Ellen Baake
Office: UHG U4-149
Phone: +49-521-106-4896
Fax: +49-521-106-6411
Email: ebaake[at]techfak.uni-bielefeld.de
Phone: +49-521-106-4896
Fax: +49-521-106-6411
Email: ebaake[at]techfak.uni-bielefeld.de
Biographical sketch
Education
- 1999 Habilitation in Zoology and Theoretical Biology, Munich University
- 1989 PhD in Theoretical Biology, Bonn University
- 1980 - 1985 Study of Biology and Mathematics, Bonn University (diploma in biology 1985)
Professional Career
- since 2004 Professor for Biomathematics and Theoretical Bioinformatics,
Faculty of Technology, Bielefeld University
(associate professor until 2012, full professor since 2012;
joint membership in Faculty of Mathematics, Bielefeld University since 2011) - 1989 - 2004 Positions/fellowships at
- Augsburg University (Mathematics Institute)
- Max-Planck-Institute for Developmental Biology (Tuebingen)
- University of Edinburgh (Institute for Cell, Animal, and Plant Biology)
- Munich University (Zoology Department)
- Greifswald University (Department of Mathematics and Computer Science)
- Bielefeld University (Faculty of Technology)
- Vienna University (Faculty of Mathematics)
Research
Research interests:
- Mathematical population genetics
- Probability theory
- Mathematical immunobiology
Current projects with third-party funding:
- since 2017 PI in DFG Collaborative Research Centre 1283
Taming uncertainty and profiting from randomness and low regularity in analysis,
stochastics and their applications
Within Bielefeld University:
- since 2006 Speaker of the Research Centre for Mathematical Modelling
Miscellanea
- 2021-2023 President of ESMTB (European Society of Mathematical and Theoretical Biology)
-
2016 Plenary talk at the BeNeLux Mathematical Congress,
Amsterdam (BeNeLuxMC 2016) - 2011-2022 Coordinator of DFG Priority Programme Probabilistic Structures in Evolution
-
2011 Offer of Chair of Biomathematics (W3) at the Department of Mathematics,
University of Erlangen-Nuernberg (declined) -
2010 Invited sectional talk at the International Congress of Mathematicians,
Hyderabad (ICM 2010) -
2008 Plenary talk at the European Conference on Mathematical and Theoretical Biology,
Edinburgh (ECMTB 2008) - 2007 Kloosterman Chair, Leiden University
Publications and preprints
Book
- E. Baake, A. Wakolbinger (eds.), Probabilistic Structures in Evolution, EMS Press, Berlin, 2021.
Preprints & Recent Articles
The more recent ones can be downloaded as pdf's or gzipped postscript files.
They are also available at http://www.arXiv.org.
Matrix functions and Markov embedding
- E. Baake, M. Baake
An alternative recursive approach to functions of simple triangular matrices
[Preprint]
- E. Baake, M. Baake
- E. Baake, M. Baake
A multiple coupon collection process and its Markov embedding structure
[Preprint]
Experimental evolution
- E. Baake, A. Wakolbinger
Microbial populations under selection
(in E. Baake, A. Walkolbinger (eds.), Probabilistic Structures in Evolution,
EMS Press, Berlin, 2021, pp.43-68)
[Preprint], [Book publication]
- E. Baake, A. González Casanova, S. Probst, A. Wakolbinger
Modelling and simulating Lenski's long-term evolution experiment
Theor. Popul. Biol., 127 (2019), 58-74
[Preprint], [Journal publication] This paper won the 2022 Feldman Prize
Mutation-selection models
-
E. Baake, F. Cordero, E. Di Gaspero
Killing versus catastrophes in birth-death processes and an application to population genetics
[Preprint] -
E. Baake, E. Di Gaspero, F. Cordero
The mutation process on the ancestral line under selection
Theor. Popul. Biol., 158 (2024), 60-75
[Preprint], [Journal publication] -
E. Baake, L. Esercito, S. Hummel
Lines of descent in a Moran model with frequency-dependent selection and mutation
Stoch. Process. their Appl., 160 (2023), 409-457
[Preprint], [Journal publication] -
E. Baake, F. Cordero, S. Hummel
Lines of descent in the deterministic mutation-selection model with pairwise interaction
Ann. Appl. Probab., 32 (2022), 2400-2447
[Preprint], [Journal publication] -
E. Baake, A. Wakolbinger
Lines of descent under selection
J. Stat. Phys., 172 (2018), 156-174
[Preprint], [Journal publication] -
E. Baake, F. Cordero, S. Hummel
A probabilistic view on the deterministic mutation-selection equation: dynamics, equilibria, and ancestry via individual lines of descent
J. Math. Biol., 77 (2018), 795-820
[Preprint], [Journal publication] -
E. Baake, U. Lenz, A. Wakolbinger
The common ancestor type distribution of a Λ-Wright-Fisher process with selection and mutation
Electron. Commun. Probab., 21 (2016), no. 59, 1–16
[Preprint], [Journal publication] -
U. Lenz, S. Kluth, E. Baake, A. Wakolbinger
Looking down in the ancestral selection graph: A probabilistic approach to the common ancestor type distribution
Theor. Pop. Biol., 103 (2015), 27-37
[Preprint], [Journal publication] -
S. Kluth, E. Baake
The Moran model with selection: Fixation probabilities, ancestral lines, and an alternative particle representation
Theor. Pop. Biol., 90 (2013), 104–112
[Preprint], [Journal publication] -
S. Kluth, T. Hustedt, E. Baake
The common ancestor process revisited
Bull. Math. Biol., 75 (2013), 2003-2027
[Preprint], [Journal publication] -
E. Baake, R. Bialowons
Ancestral processes with selection: Branching and Moran models
Banach Center Publications, 80 (2008), 33-52
[Preprint], [Journal publication] -
E. Baake, H.-O. Georgii
Mutation, selection, and ancestry in branching models: a variational approach
J. Math. Biol., 54 (2007), 257-303
[Preprint], [Journal publication] -
E. Baake, M. Baake, A. Bovier, M. Klein
An asymptotic maximum principle for essentially linear evolution models
J. Math. Biol., 50 (2005), 83-114
[Preprint], [Journal publication] -
J. Hermisson, O. Redner, H. Wagner, E. Baake
Mutation-selection Balance: Ancestry, Load, and Maximum Principle
Theor. Pop. Biol. 62 (2002), 9-46
[Preprint], [Journal publication] -
E. Baake, H. Wagner
Mutation-selection models solved exactly with methods from statistical mechanics
Gen. Res. 78 (2001), 93-117
[Preprint], [Journal publication] -
E. Baake, W. Gabriel
Biological evolution through mutation, selection, and drift: An introductory review
Ann. Rev. Comp. Phys. VII (2000), 203-264
[Preprint][Journal publication] -
H. Wagner, E. Baake, T. Gerisch
Ising quantum chain and sequence evolution
J. Stat. Phys. 92 (1998), 1017-1052
[Preprint], [Journal publication] -
E. Baake, M. Baake, H. Wagner
Quantum mechanics versus classical probabilities in biological evolution
Phys. Rev. E 57 (1998), 1191-1192
[Preprint], [Journal publication] -
H. Wagner, E. Baake
Ising quantum chain and biological evolution
Physical Applications and Mathematical Aspects of Geometry, Groups and Algebras
eds. H.-D. Doebner, P. Nattermann, W. Scherer, World Scientific, Singapore (1997), vol.II, 821
[Preprint] -
E. Baake, M. Baake, H. Wagner
Ising quantum chain is equivalent to a model of biological evolution
Phys. Rev. Lett. 78 (1997), 559-562 (size: 182 kB) + Erratum!
[Preprint], [Journal publication] -
E. Baake
Diploid Sequence Space, Dominance, and Evolution
Advances in Mathematical Population Dynamics - Molecules, Cells and Man
eds. O. Arino, D. Axelrod, M. Kimmel, World Scientific, Singapore (1997), 1-15
[Preprint] -
E. Baake, T. Wiehe
Bifurcations in haploid and diploid sequence space models
J. Math. Biol. 35 (1997), 321-343
[Preprint], [Journal publication] -
T. Wiehe, E. Baake, P. Schuster
Error propagation in reproduction of diploid organisms.
A case study on single peaked landscapes
J. Theor. Biol. 177 (1995), 1-15
[Preprint], [Journal publication] -
E. Baake
Diploid models on sequence space
J. Biol. Syst. 3 (1995), 343-349
[Journal publication]
Recombination
- F. Alberti, E. Baake
Solving the selection-recombination equation: Ancestral lines and dual processes
Doc. Math. 26 (2021), 743-793
[Preprint] [Journal publication] -
F. Alberti, C. Herrmann, E. Baake
Selection, recombination, and the ancestral initiation graph
Theor. Popul. Biol., 42 (2021), 46-56
[Preprint] [Journal publication] - F. Alberti, E. Baake, I. Letter, S. Martinez
Solving the migration-recombination equation from a genealogical point of view
J. Math. Biol. 82 (2021), article no. 41 (27 pp)
[Preprint] [Journal publication] - E. Baake, M. Baake
Ancestral lines under recombinations
(in E. Baake, A. Walkolbinger (eds.), Probabilistic Structures in Evolution, EMS Press, Berlin, 2021, pp. 365-382)
[Preprint], [Book publication] - E. Baake, M. Esser
Fragmentation Process, Pruning Poset for Rooted Forests, and Moebius Inversion
Markov Proc. Relat. Fields 24 (2018), 57-84
[Preprint] [Journal publication] - E. Baake, M. Baake
Haldane linearisation done right: Solving the nonlinear recombination equation the easy way
Discrete Contin. Dyn. Syst. 36 (2016), 6645-6656
[Preprint] [Journal publication] -
M. Esser, S. Probst, E. Baake
Partitioning, duality, and linkage disequilibria in the Moran model with recombination
J. Math. Biol. 73 (2016), 161-197
[Preprint], [Journal publication] -
E. Baake, M. Baake, M. Salamat
The general recombination equation in continuous time and its solution
Discrete Contin. Dyn. Syst. 36 (2016), 63-95
[Preprint], [Journal publication] -
E. Baake, U. von Wangenheim
Single-Crossover Recombination and Ancestral Recombination Trees
J. Math. Biol. 68 (2014), 1371-1402
[Preprint], [Journal publication] -
E. Baake, T. Hustedt
Moment closure in a Moran Model with recombination
Markov Proc. Relat. Fields 17 (2011), 429-446
[Preprint] -
E. Baake
Deterministic and stochastic aspects of single-crossover recombination
Proceedings of the International Congress of Mathematicians, Hyderabad, India, 2010, Vol. VI, 3037-3053
[Preprint] -
U. von Wangenheim, E. Baake, M. Baake
Single-crossover recombination in discrete time
J. Math. Biol. 60 (2010), 727-760
[Preprint], [Journal publication] -
E. Baake, I. Herms
Single-crossover dynamics: finite versus infinite populations
Bull. Math. Biol. 70 (2008), 603-624
[Preprint], [Journal publication] -
M. Baake, E. Baake
An exactly solved model for recombination, mutation and selection
Can. J. Math. 55 (2003),3-41
[Preprint], [Journal publication] -
E. Baake
Mutation and recombination with tight linkage
J. Math. Biol. 42 (2001), 455-488
[Preprint], [Journal publication]
Branching processes
-
H.-O. Georgii, E. Baake
Supercritical multitype branching processes: The ancestral type of typical individuals
Adv. Appl. Prob. 35 (2003), 1090-1110
[Preprint], [Journal publication]
Immune biology
-
C. Ernst, E. Baake
Rare event simulation in immune biology: Models of negative selection in T-cell maturation
Proceedings of the 10th International Workshop on Rare Event Simulation, RESIM 2014, 27-29 Aug 2014, Amsterdam, The Netherlands, p. 43.
[Preprint] -
F. Lipsmeier, E. Baake
Rare event simulation for T-cell activation
J. Stat. Phys., 134 (2009), 537-566
[Preprint], [Journal publication] -
F. Lipsmeier, E. Baake
Rare event simulation in immunobiology
Proc. 7th International Workshop on Rare Event Simulation RESIM 2008,
Rennes, France, 24-26 September 2008
[Preprint] -
N. Zint, E. Baake, F. den Hollander
How T-cells use large deviations to recognize foreign antigens
J. Math. Biol. 57 (2008), 841-861
[Preprint], [Journal publication]
Molecular phylogeny
-
E. Baake, A. v. Haeseler
Distance measures in terms of substitution processes
Theor. Pop. Biol. 55 (1999), 166-175
[Preprint], [Journal publication] -
E. Baake
What can and what cannot be inferred from pairwise sequence comparisons?
Math. Biosci. 154 (1998), 1-21
[Preprint], [Journal publication]
History of Biomathematics
-
E. Baake, A. Wakolbinger
Feller's Contributions to Mathematical Biology
Article will appear in: The Selected Papers of William Feller. Springer Verlag
[Preprint] -
E. Baake
Are mutations spontaneous or directed?
NAW 5/8 (2007), 171-174
[Preprint], >[Newsletter publication]
Parameter identification
-
E. Baake, M. Baake, E. Eich
On the role of invariants for the parameter estimation problem in Hamiltonian systems
Phys. Lett. A180 (1993), 74-822
[Journal publication] - E. Baake, M. Baake, H.G. Bock, K.M. Briggs
Fitting ordinary differential equations to chaotic data
Phys. Rev. A45 (1992), 5524-5529
[Journal publication]
Photosynthesis
- E. Baake, J. P. Schlöder
Modelling the fast fluorescence rise of photosynthesis
Bull. Math. Biol. 54 (1992), 999-1021
[Journal publication] - E. Pfündel, E. Baake
A quantitative description of fluorescence excitation spectra in intact bean leaves greened under intermittent light
Photosynth. Res. 26 (1990), 19-28
[Journal publication]
Root growth
- E. Buff, M. Baake, A. Sievers
An empirical function for the description of root growth
Plant Physiol. 83 (1987), 685-690
[Journal publication] - M. Baake, E. Buff
From cell growth to root growth
J. Theor. Biol. 123 (1986), 347-365
[Journal publication]
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