1. Current Projects

Currently, the scientific focus and researchers interests are far remote from the ideal of knowledge generation spawned through general interest and collaboration. On the contrary, science is now driven via strong ‘artificial’ competition and measured by number of publications and journal impact factors.

Among other issues, this leads to software artifacts (research or theses outputs) which are incorrect. Yet, such programs are unreflectively used in research since it is not generally possible to publish comprehensive tests of such programs. Even worse, untested tools of unknown quality are pieced together into complex data analysis workflows. 

It is my vision to develop a platform for scientific research to alleviate such problems and put scientific research, collaboration, and the strive for knowledge back at the center.  The platform, entitled, the Internet of Science, will cover the complete workflow from hypothesis to publication. All work will be performed in an integrated environment (online/offline) with all steps ready for seamless collaborative work.

Towards an Internet of Science:

https://www.ncbi.nlm.nih.gov/pubmed/31145694
https://bitbucket.org/allmer/ios/src/master/

2. Publications

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.

Publications lists

Google Scholar: https://scholar.google.de/citations?user=BHfsiQEAAAAJ&hl=de

ResearchGate: https://www.researchgate.net/profile/Jens_Allmer

PubMed: https://www.ncbi.nlm.nih.gov/pubmed?term=Jens%20Allmer%5BAuthor%20-%20Full%5D

3. Courses

Hochschule Ruhr West, University of Applied Sciences

Applied Computer Sciences and Programming Languages

Information Systems in Healthcare, Databases and data security

Personalized Healthcare 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)

Computational Biology (Izmir Institute of Technology, Izmir, Turkey)

Algorithms in Bioinformatics (Izmir Institute of Technology, Izmir, Turkey)

Proteomics Data Analysis (Izmir Institute of Technology, Izmir, Turkey)

Genomics (Izmir Institute of Technology, Izmir, Turkey)

Proteomics Data Analysis (ERASMUS, Frei University Berlin, Germany)

Computational Proteomics (ERASMUS, Bielefeld University, Germany)

Bioinformatics in Genomics and Proteomics (Invited Lecture Series, Dokuy Eylül University, Izmir, Turkey)

Bioinformatics (Izmir University of Economics, Izmir, Turkey)

Introduction to Software Engineering (Izmir University of Economics, Izmir, Turkey)

Introduction to Computers and Information (Izmir University of Economics, Izmir, Turkey)

Database Management Systems (Izmir University of Economics, Izmir, Turkey)

Data Mining (Izmir University of Economics, Izmir, Turkey)

Advanced Programming (Izmir University of Economics, Izmir, Turkey)

System Analysis and Design (Izmir University of Economics, Izmir, Turkey)

Methods in Functional Proteomics (Münster University, Münster, Germany)

4. Theses

Doctoral

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.

PhD Committee Membership

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

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.