18 papers · ranked by Valyu relevance
Shreepriya Das, Haris Vikalo
Background Next-generation DNA sequencing platforms are capable of generating millions of reads in a matter of days at rapidly reducing costs. Despite its proliferation and technological improvements, the performance of next-generation sequencing remains adversely affected by the imperfections in the underlying…
Vladimír Boža, Broňa Brejová, Tomáš Vinař, Degui Zhi
The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp were reported); however it suffers from high sequencing error rate. We present an open-source DNA base caller based on deep recurrent neural networks and show that the accuracy of base calling is much dependent on the underlying software…
Yuan Ji, Riten Mitra, Fernando Quintana, Alejandro Jara + 4 more
'Peter Mueller' 'Ping Liu' 'Yue Lu' 'Shoudan Liang'] Base calling is a critical step in the Solexa next-generation sequencing procedure. It compares the position-specific intensity measurements that reflect the signal strength of four possible bases (A, C, G, T) at each genomic position, and outputs estimates of the…
Kristof De Beuf, Joachim De Schrijver, Olivier Thas, Wim Van Criekinge + 2 more
'Wim Van Criekinge' 'Rafael A Irizarry' 'Lieven Clement'] Background 454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this platform is its sensitivity to…
Qian Lou, Sarath Chandra Janga, Lei Jiang
Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-ofthe-art base-callers adopt deep neural networks (DNNs) to translate electrical signals generated by nanopore sequencers to digital DNA symbols. A DNN-based base-caller consumes 44.5% of…
Xiaohu Shen, Haris Vikalo
Background Next-generation sequencing systems are capable of rapid and cost-effective DNA sequencing, thus enabling routine sequencing tasks and taking us one step closer to personalized medicine. Accuracy and lengths of their reads, however, are yet to surpass those provided by the conventional Sanger sequencing…
Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto + 3 more
Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real time. Through detecting the change of ion currency signals during a DNA/RNA fragment’s pass through a nanopore, genotypes are determined. Currently…
Vladimír Boža, Broňa Brejová, Tomáš Vinař
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100 kBp were reported), however it suffers from high sequencing error rate. In this paper, we show that the error rate can be reduced by improving the base calling process.
Bud Mishra
Understanding complex mammalian biology depends crucially on our ability to define a precise map of all the transcripts encoded in a genome, and to measure their relative abundances. A promising assay depends on RNASeq approaches, which builds on next generation sequencing pipelines capable of interrogating cDNAs…
Zhimeng Xu, Yuting Mai, Denghui Liu, Wenjun He + 8 more
Oxford Nanopore Technologies (ONT) is a promising sequencing technology that could generate relatively longer sequencing reads compared to the next generation sequencing (NGS) technology. The base calling process is very important for TGS. It translates the original electrical signals from the sequencer to the…
Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař + 1 more
MinION by Oxford Nanopore Technologies (ONT) is a portable DNA sequencer that measures electric current as DNA passes through nanopores. Electrical signals produced by the device need to be translated into sequences by a base caller software. In many applications of nanopore sequencing, fast and accurate base calling…
Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař
> Abstract. We developed a new base caller DeepNano-coral for nanopore sequencing, which is optimized to run on the Coral Edge Tensor Processing Unit, a small USB-attached hardware accelerator. To achieve this goal, we have designed new versions of two key components used in convolutional neural networks for speech…
Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the sequencing accuracy. The most successful nanopore base callers to date use…
Ruikai Jia, Yusha Wang, Hua Ye, Xiaoshu Ma
gene synthesis sequencing using the long-read Oxford Nanopore Technologies (ONT) provides a cost-effective option for gene synthesis quality control. Despite the advantage of using long reads, however, accurate base calling is influenced by modified bases. We introduce a method for filtering abnormal modified base…
Mehwish Nasim, Aimal Rextin, Numair Khan, Muhammad Muddassir Malik
—In this paper we predict outgoing mobile phone calls using a machine learning approach. We analyze to which extent the activity of mobile phone users is predictable. The premise is that mobile phone users exhibit temporal regularity in their interactions with majority of their contacts. In the sociological context…
Liuzhou Gao, Xinyi Liang, Linke He, Guoao Li + 5 more
Tetracoordinated boron species generated from the complexation of organoboron compounds with bases are highly important intermediates in molecular fragments coupling. The type of base significantly impacts both the reaction activity and mechanism of organoboron compounds. Herein, our structural and mechanistic insights…
Lin He, Jinyun Luo, Muze Lin, Guangfen Du + 1 more
The first catalytic vicinal thiosulfonylation of ynones has been developed. Under the catalysis of 1-10 mol% Cs2CO3, various thiosulfonates underwent Michael addition/nucleophilic substitution tandem reaction with different ynones to form C-SO2 and C-S bonds simultaneously and produce multifunctional vinyl sulfones in…
Gayan Senavirathne
Most undergraduate Organic chemistry textbooks contain a section on the general acid-base equilibria, strength of acids and bases, and predicting the equilibrium position of acid-base reactions (1-3). The students are taught to qualitatively predict the directions of these reactions using only the acid/base strengths…