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List of works by Alexander Sczyrba

AGenDA: gene prediction by cross-species sequence comparison

scientific article published on July 2004

AGenDA: homology-based gene prediction

scientific article published in August 2003

AMBER: Assessment of Metagenome BinnERs.

scientific article published in June 2018

AltAVisT: comparing alternative multiple sequence alignments

scientific article published on 01 February 2003

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant

scientific article

Analyzing large scale genomic data on the cloud with Sparkhit

scientific article

Back to the Future of Soil Metagenomics

scientific article

Binning enables efficient host genome reconstruction in cnidarian holobionts

Bioboxes: standardised containers for interchangeable bioinformatics software

scientific article

Bioinformatics for NGS-based metagenomics and the application to biogas research.

scientific article

CAMISIM: simulating metagenomes and microbial communities

scientific article published on 08 February 2019

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.

scientific article

Common ELIXIR Service for Researcher Authentication and Authorisation

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

scientific article

Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.

scientific article

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

scientific article published on 15 December 2021

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

Decontamination of MDA reagents for single cell whole genome amplification

scientific article

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

scientific article published on 30 July 2015

EMMA: a platform for consistent storage and efficient analysis of microarray data

scientific article

Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats

scientific article published in 2022

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

scientific article published on 03 June 2019

Expansion of the global RNA virome reveals diverse clades of bacteriophages

scientific article published in October 2022

F5Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota

scientific article published on 27 March 2019

Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.

scientific article published on 6 April 2016

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities.

scientific article published on 07 July 2015

GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.

scientific article

Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190.

scientific article

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres

scientific article published on 17 April 2014

Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment

scientific article published on 7 May 2016

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

scientific article

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

scientific article published on 13 November 2017

High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery

scientific article published on September 16, 2011

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

scientific article

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum

scientific article published on 17 June 2020

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea

scientific article published on 16 February 2018

Insights into the phylogeny and coding potential of microbial dark matter

scientific article

Intraspecies Transfer of the Chromosomal Acinetobacter baumannii blaNDM-1 Carbapenemase Gene

scientific article published on 7 March 2016

IsoSVM--distinguishing isoforms and paralogs on the protein level

scientific article

MeCorS: Metagenome-enabled error correction of single cell sequencing reads

scientific article published on 15 March 2016

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

scientific article

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen

scientific article (publication date: 28 January 2011)

Microarray-based analysis of early development in Xenopus laevis

scientific article published in August 2001

Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity

scientific article

Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma

scientific article

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

scientific article

Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean.

scientific article

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

scientific article published on 25 June 2013

Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type

scientific article published on 26 July 2016

RNA-related tools on the Bielefeld Bioinformatics Server

scientific article

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

scientific article

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

scientific article

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

scientific article (publication date: December 2013)

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

scientific article

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

scientific article

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

scientific article

The Role of <i>Petrimonas mucosa</i> ING2-E5A<sup>T</sup> in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

scientific article published on 17 December 2020

The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features

scientific article

Thousands of small, novel genes predicted in global phage genomes

scientific article published in 2022

Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server

scientific article published on 16 January 2008

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

scientific article

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

scientific article

XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis

scientific article

acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.

scientific article

de.NBI Cloud federation through ELIXIR AAI

scientific article published on 10 June 2019

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences

scientific article published on July 2004

miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering

scientific article published on 18 March 2016

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