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Article
Open AccessMetabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target
The genomic landscape of colorectal cancer (CRC) is shaped by inactivating mutations in tumour suppressors such as APC, and oncogenic mutations such as mutant KRAS. Here we used genetically engineered mouse model...
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Article
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer
Oncogenic KRAS mutations and inactivation of the APC tumor suppressor co-occur in colorectal cancer (CRC). Despite efforts to target mutant KRAS directly, most therapeutic approaches focus on downstream pathways,...
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Article
Open AccessAuthor Correction: Loss of BCL9/9l suppresses Wnt driven tumourigenesis in models that recapitulate human cancer
The original version of this Article contained an error in the spelling of the author Miryam Müller, which was incorrectly given as Miryam Müeller. This has now been corrected in both the PDF and HTML versions...
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Article
Open AccessLoss of BCL9/9l suppresses Wnt driven tumourigenesis in models that recapitulate human cancer
Different thresholds of Wnt signalling are thought to drive stem cell maintenance, regeneration, differentiation and cancer. However, the principle that oncogenic Wnt signalling could be specifically targeted ...
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Article
Mannose impairs tumour growth and enhances chemotherapy
It is now well established that tumours undergo changes in cellular metabolism1. As this can reveal tumour cell vulnerabilities and because many tumours exhibit enhanced glucose uptake2, we have been interested i...
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Chapter and Conference Paper
Revisiting Expression Representations for Nonlinear AMPL Models
AMPL facilitates stating and solving nonlinear programming problems involving algebraically defined objectives and constraints. For solving such problems, the AMPL/solver interface library provides routines th...
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Chapter and Conference Paper
The AMPL Modeling Language: An Aid to Formulating and Solving Optimization Problems
Optimization problems arise in many contexts. Sometimes finding a good formulation takes considerable effort. A modeling language, such as AMPL, facilitates experimenting with formulations and simplifies using...
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Chapter and Conference Paper
Using Expression Graphs in Optimization Algorithms
An expression graph, informally speaking, represents a function in a way that can be manipulated to reveal various kinds of information about the function, such as its value or partial derivatives at specified...
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Chapter and Conference Paper
Large-Scale Transient Sensitivity Analysis of a Radiation-Damaged Bipolar Junction Transistor via Automatic Differentiation
Automatic differentiation (AD) is useful in transient sensitivity analysis of a computational simulation of a bipolar junction transistor subject to radiation damage. We used forward-mode AD, implemented in a ...
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Chapter and Conference Paper
Semiautomatic Differentiation for Efficient Gradient Computations
Many large-scale computations involve a mesh and first (or sometimes higher) partial derivatives of functions of mesh elements. In principle, automatic differentiation (AD) can provide the requisite partials m...
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Chapter and Conference Paper
Automatic Differentiation of C++ Codes for Large-Scale Scientific Computing
We discuss computing first derivatives for models based on elements, such as large-scale finite-element PDE discretizations, implemented in the C++ programming language. We use a hybrid technique of automatic ...
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Chapter
Design Principles and New Developments in the AMPL Modeling Language
The design of the AMPL modeling language stresses naturalness of expressions, generality of iterating over sets, separation of model and data, ease of data manipulation, and automatic updating of derived value...
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Chapter and Conference Paper
Symbolic-Algebraic Computations in a Modeling Language for Mathematical Programming
AMPL is a language and environment for expressing and manipulating mathematical programming problems, i.e., minimizing or maximizing an algebraic objective function subject to algebraic constraints. The AMPL proc...
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Chapter
Conveying Problem Structure from an Algebraic Modeling Language to Optimization Algorithms
Optimization algorithms can exploit problem structures of various kinds, such as sparsity of derivatives, complementarity conditions, block structure, stochasticity, priorities for discrete variables, and info...
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Chapter
A Primal-dual Interior Method for Nonconvex Nonlinear Programming
Primal-dual interior methods for nonconvex nonlinear programming have recently been the subject of significant attention from the optimization community. Several different primal-dual methods have been suggest...
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Chapter
Experience with a Primal Presolve Algorithm
Sometimes an optimization problem can be simplified to a form that is faster to solve. Indeed, sometimes it is convenient to state a problem in a way that admits some obvious simplifications, such as eliminati...
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Chapter and Conference Paper
AMPL: A Mathematical Programing Language
Practical large-scale mathematical programming involves more than just the minimization or maximization of an objective function subject to constraint equations and inequalities. Considerable effort must be ex...
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Article
A variant of Karmarkar's linear programming algorithm for problems in standard form
This paper presents a variant of Karmarkar's linear programming algorithm that works directly with problems expressed in standard form and requires no a priori knowledge of the optimal objective function value...
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Chapter and Conference Paper
A trust-region approach to linearly constrained optimization
This paper suggests a class of trust-region algorithms for solving linearly constrained optimization problems. The algorithms use a “local” active-set strategy to select the steps they try. This strategy is su...
