Lista de obras - Alexander Sczyrba - Dominio Público Uruguay

AGenDA: gene prediction by cross-species sequence comparison

artículo científico publicado en 2004

AGenDA: homology-based gene prediction

artículo científico publicado en 2003

AMBER: Assessment of Metagenome BinnERs.

artículo científico publicado en 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

artículo científico publicado en 2016

Analyzing large scale genomic data on the cloud with Sparkhit

artículo científico publicado en 2018

Back to the Future of Soil Metagenomics

artículo científico publicado en 2016

Binning enables efficient host genome reconstruction in cnidarian holobionts

Bioboxes: standardised containers for interchangeable bioinformatics software

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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.

artículo científico publicado en 2018

Common ELIXIR Service for Researcher Authentication and Authorisation

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

artículo científico publicado en 2014

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

artículo científico publicado en 2014

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

artículo científico publicado en 2021

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

article

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

artículo científico publicado en 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

artículo científico publicado en 2022

Decontamination of MDA reagents for single cell whole genome amplification

artículo científico publicado en 2011

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

artículo científico publicado en 2015

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

artículo científico publicado en 2003

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

artículo científico publicado en 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

artículo científico publicado en 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.

artículo científico publicado en 2016

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

artículo científico

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

artículo científico publicado en 2008

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

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico publicado en 2016

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado el 16 de septiembre de 2011

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

Insights into the phylogeny and coding potential of microbial dark matter

artículo científico publicado en 2013

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

artículo científico publicado en 2016

IsoSVM--distinguishing isoforms and paralogs on the protein level

artículo científico publicado en 2006

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

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

artículo científico publicado en 2012

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

artículo científico publicado en 2001

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

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2012

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

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

RNA-related tools on the Bielefeld Bioinformatics Server

artículo científico publicado en 2003

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2013

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

artículo científico publicado en 2015

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2020

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

artículo científico publicado en 2014

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

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

artículo científico publicado en 2005

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

artículo científico publicado en 2016

de.NBI Cloud federation through ELIXIR AAI

artículo científico publicado en 2019

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

artículo científico publicado en 2004

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

artículo científico publicado en 2016

Lista de obras de Alexander Sczyrba

AGenDA: gene prediction by cross-species sequence comparison

AGenDA: homology-based gene prediction

AMBER: Assessment of Metagenome BinnERs.

AltAVisT: comparing alternative multiple sequence alignments

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

Analyzing large scale genomic data on the cloud with Sparkhit

Back to the Future of Soil Metagenomics

Binning enables efficient host genome reconstruction in cnidarian holobionts

Bioboxes: standardised containers for interchangeable bioinformatics software

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

CAMISIM: simulating metagenomes and microbial communities

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

Common ELIXIR Service for Researcher Authentication and Authorisation

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

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

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

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

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

Critical Assessment of Metagenome Interpretation: the second round of challenges

Decontamination of MDA reagents for single cell whole genome amplification

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

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

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

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

Expansion of the global RNA virome reveals diverse clades of bacteriophages

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

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

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

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

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

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

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

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

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

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

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

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

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

Insights into the phylogeny and coding potential of microbial dark matter

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

IsoSVM--distinguishing isoforms and paralogs on the protein level

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

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

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

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

Microarray-based analysis of early development in Xenopus laevis

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

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

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

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

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

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

RNA-related tools on the Bielefeld Bioinformatics Server

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

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

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

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

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

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

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

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

Thousands of small, novel genes predicted in global phage genomes

Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server

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

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

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

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

de.NBI Cloud federation through ELIXIR AAI

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

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