(All papers listed here are based on work partially supported by the NSF and the Alfred P. Sloan foundation).
Notes on supersymmetric and holomorphic field theories in dimensions $2$ and $4$. Dedicated to Dennis Sullivan on the occassion of his 70th birthday. This is now arXiv:1111.4234.
Quantum BCOV theory on Calabi-Yau manifolds and the higher genus B-model. Joint with Si Li. Here is the pdf.
Factorization algebras in perturbative quantum field theory, joint with Owen Gwilliam. This still requires quite a bit of work. A draft is available in two formats: either as a wiki or as a more conventional pdf file. (Last updated: December 16, 2011).
A geometric construct of the Witten genus. This is a sequence of two papers, both of which are now on the arxiv: here and here.
Abstract: I describe how the Witten genus of a complex manifold $X$ can be seen from a rigorous analysis of a certain two-dimensional quantum field theory of maps from a surface to $X$.
Renormalization and effective field theory. This is my book on the foundations of perturbative quantum field theory, from a point of view which emphasizes the Wilsonian low-energy effective field theories and the Batalin-Vilkvovisky formalism. This has now been published by the AMS, so the pdf file has been taken down from this website. Here is the AMS website from the book; you can buy it soon from your friendly online bookstore.
I also have some slides from talks I've been giving about this material.
Renormalization and the Batalin-Vilkovisky formalism arXiv:0706.1533
This paper contains an early version of some of the ideas in the longer paper above. The aim of this paper was to get, as quickly
as possible, to the construction of a non-trivial theory (perturbative
Chern-Simons theory). Unfortunately, though, this paper doesn't
do a good job of explaining the Wilsonian philosophy underlying
everything, so I wouldn't really recommend reading it.