| Issue Date | Title | Author(s) |
| 2022 | 44 Current Challenges in miRNomics | Akgül, Bünyamin ; Stadler, Peter F.; Hawkins, Liam J.; Hadj-Moussa, Hanane; Storey, Kenneth B.; Ergin, Kemal; Allmer, Jens |
| Oct-2011 | Algorithms for the de novo sequencing of peptides from tandem mass spectra | Allmer, Jens |
| 2017 | AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs | Kochetov, Alex V.; Allmer, Jens ; Klimenko, Alexandra I.; Zuraev, Bulat S.; Matushkin, Yury G.; Lashin, Sergey A. |
| 2021 | Antiviral microRNA expression signatures are altered in subacute sclerosing panencephalitis | Tüfekçi, Kemal Uğur; Allmer, Jens ; Çarman, Kürşat Bora; Bayram, Erhan; Topçu, Yasemin; Hız, Semra; Genç, Şermin; Yiş, Uluç |
| Jul-2016 | Automatic, fast and accurate sequence decontamination | Bağcı, Caner |
| 2012 | A call for benchmark data in mass spectrometry-based proteomics | Allmer, Jens |
| 2013 | Can MiRBase provide positive data for machine learning for the detection of MiRNA hairpins? | Demirci, Müşerref Duygu Saçar; Hamzeiy, Hamid; Allmer, Jens |
| Dec-2017 | Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers | Yousef, Malik; Nigatu, Dawit; Levy, Dalit; Allmer, Jens ; Henkel, Werner |
| 2015 | A cell division cycle 7-related protein kinase inhibitor suppresses glioblastoma cell growth in vitro | Erkan, E. P.; Dinç, Melike; Eren, E.; Allmer, Jens ; Yalçın, Talat ; Genç, S. |
| 2013 | Comparison of four Ab initio MicroRNA prediction tools | Saçar, Müşerref Duygu; Allmer, Jens |
| 2014 | Computational and bioinformatics methods for microRNA gene prediction | Allmer, Jens |
| Jun-2017 | Computational establishment of microRNA metabolic networks | Saçar Demirci, Müşerref Duygu |
| 2012 | Computational methods for ab initio detection of microRNAs | Allmer, Jens ; Yousef, Malik |
| 2014 | Computational methods for microRNA target prediction | Hamzeiy, Hamid; Yousef, Malik; Allmer, Jens |
| 2016 | Computational miRNomics | Allmer, Jens ; Yousef, Malik |
| 2017 | Computational miRNomics - Integrative Approaches | Hofestaedt, Ralf; Schreiber, Falk; Sommer, Bjoern; Allmer, Jens |
| Oct-2014 | Computational prediction of MicroRNAs from toxoplasma gondii potentially regulating the hosts' gene expression | Saçar, Müşerref Duygu; Bağcı, Caner; Allmer, Jens |
| 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 |
| 2016 | Database normalization is crucial for reliable protein identification in mass spectrometry-based proteomics | Has, Canan; Mungan, Mehmet Direnç; Çiftçi, Cansu; Allmer, Jens |
| 2017 | Delineating the impact of machine learning elements in pre-microRNA detection | Saçar Demirci, Müşerref Duygu; Allmer, Jens |
| Dec-2013 | Determining the C-terminal amino acid of a peptide from MS/MS data | Allmer, Jens |
| Jun-2013 | Development of EST-SSR markers for diversity and breeding studies in opium poppy | Şelale, Hatice ; Çelik, İbrahim; Gültekin, Visam; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne |
| Feb-2017 | Development of genomic simple sequence repeat markers in faba bean by next-generation sequencing | Abuzayed, Mazen A.; Göktay, Mehmet ; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne |
| Aug-2014 | Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing | Çelik, İbrahim; Gültekin, Visam; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne |
| 2018 | Development of simple sequence repeat markers in hazelnut (Corylus avellana L.) by next-generation sequencing and discrimination of Turkish hazelnut cultivars | Özturk, Süleyman Can; Göktay, Mehmet ; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne |
| 2016 | Differential expression of toxoplasma gondii microRNAs in murine and human hosts | Saçar Demirci, Müşerref Duygu; Bağcı, Caner; Allmer, Jens |
| 2017 | Distinguishing between MicroRNA targets from diverse species using sequence motifs and K-mers | Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin ; Allmer, Jens |
| 2020 | DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data | Takan, Savaş ; Allmer, Jens |
| 2009 | Enabling the quantitation of post translational modifications | Allmer, Jens |
| Dec-2016 | Enhancement and validation of current human genome annotation via novel proteogenomics algorithms | Has, Canan |
| Sep-2014 | EPO mediates neurotrophic, neuroprotective, anti-oxidant, and anti-apoptotic effects via downregulation of miR-451 and miR-885-5p in SH-SY5Y neuron-like cells | Alural, Begüm; Duran, Gizem Ayna; Tüfekçi, Kemal Uğur; Allmer, Jens ; Onkal, Zeynep; Tunalı, Doğa; Genç, Kürşad; Genç, Şermin |
| 2011 | Evaluation of protein secondary structure prediction algorithms on a new advanced benchmark dataset | Has, Canan |
| Jan-2012 | Existing bioinformatics tools for the quantitation of post-translational modifications | Allmer, Jens |
| 2011 | Exploiting fragment-ion complementarity for peptide de novo sequencing from collision induced dissociation tandem mass spectra | Aytun, Belgin |
| Jan-2018 | The expressed MicroRNA-mRNA interactions of Toxoplasma gondii | Acar, İlhan Erkin ; Saçar Demirci, Müşerref Duygu; Groß, Uwe; Allmer, Jens |
| 2016 | Feature selection for microRNA target prediction comparison of one-class feature selection methodologies | Yousef, Malik; Allmer, Jens ; Khalifa, Waleed |
| 2016 | Feature selection has a large impact on one-class classification accuracy for micrornas in plants | Yousef, Malik; Demirci, Müşerref Duygu Saçar; Khalifa, Waleed; Allmer, Jens |
| 2019 | Gen ifadesinin yeni düzenleyicileri halkasal RNA’ların apoptotik yolaklara olan etkilerinin araştırılması | Akgül, Bünyamin ; Aldanmaz, Ayten Nalbant ; Allmer, Jens |
| 2015 | Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame | Uncu, Ayşe Özgür; Gültekin, Visam; Allmer, Jens ; Frary, Anne ; Doğanlar, Sami |
| 2016 | The impact of feature selection on one and two-class classification performance for plant microRNAs | Khalifa, Waleed; Yousef, Malik; Saçar Demirci, Müşerref Duygu; Allmer, Jens |
| Dec-2016 | Importance of database normalization for reliable protein identification in mass spectrometry-based proteomics | Mungan, Mehmet Direnç |
| 2017 | Improving the quality of positive datasets for the establishment of machine learning models for pre-microRNA detection | Saçar Demirci, Müşerref Duygu; Allmer, Jens |
| 2013 | An integrative data mining approach for microRNA detection in human | Saçar, Müşerref Duygu |
| Sep-2014 | Intersection of MicroRNA and gene regulatory networks and their implication in cancer | Yousef, Malik; Trinh, Hung V.; Allmer, Jens |
| 2009 | Label-free quantitation with 2DB | Allmer, Jens |
| Apr-2010 | Label-free quantitation, an extension to 2DB | Allmer, Jens |
| Jul-2015 | A lattice-based approach for news chain construction | Toprak, Mustafa |
| 28-May-2015 | Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells | Alural, Begüm; Özerdem, Ayşegül; Allmer, Jens ; Genç, Kürşad; Genç, Şermin |
| 2016 | A machine learning approach for MicroRNA precursor prediction in retro-transcribing virus genomes | Saçar Demirci, Müşerref Duygu; Toprak, Mustafa; Allmer, Jens |
| 2014 | Machine learning methods for microRNA gene prediction | Saçar, Müşerref Duygu; Allmer, Jens |
| Mar-2017 | MicroRNA categorization using sequence motifs and k-mers | Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin ; Allmer, Jens |
| 2017 | Mikro-RNA metabolik ağ kontrol analizi için veri ambarı | Allmer, Jens ; Saçar Demirci, Müşerref Duygu; Acar, İlhan Erkin |
| Jun-2017 | Mining the Toxoplasma gondii genome for microRNA regulatory patterns | Acar, İlhan Erkin |
| 2014 | miRNomics: MicroRNA biology and computational analysis preface | Yousef, Malik; Allmer, Jens |
| 2012 | Ms Homolog özelliğe dayalı veritabanı aramalarının kapsamının genişletilmesi | Allmer, Jens ; Yılmaz, Şule |
| Aug-2017 | Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea) | Göl, Şurhan; Göktay, Mehmet ; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne |
| 2012 | De novo markup language, a standard to represent de novo sequencing results from MS/MS data | Takan, Savaş ; Allmer, Jens |
| Dec-2017 | On the performance of pre-microRNA detection algorithms | Saçar Demirci, Müşerref Duygu; Baumbach, Jan; Allmer, Jens |
| Jan-2016 | One step forward, two steps back; Xeno-MicroRNAs reported in breast milk are artifacts | Bağcı, Caner; Allmer, Jens |
| 2016 | PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes | Has, Canan; Lashin, Sergey A.; Kochetov, Alexey; Allmer, Jens |
| Apr-2017 | PGMiner: Complete proteogenomics workflow; from data acquisition to result visualization | Has, Canan; Allmer, Jens |
| 2016 | Preparing sequence databases for application in proteogenomics | Has, Canan; Mungan, Mehmet Direnç; Çiftçi, Cansu; Allmer, Jens |
| 2017 | Puccinellia distans (Jacq.) Parl.’da boron hiperakümülasyonu ve tolerans mekanizmalarının proteomiks yaklaşım kullanarak anlaşılması | Yalçın, Talat ; Frary, Anne ; Allmer, Jens |
| 2012 | Quality assessment of de novo sequence assembly tools | Gültekin, Visam |
| 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 |
| Jul-2012 | Ray: A profile-based approach for homology matching of tandem-ms spectra to sequence databases | Yılmaz, Şule |
| 2010 | Relative protein quantitation with post translational modifications in mass spectrometry based proteomics | Allmer, Jens |
| 2012 | Removing contamination from genomic sequences based on vector reference libraries | Bağcı, Caner; Allmer, Jens |
| 2009 | Systematic computational analysis of potential RNA interference regulation in Toxoplasma gondii | Çakır, Mehmet Volkan |
| 2010 | Systematic computational analysis of potential rnai regulation in toxoplasma gondii | Çakır, Mehmet Volkan; Allmer, Jens |
| May-2018 | Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans | Öztürk, Saniye Elvan; Göktay, Mehmet ; Has, Canan; Babaoğlu, Mehmet; Allmer, Jens ; Doğanlar, Sami ; Frary, Anne |
| 2017 | Visualization and analysis of MicroRNAs within KEGG pathways using VANESA | Hamzeiy, Hamid; Suluyayla, Rabia; Brinkrolf, Christoph; Janowski, Sebastian Jan; Hofestaedt, Ralf; Allmer, Jens |
| 2018 | Visualization and analysis of miRNAs implicated in amyotrophic lateral sclerosis within gene regulatory pathways | Hamzeiy, Hamid; Suluyayla, Rabia; Brinkrolf, Christoph; Janowski, Sebastian Jan; Hofestädt, Ralf; Allmer, Jens |
