2015

  1. Single-cell chromatin accessibility reveals principles of regulatory variation.
    Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y. and Greenleaf, W. J.
    (2015). Nature 523(7561): 486-490. PubMed PMID: 26083756; PubMed Central PMCID: PMCPMC4685948.

  2. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.
    Cenik, C, Cenik, E. S., Byeon, G. W., Grubert, F., Candille, S. I., Spacek, D., Alsallakh, B., Tilgner, H., Araya, C. L., Tang, H., Ricci, E. and Snyder, M. P.
    (2015). Genome Res 25(11): 1610-1621. PubMed PMID: 26297486; PubMed Central PMCID: PMCPMC4617958.

  3. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform.
    Chen, R., Im, H. and Snyder, M.
    (2015). Cold Spring Harb Protoc 2015(7): 634-641. PubMed PMID: 25762419

  4. Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform.
    Chen, R., Im, H. and Snyder, M.
    (2015). Cold Spring Harb Protoc 2015(7): 642-648. PubMed PMID: 25762418

  5. Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform.
    Chen, R., Im, H. and Snyder, M.
    (2015). Cold Spring Harb Protoc 2015(7): 626-633. PubMed PMID: 25762417

  6. Evaluating Common Humoral Responses against Fungal Infections with Yeast Protein Microarrays.
    Coelho, P. S., Im, H., Clemons, K. V., Snyder, M. P. and Stevens, D. A.
    (2015). "Evaluating Common Humoral Responses against Fungal Infections with Yeast Protein Microarrays." J Proteome Res 14(9): 3924-3931. PubMed PMID: 26258609.

  7. Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry.
    Contrepois, K., Jiang, L. and Snyder, M.
    (2015). Mol Cell Proteomics 14(6): 1684-1695. PubMed PMID: 25787789

  8. Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data
    Dewey, F. E., Grove, M. E., Priest, J. R., Waggott, D., Batra, P., Miller, C. L., Wheeler, M., Zia, A., Pan, C., Karzcewski, K. J., Miyake, C., Whirl-Carrillo, M., Klein, T. E., Datta, S., Altman, R. B., Snyder, M., Quertermous, T. and Ashley, E. A.
    (2015).PLoS Genet 11(10): e1005496. PubMed PMID: 26448358

  9. Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
    Fasolo, J., Im, H. and Snyder, M. P.
    ( 2015). J Vis Exp(102): e51872. PubMed PMID: 26274875.

  10. Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis
    Fotiou, E., Martin-Almedina, S., Simpson, M. A., Lin, S., Gordon, K., Brice, G., Atton, G., Jeffery, I., Rees, D. C., Mignot, C., Vogt, J., Homfray, T., Snyder, M. P., Rockson, S. G., Jeffery, S., Mortimer, P. S., Mansour, S. and Ostergaard, P.
    (2015). Nat Commun 6: 8085. PubMed PMID: 26333996

  11. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions
    Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., Heidari, N., Euskirchen, G., Huber, W., Pritchard, J. K., Bustamante, C. D., Steinmetz, L. M., Kundaje, A. and Snyder, M.
    (2015). Cell 162(5): 1051-1065. PubMed PMID: 26300125; PubMed Central PMCID: PMCPMC4556133.

  12. Transglutaminase 4 as a prostate autoantigen in male subfertility
    Landegren, N., Sharon, D., Shum, A. K., Khan, I. S., Fasano, K. J., Hallgren, A., Kampf, C., Freyhult, E., Ardesjo-Lundgren, B., Alimohammadi, M., Rathsman, S., Ludvigsson, J. F., Lundh, D., Motrich, R., Rivero, V., Fong, L., Giwercman, A., Gustafsson, J., Perheentupa, J., Husebye, E. S., Anderson, M. S., Snyder, M. and Kampe, O.
    (2015). Sci Transl Med 7(292): 292ra101. PubMed PMID: 26084804.

  13. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development
    Lardenois, A., Stuparevic, I., Liu, Y., Law, M. J., Becker, E., Smagulova, F., Waern, K., Guilleux, M. H., Horecka, J., Chu, A., Kervarrec, C., Strich, R., Snyder, M., Davis, R. W., Steinmetz, L. M. and Primig, M.
    (2015). Nucleic Acids Res 43(1): 115-128. PubMed PMID: 25477386; PubMed Central PMCID: PMCPMC4288150.

  14. Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders
    Li, J., Ma, Z., Shi, M., Malty, R. H., Aoki, H., Minic, Z., Phanse, S., Jin, K., Wall, D. P., Zhang, Z., Urban, A. E., Hallmayer, J., Babu, M. and Snyder, M.
    (2015). Cell Syst 1(5): 361-374. PubMed PMID: 26949739; PubMed Central PMCID: PMCPMC4776331.

  15. Exome Sequencing of Neonatal Blood Spots and the Identification of Genes Implicated in Bronchopulmonary Dysplasia
    Li, J., Yu, K. H., Oehlert, J., Jeliffe-Pawlowski, L. L., Gould, J. B., Stevenson, D. K., Snyder, M., Shaw, G. M. and O'Brodovich, H. M. (2015).Am J Respir Crit Care Med 192(5): 589-596. PubMed PMID: 26030808; PubMed Central PMCID: PMCPMC4595691.

  16. Metformin Improves Diabetic Bone Health by Re-Balancing Catabolism and Nitrogen Disposal
    Li, X., Guo, Y., Yan, W., Snyder, M. P. and Li, X.
    (2015).PLoS One 10(12): e0146152. PubMed PMID: 26716870; PubMed Central PMCID: PMCPMC4696809.

  17. Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution
    "Lin, H., Chen, M., Kundaje, A., Valouev, A., Yin, H., Liu, N., Neuenkirchen, N., Zhong, M. and Snyder, M.
    (2015). Dev Cell 32(6): 772-774. PubMed PMID: 25805139; PubMed Central PMCID: PMCPMC4472434.

  18. Metabolome progression during early gut microbial colonization of gnotobiotic mice.
    Marcobal, A., Yusufaly, T., Higginbottom, S., Snyder, M., Sonnenburg, J. L. and Mias, G. I.
    (2015). Sci Rep 5: 11589. PubMed PMID: 26118551; PubMed Central PMCID: PMCPMC4484351.

  19. Recurrent somatic mutations in regulatory regions of human cancer genomes.
    Melton, C., Reuter, J. A., Spacek, D. V. and Snyder, M.
    (2015). Nat Genet 47(7): 710-716. PubMed PMID: 26053494; PubMed Central PMCID: PMCPMC4485503.

  20. Achieving high-sensitivity for clinical applications using augmented exome sequencing
    Patwardhan, A., Harris, J., Leng, N., Bartha, G., Church, D. M., Luo, S., Haudenschild, C., Pratt, M., Zook, J., Salit, M., Tirch, J., Morra, M., Chervitz, S., Li, M., Clark, M., Garcia, S., Chandratillake, G., Kirk, S., Ashley, E., Snyder, M., Altman, R., Bustamante, C., Butte, A. J., West, J. and Chen, R.
    (2015) Genome Med 7: 71. PubMed PMID: 26269718; PubMed Central PMCID: PMCPMC4534066.

  21. Mango: a bias-correcting ChIA-PET analysis pipeline.
    Phanstiel, D. H., Boyle, A. P., Heidari, N. and Snyder, M. P.
    (2015).Bioinformatics 31(19): 3092-3098. PubMed PMID: 26034063; PubMed Central PMCID: PMCPMC4592333.

  22. High-throughput sequencing technologies
    Reuter, J. A., Spacek, D. V. and Snyder, M. P.
    (2015). Mol Cell 58(4): 586-597. PubMed PMID: 26000844; PubMed Central PMCID: PMCPMC4494749.

  23. RNA Sequencing Analysis Detection of a Novel Pathway of Endothelial Dysfunction in Pulmonary Arterial Hypertension.
    Rhodes, C. J., Im, H., Cao, A., Hennigs, J. K., Wang, L., Sa, S., Chen, P. I., Nickel, N. P., Miyagawa, K., Hopper, R. K., Tojais, N. F., Li, C. G., Gu, M., Spiekerkoetter, E., Xian, Z., Chen, R., Zhao, M., Kaschwich, M., Del Rosario, P. A., Bernstein, D., Zamanian, R. T., Wu, J. C., Snyder, M. P. and Rabinovitch, M.
    (2015). Am J Respir Crit Care Med 192(3): 356-366. PubMed PMID: 26030479; PubMed Central PMCID: PMCPMC4584250.

  24. AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.
    Song, G., Dickins, B. J., Demeter, J., Engel, S., Gallagher, J., Choe, K., Dunn, B., Snyder, M. and Cherry, J. M.
    (2015).PLoS One 10(3): e0120671. PubMed PMID: 25781462; PubMed Central PMCID: PMCPMC4363492.

  25. Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming.
    Tanaka, Y., Hysolli, E., Su, J., Xiang, Y., Kim, K. Y., Zhong, M., Li, Y., Heydari, K., Euskirchen, G., Snyder, M. P., Pan, X., Weissman, S. M. and Park, I. H.
    (2015). Stem Cell Reports 4(6): 1125-1139. PubMed PMID: 26004630; PubMed Central PMCID: PMCPMC4471828.

  26. Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events.
    Tilgner, H., Jahanbani, F., Blauwkamp, T., Moshrefi, A., Jaeger, E., Chen, F., Harel, I., Bustamante, C. D., Rasmussen, M. and Snyder, M. P.
    (2015). Nat Biotechnol 33(7): 736-742. PubMed PMID: 25985263; PubMed Central PMCID: PMCPMC4832928.

  27. Characterization of novel transcripts in pseudorabies virus
    Tombacz, D., Csabai, Z., Olah, P., Havelda, Z., Sharon, D., Snyder, M. and Boldogkoi, Z.
    (2015).Viruses 7(5): 2727-2744. PubMed PMID: 26008709; PubMed Central PMCID: PMCPMC4452928.

  28. Where Next for Genetics and Genomics?
    Tyler-Smith, C., Yang, H., Landweber, L. F., Dunham, I., Knoppers, B. M., Donnelly, P., Mardis, E. R., Snyder, M. and McVean, G. (2015). PLoS Biol 13(7): e1002216. PubMed PMID: 26225775; PubMed Central PMCID: PMCPMC4520474.

  29. Genomic analysis of mycosis fungoides and Sezary syndrome identifies recurrent alterations in TNFR2.
    Ungewickell, A., Bhaduri, A., Rios, E., Reuter, J., Lee, C. S., Mah, A., Zehnder, A., Ohgami, R., Kulkarni, S., Armstrong, R., Weng, W. K., Gratzinger, D., Tavallaee, M., Rook, A., Snyder, M., Kim, Y. and Khavari, P. A.
    (2015)." Nat Genet 47(9): 1056-1060. PubMed PMID: 26258847.

  30. Impact of allele-specific peptides in proteome quantification.
    Wu, L. and Snyder, M.
    (2015). Proteomics Clin Appl 9(3-4): 432-436. PubMed PMID: 25676416; PubMed Central PMCID: PMCPMC4448739.

  31. Genomic analysis of fibrolamellar hepatocellular carcinoma.
    Xu, L., Hazard, F. K., Zmoos, A. F., Jahchan, N., Chaib, H., Garfin, P. M., Rangaswami, A., Snyder, M. P. and Sage, J.
    (2015).
    Hum Mol Genet 24(1): 50-63. PubMed PMID: 25122662; PubMed Central PMCID: PMCPMC4262492.

  32. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.
    Yan, J. F., Kim, H., Jeong, S. K., Lee, H. J., Sethi, M. K., Lee, L. Y., Beavis, R. C., Im, H., Snyder, M. P., Hofree, M., Ideker, T., Wu, S. L., Paik, Y. K., Fanayan, S. and Hancock, W. S.
    (2015). J Proteome Res 14(12): 4995-5006. PubMed PMID: 26435392.