First week: A crash course in computational complexity heavily biased toward quantum computing can be found in [2, Part 1] or [1, Ch. 3.1-3.2]. If you are interested in more details, see the excellent textbook [4]. For a comprehensive treatment of circuit complexity I particularly recommend [5]. Reversible circuits: [3, Ch. 1.5] or [2, Ch, 7]; simulation of any classical computation with a reversible one (aka Garbage Removal Lemma): [3, Fig. 1.6] or [2, Lemma 7.2]. The physics of Landauer's principle is discussed in [1, Ch. 3.2.5], see also Wikipedia article. Matrix form of circuit computations: [3, Ch. 1.4]. Probabilistic computation: [2, Ch. 4.3] (for an in-depth treatment see [4, Ch. 1.7]). For doubly stochastic matrices, Birkhoff-von Neumann theorem and much more see e.g. [6]. Rudimentary facts and notation from linear algebra (tensor products, Hilbert spaces, adjoint operators, unitary operators, unit vectors as pure states of a quantum system etc.) can be found in any of our textbooks; I particularly recommend [1, Ch. 2.1]. Mathematics and physics of Pauli matrices are extensively discussed in the Wikipedia article. Hadamard gate. Dirac's notation.
Second week: Completeness result for exact realization: [2, Ch. 8.1]. Universal/complete bases: [2, Ch. 8.2, 8.3] or [3, Ch. 4.3, 4.4]. Simulation of probabilistic computations by quantum circuits: [3, Ch. 6.1]. Oracle separation results in complexity theory: [4, Ch. 3.4]. Oracle separation of BQP from PH (and hence BPP): [7]. Deutsch algorithm: [3, Ch. 6.3]. Our exposition of Deutsch-Jozsa closely follows the one given in [3, Ch. 6.4]. Hidden Subgroup Problem will be thoroughly discussed later in the course, for now see [8] (and do drop me a word if you know of any more recent developments). Simon's algorithm: [3, Ch. 6.5]. $BQP\subset PP$: see [1, Ch. 4.5.5] for a slightly weaker result.
Third week: Grover's search algorithm: [3, Ch. 8.1]. Shor's algorithm. The reduction of factoring to order-finding goes back to Miller (1975). Our exposition is close to [2, Ch. 13.3] but the best shot at tedious technical details is [1, Appendix 4]. In particular, the continuous fraction result that we skipped is [1, Theorem A4.16]. Normal operators: [1, Ch. 2.1.6]. Operator $U_a$, its eigenvalues and eigenvectors: [3, Ch. 7.3.3]. Eigenvalue estimation problem. Controlled operators $c-U$ (aka $\Lambda^1(U)$) and $c-U^x$: [3, Ch 7.2]. Quantum Fourier Transform $QFT_m$ and its inverse [3, Ch 7.1]. For an efficient realization of $QFT_{2^h}$ see [3, Ch. 7.3].
Fourth week: Discrete Logarithm: [3, Ch. 7.4]. For the Hidden Subgroup Problem in Abelian groups, I recommend [2, Ch. 13.8]; as I said before, [8] is a good survey in the non-Abelian case (the application to Graph Isomorphism seems to be a part of folklore). Our exposition of the hybrid method more or less follows [3, Ch. 9.3]. Mega-theorem about polynomial equivalence of various complexity measures for total functions, along with references, can be found (in bits and pieces) in the survey [9], see in particular Theorems 10, 11, 2, 7, 17 and 18.
Fifth week: Mega-theorem cntd. Approximate degree of AND-OR tree (without proof): [10,11]. The paper [12] exploits pointer functions technique for solving more open problems in the area; in particular it gives strong separations between the opposite sides of the spectrum in our mega-theorem. The solution of the sensitivity conjecture: [13]. The standard textbook in classical communication complexity is [14] (see also [4], [5] or check out my survey [15] for an exposition at a highly introductory level). Deterministic communication complexity [14, Ch. 1.4] or [15, Sct. 2].
Sixth week: The rank lower bound [14, Ch. 1.4]. Probabilistic communication complexity [14, Ch. 3]. Rabin's protocol for the equality function [14, Example 3.5]. The quantum communication complexity was introduced in [16]. The decomposition theorem for quantum communication protocols also appeared in [16], and it was further refined in [17,18]. The lower bound in terms of the spectral norm of the communication matrix is from [17]. The same lower bound for the (classical) unbounded-error case, without proof: [19]. The relation between quantum decision tree and communication complexities for block-composed functions was observed in [20]. Lower bounds for block-composed functions with the outer function symmetric (statement): [18,21].
Seventh week: For trace norm (as well as many others): [22]. Approximate trace norm was introduced in [18], and the same paper proved tight lower bounds for symmetric predicates. A simpler proof based on generalized discrepancy was given in [21]. Our exposition of Quantum Probability follows [3, Ch. 3.5] or [2, Ch. 10]. Density matrices. Concrete examples of physically realizable operators (aka superoperators): unitary action, probabilistic quantum circuits, one qubit noise models (an excellent overview of those can be found in [1, Ch. 8.3]), tracing out, projective measurements, unitary embeddings. The axiomatic definition of superoperatotrs is in [1, Ch. 8.2.4]; note that they consider a slightly more general case when the trace is allowed to decrease. Tracing-out + unitary embedding: [2, Problem 11.1]. Operator-sum representation: [1, Ch. 8.2.3.]; for another account see [2, Ch. 11.1]. [1, Theorem 8.1] provides a detailed proof of the equivalence of two definitions we sketched in class. Trace distance: [1, Ch. 9.2.1]. Superoperators do not increase trace distance: [1, Theorem 9.2].
Eighth week: Classical error-correction (concept). Projective and syndrom measurements [3, Ch. 3.4]. Three qubit bit/phase flip codes are in [1, Ch. 10.1], and the Shor code is in [1, Ch. 10.2]. This Wikipedia article provides a very good overview of those aspects of quantum error-correction we have touched in our course. Criterium of quantum recovery [1, Theorem 10.1]. Unitary equivalence for mixed states: [1, Theorem 2.6]. Unitary equivalence for operator-sum representations: [1, Theorem 8.2].
Ninth week: Criterium of quantum recovery cntd. Discretization of the errors: [1, Sct. 10.3.1]. Stabilizer codes [1, Ch. 10.5]. Quantum Merlin-Arthur: [23].