Profiles

Barbara Holland

Professor Barbara Holland

Barbara Holland

Professor in Mathematics

Room 460 , Maths-Physics Building

+61 3 6226 1990 (phone)

Barbara.Holland@utas.edu.au

Barbara Holland is a Professor in the discipline of Mathematics within the School of Natural Sciences at the University of Tasmania, Australia. She lectures mostly in Statistics.

Barbara applies mathematics and statistics to problems in evolutionary biology or population genetics. In particular, her research has focused on problems in phylogenetics. She is interested in developing tools that can assess if sequence data is well explained by a simple tree model or if more complex processes such as hybridisation, recombination or convergent selection are at work. The areas of mathematics/statistics that she uses frequently include stochastic models, continuous time Markov chains, combinatorial optimization, maximum likelihood, and simulation.

Biography

Barbara completed a PhD in Mathematical Biology at Massey University in New Zealand followed by postdoctoral studies at the Ruhr Universität Bochum (Germany) and in the Allan Wilson Centre for Molecular Ecology and Evolution (New Zealand). Prior to joining the University of Tasmania she worked as a Mathematics lecturer and researcher at Massey University.

Since beginning her PhD she has enjoyed the challenge of working with biologists in trying to translate the problems they face into the language of mathematics. Biology is awash with data since the advent of DNA sequencing technology and this has opened up a range of very interesting research questions that require a combination of skills from mathematics, biology and computer science.

Career summary

Qualifications

Degree	Thesis Title	University	Country	Date of Award
PhD	Evolutionary analyses of large data sets: Trees and beyond	Massey University	New Zealand	11/2/2002
BInfSc (1^st Class Hons)		Massey University	New Zealand	31/12/1997
BSc		Massey University	New Zealand	31/12/1996

Memberships

Professional practice

Society of Systematic Biologists
Society for Molecular Biology and Evolution

Administrative expertise

Barbara is currently the co-Associate Head of Research for the School of Natural Sciences. She has previously been the head of the Discipline for Mathematics.

Teaching

Statistics, Operations Research, Phylogenetics

Teaching expertise

At the undergraduate level Barbara teaches mostly in Statistics.

Teaching responsibility

Mathematics discipline

KMA153 - Data Handling and Statistics 1 (Unit coordinator, Semester 1)
KMA253 - Data Handling and Statistics 2 (Unit coordinator, Semester 2)
KMA457 - Advanced Topics in Mathematical Biology (Contributor, occasionally coordinator)
XBR105 – Good thinking: Reasoning skills for Life (Breadth unit, co-taught with Philosophy)
BEA140 - Data Analysis for Business (Contributor)

Research Appointments

2013: Elected to council of Society of Systematic Biologists

Research Invitations

Invited participant Workshop of Phylogenomics and Evolutionary Networks (Sumner, March, 2020)
Invited speaker, Workshop on Mathematical and Statistical Challenges in Bridging Model Development, Parameter Identification and Model Selection in the Biological Sciences. (Banff International Research Station for Mathematical Innovation and Discovery, Banff, Canada, November 2018) “Assessing model adequacy in phylogenetics”
Invited Speaker, MCEB (Porquerolles, France, June 2017) “Desirable properties of models for phylogenetic analysis”
Invited Speaker, Royal Society of Tasmania Winter Lecture Series (Hobart, July 2016) “Embracing uncertainty in Molecular Evolution”
Invited Speaker, BioInfoSummner (Adelaide, December, 2014) 'Introduction to Phylogenetic Methods'
Invited speaker and workshop leader, NSF/ CBMS conference Mathematical Phylogeny (Rockhill SC, June, 2014) 'Testing phylogenetic models – how bad and bad how? Residual diagnostics for phylogenetics'
Symposium speaker, Society for Molecular Biology and Evolution (San Juan, Puerto Rico, June, 2014) 'Markov models of convergent evolution'
Invited Speaker, BioInfoSummner (Adelaide, December, 2013) 'Introduction to Phylogenetic Methods'
Invited participant at Cass Workshop on Networks of Life. Cass, New Zealand. 'Modelling convergence' (Feb 2013)
Invited speaker at Massey University, New Zealand (joint talk to the Institute of Fundamental Sciences and Institute of Veterinary, Animal, and Biomedical Sciences) entitled 'A tour of recent work by the Phylomanians'
Invited speaker at the School of Mathematics, University of Adelaide, Australia. Current statistical challenges for molecular phylogenetics (May, 2011)
Keynote speaker at the Isaac Newton Institute for Mathematical Sciences, Cambridge, UK. Workshop on Phylogenetics: New data new challenges. Phylogenies from DArTs: A stochastic Dollo process with censored data (June, 2011)

View more on Professor Barbara Holland in WARP

Expertise

Phylogenetics
Mathematical biology
Evolutionary Biology

Research Themes

Barbara's main interests are in mathematical phylogenetics, which deals with the estimation of evolutionary trees (family trees for species). Molecular phylogenetics uses patterns in DNA sequence data to make inferences about how different species are related to each other and to uncover information about the processes of evolution. Statistical modelling of sequence data has many applications within health, agriculture and conservation.

Collaboration

Barbara’s international collaborators include David Liberles (Temple University), Vincent Moulton & Katharina Huber (University of East Anglia), Lars Jermiin (university College Dublin), Arndt von Haeseler (University of Vienna).

Within Australia she has collaborated with Andrew Francis (Western Sydney University), Nigel Bean, Jono Tuke and Stephen Crotty (University of Adelaide), David Lambert (Griffith)

At the University of Tasmania Barbara enjoys getting across Churchill Road to work with colleagues in Biological Sciences such as Bec Jones and Greg Jordan. In her own corridor her main collaborators are Jeremy Sumner, Malgorzata O’Reilly and Mike Charleston.

Awards

2010: ARC funded Future Fellowship
2008: New Zealand Mathematics Society Early Career Award
2005: Royal Society of New Zealand, Hamilton Award

Current projects

My current research interests include:

Phylogenetic approaches to associating genotype with phenotype
Stochastic models of gene family evolution
Stochastic models of gene network evolution, detecting homology between biological networks
Modelling convergent evolution

Fields of Research

Biological mathematics (490102)
Phylogeny and comparative analysis (310410)
Stochastic analysis and modelling (490510)
Microbial genetics (310704)
Molecular evolution (310510)
Applications in life sciences (460103)
Biostatistics (490502)
Biological adaptation (310403)
Genetics (310599)
Microbial ecology (310703)
Curriculum and pedagogy theory and development (390102)
Professional education and training (390305)
Plant physiology (310806)
Biogeography and phylogeography (310402)
Epidemiology (420299)
Host-parasite interactions (310407)
Proteins and peptides (340407)
Astronomical sciences (510199)
Bioinformatic methods development (310201)
Plant biology (310899)
Behavioural ecology (310301)
Environmental management (410499)
Structural biology (incl. macromolecular modelling) (310112)
Artificial life and complex adaptive systems (460201)
Statistics (490599)
Biological network analysis (310202)
Cellular interactions (incl. adhesion, matrix, cell wall) (310105)
Archaeological science (430101)
Galactic astronomy (510104)
Plant and fungus systematics and taxonomy (310411)
Palaeoclimatology (370904)
Lie groups, harmonic and Fourier analysis (490406)
Algebra and number theory (490401)
Speciation and extinction (310412)
Signal transduction (310111)
Evolutionary impacts of climate change (310406)
Plant biochemistry (310802)
Genomics (310509)
Race, ethnicity and law (480413)
Teacher education and professional development of educators (390307)
Higher education (390303)
Genetic immunology (310507)
Computational ecology and phylogenetics (310203)
Statistical theory (490509)

Research Objectives

Expanding knowledge in the biological sciences (280102)
Expanding knowledge in the mathematical sciences (280118)
Terrestrial biodiversity (180606)
Expanding knowledge in the physical sciences (280120)
Barley (260301)
Expanding knowledge in the environmental sciences (280111)
Professional development and adult education (160104)
Learner and learning (160199)
Expanding knowledge in the health sciences (280112)
Expanding knowledge in history, heritage and archaeology (280113)
Religious structures (130504)
Expanding knowledge in psychology (280121)
Pedagogy (160302)
Expanding knowledge in the agricultural, food and veterinary sciences (280101)
Air quality (180101)
Native forests (260204)
Effects of climate change on Antarctic and sub-Antarctic environments (excl. social impacts) (190503)
Public health (excl. specific population health) (200499)
Ecosystem adaptation to climate change (190102)
Teacher and instructor development (160303)
Information systems, technologies and services (220499)
Assessment, development and evaluation of curriculum (160301)
Expanding knowledge in the earth sciences (280107)

Publications

Barbara publishes in a mix of more mathematical and more biological journals. She peaked too soon by getting her name on a Science paper back when she was doing a PhD. Since then she's always particularly pleased to get her work into Systematic Biology or Molecular Biology and Evolution.

Barbara is currently an Associate Editor for Genome Biology and evolution and a Handling Editor (Applications) for the Australia and New Zealand Journal of Statistics.

Total publications

111

Highlighted publications

(11 outputs)

Year	Type	Citation
2010	Journal Article	Holland BR, Spencer HG, Worthy TH, Kennedy M, 'Identifying Cliques of Convergent Characters: Concerted Evolution in the Cormorants and Shags', Systematic Biology, 59, (4) pp. 433-445. ISSN 1063-5157 (2010) [Refereed Article] DOI: 10.1093/sysbio/syq023 [eCite] [Details] Citations: Scopus - 42Web of Science - 43 Tweet
2008	Journal Article	Holland BR, Benthin S, Lockhart PJ, Moulton V, Huber KT, 'Using supernetworks to distinguish hybridization from lineage-sorting', BMC Evolutionary Biology, 8, (1) EJ ISSN 1471-2148 (2008) [Refereed Article] DOI: 10.1186/1471-2148-8-202 [eCite] [Details] Citations: Scopus - 96Web of Science - 94 Tweet
2007	Journal Article	Holland BR, Conner G, Huber K, Moulton V, 'Imputing Supertrees and Supernetworks from Quartets', Systematic Biology, 56, (1) pp. 57-67. ISSN 1063-5157 (2007) [Refereed Article] DOI: 10.1080/10635150601167013 [eCite] [Details] Citations: Scopus - 35Web of Science - 30 Tweet
2006	Journal Article	Holland BR, Jermiin LS, Moulton V, 'Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny', Molecular Biology and Evolution, 23, (5) pp. 848-855. ISSN 0737-4038 (2006) [Refereed Article] DOI: 10.1093/molbev/msj061 [eCite] [Details] Citations: Scopus - 30Web of Science - 30 Tweet
2005	Journal Article	Goremykin V, Holland BR, Hirsch-Ernst KI, Hellwig FH, 'Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications', Molecular Biology and Evolution, 22, (9) pp. 1813-1822. ISSN 0737-4038 (2005) [Refereed Article] DOI: 10.1093/molbev/msi173 [eCite] [Details] Citations: Scopus - 120Web of Science - 120 Tweet
2005	Journal Article	Kennedy M, Holland BR, Gray RD, Spencer HG, 'Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks', Systematic Biology, 54, (4) pp. 620-633. ISSN 1063-5157 (2005) [Refereed Article] DOI: 10.1080/106351591007462 [eCite] [Details] Citations: Scopus - 51Web of Science - 49 Tweet
2004	Journal Article	Holland BR, Huber KT, Moulton V, Lockhart PJ, 'Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny', Molecular Biology and Evolution, 21, (7) pp. 1459-1461. ISSN 0737-4038 (2004) [Refereed Article] DOI: 10.1093/molbev/msh145 [eCite] [Details] Citations: Scopus - 141Web of Science - 130 Tweet
2003	Conference Publication	Holland BR, Moulton V, 'Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees', Algorithms in Bioinformatics, 15-20 September 2003, Budapest, Hungary, pp. 165-176. ISBN 3-540-20076-2 (2003) [Refereed Conference Paper] [eCite] [Details]
2003	Journal Article	Holland BR, Penny D, Hendy MD, 'Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study', Systematic Biology, 52, (2) pp. 229-238. ISSN 1063-5157 (2003) [Refereed Article] DOI: 10.1080/10635150390192771 [eCite] [Details] Citations: Web of Science - 109 Tweet
2002	Journal Article	Lambert DM, Ritchie PA, Millar CD, Holland BR, Drummond AJ, et al., 'Rates of Evolution in Ancient DNA from Adelie Penguins', Science, 295, (5563) pp. 2270-2273. ISSN 0036-8075 (2002) [Refereed Article] DOI: 10.1126/science.1068105 [eCite] [Details] Citations: Scopus - 239Web of Science - 233 Tweet
2000	Journal Article	Chor B, Hendy MD, Holland BR, Penny D, 'Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach', Molecular Biology and Evolution, 17, (10) pp. 1529-1541. ISSN 0737-4038 (2000) [Refereed Article] DOI: 10.1093/oxfordjournals.molbev.a026252 [eCite] [Details] Citations: Scopus - 72Web of Science - 65 Tweet

Journal Article

(92 outputs)

Year	Citation	Altmetrics
2023	Liu Qin, Charleston MA, Richards SA, Holland BR, 'Performance of AIC and BIC in selecting Partition Models and Mixture Models', Systematic biology pp. 1-29. ISSN 1076-836X (2023) [Refereed Article] DOI: 10.1093/sysbio/syac081 [eCite] [Details] Citations: Web of Science - 6 Co-authors: Liu Qin; Charleston MA; Richards SA Tweet
2023	Stevenson J, Holland B, Charleston M, Sumner J, 'Evaluation of the RelatiPerformance of the Subflattenings Method for Phylogenetic Inference', Bulletin of Mathematical Biology, 85, (19) pp. 1-23. ISSN 1522-9602 (2023) [Refereed Article] DOI: 10.1007/s11538-023-01120-z [eCite] [Details] Co-authors: Stevenson J; Charleston M; Sumner J Tweet
2023	Sykes J, Holland BR, Charleston MA, 'A review of visualisations of protein fold networks and their relationship with sequence and function', Biological reviews of the Cambridge Philosophical Society, 98, (1) pp. 243-262. ISSN 1469-185X (2023) [Refereed Article] DOI: 10.1111/brv.12905 [eCite] [Details] Citations: Scopus - 1 Co-authors: Sykes J; Charleston MA Tweet
2022	Crotty SM, Holland BR, 'Comparing partitioned models to mixture models: do information criteria apply?', Systematic Biology, 71, (6) pp. 1541-1548. ISSN 1063-5157 (2022) [Refereed Article] DOI: 10.1093/sysbio/syac003 [eCite] [Details] Citations: Scopus - 3Web of Science - 5 Tweet
2022	Diao J, O'Reilly MM, Holland B, 'A subfunctionalisation model of gene family evolution predicts balanced tree shapes', Molecular Phylogenetics and Evolution, 176 Article 107566. ISSN 1055-7903 (2022) [Refereed Article] DOI: 10.1016/j.ympev.2022.107566 [eCite] [Details] Co-authors: Diao J; O'Reilly MM Tweet
2022	Soewongsono AC, Holland BR, O'Reilly MM, 'The shape of phylogenies under phase-type distributed times to speciation and extinction', Bulletin of Mathematical Biology, 84 Article 118. ISSN 0092-8240 (2022) [Refereed Article] DOI: 10.1007/s11538-022-01072-w [eCite] [Details] Co-authors: Soewongsono AC; O'Reilly MM Tweet
2022	Sykes J, Holland B, Charleston M, 'Unattained geometric configurations of secondary structure elements in protein structural space', Journal of Structural Biology, 214 Article 107870. ISSN 1047-8477 (2022) [Refereed Article] DOI: 10.1016/j.jsb.2022.107870 [eCite] [Details] Co-authors: Sykes J; Charleston M Tweet
2020	Abera A, O'Reilly MM, Fackrell M, Holland BR, Heydar M, 'On the decision support model for the patient admission scheduling problem with random arrivals and departures: A solution approach', Stochastic Models, 36, (2) pp. 312-336. ISSN 1532-6349 (2020) [Refereed Article] DOI: 10.1080/15326349.2020.1742161 [eCite] [Details] Citations: Scopus - 2Web of Science - 2 Co-authors: Abera A; O'Reilly MM; Heydar M Tweet
2020	Brown MJM, Holland B, Jordan GJ, 'Hyperoverlap: detecting biological overlap in n-dimensional space', Methods in Ecology and Evolution ISSN 2041-210X (2020) [Refereed Article] DOI: 10.1111/2041-210X.13363 [eCite] [Details] Citations: Scopus - 10Web of Science - 10 Co-authors: Brown MJM; Jordan GJ Tweet
2020	Hatisaru V, Oates G, Fraser S, Murphy C, Maher N, et al., 'A peer learning circle approach to professional learning: Promoting representational fluency', Australian Mathematics Education Journal, 2, (4) pp. 4-10. ISSN 2652-0176 (2020) [Refereed Article] [eCite] [Details] Co-authors: Hatisaru V; Oates G; Fraser S; Murphy C; Maher N; Seen A
2020	Holland BR, Ketelaar-Jones S, O'Mara AR, Woodhams MD, Jordan GJ, 'Accuracy of ancestral state reconstruction for non-neutral traits', Scientific Reports, 10, (1) Article 7644. ISSN 2045-2322 (2020) [Refereed Article] DOI: 10.1038/s41598-020-64647-4 [eCite] [Details] Citations: Scopus - 13Web of Science - 13 Co-authors: Ketelaar-Jones S; O'Mara AR; Woodhams MD; Jordan GJ Tweet
2020	Jermiin LS, Catullo RA, Holland BR, 'A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics', NAR Genomics and Bioinformatics, 2, (2) pp. 1-14. ISSN 2631-9268 (2020) [Refereed Article] DOI: 10.1093/nargab/lqaa041 [eCite] [Details] Citations: Scopus - 8Web of Science - 9 Tweet
2020	Jordan GJ, Carpenter RJ, Holland BR, Beeton NJ, Woodhams MD, et al., 'Links between environment and stomatal size through evolutionary time in Proteaceae', Proceedings of the Royal Society of London. Biological Sciences, 287, (1919) Article 20192876. ISSN 0962-8452 (2020) [Refereed Article] DOI: 10.1098/rspb.2019.2876 [eCite] [Details] Citations: Scopus - 5Web of Science - 5 Co-authors: Jordan GJ; Carpenter RJ; Beeton NJ; Woodhams MD; Brodribb TJ Tweet
2020	Shore JA, Holland BR, Sumner JG, Nieselt K, Wills PR, 'The ancient operational code is embedded in the amino acid substitution matrix and aaRS phylogenies', Journal of Molecular Evolution, 88, (2) pp. 136-150. ISSN 0022-2844 (2020) [Refereed Article] DOI: 10.1007/s00239-019-09918-z [eCite] [Details] Citations: Scopus - 4Web of Science - 5 Co-authors: Shore JA; Sumner JG Tweet
2020	Shore JA, Sumner JG, Holland BR, 'The impracticalities of multiplicativelyclosed codon models: a retreat to linear alternatives', Journal of Mathematical Biology pp. 1-25. ISSN 0303-6812 (2020) [Refereed Article] DOI: 10.1007/s00285-020-01519-5 [eCite] [Details] Co-authors: Shore JA; Sumner JG Tweet
2020	Sykes J, Holland BR, Charleston MA, 'Benchmarking methods of protein structure alignment', Journal of Molecular Evolution, 88, (7) pp. 575-597. ISSN 0022-2844 (2020) [Refereed Article] DOI: 10.1007/s00239-020-09960-2 [eCite] [Details] Citations: Scopus - 4Web of Science - 4 Co-authors: Sykes J; Charleston MA Tweet
2019	Crotty SM, Minh BQ, Bean NG, Holland BR, Tuke J, et al., 'GHOST: Recovering historical signal from heterotachously-evolved sequence alignments', Systematic Biology, 69, (2) Article syz051. ISSN 1063-5157 (2019) [Refereed Article] DOI: 10.1093/sysbio/syz051 [eCite] [Details] Citations: Scopus - 60Web of Science - 59 Tweet
2019	Diao J, Stark TL, Liberles DA, O'Reilly MM, Holland BR, 'Level-dependent QBD models for the evolution of a family of gene duplicates', Stochastic Models pp. 1-28. ISSN 1532-6349 (2019) [Refereed Article] DOI: 10.1080/15326349.2019.1680296 [eCite] [Details] Citations: Scopus - 1Web of Science - 1 Co-authors: Diao J; O'Reilly MM Tweet
2019	Wasef S, Subramanian S, O'Rorke R, Huynen L, El-Marghani S, et al., 'Mitogenomic diversity in Sacred Ibis mummies sheds light on early Egyptian practices', PLoS One, 14, (11) Article e0223964. ISSN 1932-6203 (2019) [Refereed Article] DOI: 10.1371/journal.pone.0223964 [eCite] [Details] Citations: Scopus - 10Web of Science - 11 Tweet
2018	Bruniche-Olsen A, Jones ME, Burridge CP, Murchison EP, Holland BR, et al., 'Ancient DNA tracks the mainland extinction and island survival of the Tasmanian devil', Journal of Biogeography, 45, (5) pp. 963-976. ISSN 0305-0270 (2018) [Refereed Article] DOI: 10.1111/jbi.13214 [eCite] [Details] Citations: Scopus - 12Web of Science - 13 Co-authors: Jones ME; Burridge CP Tweet
2018	Mitchell JD, Sumner JG, Holland BR, 'Distinguishing between convergent evolution and violation of the molecular clock for three taxa', Systematic Biology, 67, (5) pp. 905-915. ISSN 1063-5157 (2018) [Refereed Article] DOI: 10.1093/sysbio/syy038 [eCite] [Details] Citations: Scopus - 2Web of Science - 1 Co-authors: Mitchell JD; Sumner JG Tweet
2017	Halliwell B, Uller T, Holland BR, While GM, 'Live bearing promotes the evolution of sociality in reptiles', Nature Communications, 8 Article 2030. ISSN 2041-1723 (2017) [Refereed Article] DOI: 10.1038/s41467-017-02220-w [eCite] [Details] Citations: Scopus - 29Web of Science - 28 Co-authors: Halliwell B; While GM Tweet
2017	Serdoz S, Egri-Nagy A, Sumner J, Holland BR, Jarvis PD, et al., 'Maximum likelihood estimates of pairwise rearrangement distances', Journal of Theoretical Biology, 423 pp. 31-40. ISSN 0022-5193 (2017) [Refereed Article] DOI: 10.1016/j.jtbi.2017.04.015 [eCite] [Details] Citations: Scopus - 10Web of Science - 10 Co-authors: Sumner J; Jarvis PD Tweet
2017	Stark TL, Liberles DA, Holland BR, O'Reilly MM, 'Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization', BMC Evolutionary Biology, 17, (38) pp. 1-16. ISSN 1471-2148 (2017) [Refereed Article] DOI: 10.1186/s12862-016-0848-0 [eCite] [Details] Citations: Scopus - 8Web of Science - 9 Co-authors: Stark TL; O'Reilly MM Tweet
2017	Steane DA, Potts BM, McLean EH, Collins L, Holland BR, et al., 'Genomic scans across three eucalypts suggest that adaptation to aridity is a genome-wide phenomenon', Genome Biology and Evolution, 9, (2) pp. 253-265. ISSN 1759-6653 (2017) [Refereed Article] DOI: 10.1093/gbe/evw290 [eCite] [Details] Citations: Scopus - 22Web of Science - 23 Co-authors: Steane DA; Potts BM; Vaillancourt RE Tweet
2017	Sumner JG, Taylor A, Holland BR, Jarvis PD, 'Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants', Journal of Mathematical Biology, 75, (6-7) pp. 1619-1654. ISSN 0303-6812 (2017) [Refereed Article] DOI: 10.1007/s00285-017-1129-2 [eCite] [Details] Citations: Scopus - 3Web of Science - 3 Co-authors: Sumner JG; Jarvis PD Tweet
2017	Worth JRP, Holland BR, Beeton NJ, Schonfeld B, Rossetto M, et al., 'Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway', Annuals of Botany, 120, (4) pp. 539-549. ISSN 0305-7364 (2017) [Refereed Article] DOI: 10.1093/aob/mcx086 [eCite] [Details] Citations: Scopus - 13Web of Science - 13 Co-authors: Beeton NJ; Schonfeld B; Vaillancourt RE; Jordan GJ Tweet
2016	Bruniche-Olsen A, Austin JJ, Jones ME, Holland BR, Burridge CP, 'Detecting selection on temporal and spatial scales: a genomic time-series assessment of selective responses to devil facial tumor disease', PLoS One, 11, (3) Article e0147875. ISSN 1932-6203 (2016) [Refereed Article] DOI: 10.1371/journal.pone.0147875 [eCite] [Details] Citations: Scopus - 13Web of Science - 13 Co-authors: Jones ME; Burridge CP Tweet
2016	Humphries MA, Bruno R, Lai FY, Thai PK, Holland BR, et al., 'Evaluation of monitoring schemes for wastewater-based epidemiology to identify drug use trends using cocaine, methamphetamine, MDMA and methadone', Environmental Science and Technology, 50, (9) pp. 4760-4768. ISSN 0013-936X (2016) [Refereed Article] DOI: 10.1021/acs.est.5b06126 [eCite] [Details] Citations: Scopus - 17Web of Science - 15 Co-authors: Humphries MA; Bruno R Tweet
2016	Manning EM, Holland BR, Ellingsen SP, Breen SL, Chen X, et al., 'Comparison of three statistical classification techniques for maser identification', Publications of the Astronomical Society of Australia, 33 Article e015. ISSN 1448-6083 (2016) [Refereed Article] DOI: 10.1017/pasa.2016.13 [eCite] [Details] Citations: Scopus - 2Web of Science - 2 Co-authors: Manning EM; Ellingsen SP; Humphries M Tweet
2016	Schmid J, Magee PT, Holland BR, Zhang N, Cannon RD, et al., 'Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans', Current Genetics, 62, (1) pp. 81-85. ISSN 0172-8083 (2016) [Refereed Article] DOI: 10.1007/s00294-015-0516-8 [eCite] [Details] Citations: Scopus - 6Web of Science - 5 Tweet
2016	Woodhams MD, Lockhart PJ, Holland BR, 'Simulating and summarizing sources of gene tree incongruence', Genome Biology and Evolution, 8, (5) pp. 1299-1315. ISSN 1759-6653 (2016) [Refereed Article] DOI: 10.1093/gbe/evw065 [eCite] [Details] Citations: Scopus - 8Web of Science - 7 Co-authors: Woodhams MD Tweet
2015	Fearnhead P, Yu S, Biggs P, Holland B, French N, 'Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods', The Annals of Applied Statistics, 9, (1) pp. 200-224. ISSN 1932-6157 (2015) [Refereed Article] DOI: 10.1214/14-AOAS795 [eCite] [Details] Citations: Scopus - 3Web of Science - 3 Tweet
2015	Larcombe MJ, Holland B, Steane DA, Jones RC, Nicolle D, et al., 'Patterns of reproductive isolation in Eucalyptus - a phylogenetic perspective', Molecular Biology and Evolution, 32, (7) pp. 1833-1846. ISSN 0737-4038 (2015) [Refereed Article] DOI: 10.1093/molbev/msv063 [eCite] [Details] Citations: Scopus - 44Web of Science - 45 Co-authors: Larcombe MJ; Steane DA; Jones RC; Vaillancourt RE; Potts BM Tweet
2015	Wasef S, Wood R, El Merghani S, Ikram S, Curtis C, et al., 'Radiocarbon dating of Sacred Ibis mummies from ancient Egypt', Journal of Archaeological Science: Reports, 4 pp. 355-361. ISSN 2352-409X (2015) [Refereed Article] DOI: 10.1016/j.jasrep.2015.09.020 [eCite] [Details] Citations: Scopus - 11 Tweet
2015	Zhang N, Magee BB, Magee PT, Holland BR, Rodrigues E, et al., 'Selective advantages of a parasexual cycle for the yeast Candida albicans', Genetics, 200, (4) pp. 1117-1132. ISSN 1943-2631 (2015) [Refereed Article] DOI: 10.1534/genetics.115.177170 [eCite] [Details] Citations: Scopus - 20Web of Science - 17 Tweet
2014	Baxter RB, Dobbie PD, Parker QA, Casewell SL, Lodieu N, et al., 'Component masses of young, wide, non-magnetic white dwarf binaries in the Sloan Digital Sky Survey Data Release 7', Monthly Notices of the Royal Astronomical Society, 440, (4) pp. 3184-3201. ISSN 0035-8711 (2014) [Refereed Article] DOI: 10.1093/mnras/stu464 [eCite] [Details] Citations: Scopus - 10Web of Science - 14 Co-authors: Dobbie PD Tweet
2014	Binney BM, Biggs PJ, Carter PE, Holland BR, French NP, 'Quantification of historical livestock importation into New Zealand 1860-1979', New Zealand Veterinary Journal, 62, (6) pp. 309-314. ISSN 0048-0169 (2014) [Refereed Article] DOI: 10.1080/00480169.2014.914861 [eCite] [Details] Citations: Scopus - 9Web of Science - 7 Tweet
2014	Bruniche-Olsen A, Jones ME, Austin JJ, Burridge CP, Holland BR, 'Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease', Biology Letters, 10, (11) Article 20140619. ISSN 1744-9561 (2014) [Refereed Article] DOI: 10.1098/rsbl.2014.0619 [eCite] [Details] Citations: Scopus - 53Web of Science - 52 Co-authors: Jones ME; Burridge CP Tweet
2014	Harris RL, Holland BR, Cameron EZ, Davies NW, Nicol SC, 'Chemical signals in the echidna: differences between seasons, sexes, individuals and gland types', Journal of Zoology, 293, (3) pp. 171-180. ISSN 0952-8369 (2014) [Refereed Article] DOI: 10.1111/jzo.12133 [eCite] [Details] Citations: Scopus - 11Web of Science - 11 Co-authors: Harris RL; Cameron EZ; Davies NW; Nicol SC Tweet
2014	Sumner JG, Jarvis PD, Holland BR, 'A tensorial approach to the inversion of group-based phylogenetic models', BMC Evolutionary Biology, 14 Article 236. ISSN 1471-2148 (2014) [Refereed Article] DOI: 10.1186/s12862-014-0236-6 [eCite] [Details] Citations: Scopus - 1Web of Science - 1 Co-authors: Sumner JG; Jarvis PD Tweet
2013	Blanke A, Greve C, Wipfler B, Beutel R, Holland BR, et al., 'The identification of concerted convergence in insect heads corroborates Palaeoptera', Systematic Biology, 62, (2) pp. 250-263. ISSN 1063-5157 (2013) [Refereed Article] DOI: 10.1093/sysbio/sys091 [eCite] [Details] Citations: Scopus - 29Web of Science - 34 Tweet
2013	Cox MP, Holland BR, Wilkins MC, Schmid J, 'Reconstructing past changes in locus-specific recombination rates', BMC Genetics, 14 Article 11. ISSN 1471-2156 (2013) [Refereed Article] DOI: 10.1186/1471-2156-14-11 [eCite] [Details] Citations: Scopus - 3Web of Science - 4 Tweet
2013	Grievink LS, Penny D, Holland BR, 'Missing data and influential sites: Choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice', Genome Biology and Evolution, 5, (4) pp. 681-687. ISSN 1759-6653 (2013) [Refereed Article] DOI: 10.1093/gbe/evt032 [eCite] [Details] Citations: Scopus - 14Web of Science - 13 Tweet
2013	Holland BR, 'The rise of statistical phylogenetics', Australian and New Zealand Journal of Statistics, 55, (3) pp. 205-220. ISSN 1369-1473 (2013) [Refereed Article] DOI: 10.1111/anzs.12035 [eCite] [Details] Citations: Scopus - 4Web of Science - 4 Tweet
2013	Holland BR, Jarvis PD, Sumner JG, 'Low-parameter phylogenetic inference under the general Markov model', Systematic Biology, 62, (1) pp. 78-92. ISSN 1063-5157 (2013) [Refereed Article] DOI: 10.1093/sysbio/sys072 [eCite] [Details] Citations: Scopus - 22Web of Science - 21 Co-authors: Jarvis PD; Sumner JG Tweet
2013	Mohan V, Stevenson M, Marshall J, Fearnhead P, Holland BR, et al., 'Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand', MicrobiologyOpen, 2, (4) pp. 659-673. ISSN 2045-8827 (2013) [Refereed Article] DOI: 10.1002/mbo3.102 [eCite] [Details] Citations: Scopus - 20Web of Science - 19 Tweet
2013	Woodhams M, Steane DA, Jones RC, Nicolle D, Moulton V, et al., 'Novel distances for Dollo data', Systematic Biology, 62, (1) pp. 62-77. ISSN 1063-5157 (2013) [Refereed Article] DOI: 10.1093/sysbio/sys071 [eCite] [Details] Citations: Scopus - 24Web of Science - 24 Co-authors: Woodhams M; Steane DA; Jones RC Tweet
2012	Eytan RI, Hastings PA, Holland BR, Hellberg ME, 'Reconciling molecules and morphology: Molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria)', Molecular Phylogenetics and Evolution, 62, (1) pp. 159-173. ISSN 1055-7903 (2012) [Refereed Article] DOI: 10.1016/j.ympev.2011.09.028 [eCite] [Details] Citations: Scopus - 12Web of Science - 12 Tweet
2012	Johnson KA, Holland BR, Heslewood MM, Crayn DM, 'Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data', Molecular Phylogenetics and Evolution, 62, (1) pp. 146-158. ISSN 1055-7903 (2012) [Refereed Article] DOI: 10.1016/j.ympev.2011.09.011 [eCite] [Details] Citations: Scopus - 17Web of Science - 17 Co-authors: Johnson KA Tweet
2012	Saurabh K, Holland BR, Gibb GC, Penny D, 'Gaps: an elusive source of phylogenetic information', Systematic Biology, 61, (6) pp. 1075-1082. ISSN 1063-5157 (2012) [Refereed Article] DOI: 10.1093/sysbio/sys043 [eCite] [Details] Citations: Scopus - 14Web of Science - 12 Tweet
2012	Sumner JG, Holland BR, Jarvis PD, 'The Algebra of the General Markov Model on Phylogenetic Trees and Networks', Bulletin of Mathematical Biology, 74, (4) pp. 858-880. ISSN 1522-9602 (2012) [Refereed Article] DOI: 10.1007/s11538-011-9691-z [eCite] [Details] Citations: Scopus - 11Web of Science - 11 Co-authors: Sumner JG; Jarvis PD Tweet
2012	Sumner JG, Jarvis PD, Fernandez-Sanchez J, Kaine BT, Woodhams MD, et al., 'Is the general time-reversible model bad for molecular phylogenetics?', Systematic Biology, 61, (6) pp. 1069-1074. ISSN 1063-5157 (2012) [Refereed Article] DOI: 10.1093/sysbio/sys042 [eCite] [Details] Citations: Scopus - 33Web of Science - 32 Co-authors: Sumner JG; Jarvis PD; Kaine BT; Woodhams MD Tweet
2012	Yu S, Fearnhead P, Holland BR, Biggs P, Maiden M, et al., 'Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli', Journal of Molecular Evolution, 74, (5-6) pp. 273-280. ISSN 0022-2844 (2012) [Refereed Article] DOI: 10.1007/s00239-012-9505-4 [eCite] [Details] Citations: Scopus - 7Web of Science - 7 Tweet
2011	White WTJ, Holland BR, 'Faster exact maximum parsimony search with XMP', Bioinformatics, 27, (10) pp. 1359-1367. ISSN 1367-4803 (2011) [Refereed Article] DOI: 10.1093/bioinformatics/btr147 [eCite] [Details] Citations: Scopus - 8Web of Science - 7 Tweet
2010	Grievink LS, Penny D, Hendy MD, Holland BR, 'Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree', Systematic Biology, 59, (3) pp. 288-297. ISSN 1063-5157 (2010) [Refereed Article] DOI: 10.1093/sysbio/syq003 [eCite] [Details] Citations: Scopus - 17Web of Science - 16 Tweet
2010	Holland BR, Spencer HG, Worthy TH, Kennedy M, 'Identifying Cliques of Convergent Characters: Concerted Evolution in the Cormorants and Shags', Systematic Biology, 59, (4) pp. 433-445. ISSN 1063-5157 (2010) [Refereed Article] DOI: 10.1093/sysbio/syq023 [eCite] [Details] Citations: Scopus - 42Web of Science - 43 Tweet
2010	McGaughran A, Holland BR, 'Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level', PLOS One, 5, (3) EJ ISSN 1932-6203 (2010) [Refereed Article] DOI: 10.1371/journal.pone.0009686 [eCite] [Details] Citations: Scopus - 6Web of Science - 5 Tweet
2010	McGraughran A, Stevens M, Holland BR, 'Biogeography of Circum-Antarctic springtails. ', Molecular Phylogenetics and Evolution, 57, (1) pp. 48-58. ISSN 1055-7903 (2010) [Refereed Article] DOI: 10.1016/j.ympev.2010.06.003 [eCite] [Details] Citations: Scopus - 32Web of Science - 24 Tweet
2010	Zhang N, Cannon RD, Holland BR, Patchett ML, Schmid J, 'Impact of Genetic Background on Allele Selection in a Highly Mutable Candida albicans Gene, PNG', PLOS One, 5, (3) EJ ISSN 1932-6203 (2010) [Refereed Article] DOI: 10.1371/journal.pone.0009614 [eCite] [Details] Citations: Scopus - 9Web of Science - 9 Tweet
2010	de Nooijer S, Holland BR, Penny D, 'The Emergence of Predators in Early Life: There was No Garden of Eden', PLOS One, 4, (6) EJ ISSN 1932-6203 (2010) [Refereed Article] DOI: 10.1371/journal.pone.0005507 [eCite] [Details] Citations: Scopus - 11Web of Science - 11 Tweet
2009	French NP, Midwinter A, Holland BR, Collins-Emerson J, Pattison R, et al., 'Molecular Epidemiology of Campylobacter jejuni Isolates from Wild-Bird Fecal Material in Children's Playgrounds', Applied and Environmental Microbiology, 75, (3) pp. 779-783. ISSN 0099-2240 (2009) [Refereed Article] DOI: 10.1128/AEM.01979-08 [eCite] [Details] Citations: Scopus - 107Web of Science - 106 Tweet
2009	Zhang N, Upritchard JE, Holland BR, Fenton LE, Ferguson MM, et al., 'Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes', Infection, Genetics and Evolution, 9, (4) pp. 493-500. ISSN 1567-1348 (2009) [Refereed Article] DOI: 10.1016/j.meegid.2009.01.007 [eCite] [Details] Citations: Scopus - 10Web of Science - 10 Tweet
2008	Grievink LS, Penny D, Hendy MD, Holland BR, 'LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites', BMC Evolutionary Biology, 8, (1) pp. 1-6. ISSN 1471-2148 (2008) [Refereed Article] DOI: 10.1186/1471-2148-8-317 [eCite] [Details] Citations: Scopus - 10Web of Science - 10 Tweet
2008	Holland BR, Benthin S, Lockhart PJ, Moulton V, Huber KT, 'Using supernetworks to distinguish hybridization from lineage-sorting', BMC Evolutionary Biology, 8, (1) EJ ISSN 1471-2148 (2008) [Refereed Article] DOI: 10.1186/1471-2148-8-202 [eCite] [Details] Citations: Scopus - 96Web of Science - 94 Tweet
2008	Holland BR, Clarke AC, Meudt HM, 'Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution', Systematic Biology, 57, (3) pp. 347-366. ISSN 1063-5157 (2008) [Refereed Article] DOI: 10.1080/10635150802044037 [eCite] [Details] Citations: Scopus - 104Web of Science - 104 Tweet
2008	Shepherd LD, Holland BR, Perrie LR, 'Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Aspenium ferns ', Molecular Phylogenetics and Evolution, 48, (1) pp. 176-187. ISSN 1055-7903 (2008) [Refereed Article] DOI: 10.1016/j.ympev.2008.02.023 [eCite] [Details] Citations: Scopus - 23Web of Science - 21 Tweet
2007	Holland BR, Conner G, Huber K, Moulton V, 'Imputing Supertrees and Supernetworks from Quartets', Systematic Biology, 56, (1) pp. 57-67. ISSN 1063-5157 (2007) [Refereed Article] DOI: 10.1080/10635150601167013 [eCite] [Details] Citations: Scopus - 35Web of Science - 30 Tweet
2007	Shavit L, Penny D, Hendy MD, Holland BR, 'The Problem of Rooting Rapid Radiations', Molecular Biology and Evolution, 24, (11) pp. 2400-2411. ISSN 0737-4038 (2007) [Refereed Article] DOI: 10.1093/molbev/msm178 [eCite] [Details] Citations: Scopus - 68Web of Science - 63 Tweet
2007	White WT, Hills SF, Gaddam R, Holland BR, Penny D, 'Treeness Triangles: Visualising the Loss of Phylogenetic Signal', Molecular Biology and Evolution, 24, (9) pp. 1529-1541. ISSN 0737-4038 (2007) [Refereed Article] DOI: 10.1093/molbev/msm139 [eCite] [Details] Citations: Scopus - 21Web of Science - 20 Tweet
2006	Auch AF, Henz SR, Holland BR, Goker M, 'Genome BLAST distance phylogenies inferred from whole plastic and whole mitochondrion genome sequences', BMC Bioinformatics, 7, (July) pp. 1-16. ISSN 1471-2105 (2006) [Refereed Article] DOI: 10.1186/1471-2105-7-350 [eCite] [Details] Citations: Scopus - 54Web of Science - 53 Tweet
2006	Holland BR, Jermiin LS, Moulton V, 'Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005: Improved Consensus Network Techniques for Genome-Scale Phylogeny', Molecular Biology and Evolution, 23, (5) pp. 848-855. ISSN 0737-4038 (2006) [Refereed Article] DOI: 10.1093/molbev/msj061 [eCite] [Details] Citations: Scopus - 30Web of Science - 30 Tweet
2006	Holmes AR, Tsao S, Ong SW, Lamping E, Niimi K, et al., 'Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2', Molecular Microbiology, 62, (1) pp. 170-186. ISSN 0950-382X (2006) [Refereed Article] DOI: 10.1111/j.1365-2958.2006.05357.x [eCite] [Details] Citations: Scopus - 55Web of Science - 52 Tweet
2006	Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, et al., 'Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes', Molecular Biology and Evolution, 23, (10) pp. 1966-1975. ISSN 0737-4038 (2006) [Refereed Article] DOI: 10.1093/molbev/msl063 [eCite] [Details] Citations: Scopus - 55Web of Science - 50 Tweet
2005	Dress A, Holland BR, Huber KT, Koolen JH, Moulton V, et al., 'Δ additive and Δ ultra-additive maps, Gromov's trees, and the Farris transform', Discrete Applied Mathematics: Combinatorial Operations Research and Computer Science, 146, (1) pp. 51-73. ISSN 0166-218X (2005) [Refereed Article] DOI: 10.1016/j.dam.2003.01.003 [eCite] [Details] Citations: Scopus - 19Web of Science - 15 Tweet
2005	Goremykin V, Holland BR, Hirsch-Ernst KI, Hellwig FH, 'Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications', Molecular Biology and Evolution, 22, (9) pp. 1813-1822. ISSN 0737-4038 (2005) [Refereed Article] DOI: 10.1093/molbev/msi173 [eCite] [Details] Citations: Scopus - 120Web of Science - 120 Tweet
2005	Holland BR, Delsuc F, Moulton V, 'Visualizing conflicting evolutionary hypotheses in large collections of trees: Using consensus networks to study the origins of Placentals and Hexapods', Systematic Biology, 54, (1) pp. 66-76. ISSN 1063-5157 (2005) [Refereed Article] DOI: 10.1080/10635150590906055 [eCite] [Details] Citations: Scopus - 51Web of Science - 49 Tweet
2005	Holland BR, Huber KT, Penny D, Moulton V, 'The Min/Max Squeeze: Guaranteeing a Minimal Tree for Population Data', Molecular Biology and Evolution, 22, (2) pp. 235-242. ISSN 0737-4038 (2005) [Refereed Article] DOI: 10.1093/molbev/msi010 [eCite] [Details] Citations: Scopus - 15Web of Science - 10 Tweet
2005	Holland BR, Schmid J, 'Selecting representative model micro-organisms', BMC Microbiology, 5, (May) pp. 1-11. ISSN 1471-2105 (2005) [Refereed Article] DOI: 10.1186/1471-2180-5-26 [eCite] [Details] Citations: Scopus - 7Web of Science - 7 Tweet
2005	Kennedy M, Holland BR, Gray RD, Spencer HG, 'Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks', Systematic Biology, 54, (4) pp. 620-633. ISSN 1063-5157 (2005) [Refereed Article] DOI: 10.1080/106351591007462 [eCite] [Details] Citations: Scopus - 51Web of Science - 49 Tweet
2004	Holland BR, Huber KT, Moulton V, Lockhart PJ, 'Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny', Molecular Biology and Evolution, 21, (7) pp. 1459-1461. ISSN 0737-4038 (2004) [Refereed Article] DOI: 10.1093/molbev/msh145 [eCite] [Details] Citations: Scopus - 141Web of Science - 130 Tweet
2004	Schmid J, Cannon RD, Holland BR, 'A futile act? Thoughts on the reproductive biology of Candida albicans', Mycologist, 18, (4) pp. 158-163. ISSN 0269-915X (2004) [Refereed Article] DOI: 10.1017/S0269915X0400415X [eCite] [Details] Tweet
2003	Gardner PP, Holland BR, Moulton V, Hendy M, Penny D, 'Optimal alphabets for an RNA world', Proceedings of the Royal Society of London, 270, (1520) pp. 1177-1182. ISSN 0370-1662 (2003) [Refereed Article] DOI: 10.1098/rspb.2003.2355 [eCite] [Details] Citations: Scopus - 16Web of Science - 15 Tweet
2003	Hendy MD, Holland BR, 'Upper bounds on maximum likelihood for phylogenetic trees', Bioinformatics, 19, (2) pp. ii66-ii72. ISSN 1367-4803 (2003) [Refereed Article] DOI: 10.1093/bioinformatics/btg1062 [eCite] [Details] Citations: Scopus - 7Web of Science - 4 Tweet
2003	Holland BR, Penny D, Hendy MD, 'Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock-A Simulation Study', Systematic Biology, 52, (2) pp. 229-238. ISSN 1063-5157 (2003) [Refereed Article] DOI: 10.1080/10635150390192771 [eCite] [Details] Citations: Web of Science - 109 Tweet
2003	Salemi M, De Oliveira T, Courgnaud V, Moulton V, Holland BR, et al., 'Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses', Journal of Virology, 77, (13) pp. 7202-7213. ISSN 0022-538X (2003) [Refereed Article] DOI: 10.1128/JVI.77.13.7202-7213.2003 [eCite] [Details] Citations: Scopus - 33Web of Science - 31 Tweet
2003	Strimmer K, Forslund K, Holland BR, Moulton V, 'A novel exploratory method for visual recombination detection', Genome Biology, 4, (5) pp. R33. ISSN 1465-6914 (2003) [Refereed Article] DOI: 10.1186/gb-2003-4-5-r338976 [eCite] [Details] Citations: Web of Science - 18 Tweet
2003	Wagele JW, Holland BR, Dreyer H, Hackethal B, 'Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats', Molecular Phylogenetics and Evolution, 28, (3) pp. 536-551. ISSN 1055-7903 (2003) [Refereed Article] DOI: 10.1016/S1055-7903(03)00053-8 [eCite] [Details] Citations: Scopus - 13Web of Science - 13 Tweet
2003	Zhang N, Harrex AL, Holland BR, Fenton LE, Cannon RD, et al., 'Sixty Alleles of the ALS7 Open Reading Frame in Candida albicans: ALS7 Is a Hypermutable Contingency Locus', Genome Research, 13, (9) pp. 2005-2017. ISSN 1088-9051 (2003) [Refereed Article] DOI: 10.1101/gr.1024903 [eCite] [Details] Citations: Scopus - 58Web of Science - 55 Tweet
2002	Holland BR, Huber KT, Dress A, Moulton V, 'Plots: A Tool for Analyzing Phylogenetic Distance Data', Molecular Biology and Evolution, 19, (12) pp. 2051-2059. ISSN 0737-4038 (2002) [Refereed Article] DOI: 10.1093/oxfordjournals.molbev.a004030 [eCite] [Details] Citations: Scopus - 93Web of Science - 90 Tweet
2002	Lambert DM, Ritchie PA, Millar CD, Holland BR, Drummond AJ, et al., 'Rates of Evolution in Ancient DNA from Adelie Penguins', Science, 295, (5563) pp. 2270-2273. ISSN 0036-8075 (2002) [Refereed Article] DOI: 10.1126/science.1068105 [eCite] [Details] Citations: Scopus - 239Web of Science - 233 Tweet
2000	Chor B, Hendy MD, Holland BR, Penny D, 'Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach', Molecular Biology and Evolution, 17, (10) pp. 1529-1541. ISSN 0737-4038 (2000) [Refereed Article] DOI: 10.1093/oxfordjournals.molbev.a026252 [eCite] [Details] Citations: Scopus - 72Web of Science - 65 Tweet

Chapter in Book

(4 outputs)

Year	Citation	Altmetrics
2017	Jarvis PD, Holland BR, Sumner JG, 'Phylogenetic Invariants and Markov Invariants', Reference Module in Life Sciences, Elsevier, BD Roitberg (ed), Amsterdam, Netherlands, pp. 1-3. ISBN 9780128096338 (2017) [Revised Book Chapter] DOI: 10.1016/B978-0-12-809633-8.06903-X [eCite] [Details] Co-authors: Jarvis PD; Sumner JG Tweet
2014	French N, Yu S, Biggs P, Holland B, Fearnhead P, et al., 'Evolution of Campylobacter Species in New Zealand', Campylobacter Ecology and Evolution, Caister Academic Press, SK Sheppard, G Meric (ed), United Kingdom, pp. 221-240. ISBN 978-1-908230-36-2 (2014) [Research Book Chapter] [eCite] [Details] Tweet
2013	Jarvis PD, Holland BR, Sumner JG, 'Phylogenetic Invariants', Brenner's Encyclopedia of Genetics, Academic Press Ltd Elsevier Science Ltd, S Maloy, K Hughes (ed), United Kingdom, pp. 321-323. ISBN 978-0-08-096156-9 (2013) [Other Book Chapter] DOI: 10.1016/B978-0-12-374984-0.09001-X [eCite] [Details] Co-authors: Jarvis PD; Sumner JG Tweet
2007	Penny D, Hendy MD, Holland BR, 'Phylogenetics: Parsimony, Networks, and Distance Methods', Handbook of Statistical Genetics, John Wiley & Sons, Ltd, DJ Balding, M Bishop and C Cannings (ed), West Sussex, England, pp. 489-532. ISBN 978-0-470-05830-5 (2007) [Revised Book Chapter] [eCite] [Details]

Review

(2 outputs)

Year	Citation	Altmetrics
2015	Holland BR, 'Book review - Molecular Evolution: A Statistical Approach', Systematic Biology, 64, (3) pp. 545-546. ISSN 1063-5157 (2015) [Review Single Work] DOI: 10.1093/sysbio/syv002 [eCite] [Details] Tweet
2007	Holland BR, 'Analysis of Phylogenetics and Evolution with R', Systematic Biology, 56, (4) pp. 694-696. (2007) [Review Single Work] DOI: 10.1080/10635150701475589 [eCite] [Details] Tweet

Year

Citation

Altmetrics

2015

Holland BR, 'Book review - Molecular Evolution: A Statistical Approach', Systematic Biology, 64, (3) pp. 545-546. ISSN 1063-5157 (2015) [Review Single Work]

DOI: 10.1093/sysbio/syv002 [eCite] [Details]

2007

Holland BR, 'Analysis of Phylogenetics and Evolution with R', Systematic Biology, 56, (4) pp. 694-696. (2007) [Review Single Work]

DOI: 10.1080/10635150701475589 [eCite] [Details]

Conference Publication

(12 outputs)

Year	Citation	Altmetrics
2022	Diao J, O'Reilly MM, Holland BR, 'Modelling gene content across a phylogeny to determine when genes become associated', The Eleventh International Conference on Matrix-Analytic Methods in Stochastic Models (MAM11) Proceedings, 29 June - 1 July 2022, Seoul, Republic of Korea, pp. 1-4. (2022) [Refereed Conference Paper] [eCite] [Details] Co-authors: Diao J; O'Reilly MM
2022	Soewongsono AC, Holland BR, O'Reilly MM, 'Stochastic niche-based models for the evolution of species', The Eleventh International Conference on Matrix-Analytic Methods in Stochastic Models (MAM11) Proceedings, 29 June - 1 July 2022, Seoul, Republic of Korea, pp. 1-4. (2022) [Refereed Conference Paper] [eCite] [Details] Co-authors: Soewongsono AC; O'Reilly MM
2019	Abera A, O'Reilly MM, Holland BR, Fackrell M, Heydar M, 'Decision support model for the patient admission scheduling problem with random arrivals and departures', Proceedings of the 10th International Conference on Matrix-Analytic Methods in Stochastic Models, 13-15 February 2019, Hobart, Australia, pp. 10-14. (2019) [Refereed Conference Paper] [eCite] [Details] Co-authors: Abera A; O'Reilly MM; Heydar M Tweet
2019	Reaburn R, Holland B, Oates G, Stojanovski E, 'Crossing the liminal space: students' understanding of confidence intervals', Proceedings of the 12th Delta conference on the teaching and learning of undergraduate mathematics and statistics, 24 - 29 November 2019, Fremantle, Western Australia, pp. 176. ISBN 978-1-74108-498-6 (2019) [Refereed Conference Paper] DOI: 10.26183/5d5f53ed9c926 [eCite] [Details] Co-authors: Reaburn R; Oates G Tweet
2016	Humphries MA, Holland BR, Reynolds AR, Bruno RB, 'Cognitive models in the extreme', Australian Mathematical Psychology Conference 2016, 10-12 February, 2016, Hobart, Tasmania (2016) [Conference Extract] [eCite] [Details] Co-authors: Humphries MA; Reynolds AR; Bruno RB
2012	Humphries MA, Holland BR, Karpievitch YV, Sumner JG, 'To gamma or not to gamma? Testing the fit of rates-across-sites models', Phylomania 2012, 8-9 November 2012, University of Tasmania, Hobart, pp. 7. (2012) [Conference Extract] [eCite] [Details] Co-authors: Humphries MA; Karpievitch YV; Sumner JG
2011	Kaur M, Stewart DC, Janusz A, Bowman JP, Holland BR, et al., 'Tapping into barley malt associated microbial diversity using next generation sequencing', Proceedings of the 15th Australian Barley Technical Symposium, 18-21 September 2011, Adelaide, Australia (2011) [Conference Extract] [eCite] [Details] Co-authors: Kaur M; Bowman JP; Evans E
2011	Kaur M, Stewart DC, Janusz A, Bowman JP, Holland BR, et al., 'Assessing barley malt associated microbial diversity using next generation sequencing', 2011 Australian Society for Microbiology Annual Meeting, Hobart, Australia (2011) [Conference Extract] [eCite] [Details] Co-authors: Kaur M; Bowman JP; Evans E
2006	Holland BR, Conner G, Huber KT, Moulton V, 'Imputing Supertrees and Supernetworks from Quartets', Lecture Notes in Bioinformatics: Algorithms in Bioinformatics: 6th International Workshop, WABI 2006, 11-13 September 2006, Zurich, Switzerland, pp. 162. ISBN 978-3-540-39583-6 (2006) [Conference Extract] [eCite] [Details]
2006	Holland BR, Schardl CJ, Schmid J, 'Endophyte survival without sex', Proceedings of the 6th International Symposium on Fungal Endophytes of Grasses, 25-28 March 2006, Christchurch, New Zealand, pp. 151-154. (2006) [Refereed Conference Paper] [eCite] [Details]
2003	Holland BR, Moulton V, 'Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees', Algorithms in Bioinformatics, 15-20 September 2003, Budapest, Hungary, pp. 165-176. ISBN 3-540-20076-2 (2003) [Refereed Conference Paper] [eCite] [Details]
2000	Chor B, Hendy MD, Holland BR, Penny D, 'Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach', RECOMB 2000: Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 8-11 April 2000, Tokyo, Japan, pp. 108-117. ISBN 1-58113-186-0 (2000) [Refereed Conference Paper] [eCite] [Details]

Thesis

(1 outputs)

Year	Citation	Altmetrics
2001	Holland BR, 'Evolutionary analyses of large data sets: Trees and beyond' (2001) [PhD] [eCite] [Details]

Grants & Funding

I am currently a CI in the ARC CoE for Plant Success

https://www.plantsuccess.org/
Improved phylogenetic profiling to better understand and predict the genotype to phenotype map
Homology detection, alignment and ancestral state reconstruction of genetic networks

Funding Summary

Number of grants

Total funding

$38,672,503

Projects

ARC Centre of Excellence for Plant Success in Nature and Agriculture (2020 - 2026)$35,000,000

Description: https://www.plantsuccess.org/
Funding: Australian Research Council ($35,000,000)
Scheme: Grant-ARC Centres of Excellence
Administered By: University of Queensland
Research Team: Beveridge C; Cooper M; Brodribb TJ; Bowman J; Waterhouse P; Wright I; Burrage K; Donovan D; Foo E; Hammer G; Henry R; Holland BR; Jordan D; Ortiz-Barrientos D; Sherman B; Smith SM; Weller JL
Period: 2020 - 2026
Grant Reference: CE200100015

Using the idea of multiple representations in mathematics and science classrooms (2019)$500

Description: Peer Learning Circles: Collaboration for Learning and Teaching Grant.Quality STEM education is touted as important to the nations productivity, and significant funding has been provided to education systems to enhance student learning in STEM. Effective STEM teaching practices provide opportunities for students to express concepts through multiple modes of representation to support concept development and deep learning. This PLC will review current teacher knowledge formulations in mathematics and science education including Shulmans Pedagogical Content Knowledge (PCK), Ball and colleagues Mathematical Knowledge for Teaching (MKT) and Rowland et al.s Knowledge Quartets to identify the space that we refer to as representational fluency. The PLC will enable members to reflect on their own understanding of the notion of representational fluency and how it pertains to STEM teaching, which will in turn inform their teaching practices. The process will provide a springboard for exploring how representational fluency, as part of teacher knowledge, predicts instructional quality and student learning outcomes.
Funding: University of Tasmania ($500)
Scheme: null
Administered By: University of Tasmania
Research Team: Hatisaru V; Fraser SP; Murphy C; Oates GN; Kenny JDJ; Seen AJ; Holland BR; Maher N
Year: 2019

Creating new stochastic models to understand the evolution of gene families (2018 - 2020)$317,329

Funding: Australian Research Council ($317,329)
Scheme: Grant-Discovery Projects
Administered By: University of Tasmania
Research Team: Holland BR; O'Reilly MM; Liberles D; Liu L
Period: 2018 - 2020
Grant Reference: DP180100352

Reconstructing the evolution of climatic tolerances in conifers (2016 - 2018)$357,700

Description: This project aims to trace the evolution of climate tolerance in conifers by combining evidence from fossils,phylogenies, physiology and mathematics. Innovative methods will be used to overcome significant biases inmethods currently used to trace evolutionary change. The project will integrate data from three sources: 1) theglobal fossil record; 2) new models of current climatic tolerances of conifers; and 3) mathematical simulations ofhow and when methods of reconstructing ancestral ecology fail. The combined results should show how thisimportant group of organisms has responded to past climate change and how they will respond in the future. Itshould also provide improved estimates of past terrestrial climates.
Funding: Australian Research Council ($357,700)
Scheme: Grant-Discovery Projects
Administered By: University of Tasmania
Research Team: Jordan GJ; Holland BR; Anderegg W
Period: 2016 - 2018
Grant Reference: DP160100809

Algebraically informed models of biological sequence evolution (2015 - 2017)$310,700

Description: To make sense of the patterns they see in the natural world, biologists across fields as diverse as genetics, epidemiology and biogeography need an accurate picture of evolutionary history. DNA sequences provide an exciting means to establish this picture of the past, but to decode it successfully requires mathematical models of how DNA evolves. Our team has identified mathematical inconsistencies with current approaches. In particular, understanding the effect of natural selection in different parts of the Tree of Life requires models that behave robustly in the face of shifting evolutionary processes. This project will use insights from algebraic methods to construct mathematically consistent models of wide biological utility.
Funding: Australian Research Council ($310,700)
Scheme: Grant-Discovery Projects
Administered By: University of Tasmania
Research Team: Holland BR; Sumner JG; Jarvis PD
Period: 2015 - 2017
Grant Reference: DP150100088

The 17th Annual New Zealand Phylogenomics Meeting (2013)$1,250

Funding: University of Tasmania ($1,250)
Scheme: Grant-Conference Support Scheme
Administered By: University of Tasmania
Research Team: Holland BR
Year: 2013

Redesigning the introductory statistics classroom to the 'inverted' style to improve student experience and material retention (2013)$34,000

Description: The goal of the project is to convert the flagship introductory statistics units to inverted-style. The specific aims are to: 1) develop and evaluate a teaching model for inverting an introductory statistics classroom by creating video lectures, online assessments, and interactive activities; 2) improve student experience in the introductory statistics unit and increase students' understanding and retention of material.
Funding: Office for Learning & Teaching ($34,000)
Scheme: Grant-Seed
Administered By: University of Tasmania
Research Team: Karpievitch YV; Holland BR; Chick HL
Year: 2013

Ancient Ibis Mummies from Egypt: DNA Evolution - Math Modelling (2011 - 2015)$1,231,450

Funding: International Human Frontier Science Program Organization ($1,231,450)
Scheme: Grant-Program
Administered By: International Human Frontier Science Program Organization
Research Team: Lambert D; Holland BR; Ikram S
Period: 2011 - 2015

How Will Animals Respond to Climate Change? A Genomic Approach (2011 - 2014)$875,998

Funding: Australian Research Council ($730,000)
Scheme: Grant-Linkage Projects Round 2
Administered By: Griffith University
Research Team: Lambert D; Holland BR
Period: 2011 - 2014
Grant Reference: LP110200229

Increasing Bioinformatics capability across UTas (2011)$5,000

Funding: University of Tasmania ($5,000)
Scheme: Grant-Research Enhancement (REGS)
Administered By: University of Tasmania
Research Team: Holland BR
Year: 2011

Interpreting biological sequence information: untangling hybridisation (2010 - 2014)$532,376

Description: Hybrid evolution plays a key role in speciation and adaptation, especially in plants. Hybrid species inherit genetic material from two parent species, making them hard to detect by studying single genes. Fortunately, innovations in DNA sequencing now make it affordable to study many genes simultaneously. Current methods for studying hybridisation assume that evolutionary relationships inferred for different genes are error-free, and all conflict is attributed to hybridisation. However, in reality conflict is often caused by estimation errors, the random nature of inheritance within populations, and missing data. This project will develop the computational tools necessary to analyse next generation sequence data to untangle hybrid evolution.
Funding: Australian Research Council ($532,376)
Scheme: Fellowship-Future
Administered By: University of Tasmania
Research Team: Holland BR
Period: 2010 - 2014
Grant Reference: FT100100031

Phylogenetics: Mathematics, Models and Applications - UK, 2011 (2010)$1,200

Funding: University of Tasmania ($1,200)
Scheme: Grant-Conference Support Scheme
Administered By: University of Tasmania
Research Team: Holland BR
Year: 2010

NARGS - Recovering complex evolutionary histories with censored data (2010)$5,000

Funding: University of Tasmania ($5,000)
Scheme: Grant-New Appointees Research Grant Scheme (NARGS)
Administered By: University of Tasmania
Research Team: Holland BR
Year: 2010

Research Supervision

Barbara has supervised (or co-supervised) 17 PhD students to successful completion of their doctorates. Many of her students have gone onto jobs in academia and postdoctoral positions around the globe. She is current supervising (or co-supervising) 6 PhD students. She is always on the lookout for students with a combination of mathematical and computing skills and a passion for problems in biology.

Current

Completed

Current

Degree	Title	Commenced
PhD	Model Selection and Goodness of Fit in Molecular Phylogenetics	2019
PhD	Processing and analysing Enose data	2022
PhD	Stochastic Models for the Conservation of Endangered Species	2023
PhD	New statistical methods for PhyloG2P	2023
PhD	Integrative genomic models for Eucalyptus globulus breeding	2023
PhD	Graded Rings of Markov Invariants	2023

Completed

Degree	Title	Completed
PhD	Mathematical Models for the Evolution of Species Candidate: Albert Christian Soewongsono	2023
PhD	Stochastic Modelling of Patient Flow in Hospitals Candidate: Aregawi Kiros Abera	2023
PhD	Mechanistic Markov Models for the Evolution of Gene Families Candidate: Jiahao Diao	2023
PhD	Rate Matrices: A bridge between molecular biology and linear algebra. Two way traffic between evolutionary sequence analysis and novel mathematical frameworks Candidate: Julia Alice Shore	2023
PhD	Old Plants, New Tricks: Machine learning and the conifer fossil record Candidate: Matilda Jane Munro Brown	2022
PhD	Protein Structure and Evolution Candidate: Janan Elizabeth Sykes	2021
PhD	Markov Models for the Evolution of Duplicate Genes, and Microsatellites Candidate: Tristan Lee Stark	2018
PhD	Stats, Drugs and Rock and Roll: Statistical applications to temporally autocorrelated substance use data Candidate: Melissa Ann Humphries	2017
PhD	Distinguishing Convergence on Phylogenetic Networks Candidate: Jonathan David Mitchell	2016
PhD	Demographic history of the Tasmanian devil (Sarcophilus harrisii) from Pleistocene to present Candidate: Anna Brueniche-Olsen	2015