There is an article “
Can biology lead to new theorems?
” by Sturmfels on biology and mathematics.

Phylogenetic trees are now studied by using
mathematical tools.

Other biological structures such as RNAs and proteins
are studied mathematically. For example,
[
JQR
,
PKWA
]
. A more topological one is
[
DLV
]
.

I learned the word phylogenomics in
[
PS
]
. Statistics,
combinatorics
,
probability
, and
algebraic geometry
are related to this subject.

According to Carr, Devadoss, and Forcey
[
?
]
,
graph associahedra
appear in biological statistics
[
MPS
^{
+
}
]
.

Oriented matroids
appear in biochemistry. For example,
[
OBJOD01
,
BGO
]
.

The structure called branched polymer introduced as
models in chemistry and biology seems to be
interesting. See, for example, Brydges and Imbre
[
BI03
]
, Kenyon and Winkler
[
KW
]
, and Meszaros and Postnikov
[
MP
]
. Meszaros and Postnikov found a relation to
hyperplane arrangements

When we apply Leinster’s deﬁnition of
the Euler characteristic of small categories
to
metric spaces
regarded as enriched categories, we obtain the notion
of magnitude. It appeared in a paper on biodiversity
[
SP94
]
independently.

[BGO]
C. G. Bailey, D. W. Gull, and
J. S. Oliveira. Hypergraphic Oriented Matroid
Relational Dependency Flow Models of Chemical
Reaction Networks,
arXiv:0902.0847
.

[BI03]
David C. Brydges and John Z. Imbrie.
Branched polymers and dimensional reduction.
Ann. of Math. (2)
, 158(3):1019–1039, 2003,
http://dx.doi.org/10.4007/annals.2003.158.1019
.

[DLV]
Isabel K. Darcy, John Luecke, and Mariel
Vazquez. Tangle analysis of difference topology
experiments: applications to a Mu protein-DNA
complex,
arXiv:0710.4150
.

[JQR]
Emma Y. Jin, Jing Qin, and
Christian M. Reidys. Combinatorics Of RNA
Structures With Pseudoknots,
arXiv:0704.2518
.

[KW]
Richard Kenyon and Peter Winkler. Branched Polymers,
arXiv:0709.2325
.

[MP]
Karola Meszaros and Alexander Postnikov. Branched
polymers and hyperplane arrangements,
arXiv:0909.4547
.

[MPS
^{
+
}
]
Jason Morton, Lior Pachter, Anne Shiu, Bernd
Sturmfels, and Oliver Wienand. Convex Rank Tests and
Semigraphoids,
arXiv:math/0702564
.

[OBJOD01]
Joseph Oliveira, Colin Bailey, Janet Jones-Oliveira,
and David Dixon. An algebraic-combinatorial model
for the identiﬁcation and mapping of
biochemical pathways.
Bulletin of Mathematical
Biology
, 63(6):1163–1196, November 2001.

[PKWA]
R. C. Penner, Michael Knudsen, Carsten Wiuf,
and Joergen Ellegaard Andersen. Fatgraph
Models of Proteins,
arXiv:0902.1025
.

[PS]
Lior Pachter and Bernd Sturmfels. The Mathematics of
Phylogenomics,
arXiv:math/0409132
.

[SP94]
A. Solow and S. Polasky. Measuring
biological diversity.
Environmental and Ecological Statistics
, 1:95–107, 1994.