Cluster partitions and fitness landscapes of the Drosophila fly microbiome

Journal of Mathematical Biology - Tập 79 Số 3 - Trang 861-899 - 2019
Holger Eble1, Michael Joswig1, Lisa Lamberti2, William B. Ludington3
1Institut für Mathematik MA 6-2, TU Berlin, Berlin, Germany
2Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
3Department of Embryology, Carnegie Institution for Science, Baltimore, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Assarf B, Gawrilow E, Herr K, Joswig M, Lorenz B, Paffenholz A, Rehn T (2017) Computing convex hulls and counting integer points with polymake. Math Program Comput 9(1):1–38

Beerenwinkel N, Pachter L, Sturmfels B (2007) Epistasis and shapes of fitness landscapes. Stat Sin 17(4):1317–1342

Beerenwinkel N, Pachter L, Sturmfels B, Elena SF, Lenski RE (2007) Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol 7(1):60

Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29(4):1165–1188

Brenner J, Cummings L (1972) The Hadamard maximum determinant problem. Am Math Monthly 79:626–630

Dauxois J, Hassenforder C (2004) Toutes les probabilités et les statistiques: cours et exercices corrigés. Ellipses

De Loera JA, Rambau J, Santos F (2010) Triangulations, vol 25 of algorithms and computation in mathematics. Springer, Berlin (Structures for algorithms and applications)

de Visser JAGM, Krug J (2014) Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet 15(7):480–490

Edelsbrunner H, Harer JL (2010) Computational topology. American Mathematical Society, Providence (An introduction)

Everitt BS, Skrondal A (2010) The Cambridge dictionary of statistics, 4th edn. Cambridge University Press, Cambridge

Gawrilow E, Joswig M (2000) polymake: a Framework for Analyzing Convex Polytopes. In: Kalai G, Ziegler GM (eds) Polytopes — Combinatorics and Computation. DMV Seminar, vol 29. Birkhäuser, Basel

Gentle JE (2002) Elements of computational statistics. Statistics and computing. Springer, New York

Gould AL, Zhang V, Lamberti L, Jones EW, Obadia B, Gavryushkin A, Carlson JM, Beerenwinkel N, Ludington WB (2017) High-dimensional microbiome interactions shape host fitness. bioRxiv

Hallgrímsdóttir IB, Yuster DS (2008) A complete classification of epistatic two-locus models. BMC Genet 9(1):17

Herrmann S, Joswig M (2008) Splitting polytopes. Münster J Math 1:109–141

Herrmann S, Joswig M, Speyer D (2014) Dressians, tropical Grassmannians, and their rays. Forum Math 26(6):1853–1882

Kreznar JH, Keller MP, Traeger LL, Rabaglia ME, Schueler KL, Stapleton DS, Zhao W, Vivas EI, Yandell BS, Broman AT, Hagenbuch B, Attie AD, Rey FE (2017) Host genotype and gut microbiome modulate insulin secretion and diet-induced metabolic phenotypes. Cell Rep 18(7):1739–1750

Maclagan D, Sturmfels B (2015) Introduction to tropical geometry, volume 161 of graduate studies in mathematics. American Mathematical Society, Providence

Schervish MJ (1996) Theory of statistics. Springer Series in Statistics. Springer, New York

Seidel R (2018) Convex hull computations. In: Tóth CD, Goodmann JE, Rourke JO (eds) Handbook of discrete and computational geometry, chapter 26, 23rd edn. CRC Press, Boca Raton

Tsagris M, Beneki C, Hassani H (2014) On the folded normal distribution. Mathematics 2(1):12–28

Wright Sewall (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution. In: Proceedings of the sixth international congress of genetics, vol 1, pp 356–366