BIMMER: A Bi-layer hidden Markov model for differential methylation analysis

2013 ◽  
Author(s):  
Zijing Mao ◽  
Tim H-M Huang ◽  
Yidong Chen ◽  
Yufei Huang
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Differential Methylation ◽  
Methylation Analysis ◽  
Differential Methylation Analysis

scholarly journals Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Yu-Chen Zhang ◽  
Shao-Wu Zhang ◽  
Lian Liu ◽  
Hui Liu ◽  
Lin Zhang ◽  
...  
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Statistical Significance ◽  
Simulated Data ◽  
Real Data ◽  
Differential Methylation ◽  
Methylation Site ◽  
Sequencing Data ◽  
Rna Methylation

With the development of new sequencing technology, the entire N6-methyl-adenosine (m6A) RNA methylome can now be unbiased profiled with methylated RNA immune-precipitation sequencing technique (MeRIP-Seq), making it possible to detect differential methylation states of RNA between two conditions, for example, between normal and cancerous tissue. However, as an affinity-based method, MeRIP-Seq has yet provided base-pair resolution; that is, a single methylation site determined from MeRIP-Seq data can in practice contain multiple RNA methylation residuals, some of which can be regulated by different enzymes and thus differentially methylated between two conditions. Since existing peak-based methods could not effectively differentiate multiple methylation residuals located within a single methylation site, we propose a hidden Markov model (HMM) based approach to address this issue. Specifically, the detected RNA methylation site is further divided into multiple adjacent small bins and then scanned with higher resolution using a hidden Markov model to model the dependency between spatially adjacent bins for improved accuracy. We tested the proposed algorithm on both simulated data and real data. Result suggests that the proposed algorithm clearly outperforms existing peak-based approach on simulated systems and detects differential methylation regions with higher statistical significance on real dataset.

scholarly journals HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test

2016 ◽  
Vol 15 (1) ◽  
Author(s):  
Shuying Sun ◽  
Xiaoqing Yu
Keyword(s):  
Dna Methylation ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Differential Methylation ◽  
Sequencing Data ◽  
Exact Test ◽  
Fisher's Exact Test ◽  
Fisher’S Exact Test ◽  
Methylation Patterns

AbstractDNA methylation is an epigenetic event that plays an important role in regulating gene expression. It is important to study DNA methylation, especially differential methylation patterns between two groups of samples (e.g. patients vs. normal individuals). With next generation sequencing technologies, it is now possible to identify differential methylation patterns by considering methylation at the single CG site level in an entire genome. However, it is challenging to analyze large and complex NGS data. In order to address this difficult question, we have developed a new statistical method using a hidden Markov model and Fisher’s exact test (HMM-Fisher) to identify differentially methylated cytosines and regions. We first use a hidden Markov chain to model the methylation signals to infer the methylation state as Not methylated (N), Partly methylated (P), and Fully methylated (F) for each individual sample. We then use Fisher’s exact test to identify differentially methylated CG sites. We show the HMM-Fisher method and compare it with commonly cited methods using both simulated data and real sequencing data. The results show that HMM-Fisher outperforms the current available methods to which we have compared. HMM-Fisher is efficient and robust in identifying heterogeneous DM regions.

Auscultating Diagnosis for Hemodialysis Shunt Stenosis using a Self-Organizing Map and Hidden Markov Model

2012 ◽  
Vol 132 (10) ◽  
pp. 1589-1594 ◽  
Author(s):  
Hayato Waki ◽  
Yutaka Suzuki ◽  
Osamu Sakata ◽  
Mizuya Fukasawa ◽  
Hatsuhiro Kato
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Self Organizing Map ◽  
Self Organizing

Engaging Voluntary Contributions in Online Communities: A Hidden Markov Model

MIS Quarterly ◽  
2018 ◽  
Vol 42 (1) ◽  
pp. 83-100 ◽  
Author(s):  
Wei Chen ◽  
◽  
Xiahua Wei ◽  
Kevin Xiaoguo Zhu ◽  
◽  
...  
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Online Communities ◽  
Hidden Markov ◽  
Voluntary Contributions

Implementation of Android Based Speech Recognition for Indonesian Geography Dictionary

2016 ◽  
Vol 7 (2) ◽  
pp. 76-82
Author(s):  
Hugeng Hugeng ◽  
Edbert Hansel
Keyword(s):  
Speech Recognition ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Hidden Markov ◽  
Spoken Word ◽  
Silent Condition ◽  
Word Detection ◽  
Index Terms ◽  
To Receive ◽  
Noisy Condition

We have built an application of speech recognition for Indonesian geography dictionary based on Android operating system, named GAIA. This application uses a smartphone as a device to receive input in the form of a spoken word from a user. The approach used in recognition is Hidden Markov Model which is contained in the Pocketsphinx library. The phonemes used are Indonesian phonemes’ rule. The advantage of this application is that it can be used without internet access. In the application testing, word detection is done with four conditions to determine the level of accuracy. The four conditions are near silent, near noisy, far silent, and far noisy. From the testing and analysis conducted, it can be concluded that GAIA application can be built as a speech recognition application on Android for Indonesian geography dictionary; with the results in the near silent condition accuracy of word recognition reaches an average of 52.87%, in the near noisy reaches an average of 14.5%, in the far silent condition reaches an average of 23.2%, and in the far noisy condition reaches an average of 2.8%. Index Terms—speech recognition, Indonesian geography dictionary, Hidden Markov Model, Pocketsphinx, Android.

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