Search Results - "Majidian, Sina"

NGS based haplotype assembly using matrix completion by Majidian, Sina, Kahaei, Mohammad Hossein

“…We apply matrix completion methods for haplotype assembly from NGS reads to develop the new HapSVT, HapNuc, and HapOPT algorithms. This is performed by…”
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Hap10: reconstructing accurate and long polyploid haplotypes using linked reads by Majidian, Sina, Kahaei, Mohammad Hossein, de Ridder, Dick

“…Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype…”
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Minimum error correction-based haplotype assembly: Considerations for long read data by Majidian, Sina, Kahaei, Mohammad Hossein, de Ridder, Dick

“…The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites…”
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Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek by Javan, Sara Lamei, Kashkooli, Arman Beyraghdar, Shojaeiyan, AbdolAli, Majidian, Sina

“…Medicinal plants are rich sources for treating various diseases due their bioactive secondary metabolites. Fenugreek (Trigonella foenum-graecum) is one of the…”
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Genomic variant benchmark: if you cannot measure it, you cannot improve it by Majidian, Sina, Agustinho, Daniel Paiva, Chin, Chen-Shan, Sedlazeck, Fritz J, Mahmoud, Medhat

“…Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing…”
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When less is more: sketching with minimizers in genomics by Ndiaye, Malick, Prieto-Baños, Silvia, Fitzgerald, Lucy M, Yazdizadeh Kharrazi, Ali, Oreshkov, Sergey, Dessimoz, Christophe, Sedlazeck, Fritz J, Glover, Natasha, Majidian, Sina

“…The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance,…”
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The GIAB genomic stratifications resource for human reference genomes by Dwarshuis, Nathan, Kalra, Divya, McDaniel, Jennifer, Sanio, Philippe, Alvarez Jerez, Pilar, Jadhav, Bharati, Huang, Wenyu (Eddy), Mondal, Rajarshi, Busby, Ben, Olson, Nathan D., Sedlazeck, Fritz J., Wagner, Justin, Majidian, Sina, Zook, Justin M.

“…Despite the growing variety of sequencing and variant-calling tools, no workflow performs equally well across the entire human genome. Understanding…”
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Matrix Completion Using Graph Total Variation Based on Directed Laplacian Matrix by Ahmadi, Alireza, Majidian, Sina, Kahaei, Mohammad Hossein

“…We propose two graph matrix completion algorithms called GMCM-DL and GMCR-DL, by employing a new definition of Graph Total Variation for matrices based on the…”
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Bioinformatics Evaluation of SPATA19 Gene Expression in Different Parts of Brain by Zargar, Mahsa, Majidian, Sina, Modarressi, Mohammad Hossein, Shabani, Sasan

“…Background: Determining the expression pattern of testis genes in the brain is essential for understanding tissue functions and correlation or…”
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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree by Dylus, David, Altenhoff, Adrian, Majidian, Sina, Sedlazeck, Fritz J., Dessimoz, Christophe

“…Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints…”
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OMAMO: orthology-based alternative model organism selection by Nicheperovich, Alina, Altenhoff, Adrian M, Dessimoz, Christophe, Majidian, Sina

“…Abstract Summary The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding…”
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Phylogenetic placement of whole genome duplications in yeasts through quantitative analysis of hierarchical orthologous groups [version 1; peer review: 1 approved with reservations, 1 not approved] by Moix, Samuel, Glover, Natasha, Majidian, Sina

“…Background: Whole genome duplications (WGD) are genomic events leading to formation of polyploid organisms. Resulting duplicated genes play important roles in…”
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OMAMO: orthology-based alternative model organism selection by Nicheperovich, Alina, Altenhoff, Adrian M, Dessimoz, Christophe, Majidian, Sina

“…The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology…”
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Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices by Ezazi, Robab, Ahmadzadeh, Masoud, Majidian, Sina, Stefani, Erika, Pindo, Massimo, Donati, Claudio

“…ABSTRACT The microbial communities associated to the rhizosphere (the rhizomicrobiome) have a substantial impact on plant growth and yield. Understanding the…”
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Hybrid experimental and numerical approach for assessment of non-linear dynamic behavior of soil-nailed retaining walls by Majidian, Sina, Komak Panah, Ali

“…Seismic Performance-based design demands reliable means for profound understanding of inelastic and non-linear dynamic behavior of civil structures. In this…”
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Haplotype Assembly Using Manifold Optimization and Error Correction Mechanism by Mohades, Mohamad Mahdi, Majidian, Sina, Kahaei, Mohammad Hossein

“…Recent matrix completion based methods have not been able to properly model the haplotype assembly problem for noisy observations. To deal with such cases, we…”
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Effect of fine material content on the CBR of Iran saturated soils by Pasand, Seyed Ali, Nasrollahi, Nasim, Asghari-Kaljahi, Ebrahim, Majidian, Sina

“…The California bearing ratio (CBR) is an important index of soil quality for use in road construction and base stabilization. The CBR test can be performed in…”
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OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem by Altenhoff, Adrian M, Warwick Vesztrocy, Alex, Bernard, Charles, Train, Clement-Marie, Nicheperovich, Alina, Prieto Baños, Silvia, Julca, Irene, Moi, David, Nevers, Yannis, Majidian, Sina, Dessimoz, Christophe, Glover, Natasha M

“…Abstract In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and…”
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PhaseME: Automatic rapid assessment of phasing quality and phasing improvement by Majidian, Sina, Sedlazeck, Fritz J

“…The detection of which mutations are occurring on the same DNA molecule is essential to predict their consequences. This can be achieved by phasing the genomic…”
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Anti-angiogenic effects of testis-specific gene antigen 10 on primary endothelial cells by Valipour, Elahe, Nooshabadi, Vajihe Taghdiri, Mahdipour, Shadi, Shabani, Sasan, Farhady-Tooli, Leila, Majidian, Sina, Noroozi, Zahra, Mansouri, Kamran, Motevaseli, Elaheh, Modarressi, Mohammad Hossein

“…•Reduced expression of angiogenesis-related genes in TSGA10 over-expressing HUVECs.•Inhibitory effects of over-expressing TSGA10 on VEGF-stimulated…”
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