Jingchu Luo

Jingchu Luo

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Jingchu Luo

Publications by authors named "Jingchu Luo"

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LSD 3.0: a comprehensive resource for the leaf senescence research community.

Nucleic Acids Res 2019 Oct 10. Epub 2019 Oct 10.

National Genomics Data Center, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkz898DOI Listing
October 2019

Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes.

Methods Mol Biol 2017 ;1533:315-333

State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing, 100871, China.

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http://dx.doi.org/10.1007/978-1-4939-6658-5_19DOI Listing
January 2018

GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China.

Authors:
Jingchu Luo

Genomics Proteomics Bioinformatics 2017 02 22;15(1):11-13. Epub 2017 Feb 22.

College of Life Sciences, State Key Laboratory of Protein and Plant Gene Research and Center for Bioinformatics, Peking University, Beijing 100871, China. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2017.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339405PMC
February 2017

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.

Nucleic Acids Res 2017 01 24;45(D1):D1040-D1045. Epub 2016 Oct 24.

State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Beijing 100871, P.R. China

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http://dx.doi.org/10.1093/nar/gkw982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210657PMC
January 2017

Erratum to: SorGSD: a sorghum genome SNP database.

Biotechnol Biofuels 2016 15;9:37. Epub 2016 Feb 15.

Genomics and Molecular Breeding of Biofuel Crops, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.

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http://dx.doi.org/10.1186/s13068-016-0450-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755019PMC
February 2016

An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.

Mol Biol Evol 2015 Jul 6;32(7):1767-73. Epub 2015 Mar 6.

State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, P.R. China

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http://atrm.cbi.pku.edu.cn/for_download/Mol_Biol_Evol-2015-J
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http://mbe.oxfordjournals.org/lookup/doi/10.1093/molbev/msv0
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http://dx.doi.org/10.1093/molbev/msv058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476157PMC
July 2015

GSDS 2.0: an upgraded gene feature visualization server.

Bioinformatics 2015 Apr 10;31(8):1296-7. Epub 2014 Dec 10.

State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.

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http://dx.doi.org/10.1093/bioinformatics/btu817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393523PMC
April 2015

Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics.

BMC Evol Biol 2015 Apr 18;15:66. Epub 2015 Apr 18.

State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Center for Bioinformatics, Peking University, Beijing, 100871, People's Republic of China.

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http://dx.doi.org/10.1186/s12862-015-0345-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425925PMC
April 2015

Bringing biocuration to China.

Genomics Proteomics Bioinformatics 2014 Aug 17;12(4):153-5. Epub 2014 Jul 17.

College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1016/j.gpb.2014.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411340PMC
August 2014

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors.

Nucleic Acids Res 2014 Jan 29;42(Database issue):D1182-7. Epub 2013 Oct 29.

State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics, Peking University, Beijing 100871, P.R. China.

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http://dx.doi.org/10.1093/nar/gkt1016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965000PMC
January 2014

LSD 2.0: an update of the leaf senescence database.

Nucleic Acids Res 2014 Jan 31;42(Database issue):D1200-5. Epub 2013 Oct 31.

College of Life Sciences, Peking University, Beijing 100871, People's Republic of China, The Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, People's Republic of China, Center for Life Sciences, Peking University, Beijing 100871, People's Republic of China and Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China.

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http://dx.doi.org/10.1093/nar/gkt1061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965048PMC
January 2014

A brief introduction to web-based genome browsers.

Brief Bioinform 2013 Mar 3;14(2):131-43. Epub 2012 Jul 3.

College of Life Sciences, Peking University, Beijing 100871, P.R. China.

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http://dx.doi.org/10.1093/bib/bbs029DOI Listing
March 2013

ABrowse--a customizable next-generation genome browser framework.

BMC Bioinformatics 2012 Jan 5;13. Epub 2012 Jan 5.

College of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.

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http://dx.doi.org/10.1186/1471-2105-13-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265404PMC
January 2012

Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome.

Mol Biol Evol 2011 Oct 5;28(10):2823-32. Epub 2011 May 5.

Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, PR China.

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http://dx.doi.org/10.1093/molbev/msr101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176832PMC
October 2011

Rice-Map: a new-generation rice genome browser.

BMC Genomics 2011 Mar 30;12:165. Epub 2011 Mar 30.

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China.

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http://dx.doi.org/10.1186/1471-2164-12-165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072960PMC
March 2011

AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies.

Nucleic Acids Res 2011 Jan 2;39(Database issue):D1123-9. Epub 2010 Nov 2.

National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China.

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http://dx.doi.org/10.1093/nar/gkq1066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013673PMC
January 2011

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database.

Nucleic Acids Res 2011 Jan 18;39(Database issue):D1114-7. Epub 2010 Nov 18.

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering and College of Life Sciences, Peking University, Beijing 100871, PR China.

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http://dx.doi.org/10.1093/nar/gkq1141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013715PMC
January 2011

LSD: a leaf senescence database.

Nucleic Acids Res 2011 Jan 18;39(Database issue):D1103-7. Epub 2010 Nov 18.

College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering and Center for Bioinformatics, Peking University, Beijing 100871, PR China.

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http://dx.doi.org/10.1093/nar/gkq1169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013730PMC
January 2011

Computational identification of plant transcription factors and the construction of the PlantTFDB database.

Methods Mol Biol 2010 ;674:351-68

National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, China.

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http://dx.doi.org/10.1007/978-1-60761-854-6_21DOI Listing
December 2010

WebLab: a data-centric, knowledge-sharing bioinformatic platform.

Nucleic Acids Res 2009 Jul 22;37(Web Server issue):W33-9. Epub 2009 May 22.

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1093/nar/gkp428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703900PMC
July 2009

NTAP: for NimbleGen tiling array ChIP-chip data analysis.

Bioinformatics 2009 Jul 25;25(14):1838-40. Epub 2009 May 25.

College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1093/bioinformatics/btp320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705232PMC
July 2009

Expression pattern divergence of duplicated genes in rice.

BMC Bioinformatics 2009 Jun 16;10 Suppl 6:S8. Epub 2009 Jun 16.

College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center for Bioinformatics, Peking University, Beijing 100871, PR China.

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http://dx.doi.org/10.1186/1471-2105-10-S6-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697655PMC
June 2009

Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.

Gene 2008 Jul 9;418(1-2):1-8. Epub 2008 Apr 9.

College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.

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http://linkinghub.elsevier.com/retrieve/pii/S037811190800136
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http://dx.doi.org/10.1016/j.gene.2008.03.016DOI Listing
July 2008

PlantTFDB: a comprehensive plant transcription factor database.

Nucleic Acids Res 2008 Jan 12;36(Database issue):D966-9. Epub 2007 Oct 12.

College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Center for Bioinformatics, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1093/nar/gkm841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238823PMC
January 2008

Efficient targeted anticoagulant with active RGD motif.

Thromb Res 2007 12;120(4):541-7. Epub 2007 Jan 12.

National Key Laboratory of Biomembrane and Membrane Biotechnology, College of Life Sciences, Peking University, Beijing, 100871, PR China.

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http://dx.doi.org/10.1016/j.thromres.2006.11.013DOI Listing
October 2007

ABCGrid: Application for Bioinformatics Computing Grid.

Bioinformatics 2007 May 7;23(9):1175-7. Epub 2007 Mar 7.

Center for Bioinformatics, National Laboratory of Plant Genetic Engineering and Protein Engineering and College of Life Sciences, Peking University, Beijing, PR China.

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http://dx.doi.org/10.1093/bioinformatics/btm086DOI Listing
May 2007

A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir.

Cell Res 2007 Apr;17(4):357-62

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1038/cr.2007.27DOI Listing
April 2007

Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice.

Mol Biol Evol 2007 Mar 11;24(3):875-88. Epub 2007 Jan 11.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1093/molbev/msm005DOI Listing
March 2007

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.

BMC Bioinformatics 2006 Oct 12;7:447. Epub 2006 Oct 12.

College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626491PMC
October 2006

Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias.

Gene 2006 Jul 18;376(2):199-206. Epub 2006 Mar 18.

College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China.

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http://linkinghub.elsevier.com/retrieve/pii/S037811190600212
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http://dx.doi.org/10.1016/j.gene.2006.03.003DOI Listing
July 2006

KOBAS server: a web-based platform for automated annotation and pathway identification.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W720-4

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China.

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http://dx.doi.org/10.1093/nar/gkl167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538915PMC
July 2006

DRTF: a database of rice transcription factors.

Bioinformatics 2006 May 21;22(10):1286-7. Epub 2006 Mar 21.

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing 100871, People's Republic of China.

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http://dx.doi.org/10.1093/bioinformatics/btl107DOI Listing
May 2006

The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family.

Plant Mol Biol 2006 Jan;60(1):107-24

Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, National Key Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, 100871, Beijing, People's Republic of China.

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http://link.springer.com/content/pdf/10.1007/s11103-005-2910
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http://link.springer.com/10.1007/s11103-005-2910-y
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http://dx.doi.org/10.1007/s11103-005-2910-yDOI Listing
January 2006

Systematic high-yield production of human secreted proteins in Escherichia coli.

Biochem Biophys Res Commun 2005 Jul;332(2):593-601

National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1016/j.bbrc.2005.04.163DOI Listing
July 2005

GBA server: EST-based digital gene expression profiling.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W673-6

Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China.

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http://dx.doi.org/10.1093/nar/gki480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160240PMC
July 2005

Duplication and DNA segmental loss in the rice genome: implications for diploidization.

New Phytol 2005 Mar;165(3):937-46

College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1111/j.1469-8137.2004.01293.xDOI Listing
March 2005

SPD--a web-based secreted protein database.

Nucleic Acids Res 2005 Jan;33(Database issue):D169-73

Centre of Bioinformatics, College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1093/nar/gki093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540047PMC
January 2005

Identification of a naturally occurring recombinant isolate of Sugarcane mosaic virus causing maize dwarf mosaic disease.

Virus Genes 2005 Jan;30(1):75-83

Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1007/s11262-004-4584-yDOI Listing
January 2005

RDfolder: a web server for prediction of RNA secondary structure.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W150-3

Beijing Institute of Basic Medical Sciences, PO Box 130(3), Beijing 100850, People's Republic of China.

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http://dx.doi.org/10.1093/nar/gkh445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441583PMC
July 2004

Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT.

Mamm Genome 2003 Dec;14(12):859-65

College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, and Centre of Bioinformatics, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1007/s00335-003-2296-6DOI Listing
December 2003

[MGAP-A microbe genome annotation platform].

Wei Sheng Wu Xue Bao 2003 Dec;43(6):805-8

College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Centre of Bioinformatics, Peking University, Beijing 100871, China.

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December 2003

PCAS--a precomputed proteome annotation database resource.

BMC Genomics 2003 Nov 1;4(1):42. Epub 2003 Nov 1.

College of Life Sciences, National Laboratory of Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1186/1471-2164-4-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC293463PMC
November 2003

Bioinformatics service, education and research: the EMBnet and CBI. European Molecular Biology Network Centre of Bioinformatics.

Authors:
Jingchu Luo

In Silico Biol 2002 ;2(3):173-7

Centre of Bioinformatics, Peking University, Beijing 100871, P.R. China.

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July 2003

PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide.

Mamm Genome 2003 May;14(5):341-9

Bioinformatics/Genomics Research, Schering-Plough Research Institute, 2015 Gallopjng Hill Road, Kenilworth, NJ 07033, USA.

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http://dx.doi.org/10.1007/s00335-002-3061-yDOI Listing
May 2003

The toxicity test and hypothetical model of Bacillus thuringiensis Cry1Aa helix4.

Sci China C Life Sci 2002 Dec;45(6):561-8

Peking University, Beijing, China.

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http://dx.doi.org/10.1007/BF02879743DOI Listing
December 2002

PGAAS: a prokaryotic genome assembly assistant system.

Bioinformatics 2002 May;18(5):661-5

College of Life Sciences, The National Key Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1093/bioinformatics/18.5.661DOI Listing
May 2002