As a de.NBI Cloud user you are able to add your publication to this list. Have a look at our wiki to find out how you can add your publications to this list. When doing so, please pay particular attention to the information on the desired type of citation.

Currently 159 publications with reference to de.NBI Cloud are listed.

Recently added publication

The environment drives microbial trait variability in aquatic habitats
S. Beier - A. Andersson, P. Galand, C. Hochart et al. - Wiley, 2020

Diabetes changes gene expression but not DNA methylation in cardiac cells
A. Lother - O. Bondareva, A. Saadatmand, L. Pollmeier et al. - Elsevier BV,

Congenital heart disease risk loci identified by genome-wide association study in European patients
H. Lahm - M. Jia, M. Dreßen, F. Wirth et al. - American Society for Clinical Investigation,

Electroactive microorganisms in mouse feces
L. Rago - D. Popp, J. Heiker, F. Harnisch - Elsevier BV, 2021

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
E. Redl - R. Sheibani-Tezerji, C. Cardona, P. Hamminger et al. - Life Science Alliance, LLC, 2020

MOSGA: Modular Open-Source Genome Annotator
R. Martin - T. Hackl, G. Hattab, M. Fischer - Oxford University Press (OUP), 2020

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
D. Porubsky, . - P. Ebert, P. Audano, M. Vollger et al. - Springer Science and Business Media LLC, 2020

A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans
W. Qi - E. Gromoff, F. Xu, Q. Zhao et al. - Cold Spring Harbor Laboratory,

A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
W. Liang - K. Yamahara, C. Hernando-Erhard, S. Lagies et al. - Elsevier BV,

Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages
J. Wolf - X. Zhuang, A. Hildebrand, S. Boneva et al. - Elsevier BV,

Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
I. Meyer-Cifuentes - J. Werner, N. Jehmlich, S. Will et al. - Springer Science and Business Media LLC, 2020

Survey of metaproteomics software tools for functional microbiome analysis
R. Sajulga - C. Easterly, M. Riffle, B. Mesuere et al. - Public Library of Science (PLoS),

The environment drives microbial trait variability in aquatic habitats
S. Beier - A. Andersson, P. Galand, C. Hochart et al. - Wiley, 2020

Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
P. Afouda - G. Dubourg, A. Levasseur, P. Fournier et al. - MDPI AG,

Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
R. Wirth - B. Pap, T. Böjti, P. Shetty et al. - Frontiers Media SA,

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
D. Wibberg - B. Batut, P. Belmann, J. Blom et al. - F1000 Research Ltd,

Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
M. Núñez-Sánchez - J. Colom, L. Walsh, C. Buttimer et al. - MDPI AG,

Deep learning-based diatom taxonomy on virtual slides
M. Kloster - D. Langenkämper, M. Zurowietz, B. Beszteri - Springer Science and Business Media LLC, 2020

Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
T. Wilke - T. Hauffe, E. Jovanovska, A. Cvetkoska et al. - American Association for the Advancement of Science (AAAS), 2020

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
H. Schiebenhoefer - K. Schallert, B. Renard, K. Trappe et al. - Springer Science and Business Media LLC, 2020

Training Infrastructure as a Service
H. Rasche - B. Grüning - Cold Spring Harbor Laboratory,

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
D. Baker - M. van den Beek, D. Blankenberg, D. Bouvier et al. - Public Library of Science (PLoS),

Draft Genome Sequences of Three Clostridia Isolates Involved in Lactate-Based Chain Elongation
B. Liu - D. Popp, H. Sträuber, H. Harms - American Society for Microbiology, 2020

pyGenomeTracks: reproducible plots for multivariate genomic datasets
L. Lopez-Delisle - L. Rabbani, J. Wolff, V. Bhardwaj et al. - Oxford University Press (OUP),

Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
M. Buhl - M. Marschal - Microbiology Society,

SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
S. Müller - S. Wallner, G. Schmitz, T. Loew et al. - Elsevier BV,

A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
S. Dhamija - C. Yang, J. Seiler, K. Myacheva et al. - Springer Science and Business Media LLC,

An Interactive Visualization for Feature Localization in Deep Neural Networks
M. Zurowietz - T. Nattkemper - Frontiers Media SA, 2020

Genome‐wide cooperation of EMT transcription factor ZEB 1 with YAP and AP ‐1 in breast cancer
N. Feldker - F. Ferrazzi, H. Schuhwerk, S. Widholz et al. - EMBO,

Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
C. Lange - J. Wolf, C. Auw‐Haedrich, A. Schlecht et al. - Wiley,

Lake expansion elevates equilibrium diversity via increasing colonization
T. Hauffe - D. Delicado, R. Etienne, L. Valente - Wiley, 2020

Unifying the global coding sequence space enables the study of genes with unknown function across biomes
C. Vanni - M. Schechter, S. Acinas, A. Barberán et al. - Cold Spring Harbor Laboratory, 2020

Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
T. Villa - M. Barucco, M. Martin-Niclos, A. Jacquier - Elsevier BV,

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve et al. - MDPI AG,

Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
M. Foschini - L. Morandi, A. Sanchez, A. Santoro et al. - Frontiers Media SA,

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
H. Nützmann - D. Doerr, A. Ramírez-Colmenero, J. Sotelo-Fonseca et al. - Proceedings of the National Academy of Sciences, 2020

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
V. Jalili, E. Afgan, Q. Gu, D. Clements, D. Blankenberg, J. Goecks, J. Taylor, A. Nekrutenko - Oxford University Press (OUP),

Galactic Circos: User-friendly Circos plots within the Galaxy platform
H. Rasche, S. Hiltemann - Oxford University Press (OUP),

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
A. Busch - M. Brüggemann, S. Ebersberger, K. Zarnack - Elsevier BV,

3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
S. Boneva - A. Schlecht, D. Böhringer, H. Mittelviefhaus et al. - Springer Science and Business Media LLC,

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
J. Oeyen - P. Baa-Puyoulet, J. Benoit, L. Beukeboom et al. - Oxford University Press (OUP),

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
M. Mungan, M. Alanjary, K. Blin, T. Weber, M. Medema, N. Ziemert - Oxford University Press (OUP), 2020

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
M. Mungan, M. Alanjary, K. Blin, T. Weber, M. Medema, N. Ziemert - Oxford University Press (OUP), 2020

Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
R. Winkler, I. Rosas-Román - American Chemical Society (ACS),

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
N. Blomberg - K. Lauer - Springer Science and Business Media LLC,

Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
B. Öztürk, J. Werner, J. Meier-Kolthoff, B. Bunk, C. Spröer, D. Springael - Oxford University Press (OUP), 2020

The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
M. McGill - B. Sabikunnahar, Q. Fang, C. Teuscher - Elsevier BV,

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
S. Chen - G. Sun, Y. Yan, K. Konstantinidis et al. - Proceedings of the National Academy of Sciences, 2020

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm et al. - Cold Spring Harbor Laboratory,

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
H. Lee - H. Chawla, C. Obermeier, F. Dreyer et al. - Frontiers Media SA, 2020

Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
W. Logroño - D. Popp, S. Kleinsteuber, H. Sträuber et al. - MDPI AG, 2020

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
G. Lodewijk - D. Fernandes, I. Vretzakis, J. Savage - Oxford University Press (OUP),

An epigenetic map of malaria parasite development from host to vector
K. Witmer - S. Fraschka, D. Vlachou, R. Bártfai - Springer Science and Business Media LLC,

Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
M. Tangaro, G. Donvito, M. Antonacci, M. Chiara, P. Mandreoli, G. Pesole, F. Zambelli - Oxford University Press (OUP),

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
T. McGowan, J. Johnson, P. Kumar, R. Sajulga, S. Mehta, P. Jagtap, T. Griffin - Oxford University Press (OUP),

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
F. Uellendahl-Werth - M. Wolfien, A. Franke, O. Wolkenhauer - Springer Science and Business Media LLC,

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
S. Kumaran - A. Ngo, F. Schultes, D. Tischler - Springer Science and Business Media LLC,

Identification of X-chromosomal genes that drive global X-dosage effects in embryonic stem cells
O. Genolet - A. Monaco, I. Dunkel, M. Boettcher - Cold Spring Harbor Laboratory,

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
J. Werner - E. Nour, B. Bunk, C. Spröer et al. - Frontiers Media SA, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
J. Garrido - M. Aguilar, P. Prieto - Springer Science and Business Media LLC,

Pluripotency factors select gene expression repertoire at Zygotic Genome Activation
M. Gao - M. Veil, M. Rosenblatt, A. Gebhard et al. - Cold Spring Harbor Laboratory,

Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann et al. - Springer Science and Business Media LLC,

Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
G. Farmiloe - G. Lodewijk, S. Robben, E. van Bree - The Royal Society,

Interpretable detection of novel human viruses from genome sequencing data
J. Bartoszewicz - A. Seidel, B. Renard - Cold Spring Harbor Laboratory, 2020

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
D. Hofacker - J. Broche, L. Laistner, S. Adam et al. - MDPI AG,

Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages
F. Candeliere - S. Raimondi, G. Spampinato, M. Tay et al. - American Society for Microbiology,

BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
M. Hanussek - F. Bartusch, J. Krüger - Elsevier BV, 2020

Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
M. Zurowietz - T. Nattkemper - Institute of Electrical and Electronics Engineers (IEEE), 2020

Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye - Springer International Publishing, 2020

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
G. Sevillya, D. Doerr, Y. Lerner, J. Stoye, M. Steel, S. Snir - Oxford University Press (OUP), 2019

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
M. Lewinski - Y. Bramkamp, T. Köster, D. Staiger - Cold Spring Harbor Laboratory, 2019

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger et al. - Oxford University Press (OUP), 2019

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
G. Etherington - N. Soranzo, S. Mohammed, W. Haerty et al. - Oxford University Press (OUP),

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata - Cold Spring Harbor Laboratory,

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
J. Werner - A. Géron, J. Kerssemakers, S. Matallana-Surget - Springer Science and Business Media LLC, 2019

Tool recommender system in Galaxy using deep learning
A. Kumar - B. Grüning, R. Backofen - Cold Spring Harbor Laboratory,

Highly efficient library preparation for Ion Torrent sequencing using Y-adapters
L. Forth - D. Höper - Future Science Ltd,

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
J. Torres-Paz - J. Leclercq, S. Rétaux - eLife Sciences Publications, Ltd,

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
A. Géron - J. Werner, R. Wattiez, P. Lebaron - Frontiers Media SA, 2019

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
M. Emperle - S. Adam, S. Kunert, M. Dukatz et al. - Oxford University Press (OUP),

An intrinsically disordered proteins community for ELIXIR
N. Davey - M. Babu, M. Blackledge, A. Bridge et al. - F1000 Research Ltd,

Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
S. Lambrecht - Y. Kanesaki, J. Fuss, B. Huettel et al. - Springer Science and Business Media LLC,

Development of novel microsatellite markers for Alkanna tinctoria  by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer - Wiley,

ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
M. Haas - J. Gómez Vázquez, D. Sun, H. Tran et al. - Elsevier BV,

Candida auris in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen et al. - Centers for Disease Control and Prevention (CDC),

Pheno-seq – linking visual features and gene expression in 3D cell culture systems
S. Tirier - J. Park, F. Preußer, L. Amrhein et al. - Springer Science and Business Media LLC, 2019

Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
R. Rauschmeier - C. Gustafsson, A. Reinhardt, N. A‐Gonzalez et al. - EMBO,

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
T. Wollmann - M. Gunkel, I. Chung, H. Erfle et al. - Elsevier BV, 2019

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
L. Sánchez - B. Burger, C. Horro, A. Fabregat et al. - Oxford University Press (OUP),

Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion - American Chemical Society (ACS), 2019

U2AF65assemblies drive sequence‐specific splice site recognition
M. Tari - V. Manceau, J. Matha Salone, A. Kobayashi et al. - EMBO,

A pan-cancer analysis of synonymous mutations
Y. Sharma - M. Miladi, S. Dukare, K. Boulay et al. - Springer Science and Business Media LLC,

de.NBI Cloud federation through ELIXIR AAI
P. Belmann - B. Fischer, J. Krüger, M. Procházka et al. - F1000 Research Ltd, 2019

Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells
C. Ritter - T. Wollmann, P. Bernhard, M. Gunkel et al. - Springer Science and Business Media LLC, 2019

BIIGLE2Go—A scalable image annotation system for easy deployment on cruises
M. Zurowietz - D. Langenkamper, T. Nattkemper - IEEE, 2019

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
B. Pucker - D. Holtgräwe, K. Stadermann, K. Frey et al. - Public Library of Science (PLoS), 2019

Reproducible Scientific Workflows for High Performance and Cloud Computing
F. Bartusch - M. Hanussek, J. Kruger, O. Kohlbacher - IEEE, 2019

BOOTABLE: Bioinformatics Benchmark Tool Suite
M. Hanussek - F. Bartusch, J. Kruger, O. Kohlbacher - IEEE, 2019

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
J. Espenshade - S. Thijs, S. Gawronski, H. Bové et al. - Frontiers Media SA,

Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
L. Youssar - V. Wernet, N. Hensel, X. Yu et al. - Public Library of Science (PLoS),

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
J. Teikari - R. Popin, S. Hou, M. Wahlsten et al. - Springer Science and Business Media LLC,

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi - S. Bray, C. Barnett, B. Grüning - Oxford University Press (OUP),

CAMISIM: simulating metagenomes and microbial communities
A. Fritz - P. Hofmann, S. Majda, E. Dahms et al. - Springer Science and Business Media LLC, 2019

Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis
A. Lother - L. Deng, M. Huck, D. Fürst et al. - Bioscientifica,

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
A. Bagnacani - M. Wolfien, O. Wolkenhauer - Springer New York,

Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
A. Kalmbach - C. Schröder, L. Klein-Hitpass, K. Nordström et al. - S. Karger AG,

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
P. Kumar - P. Panigrahi, J. Johnson, W. Weber et al. - American Chemical Society (ACS),

Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
S. Matallana-Surget - J. Werner, R. Wattiez, K. Lebaron et al. - Frontiers Media SA, 2018

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
S. Weise - G. Arumugam, A. Villarreal, P. Videm et al. - Springer Science and Business Media LLC,

Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation
N. Blagitko-Dorfs - P. Schlosser, G. Greve, D. Pfeifer et al. - Springer Science and Business Media LLC,

MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
M. Zurowietz - D. Langenkämper, B. Hosking, H. Ruhl - Public Library of Science (PLoS), 2018

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J. Huerta-Cepas - D. Szklarczyk, D. Heller, A. Hernández-Plaza et al. - Oxford University Press (OUP), 2018

Aequatus: an open-source homology browser
A. Thanki - N. Soranzo, J. Herrero, W. Haerty - Oxford University Press (OUP),

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
V. Piro - T. Dadi, E. Seiler, K. Reinert - Cold Spring Harbor Laboratory, 2018

Common ELIXIR Service for Researcher Authentication and Authorisation
M. Linden - M. Prochazka, I. Lappalainen, D. Bucik et al. - F1000 Research Ltd, 2018

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
I. Maus - M. Rumming, I. Bergmann, K. Heeg et al. - Springer Science and Business Media LLC, 2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J. Wolff - V. Bhardwaj, S. Nothjunge, G. Richard et al. - Oxford University Press (OUP),

Community-Driven Data Analysis Training for Biology
B. Batut - S. Hiltemann, A. Bagnacani, D. Baker et al. - Elsevier BV,

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
I. Maus - A. Bremges, Y. Stolze, S. Hahnke et al. - Springer Science and Business Media LLC, 2017

Workflows for microscopy image analysis and cellular phenotyping
T. Wollmann - H. Erfle, R. Eils, K. Rohr - Elsevier BV, 2017

Bioinformatics for NGS-based metagenomics and the application to biogas research
S. Jünemann - N. Kleinbölting, S. Jaenicke, C. Henke et al. - Elsevier BV, 2017

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper - Frontiers Media SA, 2017