| 2005 | CEC | Evolving hidden Markov models for protein secondary structure prediction. | Kyoung-Jae Won, Thomas Hamelryck, Adam Prgel-Bennett, Anders Krogh |
| 2005 | ISMB | An HMM posterior decoder for sequence feature prediction that includes homology information. | Lukas Kll, Anders Krogh, Erik L. L. Sonnhammer |
| 2004 | KES | The Block Hidden Markov Model for Biological Sequence Analysis. | Kyoung-Jae Won, Adam Prgel-Bennett, Anders Krogh |
| 2002 | ISMB | A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. | Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio |
| 2001 | ISMB | ISMB 2001. | Sren Brunak, Anders Krogh |
| 1998 | ISMB | Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model. | Henrik Nielsen, Anders Krogh |
| 1998 | ISMB | A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences. | Erik L. L. Sonnhammer, Gunnar von Heijne, Anders Krogh |
| 1997 | ICASSP | Hidden neural networks: a framework for HMM/NN hybrids. | Sren Kamaric Riis, Anders Krogh |
| 1997 | ISMB | Two Methods for Improving Performance of a HMM and their Application for Gene Finding. | Anders Krogh |
| 1995 | ISMB | Periodic Sequence Patterns in Human Exons. | Pierre Baldi, Sren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh |
| 1995 | ISMB | Maximum Entropy Weighting of Aligned Sequences of Proteins or DNA. | Anders Krogh, Graeme J. Mitchison |
| 1994 | ICPR | Hidden Markov models for labeled sequences. | Anders Krogh |
| 1993 | ISMB | Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families. | Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, Kimmen Sjlander, David Haussler |