Review
Biochemical Research Methods
Ziad Al Bkhetan, Gursharan Chana, Kotagiri Ramamohanarao, Karin Verspoor, Benjamin Goudey
Summary: This study comprehensively evaluated consensus strategies for haplotype phasing, exploring the performance of different consensus paradigms and the impact on the downstream task of genotype imputation across various datasets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Brian L. Browning, Xiaowen Tian, Ying Zhou, Sharon R. Browning
Summary: Haplotype phasing method presented in this study efficiently estimates haplotypes from genotype data using marker windowing and composite reference haplotypes. It employs a progressive phasing algorithm and two-stage phasing algorithm for high-frequency and low-frequency markers respectively. Performance comparison shows that Beagle 5.2 is over 20 times faster than SHAPEIT for TOPMed sequence data, while achieving similar accuracy and scalability for larger sample sizes.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemical Research Methods
Sepideh Mazrouee
Summary: This article proposes a novel approach called ARHap for individual human phasing based on discovery of interesting hidden relations among single variant sites. ARHap learns strong association rules among variant loci on the genome and develops a combinatorial approach for fast and accurate haplotype phasing. Extensive experimental analyses demonstrate the superiority of ARHap in diploid haplotyping compared to state-of-the-art algorithms, showing significantly better accuracy performance.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Automation & Control Systems
Yu Zhang, Zhuo Jin, Jiaqin Wei, George Yin
Summary: This paper studies closed-loop equilibrium strategies for mean-variance portfolio selection problems in a hidden Markov model with dynamic attention behavior. The investor's attention to news is introduced as a control of the accuracy of the news signal process. Equilibrium strategies are found by numerically solving an extended HJB equation using the Markov chain approximation method, and an iterative algorithm is constructed with established convergence. Numerical examples are provided to illustrate the results.
Article
Genetics & Heredity
Tomoyuki Furuta, Toshio Yamamoto, Motoyuki Ashikari
Summary: This paper introduces an error correction tool called GBScleanR, which incorporates marker-specific error rates into the hidden Markov model (HMM) to achieve robust and precise error correction for noisy RRS-based genotype data. The results indicate that GBScleanR improves accuracy by more than 25 percentage points compared to existing tools in simulation data sets and achieves the most reliable genotype estimation in real data even with error-prone markers.
Article
Chemistry, Multidisciplinary
Norah Abanmi, Heba Kurdi, Mai Alzamel
Summary: The prevalence of malware attacks targeting IoT systems has raised concerns and emphasized the need for effective detection and defense mechanisms. However, detecting malware, especially those with new or unknown behaviors, is challenging. The main issue lies in its ability to hide, making it difficult to detect. Moreover, limited information on malware families restricts the availability of big data for analysis. This paper introduces a new Profile Hidden Markov Model (PHMM) for app analysis and classification in Android systems, while also dynamically identifying suspicious calls to reduce the risk of code execution. The experimental results demonstrate that the proposed Dynamic IoT malware Detection in Android Systems using PHMM (DIP) outperforms eight rival malware detection frameworks, achieving up to 96.3% accuracy at a 5% False Positive Rate (FP rate), 3% False Negative Rate (FN rate), and 94.9% F-measure.
APPLIED SCIENCES-BASEL
(2023)
Article
Computer Science, Information Systems
Jinwen Xi, Guosheng Xu, Shihong Zou, Yueming Lu, Guoqiang Li, Jiuyun Xu, Ruisheng Wang
Summary: In this paper, we propose HMMDShard, a dynamic blockchain sharding scheme based on the hidden Markov model (HMM). HMMDShard leverages the dynamic assemblage characteristic of IoT collaborative sensing and achieves adaptive dynamic incremental updating of blockchain shards by integrating HMM, effectively reducing the proportion of cross-shard transactions (CSTs). We conduct a comprehensive analysis of the security issues and properties of HMMDShard, and evaluate its performance through the implementation of a system prototype. The results demonstrate that HMMDShard significantly reduces the proportion of CSTs and outperforms other baselines in terms of system throughput and transaction confirmation latency.
IEEE INTERNET OF THINGS JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Claire Oget-Ebrad, Naveen Kumar Kadri, Gabriel Costa Monteiro Moreira, Latifa Karim, Wouter Coppieters, Michel Georges, Tom Druet
Summary: This study evaluates several population-based haplotype phasing methods in a Holstein cattle pedigree using whole-genome sequence data. The results show that ShapeIT4.1 and Beagle5.2 are the most accurate methods, particularly for phasing long segments and in the first scenario.
Article
Biochemical Research Methods
Su Wang, Miran Kim, Xiaoqian Jiang, Arif Ozgun Harmanci
Summary: The decreasing cost of DNA sequencing has led to increased knowledge about genetic variation. In-silico genotype imputation using reference panels is a cost-effective and accurate alternative for genotyping common and uncommon variants. This study assesses the accuracy of using vicinity-based hidden Markov models (HMMs) for imputation and demonstrates that it can accurately impute both common and uncommon variants.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Artificial Intelligence
Amenah D. Abbood, Bara'a A. Attea, Ammar A. Hasan, Richard M. Everson, Clara Pizzuti
Summary: This study takes a new approach to detect the evolution of community structures by decomposing the problem into three essential components: intra-community connections, inter-community connections, and community evolution. Through a multi-objective optimization algorithm and Viterbi algorithm, the proposed model provides temporal smoothness over time for clustering dynamic networks. The results demonstrate the effectiveness of the proposed algorithm in outperforming other algorithms.
ARTIFICIAL INTELLIGENCE REVIEW
(2023)
Article
Engineering, Environmental
Silabrata Pahari, Yu-Ting Lin, Shuhao Liu, Chi Ho Lee, Mustafa Akbulut, Joseph Sang-Il Kwon
Summary: This article proposes an integrated framework for controlling self-assembling systems, which accurately captures the self-assembly process using a dissipative particle dynamics model and solves the stochastic optimal control problem by calculating the transition probabilities between states, thereby driving the system towards the desired morphology.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Automation & Control Systems
Renhai Chen, Shimin Yuan, Chenlin Ma, Huihui Zhao, Zhiyong Feng
Summary: This article discusses the advantages and disadvantages of GPS and cellular-based positioning. It highlights the challenges of cellular-based positioning and proposes a novel algorithm called THMM to improve its accuracy. The algorithm is optimized based on the characteristics of cellular-based data and the experimental results demonstrate its effectiveness.
IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS
(2022)
Article
Multidisciplinary Sciences
Carsten Wiuf, Abhishek Behera, Abhinav Singh, Manoj Gopalkrishnan
Summary: In this study, we propose a novel reaction network scheme called the Baum-Welch (BW) reaction network for learning parameters of hidden Markov models (HMMs). The scheme encodes all variables using separate species and each reaction in the scheme changes only one molecule from one species to another. We show that the BW algorithm and the reaction network scheme have the same fixed points and that the expectation step and the maximization step of the reaction network converge fast and compute the same values as the E-step and M-step of the BW algorithm. Simulation results demonstrate that our reaction network learns the same parameters as the BW algorithm and the log-likelihood increases continuously.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Biochemical Research Methods
Lars Wienbrandt, David Ellinghaus
Summary: EagleImp is a fast and accurate software for phasing and genotype imputation, with improved algorithms and technical optimizations. It outperforms other tools and servers in terms of speed and accuracy in various scenarios.
Article
Mathematics, Interdisciplinary Applications
Abdessatar Souissi, El Gheteb Soueidi
Summary: This paper aims to expand on previous research on quantum hidden Markov processes by introducing the concept of entangled hidden Markov processes. These are hidden Markov processes in which the hidden processes themselves are entangled Markov processes. The paper provides an explicit expression for the joint expectation of these processes and demonstrates that the approach also applies to the classical case.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.