All Stories

  1. The Role of MicroRNAs in HIV Infection

    Article • Genes, April 2024, MDPI AG

    Dr Jens Allmer

  2. Alternative polyadenylation and dynamic 3′ UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs

    Article • Frontiers in Molecular Biosciences, February 2024, Frontiers

    Dr Jens Allmer

  3. Deep learning in bioinformatics

    Article • TURKISH JOURNAL OF BIOLOGY, December 2023, The Scientific and Technological Research Council of Turkey (TUBITAK-ULAKBIM) - DIGITAL COMMONS JOURNALS

    Dr Jens Allmer

  4. Noncoding RNA Databases

    Article • Current Pharmaceutical Biotechnology, June 2023, Bentham Science Publishers

    Dr Jens Allmer

  5. PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach

    Article • BMC Bioinformatics, February 2023, Springer Science + Business Media

    Dr Jens Allmer

  6. Criteria for the Evaluation of Workflow Management Systems for Scientific Data Analysis

    Article • Journal of Bioinformatics and Systems Biology, January 2023, Fortune Journals

    Dr Jens Allmer

  7. IoS: A Needed Platform for Scientific Workflow Management

    Article • January 2022, Springer Science + Business Media

    Dr Jens Allmer

  8. miRNomics

    Article • January 2022, Springer Science + Business Media

    Dr Jens Allmer

  9. Systems analysis of miRNA biomarkers to inform drug safety

    Article • Archives of Toxicology, September 2021, Springer Science + Business Media

    Dr Jens Allmer

  10. 44 Current Challenges in miRNomics

    Article • August 2021, Springer Science + Business Media

    Dr Jens Allmer

  11. Ensemble Classifiers for Multiclass MicroRNA Classification

    Article • August 2021, Springer Science + Business Media

    Dr Jens Allmer

  12. Antiviral microRNA Expression Signatures are Altered in Subacute Sclerosing Panencephalitis

    Article • Neurological Sciences and Neurophysiology, July 2021, Medknow

    Dr Jens Allmer

  13. Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features

    Article • Algorithms, April 2021, MDPI AG

    Dr Jens Allmer

  14. Special issue on COVID-19 data integration opportunities and vaccine development strategies

    Article • Journal of Integrative Bioinformatics, March 2021, De Gruyter

    Dr Jens Allmer

  15. Novel perspectives for SARS-CoV-2 genome browsing

    Article • Journal of Integrative Bioinformatics, March 2021, De Gruyter

    Dr Jens Allmer

  16. DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data

    Article • PeerJ, October 2020, PeerJ

    Dr Jens Allmer

  17. A Machine Learning-based Approach for the Categorization of MicroRNAs to Their Species of Origin

    Article • January 2020, Scitepress

    Dr Jens Allmer

  18. Towards an Internet of Science

    Article • Journal of Integrative Bioinformatics, May 2019, De Gruyter

    Dr Jens Allmer

  19. maTE: discovering expressed interactions between microRNAs and their targets

    Article • Bioinformatics, March 2019, Oxford University Press (OUP)

    Dr Jens Allmer

  20. Classification of Pre-cursor microRNAs from Different Species Using a New Set of Features

    Article • January 2019, Springer Science + Business Media

    Dr Jens Allmer

  21. Computational Prediction of Functional MicroRNA–mRNA Interactions

    Article • January 2019, Springer Science + Business Media

    Dr Jens Allmer

  22. Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars

    Article • Plant Molecular Biology Reporter, November 2018, Springer Science + Business Media

    Dr Jens Allmer

  23. Transcriptomic analysis of boron hyperaccumulation mechanisms in Puccinellia distans

    Article • Chemosphere, May 2018, Elsevier

    Dr Jens Allmer

  24. The Expressed MicroRNA—mRNA Interactions of Toxoplasma gondii

    Article • Frontiers in Microbiology, January 2018, Frontiers

    Dr Jens Allmer

  25. Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers

    Article • EURASIP Journal on Advances in Signal Processing, October 2017, Springer Science + Business Media

    Dr Jens Allmer

  26. On the performance of pre-microRNA detection algorithms

    Article • Nature Communications, August 2017, Springer Science + Business Media

    Dr Jens Allmer

  27. Improving the Quality of Positive Datasets for the Establishment of Machine Learning Models for pre-microRNA Detection

    Article • Journal of Integrative Bioinformatics, June 2017, De Gruyter

    Dr Jens Allmer

  28. Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)

    Article • Molecular Genetics and Genomics, April 2017, Springer Science + Business Media

    Dr Jens Allmer

  29. PGMiner: Complete proteogenomics workflow; from data acquisition to result visualization

    Article • Information Sciences, April 2017, Elsevier

    Dr Jens Allmer

  30. Delineating the impact of machine learning elements in pre-microRNA detection

    Article • PeerJ, March 2017, PeerJ

    Dr Jens Allmer

  31. MicroRNA categorization using sequence motifs and k-mers

    Article • BMC Bioinformatics, March 2017, Springer Science + Business Media

    Dr Jens Allmer

  32. Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA

    Article • January 2017, De Gruyter

    Dr Jens Allmer

  33. Computational miRNomics – Integrative Approaches

    Article • January 2017, De Gruyter

    Dr Jens Allmer

  34. Distinguishing between MicroRNA Targets from Diverse Species using Sequence Motifs and K-mers

    Article • January 2017, Scitepress

    Dr Jens Allmer

  35. Computational miRNomics

    Article • Journal of Integrative Bioinformatics, December 2016, De Gruyter

    Dr Jens Allmer

  36. A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes

    Article • Journal of Integrative Bioinformatics, December 2016, De Gruyter

    Dr Jens Allmer

  37. The impact of feature selection on one and two-class classification performance for plant microRNAs

    Article • PeerJ, June 2016, PeerJ

    Dr Jens Allmer

  38. Exact pattern matching: Adapting the Boyer-Moore algorithm for DNA searches

    Article • February 2016, PeerJ

    Dr Jens Allmer

  39. One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts

    Article • PLOS One, January 2016, PLOS

    Dr Jens Allmer

  40. Accurate Plant MicroRNA Prediction Can Be Achieved Using Sequence Motif Features

    Article • Journal of Intelligent Learning Systems and Applications, January 2016, Scientific Research Publishing, Inc,

    Dr Jens Allmer

  41. Feature Selection Has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants

    Article • Advances in Bioinformatics, January 2016, Hindawi Publishing Corporation

    Dr Jens Allmer

  42. Feature Selection for MicroRNA Target Prediction - Comparison of One-Class Feature Selection Methodologies

    Article • January 2016, Scitepress

    Dr Jens Allmer

  43. Differential Expression of Toxoplasma gondii MicroRNAs in Murine and Human Hosts

    Article • January 2016, Springer Science + Business Media

    Dr Jens Allmer

  44. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells

    Article • Frontiers in Cellular Neuroscience, May 2015, Frontiers

    Dr Jens Allmer

  45. Genomic Simple Sequence Repeat Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame

    Article • The Plant Genome, January 2015, Crop Science Society of America

    Dr Jens Allmer

  46. Sequence Motif-Based One-Class Classifiers Can Achieve Comparable Accuracy to Two-Class Learners for Plant microRNA Detection

    Article • Journal of Biomedical Science and Engineering, January 2015, Scientific Research Publishing, Inc,

    Dr Jens Allmer

  47. Mass Spectrometry Based Proteomics

    Article • Acta Endocrinologica (Bucharest), January 2015, ACTA Endocrinologica Foundation

    Dr Jens Allmer

  48. Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression

    Article • Genomics Proteomics & Bioinformatics, October 2014, Elsevier

    Dr Jens Allmer

  49. EPO Mediates Neurotrophic, Neuroprotective, Anti-Oxidant, and Anti-Apoptotic Effects via Downregulation of miR-451 and miR-885-5p in SH-SY5Y Neuron-Like Cells

    Article • Frontiers in Immunology, September 2014, Frontiers

    Dr Jens Allmer

  50. Intersection of MicroRNA and Gene Regulatory Networks and their Implication in Cancer

    Article • Current Pharmaceutical Biotechnology, August 2014, Bentham Science Publishers

    Dr Jens Allmer

  51. Computational Methods for MicroRNA Target Prediction

    Article • Genes, August 2014, MDPI AG

    Dr Jens Allmer

  52. Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing

    Article • Molecular Breeding, February 2014, Springer Science + Business Media

    Dr Jens Allmer

  53. miRNomics: MicroRNA Biology and Computational Analysis

    Article • January 2014, Springer Science + Business Media

    Dr Jens Allmer

  54. Determining the C-Terminal Amino Acid of a Peptide from MS/MS Data

    Article • Journal of Integrated OMICS, December 2013, Proteomass

    Dr Jens Allmer

  55. Computational and Bioinformatics Methods for MicroRNA Gene Prediction

    Article • November 2013, Springer Science + Business Media

    Dr Jens Allmer

  56. Machine Learning Methods for MicroRNA Gene Prediction

    Article • November 2013, Springer Science + Business Media

    Dr Jens Allmer

  57. Data mining for microrna gene prediction: On the impact of class imbalance and feature number for microrna gene prediction

    Article • September 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jens Allmer

  58. Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches

    Article • September 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jens Allmer

  59. Development of EST-SSR markers for diversity and breeding studies in opium poppy

    Article • Plant Breeding, April 2013, Wiley

    Dr Jens Allmer

  60. Comparison of Four Ab Initio MicroRNA Prediction Tools

    Article • January 2013, Scitepress

    Dr Jens Allmer

  61. A Call for Benchmark Data in Mass Spectrometry-Based Proteomics

    Article • Journal of Integrated OMICS, December 2012, Proteomass

    Dr Jens Allmer

  62. De novo markup language, a standard to represent de novo sequencing results from MS/MS data

    Article • April 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jens Allmer

  63. Removing contamination from genomic sequences based on vector reference libraries

    Article • April 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jens Allmer

  64. Computational methods for ab initio detection of microRNAs

    Article • Frontiers in Genetics, January 2012, Frontiers

    Dr Jens Allmer

  65. Algorithms for thede novosequencing of peptides from tandem mass spectra

    Article • Expert Review of Proteomics, October 2011, Taylor & Francis

    Dr Jens Allmer

  66. Existing bioinformatics tools for the quantitation of post-translational modifications

    Article • Amino Acids, May 2010, Springer Science + Business Media

    Dr Jens Allmer

  67. Systematic computational analysis of potential RNAi regulation in Toxoplasma gondii

    Article • April 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jens Allmer

  68. Relative protein quantitation with post translational modifications in mass spectrometry based proteomics

    Article • January 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Jens Allmer

  69. Label-free quantitation, an extension to 2DB

    Article • Amino Acids, July 2009, Springer Science + Business Media

    Dr Jens Allmer

  70. Computational Systems Biology

    Article • January 2009

    Dr Jason E McDermott, Dr Jens Allmer

  71. 2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Dr Jens Allmer

  72. Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency inChlamydomonas reinhardtii

    Article • PROTEOMICS, November 2007, Wiley

    Dr Jens Allmer

  73. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

    Article • Science, October 2007, American Association for the Advancement of Science

    Diego Mauricio Riano-Pachon, Dr Jens Allmer

  74. Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways inChlamydomonas reinhardtii

    Article • PROTEOMICS, December 2006, Wiley

    Dr Jens Allmer

  75. A new approach that allows identification of intron-split peptides from mass spectrometric data in genomic databases

    Article • FEBS Letters, March 2004, Wiley

    Dr Jens Allmer