2017

Gpr124 is essential for blood brain barrier integrity in central nervous system disease
Chang J, Mancuso MR, Maier C, Liang X, Yuki K, Yang L, Kwong JW, Wang J, Rao V, Vallon M, Kosinski C, Zhang JJ, Mah AT, Xu L, Li L, Gholamin S, Reyes TF, Li R, Kuhnert F, Han X, Yuan J, Chiou SH, Brettman AD, Daly L, Corney DC, Cheshier SH, Shortliffe LD, Wu X, Snyder M, Chan P, Giffard RG, Chang HY, Andreasson K, Kuo CJ.
Nat Med. 2017 Apr;23(4):450-460. doi: 10.1038/nm.4309. Epub 2017 Mar 13.

Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression.
Contrepois K, Coudereau C, Benayoun BA, Schuler N, Roux PF, Bischof O, Courbeyrette R, Carvalho C, Thuret JY, Ma Z, Derbois C, Nevers MC, Volland H, Redon CE, Bonner WM, Deleuze JF, Wiel C, Bernard D, Snyder MP, Rube CE, Olaso R, Fenaille F, Mann C. Nat Commun. 2017 May 10;8:14995. doi: 10.1038/ncomms14995.PMID:28489069

Deficiency Is Associated with Mitochondrial Dysfunction and Exercise Intolerance in Mice
Indumathi Chennamsetty, Michael Coronado, Kevin Contrepois,Mark P. Keller, Ivan Carcamo-Orive, John Sandin, Giovanni Fajardo, Andrew J. Whittle, Mohsen Fathzadeh, Michael Snyder, Gerald Reaven, Alan D. Attie, Daniel Bernstein, Thomas Quertermous, Joshua W. Knowles

Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information
Li X, Dunn J, Salins D, Zhou G, Zhou W, Schussler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder MP.PLoS Biol. 2017 Jan 12;15(1):e2001402. doi: 10.1371/journal.pbio.2001402

Association of AHSG with alopecia and mental retardation (APMR) syndrome.
Reza Sailani M, Jahanbani F, Nasiri J, Behnam M, Salehi M, Sedghi M, Hoseinzadeh M, Takahashi S, Zia A, Gruber J, Lynch JL, Lam D, Winkelmann J, Amirkiai S, Pang B, Rego S, Mazroui S, Bernstein JA, Snyder MP. Hum Genet. 2017 Jan 4. doi: 10.1007/s00439-016-1756-5. [Epub ahead of print]

Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing.
Tombacz D, Balázs Z, Csabai Z, Moldován N, Szucs A, Sharon D, Snyder M, Boldogkoi Z.

2016

Patient-Specific iPSC-Derived Endothelial Cells Uncover Pathways that Protect against Pulmonary Hypertension in BMPR2 Mutation Carriers.
Gu M, Shao NY, Sa S, Li D, Termglinchan V, Ameen M, Karakikes I, Sosa G, Grubert F, Lee J, Cao A, Taylor S, Ma Y, Zhao Z, Chappell J, Hamid R, Austin ED, Gold JD, Wu JC, Snyder MP, Rabinovitch M. Cell Stem Cell. 2016 Dec 2. pii: S1934-5909(16)30266-1. doi: 10.1016/j.stem.2016.08.019. [Epub ahead of print] 

Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors.
Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Nucleic Acids Res. 2016 Dec 20. pii: gkw1214. doi: 10.1093/nar/gkw1214. [Epub ahead of print]

A common class of transcripts with 5'-intro depletion, distinct early coding sequence features, and N1-methyladenosine modification.
Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP.

Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling
Reuter JA, Spacek DV, Pai RK, Snyder MP. Nat Methods. 2016 Nov;13(11):953-958. doi: 10.1038/nmeth.4028. Epub 2016 Oct 10.

Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging
Li X, Snyder MP.. Bioessays. 2016 Nov;38(11):1093-1101. doi: 10.1002/bies.201600040. Epub 2016 Aug 24.

IPSC Model oaf Pulmonary Arterial Hypertension Reveals Novel Gene Expression and Patient Specificity
Sa S, Gu M, Chappell J, Shao NY, Ameen M, Elliott KA, Li D, Grubert F, Li CG, Taylor S, Cao A, Ma Y, Fong R, Nguyen L, Wu JC, Snyder MP, Rabinovitch M. Am J Respir Crit Care Med. 2016 Oct 25. [Epub ahead of print]

  1. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations.
    Araya, C. L., Cenik, C., Reuter, J. A., Kiss, G., Pande, V. S., Snyder, M. P. and Greenleaf, W. J.
    (2016). Nat Genet 48(2): 117-125. PubMed PMID: 26691984; PubMed Central PMCID: PMCPMC4731297.

  2. NIH working group report-using genomic information to guide weight management: From universal to precision treatment.
    Bray, M. S., Loos, R. J., McCaffery, J. M., Ling, C., Franks, P. W., Weinstock, G. M., Snyder, M. P., Vassy, J. L., Agurs-Collins, T. and Conference Working, G.
    (2016). Obesity (Silver Spring) 24(1): 14-22. PubMed PMID: 26692578; PubMed Central PMCID: PMCPMC4689320.

  3. Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine?
    Contrepois, K., Liang, L. and Snyder, M.
    (2016).Clin Chem 62(5): 676-678. PubMed PMID: 26960666; PubMed Central PMCID: PMCPMC4851585.

  4. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.
    Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., Majeti, R. and Chang, H. Y.
    (2016). Nat Genet. PubMed PMID: 27526324.

  5. Secure cloud computing for genomic data.
    Datta, S., Bettinger, K. and Snyder, M.
    (2016). Nat Biotechnol 34(6): 588-591. PubMed PMID: 27281411.

  6. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.
    Henn, B. M., Botigue, L. R., Peischl, S., Dupanloup, I., Lipatov, M., Maples, B. K., Martin, A. R., Musharoff, S., Cann, H., Snyder, M. P., Excoffier, L., Kidd, J. M. and Bustamante, C. D.
    (2016). Proc Natl Acad Sci U S A 113(4): E440-449. PubMed PMID: 26712023; PubMed Central PMCID: PMCPMC4743782.

  7. Effects of cellular origin on differentiation of human induced pluripotent stem cell-derived endothelial cells.
    Hu, S., Zhao, M. T., Jahanbani, F., Shao, N. Y., Lee, W. H., Chen, H., Snyder, M. P. and Wu, J. C.
    (2016). JCI Insight 1(8). PubMed PMID: 27398408; PubMed Central PMCID: PMCPMC4937999.

  8. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.
    Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S. and Snyder, M.
    (2016). "Nat Biotechnol 34(1): 64-69. PubMed PMID: 26655498; PubMed Central PMCID: PMCPMC4884093.

  9. Genome assembly from synthetic long read clouds.
    Kuleshov, V., Snyder, M. P. and Batzoglou, S.
    (2016).Bioinformatics 32(12): i216-i224. PubMed PMID: 27307620; PubMed Central PMCID: PMCPMC4908351.

  10. Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1.
    Landegren, N., Sharon, D., Freyhult, E., Hallgren, A., Eriksson, D., Edqvist, P. H., Bensing, S., Wahlberg, J., Nelson, L. M., Gustafsson, J., Husebye, E. S., Anderson, M. S., Snyder, M. and Kampe, O.
    (2016).Sci Rep 6: 20104. PubMed PMID: 26830021; PubMed Central PMCID: PMCPMC4735587.

  11. Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance.
    Lee, S., Zhang, C., Kilicarslan, M., Piening, B. D., Bjornson, E., Hallstrom, B. M., Groen, A. K., Ferrannini, E., Laakso, M., Snyder, M., Bluher, M., Uhlen, M., Nielsen, J., Smith, U., Serlie, M. J., Boren, J. and Mardinoglu, A.
    (2016). Cell Metab 24(1): 172-184. PubMed PMID: 27345421.

  12. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Li, C., Gu, L., Gao, L., Chen, C., Wei, C. Q., Qiu, Q., Chien, C. W., Wang, S., Jiang, L., Ai, L. F., Chen, C. Y., Yang, S., Nguyen, V., Qi, Y., Snyder, M. P., Burlingame, A. L., Kohalmi, S. E., Huang, S., Cao, X., Wang, Z. Y., Wu, K., Chen, X. and Cui, Y.
    (2016). Nat Genet 48(6): 687-693. PubMed PMID: 27111034.

  13. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis
    Li, G., Chen, Y., Snyder, M. P. and Zhang, M. Q.
    (2016). Nucleic Acids Res. PubMed PMID: 27625391.

  14. Yeast longevity promoted by reversing aging-associated decline in heavy isotope content.
    Li, X. and Snyder, M. P.
    (2016). Npj Aging And Mechanisms Of Disease 2: 16004.


  15. Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging.
    Li, X. and Snyder, M. P.
    (2016). Bioessays. PubMed PMID: 27554342.

  16. Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays.
    Low, J. K., Im, H., Erce, M. A., Hart-Smith, G., Snyder, M. P. and Wilkins, M. R.
    (2016).Proteomics 16(3): 465-476. PubMed PMID: 26572822.

  17. Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro.
    Matsa, E., Burridge, P. W., Yu, K. H., Ahrens, J. H., Termglinchan, V., Wu, H., Liu, C., Shukla, P., Sayed, N., Churko, J. M., Shao, N., Woo, N. A., Chao, A. S., Gold, J. D., Karakikes, I., Snyder, M. P. and Wu, J. C.
    (2016).Cell Stem Cell 19(3): 311-325. PubMed PMID: 27545504.

  18. The genetic predisposition to bronchopulmonary dysplasia.
    Yu, K. H., Li, J., Snyder, M., Shaw, G. M. and O'Brodovich, H. M.
    (2016). Curr Opin Pediatr 28(3): 318-323. PubMed PMID: 26963946; PubMed Central PMCID: PMCPMC4853271.

  19. Omics Profiling in Precision Oncology.
    Yu, K. H. and Snyder, M.
    (2016). Mol Cell Proteomics 15(8): 2525-2536. PubMed PMID: 27099341; PubMed Central PMCID: PMCPMC4974334.

  20. Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
    Zhang, Q., Zeng, X., Younkin, S., Kawli, T., Snyder, M. P. and Keles, S.
    (2016).BMC Bioinformatics 17: 96. PubMed PMID: 26908256; PubMed Central PMCID: PMCPMC4765064.