Wing-Kin Sung

Wing-Kin Sung

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Wing-Kin Sung

Wing-Kin Sung

Publications by authors named "Wing-Kin Sung"

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An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees.

J Comput Biol 2019 Sep 16;26(9):893-907. Epub 2019 Apr 16.

School of Computing, National University of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1089/cmb.2019.0033DOI Listing
September 2019

A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest Chilo suppressalis.

Mol Ecol Resour 2019 Sep 3. Epub 2019 Sep 3.

National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research, Wuhan, 430070, Hubei, China.

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http://dx.doi.org/10.1111/1755-0998.13078DOI Listing
September 2019

Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation.

Nat Commun 2019 Aug 13;10(1):3640. Epub 2019 Aug 13.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, 430070, Hubei, China.

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http://dx.doi.org/10.1038/s41467-019-11535-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692402PMC
August 2019

Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma.

J Transl Med 2019 Aug 20;17(1):273. Epub 2019 Aug 20.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.

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http://dx.doi.org/10.1186/s12967-019-2025-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701074PMC
August 2019

SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing.

Bioinformatics 2019 Apr 15. Epub 2019 Apr 15.

School of Computing, National University of Singapore, 13 Computing Drive, Singapore.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz261DOI Listing
April 2019

The Integrator Complex Prevents Dedifferentiation of Intermediate Neural Progenitors back into Neural Stem Cells.

Cell Rep 2019 Apr;27(4):987-996.e3

Neuroscience & Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.03.089DOI Listing
April 2019

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

Nat Genet 2019 02;51(2):364

Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1038/s41588-018-0341-3DOI Listing
February 2019

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

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

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http://dx.doi.org/10.1109/TCBB.2016.2609923DOI Listing
January 2019

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

Nat Genet 2019 01 10;51(1):138-150. Epub 2018 Dec 10.

Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.

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http://dx.doi.org/10.1038/s41588-018-0298-2DOI Listing
January 2019

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

BMC Bioinformatics 2019 Jan 22;20(1):47. Epub 2019 Jan 22.

National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.

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http://dx.doi.org/10.1186/s12859-018-2593-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343306PMC
January 2019

TranSurVeyor: an improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data.

Nucleic Acids Res 2018 11;46(20):e122

School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore.

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http://dx.doi.org/10.1093/nar/gky685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237741PMC
November 2018

Determining the Consistency of Resolved Triplets and Fan Triplets.

J Comput Biol 2018 07 16;25(7):740-754. Epub 2018 Feb 16.

3 School of Computing, NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore , Singapore .

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http://dx.doi.org/10.1089/cmb.2017.0256DOI Listing
July 2018

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

Cell Oncol (Dordr) 2017 Oct 19;40(5):443-456. Epub 2017 Jun 19.

Department of Surgery, The University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1007/s13402-017-0332-xDOI Listing
October 2017

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

Nat Commun 2017 10 31;8(1):1298. Epub 2017 Oct 31.

Neuroscience and Behavioural Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.

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http://dx.doi.org/10.1038/s41467-017-01017-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663954PMC
October 2017

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

Nat Commun 2017 07 25;8(1):122. Epub 2017 Jul 25.

Neuroscience & Behavioural Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.

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http://dx.doi.org/10.1038/s41467-017-00172-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526931PMC
July 2017

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

BMC Bioinformatics 2017 Mar 14;18(Suppl 3):71. Epub 2017 Mar 14.

Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore.

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http://dx.doi.org/10.1186/s12859-017-1470-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374687PMC
March 2017

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

Methods 2016 06 1;102:36-49. Epub 2016 Feb 1.

School of Computing, National University of Singapore, 117543, Singapore; Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.01.020DOI Listing
June 2016

Pan-omics analysis of biological data.

Authors:
Wing-Kin Sung

Methods 2016 06 11;102:1-2. Epub 2016 May 11.

Department of Computer Science, School of Computing, National University of Singapore, Singapore 119077; Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.05.004DOI Listing
June 2016

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

IEEE/ACM Trans Comput Biol Bioinform 2015 Jul-Aug;12(4):770-7

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http://dx.doi.org/10.1109/TCBB.2014.2385696DOI Listing
May 2016

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

IEEE/ACM Trans Comput Biol Bioinform 2014 Jan-Feb;11(1):5-6

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March 2016

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

Diagn Microbiol Infect Dis 2016 Mar 6;84(3):203-6. Epub 2015 Nov 6.

University of Colorado School of Medicine, 13001 E 17th Place, Aurora, CO 80045, USA; Center for Global Health, Colorado School of Public Health, and Children's Hospital Colorado, 13001 E 17th Place, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.diagmicrobio.2015.11.003DOI Listing
March 2016

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

PLoS One 2014 31;9(7):e103622. Epub 2014 Jul 31.

School of Computing, National University of Singapore, Singapore, Singapore; Genome Institute of Singapore, Singapore, Singapore.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103622PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117514PMC
November 2015

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

Nucleic Acids Res 2015 Sep 13;43(16):e107. Epub 2015 Jul 13.

Department of Computer Science, National University of Singapore, Singapore 117417 Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672

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http://dx.doi.org/10.1093/nar/gkv533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4652746PMC
September 2015

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

Hepatology 2014 Dec 22;60(6):1972-82. Epub 2014 Sep 22.

Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea; Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea; Department of Bioinformatics, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea.

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http://dx.doi.org/10.1002/hep.27198DOI Listing
December 2014

CWig: compressed representation of Wiggle/BedGraph format.

Bioinformatics 2014 Sep 27;30(18):2543-50. Epub 2014 May 27.

Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672 and Department of Computer Science, School of Computing, National University of Singapore, Singapore 117417 Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672 and Department of Computer Science, School of Computing, National University of Singapore, Singapore 117417.

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http://dx.doi.org/10.1093/bioinformatics/btu330DOI Listing
September 2014

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

Nature 2013 Dec 10;504(7479):306-310. Epub 2013 Nov 10.

Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature12716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954713PMC
December 2013

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

J Comput Biol 2013 Nov;20(11):831-46

1 School of Computing, National University of Singapore , Singapore, Singapore .

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http://dx.doi.org/10.1089/cmb.2013.0076DOI Listing
November 2013

Discovering interacting domains and motifs in protein-protein interactions.

Methods Mol Biol 2013 ;939:9-20

School of Computing, National University of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1007/978-1-62703-107-3_2DOI Listing
June 2013

Telomerase directly regulates NF-κB-dependent transcription.

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

Laboratory of NFκB Signaling, IMCB, Proteos, 138673, Singapore.

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http://dx.doi.org/10.1038/ncb2621DOI Listing
December 2012

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

J Comput Biol 2012 Sep;19(9):1073-88

School of Computing, National University of Singapore, Singapore.

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http://dx.doi.org/10.1089/cmb.2012.0008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440012PMC
September 2012

BatMis: a fast algorithm for k-mismatch mapping.

Bioinformatics 2012 Aug 10;28(16):2122-8. Epub 2012 Jun 10.

NUS Graduate School for Integrative Sciences and Engineering, CeLS #05-01, 28 Medical Drive, Singapore 117456, Singapore.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts339DOI Listing
August 2012

Constructing phylogenetic supernetworks based on simulated annealing.

Mol Phylogenet Evol 2012 Jun 3;63(3):738-44. Epub 2012 Mar 3.

Faculty of Mathematics, Shahid Beheshti University, GC, Tehran, Iran.

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http://dx.doi.org/10.1016/j.ympev.2012.02.009DOI Listing
June 2012

Identifying differential histone modification sites from ChIP-seq data.

Methods Mol Biol 2012 ;802:293-303

Department of Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1007/978-1-61779-400-1_19DOI Listing
April 2012

Integration of regulatory networks by NKX3-1 promotes androgen-dependent prostate cancer survival.

Mol Cell Biol 2012 Jan 14;32(2):399-414. Epub 2011 Nov 14.

Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.

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http://mcb.asm.org/content/early/2011/11/09/MCB.05958-11.ful
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http://mcb.asm.org/cgi/doi/10.1128/MCB.05958-11
Publisher Site
http://dx.doi.org/10.1128/MCB.05958-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255774PMC
January 2012

D-SLIMMER: domain-SLiM interaction motifs miner for sequence based protein-protein interaction data.

J Proteome Res 2011 Dec 1;10(12):5285-95. Epub 2011 Nov 1.

Department of Computer Science, National University of Singapore, 13 Computing Drive, 117417 Singapore.

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http://dx.doi.org/10.1021/pr200312eDOI Listing
December 2011

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

J Comput Biol 2011 Nov 19;18(11):1681-91. Epub 2011 Sep 19.

NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.

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http://dx.doi.org/10.1089/cmb.2011.0170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216105PMC
November 2011

Computing a smallest multilabeled phylogenetic tree from rooted triplets.

IEEE/ACM Trans Comput Biol Bioinform 2011 Jul-Aug;8(4):1141-7

Institut Gaspard Monge-Université Paris-Est, 5 boulevard Descartes, Champs-sur-Marne, 77454 Marne-la-Vallée, France.

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http://dx.doi.org/10.1109/TCBB.2010.77DOI Listing
September 2011

Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state.

Mol Syst Biol 2011 Aug 30;7:526. Epub 2011 Aug 30.

Cancer Biology and Pharmacology 2, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1038/msb.2011.59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202798PMC
August 2011

CENTDIST: discovery of co-associated factors by motif distribution.

Nucleic Acids Res 2011 Jul 20;39(Web Server issue):W391-9. Epub 2011 May 20.

School of Computing, National University of Singapore, Computing 1, 13 Computing Drive, Singapore 117417.

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http://dx.doi.org/10.1093/nar/gkr387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125780PMC
July 2011

AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription.

EMBO J 2011 May 13;30(13):2569-81. Epub 2011 May 13.

Cancer Biology and Pharmacology, Genome Institute of Singapore, A STAR (Agency for Science, Technology and Research), Singapore.

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http://emboj.embopress.org/cgi/doi/10.1038/emboj.2011.151
Publisher Site
http://dx.doi.org/10.1038/emboj.2011.151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155293PMC
May 2011

PE-Assembler: de novo assembler using short paired-end reads.

Bioinformatics 2011 Jan 12;27(2):167-74. Epub 2010 Dec 12.

Computational & Mathematical Biology Group, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btq626DOI Listing
January 2011

Structural alignment of RNA with complex pseudoknot structure.

J Comput Biol 2011 Jan;18(1):97-108

Department of Computer Science, University of Hong Kong, Hong Kong.

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http://dx.doi.org/10.1089/cmb.2009.0275DOI Listing
January 2011

Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification.

PLoS One 2010 Sep 28;5(9). Epub 2010 Sep 28.

Department of Computer Science, The University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012848PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946929PMC
September 2010

Lethal-7 is down-regulated by the hepatitis B virus x protein and targets signal transducer and activator of transcription 3.

J Hepatol 2010 Jul 2;53(1):57-66. Epub 2010 Apr 2.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

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http://linkinghub.elsevier.com/retrieve/pii/S016882781000186
Publisher Site
http://dx.doi.org/10.1016/j.jhep.2009.12.043DOI Listing
July 2010

Oseltamivir ring prophylaxis for containment of 2009 H1N1 influenza outbreaks.

N Engl J Med 2010 Jun;362(23):2166-74

Biodefence Centre, Ministry of Defence, Department of Epidemiology and Public Health, National University of Singapore.

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http://dx.doi.org/10.1056/NEJMoa0908482DOI Listing
June 2010

Localized motif discovery in gene regulatory sequences.

Bioinformatics 2010 May 11;26(9):1152-9. Epub 2010 Mar 11.

Department of Computer Science, National University of Singapore, Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btq106DOI Listing
May 2010

A signal-noise model for significance analysis of ChIP-seq with negative control.

Bioinformatics 2010 May 5;26(9):1199-204. Epub 2010 Apr 5.

Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btq128DOI Listing
May 2010

SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank.

Bioinformatics 2010 Apr 18;26(8):1036-42. Epub 2010 Feb 18.

Department of Computer Science, National University of Singapore, 13 Computing Drive S(117417), Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btq065DOI Listing
April 2010

Brief overview of bioinformatics activities in Singapore.

PLoS Comput Biol 2009 Sep 25;5(9):e1000508. Epub 2009 Sep 25.

BioInformatics Institute, Singapore.

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http://dx.doi.org/10.1371/journal.pcbi.1000508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737619PMC
September 2009

Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries.

PLoS One 2009 15;4(4):e5241. Epub 2009 Apr 15.

Computational and Mathematical Biology Group, Genome Institute of Singapore, Singapore, Singapore.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005241PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666154PMC
July 2009

Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages.

Cell Stem Cell 2008 Nov 18;3(5):543-54. Epub 2008 Sep 18.

Stem Cell and Developmental Biology, Genome Institute of Singapore, 138672 Singapore.

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http://dx.doi.org/10.1016/j.stem.2008.08.004DOI Listing
November 2008

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.

Bioinformatics 2008 Oct 29;24(20):2344-9. Epub 2008 Jul 29.

Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672 Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btn402DOI Listing
October 2008

MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.

Bioinformatics 2008 Oct 12;24(20):2288-95. Epub 2008 Aug 12.

School of Computing, National University of Singapore, Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btn420DOI Listing
October 2008

RB-finder: an improved distance-based sliding window method to detect recombination breakpoints.

J Comput Biol 2008 Sep;15(7):881-98

Genome Institute of Singapore and School of Computing, National University of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1089/cmb.2007.0154DOI Listing
September 2008

Spectrum-based de novo repeat detection in genomic sequences.

J Comput Biol 2008 Jun;15(5):469-87

Department of Computer Science, National University of Singapore, Singapore.

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http://dx.doi.org/10.1089/cmb.2008.0013DOI Listing
June 2008

Using indirect protein-protein interactions for protein complex prediction.

J Bioinform Comput Biol 2008 Jun;6(3):435-66

Graduate School of Integrated Sciences, National University of Singapore, Singapore.

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June 2008

Using indirect protein-protein interactions for protein complex predication.

Comput Syst Bioinformatics Conf 2007 ;6:97-109

Graduate School of Integrated Sciences, National University of Singapore, Singapore.

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December 2007

An efficient strategy for extensive integration of diverse biological data for protein function prediction.

Bioinformatics 2007 Dec 28;23(24):3364-73. Epub 2007 Nov 28.

Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btm520DOI Listing
December 2007

Reconstructing recombination network from sequence data: the small parsimony problem.

IEEE/ACM Trans Comput Biol Bioinform 2007 Jul-Sep;4(3):394-402

Department of Mathematics, National University of Singapore, Singapore.

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http://dx.doi.org/10.1109/tcbb.2007.1018DOI Listing
October 2007

Using indirect protein interactions for the prediction of Gene Ontology functions.

BMC Bioinformatics 2007 May 22;8 Suppl 4:S8. Epub 2007 May 22.

School of Computing, National University of Singapore, Singapore, Singapore.

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http://dx.doi.org/10.1186/1471-2105-8-S4-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892087PMC
May 2007