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Items: 41

1.
2.

Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features.

Huang YF, Chen TH, Chang ZT, Wang TC, Lee SJ, Kim JC, Kim JS, Chiu KP, Nai YS.

BMC Genomics. 2019 May 27;20(1):419. doi: 10.1186/s12864-019-5713-2.

3.

Single cell transcriptome analysis of MCF-7 reveals consistently and inconsistently expressed gene groups each associated with distinct cellular localization and functions.

Chiang YS, Huang YF, Midha MK, Chen TH, Shiau HC, Chiu KP.

PLoS One. 2018 Jun 19;13(6):e0199471. doi: 10.1371/journal.pone.0199471. eCollection 2018.

4.

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females.

Huang YF, Chen YJ, Fan TC, Chang NC, Chen YJ, Midha MK, Chen TH, Yang HH, Wang YT, Yu AL, Chiu KP.

BMC Med Genomics. 2018 Feb 13;11(Suppl 1):16. doi: 10.1186/s12920-018-0329-y.

5.

Enhanced Performance of GaN-based Ultraviolet Light Emitting Diodes by Photon Recycling Using Graphene Quantum Dots.

Lin TN, Santiago SRM, Yuan CT, Chiu KP, Shen JL, Wang TC, Kuo HC, Chiu CH, Yao YC, Lee YJ.

Sci Rep. 2017 Aug 2;7(1):7108. doi: 10.1038/s41598-017-07483-3.

6.

T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.

Nai YS, Chen TH, Huang YF, Midha MK, Shiau HC, Shen CY, Chen CJ, Yu AL, Chiu KP.

Sci Rep. 2017 Jan 17;7:40767. doi: 10.1038/srep40767.

7.

A Facile and Low-Cost Method to Enhance the Internal Quantum Yield and External Light-Extraction Efficiency for Flexible Light-Emitting Carbon-Dot Films.

Jiang ZC, Lin TN, Lin HT, Talite MJ, Tzeng TT, Hsu CL, Chiu KP, Lin CA, Shen JL, Yuan CT.

Sci Rep. 2016 Jan 29;6:19991. doi: 10.1038/srep19991.

8.

Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.

Huang YF, Midha M, Chen TH, Wang YT, Smith DG, Pei KJ, Chiu KP.

PLoS One. 2015 Jun 30;10(6):e0130673. doi: 10.1371/journal.pone.0130673. eCollection 2015.

9.

Global assessment of Antrodia cinnamomea-induced microRNA alterations in hepatocarcinoma cells.

Chen YJ, Thang MW, Chan YT, Huang YF, Ma N, Yu AL, Wu CY, Hu ML, Chiu KP.

PLoS One. 2013 Dec 17;8(12):e82751. doi: 10.1371/journal.pone.0082751. eCollection 2013.

10.

Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments.

Chang HJ, Jian JW, Hsu HJ, Lee YC, Chen HS, You JJ, Hou SC, Shao CY, Chen YJ, Chiu KP, Peng HP, Lee KH, Yang AS.

Structure. 2014 Jan 7;22(1):9-21. doi: 10.1016/j.str.2013.10.005. Epub 2013 Nov 21.

11.

Antibody variable domain interface and framework sequence requirements for stability and function by high-throughput experiments.

Hsu HJ, Lee KH, Jian JW, Chang HJ, Yu CM, Lee YC, Chen IC, Peng HP, Wu CY, Huang YF, Shao CY, Chiu KP, Yang AS.

Structure. 2014 Jan 7;22(1):22-34. doi: 10.1016/j.str.2013.10.006. Epub 2013 Nov 21.

12.

Concordant and discordant regulation of target genes by miR-31 and its isoforms.

Chan YT, Lin YC, Lin RJ, Kuo HH, Thang WC, Chiu KP, Yu AL.

PLoS One. 2013;8(3):e58169. doi: 10.1371/journal.pone.0058169. Epub 2013 Mar 5.

13.

Palindromic sequence impedes sequencing-by-ligation mechanism.

Huang YF, Chen SC, Chiang YS, Chen TH, Chiu KP.

BMC Syst Biol. 2012;6 Suppl 2:S10. doi: 10.1186/1752-0509-6-S2-S10. Epub 2012 Dec 12.

14.

Multiple metallic-shell nanocylinders for surface-enhanced spectroscopes.

Lu JY, Chiu KP, Chao HY, Chang YH.

Nanoscale Res Lett. 2011 Feb 24;6(1):173. doi: 10.1186/1556-276X-6-173.

15.

De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis.

Hamza MS, Pott S, Vega VB, Thomsen JS, Kandhadayar GS, Ng PW, Chiu KP, Pettersson S, Wei CL, Ruan Y, Liu ET.

PLoS One. 2009;4(3):e4907. doi: 10.1371/journal.pone.0004907. Epub 2009 Mar 20.

16.

Application of surface polariton coupling between nano recording marks to optical data storage.

Chiu KP, Lai KF, Tsai DP.

Opt Express. 2008 Sep 1;16(18):13885-92.

PMID:
18772999
17.

Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.

Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL.

Cell Stem Cell. 2007 Sep 13;1(3):286-98. doi: 10.1016/j.stem.2007.08.004.

18.

Evanescent field enhancement due to plasmonic resonances of a metamaterial slab.

Chiu KP, Kao TS, Tsai DP.

J Microsc. 2008 Feb;229(Pt 2):313-9. doi: 10.1111/j.1365-2818.2008.01906.x.

19.

The use of multiple displacement amplification to amplify complex DNA libraries.

Fullwood MJ, Tan JJ, Ng PW, Chiu KP, Liu J, Wei CL, Ruan Y.

Nucleic Acids Res. 2008 Mar;36(5):e32. doi: 10.1093/nar/gkn074. Epub 2008 Feb 19.

20.

Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation.

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.

Mol Cell. 2007 Aug 17;27(4):622-35.

21.

Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes.

Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei CL, Sung WK.

BMC Cancer. 2007 Jun 26;7:109.

22.

Effect of membrane configuration on bench-scale MF and UF fouling experiments.

Howe KJ, Marwah A, Chiu KP, Adham SS.

Water Res. 2007 Sep;41(17):3842-9. Epub 2007 May 23.

PMID:
17582459
23.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

24.

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).

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.

Genome Res. 2007 Jun;17(6):828-38.

25.

Plasmonic optical properties of a single gold nano-rod.

Huang HJ, Yu CP, Chang HC, Chiu KP, Ming Chen H, Liu RS, Tsai DP.

Opt Express. 2007 Jun 11;15(12):7132-9.

PMID:
19547031
26.

Whole-genome cartography of estrogen receptor alpha binding sites.

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.

PLoS Genet. 2007 Jun;3(6):e87. Epub 2007 Apr 17.

27.

Effect of coagulation on the size of MF and UF membrane foulants.

Howe KJ, Marwah A, Chiu KP, Adham SS.

Environ Sci Technol. 2006 Dec 15;40(24):7908-13.

PMID:
17256547
28.

Global mapping of c-Myc binding sites and target gene networks in human B cells.

Zeller KI, Zhao X, Lee CW, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL.

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17834-9. Epub 2006 Nov 8.

29.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y.

BMC Bioinformatics. 2006 Aug 25;7:390.

30.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y.

Nucleic Acids Res. 2006 Jul 13;34(12):e84.

31.

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.

Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH.

Nat Genet. 2006 Apr;38(4):431-40. Epub 2006 Mar 5.

PMID:
16518401
32.

A global map of p53 transcription-factor binding sites in the human genome.

Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y.

Cell. 2006 Jan 13;124(1):207-19.

33.

The transcriptional landscape of the mammalian genome.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).

Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713.

34.

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.

Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, Liu ET, Ruan Y.

Nat Methods. 2005 Feb;2(2):105-11. Epub 2005 Jan 9.

PMID:
15782207
35.

Surface plasmon polariton in visible frequency of a nano-slab consisting of left-handed material.

Chiu KP, Tsai DP.

Scanning. 2004 Sep-Oct;26(5 Suppl 1):I118-23.

PMID:
15540828
36.

5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation.

Wei CL, Ng P, Chiu KP, Wong CH, Ang CC, Lipovich L, Liu ET, Ruan Y.

Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11701-6. Epub 2004 Jul 22.

37.

Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection.

Ruan YJ, Wei CL, Ee AL, Vega VB, Thoreau H, Su ST, Chia JM, Ng P, Chiu KP, Lim L, Zhang T, Peng CK, Lin EO, Lee NM, Yee SL, Ng LF, Chee RE, Stanton LW, Long PM, Liu ET.

Lancet. 2003 May 24;361(9371):1779-85. Erratum in: Lancet. 2003 May 24;361(9371):1832.

PMID:
12781537
38.

Nuclear clustering in myotubes: a proposed role in acetylcholine receptor mRNA expression.

Duca KA, Chiu KP, Sullivan T, Berman SA, Bursztajn S.

Biochim Biophys Acta. 1998 Jan 2;1401(1):1-20.

39.

A novel in situ double-labeling method for simultaneous detection of mRNA and expressed protein or two different mRNAs.

Chiu KP, Duca KA, Berman SA, Sullivan T, Bursztajn S.

J Neurosci Methods. 1996 Jun;66(2):69-79.

PMID:
8835790
40.

Improved in situ hybridization: color intensity enhancement procedure for the alkaline phosphatase/Fast Red system.

Chiu KP, Sullivan T, Bursztajn S.

Biotechniques. 1996 Jun;20(6):964-6, 968. No abstract available.

41.

Intracellular amplification of proviral DNA in tissue sections using the polymerase chain reaction.

Chiu KP, Cohen SH, Morris DW, Jordan GW.

J Histochem Cytochem. 1992 Mar;40(3):333-41.

PMID:
1313061

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