- F. Rabe, M. Kohlhase, A Web-Scalable Module System for Mathematical Theories - the original paper on MMT (Journal Information & Computation, 2013)
- F. Rabe, How to Identify, Translate, and Combine Logics? - a more modern and more formal definition of MMT with special emphasis on logic (Journal of Logic and Computation, 2017)
- F. Rabe, The Future of Logic: Foundation-Independence - a high-level summary of the MMT approach (Journal Logica Universalis, Winner of the Contest “The Future of Logic” at the World Congress on Universal Logic, 2015)
- M. Kohlhase, F. Rabe, QED Reloaded: Towards a Pluralistic Formal Library of Mathematical Knowledge - our vision of the QED approach based on MMT (Journal of Formalized Reasoning, 2016)
- F. Rabe, The MMT System - the (by now somewhat outdated) main system description for MMT (CICM conference, LNCS 2013)

This list is always outdated. Most relevant papers can be found in Florian Rabe’s publication list.

There is also an entry for MMT in the swMath catalog of mathematical software.

- M. Kohlhase, F. Mance, F. Rabe, A Universal Machine for Biform Theory Graphs - biform theories (deduction and computatiton) in MMT with a practical integration of MMT and Scala (published at CICM 2013)
- D. Ginev, M. Iancu, F. Rabe, Integrating Content and Narration-Oriented Document Formats - an integration between MMT and LaTeX
- M. Iancu, M. Kohlhase, Searching the Space of Mathematical Knowledge - this application uses MMT to generate smart search indices that include inherited and computed knowledge (published at MIR 2012)
- M. Iancu, F. Rabe, Work-in-progress: An MMT-Based User-Interface - a summary of the state of editing in MMT (published at UITP 2012)
- F. Horozal, M. Kohlhase, F. Rabe, Extending MKM Formats at the Statement Level - introduces an extension of MMT with user-declared declaration types, also called pragmatic MMT (published at MKM 2012, LNCS)
- F. Rabe, A Query Language for Formal Mathematical Libraries - introduces the QMT query language for MMT (published at MKM 2012, LNCS)
- M. Iancu, F. Rabe, Management of Change in Declarative Languages - studies change management generically at the MMT level (published at AISC 2012, LNCS)
- F. Horozal, A. Iacob, C. Jucovschi, M. Kohlhase, F. Rabe, Combining Source, Content, Presentation, Narration, and Relational Representation - introduces the concept of MMT archives (published at MKM 2011, LNCS)
- M. Kohlhase, F. Rabe, C. Sacerdoti Coen, A Foundational View on Integration Problems - outlines how MMT can be used for system integration (published at Calculemus 2011, LNCS)
- M. Codescu, F. Horozal, M. Kohlhase, T. Mossakowski, F. Rabe A Proof Theoretic Interpretation of Model Theoretic Hiding - adds the hiding operation to MMT (published at WADT 2011, LNCS)
- M. Kohlhase, F. Rabe, V. Zholudev, Towards MKM in the Large: Modular Representation and Scalable Software Architecture - a high level view on MMT and its software infrastructure (published at MKM 2010, LNCS, best paper award)
- V. Zholudev, M. Kohlhase, F. Rabe, A (insert XML Format) Database for (insert cool application) - uses MMT as an example how to use TNTBase as a format-independent database (published at XMLPrague 2009)
- J. Giceva, C. Lange, F. Rabe, Integrating Web Services into Active Mathematical Documents - introduces JOBAD, a precursor to the MMT interactive web interface (published at MKM 2009, LNCS)
- F. Rabe and C. Schürmann, A Practical Module System for LF - the Twelf instantiation of the MMT module system (published at LFMTP 2009)
- M. Kohlhase, C. Müller, F. Rabe, Notations for Living Mathematical Documents - introduces a precursor to the MMT notation language and rendering engine
- F. Rabe and M. Kohlhase, An Exchange Format for Modular Knowledge - an early workshop paper on MMT (published at KEAPPA 2008)