Natrix2 – Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases

Authors: Aman Deep, Dana Bludau, Marius Welzel, Sandra Clemens, Dominik Heider, Jens Boenigk, Daniela Beisser

Source: Metabarcoding and Metagenomics, Vol 7, Iss , Pp 263-271 (2023)

Subject Terms: Ecology, QH540-549.5

File Description: electronic resource

Relation: https://mbmg.pensoft.net/article/109389/download/pdf/; https://mbmg.pensoft.net/article/109389/download/xml/; https://mbmg.pensoft.net/article/109389/; https://doaj.org/toc/2534-9708

Access URL: https://doaj.org/article/bbc8c28ceee340b081e39e62e3366953

Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates

Authors: Stephan Majda, Daniela Beisser, Jens Boenigk

Source: Communications Biology, Vol 4, Iss 1, Pp 1-11 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/0ab9fcfb9ba041fdb0be1e66657d5bfe

Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

Authors: Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk, Daniela Beisser

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-14 (2020)

Subject Terms: Amplicon sequencing, Operational Taxonomic Units, Amplicon Sequence Variants, Snakemake, Pipline, Illumina, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-03852-4; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/5c83108527fa426e9d3e97b719d37240

Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution

Authors: Daniela Frantal, Sabine Agatha, Daniela Beisser, Jens Boenigk, Tatyana Darienko, Gianna Dirren-Pitsch, Sabine Filker, Michael Gruber, Barbara Kammerlander, Laura Nachbaur, Ulrike Scheffel, Thorsten Stoeck, Kuimei Qian, Birgit Weißenbacher, Thomas Pröschold, Bettina Sonntag

Source: Frontiers in Microbiology, Vol 12 (2022)

Subject Terms: ciliate plankton, biogeography, ciliate diversity, cryptic species, microplankton, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2021.787290/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/cf1d8b1a6b564a7686f6516e69f4ae74

A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes

Authors: Sebastian Spänig, Lisa Eick, Julia K. Nuy, Daniela Beisser, Margaret Ip, Dominik Heider, Jens Boenigk

Source: Environment International, Vol 157, Iss , Pp 106821- (2021)

Subject Terms: Pathogens, Antimicrobial Resistance, Multi-Omics, European Freshwater Lakes, Environmental sciences, GE1-350

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S0160412021004463; https://doaj.org/toc/0160-4120

Access URL: https://doaj.org/article/2f35f66edf6e47aab968be8d313bdd3e

Geographic distance and mountain ranges structure freshwater protist communities on a European scalе

Authors: Jens Boenigk, Sabina Wodniok, Christina Bock, Daniela Beisser, Christopher Hempel, Lars Grossmann, Anja Lange, Manfred Jensen

Source: Metabarcoding and Metagenomics, Vol 2, Iss , Pp 1-14 (2018)

Subject Terms: protist, molecular diversity, biogeography, mic, Ecology, QH540-549.5

File Description: electronic resource

Relation: https://mbmg.pensoft.net/article/21519/; https://mbmg.pensoft.net/article/21519/download/pdf/; https://mbmg.pensoft.net/article/21519/download/xml/; https://doaj.org/toc/2534-9708

Access URL: https://doaj.org/article/90deb57e15ae4ea9afe64ef3981913c0

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

Authors: Daniela Beisser, Nadine Graupner, Lars Grossmann, Henning Timm, Jens Boenigk, Sven Rahmann

Source: BMC Genomics, Vol 18, Iss 1, Pp 1-17 (2017)

Subject Terms: Metatranscriptome analysis, Taxonomic assignment, Protists, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-017-4168-6; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/b3774f2b222a4f6cbdbfc7cdba4dac72

Functional and phylogenetic analysis of the core transcriptome of Ochromonadales

Authors: Nadine Graupner, Jens Boenigk, Christina Bock, Manfred Jensen, Sabina Marks, Sven Rahmann, Daniela Beisser

Source: Metabarcoding and Metagenomics, Vol 1, Iss , Pp 1-20 (2017)

Subject Terms: Chrysophyceae, protist, expressed sequence tags, Ecology, QH540-549.5

File Description: electronic resource

Relation: https://mbmg.pensoft.net/article/19862/; https://mbmg.pensoft.net/article/19862/download/pdf/; https://mbmg.pensoft.net/article/19862/download/xml/; https://doaj.org/toc/2534-9708

Access URL: https://doaj.org/article/e04d2a59c92c44b18698dd7e6a79bee0

Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients

Authors: Julia K. Nuy, Matthias Hoetzinger, Martin W. Hahn, Daniela Beisser, Jens Boenigk

Source: Frontiers in Microbiology, Vol 11 (2020)

Subject Terms: freshwater bacteria, Polynucleobacter, Limnohabitans, biogeography, ecological differentiation, physicochemical characteristics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.00154/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/8eac6919a35849a38e42238ff9f2b853

Interaction-Specific Changes in the Transcriptome of Polynucleobacter asymbioticus Caused by Varying Protistan Communities

Authors: Daniela Beisser, Christina Bock, Martin W. Hahn, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk

Source: Frontiers in Microbiology, Vol 10 (2019)

Subject Terms: transcriptomics, Polynucleobacter asymbioticus, chrysophyceae, predator-prey, trophic modes, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2019.01498/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/5a0fe338b57846eba8bf7171d1be8f56

Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data

Authors: Diana Kraus, Jingyun Chi, Jens Boenigk, Daniela Beisser, Nadine Graupner, Micah Dunthorn

Source: PeerJ, Vol 6, p e5894 (2019)

Subject Terms: Asexuality, Meiosis, Crossover pathways, Sex, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/5894.pdf; https://peerj.com/articles/5894/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/6a0cc5ea8d124c36b77adea8c81df041

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis.

Authors: Daniela Beisser, Farnusch Kaschani, Nadine Graupner, Lars Grossmann, Manfred Jensen, Sabrina Ninck, Florian Schulz, Sven Rahmann, Jens Boenigk, Markus Kaiser

Source: PLoS ONE, Vol 12, Iss 1, p e0168183 (2017)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0168183&type=printable; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/c1fc4fa70c3345269e409204839504fd

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

Authors: Daniela Beisser, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk

Source: PeerJ, Vol 5, p e2832 (2017)

Subject Terms: Nutritional strategy, Molecular phylogeny, Chrysophyceae, RNA-Seq, Differential expression analysis, Transcriptomics, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/2832.pdf; https://peerj.com/articles/2832/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/961c5b3387e247018d3cafa15040f25e

Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

Authors: Frank Förster, Daniela Beisser, Markus A. Grohme, Chunguang Liang, Brahim Mali, Alexander Matthias Siegl, Julia C. Engelmann, Alexander V. Shkumatov, Elham Schokraie, Tobias Müller, Martina Schnölzer, Ralph O. Schill, Marcus Frohme, Thomas Dandekar

Source: Bioinformatics and Biology Insights, Vol 2012, Iss 6, Pp 69-96 (2012)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://la-press.com/transcriptome-analysis-in-tardigrade-species-reveals-specific-molecula-a3147; https://doaj.org/toc/1177-9322

Access URL: https://doaj.org/article/8b6ee1ca35584ab2afa6e9463fa358aa

Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure.

Authors: Jens Boenigk, Daniela Beisser, Sonja Zimmermann, Christina Bock, Jurij Jakobi, Daniel Grabner, Lars Groβmann, Sven Rahmann, Stephan Barcikowski, Bernd Sures

Source: PLoS ONE, Vol 9, Iss 4, p e95340 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3995725?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/90d9414842564e2eaabfd020a6a110f5

Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

Authors: Frank Förster, Daniela Beisser, Markus A. Grohme, Chunguang Liang, Brahim Mali, Alexander Matthias Siegl, Julia C. Engelmann, Alexander V. Shkumatov, Elham Schokraie, Tobias Müller, Martina Schnölzer, Ralph O. Schill, Marcus Frohme, Thomas Dandekar

Source: Bioinformatics and Biology Insights, Vol 6 (2012)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1177-9322

Access URL: https://doaj.org/article/5f140bf4d51b4c0d86682ea571d826f9