Pruning neural networks for protein secondary structure prediction. - Sepideh Babaei; Seyyed Ali Seyyedsalehi; Amir Geranmayeh (BIBE, 2008)

Heart sound reproduction based on neural network classification of cardiac valve disorders using wavelet transforms of PCG signals. - Sepideh Babaei; Amir Geranmayeh (Comput. Biol. Medicine, 2009)

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. - Sepideh Babaei; Amir Geranmayeh; Seyyed Ali Seyyedsalehi (Comput. Methods Programs Biomed., 2010)

Integrating Protein Family Sequence Similarities with Gene Expression to Find Signature Gene Networks in Breast Cancer Metastasis. - Sepideh Babaei; Erik van den Akker 001; Jeroen de Ridder; Marcel J. T. Reinders (PRIB, 2011)

Towards designing modular recurrent neural networks in learning protein secondary structures. - Sepideh Babaei; Amir Geranmayeh; Seyyed Ali Seyyedsalehi (Expert Syst. Appl., 2012)

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion. - Sepideh Babaei; Marc Hulsman; Marcel J. T. Reinders; Jeroen de Ridder (BMC Bioinform., 2013)

Highlights from the Third European International Society for Computational Biology (ISCB) Student Council Symposium 2014. - Margherita Francescatto; Susanne M. A. Hermans; Sepideh Babaei; Esmeralda Vicedo; Alexandre Borrel; Pieter Meysman (BMC Bioinform., 2015)

Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia. - Erdogan Taskesen; Sepideh Babaei; Marcel J. T. Reinders; Jeroen de Ridder (BMC Bioinform., 2015)

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex. - Sepideh Babaei; Ahmed Mahfouz; Marc Hulsman; Boudewijn P. F. Lelieveldt; Jeroen de Ridder; Marcel J. T. Reinders (PLoS Comput. Biol., 2015)

Multi-scale network analyses for cancer omics data. - Sepideh Babaei (2015)

A review on deep learning applications in highly multiplexed tissue imaging data analysis. - Mohammed Zidane; Ahmad Makky; Matthias Bruhns; Alexander Rochwarger; Sepideh Babaei; Manfred Claassen; Christian M. Schürch (Frontiers Bioinform., 2023)

Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis. - Mohammed Zidane; Ahmad Makky; Matthias Bruhns; Alexander Rochwarger; Sepideh Babaei; Manfred Claassen; Christian M. Schürch (Frontiers Bioinform., 2023)

S3-CIMA: Supervised spatial single-cell image analysis for identifying disease-associated cell-type compositions in tissue. - Sepideh Babaei; Jonathan Christ; Vivek Sehra; Ahmad Makky; Mohammed Zidane; Kilian Wistuba-Hamprecht; Christian M. Schürch; Manfred Claassen (Patterns, 2023)