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An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.

Zhou Q, Lim JQ, Sung WK, Li G.

BMC Bioinformatics. 2019 Jan 22;20(1):47. doi: 10.1186/s12859-018-2593-4.


Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments.

Fanucchi S, Fok ET, Dalla E, Shibayama Y, Börner K, Chang EY, Stoychev S, Imakaev M, Grimm D, Wang KC, Li G, Sung WK, Mhlanga MM.

Nat Genet. 2019 Feb;51(2):364. doi: 10.1038/s41588-018-0341-3.


An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

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.

Genome Res. 2019 Feb;29(2):223-235. doi: 10.1101/gr.230243.117. Epub 2019 Jan 3.


Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments.

Fanucchi S, Fok ET, Dalla E, Shibayama Y, Börner K, Chang EY, Stoychev S, Imakaev M, Grimm D, Wang KC, Li G, Sung WK, Mhlanga MM.

Nat Genet. 2019 Jan;51(1):138-150. doi: 10.1038/s41588-018-0298-2. Epub 2018 Dec 10. Erratum in: Nat Genet. 2019 Feb;51(2):364.


Determining the Consistency of Resolved Triplets and Fan Triplets.

Jansson J, Lingas A, Rajaby R, Sung WK.

J Comput Biol. 2018 Jul;25(7):740-754. doi: 10.1089/cmb.2017.0256. Epub 2018 Feb 16.


Erratum: An intrinsic mechanism controls reactivation of neural stem cells by spindle matrix proteins.

Li S, Koe CT, Tay ST, Tan ALK, Zhang S, Zhang Y, Tan P, Sung WK, Wang H.

Nat Commun. 2017 Oct 31;8(1):1298. doi: 10.1038/s41467-017-01017-1.


An intrinsic mechanism controls reactivation of neural stem cells by spindle matrix proteins.

Li S, Koe CT, Tay ST, Tan ALK, Zhang S, Zhang Y, Tan P, Sung WK, Wang H.

Nat Commun. 2017 Jul 25;8(1):122. doi: 10.1038/s41467-017-00172-9. Erratum in: Nat Commun. 2017 Oct 31;8(1):1298.


Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma.

Shek FH, Luo R, Lam BYH, Sung WK, Lam TW, Luk JM, Leung MS, Chan KT, Wang HK, Chan CM, Poon RT, Lee NP.

Cell Oncol (Dordr). 2017 Oct;40(5):443-456. doi: 10.1007/s13402-017-0332-x. Epub 2017 Jun 19.


BATVI: Fast, sensitive and accurate detection of virus integrations.

Tennakoon C, Sung WK.

BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):71. doi: 10.1186/s12859-017-1470-x.


Enterococcus faecium FC-K Derived from Kimchi Is a Probiotic Strain That Shows Anti-Allergic Activity.

Rho MK, Kim YE, Rho HI, Kim TR, Kim YB, Sung WK, Kim TW, Kim DO, Kang H.

J Microbiol Biotechnol. 2017 Jun 28;27(6):1071-1077. doi: 10.4014/jmb.1611.11020.


Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree.

Jansson J, Rajaby R, Shen C, Sung WK.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jan-Feb;15(1):15-26. doi: 10.1109/TCBB.2016.2609923. Epub 2016 Sep 20.


Pan-omics analysis of biological data.

Sung WK.

Methods. 2016 Jun 1;102:1-2. doi: 10.1016/j.ymeth.2016.05.004. Epub 2016 May 11. No abstract available.


Structural variation detection using next-generation sequencing data: A comparative technical review.

Guan P, Sung WK.

Methods. 2016 Jun 1;102:36-49. doi: 10.1016/j.ymeth.2016.01.020. Epub 2016 Feb 1. Review.


Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny.

Maurer-Stroh S, Lee CW, Patel C, Lucero M, Nohynek H, Sung WK, Murad C, Ma J, Hibberd ML, Wong CW, Simões EA.

Diagn Microbiol Infect Dis. 2016 Mar;84(3):203-6. doi: 10.1016/j.diagmicrobio.2015.11.003. Epub 2015 Nov 6.


Fibrillary glomerulonephritis combined with chronic inflammatory demyelinating polyneuropathy.

Sung WK, Jeong JU, Bang KT, Shin JH, Yoo JH, Kim NM, Park JH, Kim JH.

Kidney Res Clin Pract. 2015 Jun;34(2):117-9. doi: 10.1016/j.krcp.2014.10.008. Epub 2015 Mar 26.


An O(m log m)-Time Algorithm for Detecting Superbubbles.

Sung WK, Sadakane K, Shibuya T, Belorkar A, Pyrogova I.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jul-Aug;12(4):770-7. doi: 10.1109/TCBB.2014.2385696.


Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.

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.

PLoS One. 2015 Sep 8;10(9):e0137526. doi: 10.1371/journal.pone.0137526. eCollection 2015.


BatAlign: an incremental method for accurate alignment of sequencing reads.

Lim JQ, Tennakoon C, Guan P, Sung WK.

Nucleic Acids Res. 2015 Sep 18;43(16):e107. doi: 10.1093/nar/gkv533. Epub 2015 Jul 13.


Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.

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.

Cell Rep. 2015 Jul 14;12(2):272-85. doi: 10.1016/j.celrep.2015.06.020. Epub 2015 Jul 2.


TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome.

Ribi S, Baumhoer D, Lee K, Edison, Teo AS, Madan B, Zhang K, Kohlmann WK, Yao F, Lee WH, Hoi Q, Cai S, Woo XY, Tan P, Jundt G, Smida J, Nathrath M, Sung WK, Schiffman JD, Virshup DM, Hillmer AM.

Oncotarget. 2015 Apr 10;6(10):7727-40.


Platform comparison for evaluation of ALK protein immunohistochemical expression, genomic copy number and hotspot mutation status in neuroblastomas.

Yan B, Kuick CH, Lim M, Venkataraman K, Tennakoon C, Loh E, Lian D, Leong MY, Lakshmanan M, Tergaonkar V, Sung WK, Soh SY, Chang KT.

PLoS One. 2014 Sep 4;9(9):e106575. doi: 10.1371/journal.pone.0106575. eCollection 2014.


Do triplets have enough information to construct the multi-labeled phylogenetic tree?

Hassanzadeh R, Eslahchi C, Sung WK.

PLoS One. 2014 Jul 31;9(7):e103622. doi: 10.1371/journal.pone.0103622. eCollection 2014.


CWig: compressed representation of Wiggle/BedGraph format.

Huy Hoang D, Sung WK.

Bioinformatics. 2014 Sep 15;30(18):2543-50. doi: 10.1093/bioinformatics/btu330. Epub 2014 May 27.


Genomic portrait of resectable hepatocellular carcinomas: implications of RB1 and FGF19 aberrations for patient stratification.

Ahn SM, Jang SJ, Shim JH, Kim D, Hong SM, Sung CO, Baek D, Haq F, Ansari AA, Lee SY, Chun SM, Choi S, Choi HJ, Kim J, Kim S, Hwang S, Lee YJ, Lee JE, Jung WR, Jang HY, Yang E, Sung WK, Lee NP, Mao M, Lee C, Zucman-Rossi J, Yu E, Lee HC, Kong G.

Hepatology. 2014 Dec;60(6):1972-82. doi: 10.1002/hep.27198. Epub 2014 Sep 22.


International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions.

Eisenhaber F, Sung WK, Wong L.

BMC Syst Biol. 2013;7 Suppl 6:I1. doi: 10.1186/1752-0509-7-S6-I1. Epub 2013 Dec 13. No abstract available.


The Brm-HDAC3-Erm repressor complex suppresses dedifferentiation in Drosophila type II neuroblast lineages.

Koe CT, Li S, Rossi F, Wong JJ, Wang Y, Zhang Z, Chen K, Aw SS, Richardson HE, Robson P, Sung WK, Yu F, Gonzalez C, Wang H.

Elife. 2014 Mar 11;3:e01906. doi: 10.7554/eLife.01906.


Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma.

Fernandez-Banet J, Lee NP, Chan KT, Gao H, Liu X, Sung WK, Tan W, Fan ST, Poon RT, Li S, Ching K, Rejto PA, Mao M, Kan Z.

Genomics. 2014 Feb-Mar;103(2-3):189-203. doi: 10.1016/j.ygeno.2014.01.003. Epub 2014 Jan 21.


Guest Editorial for the International Conference on Genome Informatics (GIW 2013).

Eisenhaber F, Sung WK, Wong L.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):5-6. No abstract available.


How to perform parathyroid 4D CT: tips and traps for technique and interpretation.

Hoang JK, Sung WK, Bahl M, Phillips CD.

Radiology. 2014 Jan;270(1):15-24. doi: 10.1148/radiol.13122661. Review.


Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

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.

Nature. 2013 Dec 12;504(7479):306-310. doi: 10.1038/nature12716. Epub 2013 Nov 10.


3D chromosome modeling with semi-definite programming and Hi-C data.

Zhang Z, Li G, Toh KC, Sung WK.

J Comput Biol. 2013 Nov;20(11):831-46. doi: 10.1089/cmb.2013.0076.


Genome-wide mutational signatures of aristolochic acid and its application as a screening tool.

Poon SL, Pang ST, McPherson JR, Yu W, Huang KK, Guan P, Weng WH, Siew EY, Liu Y, Heng HL, Chong SC, Gan A, Tay ST, Lim WK, Cutcutache I, Huang D, Ler LD, Nairismägi ML, Lee MH, Chang YH, Yu KJ, Chan-On W, Li BK, Yuan YF, Qian CN, Ng KF, Wu CF, Hsu CL, Bunte RM, Stratton MR, Futreal PA, Sung WK, Chuang CK, Ong CK, Rozen SG, Tan P, Teh BT.

Sci Transl Med. 2013 Aug 7;5(197):197ra101. doi: 10.1126/scitranslmed.3006086.


Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma.

Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, Hauptschein R, Rejto PA, Fernandez J, Wang G, Zhang Q, Wang B, Chen R, Wang J, Lee NP, Zhou W, Lin Z, Peng Z, Yi K, Chen S, Li L, Fan X, Yang J, Ye R, Ju J, Wang K, Estrella H, Deng S, Wei P, Qiu M, Wulur IH, Liu J, Ehsani ME, Zhang C, Loboda A, Sung WK, Aggarwal A, Poon RT, Fan ST, Wang J, Hardwick J, Reinhard C, Dai H, Li Y, Luk JM, Mao M.

Genome Res. 2013 Sep;23(9):1422-33. doi: 10.1101/gr.154492.113. Epub 2013 Jun 20.


Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.

Zhang Z, Chang CW, Hugo W, Cheung E, Sung WK.

J Comput Biol. 2013 Mar;20(3):237-48. doi: 10.1089/cmb.2012.0233.


Pathogen chip for respiratory tract infections.

Simões EA, Patel C, Sung WK, Lee CW, Loh KH, Lucero M, Nohynek H, Nai G, Thien PL, Koh CW, Chan YS, Ma J, Maurer-Stroh S, Carosone-Link P, Hibberd ML, Wong CW; ARIVAC Consortium.

J Clin Microbiol. 2013 Mar;51(3):945-53. doi: 10.1128/JCM.02317-12. Epub 2013 Jan 9.


Whole-genome reconstruction and mutational signatures in gastric cancer.

Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PÉ, 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.

Genome Biol. 2012 Dec 13;13(12):R115. doi: 10.1186/gb-2012-13-12-r115.


Discovering interacting domains and motifs in protein-protein interactions.

Hugo W, Sung WK, Ng SK.

Methods Mol Biol. 2013;939:9-20. doi: 10.1007/978-1-62703-107-3_2.


Telomerase directly regulates NF-κB-dependent transcription.

Ghosh A, Saginc G, Leow SC, Khattar E, Shin EM, Yan TD, Wong M, Zhang Z, Li G, Sung WK, Zhou J, Chng WJ, Li S, Liu E, Tergaonkar V.

Nat Cell Biol. 2012 Dec;14(12):1270-81. doi: 10.1038/ncb2621. Epub 2012 Nov 18.


Large-scale functional organization of long-range chromatin interaction networks.

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.

Cell Rep. 2012 Nov 29;2(5):1207-19. doi: 10.1016/j.celrep.2012.09.022. Epub 2012 Oct 25.


BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.

Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.

Genome Biol. 2012 Oct 3;13(10):R82. doi: 10.1186/gb-2012-13-10-r82.


Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

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.

PLoS One. 2012;7(9):e46152. doi: 10.1371/journal.pone.0046152. Epub 2012 Sep 28.


Polynomial-time algorithms for building a consensus MUL-tree.

Cui Y, Jansson J, Sung WK.

J Comput Biol. 2012 Sep;19(9):1073-88. doi: 10.1089/cmb.2012.0008.


ChIA-PET analysis of transcriptional chromatin interactions.

Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.

Methods. 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25.


Partial anomalous pulmonary venous return in patients with pulmonary hypertension.

Sung WK, Au V, Rose A.

J Med Imaging Radiat Oncol. 2012 Jun;56(3):324-7. doi: 10.1111/j.1754-9485.2012.02364.x.


BatMis: a fast algorithm for k-mismatch mapping.

Tennakoon C, Purbojati RW, Sung WK.

Bioinformatics. 2012 Aug 15;28(16):2122-8. doi: 10.1093/bioinformatics/bts339. Epub 2012 Jun 10.


Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma.

Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, Lee NP, Lee WH, Ariyaratne PN, Tennakoon C, Mulawadi FH, Wong KF, Liu AM, Poon RT, Fan ST, Chan KL, Gong Z, Hu Y, Lin Z, Wang G, Zhang Q, Barber TD, Chou WC, Aggarwal A, Hao K, Zhou W, Zhang C, Hardwick J, Buser C, Xu J, Kan Z, Dai H, Mao M, Reinhard C, Wang J, Luk JM.

Nat Genet. 2012 May 27;44(7):765-9. doi: 10.1038/ng.2295.


Target gene analysis by microarrays and chromatin immunoprecipitation identifies HEY proteins as highly redundant bHLH repressors.

Heisig J, Weber D, Englberger E, Winkler A, Kneitz S, Sung WK, Wolf E, Eilers M, Wei CL, Gessler M.

PLoS Genet. 2012;8(5):e1002728. doi: 10.1371/journal.pgen.1002728. Epub 2012 May 17.


Constructing phylogenetic supernetworks based on simulated annealing.

Hassanzadeh R, Eslahchi C, Sung WK.

Mol Phylogenet Evol. 2012 Jun;63(3):738-44. doi: 10.1016/j.ympev.2012.02.009. Epub 2012 Mar 3.


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