2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments. - Jens Allmer; Sebastian Kuhlgert; Michael Hippler (BMC Bioinform., 2008)

Comparison of Four Ab Initio MicroRNA Prediction Tools. - Muserref Duygu Saçar; Jens Allmer (BIOINFORMATICS, 2013)

Can MiRBase Provide Positive Data for Machine Learning for the Detection of MiRNA Hairpins? - Muserref Duygu Saçar; Hamid Hamzeiy; Jens Allmer (J. Integr. Bioinform., 2013)

Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts' Gene Expression. - Müserref Duygu Saçar; Caner Bagci; Jens Allmer (Genom. Proteom. Bioinform., 2014)

Feature Selection for MicroRNA Target Prediction - Comparison of One-Class Feature Selection Methodologies. - Malik Yousef; Jens Allmer; Waleed Khalifa (BIOINFORMATICS, 2016)

Feature Selection Has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants. - Malik Yousef; Muserref Duygu Saçar; Waleed Khalifa; Jens Allmer (Adv. Bioinformatics, 2016)

Editorial: Computational miRNomics. - Jens Allmer; Malik Yousef (J. Integr. Bioinform., 2016)

A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes. - Muserref Duygu Saçar Demirci; Mustafa Toprak; Jens Allmer (J. Integr. Bioinform., 2016)

PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes. - Canan Has; Sergey A. Lashin; Alexey V. Kochetov; Jens Allmer (J. Integr. Bioinform., 2016)

Exact pattern matching: Adapting the Boyer-Moore algorithm for DNA searches. - Jens Allmer (PeerJ Prepr., 2016)

Distinguishing between MicroRNA Targets from Diverse Species using Sequence Motifs and K-mers. - Malik Yousef; Waleed Khalifa; Ilhan Erkin Acar; Jens Allmer (BIOINFORMATICS, 2017)

AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs. - Alexey V. Kochetov; Jens Allmer; Alexandra I. Klimenko; Bulat S. Zuraev; Yury G. Matushkin; Sergey A. Lashin (Bioinform., 2017)

MicroRNA categorization using sequence motifs and k-mers. - Malik Yousef; Waleed Khalifa; Ilhan Erkin Acar; Jens Allmer (BMC Bioinform., 2017)

Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers. - Malik Yousef; Dawit Nigatu; Dalit Levy; Jens Allmer; Werner Henkel (EURASIP J. Adv. Signal Process., 2017)

PGMiner: Complete proteogenomics workflow; from data acquisition to result visualization. - Canan Has; Jens Allmer (Inf. Sci., 2017)

Improving the Quality of Positive Datasets for the Establishment of Machine Learning Models for pre-microRNA Detection. - Muserref Duygu Saçar Demirci; Jens Allmer (J. Integr. Bioinform., 2017)

Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA. - Hamid Hamzeiy; Rabia Suluyayla; Christoph Brinkrolf; Sebastian Jan Janowski; Ralf Hofestädt; Jens Allmer (J. Integr. Bioinform., 2017)

Computational miRNomics - Integrative Approaches. - Ralf Hofestädt; Falk Schreiber; Björn Sommer 001; Jens Allmer (J. Integr. Bioinform., 2017)

Species Categorization via MicroRNAs - Based on 3'UTR Target Sites using Sequence Features. - Malik Yousef; Dalit Levy; Jens Allmer (BIOINFORMATICS, 2018)

Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. - Hamid Hamzeiy; Rabia Suluyayla; Christoph Brinkrolf; Sebastian Jan Janowski; Ralf Hofestädt; Jens Allmer (GMDS, 2018)

Classification of Pre-cursor microRNAs from Different Species Using a New Set of Features. - Malik Yousef; Jens Allmer (DEXA Workshops, 2019)

maTE: discovering expressed interactions between microRNAs and their targets. - Malik Yousef; Loai AbdAllah; Jens Allmer (Bioinform., 2019)

Towards an Internet of Science. - Jens Allmer (J. Integr. Bioinform., 2019)

A Machine Learning-based Approach for the Categorization of MicroRNAs to Their Species of Origin. - Luise Odenthal; Jens Allmer; Malik Yousef (BIOINFORMATICS, 2020)

Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features. - Malik Yousef; Jens Allmer (Algorithms, 2021)

Special issue on COVID-19 data integration opportunities and vaccine development strategies. - Jens Allmer (J. Integr. Bioinform., 2021)

Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21). - Jens Allmer; Mourad Elloumi; Matteo Comin; Ralf Hofestädt (J. Integr. Bioinform., 2021)

Novel perspectives for SARS-CoV-2 genome browsing. - Visam Gültekin; Jens Allmer (J. Integr. Bioinform., 2021)

Community-wide collaboration is a must to reinstall trust in bioinformatics solutions and biomedical interpretation. - Savas Takan; Jens Allmer (J. Integr. Bioinform., 2023)

PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. - Malik Yousef; Fatma Ozdemir; Amhar Jaber; Jens Allmer; Burcu Bakir-Gungor (BMC Bioinform., 2023)