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- 42. Chen, Y.G., Kim, M.V., Chen, X., Batista, P.J., Aoyama, S., Wilusz, J.E., Iwasaki, A., Chang, H.Y. (2017) Sensing self and foreign circular RNAs by intron identity. Molecular Cell, 67, 228-238. PMC5610545.
- 41. Cenik, C., Chua, H.N., Singh, G., Akef, A., Snyder, M.P., Palazzo, A.F., Moore, M.J., Roth, F.P. (2017) A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA. 23, 270-283. PMC5311483.
- 40. Chang, J., Mancuso, M.R., Maier, C., Liang, X., Yuki, K., Yang, L., Kwong, J.W., Wang, J., Rao, V., Vallon, M., Kosinski, C., Zhang, J.J.H., Mah, A.T., Xu, L., Li, L., Gholamin, S., Reyes, T.F., Li, R., Kuhnert, F., Han, X., Yuan, J., Chiou, S-H., Brettman, A.D., Daly, L., Corney, D.C., Cheshier, S.H., Shortliffe, L.D., Wu, X., Snyder, M., Chan, P., Giffard, R.G., Chang, H.Y., Andreasson, K., Kuo, C.J. (2017) Gpr124 is essential for blood-brain barrier integrity in CNS disease. Nature Medicine, 23, 450-460. PMC5559385.
- 39. Carter, A.C., Chang, H.Y., Church, G., Dombkowski, A., Ecker, J., Gil, E., Giresi, P.G., Greely, H., Greenleaf, W.J., Hacohen, N., He, C., Hill, D.E., Ko, J., Kohane, I.S., Kundaje, A., Palmer, M., Snyder, M., Tung, J., Urban, A.E., Vidal, M., Wong, W. (2017) Challenges and recommendations for epigenomics in precision health. Nature Biotechnology, 35, 1128-1132. PMC5821229.
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- 2016
- 38. Wang, Y., Jiang, R., Wong, W-H. (2016) Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data. National Science Review, 3, 240-51, PMC5501464.
- 37. Yu, K.H., Zhang, C., Berry, G.J., Altman, R.B., Ré, C., Rubin, D.L., Snyder, M. (2016) Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features. Nat. Commun., 7, 12474. PMC4990706.
- 36. Wang K., Lee C.S., Marinkovich M.P., Chang H.Y., Oro A.E., Khavari P.A. (2016). Factors That May Promote an Effective Local Research Environment. J. Invest Dermatol. 136, 1529-1531. PMC5873952.
- 35. Tombácz, D., Csabai, Z., Oláh, P., Balázs, Z., Likó, I., Zsigmond, L., Sharon, D., Snyder, M., Boldogkői, Z. (2016) Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus. PLoS One, 11, e0162868. PMC5042381.
- 34. Reuter, J.A., Spacek, D.V., Pai, R.K., Snyder, M.P. (2016) Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. Nat Methods, 13, 953-958. PMC5734913.
- 33. Quinn, J.J., Zhang, Q.C., Georgiev, P., Ilik, I.A., Akhtar, A., Chang, H.Y. (2016) Rapid evolutionary turnover underlies conserved lncRNA-genome interactions. Genes & Development, 30, 191-207. PMC4719309. Cover article. New York Times “Telling Jewels from Junk in DNA.”
- 32. Mumbach, M.R., Rubin, A.J., Flynn, R.A., Khavari, P.A., Greenleaf, W.J., Chang, H.Y. (2016) HiChIP: Efficient and sensitive analysis of protein-directed genome architecture. Nature Methods, 13, 919-922. PMC5501173.
- 31. Lu, Z., Zhang, Q.C., Lee, B., Flynn, R.A., Smith, M.A., Robinson, J., Davidovich, C., Gooding, A.R., Goodrich, K.J., Mattick, J., Mesirov, J.P., Cech, T.R., Chang, H.Y. (2016) RNA duplex map in living cells reveals higher order transcriptome structure. Cell, 165, 1267-79. PMC5029792.
- 30. Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S., Snyder, M. (2016) Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat. Biotechnol., 34, 64-9. PMC4884093.
- 29. Kuleshov, V., Snyder, M.P., Batzoglou, S. (2016) Genome assembly from synthetic long read clouds. Bioinformatics, 32, i216-i224. PMC4908351.
- 28. Huang, W-H., Guenthner, C.J., Xu, J., Nguyen, T., Wilkinson, A.W., Gozani, O., Chang, H.Y., Shamloo, M., Luo, L. (2016) Molecular and neural functions of Rai1, the causal gene for Smith-Magenis Syndrome. Neuron, 92, 392-406. PMC5098476.
- 27. Giorgetti, L., Lajoie, B.R., Carter, A.C.,* Attia, M., Zhan, Y., Xu, J., Chen, C.J., Kaplan, N., Chang, H.Y., Heard, E., Dekker, J. (2016) Structural organization of the inactive X chromosome in the mouse. Nature, 535, 575-9. PMC5443622.
- 26. Flynn, R.A., Do, B.T., Rubin, A.J., Calo, E., Lee, B., Kuchelmeister, H., Rale, M., Chu, C., Kool, E.T., Wysocka, J., Khavari, P.A., Chang, H.Y. (2016) 7SK-BAF axis controls pervasive transcription at enhancers. Nature Structural Molecular Biology, 23, 231-8. PMC4982704.
- 25. Denny, S.K., Yang, D., Chuang, C.H., Brady, J.J., Lim, J.S., Grüner, B.M., Chiou, S.H., Schep, A.N., Baral, J., Hamard, C., Antoine, M., Wislez, M., Kong, C.S., Connolly, A.J., Park, K.S., Sage, J., Greenleaf, W.J., Winslow, M.M. (2016) Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility. Cell, 166, 328-342. PMC5004630.
- 24. 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., Chang, H.Y. (2016) Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature Genetics, 48, 1193-203. PMC5042844.
- 23. Chen, X., Shen, Y., Draper, W., Buenrostro, J.D., Litzenburger, U., Cho, S-W., Satpathy, A., Ghosh, R.P., East-Seletsky A., Doudna, J.A., Greenleaf, W.J., Liphardt, J.T., Chang, H.Y. (2016) ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nature Methods, 13, 1013-1020. PMC5509561. Highlight in Nature Reviews Genetics, “See and seq the regulome”.
- 22. Atianand, M.K., Hu, W., Satpathy, A.T., Shen, Y., Ricci, E.P., Alvarez-Dominguez, J.R., Bhatta, A., McGowan, J., S.A. Schattgen, J. Blin, J.E. Braun, P. Gandhi, M.J. Moore, Chang HY, H.F. Lodish, D.R. Caffrey, and Fitzgerald, K.A. (2016) A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation. Cell, 165, 1672-1685. PMC5289747.
- 21. Lu Z, Chang HY. (2016). Decoding the RNA structurome. Curr Opin Struct Biol. 36, 142-8. PMC4785074.
- 20. Araya, C.L., Cenik, C., Reuter, J.A., Kiss, G., Pande, V.S., Snyder, M.P., Greenleaf, W.J. (2016) Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature Genetics, 48, 117-25. PMC4731297.
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- 2015
- 19. Tilgner, H., Jahanbani, F., Blauwkamp, T., Moshrefi, A., Jaeger, E., Chen, F., Harel, I., Bustamante, C., Rasmussen, M., Snyder, M. (2015) Comprehensive transcriptome analysis using synthetic long read sequencing reveals co-association of distant splicing events. Nature Biotech, 33, 736-42. PMC4832928.
- 18. Spitale, R.C., Flynn, R.A., Zhang, Q.C., Crisalli, P., Jung, J-W., Kuchelmeister, H.Y., Torre, E.A., Batista, P.J., Kool, E.T., Chang, H.Y. (2015) Structural imprints in vivo decode RNA regulatory mechanisms. Nature, 519, 486-90. PMC4376618.
- 17. Schep, A.N., Buenrostro, J.D., Denny, S.K., Schwartz, K., Sherlock, G., Greenleaf, W.J. (2015) Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. Genome Research, 25, 1757-70. PMC4617971.
- 16. Reuter, J.A., Spacek, D.V., Snyder, M.P. (2015) High-throughput sequencing technologies. Mol. Cell 58, 586-97. PMC4494749.
- 15. 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., Snyder M. (2015). Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell. 162, 1051-65. PMC4556133.
- 14. Qu, K., Zaba, L.C., Giresi, P.G., Li, R., Longmire, M., Kim, Y.H., Greenleaf, W.J., Chang, H.Y. (2015) Individuality and variation of personal regulomes in human T cells. Cell Systems, 1, 51-61. PMC4522940. Preview in Cell Systems. News coverage Stanford Medical Report “Women’s immune system genes operate differently from men’s”.
- 13. Phanstiel, D.H., Boyle, A.P., Heidari, N., Snyder, M.P. (2015) Mango: a bias-correcting ChIA-PET analysis pipeline. Bioinformatics, 31, 3092-8. PMC4592333.
- 12. Melton, C., Reuter, J.A., Spacek, D.V., Snyder, M. (2015) Recurrent somatic mutations in regulatory regions of human cancer genomes. Nat Genet., 47, 710-6. PMC4485503.
- 11. Mazumdar, C., Shen, Y., Xavy, S., Reinisch, A., Li, R., Zhao, F., Corces-Zimmerman, M.R., Buenrostro, J.D., Chan, S., Thomas, D., Koenig, J., Hong, W-J., Chang, H.Y., and Majeti, R. (2015) Leukemia-associated cohesin mutants dominantly enforce stem cell programs and impair human hematopoietic progenitor differentiation. Cell Stem Cell, 17, 675–688. PMC4671831.
- 10. Grow, E.J., Flynn, R.A., Chavez, S.L., Bayless, N.L., Wossidlo, M., Wesche, D., Martin, L., Ware, C., Blish, C., Chang, H.Y., Reijo Pera, R.A., Wysocka, J. (2015) Intrinsic retroviral reactivation in human pre-implantation development and pluripotent cells. Nature 522, 221-5. PMC4503379. New York Times “Ancient Viruses, Once Foes, May Now Serve as Friends.”
- 9. Chu, C., Zhang, Q.C., da Rocha, S.T., Flynn, R.A., Bharadwaj, M., Calabrese, J.M., Magnuson, T., Heard, E., Chang, H.Y. (2015) Systematic discovery of Xist RNA binding proteins. Cell, 161, 404-416. PMC4425988.
- 8. Cheloufi, S., Elling, U., Hopfgartner, B., Jung, Y., Murn, J., Badeaux, A., Blanco, A., Ang, C.E., Tenen, D., Ferrari, F., Wesche, D., Abazova, N., Hogue, M., Tasdemir, N., Rathert, P., Vidal, S., Fellner, M., Wenzel, D., Zinner, M., Stadtfeld, M., Chang, H.Y., Almouzni, G., Lowe, S.W., Rinn, J.L., Wernig, M., Shi, Y., Park, P., Penninger, J.M., Zuber, J., Hochedlinger, K. (2015) The histone chaperone CAF-1 safeguards somatic cell identity. (Article) Nature, 528, 218-224. PMC4866648.
- 7. Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. (2015). RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 518, 249-53. PMC4827702.
- 6. Buenrostro, J.D., Wu, B., Chang, H.Y., Greenleaf, W.J. (2015) ATAC-seq: A method for assaying chromatin accessibility genome-wide. Current Protocols in Molecular Biology, 109, 21.29.1-21.29.9. PMC4374986.
- 5. Buenrostro, J.D., Wu, B., Litzenburger, U.M., Ruff, D., Gonzales, M., Snyder, M.P., Chang, H.Y.,* Greenleaf, W.J.*. (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature, 523, 486-90. *corresponding authors. PMC4685948. Highlight in Nature Reviews Genetics, 2015; Nature Methods, 2015.
- 4. Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR. (2015). DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. 528, 517-22. PMC4762670.
- 3. Bao, X., Rubin, A.J., Qu, K., Zhang, J., Giresi, P.G., Chang, H.Y., Khavari, P.A. (2015) A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biology, 16, 284. PMC4699366.
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- 2014
- 2. Esplin, E.D., Oei, L., Snyder, M.P. (2014) Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Pharmacogenomics, 15, 1771-1790. PMC4336568.
- 1. Li, J., Shi, M., Ma, Z., Zhao, S., Euskirchen, G., Ziskin, J., Urban, A., Hallmayer, J., Snyder, M. (2014) Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol. Syst. Biol. 10, 774. PMC4300495.
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