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Mile Sikic on Muck Rack

Mile Sikic

Asia–Pacific (APAC)
As seen in: Nature, BioRxiv
Group leader and assistant director @astar_gis, Prof @SveucilisteZG, partner @OraclumCapital. AI in Genomics
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Articles

A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines - Nature Methods

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By Ying Chen, Nadia M. Davidson, Yuk Kei Wan, Yan Su, Hasindu Gamaarachchi, Andre Sim, Laura Wratten, Christopher Hakkaart, Chelsea Sawyer, Viktoriia Iakovleva, Jiaxu Wang, Dominik Stanojevic, Hoang-Dai Tran, Shen Yon Toh, Philip Andrew Ewels, N. Gopalakrishna Iyer, Alexandre P. Thiery, Alexandre H. Thiéry, Ramanuj DasGupta, Mile Sikic, Yue Wan, Wai Leong Tam, Chiea Chuan Khor, Torsten Wüstefeld, Alexander Lezhava, Ploy N. Pratanwanich, Alicia Oshlack, SG-NEx consortium
| Nature Verified
Abstract The human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting in alternative isoforms that are highly similar and that remain difficult to quantify.
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Telomere-to-Telomere Phased Genome Assembly Using HERRO-Corrected Simplex Nanopore Reads

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By Dominik Stanojevic, Dehui Lin, Sergey Nurk, Mile Sikic
| BioRxiv
Abstract Telomere-to-telomere phased assemblies have become the norm in genomics. To achieve these for diploid and even polyploid genomes, the contemporary approach involves a combination of two long-read sequencing technologies: high-accuracy long reads, e.g. Pacific Biosciences (PacBio) HiFi or Oxford Nanopore (ONT) 'Duplex' reads, and ultra-long ONT 'Simplex' reads. Using two different technologies increases the cost and the required amount of genomic DNA.
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Telomere-to-telomere phased genome assembly using error-corrected Simplex nanopore reads

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By Dominik Stanojevic, Dehui Lin, Mile Sikic, Oxford Nanopore Techologies
| BioRxiv
Abstract Telomere-to-telomere phased assemblies are standard expectations. To achieve these for diploid and even polyploid genomes, the contemporary approach involves at least two long-read sequencing technologies: high-accuracy HiFi or Duplex nanopore long reads and ultra-long noisy nanopore reads. Using two different technologies increases the cost and the required amount of genomic DNA.
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