Naoki Nariai, Ph.D.


Work address:
    5200 Illumina Way
    San Diego, CA 92122

Research Interests:
  • Bioinformatics
  • Machine learning
  • Statistical inference
Current Position:
  • Bioinformatics Scientist, Illumina, Inc. (June 2017 - present)
Past Research Positions:
  • Assistant Project Scientist, Department of Pediatrics and Institute for Genomic Medicine, University of California, San Diego (June 2015 - May 2017)
  • Assistant Professor, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University (June 2012 - May 2015)
  • Researcher, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University (April 2012 - May 2012)
  • Project Academic Support Specialist, Institute of Medical Science, University of Tokyo (January 2012 - March 2012)
  • Ph.D. in Bioinformatics, Boston University (2010)
  • Master’s degree in Computer Science, University of Tokyo (2005)
  • Bachelor’s degree in Information Science, University of Tokyo (2003)
Awards and Honors:
  • Reviewer's Choice Abstract (scored in the top 10% of poster abstracts) at the 2016 American Society of Human Genetics Annual Meeting
  • Grant-in-Aid for Young Scientists (B) from Japan Society for the Promotion of Science, 15K20851 (April 2015 - March 2017, declined)
  • Excellent poster award, Japanese Society for Bioinformatics (October 2013)
  • Research Assistantship from Boston University (May 2006 - October 2008)
  • DC1 fellowship from Japan Society for the Promotion of Science (April 2005 - March 2008, declined)
  • Member, American Society for Human Genetics (2018 - present)
  • Member, International Society for Computational Biology (2014 - 2017)
  • Member, Japanese Society for Bioinformatics (2012 - 2017)
Selected Publications:
Mimori T, Yasuda J, Kuroki Y, Shibata TF, Katsuoka F, Saito S, Nariai N, Ono A, Nakai-Inagaki N, Misawa K, Tateno K, Kawai Y, Fuse N, Hozawa A, Kuriyama S, Sugawara J, Minegishi N, Suzuki K, Kinoshita K, Nagasaki M, Yamamoto M.
Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.
Pharmacogenomics J. 2018 Jan 19. doi: 10.1038/s41397-017-0010-4.

Nariai N, Greenwald WW, DeBoever C, Li H, Frazer KA.
Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling.
Genetics. 2017 

Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA.
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.
BMC Bioinformatics. 2017;18:207.

DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D’Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D’Antonio-Chronowska A, Farley EK, Frazer KA.

Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.
Cell Stem Cell. 2017;20(4):533-546.

Panopoulos AD, D’Antonio M, Benaglio B, Williams R, Hashem SI, 
Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O’Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Mu¨ller F, Goldstein LSB, Belmonte JC, Adler E, Loring JF, Berggren WT, D’Antonio-Chronowska A, Smith EN, Frazer KA.
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem Cell Reports. 2017;8:1086-1100.

Branham K, Matsui H, Biswas P, Guru A A, Hicks M, Suk J J, Li H, Jakubosky D, Long T, Telenti A, Nariai N, Heckenlively JR, Frazer KA, Sieving PA, Ayyagari R.
Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing.
Physiol Genomics. 2016; DOI: 10.1152/physiolgenomics.00101.2016.

Kojima K, Kawai Y, Nariai N, Mimori T, Hasegawa T, Nagasaki M.
Short tandem repeat number estimation from paired-end reads for multiple individuals by considering coalescent tree.
BMC Genomics. 2016;17 Suppl 5:494

Pan X, Nariai N, Fukuhara N, Saito S, Sato Y, Katsuoka F, Kojima K, Kuroki Y, Danjoh I, Saito R, Hasegawa S, Okitsu Y, Kondo A, Onishi Y, Nagami F, Kiyomoto H, Hozawa A, Fuse N, Nagasaki M, Shimizu R, Yasuda J, Harigae H, Yamamoto M.
Monitoring of minimal residual disease in early T-cell precursor acute lymphoblastic leukaemia by next-generation sequencing.
British Journal of Haematology. 2016; DOI: 10.1111/bjh.13948.

Nariai N, Kojima K, Mimori T, Kawai Y, Nagasaki M.
A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes.
BMC Genomics. 2016;17 Suppl 1:2.

Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjo I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Engel JD, Kinoshita K, Kure S, Yaegashi N, ToMMo Japanese Reference Panel Project, Yamamoto M.
Rare variant discovery by deep whole-genome sequencing of 1070 Japanese individuals.
Nature Communications. 2015;6:8018.

Kawai Y, Mimori T, Kojima K, Nariai N, Danjoh I, Saito R, Yasuda J, Yamamoto M, Nagasaki M.
Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals.
Journal of Human Genetics. 2015;60:581-587.

Nariai N, Kojima K, Saito S, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Yasuda J, Nagasaki M.
HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data.
BMC Genomics. 2015;16 Suppl 2:S7.

Mimori T, Nariai N, Kojima K, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Nagasaki M.
Estimating copy numbers of alleles from population-scale high-throughput sequencing data.
BMC Bioinformatics. 2015;16 Suppl 1:S4.

Nariai N, Kojima K, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Nagasaki M.
TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads.
BMC Genomics. 2014;15 Suppl 10:S5.

Fujiwara T, Fukuhara N, Funayama R, Nariai N, Kamata M, Nagashima T, Kojima K, Onishi Y, Sasahara Y, Ishizawa K, Nagasaki M,
Nakayama K, Harigae H.
Identification of acquired mutations by whole-genome sequencing in GATA-2 deficiency evolving into myelodysplasia and
acute leukemia.
Annals of Hematology. 2014;93(9):1515-22.

Mimori T, Nariai N, Kojima K, Takahashi M, Ono A, Sato Y, Yamaguchi-Kabata Y, Nagasaki M.
iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.
BMC Systems Biology. 2013;7 Suppl 6:S8.

Kojima K, Nariai N, Mimori T, Takahashi M, Yamaguchi-Kabata Y, Sato Y, Nagasaki M.
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads.
Bioinformatics. 2013;29(22):2835-43.

Nariai N, Hirose O, Kojima K, Nagasaki M.
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.
Bioinformatics. 2013;29(18):2292-9.

Koso H, Takeda H, Yew CC, Ward JM, Nariai N, Ueno K, Nagasaki M, Watanabe S, Rust AG, Adams DJ, Copeland NG, Jenkins NA.
Transposon mutagenesis identifies genes that transform neural stem cells into glioma-initiating cells.
Proceedings of the National Academy of Sciences of the United States of America. 2012;109(44):E2998-3007.

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED.
Integration of relational and hierarchical network information for protein function prediction.
BMC Bioinformatics. 2008;9:350.

Nariai N, Kolaczyk ED, Kasif S.
Probabilistic protein function prediction from heterogeneous genome-wide data.
PLoS One. 2007;2(3):e337.

Nariai N, Kim S, Imoto S, Miyano S.
Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks.
Pacific Symposium on Biocomputing. 2004:336-47.

A complete list of publications is available below:

Google Scholar Citations

NCBI Pubmed


Professional Talks:

  • 2016 The Fourteenth Asia Pacific Bioinformatics Conference, San Francisco, USA
  • 2015 The Thirteenth Asia Pacific Bioinformatics Conference, HsinChu, Taiwan
  • 2014 The 25th International Conference on Genome Informatics, Tokyo, Japan
  • 2014 Multidisciplinary Approach Forum, Miyagi, Japan
  • 2014 The First International Conference on Algorithms for Computational Biology, Tarragona, Spain
  • 2014 NGS Data Analysis Seminar, Kyushu University, Fukuoka, Japan
  • 2013 Japanese Society for Bioinformatics, Tokyo, Japan
  • 2012 In Silico Megabank Research Seminar, Tohoku University, Miyagi, Japan
  • 2007 The Seventh Annual International Workshop on Bioinformatics and Systems Biology, Tokyo, Japan
  • 2004 Pacific Symposium on Biocomputing, Hawaii, USA
Recent poster/oral abstracts:
  • X. Chen; N. Nariai; A. Gross; S. Ji; C. Saunders "Manta: Improving the accuracy of structural variant calling", ASHG2018
  • A.M. Gross; A. Chawla; S.S. Ajay; N. Nariai; X. Chen; C.T. Saunders; D.R. Bentley; R.J. Taft "Development of structural variation calling in clinical whole genome sequencing: A progress report", ASHG2018
  • Y. Qiu; J. Yan; A.M. Ribeiro-dos-Santos; Y. Yin; Y. Li; N. Vinckier; N. Nariai; A. Raman; E. Morgunova; A. Mahajan; K.J. Gaulton; M.I McCarthy; K.A. Frazer; M. Sander; J. Taipale; B. Ren "Systematic analysis of genetic variants with allelic effects on transcription factor binding.", ASHG2018
  • P. Benaglio; J. Yan; J. Chiou; N. Nariai; M. Sander; B. Ren; K. Gaulton; K. Frazer "Systematic characterization of genetic variants associated with type 1 diabetes for differential binding of 530 transcription factors", ASHG2018
  • Japanese Patent Application (No. 2015-256860, application date: December 28th, 2015)
  • Nagasaki M, Nariai N, Kojima K. "Method for determining genotype of particular gene locus group or individual gene locus, determination computer system and determination program", Japanese PCT Patent Application (No. PCT/JP2015/86194, application date: December 25th, 2015), WO2016104688 A1
  • Nagasaki M, Kojima K, Nariai N, Mimori T, Kawai Y. "Method, computer system and software for selecting Tag SNP, and DNA microarray equipped with nucleic acid probe corresponding to Tag SNP selected by said selection method", Japanese PCT Patent Application (No. PCT/JP2015/067686, application date: June 19th, 2015), WO2015194655 A1
Review Articles:
  • Nariai N. "Bioinformatics methods in the era of personal sequencing", Jikken Igaku, Vol. 34(16), p2652-2656, October 2016
  • Nariai N. "HLA typing from whole-genome sequencing data", "Society of Evolutionary Studies, Japan" News, Vol.17 No.1, p15-23, March 2016
  • Kawai Y, Mimori T, Kojima K, Nariai N, Nagasaki M. "Design of Japonica array and its application to genotype imputation", Medical Science Digest, Vol. 41(5), p226-229, May 2015
  • Nariai N. "Genome-wide analysis of transcriptome by RNA-seq", "Society of Evolutionary Studies, Japan" News, Vol.15 No.2, p10-15, July 2014

Referee Services:

  • Bioinformatics (2014, 2015, 2016, 2017)
  • Journal of the American Statistical Association (2017)
  • Statistical Applications in Genetics and Molecular Biology (2017)
  • IEEE/ACM Transactions on Computational Biology and Bioinformatics (2015)
  • Grant proposal for the University of Strasbourg Institute for Advanced Study (2013)
  • RECOMB (2005)

Open source software contributions:

  • Manta Structural Variant Caller (