J
Jens Allmer
Researcher at İzmir Institute of Technology
Publications - 79
Citations - 3872
Jens Allmer is an academic researcher from İzmir Institute of Technology. The author has contributed to research in topics: MiRBase & Regulation of gene expression. The author has an hindex of 19, co-authored 75 publications receiving 3465 citations. Previous affiliations of Jens Allmer include İzmir University of Economics & University of Pennsylvania.
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Exact pattern matching: Adapting the Boyer-Moore algorithm for DNA searches
TL;DR: In this paper, a portion of the Chlamydomonas reinhardtii genome (30 mega bases) was searched with queries ranging from 10 to 2000 nucleotides and an alternating number of matches between one and 25000.
Proceedings ArticleDOI
Species categorization via MicroRNAs based on 3’UTR target sites using sequence features
TL;DR: This work investigated whether miRNA targets sites within the 3’UTR can be differentiated between species based on k-mer features only and found the simplicity of the approach, based on just k-mers, is promising for automatic categorization systems.
Posted ContentDOI
Boron Hyperaccumulation Mechanisms in Puccinellia distans as Revealed by Transcriptomic Analysis
Saniye Elvan Ozturk,Mehmet Göktay,Canan Has,Mehmet Babaoglu,Jens Allmer,Sami Doganlar,Anne Frary +6 more
TL;DR: The results indicated that the hyperaccumulation mechanism of P. distans involves many transcriptomic changes including those that lead to: alterations in the malate pathway, changes in cell wall components that allow sequestration of excess boron without toxic effects, and increased expression of at least one putative borons transporter and two putative aquaporins.
Posted ContentDOI
Detection of pre-microRNA with Convolutional Neural Networks
TL;DR: A method is proposed that uses domain knowledge to create an efficient image representation of miRNA molecules encoding sequence, structure, and implicitly some thermodynamic information and uses this low-level feature representation of the molecules to develop a hierarchical deep representation using a convolutional neural network model, which directly detects precursor miRNAs.
Journal ArticleDOI
Towards an Internet of Science.
TL;DR: The opportunity to build a new system, which will overcome current duplications of effort, introduce proper testing, allow for development and analysis in public and private clouds, and include reporting features leading to interactive documents is presented.