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Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development

Sarah A Pendergrass, Alex Frase, John Wallace, Daniel Wolfe, Neerja Katiyar, Carrie Moore, Marylyn D Ritchie
2013 BioData Mining  
Via Biofilter 2.0 researchers can: Annotate genomic location or region based data, such as results from association studies, or CNV analyses, with relevant biological knowledge for deeper interpretation  ...  Conclusions: Biofilter is a software tool that provides a flexible way to use the ever-expanding expert biological knowledge that exists to direct filtering, annotation, and complex predictive model development  ...  We provide here further details and examples of filtering, annotating, and modeling within Biofilter, although it is important to note that annotation, filtering, and modeling with Biofilter are not exclusive  ... 
doi:10.1186/1756-0381-6-25 pmid:24378202 pmcid:PMC3917600 fatcat:qld5e2yncrctrkep2zv5a2f7hy

Polygenic inheritance of paclitaxel-induced sensory peripheral neuropathy driven by axon outgrowth gene sets in CALGB 40101 (Alliance)

A Chhibber, J Mefford, E A Stahl, S A Pendergrass, R M Baldwin, K Owzar, M Li, E P Winer, C A Hudis, H Zembutsu, M Kubo, Y Nakamura (+7 others)
2014 The Pharmacogenomics Journal  
Peripheral neuropathy is a common dose-limiting toxicity for patients treated with paclitaxel.  ...  Our results suggest that paclitaxel-induced neuropathy has a heritable component, driven in part by genes involved in axon outgrowth.  ...  The genotyping used for this work was generated as part of the NIH Pharmacogenomics Research Network-RIKEN Center for Genomic Medicine Global Alliance.  ... 
doi:10.1038/tpj.2014.2 pmid:24513692 pmcid:PMC4111770 fatcat:5z2gg2k2grenndm3ee44lfqg74

A Biologically Informed Method for Detecting Associations with Rare Variants [chapter]

Carrie C. Buchanan, John R. Wallace, Alex T. Frase, Eric S. Torstenson, Sarah A. Pendergrass, Marylyn D. Ritchie
2012 Lecture Notes in Computer Science  
To three very important educators and mentors, my mother, grandmother, and sister.  ...  This project has benefitted immensely from their advice and input.  ...  Gene annotations were found in UCSC Genome Browser and the NCBI database [71, 133] with ion channel regulation.  ... 
doi:10.1007/978-3-642-29066-4_18 fatcat:hd3xix7mozaxhddpsc4fssj6ey

Forebrain Transcriptional Response to Transient Changes in Circulating Androgens in a Cichlid Fish

Ana S Félix, Sara D Cardoso, António Roleira, Rui F Oliveira
2020 G3: Genes, Genomes, Genetics  
neuroendocrinology by injecting 11-ketotestosterone or testosterone, and compared the forebrain transcriptome of these individuals to control fish injected with vehicle.  ...  Forebrain samples were collected 30 min and 60 min after injection and analyzed using RNAseq.  ...  Instituto Gulbenkian de Ciência for performing the initial stages of RNAseq data analysis (quality control, alignment to reference genome, generation of table of counts).  ... 
doi:10.1534/g3.119.400947 pmid:32276961 pmcid:PMC7263668 fatcat:bv2kzi7yqjculjutloquas76pe

Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology

Pavel Dvořák, Pablo I. Nikel, Jiří Damborský, Víctor de Lorenzo
2017 Biotechnology Advances  
The complexity of this endeavour and the lack of 15 fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant 16 DNA-based bioremediation only a decade later.  ...  Whereas naturally occurring microbes already have 11 considerable ability to remove many environmental pollutants with no external intervention, 12 the onset of genetic engineering in the 1980s allowed  ...  The reconstructed genome-scale 36 metabolic models, together with transcriptomic, proteomic, metabolomic, and flux analyses in 37 various growth and stress conditions, completely changed our view of popular  ... 
doi:10.1016/j.biotechadv.2017.08.001 pmid:28789939 fatcat:snmm6z3j4fajticae2sujhqxpe

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes

Georgina Robinson, Gary S. Caldwell, Matthew J. Wade, Andrew Free, Clifford L. W. Jones, Selina M. Stead
2016 Scientific Reports  
Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved  ...  To date, a lack of understanding of the complex interactions between bacteria and deposit-feeders has created a knowledge gap in microbial mineralization within aquaculture systems.  ...  The FastTree Greengenes (gg_13_08) phylogeny 53 annotated with these organisms' genomes was used to pick closed-reference OTUs based on 65% of the total sequences from the de-multiplexed and quality-filtered  ... 
doi:10.1038/srep38850 pmid:27941918 pmcid:PMC5150640 fatcat:nyxevifnjvf25b5l522pazsnie

Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles

Rob A Schmitz, Stijn H Peeters, Wouter Versantvoort, Nunzia Picone, Arjan Pol, Mike S M Jetten, Huub J M Op den Camp
2021 FEMS Microbiology Reviews  
However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically  ...  Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment  ...  Glöckner 2012) and a tree that was constructed using FastTree v2.1 (Price, Dehal and Arkin 2010) with 1000 bootstraps and substitution model GTR-gamma.  ... 
doi:10.1093/femsre/fuab007 pmid:33524112 pmcid:PMC8498564 fatcat:l45wanx4dndedhffnmqpxqnzyu

Polygenic inheritance of paclitaxel-induced sensory peripheral neuropathy driven by axon outgrowth gene sets in CALGB 40101 (Alliance)

J S Witte, E A Stahl, A Chhibber, E P Winer, M D Ritchie, L N Shulman, H L McLeod, R M Plenge, M J Ratain, D L Kroetz, H Zembutsu, J Mefford (+7 others)
Peripheral neuropathy is a common dose-limiting toxicity for patients treated with paclitaxel.  ...  Our results suggest that paclitaxel-induced neuropathy has a heritable component, driven in part by genes involved in axon outgrowth.  ...  The genotyping used for this work was generated as part of the NIH Pharmacogenomics Research Network-RIKEN Center for Genomic Medicine Global Alliance.  ... 
doi:10.17615/q0qy-yd04 fatcat:gjryp4ah7nfz5c6w6aixd6jrge

Twentieth Annual Meeting of the Association for Chemoreception Sciences

1998 Chemical Senses  
models in developmental biology.  ...  Ecdysteroids regulate many developmental events in M. sexta; during adult development hormone levels rise early and fall late.  ...  Each urine sample was made acidic and extracted with methylene chloride (CH2Cl2); the sample was then made neutral and extracted with CH2Cl2; the sample was then made basic and again extracted with CH2Cl2  ... 
doi:10.1093/chemse/23.5.545 fatcat:v2hv5w77onan7f6cs3tclcwmly

Ecological role of Thaumarchaeota in pelagic redox gradients of the Baltic Sea

Carlo Berg
In the scope of this thesis, metatranscriptomic analyses, biogeochemical rate measurements, and group-specific quantifications in environmental samples as well as investigations of enrichment cultures  ...  The amoA neighbor-joining tree was generated based on the protein alignment, using Phylip with a Fitch model and Ca. N. maritimus SCM1 as a filter.  ...  The filter surface was gold-sputter-coated with an Agar sputter coater (model 108) for 120 s, resulting in a 20-to 40-nm thin layer of gold.  ... 
doi:10.18453/rosdok_id00001600 fatcat:2cnby54yofgdll5kt7yvojqtpy

Exploring the actions of citizens as scientists through experimentation with aquaponics

Ria Follett
Scientists are increasingly collaborating with citizens to engage in science where, on their own, they lack the resources to collect or analyse the data.  ...  The ways the citizens research was compared and contrasted with the way scientists researched in the field of aquaponics, providing insights into areas that need further consideration when endeavouring  ...  I appreciate his insightful guidance into this research and  ... 
doi:10.25949/19440110.v1 fatcat:bm4gmpbgdnfmxiumxhpvhjsozi

Microbial Phosphorus Transformation Pathways in Piggery Waste Treatment Systems [article]

Maha Laksha Mudiyanselage Anjani Wathsala Weerasekara
MLMAW Weerasekara iv ACKNOWLEDGEMENT The entire work of this study has endowed me with much knowledge and experience.  ...  So take this opportunity to acknowledge everyone for their contributions with great pleasure. I wish to express my first and foremost gratitude to my supervisors, Winthrop Professor  ...  High colonisation % was observed for Balance® 100 kg ha -1 and control and low colonisation % was observed for Agras® 100 kg ha -1 and Balance® 50 kg ha -1 +Agras® 50 kg ha -1 ).  ... 
doi:10.26182/5d350c46ecc00 fatcat:ebl6qpgb5vef7as62f7pkxvrlq

Cobia (Rachycentron canadum): A Selected Annotated Bibliography on Aquaculture, General Biology and Fisheries 1967–2015

Uriel Rodriguez Estrada, Fanny Ayumi Yasumaru, Albert G. J. Tacon, Daniel Lemos
2015 Reviews in Fisheries Science & Aquaculture  
, and the industry.  ...  The present compilation covers the period between 1967 and 2015 and includes publications on cobia general biology, fisheries and aquaculture for the potential benefit of students, researchers, farmers  ...  Acknowledgments The project has been funded by CNPq (Brazilian Council for Scientific and Technological Development) Science without Borders À Special Visiting Researcher" programme (400713/2012-8).  ... 
doi:10.1080/23308249.2015.1088821 fatcat:vsjuenaicfgq3jiy6lqilz7hsy

Linking Metabolic Capacity and Molecular Biology of Methylocystis sp. Strain SC2 by a Newly Developed Proteomics Workflow

Anna Hakobyan, Biologie, Liesack, Werner (PD Dr.)
To successfully develop the proteomics workflow, we particularly focused on an efficient solubilization and digestion of the integral membrane proteins of strain SC2 for further downstream analysis.  ...  In this study, we therefore aimed to develop an efficient proteomics workflow for strain SC2 and to apply this state-of-the-art tool for investigation of the strain SC2 response to environmental factors  ...  Our model organism, strain SC2, is one of the very few Methylocystis spp. with a well-annotated gap-closured genome sequence .  ... 
doi:10.17192/z2020.0125 fatcat:cs6d4ctuvbf6zfumqi6ydp2qei


R.S. Azzoni
In particular, for the great help on field activities and data processing, I gratefully thank We are also kindly grateful to the Stelvio Park management staff, the municipality of Valfurva and the Italian  ...  Acknowledgements Authors thank Parco Tecnologico Padano (Lodi, Italy) for technical assistance and sequencing.  ...  Genomes annotation revealed widespread presence of CO dehydrogenase and absence of a complete CO2 fixation pathway, consistently with the complete genome of Polaromonas JS666.  ... 
doi:10.13130/r-s-azzoni_phd2017-02-24 fatcat:3r6ldth2vbfzjhvfnnk7526hnu
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