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ORCIDJens Allmer
Person information
- affiliation: Izmir Institute of Technology, Urla, Izmir, Turkey
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Journal Articles
- 2023
[j22]Malik Yousef
, Fatma Ozdemir, Amhar Jaber, Jens Allmer, Burcu Bakir-Gungor:
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. BMC Bioinform. 24(1): 60 (2023)- [j21]Savas Takan, Jens Allmer:
Community-wide collaboration is a must to reinstall trust in bioinformatics solutions and biomedical interpretation. J. Integr. Bioinform. 20(1) (2023) - 2021
- [j20]Malik Yousef, Jens Allmer:
Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features. Algorithms 14(5): 132 (2021) - [j19]Jens Allmer:
Special issue on COVID-19 data integration opportunities and vaccine development strategies. J. Integr. Bioinform. 18(1): 1-2 (2021) - [j18]Visam Gültekin, Jens Allmer:
Novel perspectives for SARS-CoV-2 genome browsing. J. Integr. Bioinform. 18(1): 19-26 (2021) - [j17]Jens Allmer, Mourad Elloumi, Matteo Comin, Ralf Hofestädt:
Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21). J. Integr. Bioinform. 18(4) (2021) - 2019
- [j16]Malik Yousef, Loai AbdAllah, Jens Allmer:
maTE: discovering expressed interactions between microRNAs and their targets. Bioinform. 35(20): 4020-4028 (2019) - [j15]Jens Allmer:
Towards an Internet of Science. J. Integr. Bioinform. 16(3) (2019) - 2017
- [j14]Alexey V. Kochetov, Jens Allmer, Alexandra I. Klimenko, Bulat S. Zuraev, Yury G. Matushkin, Sergey A. Lashin:
AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs. Bioinform. 33(6): 923-925 (2017) - [j13]Malik Yousef, Waleed Khalifa, Ilhan Erkin Acar, Jens Allmer:
MicroRNA categorization using sequence motifs and k-mers. BMC Bioinform. 18(1): 170:1-170:9 (2017) - [j12]Malik Yousef, Dawit Nigatu, Dalit Levy, Jens Allmer, Werner Henkel:
Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers. EURASIP J. Adv. Signal Process. 2017: 70 (2017) - [j11]Canan Has, Jens Allmer:
PGMiner: Complete proteogenomics workflow; from data acquisition to result visualization. Inf. Sci. 384: 126-134 (2017) - [j10]Hamid Hamzeiy, Rabia Suluyayla, Christoph Brinkrolf, Sebastian Jan Janowski, Ralf Hofestädt, Jens Allmer:
Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA. J. Integr. Bioinform. 14(1) (2017) - [j9]Ralf Hofestädt, Falk Schreiber, Björn Sommer, Jens Allmer:
Computational miRNomics - Integrative Approaches. J. Integr. Bioinform. 14(1) (2017) - [j8]Muserref Duygu Saçar Demirci, Jens Allmer:
Improving the Quality of Positive Datasets for the Establishment of Machine Learning Models for pre-microRNA Detection. J. Integr. Bioinform. 14(2) (2017) - 2016
- [j7]Malik Yousef, Muserref Duygu Saçar, Waleed Khalifa, Jens Allmer:
Feature Selection Has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants. Adv. Bioinformatics 2016: 5670851:1-5670851:6 (2016) - [j6]Canan Has, Sergey A. Lashin, Alexey V. Kochetov, Jens Allmer:
PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes. J. Integr. Bioinform. 13(4) (2016) - [j5]Jens Allmer, Malik Yousef:
Editorial: Computational miRNomics. J. Integr. Bioinform. 13(5) (2016) - [j4]Muserref Duygu Saçar Demirci, Mustafa Toprak, Jens Allmer:
A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes. J. Integr. Bioinform. 13(5) (2016) - 2014
- [j3]Müserref Duygu Saçar, Caner Bagci, Jens Allmer:
Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts' Gene Expression. Genom. Proteom. Bioinform. 12(5): 228-238 (2014) - 2013
- [j2]Muserref Duygu Saçar, Hamid Hamzeiy, Jens Allmer:
Can MiRBase Provide Positive Data for Machine Learning for the Detection of MiRNA Hairpins? J. Integr. Bioinform. 10(2) (2013) - 2008
- [j1]Jens Allmer, Sebastian Kuhlgert, Michael Hippler:
2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments. BMC Bioinform. 9 (2008)
Conference and Workshop Papers
- 2020
- [c7]Luise Odenthal, Jens Allmer, Malik Yousef:
A Machine Learning-based Approach for the Categorization of MicroRNAs to Their Species of Origin. BIOINFORMATICS 2020: 150-157 - 2019
- [c6]Malik Yousef, Jens Allmer:
Classification of Pre-cursor microRNAs from Different Species Using a New Set of Features. DEXA Workshops 2019: 15-20 - 2018
- [c5]Malik Yousef, Dalit Levy, Jens Allmer:
Species Categorization via MicroRNAs - Based on 3'UTR Target Sites using Sequence Features. BIOINFORMATICS 2018: 112-118 - [c4]Hamid Hamzeiy, Rabia Suluyayla, Christoph Brinkrolf, Sebastian Jan Janowski, Ralf Hofestädt, Jens Allmer:
Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways. GMDS 2018: 183-187 - 2017
- [c3]Malik Yousef, Waleed Khalifa, Ilhan Erkin Acar, Jens Allmer:
Distinguishing between MicroRNA Targets from Diverse Species using Sequence Motifs and K-mers. BIOINFORMATICS 2017: 133-139 - 2016
- [c2]Malik Yousef, Jens Allmer, Waleed Khalifa:
Feature Selection for MicroRNA Target Prediction - Comparison of One-Class Feature Selection Methodologies. BIOINFORMATICS 2016: 216-225 - 2013
- [c1]Muserref Duygu Saçar, Jens Allmer:
Comparison of Four Ab Initio MicroRNA Prediction Tools. BIOINFORMATICS 2013: 190-195
Informal and Other Publications
- 2016
- [i1]Jens Allmer:
Exact pattern matching: Adapting the Boyer-Moore algorithm for DNA searches. PeerJ Prepr. 4: e1758 (2016)
Coauthor Index
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