Publications by authors named "Runsheng Chen"

100Publications

NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants.

Nucleic Acids Res 2020 Nov 16. Epub 2020 Nov 16.

Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkaa1046DOI Listing
November 2020

Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division.

Genome Res 2020 Nov 15;30(11):1570-1582. Epub 2020 Oct 15.

Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, 100101, China.

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http://dx.doi.org/10.1101/gr.256131.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605247PMC
November 2020

Genetic variations associated with long noncoding RNAs.

Essays Biochem 2020 Oct 9. Epub 2020 Oct 9.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1042/EBC20200033DOI Listing
October 2020

LRIK interacts with the Ku70-Ku80 heterodimer enhancing the efficiency of NHEJ repair.

Cell Death Differ 2020 Jun 25. Epub 2020 Jun 25.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China.

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http://dx.doi.org/10.1038/s41418-020-0581-5DOI Listing
June 2020

Noncoding RNA: from dark matter to bright star.

Sci China Life Sci 2020 Apr 13;63(4):463-468. Epub 2020 Mar 13.

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1007/s11427-020-1676-5DOI Listing
April 2020

LncRNA HRCEG, regulated by HDAC1, inhibits cells proliferation and epithelial-mesenchymal-transition in gastric cancer.

Cancer Genet 2020 02 8;241:25-33. Epub 2020 Jan 8.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan, 528316, China. Electronic address:

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http://dx.doi.org/10.1016/j.cancergen.2019.12.007DOI Listing
February 2020

Association of the Polymorphism rs13259960 in SLEAR With Predisposition to Systemic Lupus Erythematosus.

Arthritis Rheumatol 2020 06 26;72(6):985-996. Epub 2020 Apr 26.

Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China, and Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan, China.

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http://dx.doi.org/10.1002/art.41200DOI Listing
June 2020

SpatialDB: a database for spatially resolved transcriptomes.

Nucleic Acids Res 2020 01;48(D1):D233-D237

Center for High Throughput Sequencing, Core Facility for Protein Research, Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkz934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145543PMC
January 2020

NPInter v4.0: an integrated database of ncRNA interactions.

Nucleic Acids Res 2020 01;48(D1):D160-D165

Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkz969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145607PMC
January 2020

ER-residential Nogo-B accelerates NAFLD-associated HCC mediated by metabolic reprogramming of oxLDL lipophagy.

Nat Commun 2019 07 29;10(1):3391. Epub 2019 Jul 29.

Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.

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http://dx.doi.org/10.1038/s41467-019-11274-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662851PMC
July 2019

LncRNA HAND2-AS1 promotes liver cancer stem cell self-renewal via BMP signaling.

EMBO J 2019 09 23;38(17):e101110. Epub 2019 Jul 23.

CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.15252/embj.2018101110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717889PMC
September 2019

LincK contributes to breast tumorigenesis by promoting proliferation and epithelial-to-mesenchymal transition.

J Hematol Oncol 2019 02 22;12(1):19. Epub 2019 Feb 22.

Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Peking Union Medical College Hospital, Center of Excellence in Tissue Engineering Chinese Academy of Medical Sciences, Beijing Key Laboratory (No. BZO381), Beijing, 100005, China.

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https://jhoonline.biomedcentral.com/articles/10.1186/s13045-
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http://dx.doi.org/10.1186/s13045-019-0707-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387548PMC
February 2019

LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes.

Methods Mol Biol 2019 ;1870:189-198

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://link.springer.com/10.1007/978-1-4939-8808-2_14
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http://dx.doi.org/10.1007/978-1-4939-8808-2_14DOI Listing
May 2019

Long noncoding RNA SMRG regulates Drosophila macrochaetes by antagonizing scute through E(spl)mβ.

RNA Biol 2019 01 17;16(1):42-53. Epub 2018 Dec 17.

a State Key Laboratory of Brain and Cognitive Science , Institute of Biophysics, Chinese Academy of Sciences , Beijing , China.

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http://dx.doi.org/10.1080/15476286.2018.1556148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380328PMC
January 2019

Toward Automated Identification of Glycan Branching Patterns Using Multistage Mass Spectrometry with Intelligent Precursor Selection.

Anal Chem 2018 12 30;90(24):14412-14422. Epub 2018 Nov 30.

Key Laboratory of Intelligent Information Processing, Institute of Computing Technology , Chinese Academy of Sciences , 6 Kexueyuan South Road , Beijing 100080 , China.

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http://dx.doi.org/10.1021/acs.analchem.8b03967DOI Listing
December 2018

piRBase: a comprehensive database of piRNA sequences.

Nucleic Acids Res 2019 01;47(D1):D175-D180

Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky1043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323959PMC
January 2019

Identification and functional characterization of intermediate-size non-coding RNAs in maize.

BMC Genomics 2018 Oct 4;19(1):730. Epub 2018 Oct 4.

China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-018-5103-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172812PMC
October 2018

Long noncoding RNA lncHand2 promotes liver repopulation via c-Met signaling.

J Hepatol 2018 Oct 11;69(4):861-872. Epub 2018 Apr 11.

CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01688278183197
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http://dx.doi.org/10.1016/j.jhep.2018.03.029DOI Listing
October 2018

XPF plays an indispensable role in relieving silver nanoparticle induced DNA damage stress in human cells.

Toxicol Lett 2018 May 17;288:44-54. Epub 2018 Feb 17.

Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03784274183006
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http://dx.doi.org/10.1016/j.toxlet.2018.02.022DOI Listing
May 2018

A novel antisense long noncoding RNA, TWISTED LEAF, maintains leaf blade flattening by regulating its associated sense R2R3-MYB gene in rice.

New Phytol 2018 04 7;218(2):774-788. Epub 2018 Feb 7.

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1111/nph.15023DOI Listing
April 2018

NONCODEV5: a comprehensive annotation database for long non-coding RNAs.

Nucleic Acids Res 2018 01;46(D1):D308-D314

Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.

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http://dx.doi.org/10.1093/nar/gkx1107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753287PMC
January 2018

TDP-43 regulates cancer-associated microRNAs.

Protein Cell 2018 10 26;9(10):848-866. Epub 2017 Sep 26.

State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1007/s13238-017-0480-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6160384PMC
October 2018

Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA-MUF Interaction with ANXA2 and miR-34a.

Cancer Res 2017 12 25;77(23):6704-6716. Epub 2017 Sep 25.

Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1915DOI Listing
December 2017

Using the NONCODE Database Resource.

Curr Protoc Bioinformatics 2017 06 27;58:12.16.1-12.16.19. Epub 2017 Jun 27.

Institute of Computing Technology Chinese Academy of Sciences, Bioinformatics Research Group, Advanced Computing Research Laboratory, Beijing, China.

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http://dx.doi.org/10.1002/cpbi.25DOI Listing
June 2017

Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data.

Brief Bioinform 2018 11;19(6):1302-1309

Key Laboratory of RNA Biology, Institute of Biophysics and University of the Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1093/bib/bbx059DOI Listing
November 2018

Long noncoding RNA lncKdm2b is required for ILC3 maintenance by initiation of Zfp292 expression.

Nat Immunol 2017 05 20;18(5):499-508. Epub 2017 Mar 20.

Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1038/ni.3712DOI Listing
May 2017

Identification and analysis of intermediate-size noncoding RNAs in the rhesus macaque fetal brain.

J Genet Genomics 2017 03 27;44(3):171-174. Epub 2017 Jan 27.

State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China. Electronic address:

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http://pubmedcentralcanada.ca/pmcc/articles/PMC3138756/pdf/p
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http://linkinghub.elsevier.com/retrieve/pii/S167385271730018
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http://dx.doi.org/10.1016/j.jgg.2017.01.003DOI Listing
March 2017

SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci.

Brief Bioinform 2018 07;19(4):636-643

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1093/bib/bbx005DOI Listing
July 2018

Long noncoding RNA LINC01186, regulated by TGF-β/SMAD3, inhibits migration and invasion through Epithelial-Mesenchymal-Transition in lung cancer.

Gene 2017 Apr 22;608:1-12. Epub 2017 Jan 22.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2017.01.023DOI Listing
April 2017

LncRNA16 is a potential biomarker for diagnosis of early-stage lung cancer that promotes cell proliferation by regulating the cell cycle.

Oncotarget 2017 Jan;8(5):7867-7877

Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China.

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http://dx.doi.org/10.18632/oncotarget.13980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5352366PMC
January 2017

The Landscape of Viral Expression Reveals Clinically Relevant Viruses with Potential Capability of Promoting Malignancy in Lower-Grade Glioma.

Clin Cancer Res 2017 May 18;23(9):2177-2185. Epub 2016 Nov 18.

Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.

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http://dx.doi.org/10.1158/1078-0432.CCR-16-1495DOI Listing
May 2017

Lateralization of gene expression in the honeybee brain during olfactory learning.

Sci Rep 2016 10 5;6:34727. Epub 2016 Oct 5.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1038/srep34727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5050455PMC
October 2016

LncVar: a database of genetic variation associated with long non-coding genes.

Bioinformatics 2017 01 6;33(1):112-118. Epub 2016 Sep 6.

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences.

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http://dx.doi.org/10.1093/bioinformatics/btw581DOI Listing
January 2017

The long noncoding RNA ASNR regulates degradation of Bcl-2 mRNA through its interaction with AUF1.

Sci Rep 2016 08 31;6:32189. Epub 2016 Aug 31.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1038/srep32189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006016PMC
August 2016

Expression profiling and functional prediction of long noncoding RNAs in nasopharyngeal nonkeratinizing carcinoma.

Discov Med 2016 04;21(116):239-50

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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April 2016

Systematic study of novel lncRNAs in different gastrointestinal cancer cells.

Discov Med 2016 03;21(115):159-71

Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China.

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March 2016

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.

Database (Oxford) 2016 17;2016. Epub 2016 Apr 17.

Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China

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http://dx.doi.org/10.1093/database/baw057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834207PMC
January 2017

DRME: Count-based differential RNA methylation analysis at small sample size scenario.

Anal Biochem 2016 Apr 4;499:15-23. Epub 2016 Feb 4.

Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China. Electronic address:

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http://dx.doi.org/10.1016/j.ab.2016.01.014DOI Listing
April 2016

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

Bioinformatics 2016 06 27;32(11):1740-2. Epub 2016 Jan 27.

Key Laboratory of RNA Biology, Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, Research Network of Computational Biology, RNCB, Beijing 100101, China.

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http://dx.doi.org/10.1093/bioinformatics/btw041DOI Listing
June 2016

NONCODEv4: Annotation of Noncoding RNAs with Emphasis on Long Noncoding RNAs.

Methods Mol Biol 2016 ;1402:243-254

Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1007/978-1-4939-3378-5_19DOI Listing
October 2016

Computational identification of piRNA targets on mouse mRNAs.

Bioinformatics 2016 04 16;32(8):1170-7. Epub 2015 Dec 16.

Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology and.

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http://dx.doi.org/10.1093/bioinformatics/btv729DOI Listing
April 2016

GADD45A inhibits autophagy by regulating the interaction between BECN1 and PIK3C3.

Autophagy 2015 ;11(12):2247-58

a State Key Laboratory of Molecular Oncology; Cancer Institute and Hospital; Chinese Academy of Medical Sciences & Peking Union Medical College ; Beijing , China.

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https://www.tandfonline.com/doi/full/10.1080/15548627.2015.1
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http://dx.doi.org/10.1080/15548627.2015.1112484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835191PMC
October 2016

NONCODE 2016: an informative and valuable data source of long non-coding RNAs.

Nucleic Acids Res 2016 Jan 19;44(D1):D203-8. Epub 2015 Nov 19.

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China

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http://dx.doi.org/10.1093/nar/gkv1252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702886PMC
January 2016

Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBPα.

Stem Cell Reports 2015 Nov 17;5(5):856-865. Epub 2015 Oct 17.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2015.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649137PMC
November 2015

Transcriptome profiling of esophageal squamous cell carcinoma reveals a long noncoding RNA acting as a tumor suppressor.

Oncotarget 2015 Jul;6(19):17065-80

Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627292PMC
http://dx.doi.org/10.18632/oncotarget.4185DOI Listing
July 2015

Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells.

Biochemistry 2015 May 28;54(18):2895-902. Epub 2015 Apr 28.

†CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun, Chaoyang District, Beijing 100101, China.

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http://dx.doi.org/10.1021/acs.biochem.5b00259DOI Listing
May 2015

The long noncoding RNA lncTCF7 promotes self-renewal of human liver cancer stem cells through activation of Wnt signaling.

Cell Stem Cell 2015 Apr;16(4):413-25

CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.03.003DOI Listing
April 2015

On bioinformatic resources.

Authors:
Runsheng Chen

Genomics Proteomics Bioinformatics 2015 Feb 2;13(1):1-3. Epub 2015 Mar 2.

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

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http://dx.doi.org/10.1016/j.gpb.2015.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411502PMC
February 2015

Epigenetic changes and functional study of HOXA11 in human gastric cancer.

Epigenomics 2015 15;7(2):201-13. Epub 2015 Jan 15.

Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China.

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http://dx.doi.org/10.2217/epi.14.92DOI Listing
September 2015

MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes.

Cell Res 2015 Feb 13;25(2):193-207. Epub 2015 Jan 13.

Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1038/cr.2015.4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650574PMC
February 2015

piRBase: a web resource assisting piRNA functional study.

Database (Oxford) 2014 25;2014:bau110. Epub 2014 Nov 25.

Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Science, Beijing 100049, China, Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, College of Life Sciences, Hebei University, Baoding 071002, Hebei, China and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Science, Beijing 100049, China, Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, College of Life Sciences, Hebei University, Baoding 071002, Hebei, China and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China

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http://dx.doi.org/10.1093/database/bau110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243270PMC
July 2015

Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome.

Mol Biosyst 2015 Jan 5;11(1):262-74. Epub 2014 Nov 5.

Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, Shaanxi 710027, China.

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http://dx.doi.org/10.1039/c4mb00604fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253022PMC
January 2015

Association of echocardiographic left ventricular structure and -344C/T aldosterone synthase gene variant: A meta-analysis.

J Renin Angiotensin Aldosterone Syst 2015 Dec 10;16(4):858-71. Epub 2014 Sep 10.

Beijing Anzhen Hospital, Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel Diseases, China

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http://dx.doi.org/10.1177/1470320314535459DOI Listing
December 2015

Computational methods to predict long noncoding RNA functions based on co-expression network.

Methods Mol Biol 2014 ;1182:209-18

Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190, People's Republic of China.

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http://dx.doi.org/10.1007/978-1-4939-1062-5_19DOI Listing
March 2015

De novo approach to classify protein-coding and noncoding transcripts based on sequence composition.

Methods Mol Biol 2014 ;1182:203-7

Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190, People's Republic of China.

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http://dx.doi.org/10.1007/978-1-4939-1062-5_18DOI Listing
March 2015

The influences of PRG-1 on the expression of small RNAs and mRNAs.

BMC Genomics 2014 Apr 30;15:321. Epub 2014 Apr 30.

School of Life Science, Hebei University, Hebei 071002, People's Republic of China.

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http://dx.doi.org/10.1186/1471-2164-15-321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035053PMC
April 2014

Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy.

Protein Cell 2014 Oct 21;5(10):770-82. Epub 2014 May 21.

Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1007/s13238-014-0071-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180458PMC
October 2014

Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum.

PLoS One 2014 8;9(4):e92946. Epub 2014 Apr 8.

Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092946PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3979661PMC
November 2014

One novel long noncoding RNA lnc10 in Drosophila.

J Genet Genomics 2014 Feb 13;41(2):79-82. Epub 2014 Jan 13.

State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1016/j.jgg.2013.12.007DOI Listing
February 2014

Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis.

Mol Plant 2014 Mar 7;7(3):514-27. Epub 2014 Jan 7.

College of Life Sciences, Beijing Normal University, Beijing 100875, China.

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http://dx.doi.org/10.1093/mp/sst177DOI Listing
March 2014

Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum.

BMC Genomics 2013 Dec 30;14:931. Epub 2013 Dec 30.

MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China.

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http://dx.doi.org/10.1186/1471-2164-14-931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890542PMC
December 2013

Recipe for a busy bee: microRNAs in Honey Bee caste determination.

PLoS One 2013 11;8(12):e81661. Epub 2013 Dec 11.

Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081661PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3862878PMC
September 2014

Light-induced protein translocation by genetically encoded unnatural amino acid in Caenorhabditis elegans.

Protein Cell 2013 Dec;4(12):883-6

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1007/s13238-013-3118-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875405PMC
December 2013

NONCODEv4: exploring the world of long non-coding RNA genes.

Nucleic Acids Res 2014 Jan 26;42(Database issue):D98-103. Epub 2013 Nov 26.

Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China, University of Chinese Academy of Sciences, Beijing 100049, China, Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and Taicang Institute of Life Sciences Information, Suzhou 215400, China.

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http://dx.doi.org/10.1093/nar/gkt1222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965073PMC
January 2014

NPInter v2.0: an updated database of ncRNA interactions.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D104-8. Epub 2013 Nov 11.

Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Sciences, Beijing 100049, China and Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.

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http://dx.doi.org/10.1093/nar/gkt1057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965026PMC
January 2014

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.

Nucleic Acids Res 2013 Sep 27;41(17):e166. Epub 2013 Jul 27.

Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China, College of Computer Science and Technology, Jilin University, Changchun 130012, China and Laboratory of Bioinformatics and Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkt646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783192PMC
September 2013

Transcriptome-wide analysis of TDP-43 binding small RNAs identifies miR-NID1 (miR-8485), a novel miRNA that represses NRXN1 expression.

Genomics 2014 Jan 1;103(1):76-82. Epub 2013 Jul 1.

Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2013.06.006DOI Listing
January 2014

Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines.

Sci China Life Sci 2013 Jun 11;56(6):503-12. Epub 2013 May 11.

Bioinformatic Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.

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http://dx.doi.org/10.1007/s11427-013-4485-1DOI Listing
June 2013

Genome comparisons as a tool for antimicrobial target discovery.

Methods Mol Biol 2013 ;993:31-8

Shanghai Center for Bioinformation Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1007/978-1-62703-342-8_3DOI Listing
September 2013

De novo prediction of RNA-protein interactions from sequence information.

Mol Biosyst 2013 Jan 9;9(1):133-42. Epub 2012 Nov 9.

School of Science, Dalian Jiaotong University, Dalian 116028, China.

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http://dx.doi.org/10.1039/c2mb25292aDOI Listing
January 2013

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks.

Nucleic Acids Res 2013 Jan 5;41(2):e35. Epub 2012 Nov 5.

School of computer science and technology, Xidian University, 2 South Taibai Road, Xi'an Shaanxi, 710071, PR China.

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http://dx.doi.org/10.1093/nar/gks967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554231PMC
January 2013

The novel long non-coding RNA CRG regulates Drosophila locomotor behavior.

Nucleic Acids Res 2012 Dec 15;40(22):11714-27. Epub 2012 Oct 15.

State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gks943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526303PMC
December 2012

A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa.

Mol Plant 2013 May 17;6(3):830-46. Epub 2012 Sep 17.

Peking-Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1093/mp/sss087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716300PMC
May 2013

Regulatory elements of Caenorhabditis elegans ribosomal protein genes.

BMC Genomics 2012 Aug 28;13:433. Epub 2012 Aug 28.

Bioinformatics Division, Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Tsinghua University, Beijing, China.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575287PMC
August 2012

The human microbiome: a hot spot of microbial horizontal gene transfer.

Genomics 2012 Nov 25;100(5):265-70. Epub 2012 Jul 25.

Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.

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http://dx.doi.org/10.1016/j.ygeno.2012.07.012DOI Listing
November 2012

Transcription network analysis by a sparse binary factor analysis algorithm.

J Integr Bioinform 2012 Jul 23;9(2):198. Epub 2012 Jul 23.

Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.

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https://doi.org/10.1515/jib-2012-198
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http://dx.doi.org/10.2390/biecoll-jib-2012-198DOI Listing
July 2012

Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells.

Int J Cell Biol 2012 12;2012:672462. Epub 2012 Feb 12.

Laboratory of Bioinformation and Noncoding RNA and Center for Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1155/2012/672462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296955PMC
August 2012

Integrated sequence-structure motifs suffice to identify microRNA precursors.

PLoS One 2012 15;7(3):e32797. Epub 2012 Mar 15.

School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, PR China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032797PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305290PMC
August 2012

CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing.

Protein Cell 2012 Feb 17;3(2):148-52. Epub 2012 Mar 17.

Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.

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http://dx.doi.org/10.1007/s13238-012-2015-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875413PMC
February 2012

A differential sequencing-based analysis of the C. elegans noncoding transcriptome.

RNA 2012 Apr 16;18(4):626-39. Epub 2012 Feb 16.

Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1261/rna.030965.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312551PMC
April 2012

A binary matrix factorization algorithm for protein complex prediction.

Proteome Sci 2011 Oct 14;9 Suppl 1:S18. Epub 2011 Oct 14.

Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.

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http://proteomesci.biomedcentral.com/articles/10.1186/1477-5
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http://dx.doi.org/10.1186/1477-5956-9-S1-S18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724484PMC
October 2011

NONCODE v3.0: integrative annotation of long noncoding RNAs.

Nucleic Acids Res 2012 Jan 1;40(Database issue):D210-5. Epub 2011 Dec 1.

Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China.

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http://dx.doi.org/10.1093/nar/gkr1175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245065PMC
January 2012

ncFANs: a web server for functional annotation of long non-coding RNAs.

Nucleic Acids Res 2011 Jul;39(Web Server issue):W118-24

Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125796PMC
July 2011

Identification and analysis of intermediate size noncoding RNAs in the human fetal brain.

PLoS One 2011 18;6(7):e21652. Epub 2011 Jul 18.

Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021652PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138756PMC
November 2011

Predicting housekeeping genes based on Fourier analysis.

PLoS One 2011 8;6(6):e21012. Epub 2011 Jun 8.

Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021012PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110801PMC
October 2011

The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression.

Nucleic Acids Res 2011 Jul 4;39(12):5203-14. Epub 2011 Mar 4.

Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

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http://dx.doi.org/10.1093/nar/gkr102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130273PMC
July 2011