51. Yablonovitch A, Deng P, Jacobson D, Li JB (2017) The evolution and adaptation of A-to-I RNA editing.  PLoS Genetics. 13(11):e1007064. doi: 10.1371/journal.pgen.1007064

50. Yablonovitch A, Fu J, Li K, Mahato S, Kang L, Rashkovestsky E, Korol AB, Tang H, Michalak P, Zelhof AC, Nevo E, Li JB (2017) Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates.  Nature Communications. 8(1):1570. doi: 10.1038/s41467-017-01658-2

49. Walkley CR, Li JB (2017) Rewriting the transcriptome: adenosine-to-inosine RNA editing by ADARs.  Genome Biology. 18(1):205

48. Tan MH*, Li Q*, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, GTEx Consortium, Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB (2017) Dynamic landscape and regulation of RNA editing in mammals.  Nature. 550(7675):249-254

47. Heraud-Farlow JE, Chalk AM, Linder SE, Li Q, Taylor S, White JM, Pang L, Liddicoat BJ, Gupte A, Li JB, Walkley CR. (2017) Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis.  Genome Biology. 2017 Sep 5;18(1):166

46. Lumb JH, Li Q, Popov LM, Ding S, Keith MT, Merrill BD, Greenberg HB, Li JB, Carette JE (2017) DDX6 Represses Aberrant Activation of Interferon-Stimulated Genes.  Cell Reports. 20(4):819-831

45. Gal-Mark N, Shallev L, Sweetat S, Barak M, Li JB, Levanon EY, Eisenberg E, Behar O (2017) Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition.  Scientific Reports. 2017 Mar 7;7:43421. doi: 10.1038/srep43421.

44. Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Ma RK, Caswell DR, Chiou SH, Winters AF, Grüner BM, Ramaswami G, Spencley AL, Kopecky KE, Sayles LC, Sweet-Cordero EA, Li JB, Kundaje A, Winslow MM (2017) Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis.  Nature Medicine. 23(3):291-300

43. Zhang R^, Deng P, Jacobson D, Li JB^. Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing (2017) .  PLoS Genetics. 2017 Feb 6;13(2):e1006563. doi: 10.1371/journal.pgen.1006563. [Highlighted in Science Vol 355, Issue 6331, "The evolution of edited RNA transcripts" by Laura Zahn]

42. Choi YJ, Lin CP, Risso D, Chen S, Kim TA, Tan MH, Li JB, Wu Y, Chen C, Xuan Z, Macfarlan T, Peng W, Lloyd KC, Kim SY, Speed TP, He L (2017) Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells. Science. 355(6325). pii: eaag1927.

2016

41. Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR (2016) Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis.  Experimental Hematology. 44(10):947-963

40. Ramaswami G, Li JB^ (2016) Identification of human RNA editing sites: A historical perspective.  Methods. 107:42-47

39. Reid CD, Karra K, Chang J, Piskol R, Li Q, Li JB, Cherry JM, Baker JC (2016) XenMine: A genomic interaction tool for the Xenopus community.  Developmental Biology. pii: S0012-1606(15)30264-5

38. George CX, Ramaswami G, Li JB, Samuel CE (2016) Editing of Cellular Self-RNAs by Adenosine Deaminase ADAR1 Suppresses Innate Immune Stress Responses.  Journal of Biological Chemistry. 291(12):6158-6168

37. Han L, Diao L, Yu S, Xu X, Li J, Zhang R, Yang Y, Werner HM, Eterovic AK, Yuan Y, Li J, Nair N, Minelli R, Tsang YH, Cheung LW, Jeong KJ, Roszik J, Ju Z, Woodman SE, Lu Y, Scott KL, Li JB, Mills GB, Liang H (2015) The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers.  Cancer Cell. 28(4):515-528

36. Ramaswami G*, Deng P*, Zhang R, Carbone MA, Mackay TF, Li JB^ (2015) Genetic mapping uncovers cis-regulatory landscape of RNA editing.  Nature Communications. 6:8194. doi: 10.1038/ncomms9194

35. Liddicoat B, Piskol R, Chalk A, Ramaswami G, Higuchi M, Hartner J, Li JB*, Seeburg PH*, Walkley C* (2015) RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as non-self.  Science, published online July 23 2015 [* equal contribution]

34. Sapiro AL, Deng P, Zhang R, Li JB^ (2015) Cis regulatory effects on A-to-I RNA editing in related Drosophila species.  Cell Reports, 11:697-703

33. Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang E, Karczewski K, Maller J, Kukurba KR, DeLuca D, Fromer M, Ferreira P, Smith KS, Zhang R, Zhao F, Banks E, Poplin R., Ruderfer D., Tukianen T, Stenson P, Cooper D, the GTEx Consortium, the Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG (2015) Impact of predicted protein-truncating genetic variants on the human transcriptome.  Science, 348:666-669

32. Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C; GTEx Consortium, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T (2015) The landscape of genomic imprinting across diverse adult human tissues.  Genome Research, pii: gr.192278.115. [Epub ahead of print]

31. Babak T, DeVeale E, Tsang E, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, Montgomery SB, Fraser HB (2015) Genetic conflict reflected in tissue-specific maps of genomic imprinting.  Nature Genetics, 47:544-549

30.Zheng M, Zhang H, Dill DL, Clark JD, Tu S, Yablonovitch AL, Tan MH, Zhang R, Rujescu D, Wu M, Tessarollo L, Vieira W, Gottesman MM, Deng S, Eberlin LS, Zare RN, Billard JM, Gillet JP, Li JB^, Peltz G^ (2015) The role of abcb5 alleles in susceptibility to haloperidol-induced toxicity in mice and humans.  PLoS Medicine, 12(2):e1001782

29. Satterlee JS, Basanta-Sanchez M, Blanco S, Li JB, Meyer K, Pollock J, Sadri-Vakili G, Rybak-Wolf A (2014) Novel RNA modifications in the nervous system: form and function.  Journal of Neuroscience, 34:15170-15177

28. Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB^, Ni JQ^ (2014) Enhanced Specificity and Efficiency of the CRISPR/Cas9 System with Optimized sgRNA Parameters in Drosophila.  Cell Reports, 9:1151-1162

27. Kukurba KR, Zhang R, Li X, Smith KS, Knowles DA, Tan MH, Piskol R, Lek M, Snyder M, MacArthur DG, Li JB^, Montgomery SB^ (2014) Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues.  PLoS Genetics, 10(5): e1004304. doi:10.1371/journal.pgen.1004304

26. Zhang R, Li X, Ramaswami G, Smith KS, Turecki G, Montgomery SB^, Li JB^ (2014) Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing. Nature Methods, 11:51-54

25. Bazak L, Haviv A, Barak M, Jacob-Hirsch J, Deng P, Zhang R, Isaacs FJ, Rechavi G, Li JB, Eisenberg E, Levanon EY (2013) A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.  Genome Research, 34:365-376

24. Ramaswami G^, Li JB^ (2014) RADAR: a rigorously annotated database of A-to-I RNA editing.  Nucleic Acids Research, 42: D109-D113. [RADAR website]

23. Li JB^, Church GM (2013) Deciphering the functions and regulation of brain-enriched A-to-I RNA editing.  Nature Neuroscience, 16:1518-1522

22. Piskol R, Ramaswami G, Li JB^ (2013) Reliable Identification of Genomic Variants from RNA-Seq Data.  American Journal of Human Genetics, 93:641-651 [Supporting documentation]

21. Ramaswami G*, Zhang R*, Piskol R, Keegan LP, Deng P, O'Connell MA, Li JB^ (2013) Identifying RNA editing sites using RNA sequencing data alone.  Nature Methods, 10:128-132

20. Piskol R*, Peng Z*, Wang J, Li JB^ (2013) Lack of evidence for existence of non-canonical RNA editing. Nature Biotechnology, 31:19-20

19.Tan MH*^, Au KF*, Yablonovitch AL*, Wills AE, Chuang J, Baker JC, Wong WH, Li JB^ (2013) RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.  Genome Research, 23:201-216

18. Bass B, Hundley H, Li JB, Peng Z, Pickrell, Xiao XG, Yang L (2012) The difficult calls in RNA editing.  Nature Biotechnology, 30:1207-1209

17. Eran A, Li JB, Vatalaro K, McCarthy J, Rahimov F, Collins C, Markianos K, Margulies DM, Brown EN, Calvo SE, Kohane IS, Kunkel LM (2012) Comparative RNA editing in autistic and neurotypical cerebella.  Molecular Psychiatry, August 7 2012 doi: 10.1038/mp.2012.118 [Epub ahead of print]

16. Sanjana NE^, Levanon EY^, Hueske EA, Ambrose JM, Li JB^ (2012) Activity-dependent A-to-I RNA Editing in Rat Cortical Neurons.  Genetics, 192:281-287 [Cover story]

15. Ramaswami G*, Lin W*, Piskol R*, Tan MH, Davis C, Li JB^ (2012) Accurate Identification of Human Alu and non-Alu RNA Editing Sites.  Nature Methods,9:579-581

14. Lin W*, Piskol R*, Tan MH, Li JB^ (2012) Comment on “Widespread RNA and DNA sequence differences in the human transcriptome”.  Science, 335:1302

13. Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT (2012). A versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.  Proc Natl Acad Sci USA, 109:21301-21306

12. Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM (2012) A public resource facilitating clinical use of genomes. Proc Natl Acad Sci USA, 109:11920-11927

11. Kosuri S*, Eroshenko N*, LeProust E, Super M, Way J, Li JB, Church GM (2010) A Scalable Gene Synthesis Platform Using High-Fidelity DNA Microchips.  Nature Biotechnology 28:1295-1299

10. Eisenberg E, Li JB, Levanon EY (2010) Sequence based identification of RNA editing sites. RNA Biology 7(2):248-252

9. Lee JH*, Park IH*, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM (2009) A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.   PLoS Genetics 5(11):e1000718

8.Li JB*, Levanon EY*, Yoon JK, Aach J, Xie B, LeProust E, Zhang K, Gao Y, Church GM (2009) Genome-wide identification of human RNA editing sites by massively parallel DNA capturing and sequencing.  Science 324:1210-1213

7. Zhang K*, Li JB*, Gao Y*, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM (2009) Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human.  Nature Methods 6:613-618

6. Li JB*^, Gao Y*, Aach J*, Zhang K*, Kryukov GV*, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM^ (2009) Multiplex padlock targeted sequencing reveal human hypermutable CpG variations.  Genome Research 19:1606-1615

5. Ball MP*, Li JB*^, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM^ (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.  Nature Biotechnology 27:361-368

4. Porreca GJ*, Zhang K*, Li JB, Leproust EM, Peck BJ, Vassallo S, Emig C, Gao Y, Church GM, Shendure J (2007) Multiplex amplification of large sets of human exons".  Nature Methods 4:931-936

3. Li JB*, Zhang M*, Dutcher SK, Stormo GD (2005) Procom: a web-based tool to compare multiple eukaryotic proteomes.  Bioinformatics 21:1693-1694

2. Li JB, Gerdes JM, Haycraft CJ, Fan Y, Teslovich TM, May-Simera H, Li H, Blacque OE, Li L, Leitch CC, Lewis RA, Green JS, Parfrey PS, Leroux MR, Davidson WS, Beales PL, Guay-Woodford LM, Yoder BK, Stormo GD, Katsanis N, Dutcher SK (2004) Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene.  Cell 117:541-552 [Cover story]

1. Li JB*, Lin S*, Jia H, Wu H, Roe BA, Kulp D, Stormo GD, Dutcher SK (2003) Analysis of Chlamydomonas reinhardtii genome structure using large-scale sequencing of regions on linkage groups I and III.  Journal of Eukaryotic Microbiology 50:145-155 ["Paper of the Year" Award]

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Book Chapters

1.Tan MH, Li JB (2013) Identification of RNA Editing Sites: a Survey of the Past, Present, and Future. In: RNA Editing: Current Research and Future Trends (ed. S. Maas), Horizon Press: Norwich.