow, N and Tzeng, HF and Anders, MW and Blackburn, AC (2001) 'Identification of novel glutathione transferases and polymorphic variants by expressed sequence tag database analysis'. Drug Metabolism and Disposition, 29 (4 II):544-547 [Details]
(2000) 'Identification, characterization, and crystal structure of the omega class glutathione transferases'
Board, PG and Coggan, M and Chelvanayagam, G and Easteal, S and Jermiin, LS and Schulte, GK and Danley, DE and Hoth, LR and Griffor, MC and Kamath, AV and Rosner, MH and Chrunyk, BA and Perregaux, DE and Gabel, CA and Geoghegan, KF and Pandit, J (2000) 'Identification, characterization, and crystal structure of the omega class glutathione transferases'. Journal of Biological Chemistry, 275 (32):24798-24806 [DOI] [Details]
(2000) 'TrExML: A maximum-likelihood approach for extensive tree-space exploration'
Wolf, MJ and Easteal, S and Kahn, M and McKay, BD and Jermiin, LS (2000) 'TrExML: A maximum-likelihood approach for extensive tree-space exploration'. Bioinformatics, 16 (4):383-394 [DOI] [Details]
(2000) 'A molecular framework for the phylogeny of the ant subfamily Dolichoderinae'
Chiotis, M and Jermiin, LS and Crozier, RH (2000) 'A molecular framework for the phylogeny of the ant subfamily Dolichoderinae'. Molecular Phylogenetics and Evolution, 17 (1):108-116 [DOI] [Details]
(2000) 'Identification and characterization of the Zeta class of glutathione transferases'
Board, PG and Chelvanyagam, G and Jermiin, LS and Blackburn, A (2000) 'Identification and characterization of the Zeta class of glutathione transferases'. Clinical Chemistry and Enzymology Communications, 8 (4-6):379-384 [Details]
(1999) 'Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium'
Jones, RA and Jermiin, LS and Easteal, S and Patel, BKC and Beacham, IR (1999) 'Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium'. Journal of Applied Microbiology, 86 (1):93-107 [DOI] [Details]
(1998) 'Accelerated evolution of cytochrome b in simian primates: Adaptive evolution in concert with other mitochondrial proteins?'
Andrews, TD and Jermiin, LS and Easteal, S (1998) 'Accelerated evolution of cytochrome b in simian primates: Adaptive evolution in concert with other mitochondrial proteins?'. Journal of Molecular Evolution, 47 (3):249-257 [DOI] [Details]
(1998) 'A novel transcription factor, ELF5, 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'
Zhou, J and Ng, AYN and Tymms, MJ and Jermiin, LS and Seth, AK and Thomas, RS and Kola, I (1998) 'A novel transcription factor, ELF5, 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 (21):2719-2732 [DOI] [Details]
(1997) 'Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria'
Foster, PG and Jermiin, LS and Hickey, DA (1997) 'Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria'. Journal of Molecular Evolution, 44 (3):282-288 [DOI] [Details]
(1997) 'Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis'
Jermiin, LS and Olsen, GJ and Mengersen, KL and Easteal, S (1997) 'Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis'. Molecular Biology and Evolution, 14 (12):1296-1302 [DOI] [Details]
(1997) 'Molecular evidence for a Jurassic origin of ants'
Crozier, RH and Jermiin, LS and Chiotis, M (1997) 'Molecular evidence for a Jurassic origin of ants'. Naturwissenschaften, 84 (1):22-23 [DOI] [Details]
(1997) 'Erratum: Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA (Journal of Molecular Evolution (1996) 42 (476-480))'
Jermiin, LS and Foster, PG and Graur, D and Lowe, RM and Crozier, RH (1997) 'Erratum: Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA (Journal of Molecular Evolution (1996) 42 (476-480))'. Journal of Molecular Evolution, 44 (4) [DOI] [Details]
(1997) 'Zeta, a novel class of glutathione transferases in a range of species from plants to humans'
Board, PG and Baker, RT and Chelvanayagam, G and Jermiin, LS (1997) 'Zeta, a novel class of glutathione transferases in a range of species from plants to humans'. Biochemical Journal, 328 (3):929-935 [DOI] [Details]
(1996) 'Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA'
Jermiin, LS and Foster, PG and Graur, D and Lowe, RM and Crozier, RH (1996) 'Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA'. Journal of Molecular Evolution, 42 (4):476-480 [DOI] [Details]
(1995) 'Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA'
Jermiin, LS and Graur, D and Crozier, RH (1995) 'Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA'. Molecular Biology and Evolution, 12 (4):558-563 [Details]
(1994) 'A comparative analysis of some life-history traits between cooperatively and non-cooperatively breeding Australian passerines'
Poiani, A and Jermiin, LS (1994) 'A comparative analysis of some life-history traits between cooperatively and non-cooperatively breeding Australian passerines'. Evolutionary Ecology, 8 (5):471-488 [DOI] [Details]
(1994) 'Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes'
Jermiin, LS and Graur, D and Lowe, RM and Crozier, RH (1994) 'Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes'. Journal of Molecular Evolution, 39 (2):160-173 [DOI] [Details]
(1994) 'The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: Sequence divergence in hymenoptera may be associated with nucleotide content'
Jermiin, LS and Crozier, RH (1994) 'The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: Sequence divergence in hymenoptera may be associated with nucleotide content'. Journal of Molecular Evolution, 38 (3):282-294 [DOI] [Details]
(1993) 'Counterselection on sex chromosomes in the Mus musculus European hybrid zone'
Dod, B and Jermiin, LS and Boursot, P and Chapman, VH and Nielsen, JT and Bonhomme, F (1993) 'Counterselection on sex chromosomes in the Mus musculus European hybrid zone'. Journal of Evolutionary Biology, 6 (4):529-546 [DOI] [Details]
(1993) 'Revised descriptions of the morphology of Trachyphloeus bifoveolatus, T. angustisetulus, T. spinimanus and T. digitalis (Coleoptera: Curculionidae)'
Jermiin, LS and Mahler, V (1993) 'Revised descriptions of the morphology of Trachyphloeus bifoveolatus, T. angustisetulus, T. spinimanus and T. digitalis (Coleoptera: Curculionidae)'. Entomologist's Gazette, 44 :139-153 [Details]
(1991) 'Changes in relative mobility of pancreatic amylase variants in isoelectric focusing'
Tomiuk, J and Jermiin, LS (1991) 'Changes in relative mobility of pancreatic amylase variants in isoelectric focusing'. Primates, 32 :119-123 [Details]
(1991) 'Electrophoretic and morphometric analyses of two sibling species pairs in Trachyphloeus (Coleoptera: Curculionidae)'
Jermiin, LS and Loeschcke, V and Simonsen, V and Mahler, V (1991) 'Electrophoretic and morphometric analyses of two sibling species pairs in Trachyphloeus (Coleoptera: Curculionidae)'. Entomologica Scandinavica, 22 (2):159-170 [DOI] [Details]

Book Chapters

  Year Publication
(2017) 'Identifying optimal models of evolution'
Jermiin, LS and Jayaswal, V and Ababneh, FM and Robinson, J (2017) 'Identifying optimal models of evolution' In: :379-420 Humana Press. [Details]
(2009) 'SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences'
Jermiin, LS and Ho, JWK and Lau, KW and Jayaswal, V (2009) 'SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences' In: :65-91 Humana Press. [Details]
(2008) 'Phylogenetic model evaluation'
Jermiin, L and Jayaswal, V and Ababneh, F and Robinson, J (2008) 'Phylogenetic model evaluation' In: :331-363 Humana Press. [Details]

Conference Publications

  Year Publication
(2007) 2007 IEEE Congress on Evolutionary Computation, CEC 2007
Jayaswal, V and Poladian, L and Jermiin, LS (2007) Single- and multi-objective phylogenetic analysis of primate evolution using a genetic algorithm 2007 IEEE Congress on Evolutionary Computation, CEC 2007 , pp.4146-4153 [Details]
(2007) Photosynthesis Research
Larkum, A and Ip, C and Chen, M and Jermiin, L (2007) Phylogeny of Prochlorococcus marinus: how is this species related to the rest of the Cyanobacteria? Photosynthesis Research , pp.272-273 [Details]
(2007) Photosynthesis Research
Larkum, A and Zhang, Y and Churdh, B and Jermiin, L (2007) Modelling the IsiA-PSI supermolecular complex of cyanobacteria Photosynthesis Research , pp.172-172 [Details]
(2007) 2007 IEEE Congress on Evolutionary Computation
Jayaswal, V and Poladian, L and Jermiin, LS (2007) Single- and multi-objective phylogenetic analysis of primate evolution using a genetic algorithm 2007 IEEE Congress on Evolutionary Computation , pp.4146-4153 [Details]
(2005) IQEC, International Quantum Electronics Conference Proceedings
Large, M and Wickham, S and Poladian, L and Jermiin, LS (2005) Iridescence control in low contrast biological microstructures IQEC, International Quantum Electronics Conference Proceedings , pp.357-359 [Details]
(2004) Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2004 (Abstracts and CD-ROM)
Zhou, BB and Till, M and Zomaya, A and Jermiin, LS (2004) Parallel implementation of maximum likelihood methods for phylogenetic analysis Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2004 (Abstracts and CD-ROM) , pp.3269-3274 [Details]
(1998) Toxicology Letters
Board, P and Blackburn, A and Jermiin, LS and Chelvanayagam, G (1998) Polymorphism of phase II enzymes: Identification of new enzymes and polymorphic variants by database analysis Toxicology Letters , pp.149-154 [Details]

Honours and Awards

  Year Title Awarding Body
2009 OCE Science Leader Commonwealth Scientific and Industrial Research Organisation (CSIRO)
1998 U2000 Research Fellow University of Sydney

Professional Associations

  Association Function From / To
Systematic Biology Associate Editor 01-JAN-07 / 31-DEC-23
Molecular Biology and Evolution Editor 01-JAN-13 / 31-DEC-17

Patents

  Patent Number Title Granted
AU2014280850A1 Transaminase Biocatalysts 14-JUN-14

Education

  Year Institution Qualification Subject
1994 La Trobe University PhD Molecular Evolution
1989 Aarhus University MSc Population Genetics

Languages

  Language
English
Danish

Modules Taught

  Term/Year Module Title Module Code Subject / Desc
2023-2024 Programming for Biologists MA5114
2023-2024 Introduction to Bioinformatics MA324