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3 results on '"Shubhi Saini"'

1. DAVI:Deep Learning Based Tool for Alignment and Single Nucleotide Variant identification

Author

Shubhi Saini and Gaurav Gupta

Subjects
Smith–Waterman algorithm, chemistry.chemical_classification, Computer science, business.industry, Deep learning, Machine learning, computer.software_genre, DNA sequencing, Task (project management), Identification (information), chemistry, Nucleotide, State (computer science), Artificial intelligence, business, computer
Abstract

The Next Generation Sequencing (NGS) technologies have provided affordable ways to generate errorful raw genetical data. To extract Variant Information from billions of NGS reads is still a daunting task which involves various hand-crafted and parameterized statistical tools. Here we propose a Deep Neural Networks (DNN) based alignment and SNV tool known as DAVI. DAVI consists of models for both global and local alignment and for Variant Calling. We have evaluated the performance of DAVI against existing state of the art tool-set and found that its accuracy and performance is comparable to existing tools used for benchmarking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies. Moreover, this approach is a migration from expert driven statistical models to generic, automated, self-learning models.

Published
2019
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2. Nucl2Vec : Local alignment of DNA sequences using Distributed Vector Representation

Author

Shubhi Saini, Gaurav Gupta, Kolin Paul, and Prakhar Ganesh

Subjects
Smith–Waterman algorithm, Whole genome sequencing, Computer science, Genomics, computer.software_genre, DNA sequencing, chemistry.chemical_compound, ComputingMethodologies_PATTERNRECOGNITION, chemistry, Data mining, Representation (mathematics), computer, DNA, Reference genome
Abstract

The Next Generation Sequencing Technique (NGS) has provided affordable and fast method for generating genetic data. Generation of whole Genome Sequence and extract relevant information from this data is still a computationally expensive process. In this paper we demonstrate a novel approach for local alignment of DNA reads with respect to reference genome. For this process we have used Skip-gram model for creating encoding(Nucl2Vec) and k-nearest neighbor for the alignment. With our new approach we have reduced computation cost for local alignment, while achieving accuracy comparable to existing defacto standard BWA-MEM tool.Index TermsGenome, Alignment, Local Alignment, k-nearest Neighbor, Distributed vector representation, Skip-gram

Published
2018
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3. Morphological and neurochemical changes in GABAergic neurons of the aging human inferior colliculus.

Author

Pal, Indra, Paltati, Chaitanya Rama Bai, Kaur, Charanjeet, Shubhi Saini, Kumar, Punit, Jacob, Tony George, Bhardwaj, Daya Nand, and Roy, Tara Sankar

Subjects
*INFERIOR colliculus, *GABAERGIC neurons, *GLUTAMATE decarboxylase, *AUDITORY pathways, *OLDER people
Abstract

It is well known that quality of hearing decreases with increasing age due to changes in the peripheral or central auditory pathway. Along with the decrease in the number of neurons the neurotransmitter profile is also affected in the various parts of the auditory system. Particularly, changes in the inhibitory neurons in the inferior colliculus (IC) are known to affect quality of hearing with aging. To date, there is no information about the status of the inhibitory neurotransmitter GABA in the human IC during aging. We have collected and processed inferior colliculi of persons aged 11–97 years at the time of death for morphometry and immunohistochemical expression of glutamic acid decarboxylase (GAD67) and parvalbumin. We used unbiased stereology to estimate the number of cresyl-violet and immunostained neurons. Quantitative real-time PCR was used to measure the relative expression of the GAD67 mRNA. We found that the number of total, GABAergic and PV-positive neurons significantly decreased with increasing age (p < 0.05). The proportion of GAD67-ir neurons to total number of neurons was also negatively associated with increasing age (p = 0.004), but there was no change observed in the proportion of PV-ir neurons relative to GABAergic neurons (p = 0.25). Further, the fold change in the levels of GAD67 mRNA was negatively correlated to age (p = 0.024). We conclude that the poorer quality of hearing with increasing age may be due to decreased expression of inhibitory neurotransmitters and the decline in the number of inhibitory neurons in the IC. • A total number of neurons, GAD67, and PV-positive neurons in human IC was estimated using optical fractionator. • Total neuronal population, GAD67 and PV-positive neurons were negatively correlated with increasing age. • The relative gene expression of GAD67 mRNA decreased with aging. [ABSTRACT FROM AUTHOR]

Published
2019
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