Aktuelle Projekte

Derweil entfernt sich der Fokus der Wissenschaft und der Wissenschaftler immer weiter vom Ideal der Wissensfindung durch Neugierde und Kollaboration. Vielmehr ist wichtig wie viele Publikationen in Journalen mit hohen Impaktfaktoren platziert werden können (starker Konkurrenzkampf).

Dies führt unter anderem auch zu Softwareartefakten (aus Forschung und Abschlussarbeiten) die grob fehlerhaft sind. Dennoch werden solche Programme in der wissenschaftlichen Forschung eingesetzt, da z.B. die Überprüfung solcher Programme nicht hoch publiziert werden kann. Schlimmer noch, solche ungetesteten Programme werden zu komplexen Datenanalyseworkflows zusammengesetzt.

Meine Vision ist es durch die Entwicklung einer Plattform zum wissenschaftlichen Arbeiten den Fokus wieder auf die Wissensfindung zu lenken. Die Plattform, das Internet of Science (IoS), wird den vollständigen wissenschaftlichen Ablauf von Hypothese bis Publikation abbilden. Dieser Ablauf wird auf einer integrierten Oberfläche (Online/Offline) stattfinden, welche für jede Aufgabe Kollaborationsmöglichkeiten bereithält.

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

Um das Internet of Science weiter zu fördern richten wir eine Konferenz zum Thema angewandte Bioinformatik und integrative Bioinformatik aus:
1. International Applied Bioinformatics Conference (iABC’20) & 16. International Integrative Bioinformatics Conference.

Publikationen

Ausgewählte Publikationen

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.

Publikationslisten

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

Lehrveranstaltungen

Hochschule Ruhr West

• Grundlagen der Informatik und Programmiersprachen
• Informationssysteme im Gesundheitswesen, Datenbanken, Datensicherheit
• Personalisierte Gesundheitstechnologien
• Semantische und Syntaktische Interoperabilität / Standards
• Data Mining und Maschinelles Lernen

Zuvor

• Einführung in die Programmierung (Izmir Institute of Technology, Izmir, Türkei)
• Angewandte Bioinformatik (Izmir Institute of Technology, Izmir, Türkei)
• Bioinformatik (Izmir Institute of Technology, Izmir, Türkei)
• Algorithmen in der Bioinformatik (Izmir Institute of Technology, Izmir, Türkei)
• Proteomische Datenanalyse (Izmir Institute of Technology, Izmir, Türkei)
• Genomik (Izmir Institute of Technology, Izmir, Türkei)
• Proteomische Datenanalyse (ERASMUS, Freie Universität Berlin, Deutschland)
• Computergestützte Proteomik (ERASMUS, Bielefeld Universität, Deutschland)
• Bioinformatik für Genomik und Proteomik (Kurs auf Einladung, Dokuy Eylül University, Izmir, Türkei)
• Bioinformatik (Izmir University of Economics, Izmir, Türkei)
• Grundlagen des Software-Engineering (Izmir University of Economics, Izmir, Türkei)
• Einführung in Computer und Informationstheorie (Izmir University of Economics, Izmir, Türkei)
• Datenbanksysteme (Izmir University of Economics, Izmir, Türkei)
• Data Mining (Izmir University of Economics, Izmir, Türkei)
• Fortgeschrittene Programmierung (Izmir University of Economics, Izmir, Türkei)
• System Analyse und Design (Izmir University of Economics, Izmir, Türkei)
• Methoden der Funktionalen Proteomik (Münster University, Münster, Deutschland

Abschlussarbeiten

Abgeschlossene Doktorarbeiten

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.

Gutachter für Doktorarbeiten

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).

Masterarbeiten

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.