| Issue Date | Title | Author(s) |
| 1 | 2013 | Comparison of four Ab initio MicroRNA prediction tools | Saçar, Müşerref Duygu; Allmer, Jens |
| 2 | 2013 | Data mining for microrna gene prediction: On the impact of class imbalance and feature number for microrna gene prediction | Saçar, Müşerref Duygu; Allmer, Jens |
| 3 | 2016 | Database normalization is crucial for reliable protein identification in mass spectrometry-based proteomics | Has, Canan; Mungan, Mehmet Direnç; Çiftçi, Cansu; Allmer, Jens |
| 4 | 2017 | Distinguishing between MicroRNA targets from diverse species using sequence motifs and K-mers | Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin ; Allmer, Jens |
| 5 | 2016 | Feature selection for microRNA target prediction comparison of one-class feature selection methodologies | Yousef, Malik; Allmer, Jens ; Khalifa, Waleed |
| 6 | 2012 | De novo markup language, a standard to represent de novo sequencing results from MS/MS data | Takan, Savaş ; Allmer, Jens |
| 7 | 2016 | Preparing sequence databases for application in proteogenomics | Has, Canan; Mungan, Mehmet Direnç; Çiftçi, Cansu; Allmer, Jens |
| 8 | 2013 | Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches | Has, Canan; Kundakçı, Cemal Ulaş; Altay, Aybuge; Allmer, Jens |
| 9 | 2010 | Relative protein quantitation with post translational modifications in mass spectrometry based proteomics | Allmer, Jens |
| 10 | 2012 | Removing contamination from genomic sequences based on vector reference libraries | Bağcı, Caner; Allmer, Jens |
| 11 | 2010 | Systematic computational analysis of potential rnai regulation in toxoplasma gondii | Çakır, Mehmet Volkan; Allmer, Jens |
