Prof. Dr. Jens Allmer

Institut Mess- und Sensortechnik

Startseite // Allmer, Jens

Occupation:
Field of expertise: Medical Informatics and Bioinformatics

Medical Informatics and Bioinformatics

Jens Allmer is Professor of Medical Informatics and Bioinformatics at Hochschule Ruhr West (HRW), Mülheim an der Ruhr, Germany. Previously, he held positions as Cluster Leader at Wageningen University and Research, Wageningen, Netherlands (2017–2018), and as Assistant and Associate Professor at Izmir Institute of Technology, Izmir, Turkey (2008–2016). Prof. Allmer earned his doctorate (2006) in Biology with distinction from the University of Münster, where he also obtained his diploma. In 2010, he was recognised as an outstanding young scientist in the field of Bioinformatics by the Turkish Academy of Sciences. Prof. Allmer has published more than 80 manuscripts in relevant peer-reviewed journals with a cumulative impact factor exceeding 130. He has also secured over €650,000 in research funding.

Prof. Allmer’s research interests encompass most areas of omics. Currently, his primary focus is on microRNA regulation and pathogen-host interaction. He employs machine learning to investigate these topics.

Teaching

HOCHSCHULE RUHR WEST

Fundamentals of Computer Science and Programming Languages
Information Systems in Healthcare, Databases, Data Security
Personalised Health Technologies
Semantic and Syntactic Interoperability / Standards
Data Mining and Machine Learning

PREVIOUSLY

Introduction to Programming (Izmir Institute of Technology, Izmir, Turkey)
Applied Bioinformatics (Izmir Institute of Technology, Izmir, Turkey)
Bioinformatics (Izmir Institute of Technology, Izmir, Turkey)
Algorithms in Bioinformatics (Izmir Institute of Technology, Izmir, Turkey)
Proteomic Data Analysis (Izmir Institute of Technology, Izmir, Turkey)
Genomics (Izmir Institute of Technology, Izmir, Turkey)
Proteomic Data Analysis (ERASMUS, Free University Berlin, Germany)
Computer-Aided Proteomics (ERASMUS, Bielefeld University, Germany)
Bioinformatics for Genomics and Proteomics (Invited Course, Dokuz Eylül University, Izmir, Turkey)
Bioinformatics (Izmir University of Economics, Izmir, Turkey)
Fundamentals of Software Engineering (Izmir University of Economics, Izmir, Turkey)
Introduction to Computer and Information Theory (Izmir University of Economics, Izmir, Turkey)
Database Systems (Izmir University of Economics, Izmir, Turkey)
Data Mining (Izmir University of Economics, Izmir, Turkey)
Advanced Programming (Izmir University of Economics, Izmir, Turkey)
Systems Analysis and Design (Izmir University of Economics, Izmir, Turkey)
Methods of Functional Proteomics (Münster University, Münster, Germany)

Completed Doctoral Theses

Müşerref Duygu Saçar Demirci (2013 - 2017) Computational Establishment of MicroRNA Metabolic Networks, Department of Molecular Biology and Genetics, IYTE.

Canan Has (2012 - 2017) Enhancement and validation of current human genome annotation via new proteogenomic methods, Department of Molecular Biology and Genetics, IYTE.

Reviewer for Doctoral Theses

Florent Jouy, Effects of Chemicals on Human Immune Cells Through Quantitative Proteomics, Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany (2017).

Nimet İlke Akçay, Petri Net-Based Quantitative Modeling and Validation of p16-mediated Signaling Pathway, Applied Mathematics and Computer Science, Eastern Mediterranean University, Famagusta, North Cyprus (2016).

Çağdaş Taşoğlu, Fragmentation Reaction Mechanism of Peptides Containing Glutamic Acid and Glutamine in Gas Phase: Comparison of Electron Transfer Dissociation with Collision-Induced Dissociation using Mass Spectrometry, Chemistry Izmir Institute of Technology, Izmir, Turkey (2015).

Ahmet Emin Atik, Gas-Phase Fragmentation Mechanisms of Peptides by Mass Spectrometry, Chemistry, Izmir Institute of Technology, Izmir, Turkey (2013).

Tunca Doğan, Automatic Identification of Evolutionary and Sequence Relationships in Large Scale Protein Data Using Computational and Graph-Theoretical Analyses, Bioengineering, Izmir Institute of Technology, Izmir, Turkey (2012).

Master’s Theses

Jorge Cordero (2018 - 2019) Application of deep learning to pre-miRNA detection using Google Tensor Flow (Co-Advisor with Vlado Menkowski, Technical University Eindhoven).

Luise Odenthal (2018 - 2019) Framework for the automatic categorization of hairpins to their species of origin (Co-Advisor with Malik Yousef and Ralf Hofestädt), Department of Computer Engineering, IYTE.

İlhan Erkin Acar (2015 - 2017) Improving MicroRNA Target Prediction Employing Integrative Data Mining, Department of Biotechnology, IYTE.

Mehmet Direnç Mungan (2014 - 2017) Importance of Database Normalization for Reliable Protein Identification in Mass Spectrometry-Based Proteomics, Department of Biotechnology, IYTE.

Caner Bağcı, Biotechnology (2013 - 2016) Automatic, Fast and Accurate Sequence Decontamination (co-Advisor with Dr. Selma Tekir, Department of Computer Engineering, IYTE), Biotechnology, IYTE.

Rabia Suluyayla (2013 - 2016) Cost and Benefit Analysis of Features used in Machine Learning based pre-miRNA Detection, Department of Molecular Biology and Genetics, IYTE.

Mustafa Toprak (2013 - 2015 ) A Detailed Analysis on Infrastructure and Programming Dependencies of Selected Data Mining Algorithms (co-Advisor with Dr. Selma Tekir, Department of Computer Engineering, IYTE), Department of Computer Engineering, IYTE.

Mehmet Göktay (2013 - 2015) Characterization of World Spinach Genetic Collection by Using Molecular Markers (co-Advisor with Dr. Sami Doğanlar, Department of Molecular Biology and Genetics, IYTE), Department of Molecular Biology and Genetics, IYTE.

Müşerref Duygu Saçar (2011 - 2013) An Integrative Data Mining Approach for MicroRNA Detection in Human, Department of Molecular Biology and Genetics, IYTE.

Visam Gültekin, (2010 - 2013) Quality Assessment of De Novo Sequence Assembly Tools, Department of Molecular Biology and Genetics, IYTE.

Savaş Takan (2010 - 2013) A Common Representation, Standardization, Analysis for De Novo Sequencing Results (co-Advisor with Dr. Sıtkı Aytaç, Computer Engineering, IYTE), Department of Computer Engineering, IYTE.

Şule Yılmaz (2010 - 2012) RAy: A Profile-based Approach for Homology Matching of Tandem-MS Spectra to Sequence Databases (co-Advisor with Dr. Bilge Karaçalı), Department of Biotechnology, IYTE.

Canan Has (2009 - 2012) Evaluations of Protein Secondary Structure Prediction Algorithms on a New Advanced Benchmark DataSet, Department of Molecular Biology and Genetics, IYTE.

Belgin Aytun (2009 - 2011) Exploiting Fragment-Ion Complementarity for Peptide De Novo Sequencing From Collision Induced Dissociations Tandem Mass Spectra, Department of Molecular Biology and Genetics, IYTE.

Mehmet Volkan Çakır (2007 - 2009) Systematic Computational Analysis of Potential RNAi Regulation in Toxoplasma gondii, Department of Molecular Biology and Genetics, IYTE.

Research and Cooperation

Meanwhile, the focus of science and scientists is drifting further away from the ideal of knowledge discovery through curiosity and collaboration. Instead, the emphasis is on how many publications can be placed in high-impact journals, leading to intense competition.

This has resulted, among other things, in software artefacts (from research and theses) that are fundamentally flawed. Nevertheless, such programs are used in scientific research because, for example, the validation of these programs cannot be highly published. Worse still, these untested programs are combined into complex data analysis workflows.

My vision is to refocus on knowledge discovery through the development of a platform for scientific work. The platform, the Internet of Science (IoS), will map the entire scientific process from hypothesis to publication. This process will take place on an integrated interface (online/offline), providing collaboration opportunities for every task.

Towards an Internet of Science:
https://www.ncbi.nlm.nih.gov/pubmed/31145694
https://bitbucket.org/allmer/ios/src/master/

To further promote the Internet of Science, we are organising a conference on applied bioinformatics and integrative bioinformatics:
1st International Applied Bioinformatics Conference (iABC’20) & 16th International Integrative Bioinformatics Conference.

Selected Publications

1. Saçar Demirci MD, Baumbach J, and Allmer J (2017) On the performance of pre-microRNA detection algorithms, Nature Communications (IF: 12.124), 8(1):330, doi: 10.1038/s41467-017-00403-z.

2. Allmer J (2010) Existing bioinformatics tools for the quantitation of post translational modifications, Amino Acids (IF: 3.173), 42(1):129-138, doi: 10.1007/s00726-010-0614-3.

3. Bağcı C, and Allmer J (2016) One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk are Artifacts, PLOS One (IF: 3.061), doi: 10.1371/journal.pone.0145065.

4. Acar IE, Sacar Demirci MD, Gross U, and Allmer J (2018) The Expressed MicroRNA - mRNA Interactions of Toxoplasma gondii, Frontiers in Microbiology (IF: 4.076), doi: 10.3389/fmicb.2017.02630

5. Yousef M, Abddallah L, and Allmer J (2019) maTE: Discovering Expressed MicroRNA - Target Interactions, Bioinformatics (IF: 5,481) doi:.10.1093/bioinformatics/btz204.

6. Jans Allmer, Abhishek Kumar (2025) Proteogenomics - Methods and Protocols