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RTK: efficient rarefaction analysis of large datasets

Paul Saary, Kristoffer Forslund, Peer Bork, Falk Hildebrand, Inanc Birol
2017 Bioinformatics  
Results: Here we present a software package for rarefaction analysis of large count matrices, as well as estimation and visualization of diversity, richness and evenness.  ...  tasks, like rarefaction and associated analysis.  ...  Here, we present the rarefaction toolkit (RTK), which can perform fast rarefaction on very large datasets comprising millions of features even on a laptop computer, computes estimates of ecological diversity  ... 
doi:10.1093/bioinformatics/btx206 pmid:28398468 pmcid:PMC5870771 fatcat:3b52nh2fmfbc7cugu657hbrjtq

LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis [article]

Ezgi Ozkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y.K. Ng, Robert P. Davey, Mohammad Bahram, Falk Hildebrand
2021 bioRxiv   pre-print
Amplicon sequencing is an established and cost-efficient method for profiling microbiomes.  ...  To bridge this gap, we developed the LotuS2 (Less OTU Scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences.  ...  We also would like to acknowledge CyVerse UK for the hosting of the LotuS2 website.  ... 
doi:10.1101/2021.12.24.474111 fatcat:i2abe33efbdp3jysx33ycymr4e

High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo

Julia C. Pringle, Amy Wesolowski, Sophie Berube, Tamaki Kobayashi, Mary E. Gebhardt, Modest Mulenga, Mike Chaponda, Thierry Bobanga, Jonathan J. Juliano, Steven Meshnick, William J. Moss, Giovanna Carpi (+1 others)
2019 Malaria Journal  
programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.  ...  No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone.  ...  Acknowledgements We gratefully acknowledge Anne Jedlicka and Amanda Dziedzic in the Johns Hopkins Bloomberg School of Public Health Genomic Analysis and Sequencing Core for assistance with amplicon library  ... 
doi:10.1186/s12936-019-3023-4 pmid:31801548 pmcid:PMC6894251 fatcat:7sj5p4oefvffjloibzluy6dz5i

Kidney Regeneration: Lessons from Development

Takuto Chiba, Neil Hukriede, Mark P. de Caestecker
2015 Current Pathobiology Reports  
based on public datasets from recent AKI translational profiling studies.  ...  A number of genes involved in kidney development are reactivated in the adult after acute kidney injury (AKI).  ...  The laboratory of Mark de Caestecker was supported by National Institutes of Health Grants 1R01 HL093057 and 1RC4DK090770.  ... 
doi:10.1007/s40139-015-0069-z pmid:26120499 pmcid:PMC4477536 fatcat:qj2fyysopvdtxdno4f4zx6mna4

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments [article]

Satoshi Hiraoka, Miho Hirai, Yohei Matsui, Akiko Makabe, Hiroaki Minegishi, Miwako Tsuda, Juliarni Juliarni, Eugenio Rastelli, Roberto Danovaro, Cinzia Corinaldesi, Tomo Kitahashi, Eiji Tasumi (+4 others)
2019 bioRxiv   pre-print
Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultra-deep-sea microbial  ...  ecology, one of the last frontiers on our planet.  ...  RTK: efficient rarefaction analysis of large datasets. 582 Bioinformatics 2017; 33: 2594-2595. 583 35. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al.  ... 
doi:10.1101/729517 fatcat:y5wft37qhfcopcmdbqmctbjyfu

Predicting Tree-Related Microhabitats by Multisensor Close-Range Remote Sensing Structural Parameters for the Selection of Retention Elements

Julian Frey, Thomas Asbeck, Jürgen Bauhus
2020 Remote Sensing  
The aim to predict TreMs based on remote sensing (RS) parameters is supposed to assist a more objective and efficient selection of retention elements.  ...  This method allows a more efficient and objective selection of retention elements such as habitat trees that are keystone features for biodiversity conservation, even if it cannot be considered a full  ...  An assessment of all trees in the plots was not feasible for logistic reasons, but by selecting 15 large trees, we captured most of the variation (80% based on a rarefaction analysis) of TreMs in the plots  ... 
doi:10.3390/rs12050867 fatcat:hkgmlurx3rbgxnprqlthc5i24q

Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

Julia Kleinteich, Falk Hildebrand, Mohammad Bahram, Anita Y. Voigt, Susanna A. Wood, Anne D. Jungblut, Frithjof C. Küpper, Antonio Quesada, Antonio Camacho, David A. Pearce, Peter Convey, Warwick F. Vincent (+3 others)
2017 Frontiers in Ecology and Evolution  
Rarefaction Sample count matrices were rarefied using the R implementation of rtk toolkit (Saary et al., 2017) .  ...  To do so, we undertook a large-scale microbial community analysis using standardized methods.  ...  Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
doi:10.3389/fevo.2017.00137 fatcat:lw3lwo4c5jdnharwytewwevqkm

Structure and function of the global topsoil microbiome

Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema (+9 others)
2018 Nature  
In this pilot research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act are distributed online and free of cost or  ...  time after the work was first published, provided that clear reference is made to the source of the first publication of the work.  ...  Hercog and other members of the EMBL GeneCore (Heidelberg), who provided assistance and facilities for sequencing.  ... 
doi:10.1038/s41586-018-0386-6 pmid:30069051 fatcat:t4c25q37wnhs5owamf4deytm3i

Dispersal strategies shape persistence and evolution of human gut bacteria

Falk Hildebrand, Toni I. Gossmann, Clémence Frioux, Ezgi Özkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, Peer Bork
2021 Cell Host and Microbe  
These "tenacious" bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions.  ...  Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota.  ...  RTK: efficient rarefaction analysis of large datasets. Bioinformatics 33, 2594-2595.  ... 
doi:10.1016/j.chom.2021.05.008 pmid:34111423 pmcid:PMC8288446 fatcat:4h5p2eyjpjditbrtoowjv2toly

Latest Developments in Sustainable Water Management
Najnovija dostignuca u održivom gospodarenju vodama

Ivan Halkijevic, Damir Bekic, Goran Loncar, Kristina Potocki, Gordon Gilja, Dalibor Carevic
2019 Future Trends in Civil Engineering   unpublished
A brief account of the application and limitations of remote sensing techniques in monitoring meteorological and hydrological data, in efficient irrigation planning, and in improvement of water use in  ...  Several new water treatment technologies with a large-scale application potential are presented, and the use of numerical modelling in water treatment, 'green' infrastructure, and coastal engineering planning  ...  [28] evaluated the capability of different datasets for soil drainage mapping in agricultural fields.  ... 
doi:10.5592/co/ftce.2019.07 fatcat:kgs25l3cv5gubde67a5zgv3n34

Effect of a Wood-Based Carrier of Trichoderma atroviride SC1 on the Microorganisms of the Soil

Hamza Chammem, Livio Antonielli, Andrea Nesler, Massimo Pindo, Ilaria Pertot
2021 Journal of Fungi  
Trichoderma atroviride SC1 coated wood pellets and non-coated pellets were applied at the level of 10 g∙kg−1 of soil and at the final concentration of 5 × 103 conidia∙g−1 of soil and compared to a conidial  ...  The aims of this study were to evaluate the effect of wood pellets on the growth of Trichoderma spp. in bulk soil and on the soil microbial population's composition and diversity.  ...  Alpha-diversity values were calculated adopting a multiple rarefaction method, implemented in the rtk R package [53] .  ... 
doi:10.3390/jof7090751 pmid:34575789 fatcat:utmfin2ikndtzbogj3iun7urqi

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures

Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund
2019 Frontiers in Microbiology  
Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways  ...  Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle.  ...  We thank the lab of Dr. Hailiang Dong at Miami University for analyzing samples for major anions, cations, and trace elements. We also thank Dr.  ... 
doi:10.3389/fmicb.2019.01427 pmid:31333598 pmcid:PMC6624737 fatcat:fyzgtsus2bf33m3wa6mpfhe4um

34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): part 1

2019 Journal for ImmunoTherapy of Cancer  
As this is preliminary, further analysis is underway and will be validated on the larger cohort of patients.  ...  Further, tissue based analysis of PMNs does not correlate with serum NLR allowing potential for composite biomarkers.  ...  Acknowledgements Writing support was provided by Analysis Group, Inc. and editorial support was provided by Parexel, funded by Bristol-Myers Squibb.  ... 
doi:10.1186/s40425-019-0763-1 pmid:31694725 pmcid:PMC6833189 fatcat:y2lipm7rwrav3jdwdo3um27qhu

Abstract

2021 European Journal of Clinical Investigation  
The newest mitochondrial assays measure more than 50 aspects of mitochondrial function, profiling the rates of metabolism of mitochondrial substrates and the sensitivity of metabolism of these substrates  ...  This presentation will review the technology and show examples of how it can inform basic and advanced cellular studies.  ...  The development of in-house tools that allow for the integration of heterogeneous datasets into a standardized dataset architecture, automates data visualization and statistical analysis, removing human  ... 
doi:10.1111/eci.13567 fatcat:casumfo4afhklgo42swkednpya

Genetic Landscape of Electron Transport Chain Complex I Dependency in Acute Myeloid Leukemia [article]

Irene Baccelli, Yves Gareau, Bernhard Lehnertz, Stephane Gingras, Jean-Francois Spinella, Alexandre Beautrait, Sophie Corneau, Nadine Mayotte, Isabel Boivin, Simon Girard, Tara MacRae, Melanie Frechette (+17 others)
2019 bioRxiv   pre-print
Through chemically interrogation of 200 sequenced specimens, we identified Mubritinib as a strong in vitro and in vivo anti-leukemic compound, acting through ubiquinone-dependent inhibition of Electron  ...  ETC1 targeting showed selective toxicity against a subgroup of chemotherapy-resistant leukemias exhibiting OXPHOS hyperactivity, high expression of mitochondrial activity-related genes, and mutations affecting  ...  Start of  ... 
doi:10.1101/513887 fatcat:m2xuui4frbf2rhbfnb2hmuhayu
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