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Mark MuldoonSenior Lecturer, School of MathematicsTeaching:
Schedule, Winter & Spring 2012 Things to download:
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From a
reminiscence
by
Gian-Carlo Rota about
Alonzo Church:
It may be asked why anyone would bother to sit in a
lecture which was the literal repetition of an available
text. Such a question would betray an oversimplified view
of what goes on in a classroom. What one really learns in
class is what one does not know at the time one is
learning. The person lecturing to us was logic incarnate.
His pauses, hesitations, emphases, his betrayals of
emotion (however rare), and sundry other nonverbal
phenomena taught us a lot more logic than any written
text could. We learned to think in unison with him as he
spoke, as if following the demonstration of a
calisthenics instructor. Church's course permanently
improved the rigor of our reasoning.
Schedule, Winter & Spring 2012| Weekday | 9:00 → 10:00 | 10:00 → 11:00 | 11:00 → 12:00 | 12:00 → 1:00 | 1:00 → 2:00 | 2:00 → 3:00 | 3:00 → 4:00 | 4:00 → 5:00 |
|---|---|---|---|---|---|---|---|---|
| Monday |
Discrete Maths Problems Class Zochonis: Theatre D |
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| Tuesday |
Tropical Maths Reading Group Frank Adams Room 2 |
CICADA Seminar Frank Adams Room 1 Alan Turing Bldg. |
Connar Baird (Project Student) |
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| Wednesday |
Discrete Maths Lecture Chemsitry: G.54 |
Discrete Maths Problems Class Zochonis: Theatre D |
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| Thursday |
Jackson Lab Group Meeting, Smith Bldg from 9:15 |
Discrete Maths Lecture Chemsitry: G.54 |
Mathematical Biology Lecture/Problems Class Alan Turing: G.209 |
Mathematical Biology Lecture/Problems Class Alan Turing: G.209 |
Sam Barlow (Project Student) |
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| Friday |
Discrete Maths Problems Class Zochonis: Theatre C |
Joe Mellor |
Kelly Freeman (Project Student) |
Mathematical Biology Lecture Alan Turing: G.207 |
Complex Systems & Statistical Physics Seminar Niels Bohr Common Room |
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Free SoftwareJ.L. Thorne, H. Kishino and J.S. Painter, "Estimating the rate of evolution of the rate of molecular evolution", Mol. Bio. Evol., 15, pp. 1647-1657, (1998).
Source Release (useful on both Macs and unix machines)
sp.gz is tarred, gzipped archive that contains complete sources and instructions to compile the unix version of the program, divt. There is also a Metrowerks CodeWarrior project to build a Macintosh version, MacDivT. Both versions are command-line affairs: they read and write text files and have only the most rudimentary of user interfaces. The distribution also includes a perl script, LANL2divt.pl, that helps one prepares input files for either divt and MacDivT.
HD Tools: HDent and HDdist are a pair of programs for the analysis of data from heteroduplex mobility and tracking assays (HDA and HTA). There are two versions available, one for older Macs and a simpler, command-line version for windows and unix machines (including modern Macs).
A Binary-only release for Windows
winHDent.zip is a zipped archive that contains a command-line version of HDent, the entropy tool for HMA data.
Source Releases (useful on both Macs and unix machines)
HD_Tools_src1.1.tgz.uu is a uuencoded, tarred, gzipped archive that contains complete sources and instructions to compile both the unix, command-line versions of the programs and the Macintosh versions, which present a standard Mac-like interface.
HD_Tools_src1.1.sea.hqx is a version of the source distribution compressed and encoded in standard Macintosh formats suited for unpacking with StuffIt Expander.
A Binary-only Release (useful only on old Macs)
Mac_HD_Tools1.1.sea.hqx is a binhexed, self-extracting archive of the Macintosh programs. It includes some test files and sample output as well as binaries for both Power PC and 68K machines.
PerOrb: PerOrb, or po for short, is a program to find periodic orbits of the complex mapping T(z) = z^2 + c.
Julia.tgz is a tarred, gzipped archive that contains complete sources for the program, along with instructions about how to compile it. A ReadMe file is also available here on the web.
Preprints & PapersYunjiao Wang, Pawel Paszek, Caroline A. Horton, Yue Hong, Michael R. H. White, Douglas B. Kell, Mark R. Muldoon and David S. Broomhead, A systematic survey of the response of a model NF-κB signalling pathway to TNFα stimulation, Journal of Theoretical Biology, 297, (2012).
Mark Muldoon, Jeremy Huke and Kieran Smallbone, Dave Broomhead's 60th Birthday, Mathematics Today, 47, (2011).
Yunjiao Wang, Pawel Paszek, Caroline A. Horton, Douglas B. Kell, Michael R. H. White, David S. Broomhead and Mark R. Muldoon, Interactions among oscillatory pathways in NF-κB signalling, BMC Systems Biology, 5, (2011).
Jennifer L. Kirchherr, Jennifer Hamilton, Xiaozhi Lu, S. Gnanakaran, Mark Muldoon, Marcus Daniels, Webster Kasongo, Victor Chalwe, Chanda Mulenga, Lawrence Mwananyanda, Rosemary M. Musonda, Xing Yuan, David C. Montefiori, Bette T. Korber, Barton F. Haynes and Feng Gao, Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120, Virology, 409, (2011).
Andrew D. Isaac, Mark Muldoon, Keri A. Brown and Terence A. Brown, Genetic analysis of wheat landraces enables the location of the first agricultural sites in Italy to be identified, Journal of Archaeological Science, 37, (2010).
Rigmor C. Baraas, Janus J. Kulikowski and Mark R. Muldoon, Bar-like S-cone stimuli reveal the importance of an intermediate temporal filter, Journal of the Optical Society of America A, 27, (2010).
Dan H. Barouch, Kara L. O'Brien, Nathaniel L. Simmons, Sharon L. King, Peter Abbink, Lori F. Maxfield, Ying-Hua Sun, Annalena La Porte, Ambryice M. Riggs, Diana M. Lynch, Sarah L. Clark, Katherine Backus, James R. Perry, Michael S. Seaman, Angela Carville, Keith G. Mansfield, James J. Szinger, Will Fischer, Mark Muldoon and Bette Korber, Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys, Nature Medicine, 16, (2010).
Sampa Santra, Hua-Xin Liao, Ruijin Zhang, Mark Muldoon, Sydeaka Watson, Will Fischer, James Theiler, James Szinger, Harikrishnan Balachandran, Adam Buzby, David Quinn, Robert J. Parks, Chun-Yen Tsao, Angela Carville, Keith G. Mansfield, George N. Pavlakis, Barbara K. Felber, Barton F. Haynes, Bette T. Korber and Norman L. Letvin, Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys, Nature Medicine, 16, (2010).
Jasmina Cehajic-Kapetanovic, Paul N. Bishop, Sidath Liyanage, Trevor King, Mark Muldoon and Ian M. Wearne, A novel Ocular Anaesthetic Scoring System, OASS, tool to measure both motor and sensory function following local anaesthesia, British Journal of Ophthalmology, 94, (2010).
Mark Muldoon, External Examiners, Mathematics Today, (2009).
Sampa Santra, Bette T. Korber, Mark Muldoon, Dan H. Barouch, Gary J. Nabel, Feng Gao, Beatrice H. Hahn, Barton F. Haynes and Norman L. Letvin, A centralized gene-based HIV-1 vaccine elicits broad cross-clade cellular immune responses in rhesus monkeys, Proceedings of the National Academy of Sciences of the USA, 105, (2008).
M. J. Conyon and M. R. Muldoon, Ownership and Control: A Small-World Analysis, (2008).
Nicole Frahm, Daniel E. Kaufmann, Karina Yusim, Mark Muldoon, Can Kesmir, Caitlyn H. Linde, Will Fischer, Todd M. Allen, Bin Li, Ben H. McMahon, Kellie L. Faircloth, Hannah S. Hewitt, Elizabeth W. Mackey, Toshiyuki Miura, Ashok Khatri, Steven Wolinsky, Andrew McMichael, Robert K. Funkhouser, Bruce D. Walker, Christian Brander and Bette T. Korber, Increased Sequence Diversity Coverage Improves Detection of HIV-Specific T Cell Responses, Journal of Immunology, 179, (2007).
Rong Rong, S. Gnanakaran, Julie M. Decker, Frederic Bibollet-Ruche, Jesse Taylor, Jeffrey N. Sfakianos, John L. Mokili, Mark Muldoon, Joseph Mulenga, Susan Allen, Beatrice H. Hahn, George M. Shaw, Jerry L. Blackwell, Bette T. Korber, Eric Hunter and Cynthia A. Derdeyn, Unique Mutational Patterns in the Envelope α2 Amphipathic Helix and Acquisition of Length in gp120 Hypervariable Domains Are Associated with Resistance to Autologous Neutralization of Subtype C Human Immunodeficiency Virus Type 1, Journal of Virology, 81, (2007).
Denise L. Kothe, Julie M. Decker, Yingying Li, Zhiping Weng, Frederic Bibollet-Ruche, Kenneth P. Zammit, Maraia G. Slazar, Yalu Chen, Jesus F. Salazar-Gonzalez, Zina Moldoveanu, Jiri Mestecky, Feng Gao, Barton F. Haynes, George M. Shaw, Mark Muldoon, Bette T. M. Korber and Beatrice H. Hahn, Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins, Virology, 360, (2007).
M. J. Conyon and M. R. Muldoon, The Small World of Corporate Boards, Journal of Business Finance and Accounting, 33, (2006).
J. E. Forster, R. V. Abadi, M. Muldoon and I. C. Lloyd, Grading infantile cataracts, Ophthalmic and Physiological Optics, 26, (2006).
Eric A. Weaver, Zhongjing Lu, Zenadio T. Camacho, Fatiha Moukdar, Hua-Xin Liao, Ben-Jiang Ma, Mark Muldoon, James Theiler, Gary J. Nabel, Norman L. Letvin, Bette T. Korber, Beatrice H. Hahn, Barton F. Haynes and Feng Gao, Cross-Subtype T-Cell Immune Responses Induced by a Human Immunodeficiency Virus Type 1 Group M Consensus Env Immunogen, Journal of Virology, 80, (2006).
D. S. Broomhead, J. P. Huke, M. R. Muldoon and J. Stark, Iterated Function System Models of Digital Channels, Proceedings of the Royal Society of London, Series A, 460, (2004).
Cynthia A. Derdeyn, Julie M. Decker, Frederic Bibollet-Ruche, John L. Mokili, Mark Muldoon, Scott A. Denham, Marintha L. Heil, Francis Kasolo, Rosemary Musonda, Beatrice H. Hahn, George M. Shaw, Bette T. Korber, Susan Allen and Eric Hunter, Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission, Science, 303, (2004).
K. Berthelot, M. Muldoon, L. Rajkowitsch, J. Hughes and J. E. G. McCarthy, Dynamics and processivity of 40S ribosome scanning on mRNA in yeast, Molecular Microbiology, 51, (2004).
R. A. Clement, J. P. Whittle, M. R. Muldoon, R. V. Abadi, D. S. Broomhead and O. Akman, Characterisation of congenital nystagmus waveforms in terms of periodic orbits, Vision Research, 42, (2002).
Karina Yusim, Martine Peters, Oliver Pybus, Tanmoy Bhattacharya, Eric Delaporte, Claire Mulanaga, Mark Muldoon, James Theiler and Bette Korber, Using human immunodeficiency virus type 1 sequences to infer historical features of the acquired immune deficiency syndrome epidemic and human immunodeficiency virus evolution, Philosophical Transactions of the Royal Society of London, B, 356, (2001).
M. C. Readman, M. R. Muldoon, L. Reynolds, R. Morris, M. Bayliss, D. Wood and I. Stewart, Control of free length when coiling a helical spring, IEE Proceedings-Control Theory and Applications, 148, (2001).
B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinsky and T. Bhattacharya, Timing the Ancestor of the HIV-1 Pandemic Strains, Science, 288, (2000).
D. S. Broomhead, R. A. Clement, M. R. Muldoon, J. P. Whittle, C. Scallan and R. V. Abadi, Modelling of congenital nystagmus waveforms produced by saccadic system abnormalities, Biological Cybernetics, 82, (2000).
D. S. Broomhead, J. P. Huke and M. R. Muldoon, Codes for spread spectrum applications generated using chaotic dynamical systems, Dynamics and Stability of Systems, 14, (1999).
R. B. Van Dyke, B. T. Korber, E. Popek, C. Macken, S. M. Widmayer, A. Bardeguez, I. C. Hanson, A. Wiznia, K. Luzuriaga, R. R. Viscarello, S. Wolinsky and the Ariel Core Investigators, The Ariel Project: A prospective cohort study of maternal-child transmission of human immunodeficiency virus type 1 in the era of maternal antiretroviral therapy, Journal of Infectious Diseases, 179, (1999).
Xia Jin, Caroline G. P. Roberts, Douglas F. Nixon, Yunzhen Cao, David D. Ho, Bruce D. Walker, Mark Muldoon, Bette T. M. Korber, Richard A. Koup and the ARIEL Project Investigators, Longitudinal and Cross-Sectional Analysis of Cytotoxic T Lymphocyte (CTL) Responses and their Relationship to Vertical HIV Transmission, Journal of Infectious Diseases, 178, (1998).
M. R. Muldoon, D. S. Broomhead, J. P. Huke and R. Hegger, Delay embedding in the presence of dynamical noise, Dynamics and Stability of Systems, 13, (1998).
Yunzhen Cao, Paul Krogstad, Bette T. Korber, Richard A. Koup, Mark Muldoon, Catherine Macken, Jia-Li Song, Zhanqun Jin, Jla-Qi Zhao, Sheila Clapp, Irvin S. Y. Chen, David D. Ho, Arthur J. Ammann and the Ariel Project Investigators, Maternal HIV-1 viral load and vertical transmission of infection: The Ariel Project for the prevention of HIV transmission from mother to infant, Nature Medicine, 3, (1997).
N. Martin, R. Koup, R. Kaslow, A. A. Ammann, A. J. Ammann, D. Asthana, A. Baur, Y. Bryson, S. Clapp, S. DeLaurentis, T. Devine, M. Feinberg, J. E. Fitzgibbon, M. G. Fowler, E. M. Garratty, R. Geffin, A. Gonzaga, M. Gray, S. Hetherington, J. K. Jansen, R. A. Kaslow, A. Keller, M. E. Klotman, B. Korber, A. Louzao, K. Luzuriaga, C. Macken, B. Mathieson, G. McSherry, M. Muldoon, J. I. Mullins, K. Nielsen, J. Oleske, P. Palumbo, A. Petru, S. Plaeger, Y. Riviere, P. Rossi, G. Scott, J. L. Sullivan, S. H. Vermund, D. Wara, R. J. Winchester, C. Winkler and S. Zeegen, Workshop on perinatally acquired human immuno-deficiency virus infection in long-term surviving children: A collaborative study of factors contributing to slow disease progression, Aids Research and Human Retroviruses, 12, (1996).
Mark R. Muldoon, David S. Broomhead and Jeremy P. Huke, Delay reconstruction for multiprobe signals, (1994).
R. S. MacKay and M. R. Muldoon, Diffusing through spectres: ridge curves, ghost circles and a partition of phase space, Physics Letters A, 178, (1993).
M. R. Muldoon, R. S. MacKay, J. P. Huke and D. S. Broomhead, Topology from time series, Physica D, 65, (1993).
D. S. Broomhead, J. Huke and M. R. Muldoon, Linear Filters and Non-linear Systems, Journal of the Royal Statistical Society. Series B, 54, (1992).
This page last changed Monday, 16 April 2012