Publications
2022
1. Yuliang Feng, Ping Wang, Liuyang Cai, Meixiao Zhan, Fan He, Jiahui Wang, Yong Li, Eva Gega, Wei Zhang, Wei Zhao, Yongjie Xin, Xudong Chen, Yijun Ruan, and Ligong Lu (2022). 3D-Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma. Advanced Genetics 2022, 2100010. DOI:10.1002/ggn2.202100010
2021
2. Ping Wang, Yuliang Feng, Kun Zhu, Haoxi Chai, Ya-ting Chang, Xiaofei Yang, Xiyuan Liu,1,7 Chen Shen, Eva Gega, Byoungkoo Lee, Minji Kim, Xiaoan Ruan, and Yijun Ruan (2021). In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing. Current Protocols. E174, Volume 1. DOI: 10.1002/cpz1.174
2020
3. Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei CL, Ruan Y, Li S. (2020). ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. Sci Adv. PMID: 32832596.
4. Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Ruan Y, Yue F. (2020) A supervised learning framework for chromatin loop detection in genome-wide contact maps. Nat Commun. PMID: 32647330.
5. Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D. (2020). 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. Nucleic Acids Res. PMID: 32442297.
6. Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. (2020). Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. Genome Biol. PMID: 32393309.
7. Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Śliwińska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczyński GM. (2020). Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. Nat Commun. PMID: 32358536.
8. Luo H, Yu Q, Liu Y, Tang M, Liang M, Zhang D, Xiao TS, Wu L, Tan M, Ruan Y, Bungert J, Lu J. (2020). LATS kinase-mediated CTCF phosphorylation and selective loss of genomic binding. Sci Adv. PMID: 32128389.
9. Ashoor H, Chen X, Rosikiewicz W, Wang J, Cheng A, Wang P, Ruan Y, Li S. (2020). Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data. Nat Commun. PMID: 32127534.
10. Higashijima Y, Matsui Y, Shimamura T, Nakaki R, Nagai N, Tsutsumi S, Abe Y, Link VM, Osaka M, Yoshida M, Watanabe R, Tanaka T, Taguchi A, Miura M, Ruan X, Li G, Inoue T, Nangaku M, Kimura H, Furukawa T, Aburatani H, Wada Y, Ruan Y, Glass CK, Kanki Y. (2020). Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells. EMBO J. PMID: 32125007.
11. Zhang HB, Kim M, Chuang JH, Ruan Y. (2020). pyBedGraph: a python package for fast operations on 1D genomic signal tracks. Bioinformatics. PMID: 32044918
12. Capurso D, Tang Z, Ruan Y. Methods for comparative ChIA-PET and Hi-C data analysis. Methods. PMID: 31629084.
2019
13. Simon Zhongyuan Tian, Daniel Capurso, Minji Kim, Byoungkoo Lee, Meizhen Zheng, Yijun Ruan (2019). ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions.BioRxiv doi: https://doi.org/10.1101/613034
14. Kim M, Zheng M, Tian SZ, Lee B, Chuang J, and Ruan Y (2019). MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms. Genome Biology. PMID: 31767038.
15. Michal Sadowski, Agnieszka Kraft, Przemyslaw Szalaj, Michal Wlasnowolski, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski (2019). Spatial chromatin architecture alteration by structural variations in human genomes at the population scale. Genome Biology. PMID: 31362752.
16. Zheng M, Tian SZ, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu JJ, Li Z, Wong CH, Ngan CY, Wang P, Ruan X, Wei CL, Ruan Y (2019). Multiplex chromatin interactions with single-molecule precision. Nature. 2019 Feb;566(7745):558-562. doi: 10.1038/s41586-019-0949-1. Epub 2019 Feb 18. PMID: 30778195.
17. Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, Piecuch E, Luo O, Chines PS, Fuchbserger C; NIH Intramural Sequencing Center, Sethupathy P, Aiden AP, Ruan Y, Aiden EL, Collins FS, Ucar D, Parker SCJ, Stitzel ML (2019). Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function. Cell Rep. 2019 Jan 15;26(3):788-801.e6. doi: 10.1016/j.celrep.2018.12.083. PMID: 30650367
18. Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E (2019). An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. Genome Res. PMID: 30606742
2018
19. Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R (2018). The Energetics and Physiological Impact of Cohesin Extrusion. Cell. PMID: 30241609
20. Menghi F, Barthel FP, Yadav V, Tang M, Ji B, Tang Z, Carter GW, Ruan Y, Scully R, Verhaak RGW, Jonkers J, Liu ET (2018). The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. Cancer Cell. PMID: 30017478
21. Buisine N, Ruan X, Ruan Y, Sachs LM. (2018). Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues. Cold Spring Harbor Protocols. PMID: 29895565
22. Buisine N, Ruan X, Ruan Y, Sachs LM. Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues (2018). Cold Spring Harbor Protocols. PMID: 29895563
23. Lin D, Hong P, Zhang S, Xu W, Jamal M, Yan K, Lei Y, Li L, Ruan Y, Fu ZF, Li G, Cao G (2018).
Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature Genetics. 2018; 50(5):754-763. PMID: 29700467
2017
24. Li P, Mitra S, Spolski R, Oh J, Liao W, Tang Z, Mo F, Li X, West EE, Gromer D, Lin JX, Liu C, Ruan Y, Leonard WJ (2017). STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus. Proceedings of the National Academy of Sciences of the United States of America. PMID: 29078395; PMCID: PMC5699083
25. Rowley MJ, Nichols MH, Lyu X, Ando-Kuri M, Rivera ISM, Hermetz K, Wang P, Ruan Y, Corces VG (2017). Evolutionarily Conserved Principles Predict 3D Chromatin Organization. Molecular cell. PMID: 28826674 PMCID: PMC5591081
26. Li Z, Zhang P, Yan A, Guo Z, Ban Y, Li J, Chen S, Yang H, He Y, Li J, Guo Y, Zhang W, Hajiramezanali E, An H, Fajardo D, Harbour JW, Ruan Y, Nimer SD, Yu P, Chen X, Xu M, Yang FC (2017). ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis.Sci Adv. PMID: 28116354.
27. Li X, Luo OJ, Wang P, Zheng M, Wang D, Piecuch E, Zhu JJ, Tian SZ, Tang Z, Li G, Ruan Y.Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions.
Nature Protocols. PMID: 28358394.
2016
28. Szalaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D. 2016. An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Genome Res. 2016 Dec;26(12):1697-1709
29. Szalaj P, Michalski PJ, Wroblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczynski D. (2016). 3D-GNOME: an integrated web service for structural modeling of the 3D genome. Nucleic Acids Res. 2016 Jul 8;44(W1):W288-93.
30. Thibodeau A, Marquez EJ, Luo O, Ruan Y, Menghi F, Shin DG, Stitzel ML, Vera-Licona P, Ucar D. (2016). QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol. 2016 Jun 23;12(6):e1004809
31. Ricaño-Ponce I, Zhernakova DV, Deelen P, Luo O, Li X, Isaacs A, Karjalainen J, Di Tommaso J, Borek ZA, Zorro MM, Gutierrez-Achury J, Uitterlinden AG, Hofman A, van Meurs J; BIOS Consortium; Lifelines Cohort Study, Netea MG, Jonkers IH, Withoff S, van Duijn CM, Li Y, Ruan Y, Franke L, Wijmenga C, Kumar V. (2016). Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs. J Autoimmun. 2016 Apr;68:62-74.
2015
32. Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei C-L, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y. (2015). CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell. 2015 Dec 17;163(7): 1611–1627
33. Yao F, Kausalya JP, Sia YY, Teo AS, Lee WH, Ong AG, Zhang Z, Tan JH, Li G, Bertrand D, Liu X, Poh HM, Guan P, Zhu F, Pathiraja TN, Ariyaratne PN, Rao J, Woo XY, Cai S, Mulawadi FH, Poh WT, Veeravalli L, Chan CS, Lim SS, Leong ST, Neo SC, Choi PS, Chew EG, Nagarajan N, Jacques PÉ, So JB, Ruan X, Yeoh KG, Tan P, Sung WK, Hunziker W, Ruan Y, Hillmer AM. (2015). Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.Cell Rep. 2015 Jul 14;12(2):272-85.
34. Vahedi G, Kanno Y, Furumoto Y, Jiang K, Parker SC, Erdos MR, Davis SR, Roychoudhuri R, Restifo NP, Gadina M, Tang Z, Ruan Y, Collins FS, Sartorelli V, O'Shea JJ. (2015). Super-enhancers delineate disease-associated regulatory nodes in T cells.Nature. 2015 Apr 23;520(7548):558-62. Epub 2015 Feb 16.
35. Yuan D, Tang Z, Wang M, Gao W, Tu L, Jin X, Chen L, He Y, Zhang L, Zhu L, Li Y, Liang Q, Lin Z, Yang X, Liu N, Jin S, Lei Y, Ding Y, Li G, Ruan X, Ruan Y, Zhang X. (2015). The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Sci Rep. 2015 Dec 4;5:17662. doi: 10.1038/srep17662. PMID: 26634818
36. Kuznetsova T, Wang SY, Rao NA, Mandoli A, Martens JH, Rother N, Aartse A, Groh L, Janssen-Megens EM, Li G, Ruan Y, Logie C, Stunnenberg HG. (2015). Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization. Genome Biol. 2015 Dec 1;16:264. doi: 10.1186/s13059-015-0832-9. PMID: 26619937
37. Buisine N, Ruan X, Bilesimo P, Grimaldi A, Alfama G, Ariyaratne P, Mulawadi F, Chen J, Sung WK, Liu ET, Demeneix BA, Ruan Y, Sachs LM. (2015). Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis. PLoS One. 2015 Sep 8;10(9):e0137526. doi: 10.1371/journal.pone.0137526. eCollection 2015. PMID: 26348928
38. Bagamasbad PD, Bonett RM, Sachs L, Buisine N, Raj S, Knoedler JR, Kyono Y, Ruan Y, Ruan X, Denver RJ. (2015). Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module. Mol Endocrinol. 2015 Jun;29(6):856-72. doi: 10.1210/me.2014-1349. Epub 2015 Apr 13. PMID: 25866873
39. Xiao, JH., Wu, CY., Yuan, M., Wang N., Fan, YR., Yang, M., Ouyang, Y., Ruan, Y., Zhang, Q. (2015). The progress and perspective of rice functional genomics research in China. Chinese Science Bulletin (科学通报), Volume 60, Issue 18: Pages 1711-1722 (2015). doi.org/10.1360/N972015-00391
40.
2014
41. Li G, Cai L, Chang H, Hong P, Zhou Q, Kulakova EV, Kolchanov NA, Ruan Y. (2014). Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application. BMC Genomics. 2014;15 Suppl 12:S11. doi: 10.1186/1471-2164-15-S12-S11. Epub 2014 Dec 19. PMID: 25563301
42. Li, G., Ruan, Y., Gu, R., Du, S. (2014) Emergence of 3D genomics. Chinese Journal (科学通报) 59(13):1165. DOI:10.1360/N972014-00163.
43. Peng, C., Li, G. Zhang, H-Y, Ruan, Y. (2014) Reconstruction of Three-Dimensional Structures of Chromatin and Its Biological Implications. Scientia Sinica Vitae (中国科学) 44(8):794. DOI:10.1360/052014-108
44. Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, Liang G, Tang Z, Mathé E, Benner C, Dubois W, Nelson S, Vian L, Oliveira TY, Jankovic M, Hakim O, Gazumyan A, Pavri R, Awasthi P, Song B, Liu G, Chen L, Zhu S, Feigenbaum L, Staudt L, Murre C, Ruan Y, Robbiani DF, Pan-Hammarström Q, Nussenzweig MC, Casellas R. (2014). B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity. Cell. 2014 Dec 18;159(7):1524-37.
45. Jiang Z, Sun J, Dong H, Luo O, Zheng X, Obergfell C, Tang Y, Bi J, O'Neill R, Ruan Y, Chen J, Tian XC. (2014). Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics. 2014 Sep 4;15:756. doi: 10.1186/1471-2164-15-756.
46. Maejima T, Inoue T, Kanki Y, Kohro T, Li G, Ohta Y, Kimura H, Kobayashi M, Taguchi A, Tsutsumi S, Iwanari H, Yamamoto S, Aruga H, Dong S, Stevens JF, Poh HM, Yamamoto K, Kawamura T, Mimura I, Suehiro J, Sugiyama A, Kaneki K, Shibata H, Yoshinaka Y, Doi T, Asanuma A, Tanabe S, Tanaka T, Minami T, Hamakubo T, Sakai J, Nozaki N, Aburatani H, Nangaku M, Ruan X, Tanabe H, Ruan Y, Ihara S, Endo A, Kodama T, Wada Y. (2014). Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells. PLoS One. 2014;9(6):e99749.
47. Inoue T, Kohro T, Tanaka T, Kanki Y, Li G, Poh HM, Mimura I, Kobayashi M, Taguchi A, Maejima T, Suehiro J, Sugiyama A, Kaneki K, Aruga H, Dong S, Stevens JF, Yamamoto S, Tsutsumi S, Fujita T, Ruan X, Aburatani H, Nangaku M, Ruan Y, Kodama T, Wada Y. (2014). Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements. Genome Biol. 10;15(4):R63.
48. Utami KH, Hillmer AM, Aksoy I, Chew EG, Teo AS, Zhang Z, Lee CW, Chen PJ, Seng CC, Ariyaratne PN, Rouam SL, Soo LS, Yousoof S, Prokudin I, Peters G, Collins F, Wilson M, Kakakios A, Haddad G, Menuet A, Perche O, Tay SK, Sung KW, Ruan X, Ruan Y, Liu ET, Briault S, Jamieson RV, Davila S, Cacheux V. (2014). Detection of chromosomal breakpoints in patients with developmental delay and speech disorders. PLoS One. 6;9(6):e90852.
49. Chen D, Fu LY, Zhang Z, Li G, Zhang H, Jiang L, Harrison AP, Shanahan HP, Klukas C, Zhang HY, Ruan Y, Chen LL, Chen M. (2014). Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res. 42(5):3028-43.
2013
50. Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. (2013). Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell. 155(7):1507-20.
51. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL. (2013). Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 504(7479):306-10. doi: 10.1038/nature12716.
52. Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA. (2013). DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nature Genetics. 45(8):852-9. doi: 10.1038/ng.2677. Epub 2013 Jun 23.
53. Wang X, Zhao Z, Muller J, Iyu A, Khng AJ, Guccione E, Ruan Y, Ingham PW. (2013) Targeted inactivation and identification of targets of the Gli2a transcription factor in the zebrafish. Biol Open. 2(11):1203-13.
2012
54. Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Tean Teh B, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y*. (2012) Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biol. 13(12):R115. [Epub ahead of print]
55. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y* (2012) The draft genome of sweet orange (Citrus sinensis). Nature Genetics. 45(1):59-66
56. Papantonis A, Kohro T, Baboo S, Larkin JD, Deng B, Short P, Tsutsumi S, Taylor S, Kanki Y, Kobayashi M, Li G, Poh HM, Ruan X, Aburatani H, Ruan Y, Kodama T, Wada Y, Cook PR. (2012) TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed. EMBO J. 31(23):4404-14. doi: 10.1038/emboj.2012.288. Epub 2012 Oct 26.
57. Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fullwood MJ, Liu E, Csermely P, Ruan Y* (2012) Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks. Cell Reports 2012 Oct 24. pii: S2211-1247(12)00326-9. doi: 10.1016/j.celrep.2012.09.022. [Epub ahead of print]
58. Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK. (2012) BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol. 13(10): R82.
59. Yao F, Ariyaratne PN, Hillmer AM, Lee WH, Li G, Teo AS, Woo XY, Zhang Z, Chen JP, Poh WT, Zawack KF, Chan CS, Leong ST, Neo SC, Choi PS, Gao S, Nagarajan N, Thoreau H, Shahab A, Ruan X, Cacheux-Rataboul V, Wei CL, Bourque G, Sung WK, Liu ET, Ruan Y* (2012) Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS One. 7(9): e46152. doi: 10.1371/journal.pone.0046152.
60. Ohta Y, Nishiyama A, Wada Y, Ruan Y, Kodama T, Tsuboi T, Tokihiro T, Ihara S. (2012) Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells. Phys Rev E Stat Nonlin Soft Matter Phys. 86(2 Pt 1): 021918. Epub 2012 Aug 21.
61. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111.
62. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. Genome Res. 2012 Sep;22(9):1658-67. doi: 10.1101/gr.136838.111.
63. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. (2012) Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.
64. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.
65. Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y* (2012). ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25.
66. Goh Y, Fullwood MJ, Poh HM, Peh SQ, Ong CT, Zhang J, Ruan X, Ruan Y*. (2012) Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation. J Vis Exp. 2012 Apr 30;(62). pii: 3770. doi: 10.3791/3770.
67. Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS. (2012) Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.
68. Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, Rajasegaran V, Heng HL, Deng N, Gan A, Lim KH, Ong CK, Huang D, Chin SY, Tan IB, Ng CC, Yu W, Wu Y, Lee M, Wu J, Poh D, Wan WK, Rha SY, So J, Salto-Tellez M, Yeoh KG, Wong WK, Zhu YJ, Futreal PA, Pang B, Ruan Y, Hillmer AM, Bertrand D, Nagarajan N, Rozen S, Teh BT, Tan P. (2012) Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nature Genetics. 2012 May;44(5):570-4. doi: 10.1038/ng.2246.
69. Ng KP, Hillmer AM, Chuah CT, Juan WC, Ko TK, Teo AS, Ariyaratne PN, Takahashi N, Sawada K, Fei Y, Soh S, Lee WH, Huang JW, Allen JC Jr, Woo XY, Nagarajan N, Kumar V, Thalamuthu A, Poh WT, Ang AL, Mya HT, How GF, Yang LY, Koh LP, Chowbay B, Chang CT, Nadarajan VS, Chng WJ, Than H, Lim LC, Goh YT, Zhang S, Poh D, Tan P, Seet JE, Ang MK, Chau NM, Ng QS, Tan DS, Soda M, Isobe K, Nöthen MM, Wong TY, Shahab A, Ruan X, Cacheux-Rataboul V, Sung WK, Tan EH, Yatabe Y, Mano H, Soo RA, Chin TM, Lim WT, Ruan Y*, Ong ST*. (2012) A common BCL2L11 deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nature Medicine 18(4): 521-528
70. Guoliang Li, Xiaoan Ruan, Raymond K. Auerbach, Kuljeet Singh Sandhu, Meizhen Zheng, Ping Wang, Huay Mei Poh, Yufen Goh, Joanne Lim, Jingyao Zhang, Hui Shan Sim, Su Qin Peh, Fabianus Hendriyan Mulawadi, Chin Thing Ong, Yuriy L. Orlov, Shuzhen Hong, Zhizhuo Zhang, Steve Landt, Debasish Raha, Ghia Euskirchen, Chia-Lin Wei, Weihong Ge, Huaien Wang, Carrie Davis, Katherine Fisher, Ali Mortazavi, Mark Gerstein, Thomas Gingeras, Barbara Wold, Yi Sun, Melissa J. Fullwood, Edwin Cheung, Edison Liu, Wing-Kin Sung, Michael Snyder, Yijun Ruan* (2012) Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell 148: 84-98
71. Ruan X, Ruan Y. (2012) Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. doi: 10.1007/978-1-61779-376-9_35.
2011
72. Lusy Handoko, Han Xu, Guoliang Li, Chew Yee Ngan, Elaine Chew, Charlie Wah Heng Lee, Chaopeng Ye, Eleanor Wong, Yubo Zhang, Fabianus Mulawadi, Jianpeng Sheng, Thompson Poh, Chee Seng Chan, Galih Kunarso, Atif Shahab, Guillaume Bourque, Valere Cacheux-Rataboul, Wing-Kin Sung, Yijun Ruan*, Chia-Lin Wei* (2011) Functional Genome Architecture Revealed by CTCF-Associated Chromatin Interactome in Pluripotent Cells. Nature Genetics 43: 630–638 (June 19, 2011)
73. Ng TF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M. (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes PLoS One. 6(6):e20579. doi: 10.1371/journal.pone.0020579. Epub 2011 Jun 6.
74. ENCODE Project Consortium. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9(4): e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.
75. Kuljeet Singh Sandhu, Guoliang Li, Wing-Kin Sung, Yijun Ruan* (2011) Chromatin Interaction Networks and Higher Order Architectures of Eukaryotic Genomes (Prospects). Journal of Cellular Biochemistry 112, 2218-2221
76. Axel M. Hillmer, Yao Fei1, Koichiro Inaki, Wah Heng Lee, Pramila N. Ariyaratne, Audrey S.M. Teo, Xing Yi Woo, Zhenshui Zhang, Zhao Hao, Leena Ukil, Jieqi P. Chen, Zhu Feng, Jimmy B.Y. So, Manuel Salto-Tellez, Wan Ting Poh, Kelson F.B. Zawack, Hui Ping J. Lim, Yee Yen Sia, Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D. Choi, Hervé Thoreau, Patrick B.O. Tan, Atif Shahab, Xiaoan Ruan, Jonas Bergh, Per Hall, Valère Cacheux-Rataboul, Chia-Lin Wei, Khay Guan Yeoh, Wing-Kin Sung, Guillaume Bourque, Edison T. Liu, Yijun Ruan*(2011) Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. Genome Research 21 (5): 665-675 (May 01, 2011)
77. Koichiro Inaki, Axel Hillmer, Leena Ukil, Fei Yao, Xing Yi Woo, Leah Vardy, Kelson Folkvard Braaten Zawack, Charlie Wah Heng Lee, Pramila Nuwantha Ariyaratne, Yang Sun Chan, Kartiki Vasant Desai, Jonas Bergh, Per Hall, Thomas Choudary Putti, Wai Loon Ong, Atif Shahab, Valere Cacheux-Rataboul, Radha Krishna Murthy Karuturi, Wing-Kin Sung, Xiaoan Ruan, Guillaume Bourque, Yijun Ruan, Edison T. Liu. (2011) Transcriptional Consequences of Genomic Structural Aberrations in Breast Cancer. Genome Research 21 (5): 676-687 (May 01, 2011)
78. Yijun Ruan (2011) Genome-sequencing anniversary. Presenting the human genome: now in 3D! Science 2011 Feb 25; 331(6020): 1025-6. doi: 10.1126/science.1203602.
79. Edwin Cheung and Yijun Ruan* (2011) Determination of transcription factor binding. Nature Genetics 43: 11-12 (January 2011)
2010
80. Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, Pan YF, Li G, Lim M, Thomsen JS, Ruan Y, Clarke ND, Prabhakar S, Cheung E, Liu ET. (2010) Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol. 2010 Dec 21;6:456. doi: 10.1038/msb.2010.109.
81. Phillips Yao Hui Huang, Yuyuan Han, Lusy Handoko, Stoyan Velkov, Eleanor Wong, Edwin Cheung, Xiaoan Ruan, Chia-Lin Wei, Melissa Jane Fullwood*, Yijun Ruan*. (2011) Protocol: Sonication-based Circular Chromosome Conformation Capture with next generation sequencing analysis for the detection of chromatin interactions. Nature Protocols (December 14, 2010) doi:10.1038/protex.2010.207
82. Hao Wu, Jifang Tao, Pauline J. Chen , Atif Shahab, Weihong Ge, Ronald P. Hart, Xiaoan Ruan, Yijun Ruan, Yi E. Sun (2010) Systematic screening identifies microRNAs dys-regulated in a mouse model of Rett syndrome. PNAS 107 (42) 18161-18166 (ahead of print October 4, 2010, doi:10.1073/pnas.1005595107)
83. Ruan Y, Wei CL. (2010) Multiplex parallel pair-end-ditag sequencing approaches in system biology. Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):224-34. doi: 10.1002/wsbm.40. Review.
84. The International Cancer Genome Consortium (2010). International network of cancer genome projects. Nature 464, 993-998.
85. Nandi T, Ong C, Singh AP, Boddey J, Atkins T, Sarkar-Tyson M, Essex-Lopresti AE, Chua HH, Pearson T, Kreisberg JF, Nilsson C, Ariyaratne P, Ronning C, Losada L, Ruan Y, Sung WK, Woods D, Titball RW, Beacham I, Peak I, Keim P, Nierman WC, Tan P. (2010). A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog. 6(4): e1000845.
86. Guoliang Li, Melissa J. Fullwood, Han Xu, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Vinsensius B Vega S N, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong-Sain Ooi, Chandana Tennakoon, Chia-Lin Wei1, Yijun Ruan*, Wing-Kin Sung* (2010). ChIA-PET Tool: A comprehensive software for chromatin interaction analysis with paired-end-tag sequencing. Genome Biology 11:R22
87. Melissa J. Fullwood, Yuyuan Han, Chia-Lin Wei, Xiaoan Ruan, Yijun Ruan* (2010). Chromatin Interaction Analysis using Paired-End Tag Sequencing. Current Protocols in Molecular Biology: Chapter 21: Unit 21.15.1-25.
88. Stefan Schoenfelder, Tom Sexton, Lyubomira Chakalova, Nathan F. Cope, Alice Horton, Simon Andrews, Sreenivasulu Kurukuti, Jennifer A. Mitchell, David Umlauf, Daniela S. Dimitrova, Christopher H. Eskiw, Yanquan Luo, Chia-Lin Wei, Yijun Ruan, James J. Bieker, and Peter Fraser (2010). Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genetics 42: 53-62.
2009
89. Melissa J. Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Xu Han, Yusoff Bin Mohamed, Yuriy L. Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei, Elaine G. Y. Chew, Phillips Yao Hui Huang, Willem-Jan Welboren, Yuyuan Han, Hong-Sain Ooi, Pramila N. Ariyaratne, Vinsensius B. Vega, Yanquan Luo, Peck Yean Tan, Pei Ye Choy, K. D. Senali Abayratna Wansa, Bing Zhao, Kar Sian Lim, Shi Chi Leow, Jit Sin Yow, Roy Joseph, Haixia Li, Kartiki V. Desai, Jane S. Thomsen, Yew Kok Lee, R. Krishna Murthy Karuturi, Thoreau Herve, Guillaume Bourque, Hendrik G. Stunnenberg, Xiaoan Ruan, Valere Cacheux-Rataboul, Wing-Kin Sung, Edison T. Liu, Chia-Lin Wei, Edwin Cheung, and Yijun Ruan* (2009). An oestrogen-receptor-α-bound human chromatin interactome. Nature 462: 58-64.
90. The Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium, Yan Zhou, Huajun Zheng, Yangyi Chen, Lei Zhang, Kai Wang, Jing Guo, Zhen Huang, Bo Zhang, Wei Huang, Ke Jin, Tonghai Dou, Masami Hasegawa, Li Wang, Yuan Zhang, Jie Zhou, Lin Tao, Zhiwei Cao, Yixue Li, Tomas Vinar, Brona Brejova, Dan Brown, Ming Li, David J. Miller, David Blair, Yang Zhong, Zhu Chen, Feng Liu, Wei H7, Zhi-Qin Wang, Qin-Hua Zhang, Huai-Dong Song, Saijuan Chen, Xuenian Xu, Bin Xu, Chuan Ju, Yucheng Huang, Paul J. Brindley, Donald P. McManus, Zheng Feng, Ze-Guang Han, Gang Lu, Shuangxi Ren, Yuezhu Wang, Wenyi Gu, Hui Kang, Jie Chen, Xiaoyun Chen, Shuting Chen, Lijun Wang, Jie Yan , Biyun Wang, Xinyan Lv, Lei Jin, Bofei Wang, Shiyin Pu, Xianglin Zhang, Wei Zhang, Qiuping Hu, Genfeng Zhu, Jun Wang, Jun Yu1, Jian Wang, Huanming Yang, Zemin Ning, Matthew Beriman, Chia-Lin Wei, Yijun Ruan, Guoping Zhao, Shengyue Wang (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature 460: 345-351.
91. Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. (2009) Metagenomic analysis of viruses in reclaimed water. Environmental Microbiology 11: 2806–2820.
92. Hillmer AM, Freudenberg J, Myles S, Herms S, Tang K, Hughes DA, Brockschmidt FF, Ruan Y, Stoneking M, Nöthen MM (2009). Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness. Hum Genet. 2009 Aug; 126(2):255-64.
93. Melissa J. Fullwood, Chia Lin Wei, Edison T. Liu, and Yijun Ruan* (2009) Next-Generation DNA Sequencing of Paired End diTags for Transcriptome and Genome Analysis (Review) Genome Research 19: 521-532.
94. Hamza MS, Pott S, Vega VB, Thomsen JS, Kandhadayar GS, Ng PW, Chiu KP, Pettersson S, Wei CL, Ruan Y, Liu ET (2009). De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis. PLoS One. 4(3):e4907.
95. Melissa Fullwood and Yijun Ruan* (2009) ChIP-based methods for the identification of long-range chromatin interactions. J. Cellular Biochemistry 107: 30-39.
96. Chia-Lin Wei and Yijun Ruan (2009). Transcriptome and Genome Characterization Using Massively Parallel Paired End Tag (PET) Sequencing Analysis, Cap-Analysis Gene Expression (CAGE): The Science of Decoding Gene Transcription 978-981-4241-34-2
2008
97. Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, Liu ET (2008). Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Research 18(11):1752-62.
98. Zhao X, Ruan Y, Wei CL (2008). Tackling the epigenome in the pluripotent stem cells. J Genet Genomics. 35(7): 403-12. Review
99. Xi Chen, Han Xu, Ping Yuan, Fang Fang, Mikael Huss, Vinsensius B. Vega, Eleanor Wong, Yuriy L. Orlov, Weiwei Zhang, Jianming Jiang, Yuin-Han Loh, Hock Chuan Yeo, Zhen Xuan Yeo, Vipin Narang, Kunde Ramamoorthy Govindarajan, Bernard Leong, Atif Shahab, Yijun Ruan, Guillaume Bourque, Wing-Kin Sung, Neil D. Clarke, Chia-Lin Wei, and Huck-Hui Ng (2008) Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells. Cell 133: 1106-1117.
100. Susannah G. Tringe, Tao Zhang, Xuguo Liu, Yiting Yu, Wah Heng Lee, Jennifer Yap, Fei Yao, Sim Tiow Suan, Seah Keng Ing, Matthew Haynes, Forest Rohwer, Chia Lin Wei, Patrick Tan, James Bristow, Edward M. Rubin, Yijun Ruan* (2008) The Airborne Metagenome in an Indoor Urban Environment. PLoS One 3(4): e1862
101. Melissa J. Fullwood, Jack J. S. Tan, Patrick W. P. Ng, Kuo Ping Chiu, Liu Jun, Chia Lin Wei, and Yijun Ruan* (2008). The use of multiple displacement amplification to amplify complex DNA libraries. Nucleic Acid Research (doi:10.1093/nar/gkn074).
102. Elizabeth A. Dinsdale, Robert A. Edwards, Dana Hall1, Florent Angly, Mya Breitbart, Jennifer M. Brulc, Mike Furlan, Christelle Desnues, Matthew Haynes1, Linlin Li1, Lauren McDanie, Mary Ann Moran, Karen E. Nelson, Christina Nilsson, Robert Olson, John Paul, Beltran Rodriguez Brito, Yijun Ruan, Brandon K. Swan, Rick Stevens, David L. Valentine, Rebecca Vega Thurber, Linda Wegley, Bryan A. White, Forest Rohwer (2008) Functional metagenomic profiling of nine biomes Nature 452: 629-632.
103. Christelle Desnues, Beltran Rodriguez-Brito, Steve Rayhawk, Scott Kelley, Tuong Tran, Matthew Haynes, Hong Liu, Mike Furlan, Linda Wegley, Betty Chau, Yijun Ruan, Dana Hall, Florent E. Angly, Robert A. Edwards, Linlin Li, Rebecca Vega Thurber, R. Pamela Reid, Janet Siefert, Valeria Souza, David L. Valentine, Brandon K. Swan, Mya Breitbart, Forest Rohwer (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452: 340-343.
2007
104. Kuznetsov VA, Orlov YL, Wei CL, Ruan Y (2007). Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments. Genome Inform. 19: 83-94.
105. Ng P, Wei CL, Ruan Y* (2007). Paired-end diTagging for transcriptome and genome analysis. Curr Protoc Mol Biol. Chapter 21: Unit 21.12.
106. Xiao Dong Zhao, Xu Han, Joon Lin Chew, Jun Liu, Kuo Ping Chiu, Andre Choo, Yuriy L. Orlov, Wing-Kin Sung, Atif Shahab, Vladimir A. Kuznetsov, Guillaume Bourque, Steve Oh, Yijun Ruan, Huck-Hui Ng, and Chia-Lin Wei (2007) Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells. Cell Stem Cell 1 (3): 286-298.
107. Lim CA, Yao F, Wong JJ, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, Ng HH, Ruan Y*, Chin KC*. (2007) Genome-wide Mapping of RELA (p65) Binding Identifies E2F1 as a Transcriptional Activator Recruited by NF-kappaB upon TLR4 Activation. Mol Cell 27(4): 622-35.
108. Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei CL, Sung WK. (2007) Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer 7: 109 (doi: 10.1186/1471-2407-7-109).
109. ENCODE (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (7146): 799-816.
110. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Research 17(6): 898-909.
111. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigo R, Harrow J, Gerstein MB. (2007) Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research 17(6): 839-851.
112. Ruan Y*, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. (2007) Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Research 17(6): 828-838.
113. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET. (2007) Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet. 3(6): e87
2006
114. Hibberd ML, Ling L, Tolfvenstam T, Mitchell W, Wong C, Kuznetsov VA, George J, Ong SH, Ruan Y, Wei CL, Gu F, Fink J, Yip A, Liu W, Schreiber M, Vasudevan SG. (2006). A genomics approach to understanding host response during dengue infection. Novartis Found Symp. 277: 206-214.
115. Karen I. Zeller, XiaoDong Zhao, Charlie W. H. Lee, Kuo Ping Chiu, Hong Sain Ooi, Fei Yao, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Vladimir A. Kuznetsov, Wing-Kin Sung, Yijun Ruan, Chi V. Dang, and Chia-Lin Wei (2006) Global Mapping of c-Myc Binding Sites and Target Gene Networks in Human B Cells. Proc Natl Acad Sci USA. 103: 17834-17839.
116. Kuo Ping Chiu, Chee-Hong Wong, Qiong Yu Chen, Chia Lin Wei, Wing-Kin Sung, and Yijun Ruan* (2006) PET-Tool: A Software Suite for Comprehensive Processing and Managing of Paired-End diTag Sequence Data. BMC Bioinformatics 7: 390 (doi:10.1186/1471-2105-7-390).
117. Patrick Ng, Jack J.S. Tan, K.-P. Chiu, H.S. Ooi, Y.L. Lee, Melissa J. Fullwoods, Lie Du, W.-K. Sung, Chia Lin Wei, Yijun Ruan* (2006) Multiplex Sequencing of Paired-End diTag for Human Transcriptome and Genome Characterization. Nucleic Acid Research 34: No. 12, e84.
118. Patrick Ng, Chia Lin Wei, Yijun Ruan* (2006) Paired-End diTagging for Transcriptome and Genome Analysis. Current Protocols in Molecular Biology UNIT 21.12.
119. Yuin-Han Loh, Qiang Wu,Joon-Lin Chew,Vinsensius B. Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque,Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Ken W. Sung, Leonard Lipovich, Vladimir A. Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin Wei, Yijun Ruan*, Bing Lim, Huck-Hui Ng*, (2006) The Oct4 and Nanog transcription network that regulates pluripotency in mouse embryonic stem cells.Nature Genetics 38: 431-440.
120. Chia Lin Wei, Qiang Wu, Vinsensius Vega, Kuo Ping Chiu, Patrick Ng, Tao Zhang, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Jian Jun Liu, XiaoDong Zhao, Yen Ling Lee, Vladimir A. Kuznetsov, Ken Sung, Bing Lim, Edison T. Liu, Qiang Yu, Huck Hui Ng, and Yijun Ruan* (2006) A Global Map of p53 Transcription Factor Binding Sites in the Human Genome. Cell 124: 207-219.
121. Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh, Martin L. Hibberd1, Edison T. Liu, Forest Rohwer, and Yijun Ruan* (2006) RNA Viral Community in the Human Gut: Prevalence of plant pathogenic viruses. PLoS Biology 4: Issue 1, e3.
2005
122. Sinnakaruppan Mathavan, Serene G. P. Lee, Alicia Mak, Lance D. Miller, Karuturi Radha Krishna Murthy, Kunde R. Govindarajan, Yan Tong, Yi Lian Wu, Siew Hong Lam, Henry Yang, Yijun Ruan, Vladimir Korzh, Zhiyuan Gong, Edison T. Liu, and Thomas Lufkin (2005) Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays. PLoS Genetics 1: Issue 2, e29. (IF 8.883)
123. Patrick Ng, Chia-Lin Wei, Wing-Kin Sung, Kuo Ping Chiu, Leonard Lipovich, Chin Chin Ang, Sanjay Gupta, Atif Shahab, Azmi Ridwan, Chee Hong Wong, Edison T. Liu, and Yijun Ruan* (2005) Gene Identification Signature (GIS) Analysis for Transcriptome Characterization and Genome Annotation. Nature Methods 2: 105-111.
124. Wei Chia Lin, Takumi Miura, Robson Paul, Lim Sai-Kiang, Xiu-qin Xu, Mathia Yu-Chuan Lee, Gupta Sanjay, Stanton W Lawrence, Yongquan Luo, Jacqui Schmitt, Scott Thies, Wei Wang, Irina Khrebtukova, Daixing Zhou, Liu Tak-Bun Edison, Ruan Yijun, Mahendra Rao, and Lim Bing (2005) Transcriptome Profiling of Murine and Human ES Cells Identifies Divergent Paths Required to Maintain the Stem Cell State. Stem Cells 23: 166-185.
125. The FANTOM Consortium, P. Carninci, ..., Kuo Ping CHIU, Edison Tak-Bun LIU, Yijun RUAN, Chia Lin WEI, Leonard LIPOVICH, et al, RIKEN Genome Exploration Research Group, Genome Science Group - Genome Network Project Core Group (2005) The Transcriptional Landscape of the Mammalian Genome Science 309 1559-1563
126. Jianjun LIU, SL Lim, Yijun RUAN, Ling AE, Ng LF, C Drostein, Edison Tak-Bun LIU, Lawrence STANTON, Martin Lloyd HIBBERD (2005) SARS Transmission Pattern in Singapore Reassessed by Viral Sequence Variation Analysis PLoS Med 2(2) 162-168
2004
127. Liu Jianjun, Lam L.S., Ruan Yijun, Ling A.E., Dorsten C., Liu Tak-Bun Edison, Stanton W Lawrence, and Hibberd Lloyd Martin (2004) SARS-CoV transmission epidemiology revealed by MALDI-TOF mass spectrometry-based viral genotyping. PLoS Medicine 2: e43.
128. MGC Project Team (2004) The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Research 14: 2121-2127
129. Wei Chia Lin, Ng Patrick Wei Pern, Chiu Kuo Ping, Chee Hong Wong, Chin Chin Ang, Lipovich Leonard, Liu Edison Tak-Bun, and Ruan Yijun* (2004) 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A. 101:11701-11706
130. Lim P.L., Kurup A., Gopalakrishna G., Chan K.P., Wong Wing-Cheong Christopher, Ng L.C., Su Yun S.T., Oon L., Bai X., Stanton W Lawrence, Ruan Yijun, Miller D Lance, Vinsensius B Vega S, James L., Ooi P.L., Kai C.S., Olsen S.J., Ang B., Leo Y.S. (2004) Laboratory-acquired SARS-Singapore 2003. New Eng J Med 350: 1740-1745
131. Vinsensius B Vega S, Ruan Yijun, Liu Jianjun, Lee W.H., Wei Chia Lin, Su Yun S.T., Tang K.F., Zhang Tao, Lin S., Kolatkar R Prasanna, Eong O.E., Ling A.E., Stanton W Lawrence, Long P.M., Liu Tak-Bun Edison (2004) Mutational dynamics of the SARS corona virus in cell culture and human population. BMC Infectious Diseases 4(1): 32-40
132. Ruan Y, Le Ber P, Ng HH, and Liu ET. (2004) Interrogating the transcriptome. Trends in Biotechnology 22(1): 23-30
2003 and earlier
133. Ruan Yijun, Wei Chia Lin, Ling Ai Ee, Vinsensius Vega S B, Thoreau Herve, Su Yun Se Thoe, Chia Jer-Ming, Ng Wei Pern Patrick, Chiu Kuo Ping, Lim Landri, Zhang Tao, Chan Kwai Peng, Lynette Oon Lin Ean, Ng Mah Lee, Leo Yee Sin, Ng Fong-Poh Lisa, Ren Chee Ee, Stanton W Lawrence, Long M. Philip, Liu Tak-Bun Edison (2003) Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection. Lancet 361 (9371): 1779-1785
134. Ruan, Y., Gilmore, J., and Conner, T.W. (2001) Plant Genome Analysis Using cDNA Microarrays. In Biochip Technology (edit by Jing Cheng and Larry Kricka, published in April 2001 by Gordon and Breach Publishing).
135. Ruan, Y., Gilmore, J., and Conner, T.W. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. The Plant Journal 15: 821-833.
136. Ruan, Y. and Straney, D.C. (1995) Identification of elements in the PDA1 promoter of Nectria haematococca necessary for a high level of transcription in vitro. Molecular and General Genetics 250: 29-38.
137. He, J., Ruan, Y. and Straney, D.C. 1995. Analysis of determinants of binding and transcriptional activation of the pisatin-responsive DNA binding factor of Nectria Haematococca. Molecular Plant-Microbe Interaction 9: 171-179.
138. Ruan, Y. and Straney, D.C. (1995) Flavonoids stimulate spore germination in Fusarium solani pathogenic on legumes in a manner sensitive to inhibitors of cAMP-dependent protein kinase. Molecular Plant-Microbe Interaction 8: 929-938.
139. Ruan, Y. and Straney, D.C. (1994) In vitro transcription from Nectria haematococca PDA1 promoter in homo-logous extract reflects in vivo pisatin-responsive regulation. Current Genetics 27: 46-53.
140. Ruan, Y. and Straney, D.C. (1994) PCR-based construction of G-free template/promoter fusions for in vitro transcription analysis allows selection of plasmids with optimal template activity. Gene 146: 227-232.
141. Straney, D.C.; Ruan, Y. and He, J. (1994) In vitro transcription and binding analysis of promoter regulation by a host specific signal in a phytopathogenic fungus. Antonie van Leewenhoek 65: 183-189
