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  1. Lister R, Gregory BD and Ecker JR. (2009) Next is now: new technologies for sequencing of genomes transcriptomes and beyond. Curr Opin Plant Biol. 2009 Apr;12(2):107-18.
    Article
  2. Lister R. and Ecker JR. (2009) Finding the fifth base: Genome-wide sequencing of cytosine Genome Res. 2009 Mar 9.
    Article
  3. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo LQ, Edsall LE, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B and Ecker JR. (2009) Human DNA methylomes at base resolution show widespread epigenomic difference. Nature. 20 Nov 19;462:315-322.
    Article                 Data
  4. Smith AD, Chung W, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z and MQ Zhang. (2009) Updates to the rmap short-read mapping software. Bioinformatics, 25(21):2841–2, N 2009.
    Article
  5. Hon GC, Wang W and Ren B (2009) Discovery and Annotation of Functional Chromatin Signatures in the Human Genome. PLoS Comput Biol, 2009, 5(11): e1000566.
    Article
  6. Hon GC, Hawkins RD and Ren B. (2009) Predictive chromatin signatures in the mammalian genome. Hum Mol Genet. 2009 Oct 15;18(R2):R195-201.
    Article
  7. Heintzman ND and Ren B. (2009) Finding distal regulatory elements in the human genome. Curr Opin Genet Dev. 2009 Oct 23.
    Article
  8. Won KJ, Ren B and Wang W. (2010) Genome-wide prediction of transcription factor binding sites using an integrated model. Genome Biology, 2010 Jan 22;11(1):R7.
    Article
  9. Hawkins R, Hon G, Lee L, Ngo Q, Lister R, Pelizzola M, Kuan S, Edsall L, Ye Z, Espinoza C, Antosiewicz-Bourget J, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson J, Ecker J, Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cell.w Cell Stem Cell, 7;6(5):479-91.
    Article
  10. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS and Thomson JA. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 28:1045-1048.
    Article
  11. Chen G, Hou Z, Gulbranson DR and Thomson JA. (2010) Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells. Cell Stem Cell. 2010 Aug 6;7(2):240-8.
    Article
  12. Chen G, Gulbranson DR, Hou Z, Bolin JM, Ruotti V, Probasco MD, Smuga-Otto K, Howden SE, Diol NR, Propson NE, Wagner R, Lee GO, Antosiewicz-Bourget J, Teng JM and Thomson JA. (2011) Chemically defined conditions for human iPSC derivation and culture. Nat Methods. 2011 Apr 10.
    Article
  13. Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD and Lieb JD (2011). An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan;18(1):91-3.
    Article
  14. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A and Costello JF. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct;28(10):1097-105.
    Article
  15. Hawkins RD, Hon GC and Ren B. (2010) Next-generation genomics: an integrative approach. Nat Rev Genet. 2010 Jul;11(7):476-86.
    Article
  16. Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM and Ecker JR. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011 Mar 3;471(7336):68-73.
    Article
  17. Pelizzola M and Ecker JR. (2011) The DNA methylome. FEBS Lett. 2011 Jul 7;585(13):1994-2000.
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  18. Shoemaker R, Wang W and Zhang K. (2011) Mediators and dynamics of DNA methylation. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2011, 3, 281-298.
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  19. Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, and Zhao Y (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146(6):1016-28.
    Article
  20. Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA and Ren B. (2011) Dynamic Chromatin States in Human ES Cells Reveal Potential Regulatory Sequences and Genes Involved in Pluripotency. Cell Research 21(10):1393-409.
    Article
  21. Chang R, Shoemaker R and Wang W. (2011) Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells. Plos Computational Biology, 2011, 7, 12, e1002300.
    Article
  22. Chang R, Shoemaker R and Wang W. (2011) A novel knowledge-driven systems biology approach for phenotype prediction upon genetic intervention. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8, 1170-1182.
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  23. Ding S and Wang W. (2011) Recipes and mechanisms of cellular reprogramming: a case study on budding yeast Saccharomyces cerevisiae. BMC System Biology, 2011, 5:50
    Article
  24. Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL and Ren B. (2012) Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell. 148(4):816-31.
    Article
  25. Yu M, Hon GC, Szulwach KE, Song C, Zhang L, Kim A, Li X, Dai Q, Park B, Min JH, Jin P, Ren B and He C. (2012). Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell, 149(6):1368-80. Epub 2012 May 17.
    Article
  26. Chen G, Gulbranson DR, Yu P, Hou Z and Thomson JA. (2012) Thermal stability of fibroblast growth factor protein is a determinant factor in regulating self-renewal, differentiation, and reprogramming in human pluripotent stem cells. Stem Cells, 30(4):623-30.
    Article
  27. Won KJ, Xu Z, Zhang X, Whitaker JW, Shoemaker R, Ren B, Xu Y and Wang W. (2012) Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells. Nucleic Acids Res. 40(17):8199-8209.
    Article
  28. Liu GH, Qu J, Suzuki K, Nivet E, Li M, Montserrat N, Yi F, Xu X, Ruiz S, Zhang W, Wagner U, Kim A, Ren B, Li Y, Goebl A, Kim J, Soligalla RD, Dubova I, Thompson J, Yates J 3rd, Esteban CR, Sancho-Martinez I and Izpisua Belmonte JC. (2012) Progressive degeneration of human neural stem cells caused by pathogenic LRRK2. Nature. 491(7425):603-7. doi: 10.1038/nature11557.
    Article