Works by Allmer, Jens

Results: 33

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

Published in:

Amino Acids, 2012, v. 42, n. 1, p. 129, doi. 10.1007/s00726-010-0614-3

By:

Allmer, Jens

Publication type:

Article

Label-free quantitation, an extension to 2DB.

Published in:

Amino Acids, 2010, v. 38, n. 4, p. 1075, doi. 10.1007/s00726-009-0317-9

By:

Allmer, Jens

Publication type:

Article

AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs.

Published in:

Bioinformatics, 2017, v. 33, n. 6, p. 923, doi. 10.1093/bioinformatics/btw736

By:

Kochetov, Alex V.;
Allmer, Jens;
Klimenko, Alexandra I.;
Zuraev, Bulat S.;
Matushkin, Yury G.;
Lashin, Sergey A.

Publication type:

Article

The Role of MicroRNAs in HIV Infection.

Published in:

Genes, 2024, v. 15, n. 5, p. 574, doi. 10.3390/genes15050574

By:

Morando, Nicolas;
Rosenzvit, Mara Cecilia;
Pando, Maria A.;
Allmer, Jens

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05187-2

By:

Yousef, Malik;
Ozdemir, Fatma;
Jaber, Amhar;
Allmer, Jens;
Bakir-Gungor, Burcu

Publication type:

Article

Deep learning in bioinformatics.

Published in:

Turkish Journal of Biology, 2023, v. 47, n. 6, p. 366, doi. 10.55730/1300-0152.2671

By:

YOUSEF, Malik;
ALLMER, Jens

Publication type:

Article

Medical Omics.

Published in:

GMS Medizinische Informatik, Biometrie und Epidemiologie, 2023, v. 19, p. 1, doi. 10.3205/mibe000246

By:

Allmer, Jens;
Hofestädt, Ralf

Publication type:

Article

Challenges for the development of automated RNA-seq analyses pipelines.

Published in:

GMS Medizinische Informatik, Biometrie und Epidemiologie, 2023, v. 19, p. 1, doi. 10.3205/mibe000245

By:

Beukers, Matthieu;
Allmer, Jens

Publication type:

Article

Systems analysis of miRNA biomarkers to inform drug safety.

Published in:

Archives of Toxicology, 2021, v. 95, n. 11, p. 3475, doi. 10.1007/s00204-021-03150-9

By:

Schofield, Amy L.;
Brown, Joseph P.;
Brown, Jack;
Wilczynska, Ania;
Bell, Catherine;
Glaab, Warren E.;
Hackl, Matthias;
Howell, Lawrence;
Lee, Stephen;
Dear, James W.;
Remes, Mika;
Reeves, Paul;
Zhang, Eunice;
Allmer, Jens;
Norris, Alan;
Falciani, Francesco;
Takeshita, Louise Y.;
Seyed Forootan, Shiva;
Sutton, Robert;
Park, B. Kevin

Publication type:

Article

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

Published in:

Plant Molecular Biology Reporter, 2018, v. 36, n. 5/6, p. 800, doi. 10.1007/s11105-018-1120-0

By:

Öztürk, Süleyman Can;
Göktay, Mehmet;
Allmer, Jens;
Doğanlar, Sami;
Frary, Anne

Publication type:

Article

Development of genomic simple sequence repeat markers in faba bean by next-generation sequencing.

Published in:

Plant Molecular Biology Reporter, 2017, v. 35, n. 1, p. 61, doi. 10.1007/s11105-016-1003-1

By:

Abuzayed, Mazen;
Goktay, Mehmet;
Allmer, Jens;
Doganlar, Sami;
Frary, Anne

Publication type:

Article

Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii.

Published in:

Proteomics, 2006, v. 6, n. 23, p. 6207, doi. 10.1002/pmic.200600208

By:

Allmer, Jens;
Naumann, Bianca;
Markert, Christine;
Zhang, Monica;
Hippler, Michael

Publication type:

Article

Community-wide collaboration is a must to reinstall trust in bioinformatics solutions and biomedical interpretation.

Published in:

Journal of Integrative Bioinformatics, 2023, v. 20, n. 1, p. 1, doi. 10.1515/jib-2022-0028

By:

Takan, Savaş;
Allmer, Jens

Publication type:

Article

Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21).

Published in:

2021

By:

Allmer, Jens;
Elloumi, Mourad;
Comin, Matteo;
Hofestädt, Ralf

Publication type:

Editorial

Novel perspectives for SARS-CoV-2 genome browsing.

Published in:

Journal of Integrative Bioinformatics, 2021, v. 18, n. 1, p. 19, doi. 10.1515/jib-2021-0001

By:

Gültekin, Visam;
Allmer, Jens

Publication type:

Article

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

Published in:

Journal of Integrative Bioinformatics, 2021, v. 18, n. 1, p. 1, doi. 10.1515/jib-2021-0006

By:

Allmer, Jens

Publication type:

Article

Towards an Internet of Science.

Published in:

Journal of Integrative Bioinformatics, 2019, v. 16, n. 3, p. 1, doi. 10.1515/jib-2019-0024

By:

Allmer, Jens

Publication type:

Article

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

Published in:

FEBS Letters, 2004, v. 562, n. 1-3, p. 202, doi. 10.1016/S0014-5793(04)00212-1

By:

Allmer, Jens;
Markert, Christine;
Stauber, Einar J.;
Hippler, Michael

Publication type:

Article

MicroRNA categorization using sequence motifs and k-mers.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1584-1

By:

Yousef, Malik;
Khalifa, Waleed;
Acar, Ílhan Erkin;
Allmer, Jens

Publication type:

Article

Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii.

Published in:

Proteomics, 2007, v. 7, n. 21, p. 3964, doi. 10.1002/pmic.200700407

By:

Naumann, Bianca;
Busch, Andreas;
Allmer, Jens;
Ostendorf, Elisabeth;
Zeller, Martin;
Kirchhoff, Helmut;
Hippler, Michael

Publication type:

Article

The Expressed MicroRNA--mRNA Interactions of Toxoplasma gondii.

Published in:

Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2017.02630

By:

Acar, İlhan E.;
Saçar Demirci, Müşerref D.;
Groß, Uwe;
Allmer, Jens

Publication type:

Article

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.

Published in:

Frontiers in Immunology, 2014, v. 5, p. 1, doi. 10.3389/fimmu.2014.00475

By:

Alural, Begum;
Duran, Gizem Ayna;
Tufekci, Kemal Ugur;
Allmer, Jens;
Onkal, Zeynep;
Tunali, Dogan;
Genc, Kursad;
Genc, Sermin

Publication type:

Article

On the performance of pre-microRNA detection algorithms.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-00403-z

By:

Demirci, Müşerref Duygu Saçar;
Baumbach, Jan;
Allmer, Jens

Publication type:

Article

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

Published in:

PLoS ONE, 2016, v. 11, n. 1, p. 1, doi. 10.1371/journal.pone.0145065

By:

Bağcı, Caner;
Allmer, Jens

Publication type:

Article

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

Published in:

EURASIP Journal on Advances in Signal Processing, 2017, v. 2017, n. 1, p. 1, doi. 10.1186/s13634-017-0506-8

By:

Yousef, Malik;
Nigatu, Dawit;
Levy, Dalit;
Allmer, Jens;
Henkel, Werner

Publication type:

Article

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

Published in:

Plant Breeding, 2013, v. 132, n. 3, p. 344, doi. 10.1111/pbr.12059

By:

Şelale, Hatice;
Çelik, Ibrahim;
Gültekin, Visam;
Allmer, Jens;
Doğanlar, Sami;
Frary, Anne;
Debener, T.

Publication type:

Article

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

Published in:

Algorithms, 2021, v. 14, n. 5, p. 132, doi. 10.3390/a14050132

By:

Yousef, Malik;
Allmer, Jens;
Verzotto, Davide

Publication type:

Article

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

Published in:

Advances in Bioinformatics, 2016, p. 1, doi. 10.1155/2016/5670851

By:

Yousef, Malik;
Saçar Demirci, Müşerref Duygu;
Khalifa, Waleed;
Allmer, Jens

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-302

By:

Allmer, Jens;
Kuhlgert, Sebastian;
Hippler, Michael

Publication type:

Article

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

Published in:

Molecular Breeding, 2014, v. 34, n. 2, p. 323, doi. 10.1007/s11032-014-0036-0

By:

Celik, Ibrahim;
Gultekin, Visam;
Allmer, Jens;
Doganlar, Sami;
Frary, Anne

Publication type:

Article

maTE: discovering expressed interactions between microRNAs and their targets.

Published in:

Bioinformatics, 2019, v. 35, n. 20, p. 4020, doi. 10.1093/bioinformatics/btz204

By:

Yousef, Malik;
Abdallah, Loai;
Allmer, Jens

Publication type:

Article

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

Published in:

Molecular Genetics & Genomics, 2017, v. 292, n. 4, p. 847, doi. 10.1007/s00438-017-1314-4

By:

Göl, Şurhan;
Göktay, Mehmet;
Allmer, Jens;
Doğanlar, Sami;
Frary, Anne

Publication type:

Article

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

Published in:

Frontiers in Molecular Biosciences, 2024, p. 1, doi. 10.3389/fmolb.2024.1336336

By:

Hansel-Frose, Aruana F. F.;
Allmer, Jens;
Friedrichs, Marcel;
Geremias dos Santos, Hellen;
Dallagiovanna, Bruno;
Spangenberg, Lucía

Publication type:

Article