Conrad Burden
Conrad Burden
Honorary Associate Professor
email conrad.burden@anu.edu.au
call +61 2 6125 0730

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About

Conrad Burden is an Honorary Associate Professor in the Mathematical Sciences Institute at the Australian National University.  His current research interests are in  mathematical population genetics.  Previous research interests include aligment-free sequence comparison, the analysis of high-throughput sequencing data, and the physico-chemical modelling of microarrays.  

Before making the move into bioinformatics in 2003 he spent 20 years as a theoretical physicist followed by a short stint working in the IT industry: 

He graduated from the University of Queensland with 1st class honours in Applied Mathematics in 1979 and The Australian National University with a PhD in Theoretical Physics in 1983.  

Between 1983 and 1988 he held postdoctoral fellowships in theoretical physics at the Weizmann Institute of Science, Glasgow University, The Australian National University and Flinders University. 

Between 1988 and 1999 he held a research position in the Department of Theoretical Physics, Australian National University, working mainly in quantum field theory and subatomic particle physics.  

Between 1999 and 2002 I was a programmer/developer in the IT industry. 

Between 2003 and 2020 I held positions as Research Fellow, Fellow and Associate Professor in the Mathematical Sciences Institute, Australian National University.

Conrad is a Fellow of the Australian Institute of Physics.  

Read more about Conrad's biography and research interests.

Affiliations

  Groups

Research interests

Currently interested in Mathematical Population Genetics. 

Previous research interests since 2003 include physico-chemical modelling of microarrays, pairwise word-match counts in random sequences, and the analysis of high-throughput genomic sequencing data.  

Research interests up to 1999 were in quantum field theory and subatomic particle physics. 

ORCiD: 0000-0003-0015-319X

ResearcherID: D-5556-2016 via Web of Science

Projects

Teaching information

Courses previously developed and taught:

MATH3353 and MATH6208 Topics in Bioinformatics (2006, 2007, 2012 to 2021)

MATH2307 and MATH6100 Bioinformatics and Biological Modelling (2010 to 2019)

BIOL2001 Introduction to Quantitative Biology (2017)

BIOL8002 Advanced Topics in Quantitative Biology, module 1: Mathematical and Progamming Background (2018 to 2020)

Special relativity, general relativity, relativistic quantum mechanics and quantum field theory components of various 2nd and 3rd year undergraduate physics courses during the period 1988 to 1999 and in 2003, 2005

Location

Room 4.74, Hanna Neumann Building 145

Publications

     Journal Articles

  • [1]  Conrad J. Burden and Robert C. Griffiths. The stationary and quasi-stationary properties of neutral multi-type branching process diffusions. Stochastic Models, 39(1):185– 218, 2023.

  • [2]  Xia Hua, Tyara Herdha, and Conrad J Burden. Protracted speciation under the state-dependent speciation and extinction approach. Systematic Biology, 71(6):1362–1377, 2022.

  • [3]  Claus Vogl, Lynette C. Mikula, and Conrad J. Burden. Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation–drift model. Theoretical Population Biology, 134:106–118, 2020.

  • [4]  Conrad J. Burden and Albert C. Soewongsono. Coalescence in the diffusion limit of a Bienaymé–Galton–Watson branching process. Theoretical Population Biology, 130:50–59, 2019.

  • [5]  Conrad J. Burden and Robert C. Griffiths. The transition distribution of a sample from a Wright–Fisher diffusion with general small mutation rates. Journal of Mathematical Biology, 79(6-7):2315–2342, sep 2019.

  • [6]  Conrad J. Burden and Robert C. Griffiths. The stationary distribution of a sample from the Wright-Fisher diffusion model with general small mutation rates. Journal of Mathematical Biology, 78(4):1211–1224, nov 2019.

  • [7]  Conrad J. Burden and Robert C. Griffiths. Stationary distribution of a 2-island 2-allele Wright–Fisher diffusion model with slow mutation and migration rates. Theoretical Population Biology, 124:70–80, 2018.

  • [8]  Conrad J. Burden and Yi Wei. Mutation in populations governed by a Galton-Watson branching process. Theoretical Population Biology, 120:52–61, 2018.

  • [9]  Conrad J. Burden and Yurong Tang. Rate matrix estimation from site frequency data. Theoretical Population Biology, 113:23–33, 2017.

  • [10]  Conrad J. Burden and Yurong Tang. An approximate stationary solution for multi-allele neutral diffusion with low mutation rates. Theoretical Population Biology, 112:22–32, 2016.

  • [11]  Conrad J. Burden and Helmut Simon. Genetic drift in populations governed by a Galton-Watson branching process. Theoretical Population Biology, 109:63–74, 2016.

  • [12]  Peijie Lin, Sylvain Forêt, Susan R Wilson, and Conrad J Burden. Estimation of the methylation pattern distribution from deep sequencing data. BMC Bioinformatics, 16(1), may 2015.

  • [13]  Conrad J. Burden, Sumaira E. Qureshi, and Susan R. Wilson. Error estimates for the analysis of differential expression from RNA-seq count data. PeerJ, 2:e576, sep 2014.

  • [14]  Conrad J. Burden, Paul Leopardi, and Sylvain Forêt. The distribution of word matches between markovian sequences with periodic boundary conditions. Journal of Computational Biology, 21(1):41–63, jan 2014.

  • [15]  A. Harrison, H. Binder, A. Buhot, C. J. Burden, E. Carlon, C. Gibas, L. J. Gamble, A. Halperin, J. Hooyberghs, D. P. Kreil, R. Levicky, P. A. Noble, A. Ott, B. M. Pettitt, D. Tautz, and A. E. Pozhitkov. Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. Nucleic Acids Research, 41(5):2779– 2796, jan 2013.

  • [16]  Conrad J. Burden, Junmei Jing, and Susan R. Wilson. Alignment-free sequence com- parison for biologically realistic sequences of moderate length. Statistical Applications in Genetics and Molecular Biology, 11(1):1–28, jan 2012.

  • [17]  José A Robles, Sumaira E Qureshi, Stuart J Stephen, Susan R Wilson, Conrad J Burden, and Jennifer M Taylor. Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing. BMC Genomics, 13(1), sep 2012.

  • [18]  Junmei Jing, Susan R. Wilson, and Conrad J. Burden. Weighted k-word matches: a sequence comparison tool for proteins. ANZIAM Journal, 51:172, jun 2011.

  • [19]  Numanul Subhani, Luis Rueda, Alioune Ngom, and Conrad J. Burden. Multiple gene expression profile alignment for microarray time-series data clustering. Bioinformatics, 26(18):2281–2288, jul 2010.

  • [20]  Junmei Jing, Conrad J. Burden, Sylvain Forêt, and Susan R. Wilson. Statistical considerations underpinning an alignment-free sequence comparison method. Journal of the Korean Statistical Society, 39(3):325–335, 2010. Special Issue: Papers inspired by the first IMS-APRM.

  • [21]  Hans Binder, Knut Krohn, and Conrad J Burden. Washing scaling of GeneChip microarray expression. BMC Bioinformatics, 11(1), may 2010.

  • [22]  Conrad J Burden and Hans Binder. Reply to ‘Linking probe thermodynamics to microarray quantification’. Physical Biology, 7(4):048002, nov 2010.

  • [23]  Conrad J Burden and Hans Binder. Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays. Physical Biology, 7(1):016004, dec 2010.

  • [24]  Hans Binder, Jan Bru ̈cker, and Conrad J. Burden. Nonspecific hybridization scaling of microarray expression estimates: A physicochemical approach for chip-to-chip normalization. The Journal of Physical Chemistry B, 113(9):2874–2895, feb 2009.

  • [25]  Sylvain Forˆet, Susan R Wilson, and Conrad J Burden. Characterizing the d2 statis- tic: Word matches in biological sequences. Statistical Applications in Genetics and Molecular Biology, 8(1):1–21, jan 2009.

  • [26]  Sylvain Forêt, Susan R. Wilson, and Conrad J. Burden. Empirical distribution of k-word matches in biological sequences. Pattern Recognition, 42(4):539–548, 2009. Pattern Recognition in Computational Life Sciences.

  • [27]  Conrad J Burden. Understanding the physics of oligonucleotide microarrays: the affymetrix spike-in data reanalysed. Physical Biology, 5(1):016004, mar 2008.

  • [28]  Conrad J. Burden. Comment on “Stationary rotating strings as relativistic particle mechanics”. Physical Review D, 78(12), 2008.

  • [29]  Conrad J. Burden, Miriam R. Kantorovitz, and Susan R. Wilson. Approximate word matches between two random sequences. The Annals of Applied Probability, 18(1):1– 21, 2008.

  • [30]  Conrad J Burden and Aaron J Oakley. Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations. Physical Biology, 4(2):79–90, jun 2007.

  • [31]  Markus Hegland, Conrad Burden, Lucia Santoso, Shev MacNamara, and Hilary Booth. A solver for the stochastic master equation applied to gene regulatory networks. Jour- nal of Computational and Applied Mathematics, 205(2):708–724, 2007. Special issue on evolutionary problems.

  • [32]  M. R. Kantorovitz, H. S. Booth, C. J. Burden, and S. R. Wilson. Asymptotic behavior of k-word matches between two uniformly distributed sequences. Journal of Applied Probability, 44(3):788–805, 2007.

  • [33]  Sylvain Forˆet, Miriam R Kantorovitz, and Conrad J Burden. Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences. BMC Bioinformatics, 7(S5), dec 2006.

  • [34]  Conrad J Burden, Yvonne Pittelkow, and Susan R Wilson. Adsorption models of hy- bridization and post-hybridization behaviour on oligonucleotide microarrays. Journal of Physics: Condensed Matter, 18(23):5545–5565, may 2006.

  • [35]  Lucia Santoso, Hilary S. Booth, Conrad J. Burden, and Markus Hegland. A stochastic model of gene switches. ANZIAM Journal, 46:530, jun 2005.

  • [36]  J. H. Maindonald and C. J. Burden. Selection bias in plots of microarray or other data that have been sampled from a high-dimensional space. ANZIAM Journal, 46:59, mar 2005.

  • [37]  Hilary S. Booth, Conrad J. Burden, John H. Maindonald, Lucia Santoso, Matthew J. Wakefield, and Susan R. Wilson. Discussion of “A bayesian approach to DNA sequence segmentation”. Biometrics, 61(2):635–637, 2005.

  • [38]  Conrad J Burden, Yvonne E Pittelkow, and Susan R Wilson. Statistical analysis of adsorption models for oligonucleotide microarrays. Statistical Applications in Genetics and Molecular Biology, 3(1):1–27, jan 2004.

  • [39]  C. J. Burden and M. A. Pichowsky. J P C -exotic mesons from the Bethe-Salpeter equation. Few-Body-Systems, 32(3):119–126, oct 2002.

  • [40]  M. L. Walker and C. J. Burden. Nonperturbative vertices in supersymmetric quantum electrodynamics. Physical Review D, 60(10), 1999.

  • [41]  M. L. Walker and C. J. Burden. Chiral symmetry in supersymmetric three dimensional quantum electrodynamics. Physical Review D, 59(12), 1999.

  • [42]  C. J. Burden. Effect of the ultraviolet part of the gluon propagator on the heavy quark propagator. Physical Review D, 59(3), 1999.

  • [43]  C. J. Burden. Analytic structure of heavy quark propagators. Physical Review D, 57(1):276–286, 1998.

  • [44]  C. J. Burden and P. C. Tjiang. Deconstructing the vertex Ansatz in three-dimensional quantum electrodynamics. Physical Review D, 58(8), 1998.

  • [45]  C. J. Burden, Lu Qian, C. D. Roberts, P. C. Tandy, and M. J. Thomson. Ground-state spectrum of light-quark mesons. Physical Review C, 55(5):2649–2664, 1997.

  • [46]  T. W. Allen and C. J. Burden. Vector positronium states in three-dimensional QED. Physical Review D, 55(8):4954–4966, 1997.

  • [47]  C. J. Burden and D.-S. Liu. Nonperturbative treatment of heavy quarks and mesons. Physical Review D, 55(1):367–376, 1997.

  • [48]  T. W. Allen and C. J. Burden. Positronium states in three-dimensional QED. Physical Review D, 53(10):5842–5855, 1996.

  • [49]  C.J. Burden, C.D. Roberts, and M.J. Thomson. Electromagnetic from factors of charged and neutral kaons. Physics Letters B, 371(3):163–168, 1996.

  • [50]  C. J. Burden and C. D. Roberts. Gauge covariance and the fermion-photon vertex in three- and four-dimensional, massless quantum electrodynamics. Physical Review D, 47(12):5581–5588, 1993.

  • [51]  D. O’Shaughnessy and C. J. Burden. Variational wavefunctions for non-compact u(1) lattice gauge theory: Comparison with exact result. Australian Journal of Physics, 46(2):231, 1993.

  • [52]  C. J. Burden and C. D. Roberts. Photon polarization tensor and gauge dependence in three-dimensional quantum electrodynamics. Physical Review D, 46(6):2695–2702, 1992.

  • [53]  Conrad J. Burden, Craig D. Roberts, and Anthony G. Williams. Singularity structure of a model quark propagator. Physics Letters B, 285(4):347–353, 1992.

  • [54]  C.J. Burden. Bound states from the bethe-salpeter equation in QED3. Nuclear Physics B, 387(2):419–446, 1992.

  • [55]  Conrad J. Burden and Craig D. Roberts. Light-cone regular vertex in three-dimensional quenched QED. Physical Review D, 44(2):540–550, 1991.

  • [56]  C. J. Burden. Nambu-Jona-Lasinio terms in Hamiltonian lattice gauge theory. Physical Review D, 41(8):2591–2597, 1990.

  • [57]  R. T. Cahill, J. Praschifka, and C. J. Burden. Diquarks and the bosonisation of QCD. Australian Journal of Physics, 42(2):161, 1989.

  • [58]  C. J. Burden, R. T. CahillT Cahill, and J. Praschifka. Baryon structure and QCD: Nucleon calculations. Australian Journal of Physics, 42(2):147, 1989.

  • [59]  C.J. Burden. The phase diagram of hamiltonian lattice QED with a 4-fermion coupling. Physics Letters B, 229(3):269–274, 1989.

  • [60]  C. J. Burden. Hamiltonian strong-coupling expansions for (2+1)-dimensional quantum electrodynamics. Physical Review D, 37(2):479–492, 1988.

  • [61]  C.J. Burden. Estimate of the lattice QED phase transition from Hamiltonian strong coupling expansions. Physics Letters B, 198(4):525–530, 1987.

  • [62]  C Burden and A. N Burkitt. Lattice fermions in odd dimensions. Europhysics Letters, 3(5):545–552, 1987.

  • [63]  C.J. Burden. Gravitational radiation from a particular class of cosmic strings. Physics Letters B, 164(4):277–281, 1985.

  • [64]  I.M. Barbour and C.J. Burden. Measurement of finite temperature chiral symmetry restoration in lattice gauge theory. Physics Letters B, 161(4):357–362, 1985.

  • [65]  C.J. Burden. Finite-temperature analysis of su(2)/z2 lattice gauge theory. Nuclear Physics B, 257:663–694, 1985.

  • [66]  C. J. Burden. Surface description of QCD with fermionic quark boundaries. Il Nuovo Cimento A, 80(4):461–476, apr 1984.

  • [67]  CJ Burden and LJ Tassie. Additional rigidly rotating solutions in the string model of hadrons. Australian Journal of Physics, 37(1):1, 1984.

  • [68]  C. J. Burden and L. J. Tassie. The De Broglie fusion method applied to quarks at the ends of strings. Annales de l’I.H.P. Physique th ́eorique, 38(3):199–213, 1983.

  • [69]  C.J. Burden a and L.J. Tassie. Quarks and diquarks in a baryon string model. Nuclear Physics B, 204(2):204–212, 1982.

  • [70]  CJ Burden and LJ Tassie. Rotating strings, glueballs and exotic mesons. Australian Journal of Physics, 35(3):223, 1982.

  • [71]  C.J. Burden and L.J. Tassie. Some exotic mesons and glueballs from the string model. Physics Letters B, 110(1):64–66, 1982.