Publications

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Currently 1029 publications with reference to de.NBI Cloud are listed.

Recently added publication

Rapid detection and online analysis of microbial changes through flow cytometry
J. Kupschus - S. Janssen, A. Hoek, J. Kuska, et al. - Wiley, 2022


Bioelectrochemical protein production valorising NH3-rich pig manure-derived wastewater and CO2 from anaerobic digestion
G. Soggia - A. Goglio, P. Cristiani, I. Luciani, et al. - Renewable Energy, 2024 usegalaxy.eu

Characterization of a highly thermostable recombinant xylanase from Anoxybacillus ayderensis
Z. Akpinar - H. Karaoglu, - Protein Expression and Purification, 2024 usegalaxy.eu

Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient
R. AlJindan - N. Mahmoud, D. AlEraky, N. Almandil, et al. - Journal of Infection and Public Health, 2024 usegalaxy.eu

Complete genome sequence of the <i>Microbacterium enclense</i> bacteriophage phiMiGM15
E. Camacho-Beltrán - J. Morales-Aguilar, M. López-Meyer, G. Rincón-Enríquez, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders
L. Jovović - J. Bedek, F. Malard, H. Bilandžija, et al. - Scientific Data, 2024 usegalaxy.eu

Nuclear position and local acetyl-CoA production regulate chromatin state
P. Willnow - A. Teleman, - Nature, 2024 usegalaxy.eu

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study
J. Pirnay - S. Djebara, G. Steurs, J. Griselain, et al. - Nature Microbiology, 2024 usegalaxy.eu

Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies
A. Pustam - J. Jayaraman, A. Ramsubhag, - Journal of Global Antimicrobial Resistance, 2024 usegalaxy.eu

SmCYP71D373 of Salvia miltiorrhiza catalyzes the methyl oxidation reaction of tanshinone IIA-19 position
X. Qiu - Y. Zhang, Y. Luo, Y. Zhang, et al. - Industrial Crops and Products, 2024 usegalaxy.eu

Carbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain
R. Sabala - A. Fukuda, C. Nakajima, Y. Suzuki, et al. - Journal of Infection and Public Health, 2024 usegalaxy.eu

Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae
I. Kandinov - B. Shaskolskiy, D. Kravtsov, M. Filippova, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Elucidating the impact of Y chromosome microdeletions and altered gene expression on male fertility in assisted reproduction
N. Pazoki - M. Salehi, S. Angaji, M. Abdollahpour-Alitappeh, et al. - Human Molecular Genetics, 2024 usegalaxy.eu

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs
R. Pachanon - N. Khine, N. Phumthanakorn, T. Wongsurawat, et al. - Frontiers in Veterinary Science, 2024 usegalaxy.eu

Divergence within the Taxon ‘Candidatus Phytoplasma asteris’ Confirmed by Comparative Genome Analysis of Carrot Strains
R. Toth - A. Ilic, B. Huettel, B. Duduk, et al. - Microorganisms, 2024 usegalaxy.eu

Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
L. Dossmann - M. Emperle, M. Dukatz, A. de Mendoza, et al. - Communications Biology, 2024 usegalaxy.eu

Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response
C. Ehle - A. Iyer-Bierhoff, Y. Wu, S. Xing, et al. - Communications Biology, 2024 usegalaxy.eu

Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca)
M. López - B. Denoyes, E. Bucher, - BMC Plant Biology, 2024 usegalaxy.eu

A practical guide to bioimaging research data management in core facilities
C. Schmidt - T. Boissonnet, J. Dohle, K. Bernhardt, et al. - Journal of Microscopy, 2024 usegalaxy.eu

Cluster efficient pangenome graph construction with nf-core/pangenome
S. Heumos - M. Heuer, F. Hanssen, L. Heumos, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression
C. Bode - S. Preissl, L. Hein, A. Lother, et al. - Intensive Care Medicine Experimental, 2024 usegalaxy.eu

Reduction of APOE accounts for neurobehavioral deficits in fetal alcohol spectrum disorders
H. Hwang - S. Yamashita, Y. Matsumoto, M. Ito, et al. - Molecular Psychiatry, 2024 usegalaxy.eu

Assessment and Partial Characterization of Candidate Genes in Dihydrochalcone and Arbutin Biosynthesis in an Apple–Pear Hybrid by <i>De Novo</i> Transcriptome Assembly
S. Miranda - M. Koop, A. Angeli, J. Lagrèze, et al. - Journal of Agricultural and Food Chemistry, 2024 usegalaxy.eu

Evaluation of novel pyridoxal isonicotinoyl hydrazone (<scp>PIH</scp>) derivatives as potential <scp>anti‐tuberculosis</scp> agents: An in silico investigation
M. Hossain - S. Al Abbad, Z. Alsunaidi, S. Rahman, et al. - International Journal of Quantum Chemistry, 2024 usegalaxy.eu

Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer
S. Joshi - R. Srivastava, - Vietnam Journal of Chemistry, 2024 usegalaxy.eu

The Damietta Server: a comprehensive protein design toolkit
I. Grin - K. Maksymenko, T. Wörtwein, M. ElGamacy, et al. - Nucleic Acids Research, 2024

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
J. Galvis - J. Guyon, B. Dartigues, H. Hecht, et al. - Bioinformatics, 2024 usegalaxy.eu

Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue
J. Fischer - A. Fedotova, C. Bühler, L. Darriba, et al. - Viruses, 2024 usegalaxy.eu

Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells
S. Watson - H. Porter, I. Sudbery, R. Thompson, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

The Celiac‐Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model
M. Herrera - M. Amundarain, P. Dörfler, V. Dodero, et al. - Angewandte Chemie International Edition, 2024

A Minimal Metadata Schema and Its Tool to Improve the Searchableness of Research Data in Bioinformatics
O. Brandt - H. Gauza, J. Kaltenbach, M. Müller, et al. - Journal of Library Metadata, 2024

Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice
B. Oakes - M. Famelis, H. Sahraoui, - ACM Transactions on Software Engineering and Methodology, 2024 usegalaxy.eu

In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae
J. Aribisala - N. S’thebe, S. Sabiu, - Scientific Reports, 2024 usegalaxy.eu

Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
K. Tóth - I. Damjanova, L. Laczkó, L. Buzgó, et al. - Antibiotics, 2024 usegalaxy.eu

Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients
S. Castellana - V. De Laurentiis, A. Bianco, L. Del Sambro, et al. - Microorganisms, 2024 usegalaxy.eu

Complete genome sequence of <i>Pseudomonas aeruginosa</i> phage Knedl
E. Maffei - C. Manner, U. Jenal, A. Harms, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

Complete genome sequence of <i>Escherichia coli</i> MP1
K. Pick - P. Stothard, T. Raivio, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Enhancing the image analysis community in Galaxy
L. Kostrykin - T. Woller, M. Kalaš, B. Özdemir, et al. - Center for Open Science, 2024 usegalaxy.eu

The Intellectual Disability Risk Gene<i>Kdm5b</i>Regulates Long-Term Memory Consolidation in the Hippocampus
L. Pérez-Sisqués - S. Bhatt, R. Matuleviciute, T. Gileadi, et al. - The Journal of Neuroscience, 2024 usegalaxy.eu

Dataset from RNAseq analysis of differential gene expression among developmental stages of two non-marine ostracodes
M. Vences - S. Anslan, J. Sabino-Pinto, M. Bonilla-Flores, et al. - Data in Brief, 2024

ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3
F. Dehghanian - P. Bovio, F. Gather, S. Probst, et al. - Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2024 usegalaxy.eu

The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis
T. Zhu - C. Wei, Y. Yu, Z. Zhang, et al. - Developmental Cell, 2024 usegalaxy.eu

Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation
D. Pinto - G. Themudo, A. Pereira, A. Botelho, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria
A. Palacios-Rodriguez - A. Espinoza-Culupú, Y. Durán, T. Sánchez-Rojas, et al. - Antibiotics, 2024 usegalaxy.eu

First detection of a cefiderocol-resistant and extensively drug-resistant Acinetobacter baumannii clinical isolate in Bulgaria
T. Strateva - S. Peykov, - Acta Microbiologica et Immunologica Hungarica, 2024 usegalaxy.eu

An <scp>RRM</scp> domain protein <scp>SOE</scp> suppresses transgene silencing in rice
R. Zhao - W. Wu, Y. Huang, X. Li, et al. - New Phytologist, 2024 usegalaxy.eu

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress
S. Hosseinzadeh - K. Hasanpur, - Scientific Reports, 2024 usegalaxy.eu

Private and well drinking water are reservoirs for antimicrobial resistant bacteria
M. Alawi - C. Smyth, D. Drissner, A. Zimmerer, et al. - npj Antimicrobials and Resistance, 2024 usegalaxy.eu

Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes
G. Zhang - T. Xu, Y. Chen, W. Xu, et al. - Current Issues in Molecular Biology, 2024 usegalaxy.eu

Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
Ö. Kahraman-Ilıkkan - - Molecular Genetics and Genomics, 2024 usegalaxy.eu

The altered TBI fecal microbiome is stable and functionally distinct
R. Pyles - A. Miller, R. Urban, M. Sheffield-Moore, et al. - Frontiers in Molecular Neuroscience, 2024 usegalaxy.eu

Pangeo environment in Galaxy Earth System supported by Fair-Ease
T. Carval - M. Jossé, J. Detoc, - Copernicus GmbH, 2024 usegalaxy.eu

Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression
L. Deng - L. Pollmeier, R. Bednarz, C. Cao, et al. - Science Advances, 2024 usegalaxy.eu

Human Metagenome Analysis with COVID-19 Infectious Disease
K. Jain - R. Yadav, - Current Trends in Biotechnology and Pharmacy, 2024 usegalaxy.eu

Characterization of the major autolysin (AtlC) of Staphylococcus carnosus
M. Merz - C. Schiffer, A. Klingl, M. Ehrmann, et al. - BMC Microbiology, 2024 usegalaxy.eu

CD38–RyR2 axis–mediated signaling impedes CD8 <sup>+</sup> T cell response to anti-PD1 therapy in cancer
A. Kar - P. Ghosh, A. Gautam, S. Chowdhury, et al. - Proceedings of the National Academy of Sciences, 2024

Decoding chromatin states by proteomic profiling of nucleosome readers
S. Lukauskas - A. Tvardovskiy, N. Nguyen, M. Stadler, et al. - Nature, 2024

Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans
F. Candeliere - E. Musmeci, L. Sola, A. Amaretti, et al. - Frontiers in Microbiology, 2024 usegalaxy.eu

A synthetic biology approach to assemble and reboot clinically relevant <i>Pseudomonas aeruginosa</i> tailed phages
T. Ipoutcha - R. Racharaks, S. Huttelmaier, C. Wilson, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

Targeted RNAseq Revealed the Gene Expression Signature of Ferroptosis-Related Processes Associated with Disease Severity in Patients with Multiple Sclerosis
L. Stojkovic - I. Jovanovic, E. Dincic, A. Djordjevic, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Identification of genetic determinants of bedaquiline resistance in <i>Mycobacterium tuberculosis</i> in Ural region, Russia
T. Umpeleva - E. Chetverikova, D. Belyaev, N. Eremeeva, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins
H. Bastide - H. Legout, N. Dogbo, D. Ogereau, et al. - Current Biology, 2024 usegalaxy.eu

PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency
R. Crespo - E. Ne, J. Reinders, J. Meier, et al. - iScience, 2024 usegalaxy.eu

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances
A. Rain-Franco - H. Peter, G. Pavan de Moraes, S. Beier, et al. - mSphere, 2024

Identification and functional characterisation of a locus for target site integration in Fusarium graminearum
M. Darino - M. Urban, N. Kaur, A. Machado Wood, et al. - Fungal Biology and Biotechnology, 2024 usegalaxy.eu

Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits
D. Beerling - D. Epihov, I. Kantola, M. Masters, et al. - Proceedings of the National Academy of Sciences, 2024 usegalaxy.eu

Changes in the Expression of Proteins Associated with Neurodegeneration in the Brains of Mice after Infection with Influenza A Virus with Wild Type and Truncated NS1
K. Donátová - M. Mladá, K. Lopušná, F. Baran, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications
P. Singh - P. Gopi, M. Rani, S. Singh, et al. - Journal of Molecular Recognition, 2024 usegalaxy.eu

Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes
S. Tetzlaff - A. Hillebrand, N. Drakoulis, Z. Gluhic, et al. - eLife, 2024 usegalaxy.eu

Genome sequence of the medicinal and ornamental plant<i>Digitalis purpurea</i>reveals the molecular basis of flower color variation
K. Wolff - R. Friedhoff, J. Horz, B. Pucker, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
N. Rahman - C. O'Cathail, A. Zyoud, A. Sokolov, et al. - Microbial Genomics, 2024 usegalaxy.eu

Draft genome sequence of <i>Streptomyces poriferorum</i> RTGN2, a bacterial endophyte isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Draft genome sequences of five <i>Mycobacterium</i> strains, isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Effect of <scp>Anti‐S100A4</scp> Monoclonal Antibody Treatment on Experimental Skin Fibrosis and Systemic Sclerosis–Specific Transcriptional Signatures in Human Skin
T. Trinh‐Minh - A. Györfi, M. Tomcik, C. Tran‐Manh, et al. - Arthritis &amp; Rheumatology, 2024 usegalaxy.eu

Anthropogenic contamination sources drive differences in antimicrobial-resistant <i>Escherichia coli</i> in three urban lakes
J. Wight - A. Byrne, K. Tahlan, A. Lang, et al. - Applied and Environmental Microbiology, 2024 usegalaxy.eu

Anthropogenic contamination sources drive differences in antimicrobial-resistant <i>Escherichia coli</i> in three urban lakes
J. Wight - A. Byrne, K. Tahlan, A. Lang, et al. - Applied and Environmental Microbiology, 2024 usegalaxy.eu

Developmental pathways underlying sexual differentiation in a U/V sex chromosome system
D. Liesner - G. Cossard, M. Zheng, O. Godfroy, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Restraining Wnt activation and intestinal tumorigenesis by a Rab35 dependent GTPase relay
S. Redhai - T. Wang, K. Boonekamp, S. Reuter, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

The Genome of Arsenophonus sp. and Its Potential Contribution in the Corn Planthopper, Peregrinus maidis
Y. Wang - A. Mikaelyan, B. Coates, M. Lorenzen, et al. - Insects, 2024 usegalaxy.eu

The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient
Y. de Souza - M. Schloter, W. Weisser, Y. Huang, et al. - Environmental Microbiome, 2024 usegalaxy.eu

From Complexity to Precision—Charting Decision-Making Through Normative Modeling
P. Kumar - P. Dayan, T. Wolfers, - JAMA Psychiatry, 2024

Predicting the Identities of su(met-2) and met-3 in Neurospora crassa by Genome Resequencing
K. McCluskey - D. Brown, E. Bredeweg, S. Baker, et al. - Fungal Genetics Reports, 2024 usegalaxy.eu

Cocoa Apoplastome Contains Defense Proteins Against Pathogens
I. de Oliveira - I. Moura, J. Santana, K. Gramacho, et al. - Phytopathology®, 2024 usegalaxy.eu

A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides
L. Ostenfeld - A. Sørensen, H. Neve, A. Vitt, et al. - Frontiers in Microbiology, 2024 usegalaxy.eu

Acute Hypoxia Does Not Alter Tumor Sensitivity to FLASH Radiation Therapy
R. Leavitt - A. Almeida, V. Grilj, P. Montay-Gruel, et al. - International Journal of Radiation Oncology*Biology*Physics, 2024 usegalaxy.eu

Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing
A. Nugroho - I. Siregar, D. Matra, U. Siregar, et al. - Data in Brief, 2024 usegalaxy.eu

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
M. Shankar - M. Rani, P. Gopi, A. P, et al. - Computational Biology and Chemistry, 2024 usegalaxy.eu

Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation
P. Volkova - A. Prazyan, M. Podlutskii, V. Saburov, et al. - Environmental and Experimental Botany, 2024 usegalaxy.eu

TcSERPIN, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens
M. Ferreira - K. Farias, M. Zugaib, A. Alves, et al. - Frontiers in Plant Science, 2024 usegalaxy.eu

Rat1 promotes premature transcription termination at R-loops
J. Mérida-Cerro - P. Maraver-Cárdenas, A. Rondón, A. Aguilera, et al. - Nucleic Acids Research, 2024 usegalaxy.eu

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
D. Larivière - L. Abueg, N. Brajuka, C. Gallardo-Alba, et al. - Nature Biotechnology, 2024 usegalaxy.eu

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models
O. Ishola - S. Kublik, A. Durai Raj, C. Ohnmacht, et al. - Microorganisms, 2024 usegalaxy.eu

Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga
V. Moris - L. Bruneau, J. Berthe, A. Heuskin, et al. - BMC Biology, 2024 usegalaxy.eu

SimLivA–Modeling ischemia‐reperfusion injury in the liver: A first step towards a clinical decision support tool
H. Tautenhahn - T. Ricken, U. Dahmen, L. Mandl, et al. - GAMM-Mitteilungen, 2024

Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity
T. Oliveira - J. Freitas, V. de Medeiros, T. Xavier, et al. - Life Science Alliance, 2024 usegalaxy.eu

Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates
T. Vieira - C. Dos Santos, A. de Jesus Bertani, G. Costa, et al. - Antibiotics, 2024 usegalaxy.eu

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
L. Dony - A. Krontira, L. Kaspar, R. Ahmad, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis
V. Pilliol - M. Beye, L. Terlier, J. Balmelle, et al. - Microorganisms, 2024 usegalaxy.eu

Transcriptomic characterization of the human segmental endotoxin challenge model
C. Gress - T. Litzenburger, R. Schmid, K. Xiao, et al. - Scientific Reports, 2024 usegalaxy.eu

Mitochondrial genome of Hancornia speciosa gomes: intergenic regions containing retrotransposons and predicted genes
F. de Souza - A. Marques, C. Almeida, - Molecular Biology Reports, 2024 usegalaxy.eu

Draft genome sequence of <i>Amycolatopsis camponoti</i> RTGN1, a bacterial endophyte isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Origin and evolutionary trajectories of brown algal sex chromosomes
J. Barrera-Redondo - A. Lipinska, P. Liu, E. Dinatale, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice
B. Herwibawa - C. Lekklar, S. Chadchawan, T. Buaboocha, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis
T. Lapp - P. Kammrath Betancor, G. Schlunck, C. Auw-Hädrich, et al. - Frontiers in Cellular and Infection Microbiology, 2024 usegalaxy.eu

Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy
A. Garcia-Fernandez - A. Janowicz, F. Marotta, M. Napoleoni, et al. - Frontiers in Microbiology, 2024 usegalaxy.eu

Oncostatin M Reduces Pathological Neovascularization in the Retina Through Müller Cell Activation
J. Rapp - A. Hospach, P. Liang, M. Schwämmle, et al. - Investigative Opthalmology &amp; Visual Science, 2024 usegalaxy.eu

hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS)
H. Salapa - P. Thibault, C. Libner, Y. Ding, et al. - Nature Communications, 2024 usegalaxy.eu

Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses
P. Kruse - G. Brandes, H. Hemeling, Z. Huang, et al. - Cells, 2024 usegalaxy.eu

Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk
P. Andriyanov - D. Kashina, A. Menshikova, - Frontiers in Microbiology, 2024 usegalaxy.eu

Postnatal persistence of hippocampal Cajal-Retzius cells has a crucial role in the establishment of the hippocampal circuit
I. Glærum - K. Dunville, K. Moan, M. Krause, et al. - Development, 2024 usegalaxy.eu

Two male-killing <i>Wolbachia</i> from <i>Drosophila birauraia</i> that are closely related but distinct in genome structure
H. Arai - M. Watada, D. Kageyama, - Royal Society Open Science, 2024 usegalaxy.eu

Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin
F. Bruno - C. Coronel-Guisado, C. González-Aguilera, - Molecular Cell, 2024 usegalaxy.eu

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells
O. Kalnytska - P. Qvist, S. Kunz, T. Conrad, et al. - iScience, 2024 usegalaxy.eu

Development of Similarity Measures From Graph-Structured Bibliographic Metadata: An Application to Identify Scientific Convergence
T. Melnychuk - L. Galke, E. Seidlmayer, S. Bröring, et al. - IEEE Transactions on Engineering Management, 2024

Biofoams with Untapped Enzymatic Potential Produced from Beer Bagasse by Indigenous Fungal Strains
C. Aguirre Pranzoni - J. Bonilla, Á. Carrillo, M. López-Vidal, et al. - Elsevier BV, 2024 usegalaxy.eu

Evolutionary Structure Conservation and Covariance Scores
F. Eggenhofer - C. Höner zu Siederdissen, - Springer US, 2024 usegalaxy.eu

Salmonella phylogenomics
C. Jia - H. Zhou, Z. Wang, Y. Liu, et al. - Elsevier, 2024 usegalaxy.eu

Description of eight new mitochondrial genomes for the genus Neoarius and phylogenetic considerations for the family Ariidae (Siluriformes)
L. Pimentel - I. da Silva, I. Rodrigues-Oliveira, R. Pasa, et al. - Genomics &amp; Informatics, 2023 usegalaxy.eu

Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistron
M. Cedeño-Sanchez - T. Cheng, C. Lambert, M. Kolarík, et al. - Mycological Progress, 2023

Cross-Species Variability in Lobular Geometry and Cytochrome P450 Hepatic Zonation: Insights into CYP1A2, CYP2E1, CYP2D6 and CYP3A4
M. Albadry - J. Küttner, J. Grzegorzewski, O. Dirsch, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Detailing Early Shoot Growth Arrest in Kro-0 x BG-5 Hybrids of <i>Arabidopsis thaliana</i>
K. Sageman-Furnas - G. Duarte, R. Laitinen, - Plant And Cell Physiology, 2023 usegalaxy.eu

Ribosome profiling reveals the fine-tuned response of <i>Escherichia coli</i> to mild and severe acid stress
K. Schumacher - R. Gelhausen, W. Kion-Crosby, L. Barquist, et al. - mSystems, 2023

USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder
J. Cheron - L. Beccari, P. Hagué, R. Icick, et al. - Nature Communications, 2023 usegalaxy.eu

Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae
A. Vieira Da Cruz - J. Jiménez-Castellanos, C. Börnsen, L. Van Maele, et al. - EMBO Molecular Medicine, 2023 usegalaxy.eu

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities
P. Müller - J. de la Cuesta-Zuluaga, M. Kuhn, M. Baghai Arassi, et al. - Nature Protocols, 2023

Construction and analysis of pseudogene-related ceRNA network in breast cancer
H. Mohebifar - A. Sabbaghian, T. Farazmandfar, M. Golalipour, et al. - Scientific Reports, 2023 usegalaxy.eu

Resin acids play key roles in shaping microbial communities during degradation of spruce bark
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Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring blaCMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal
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Mouse models of pediatric high-grade gliomas with MYCN amplification reveal intratumoral heterogeneity and lineage signatures
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Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach
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A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy
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Phage DNA Extraction, Genome Assembly, and Genome Closure
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Exploring the potential of fluoro‐flavonoid derivatives as <scp>anti‐lung</scp> cancer agents: <scp>DFT</scp>, molecular docking, and molecular dynamics techniques
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Parallel loss of sex in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
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Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep’s Milk
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Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets
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Whole genome sequencing of Bacillus anthracis isolated from animal in the 1960s, Brazil, belonging to the South America subclade
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DNA-directed termination of RNA polymerase II transcription
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A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing
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Precision Genome Engineering in <i>Streptococcus suis</i> Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
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The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication
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Volatile Organic Compounds Emitted by the Biocontrol Agent Pythium oligandrum Contribute to Ginger Plant Growth and Disease Resistance
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Regional, circuit and network heterogeneity of brain abnormalities in psychiatric disorders
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A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome
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Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study
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Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning
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A translational regulator MHZ9 modulates ethylene signaling in rice
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A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell
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Pathovar-Specific PCR Method for Detection and Identification of <i>Xanthomonas translucens</i> pv. <i>undulosa</i>
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A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (<i>Rissa tridactyla</i>), a Declining Circumpolar Seabird
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The design of functional proteins using tensorized energy calculations
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Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet
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Insight into the nodal cells transcriptome of the streptophyte green alga <i>Chara braunii</i> S276
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Proteogenomic data and resources for pan-cancer analysis
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Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage
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Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae)
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Unified fate mapping in multiview single-cell data
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BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa
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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
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Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans
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Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil
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Integrative meta-omics in Galaxy and beyond
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EODIE — Earth Observation Data Information Extractor
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The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses
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Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48
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A biologist’s guide to planning and performing quantitative bioimaging experiments
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MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
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The autoPET challenge: Towards fully automated lesion segmentation in oncologic PET/CT imaging
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Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone
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A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland
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In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut
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Su(Hw) interacts with Combgap to establish long-range chromatin contacts
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Genetic factors explaining anthocyanin pigmentation differences
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Ribosome profiling reveals the fine-tuned response of<i>Escherichia coli</i>to mild and severe acid stress
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Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması
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A Roadmap for the Human Gut Cell Atlas
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CpG DNA methylation changes during epididymal sperm maturation in bulls
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SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022
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Species Delineation and Comparative Genomics within the<i>Campylobacter ureolyticus</i>Complex
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β-Cell–Specific <i>E2f1</i> Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
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<i>De Novo</i> Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte -<i>Alternaria burnsii</i>NCIM 1409
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Single‐heartbeat cardiac cine imaging via jointly regularized nonrigid motion‐corrected reconstruction
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Mapping cells through time and space with moscot
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MpoxRadar: a worldwide MPXV genomic surveillance dashboard
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Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
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Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge
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Genetic architecture of brain age and its causal relations with brain and mental disorders
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A draft human pangenome reference
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Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
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Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
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Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia
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Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum
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Automatic annotation of the bHLH gene family in plants
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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
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ODNA: identification of organellar DNA by machine learning
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
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Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
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Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
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Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
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Increasing complexity of opsin expression across stomatopod development
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How does particulate matter affect plant transcriptome and microbiome?
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Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
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Mapping lineage-traced cells across time points with moslin
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A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
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Aircraft surveys for air eDNA: probing biodiversity in the sky
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Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion
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Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient
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Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections
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Building pangenome graphs
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The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops
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Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
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Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
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Proteome alterations in human autopsy tissues in relation to time after death
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The complete reference genome for grapevine (<i>Vitis vinifera</i>L.) genetics and breeding
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mlf-core: a framework for deterministic machine learning
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Mapping Normative Trajectories of Cognitive Function and Its Relation to Psychopathology Symptoms and Genetic Risk in Youth
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Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)
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DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
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Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin
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Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
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External <scp>DNA</scp> contamination and efficiency of bleach decontamination for arthropod diet analysis
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An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
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Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes
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Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses
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IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides
M. Amundarain - A. Vietri, V. Dodero, M. Costabel, et al. - The Journal of Physical Chemistry B, 2023

The giant diploid faba genome unlocks variation in a global protein crop
M. Jayakodi - A. Golicz, J. Kreplak, L. Fechete, et al. - Nature, 2023

Sex-biased gene expression in nutrient-sensing pathways
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Sex-biased gene expression in nutrient-sensing pathways
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Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
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Identification of Radiomic Biomarkers in a Set of Four Skeletal Muscle Groups on Dixon MRI of the NAKO MR study
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Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022)
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Evaluating Tuning Strategies for Sequence Generation with Protein Language Models
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Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43
M. Herrera - M. Amundarain, J. Santos, - Archives of Biochemistry and Biophysics, 2023

Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease
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Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region
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A comprehensive review of bioinformatics tools for chromatin loop calling
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MeganServer: facilitating interactive access to metagenomic data on a server
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Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru
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S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
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Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
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Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution
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Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources
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DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage
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MpoxRadar: a worldwide Mpox genomic surveillance dashboard
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Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera
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Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach
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Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression
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Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents
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A Physcomitrella <scp>PIN</scp> protein acts in spermatogenesis and sporophyte retention
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Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
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Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue
M. Sulyok - J. Luibrand, J. Strohäker, P. Karacsonyi, et al. - Parasites &amp; Vectors, 2023

The Full Genome Sequences of Pseudomonas sp. Strain MM221 and <i>Pseudoarthrobacter</i> sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
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Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine
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Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat
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nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plant root tissue
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A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis
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Genome-wide characterization of Ficus carica MADS-box transcription factors with a focus on their roles during fruit development
N. Kmeli - J. Hamdi, D. Bouktila, - Horticulture, Environment, and Biotechnology, 2023 usegalaxy.eu

Endosomal vesicle fusion machinery is involved with the contractile vacuole in <i>Dictyostelium discoideum</i>
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Azithromycin Susceptibility Testing and Molecular Investigation of Neisseria gonorrhoeae Isolates Collected in Russia, 2020–2021
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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
E. Deutsch - J. Vizcaíno, A. Jones, P. Binz, et al. - Journal of Proteome Research, 2023

A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
G. Hattab - A. Anžel, S. Spänig, N. Neumann, et al. - NAR Genomics and Bioinformatics, 2023

MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments
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Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma
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MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
W. Zeng - A. Gautam, D. Huson, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome
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Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
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Physics-Driven Deep Learning for Computational Magnetic Resonance Imaging: Combining physics and machine learning for improved medical imaging
K. Hammernik - T. Kustner, B. Yaman, Z. Huang, et al. - IEEE Signal Processing Magazine, 2023

CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway
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RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.
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The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves
B. Seckin Dinler - H. Cetinkaya, Z. Secgin, - Physiology and Molecular Biology of Plants, 2023 usegalaxy.eu

Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation
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Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
A. Andersson - A. Behanova, C. Wählby, F. Malmberg, et al. - Springer Nature Switzerland, 2023

DIAMOND +  MEGAN Microbiome Analysis
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A bibliometric analysis and visualization of spatially resolved transcriptomics
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Characterization of mercury species and microbial communities in sediments and suspended particulate matter from historically contaminated river systems
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Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions
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Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
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Avoiding Shortcut-Learning by Mutual Information Minimization in Deep Learning-Based Image Processing
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Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland
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Hybrid Genome Assembly of Short and Long Reads in Galaxy
T. Ohta - Y. Shiwa, - Springer US, 2023 usegalaxy.eu

Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan
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Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
M. Suzuki - Y. Hashimoto, A. Hirabayashi, K. Yahara, et al. - Springer US, 2023 usegalaxy.eu

Analysis of RNA Sequences and Modifications Using NASE
S. Wein - - Springer US, 2023 usegalaxy.eu

Exploring Scutellaria baicalensis bioactives as EGFR tyrosine kinase inhibitors: Cheminformatics and molecular docking studies
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NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming
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Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
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Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
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An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
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Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea
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Guiding the choice of informatics software and tools for lipidomics research applications
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The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
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Better Together
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Better Together
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Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
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Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium
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Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
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MGnify: the microbiome sequence data analysis resource in 2023
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STAT3 signaling induced by IL-6 family cytokines modulates angiogenesis
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Rapid detection and online analysis of microbial changes through flow cytometry
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Renewal of planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction by benthic colonizers
R. Morard - C. Hassenrück, M. Greco, A. Fernandez-Guerra, et al. - Nature Communications, 2022

Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
M. Orantes-Bonilla - M. Makhoul, H. Lee, H. Chawla, et al. - Frontiers in Plant Science, 2022

MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
M. Nata’ala - A. Avila Santos, J. Coelho Kasmanas, A. Bartholomäus, et al. - Environmental Microbiome, 2022

Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink
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Revisiting pangenome openness with k-mers
L. Parmigiani - R. Wittler, J. Stoye, - bioRxiv - Cold Spring Harbor Laboratory, 2022

Replication collisions induced by de-repressed S-phase transcription are connected with malignant transformation of adult stem cells
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Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Antibiotics, 2022

Small proteome of the nitrogen-fixing plant symbiont<i>Sinorhizobium meliloti</i>
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
A. Afrizal - S. Jennings, T. Hitch, T. Riedel, et al. - Cell Host &amp; Microbe, 2022

Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium
J. Breidenbach - B. French, T. Gordon, A. Kleinhenz, et al. - Environment International, 2022 usegalaxy.eu

Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism
A. Soriano-Sexto - D. Gallego, F. Leal, N. Castejón-Fernández, et al. - International Journal of Molecular Sciences, 2022 usegalaxy.eu

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
S. Beier - J. Werner, T. Bouvier, N. Mouquet, et al. - Frontiers in Microbiology, 2022

Multi-histone ChIP-Seq Analysis with DecoDen
T. Narendra - G. Visonà, C. de Jesus Cardona, G. Schweikert, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower
M. Gallus - I. Beer, N. Ivleva, M. Ehrmann, et al. - International Journal of Systematic and Evolutionary Microbiology, 2022 usegalaxy.eu

Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
J. Singh - H. Elhabashy, P. Muthukottiappan, M. Stepath, et al. - Nature Communications, 2022

Semi-automated assembly of high-quality diploid human reference genomes
E. Jarvis - G. Formenti, A. Rhie, A. Guarracino, et al. - Nature, 2022 usegalaxy.eu

Thin‐Plate Superstructures of the Immunogenic 33‐mer Gliadin Peptide
M. Herrera - M. Amundarain, F. Nicoletti, M. Drechsler, et al. - ChemBioChem, 2022

A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use
A. Ardisasmita - I. Schene, I. Joore, G. Kok, et al. - Communications Biology, 2022 usegalaxy.eu

Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
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The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia
E. Valadez-Moctezuma - S. Samah, J. Mascorro-Gallardo, N. Marbán-Mendoza, et al. - Genetic Resources and Crop Evolution, 2022 usegalaxy.eu

Epigenetic nature of <i>Arabidopsis thaliana</i> telomeres
M. Vaquero-Sedas - M. Vega-Palas, - Plant Physiology, 2022 usegalaxy.eu

Multivalent binding kinetics resolved by fluorescence proximity sensing
C. Schulte - A. Soldà, S. Spänig, N. Adams, et al. - Communications Biology, 2022

A whole-body FDG-PET/CT Dataset with manually annotated Tumor Lesions
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Self-supervised learning for automated anatomical tracking in medical image data with minimal human labeling effort
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Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent
K. Korfmann - T. Sellinger, F. Freund, M. Fumagalli, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica
M. Tabarelli - M. Malnoy, K. Janik, - Genes, 2022 usegalaxy.eu

Transgressive and parental dominant gene expression and cytosine methylation during seed development in<i>Brassica napus</i>hybrids
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On the way to plant data commons – a genotyping use case
M. Feser - P. König, A. Fiebig, D. Arend, et al. - Journal of Integrative Bioinformatics, 2022

Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
A. Nasereddin - H. Golan Berman, D. Wolf, E. Oiknine-Djian, et al. - Microbiology Spectrum, 2022 usegalaxy.eu

Biogenesis of <i>C. elegans</i> spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease
H. Tsai - H. Cheng, Y. Tsai, - Science Advances, 2022 usegalaxy.eu

Phased grapevine genome sequence of an<i>Rpv12</i>carrier for biotechnological exploration of resistance to<i>Plasmopara viticola</i>
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An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
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Genetic and genomic diversity in the sorghum gene bank collection of Uganda
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Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
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Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
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Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat
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A Draft Human Pangenome Reference
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MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
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Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
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Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
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KIPEs3: Automatic annotation of biosynthesis pathways
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Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response
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Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
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A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
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Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)
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MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
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Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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Structural analysis of microbiomes from salt caverns used for underground gas storage
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Sequence-based pangenomic core detection
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Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
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Association of DNA methylation and genetic variations of the <i>APOE</i> gene with the risk of diabetic dyslipidemia
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A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
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Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
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Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
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Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation
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ODGI: understanding pangenome graphs
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Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
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Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
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Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021
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MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
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The potential of bacterial key species as a tool for monitoring peatland quality
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Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau
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Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum)
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Age-related brain deviations and aggression
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Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water
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A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
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Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
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Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
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Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
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Identification and annotation of peptide allergens in Prunus dulcis
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NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
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Critical Assessment of Metagenome Interpretation: the second round of challenges
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Unifying the known and unknown microbial coding sequence space
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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation
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Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
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Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
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Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
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Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
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Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
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Pluripotency factors determine gene expression repertoire at zygotic genome activation
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Unsupervised encoding selection through ensemble pruning for biomedical classification
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STENCIL: A web templating engine for visualizing and sharing life science datasets
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Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
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Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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Drivers of diversification in freshwater gastropods vary over deep time
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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
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Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
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sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens
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What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach
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SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
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Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
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Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
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Expanding the Galaxy’s reference data
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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A Tetragenococcus halophilus human gut isolate
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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Canonical Workflows to Make Data FAIR
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
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Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
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PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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An ecological perspective on microbial genes of unknown function in soil
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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
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LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
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Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
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Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
A. Gautam - H. Felderhoff, C. Bağci, D. Huson, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Expression Atlas update: gene and protein expression in multiple species
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Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
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New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
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Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
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Peakhood: individual site context extraction for CLIP-seq peak regions
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The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
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ARTS-DB: a database for antibiotic resistant targets
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Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
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Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
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Automatic identification and annotation of MYB gene family members in plants
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Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
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Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
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TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
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Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
C. Cantalapiedra - A. Hernández-Plaza, I. Letunic, P. Bork, et al. - Molecular Biology and Evolution, 2021

Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
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Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
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OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
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Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
K. Peters - S. Herman, P. Khoonsari, J. Burman, et al. - Scientific Reports, 2021 usegalaxy.eu

Genomic impact of stress-induced transposable element mobility in Arabidopsis
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Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
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Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
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FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
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Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
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The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
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Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
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First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
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Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
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Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
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Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
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Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
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Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
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RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
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Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
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Single‐cell omics: Overview, analysis, and application in biomedical science
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Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
D. Vazquez - H. Schilbert, V. Dodero, - International Journal of Molecular Sciences, 2021

Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
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Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
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Haplotype-resolved diverse human genomes and integrated analysis of structural variation
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Replication of a Novel Parkinson's Locus in a European Ancestry Population
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Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (<i>Pimephales promelas</i>)
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Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate
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WASP: a versatile, web-accessible single cell RNA-Seq processing platform
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Single-Cell RNA Sequencing Procedures and Data Analysis
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Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis
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The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm,Antheraea pernyi (Lepidoptera: Saturniidae)
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Updates on metaQuantome Software for Quantitative Metaproteomics
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Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
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Large scale genomic rearrangements in selected <i>Arabidopsis thaliana</i> T-DNA lines are caused by T-DNA insertion mutagenesis
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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
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AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
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Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
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Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
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Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
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