| 1999 | ISMB | Metrics and Similarity Measures for Hidden Markov Models. | Rune B. Lyngs, Christian N. S. Pedersen, Henrik Nielsen |
| 1998 | ISMB | Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model. | Henrik Nielsen, Anders Krogh |
| 1997 | ISMB | Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome Analysis. | Anders Gorm Pedersen, Henrik Nielsen |
| 1995 | CAIP | Using Mirror Cameras for Estimating Depth. | Jens Arnspang, Henrik Nielsen, Morten Christensen, Knud Henriksen |
| 1995 | ICASSP | Quantization of non-linear predictors in speech coding. | Jes Thyssen, Henrik Nielsen, Steffen Duus Hansen |
| 1994 | ICASSP | Non-linear short-term prediction in speech coding. | Jes Thyssen, Henrik Nielsen, Steffen Duus Hansen |
| 1993 | Interspeech | Improving the spectral balance of digital speech synthesis applied to a female, synthetic voice. | Ida Frehr, Marianne Elmlund, Henrik Nielsen |
| 1992 | ICASSP | Improvements in 2.4 kbps high-quality speech coding. | Jesper Haagen, Henrik Nielsen, Steffen Duus Hansen |
| 1992 | ICASSP | Comparative study of error correction coding schemes for the GSM half-rate channel. | Henrik Nielsen, Keld B. Mikkelsen, Henrik B. Hansen, Yuhang Wu, Knud J. Larsen, John Aasted Srensen |
| 1991 | ICASSP | A 2.4 kbps high-quality speech coder. | Jesper Haagen, Henrik Nielsen, Steffen Duus Hansen |
| 1991 | ICASSP | High performance coder: a possible candidate for the GSM half-rate system. | Yuhang Wu, Henrik B. Hansen, Knud J. Larsen, Henrik Nielsen, John Aasted Srensen |