Academic Appointments


All Publications


  • Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis NATURE COMMUNICATIONS Sahraeian, S., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar, P. T., Au, K., Asadi, N., Gerstein, M. B., Wong, W., Snyder, M. P., Schadt, E., Lam, H. K. 2017; 8: 59

    Abstract

    RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest available tools, they have not evaluated the analysis workflows comprehensively to unleash the power within RNA-seq. Here we conduct an extensive study analysing a broad spectrum of RNA-seq workflows. Surpassing the expression analysis scope, our work also includes assessment of RNA variant-calling, RNA editing and RNA fusion detection techniques. Specifically, we examine both short- and long-read RNA-seq technologies, 39 analysis tools resulting in ~120 combinations, and ~490 analyses involving 15 samples with a variety of germline, cancer and stem cell data sets. We report the performance and propose a comprehensive RNA-seq analysis protocol, named RNACocktail, along with a computational pipeline achieving high accuracy. Validation on different samples reveals that our proposed protocol could help researchers extract more biologically relevant predictions by broad analysis of the transcriptome.RNA-seq is widely used for transcriptome analysis. Here, the authors analyse a wide spectrum of RNA-seq workflows and present a comprehensive analysis protocol named RNACocktail as well as a computational pipeline leveraging the widely used tools for accurate RNA-seq analysis.

    View details for PubMedID 28680106

  • MetaSV: an accurate and integrative structural-variant caller for next generation sequencing BIOINFORMATICS Mohiyuddin, M., Mu, J. C., Li, J., Asadi, N. B., Gerstein, M. B., Abyzov, A., Wong, W. H., Lam, H. Y. 2015; 31 (16): 2741-2744

    Abstract

    Structural variations (SVs) are large genomic rearrangements that vary significantly in size, making them challenging to detect with the relatively short reads from next-generation sequencing (NGS). Different SV detection methods have been developed; however, each is limited to specific kinds of SVs with varying accuracy and resolution. Previous works have attempted to combine different methods, but they still suffer from poor accuracy particularly for insertions. We propose MetaSV, an integrated SV caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes. Using simulation and experimental data, we demonstrate the effectiveness of MetaSV across various SV types and sizes.Code in Python is at http://bioinform.github.io/metasv/.rd@bina.comSupplementary data are available at Bioinformatics online.

    View details for DOI 10.1093/bioinformatics/btv204

    View details for Web of Science ID 000359666600020

    View details for PubMedID 25861968

    View details for PubMedCentralID PMC4528635

  • VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications BIOINFORMATICS Mu, J. C., Mohiyuddin, M., Li, J., Asadi, N. B., Gerstein, M. B., Abyzov, A., Wong, W. H., Lam, H. Y. 2015; 31 (9): 1469-1471

    Abstract

    VarSim is a framework for assessing alignment and variant calling accuracy in high-throughput genome sequencing through simulation or real data. In contrast to simulating a random mutation spectrum, it synthesizes diploid genomes with germline and somatic mutations based on a realistic model. This model leverages information such as previously reported mutations to make the synthetic genomes biologically relevant. VarSim simulates and validates a wide range of variants, including single nucleotide variants, small indels and large structural variants. It is an automated, comprehensive compute framework supporting parallel computation and multiple read simulators. Furthermore, we developed a novel map data structure to validate read alignments, a strategy to compare variants binned in size ranges and a lightweight, interactive, graphical report to visualize validation results with detailed statistics. Thus far, it is the most comprehensive validation tool for secondary analysis in next generation sequencing.Code in Java and Python along with instructions to download the reads and variants is at http://bioinform.github.io/varsim.rd@bina.comSupplementary data are available at Bioinformatics online.

    View details for DOI 10.1093/bioinformatics/btu828

    View details for Web of Science ID 000355665800019

    View details for PubMedID 25524895

    View details for PubMedCentralID PMC4410653

  • Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods. Scientific reports Mu, J. C., Tootoonchi Afshar, P., Mohiyuddin, M., Chen, X., Li, J., Bani Asadi, N., Gerstein, M. B., Wong, W. H., Lam, H. Y. 2015; 5: 14493-?

    Abstract

    A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput sequencing. Although recent works have attempted to provide such a resource, they still do not encompass all major types of variants including structural variants (SVs). Thus, we leveraged the massive high-quality Sanger sequences from the HuRef genome to construct by far the most comprehensive gold set of a single individual, which was cross validated with deep Illumina sequencing, population datasets, and well-established algorithms. It was a necessary effort to completely reanalyze the HuRef genome as its previously published variants were mostly reported five years ago, suffering from compatibility, organization, and accuracy issues that prevent their direct use in benchmarking. Our extensive analysis and validation resulted in a gold set with high specificity and sensitivity. In contrast to the current gold sets of the NA12878 or HS1011 genomes, our gold set is the first that includes small variants, deletion SVs and insertion SVs up to a hundred thousand base-pairs. We demonstrate the utility of our HuRef gold set to benchmark several published SV detection tools.

    View details for DOI 10.1038/srep14493

    View details for PubMedID 26412485

    View details for PubMedCentralID PMC4585973

  • Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods. Scientific reports Mu, J. C., Tootoonchi Afshar, P., Mohiyuddin, M., Chen, X., Li, J., Bani Asadi, N., Gerstein, M. B., Wong, W. H., Lam, H. Y. 2015; 5: 14493-?

    Abstract

    A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput sequencing. Although recent works have attempted to provide such a resource, they still do not encompass all major types of variants including structural variants (SVs). Thus, we leveraged the massive high-quality Sanger sequences from the HuRef genome to construct by far the most comprehensive gold set of a single individual, which was cross validated with deep Illumina sequencing, population datasets, and well-established algorithms. It was a necessary effort to completely reanalyze the HuRef genome as its previously published variants were mostly reported five years ago, suffering from compatibility, organization, and accuracy issues that prevent their direct use in benchmarking. Our extensive analysis and validation resulted in a gold set with high specificity and sensitivity. In contrast to the current gold sets of the NA12878 or HS1011 genomes, our gold set is the first that includes small variants, deletion SVs and insertion SVs up to a hundred thousand base-pairs. We demonstrate the utility of our HuRef gold set to benchmark several published SV detection tools.

    View details for DOI 10.1038/srep14493

    View details for PubMedID 26412485

    View details for PubMedCentralID PMC4585973

  • Fast and accurate read alignment for resequencing BIOINFORMATICS Mu, J. C., Jiang, H., Kiani, A., Mohiyuddin, M., Asadi, N. B., Wong, W. H. 2012; 28 (18): 2366-2373

    Abstract

    Next-generation sequence analysis has become an important task both in laboratory and clinical settings. A key stage in the majority sequence analysis workflows, such as resequencing, is the alignment of genomic reads to a reference genome. The accurate alignment of reads with large indels is a computationally challenging task for researchers.We introduce SeqAlto as a new algorithm for read alignment. For reads longer than or equal to 100 bp, SeqAlto is up to 10 × faster than existing algorithms, while retaining high accuracy and the ability to align reads with large (up to 50 bp) indels. This improvement in efficiency is particularly important in the analysis of future sequencing data where the number of reads approaches many billions. Furthermore, SeqAlto uses less than 8 GB of memory to align against the human genome. SeqAlto is benchmarked against several existing tools with both real and simulated data.Linux and Mac OS X binaries free for academic use are available at http://www.stanford.edu/group/wonglab/seqaltowhwong@stanford.edu.

    View details for DOI 10.1093/bioinformatics/bts450

    View details for Web of Science ID 000308532300059

    View details for PubMedID 22811546

    View details for PubMedCentralID PMC3436849