Refereed Journal Articles
- 2024 Morando N, Rosenzvit MC, Pando MA, Allmer J, The Role of MicroRNAs in HIV Infection, Genes, doi: 10.3390/genes15050574.
- 2024 Hansel-Frose AFF, Allmer J, Friedrichs M, dos Santos HG, Dallagiovanna B, and Spangenberg L, Alternative polyadenylation and dynamic 3′ UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs, Frontiers in Molecular Biosciences, doi: 10.3389/fmolb.2024.1336336.
- 2023 Yousef M, Ozdemir F, Jaber A, Allmer J, and Bakir-Gungor B, PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach, BMC Bioinformatics, doi: 10.1186/s12859-023-05187-2.
- 2023 Kiran AD, Ay MC, Allmer J, Criteria for the Evaluation of Workflow Management Systems for Scientific Data Analysis, Journal of Bioinformatics and Systems Biology, doi: 10.26502/jbsb.5107055.
- 2023 Allmer J, Noncoding RNA Databases, Current Pharmaceutical Biotechnology, doi: 10.2174/1570180819666220520124511.
- 2023 Beukers M and Allmer J, Challenges for the Development of Automated RNA-seq Analyses Pipelines, GMS Medical Informatics, Biometry and Epidemiology, doi: 10.3205/mibe000245.
- 2023 Yousef M, and Allmer J, Deep Learning in Bioinformatics, Turkish Journal of Biology, doi: 10.55730/1300-0152.2671.
- 2021 Tüfekci KU, Allmer J, Carman KB, Bayram E, Topcu Y, Kurul SH, Genc S, and Yis U, Antiviral MicroRNA Expression Signatures are Altered in Subacute Sclerosing Panencephalitis, Neurological Sciences and Neurophysiology, doi: 10.4103/nsn.nsn_57_21.
- 2021 Schofield AL, Brown JP, Brown J, Wilczynska A, Bell C, Glaab WE, Hackl M, Howell L, Lee S, Dear JW, Remes M, Reeves P, Zhang E, Allmer J, Norris A, Falciani F, Takeshita LY, Forootan SS, Sutton R, Park BK, and Goldring C, Systems analysis of miRNA biomarkers to inform drug safety, Archives of Toxicology, doi: 10.1007/s00204-021-03150-9.
- 2021 Yousef M, and Allmer J, Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features, Algorithms, doi: 10.3390/a14050132.
- 2021 Gültekin V and Allmer J, Novel Perspectives for SARS-CoV-2 Genome Browsing, Journal of Integrative Bioinformatics, doi: 10.1515/jib-2021-0001.
- 2020 Takan T and Allmer J, DNMSO; an ontology for representing de novo sequencing results from TandemMS data, PeerJ, doi: 10.7717/peerj.10216.
- 2019 Allmer J, Towards and Internet of Science, Journal of Integrative Bioinformatics, doi: 10.1515/jib-2019-0024.
- 2019 Yousef M, Abddallah L, and Allmer J, maTE: Discovering Expressed MicroRNA - Target Interactions, Bioinformatics, doi: 10.1093/bioinformatics/btz204.
- 2018 Öztürk SC, Göktay M, Allmer J, Doğanlar S, and Frary A, Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars, Plant Molecular Biology Reporter, doi: 10.1007/s11105-018-1120-0.
- 2018 Öztürk SE, Göktay M, Has C, Babaoğlu M, Allmer J, Doğanlar S, Frary A, Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans, Chemosphere, doi: 10.1016/j.chemosphere.2018.02.070.
- 2018 Acar IE, Sacar Demirci MD, Gross U, and Allmer J, The Expressed MicroRNA - mRNA Interactions of Toxoplasma gondii, Frontiers in Microbiology, doi: 10.3389/fmicb.2017.02630.
- 2017 Saçar Demirci MD, Baumbach J, and Allmer J On the performance of pre-microRNA detection algorithms, Nature Communications, doi: 10.1038/s41467-017-00403-z.
- 2017 Yousef M, Nigatu D, Levy D, Allmer J, and Henkel W, Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers, Journal on Advances in Signal Processing, doi: 10.1186/s13634-017-0506-8.