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HPG pore: an efficient and scalable framework for nanopore sequencing data

Joaquin Tarraga, Asunción Gallego, Vicente Arnau, Ignacio Medina, Joaquin Dopazo
2016 BMC Bioinformatics  
Results: Here we present HPG Pore, a toolkit for exploring and analysing nanopore sequencing data.  ...  Conclusions: HPG Pore allows for virtually unlimited sequencing data scalability, thus guaranteeing its continued management in near future scenarios. HPG Pore is available in GitHub at  ...  Acknowledgements This work was supported by grants BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness (MINECO) and Plataforma de Recursos Biomoleculares y Bioinformáticos PT 13/0001  ... 
doi:10.1186/s12859-016-0966-0 pmid:26921234 pmcid:PMC4769497 fatcat:ajbrfmiqfvb6lmd2dmtwnwjpie

Nanopore sequencing data analysis: state of the art, applications and challenges

Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
2017 Briefings in Bioinformatics  
Our analyses demonstrate that the use of nanopore data dramatically improves the de novo assembly of genomes and allows for the exploration of structural variants with an unprecedented accuracy and resolution  ...  short sequences for mitigating the intrinsic biases of nanopore sequencing technology.  ...  [29] introduced a novel tool for exploring and converting FAST5 files, HPG Pore, that can run locally on individual computer or on a computer cluster exploiting the Hadoop distributed computing framework  ... 
doi:10.1093/bib/bbx062 pmid:28637243 fatcat:lxiyn4exdfaibf4helkij43p2q

Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets

Ratanond Koonchanok, Swapna Vidhur Daulatabad, Quoseena Mir, Khairi Reda, Sarath Chandra Janga
2021 BMC Genomics  
Sequoia combines a Python-based backend with a multi-view visualization interface, enabling users to import raw nanopore sequencing data in a Fast5 format, cluster sequences based on electric-current similarities  ...  We demonstrate the application of Sequoia by generating and analyzing ~ 500k reads from direct RNA sequencing data of human HeLa cell line.  ...  QM, SD, and RK generated, extracted, and analyzed data for case studies respectively. KR and SJ supervised the overall study. RK, SD, and QM wrote the paper.  ... 
doi:10.1186/s12864-021-07791-z pmid:34233619 pmcid:PMC8262049 fatcat:rtimjdv7b5fj7h54y3hycmyvjq

13th EBSA congress, July 24–28, 2021, Vienna, Austria

2021 European Biophysics Journal  
Elena Pohl, from University of Veterinary Medicine Vienna, and her team, for taking the lead to assemble an attractive scientific programme, in the tradition of the spectacular past European Congresses  ...  EBSA is also indebted to Springer-Nature, the publisher of the European Biophysics Journal (EBJ), for its commitment to disseminate Biophysics across Europe and beyond, with its support for our Congress  ...  O-88 Biomimetic membrane nanopores for nextgeneration sensing Stefan Howorka University College London, UK Biological membrane nanopores have brought about a stepchange in portable, scalable DNA sequencing  ... 
doi:10.1007/s00249-021-01558-w pmid:34245338 pmcid:PMC8272448 fatcat:z2svytd4kbamrmvarle4lxwtxm

A Chronicle Review of Nonsilicon (Sn, Sb, Ge)‐Based Lithium/Sodium‐Ion Battery Alloying Anodes

Suzhe Liang, Ya‐Jun Cheng, Jin Zhu, Yonggao Xia, Peter Müller‐Buschbaum
2020 Small Methods  
better efficiency.  ...  small volume change during cycling, carbon materials were considered as an ideal choice of anodes which was researched for many years by countless researchers.  ...  [316] Synthesis of the HPG material was based on an ion-exchange resin-based technology.  ... 
doi:10.1002/smtd.202000218 fatcat:7iyq7ykn5vgirhxbqf5zdymyzy

Synthesis of Biomaterials Utilizing Microfluidic Technology

Xiaohong Wang, Jinfeng Liu, Peizhou Wang, Andrew deMello, Lingyan Feng, Xiaoli Zhu, Weijia Wen, Rimantas Kodzius, Xiuqing Gong
2018 Genes  
Recently, microfluidic technologies have attracted an enormous amount of interest as potential new tools for a large range of applications including materials synthesis, chemical and biological detection  ...  Their ability to handle extremely small volumes of fluids is accompanied by additional benefits, most notably, rapid and efficient mass and heat transfer.  ...  Acknowledgments: This work was sponsored by the Shanghai Pujiang Program (17PJ1402800) and the National Natural Science Foundation of China (21775101).  ... 
doi:10.3390/genes9060283 pmid:29874840 pmcid:PMC6027171 fatcat:oti624rizjevzcyz3gqu2yswka

Synthesis of model nanocatalysts for industrial applications [article]

Xiao Xie, Technische Universität Berlin, Technische Universität Berlin, Reinhard Schomäcker, Arne Thomas
An optimized catalyst, Ni0.05Mn0.95O/SiO2 (calcined at 750 °C), at the conditions of 600 °C and GHSV 80 L h-1 gcat-1, is stable for 5 days and the conversion of methane is still 50% after 120 h time on  ...  The polymer is removed completely by water extraction and can be reused for the next preparation.  ...  Compared to other tedious methods, one-pot synthesis is efficient and scalable.  ... 
doi:10.14279/depositonce-3959 fatcat:u4xkopduczhkfpiof4yq7lcobi

Polymer nanoparticles and nanofibers: Drug delivery and environmental applications [article]

The advantages of the electrospraying include increased scalable synthesis, reproducibility and high encapsulation efficiency.  ...  Template synthesize This method entails synthesizing the desired material within the pores of a nanoporous membrane. The membranes employed have cylindrical pores of uniform diameter.  ... 
doi:10.15167/forouharshad-mahdi_phd2018-03-15 fatcat:qkgmmhlrkzgq7l22pnqtteydxu

Proceedings International Sorption Heat Pump Conference 2021 - Part II Call 2021

(:Unkn) Unknown, Technische Universität Berlin, Thomas Meyer, José Corrales, Walther Hüls, Roland Kühn, Felix Ziegler
The current transition to an energy system based on renewables changes the boundary conditions.  ...  Sorption heat pumps will have an indispensable place in this context, especially due to their potential to make use of waste heat.  ...  We also thank the German Federal Ministry of Education and Research and the EU joint program "Eurostars-2" for supporting further research into solar thermal driven adsorption refrigerators for hot climate  ... 
doi:10.14279/depositonce-12278 fatcat:btae3shaifgw3lwx7wwwllvwre