Publication information in a researcher’s academic homepage provides insights about the researcher’s expertise, research interests, and collaboration networks. We aim to extract all the publication strings from a given academic homepage. This is a challenging task because the publication strings in different academic homepages may be located at different positions with different structures. To capture the positional and structural diversity, we propose an end-to-end hierarchical model named PubSE based on Bi-LSTM-CRF. We further propose an alternating training method for training the model. Experiments on real data show that PubSE outperforms the state-of-the-art models by up to 11.8% in F1-score.