Here is a partial bibliography of Cell Matrix-related work; this is from the original technical website. Below is a collection of direct links to various Cell Matrix-related papers.

Conference Papers

CEC-99 (Congress on Evolutionary Computing): Implementing a Ringed GA on the Cell Matrix

EH-99 (NASA/DoD Conference on Evolvable Hardware): Introdution to the Cell Matrix

EH-02: Paper summariing work on a NASA SBIR on Autonomous Fault Handling

EH-05: Paper presenting the commercially-available MOD-88 (an 8x8 implementation of the Cell Matrix).

AHS-2007: Conference on Adaptive Hardware Systems. Paper on self-replication and parallel configuration. 

Paper on InfoSec implications of the Cell Matrix (BLISS 2009)

Other Publications

2001 Nanotechnology Conference: Journal paper describing the Cell Matrix and how it might utuilize nanotechnology. This paper was also translated into French by Aurélien Sagnier as part of his degree work.

A book chapter on Introspective Circuits

Book chapter on Quadrillion-Element Circuits

A book chapter that discusses self-awareness in digital systems

A book chapter on self-organizing digital systems This is also the first written work on the Songline Processor.

Technical Reports

Unpublished paper describing the concept of Magic Polygons as a graphical language for describing self-modifying circuitry.

Reports from a 2003-2006 LANL project on scalable architectures.

Final report on a 2001 NASA SBIR on self-repairing systems.

Paper based on Bin Wang's thesis on DNA sequence alignment using a Cell Matrix

Very early paper describing dynamic circuit building techniques on the Cell Matrix

Really early paper (1998) trying to pitch the unique advantages of the Cell Matrix. Frustration over the inability to interest anyone in this caused a change of gears, leading to the filing of patent paperwork.

Unpublished paper on parallel bootstrap using Medusa circuitry on the Cell Matrix.  The paper was submitted electronically and had a movie embedded inside the PDF; but one reviewer freaked out because the paper "asks the reader to 'click on a figure'" and they couldn't understand how to click on a piece of paper.

Master's Thesis

Dimitri Yatsenko: Thesis on a place-and-route toolchain developed for Cell Matrix circuit synthesis.

Bin Wang: Thesis on using the Cell Matrix to implement a parallel DNA sequence allignment algorithm.

Patents

Four patents related to the Cell Matrix.