Ling-Ling Chen, Ph.D. - Publications

Affiliations: 
2009 University of Connecticut, Storrs, CT, United States 
Area:
Genetics, Molecular Biology

233 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Tseng CH, Chen LL, Su SM. Development of a system dynamics model for dioxin flow and its application to the energy sector. Heliyon. 7: e08361. PMID 34841101 DOI: 10.1016/j.heliyon.2021.e08361  1
2021 Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34791665 DOI: 10.1111/nyas.14713  1
2021 Wang S, Xiao Y, Zhou ZW, Yuan J, Guo H, Yang Z, Yang J, Sun P, Sun L, Deng Y, Xie WZ, Song JM, Qamar MTU, Xia W, Liu R, ... ... Chen LL, et al. High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height. Genome Biology. 22: 304. PMID 34736486 DOI: 10.1186/s13059-021-02522-9  1
2021 Song JM, Zhang Y, Zhou ZW, Lu S, Ma W, Lu C, Chen LL, Guo L. Oil plant genomes: current state of the science. Journal of Experimental Botany. PMID 34727176 DOI: 10.1093/jxb/erab472  1
2021 Liu CX, Chen LL. Expanded regulation of circular RNA translation. Molecular Cell. 81: 4111-4113. PMID 34686312 DOI: 10.1016/j.molcel.2021.09.023  1
2021 Tahir Ul Qamar M, Ahmad S, Khan A, Mirza MU, Ahmad S, Abro A, Chen LL, Almatroudi A, Wei DQ. Structural probing of HapR to identify potent phytochemicals to control Vibrio cholera through integrated computational approaches. Computers in Biology and Medicine. 138: 104929. PMID 34655900 DOI: 10.1016/j.compbiomed.2021.104929  1
2021 Chen LL, Wilusz JE. Methods for circular RNAs. Methods (San Diego, Calif.). PMID 34601050 DOI: 10.1016/j.ymeth.2021.09.011  1
2021 Wu M, Yang LZ, Chen LL. Long noncoding RNA and protein abundance in lncRNPs. Rna (New York, N.Y.). PMID 34526358 DOI: 10.1261/rna.078971.121  1
2021 Li X, Zhang JL, Lei YN, Liu XQ, Xue W, Zhang Y, Nan F, Gao X, Zhang J, Wei J, Yang L, Chen LL. Linking circular intronic RNA degradation and function in transcription by RNase H1. Science China. Life Sciences. PMID 34453665 DOI: 10.1007/s11427-021-1993-6  1
2021 Zhang Y, Yang L, Chen LL. Characterization of Circular RNAs. Methods in Molecular Biology (Clifton, N.J.). 2372: 179-192. PMID 34417752 DOI: 10.1007/978-1-0716-1697-0_16  1
2021 Li GW, Nan F, Yuan GH, Liu CX, Liu X, Chen LL, Tian B, Yang L. SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells. Genome Biology. 22: 221. PMID 34376223 DOI: 10.1186/s13059-021-02437-5  1
2021 Feng JW, Lu Y, Shao L, Zhang J, Li H, Chen LL. Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation. Plant Communications. 2: 100185. PMID 34327321 DOI: 10.1016/j.xplc.2021.100185  1
2021 Wu M, Xu G, Han C, Luan PF, Xing YH, Nan F, Yang LZ, Huang Y, Yang ZH, Shan L, Yang L, Liu J, Chen LL. lncRNA controls phase separation of FC/DFCs to facilitate Pol I transcription. Science (New York, N.Y.). 373: 547-555. PMID 34326237 DOI: 10.1126/science.abf6582  1
2021 He C, Liu H, Chen D, Xie WZ, Wang M, Li Y, Gong X, Yan W, Chen LL. CRISPR-Cereal: A Guide RNA Design Tool Integrating Regulome and Genomic Variation for Wheat, Maize and Rice. Plant Biotechnology Journal. PMID 34310056 DOI: 10.1111/pbi.13675  0.01
2021 Tahir Ul Qamar M, Ismail S, Ahmad S, Mirza MU, Abbasi SW, Ashfaq UA, Chen LL. Development of a Novel Multi-Epitope Vaccine Against Crimean-Congo Hemorrhagic Fever Virus: An Integrated Reverse Vaccinology, Vaccine Informatics and Biophysics Approach. Frontiers in Immunology. 12: 669812. PMID 34220816 DOI: 10.3389/fimmu.2021.669812  1
2021 Zhao H, Li J, Yang L, Qin G, Xia C, Xu X, Su Y, Liu Y, Ming L, Chen LL, Xiong L, Xie W. An inferred functional impact map of genetic variants in rice. Molecular Plant. PMID 34214659 DOI: 10.1016/j.molp.2021.06.025  1
2021 Zhou C, Chen LL, Lu RQ, Ma WW, Xiao R. Alteration of Intestinal Microbiota Composition in Oral Sensitized C3H/HeJ Mice Is Associated With Changes in Dendritic Cells and T Cells in Mesenteric Lymph Nodes. Frontiers in Immunology. 12: 631494. PMID 34177885 DOI: 10.3389/fimmu.2021.631494  0.01
2021 Wang XW, Liu CX, Chen LL, Zhang QC. RNA structure probing uncovers RNA structure-dependent biological functions. Nature Chemical Biology. 17: 755-766. PMID 34172967 DOI: 10.1038/s41589-021-00805-7  1
2021 Song JM, Xie WZ, Wang S, Guo YX, Koo DH, Kudrna D, Gong C, Huang Y, Feng JW, Zhang W, Zhou Y, Zuccolo A, Long E, Lee S, Talag J, ... ... Chen LL, et al. Two Gap-free Reference Genomes and a Global View of the Centromere Architecture in Rice. Molecular Plant. PMID 34171480 DOI: 10.1016/j.molp.2021.06.018  1
2021 Liu Y, Li ZF, Zhong YH, Zhao ZH, Deng WX, Chen LL, Liu BB, Du TJ, Zhang Y. Early combined rehabilitation intervention to improve the short-term prognosis of premature infants. Bmc Pediatrics. 21: 269. PMID 34107905 DOI: 10.1186/s12887-021-02727-8  1
2021 Shi F, Guo LC, Zhu WD, Cai MH, Chen LL, Wu L, Chen XJ, Zhu HY, Wu J. Human adipose tissue-derived MSCs improve psoriasis-like skin inflammation in mice by negatively regulating ROS. The Journal of Dermatological Treatment. 1-8. PMID 34060412 DOI: 10.1080/09546634.2021.1925622  1
2021 Xu G, Wu M, Chen LL. LETN and NPM1 tango in human nucleoli. Cell Research. PMID 33981018 DOI: 10.1038/s41422-021-00471-3  1
2021 Li J, Yuan D, Wang P, Wang Q, Sun M, Liu Z, Si H, Xu Z, Ma Y, Zhang B, Pei L, Tu L, Zhu L, Chen LL, Lindsey K, et al. Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology. 22: 119. PMID 33892774 DOI: 10.1186/s13059-021-02351-w  1
2021 Tahir Ul Qamar M, Ahmad S, Fatima I, Ahmad F, Shahid F, Naz A, Abbasi SW, Khan A, Mirza MU, Ashfaq UA, Chen LL. Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches. Computers in Biology and Medicine. 132: 104389. PMID 33866250 DOI: 10.1016/j.compbiomed.2021.104389  1
2021 Yao RW, Luan PF, Chen LL. An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies. Rna (New York, N.Y.). PMID 33846273 DOI: 10.1261/rna.078671.120  1
2021 Chen LL, Zhang DR, Li J, Wang HM, Song CH, Tang X, Guan Y, Chang Y, Wang WF. Albicanol Alleviates D-Galactose-Induced Aging and Improves Behavioral Ability Via by Alleviating Oxidative Stress-Induced Damage. Neurochemical Research. PMID 33761044 DOI: 10.1007/s11064-020-03220-x  1
2021 Shen Y, Chen LL, Gao J. CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes. Genomics, Proteomics & Bioinformatics. PMID 33662624 DOI: 10.1016/j.gpb.2020.06.021  1
2021 Ma XK, Xue W, Chen LL, Yang L. CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets. Methods (San Diego, Calif.). PMID 33588028 DOI: 10.1016/j.ymeth.2021.02.008  1
2021 Guo SK, Nan F, Liu CX, Yang L, Chen LL. Mapping circular RNA structures in living cells by SHAPE-MaP. Methods (San Diego, Calif.). PMID 33571668 DOI: 10.1016/j.ymeth.2021.01.011  1
2021 Zhou R, Sanz-Jimenez P, Zhu XT, Feng JW, Shao L, Song JM, Chen LL. Analysis of Rice Transcriptome Reveals the LncRNA/CircRNA Regulation in Tissue Development. Rice (New York, N.Y.). 14: 14. PMID 33507446 DOI: 10.1186/s12284-021-00455-2  1
2021 Statello L, Guo CJ, Chen LL, Huarte M. Author Correction: Gene regulation by long non-coding RNAs and its biological functions. Nature Reviews. Molecular Cell Biology. 22: 159. PMID 33420484 DOI: 10.1038/s41580-021-00330-4  1
2020 Statello L, Guo CJ, Chen LL, Huarte M. Gene regulation by long non-coding RNAs and its biological functions. Nature Reviews. Molecular Cell Biology. PMID 33353982 DOI: 10.1038/s41580-020-00315-9  1
2020 Tahir Ul Qamar M, Rehman A, Tusleem K, Ashfaq UA, Qasim M, Zhu X, Fatima I, Shahid F, Chen LL. Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches. Plos One. 15: e0244176. PMID 33351863 DOI: 10.1371/journal.pone.0244176  1
2020 Yang L, Xing F, He Q, Tahir Ul Qamar M, Chen LL, Xing Y. Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. International Journal of Molecular Sciences. 21. PMID 33348666 DOI: 10.3390/ijms21249618  1
2020 Zhan C, Lei L, Liu Z, Zhou S, Yang C, Zhu X, Guo H, Zhang F, Peng M, Zhang M, Li Y, Yang Z, Sun Y, Shi Y, Li K, ... ... Chen LL, et al. Author Correction: Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance. Nature Plants. PMID 33328597 DOI: 10.1038/s41477-020-00838-1  1
2020 Zhan C, Lei L, Liu Z, Zhou S, Yang C, Zhu X, Guo H, Zhang F, Peng M, Zhang M, Li Y, Yang Z, Sun Y, Shi Y, Li K, ... ... Chen LL, et al. Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance. Nature Plants. 6: 1447-1454. PMID 33299150 DOI: 10.1038/s41477-020-00816-7  1
2020 Li S, Li X, Xue W, Zhang L, Yang LZ, Cao SM, Lei YN, Liu CX, Guo SK, Shan L, Wu M, Tao X, Zhang JL, Gao X, Zhang J, ... ... Chen LL, et al. Screening for functional circular RNAs using the CRISPR-Cas13 system. Nature Methods. PMID 33288960 DOI: 10.1038/s41592-020-01011-4  1
2020 Li B, Wei WN, Wan QC, Peng K, Chen LL. Numerical Investigation into the Development Performance of Gas Hydrate by Depressurization Based on Heat Transfer and Entropy Generation Analyses. Entropy (Basel, Switzerland). 22. PMID 33286980 DOI: 10.3390/e22111212  0.01
2020 Jin XH, Zhou HL, Chen LL, Wang GF, Han QY, Zhang JG, Zhang X, Chen QY, Ye YH, Lin A, Yan WH. Peripheral immunological features of COVID-19 patients in Taizhou, China: A retrospective study. Clinical Immunology (Orlando, Fla.). 108642. PMID 33253854 DOI: 10.1016/j.clim.2020.108642  0.01
2020 Tahir Ul Qamar M, Zhu X, Khan MS, Xing F, Chen LL. Pan-genome: A promising resource for noncoding RNA discovery in plants. The Plant Genome. 13: e20046. PMID 33217199 DOI: 10.1002/Tpg2.20046  1
2020 Wang Y, Yang LZ, Chen LL. Protocol for Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 System. Star Protocols. 1: 100037. PMID 33111085 DOI: 10.1016/j.xpro.2020.100037  1
2020 Song JM, Liu DX, Xie WZ, Yang Z, Guo L, Liu K, Yang QY, Chen LL. BnPIR: Brassica napus Pan-genome Information Resource for 1,689 accessions. Plant Biotechnology Journal. PMID 33068485 DOI: 10.1111/pbi.13491  1
2020 Song Q, Bari A, Li H, Chen LL. Identification and analysis of micro-exons in AP2/ERF and MADS gene families. Febs Open Bio. PMID 32986930 DOI: 10.1002/2211-5463.12990  1
2020 Tahir Ul Qamar M, Shahid F, Aslam S, Ashfaq UA, Aslam S, Fatima I, Fareed MM, Zohaib A, Chen LL. Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2. Infectious Diseases of Poverty. 9: 132. PMID 32938504 DOI: 10.1186/S40249-020-00752-W  1
2020 Alamri MA, Tahir Ul Qamar M, Mirza MU, Alqahtani SM, Froeyen M, Chen LL. Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches. Journal of Pharmaceutical Analysis. PMID 32874702 DOI: 10.1016/J.Jpha.2020.08.012  1
2020 Wang Y, Chen LL. Organization and function of paraspeckles. Essays in Biochemistry. PMID 32830222 DOI: 10.1042/Ebc20200010  1
2020 Guo CJ, Xu G, Chen LL. Mechanisms of Long Noncoding RNA Nuclear Retention. Trends in Biochemical Sciences. PMID 32800670 DOI: 10.1016/J.Tibs.2020.07.001  1
2020 Chen LL. The expanding regulatory mechanisms and cellular functions of circular RNAs. Nature Reviews. Molecular Cell Biology. PMID 32366901 DOI: 10.1038/S41580-020-0243-Y  0.01
2020 Zhang Q, Hu J, Feng JW, Hu XT, Wang T, Gong WX, Huang K, Guo YX, Zou Z, Lin X, Zhou R, Yuan YQ, Zhang AD, Wei H, Cao G, ... ... Chen LL, et al. Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection. Genome Biology. 21: 99. PMID 32345342 DOI: 10.1186/s13059-020-02007-1  1
2020 Ul Qamar MT, Alqahtani SM, Alamri MA, Chen LL. Structural basis of SARS-CoV-2 3CL and anti-COVID-19 drug discovery from medicinal plants. Journal of Pharmaceutical Analysis. PMID 32296570 DOI: 10.1016/j.jpha.2020.03.009  1
2020 Guo CJ, Ma XK, Xing YH, Zheng CC, Xu YF, Shan L, Zhang J, Wang S, Wang Y, Carmichael GG, Yang L, Chen LL. Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells. Cell. PMID 32259487 DOI: 10.1016/J.Cell.2020.03.006  1
2020 Sturtevant D, Lu S, Zhou ZW, Shen Y, Wang S, Song JM, Zhong J, Burks DJ, Yang ZQ, Yang QY, Cannon AE, Herrfurth C, Feussner I, Borisjuk L, Munz E, ... ... Chen LL, et al. The genome of jojoba (): A taxonomically isolated species that directs wax ester accumulation in its seeds. Science Advances. 6: eaay3240. PMID 32195345 DOI: 10.1126/Sciadv.Aay3240  1
2020 Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. The Embo Journal. e103777. PMID 32090359 DOI: 10.15252/Embj.2019103777  0.01
2020 Yao RW, Liu CX, Chen LL. Linking RNA Processing and Function. Cold Spring Harbor Symposia On Quantitative Biology. PMID 32019863 DOI: 10.1101/Sqb.2019.84.039495  1
2020 Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie WZ, Cheng Y, Zhang Y, Liu K, Yang QY, ... Chen LL, et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants. PMID 31932676 DOI: 10.1038/S41477-019-0577-7  1
2020 Kong LY, Chen LL, Xiang W, Liu F. Intravenous Leiomyomatosis With Paradoxical Embolism: Unusual Presentation of Uterine Leiomyoma. Circulation. Cardiovascular Imaging. 13: e009930. PMID 31910667 DOI: 10.1161/CIRCIMAGING.119.009930  1
2020 Ma XK, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL, Yang L. CIRCexplorer3-CLEAR: A Pipeline for Direct Comparison of Circular and Linear RNA Expression. Genomics, Proteomics & Bioinformatics. PMID 31904419 DOI: 10.1016/J.Gpb.2019.11.004  1
2019 Li L, Cheng X, Chen L, Li J, Luo W, Li C. Long Noncoding Ribonucleic Acid MSTRG.59589 Promotes Porcine Skeletal Muscle Satellite Cells Differentiation by Enhancing the Function of . Frontiers in Genetics. 10: 1220. PMID 31850071 DOI: 10.3389/fgene.2019.01220  1
2019 Kong LY, Sun LL, Chen LL, Lv X, Liu F. Value of Index Beat in Evaluating Left Ventricular Systolic and Diastolic Function in Patients with Atrial Fibrillation: A Dual Pulsed-Wave Doppler Study. Ultrasound in Medicine & Biology. PMID 31784201 DOI: 10.1016/j.ultrasmedbio.2019.10.028  1
2019 Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL. Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Molecular Cell. PMID 31757757 DOI: 10.1016/J.Molcel.2019.10.024  1
2019 Chen LL, He XL, Chen KK. [Congenital deaf-mutism with pale complexion and anemia for 1 year in a school-aged girl]. Zhongguo Dang Dai Er Ke Za Zhi = Chinese Journal of Contemporary Pediatrics. 21: 1105-1109. PMID 31753093 DOI: 10.7499/j.issn.1008-8830.2019.11.010  0.01
2019 Yao RW, Xu G, Wang Y, Shan L, Luan PF, Wang Y, Wu M, Yang LZ, Xing YH, Yang L, Chen LL. Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus. Molecular Cell. PMID 31540874 DOI: 10.1016/J.Molcel.2019.08.014  1
2019 Song Q, Lv F, Tahir Ul Qamar M, Xing F, Zhou R, Li H, Chen LL. Identification and Analysis of Micro-Exon Genes in the Rice Genome. International Journal of Molecular Sciences. 20. PMID 31159166 DOI: 10.3390/ijms20112685  1
2019 Yao RW, Wang Y, Chen LL. Cellular functions of long noncoding RNAs. Nature Cell Biology. 21: 542-551. PMID 31048766 DOI: 10.1038/S41556-019-0311-8  1
2019 Liu CX, Li X, Nan F, Jiang S, Gao X, Guo SK, Xue W, Cui Y, Dong K, Ding H, Qu B, Zhou Z, Shen N, Yang L, Chen LL. Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity. Cell. PMID 31031002 DOI: 10.1016/J.Cell.2019.03.046  1
2019 Liu Y, Tahir Ul Qamar M, Feng JW, Ding Y, Wang S, Wu G, Ke L, Xu Q, Chen LL. Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species. Bmc Plant Biology. 19: 140. PMID 30987586 DOI: 10.1186/s12870-019-1757-3  1
2019 Chang JW, Ding Y, Tahir Ul Qamar M, Shen Y, Gao J, Chen LL. A deep learning model based on sparse auto-encoder for prioritizing cancer-related genes and drug target combinations. Carcinogenesis. PMID 30944926 DOI: 10.1093/carcin/bgz044  1
2019 Tahir Ul Qamar M, Zhu X, Xing F, Chen LL. ppsPCP: A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline. Bioinformatics (Oxford, England). PMID 30851098 DOI: 10.1093/bioinformatics/btz168  1
2019 Shao L, Xing F, Xu C, Zhang Q, Che J, Wang X, Song J, Li X, Xiao J, Chen LL, Ouyang Y, Zhang Q. Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 30833384 DOI: 10.1073/Pnas.1820513116  1
2019 Chen LL, Hu T, Xing ZY, Lu JS, Yang H, Huang X. Taibaiella helva sp. nov., isolated from farmland soil in China. International Journal of Systematic and Evolutionary Microbiology. PMID 30758282 DOI: 10.1099/ijsem.0.003281  1
2019 Ke L, Zhou Z, Xu XW, Wang X, Liu Y, Xu Y, Huang Y, Wang S, Deng X, Chen LL, Xu Q. Evolutionary dynamics of lincRNA transcription in nine citrus species. The Plant Journal : For Cell and Molecular Biology. PMID 30739398 DOI: 10.1111/tpj.14279  1
2019 Feng JW, Huang S, Guo YX, Liu D, Song JM, Gao J, Li H, Chen LL. Plant ISOform sequencing database (PISO): a comprehensive repertory of full-length transcripts in plants. Plant Biotechnology Journal. PMID 30633419 DOI: 10.1111/pbi.13076  1
2019 Dong R, Ma XK, Chen LL, Yang L. Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline. Methods in Molecular Biology (Clifton, N.J.). 1870: 137-149. PMID 30539552 DOI: 10.1007/978-1-4939-8808-2_10  1
2018 Tseng CH, Chen LL, Yeh PC. Modeling contamination conditions in small-scale industrial areas to estimate health savings benefits associated with remediation. Heliyon. 4: e00995. PMID 30623125 DOI: 10.1016/j.heliyon.2018.e00995  1
2018 Wang M, Tu L, Yuan D, Zhu, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G, Ye Z, Huang H, Yan F, Ma Y, Zhang L, ... ... Chen LL, et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature Genetics. PMID 30510239 DOI: 10.1038/S41588-018-0282-X  1
2018 Sun J, Liu H, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu HJ, Chen LL. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics (Oxford, England). PMID 30500879 DOI: 10.1093/bioinformatics/bty970  1
2018 Chen LL, Tseng CH, Tseng WJ. Development of a system dynamics model for polycyclic aromatic hydrocarbons and its application to assess the benefits of pollution reduction. Ecotoxicology and Environmental Safety. 166: 231-236. PMID 30273845 DOI: 10.1016/j.ecoenv.2018.09.072  1
2018 Xing YH, Chen LL. Processing and roles of snoRNA-ended long noncoding RNAs. Critical Reviews in Biochemistry and Molecular Biology. 1-11. PMID 30252509 DOI: 10.1080/10409238.2018.1508411  1
2018 Wang Y, Hu SB, Wang MR, Yao RW, Wu D, Yang L, Chen LL. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria. Nature Cell Biology. PMID 30250064 DOI: 10.1038/S41556-018-0204-2  0.01
2018 Chen LL, Chen F, Zhao HZ, Feng ZZ, Zhang H, Huang X. Aestuariimicrobium soli sp. nov., isolated from farmland soil, and emended description of the genus Aestuariimicrobium. International Journal of Systematic and Evolutionary Microbiology. PMID 30141771 DOI: 10.1099/ijsem.0.002986  1
2018 Yang SC, Guo YJ, Yu FY, Chen LL, Li WY, Ji ES. [Bosentan ameliorates hypertension in rats exposed to chronic intermittent hypoxia through inhibiting renal sympathetic nerve activity]. Sheng Li Xue Bao : [Acta Physiologica Sinica]. 70: 354-360. PMID 30112560  1
2018 Li X, Yang L, Chen LL. The Biogenesis, Functions, and Challenges of Circular RNAs. Molecular Cell. 71: 428-442. PMID 30057200 DOI: 10.1016/J.Molcel.2018.06.034  1
2018 Yang SC, Chen LL, Fu T, Li WY, Ji ES. [Improvement of hydrogen on liver oxidative stress injury in chronic intermittent hypoxia rats]. Zhongguo Ying Yong Sheng Li Xue Za Zhi = Zhongguo Yingyong Shenglixue Zazhi = Chinese Journal of Applied Physiology. 34: 61-64. PMID 29926661 DOI: 10.12047/j.cjap.5484.2018.016  1
2018 Lu LY, Chen LL, Xing ZY, Hu T, Lu JS, Huang X. Paenibacillus yanchengensis sp. nov., isolated from farmland soil. International Journal of Systematic and Evolutionary Microbiology. PMID 29664363 DOI: 10.1099/ijsem.0.002763  1
2018 Shu CC, Wang D, Guo J, Song JM, Chen SW, Chen LL, Gao JX. Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing ofDW2. Frontiers in Microbiology. 9: 307. PMID 29599755 DOI: 10.3389/fmicb.2018.00307  1
2018 Xiang JF, Yang Q, Liu CX, Wu M, Chen LL, Yang L. N6-Methyladenosines Modulate A-to-I RNA Editing. Molecular Cell. 69: 126-135.e6. PMID 29304330 DOI: 10.1016/J.Molcel.2017.12.006  1
2017 Yang N, Xu XW, Wang RR, Peng WL, Cai L, Song JM, Li W, Luo X, Niu L, Wang Y, Jin M, Chen L, Luo J, Deng M, Wang L, ... Chen LL, et al. Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nature Communications. 8: 1874. PMID 29187731 DOI: 10.1038/S41467-017-02063-5  1
2017 Liang D, Tatomer DC, Luo Z, Wu H, Yang L, Chen LL, Cherry S, Wilusz JE. The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting. Molecular Cell. 68: 940-954.e3. PMID 29174924 DOI: 10.1016/J.Molcel.2017.10.034  1
2017 Yang L, Chen LL. Enhancing the RNA engineering toolkit. Science (New York, N.Y.). 358: 996-997. PMID 29170221 DOI: 10.1126/Science.Aar2400  1
2017 Song JM, Lei Y, Shu CC, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J, Chen LL. Rice Information GateWay (RIGW): A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Molecular Plant. PMID 29042268 DOI: 10.1016/j.molp.2017.10.003  1
2017 Liu JX, Xu QH, Li S, Yu X, Liu W, Ouyang G, Zhang T, Chen LL. Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling. Biochimica Et Biophysica Acta. PMID 28887217 DOI: 10.1016/j.bbagrm.2017.09.001  1
2017 Wu H, Yang L, Chen LL. The Diversity of Long Noncoding RNAs and Their Generation. Trends in Genetics : Tig. PMID 28629949 DOI: 10.1016/J.Tig.2017.05.004  1
2017 Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Molecular Cell. PMID 28625552 DOI: 10.1016/J.Molcel.2017.05.023  1
2017 Wang JY, Chen LL, Zhou XH. Identifying prognostic signature in ovarian cancer using DirGenerank. Oncotarget. PMID 28615526 DOI: 10.18632/oncotarget.18189  1
2017 Xing YH, Yao RW, Zhang Y, Guo CJ, Jiang S, Xu G, Dong R, Yang L, Chen LL. SLERT Regulates DDX21 Rings Associated with Pol I Transcription. Cell. 169: 664-678.e16. PMID 28475895 DOI: 10.1016/J.Cell.2017.04.011  1
2017 Wang X, Xu Y, Zhang S, Cao L, Huang Y, Cheng J, Wu G, Tian S, Chen C, Liu Y, Yu H, Yang X, Lan H, Wang N, Wang L, ... ... Chen LL, et al. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nature Genetics. PMID 28394353 DOI: 10.1038/Ng.3839  1
2017 Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen L, Wang Y, Wong CC, Xiao X, Wang Z. Extensive translation of circular RNAs driven by N(6)-methyladenosine. Cell Research. PMID 28281539 DOI: 10.1038/Cr.2017.31  1
2017 Chen LL, Yang L. ALUternative Regulation for Gene Expression. Trends in Cell Biology. PMID 28209295 DOI: 10.1016/J.Tcb.2017.01.002  1
2017 Niu N, Xiang JF, Yang Q, Wang L, Wei Z, Chen LL, Yang L, Zou W. RNA-binding protein SAMD4 regulates skeleton development through translational inhibition of Mig6 expression. Cell Discovery. 3: 16050. PMID 28163927 DOI: 10.1038/Celldisc.2016.50  1
2017 Lee WH, Zhang E, Chiang CY, Yen YL, Chen LL, Liu MH, Kung CT, Hung SC. Comparing the Outcomes of Reporting and Trigger Tool Methods to Capture Adverse Events in the Emergency Department. Journal of Patient Safety. PMID 28098586 DOI: 10.1097/PTS.0000000000000341  1
2017 Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen LL. CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants. Molecular Plant. PMID 28089950 DOI: 10.1016/j.molp.2017.01.003  1
2017 Wang L, Guo J, Chang J, Qamar MTu, Chen L. Inference of Transcriptional Regulation from Expression Data Using Model Integration Current Bioinformatics. 12: 426-434. DOI: 10.2174/1574893612666171006162012  1
2016 Dong R, Ma XK, Chen LL, Yang L. Increased complexity of circRNA expression during species evolution. Rna Biology. 0. PMID 27982734 DOI: 10.1080/15476286.2016.1269999  1
2016 Zhang E, Hung SC, Wu CH, Chen LL, Tsai MT, Lee WH. Adverse event and error of unexpected life-threatening events within 24h of emergency department admission. The American Journal of Emergency Medicine. PMID 27974226 DOI: 10.1016/j.ajem.2016.11.062  1
2016 Chang JW, Zhou YQ, Ul Qamar MT, Chen LL, Ding YD. Prediction of Protein-Protein Interactions by Evidence Combining Methods. International Journal of Molecular Sciences. 17. PMID 27879651 DOI: 10.3390/ijms17111946  1
2016 Wu H, Yin QF, Luo Z, Yao RW, Zheng CC, Zhang J, Xiang JF, Yang L, Chen LL. Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. Molecular Cell. 64: 534-548. PMID 27871485 DOI: 10.1016/J.Molcel.2016.10.007  1
2016 Chen LL, Claw KG, Ramachandran S. A two-fold challenge: the experience of women of color in genomics. Genome Biology. 17: 210. PMID 27729075 DOI: 10.1186/S13059-016-1075-0  0.01
2016 Ye YN, Ma BG, Dong C, Zhang H, Chen LL, Guo FB. A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network. Scientific Reports. 6: 35082. PMID 27713529 DOI: 10.1038/srep35082  1
2016 Xing YH, Bai Z, Liu CX, Hu SB, Ruan M, Chen LL. Research progress of long noncoding RNA in China. Iubmb Life. PMID 27699981 DOI: 10.1002/Iub.1564  1
2016 Hu SB, Yao RW, Chen LL. Shedding light on paraspeckle structure by super-resolution microscopy. The Journal of Cell Biology. PMID 27646270 DOI: 10.1083/Jcb.201609008  1
2016 Zhang J, Chen LL, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao WB, Xing F, Lee S, Talag J, Song JM, Du B, Xie W, Luo M, et al. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Scientific Data. 3: 160076. PMID 27622467 DOI: 10.1038/Sdata.2016.76  1
2016 Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proceedings of the National Academy of Sciences of the United States of America. PMID 27535938 DOI: 10.1073/Pnas.1611012113  1
2016 Chen LL. Linking Long Noncoding RNA Localization and Function. Trends in Biochemical Sciences. PMID 27499234 DOI: 10.1016/J.Tibs.2016.07.003  0.01
2016 Chen LL. Ling-Ling Chen: Linking Long Noncoding RNA Processing and Function to RNA Biology. Trends in Biochemical Sciences. PMID 27473297 DOI: 10.1016/J.Tibs.2016.07.006  0.01
2016 Wang XX, Chen LL, Zhang YW, Mao PS. [Determination of Hard Rate of Alfalfa (Medicago sativa L.) Seeds with Near Infrared Spectroscopy]. Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. 36: 702-5. PMID 27400509 DOI: 10.3964/j.issn.1000-0593(2016)03-0702-04  1
2016 Guo J, Jing X, Peng WL, Nie Q, Zhai Y, Shao Z, Zheng L, Cai M, Li G, Zuo H, Zhang Z, Wang RR, Huang D, Cheng W, Yu Z, Chen LL, et al. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316. Scientific Reports. 6: 29211. PMID 27384076 DOI: 10.1038/srep29211  1
2016 Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Research. PMID 27365365 DOI: 10.1101/Gr.202895.115  1
2016 Ding Y, Li H, Chen LL, Xie K. Recent Advances in Genome Editing Using CRISPR/Cas9. Frontiers in Plant Science. 7: 703. PMID 27252719 DOI: 10.3389/fpls.2016.00703  1
2016 Zhang Y, Xue W, Li X, Zhang J, Chen S, Zhang JL, Yang L, Chen LL. The Biogenesis of Nascent Circular RNAs. Cell Reports. PMID 27068474 DOI: 10.1016/J.Celrep.2016.03.058  1
2016 Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL, Yang L. CircRNA-derived pseudogenes. Cell Research. PMID 27021280 DOI: 10.1038/Cr.2016.42  1
2016 Chen LL. The biogenesis and emerging roles of circular RNAs. Nature Reviews. Molecular Cell Biology. PMID 26908011 DOI: 10.1038/Nrm.2015.32  1
2016 Xu XW, Zhou XH, Wang RR, Peng WL, An Y, Chen LL. Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network. Scientific Reports. 6: 20715. PMID 26860696 DOI: 10.1038/srep20715  1
2016 Han YC, Song JM, Wang L, Shu CC, Guo J, Chen LL. Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. Scientific Reports. 6: 19486. PMID 26782814 DOI: 10.1038/srep19486  1
2016 Guo J, Zhang H, Wang C, Chang JW, Chen LL. Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02. Research in Microbiology. PMID 26776566 DOI: 10.1016/j.resmic.2015.12.005  1
2016 Zhang Y, Yang L, Chen LL. Characterization of Circular RNAs. Methods in Molecular Biology (Clifton, N.J.). 1402: 215-27. PMID 26721494 DOI: 10.1007/978-1-4939-3378-5_17  1
2015 Xiang JF, Yang L, Chen LL. The long noncoding RNA regulation at the MYC locus. Current Opinion in Genetics & Development. 33: 41-48. PMID 26254776 DOI: 10.1016/J.Gde.2015.07.001  1
2015 Guo J, Cheng G, Gou XY, Xing F, Li S, Han YC, Wang L, Song JM, Shu CC, Chen SW, Chen LL. Comprehensive transcriptome and improved genome annotation of Bacillus licheniformis WX-02. Febs Letters. PMID 26226425 DOI: 10.1016/j.febslet.2015.07.029  1
2015 Zhong C, Yin Q, Xie Z, Bai M, Dong R, Tang W, Xing YH, Zhang H, Yang S, Chen LL, Bartolomei MS, Ferguson-Smith A, Li D, Yang L, Wu Y, et al. CRISPR-Cas9-Mediated Genetic Screening in Mice with Haploid Embryonic Stem Cells Carrying a Guide RNA Library. Cell Stem Cell. PMID 26165924 DOI: 10.1016/J.Stem.2015.06.005  1
2015 Chen LL, Yang L. Gear Up in Circles. Molecular Cell. 58: 715-7. PMID 26046645 DOI: 10.1016/J.Molcel.2015.05.027  1
2015 Chen G, Gorelik L, Simon KJ, Pavlenco A, Cheung A, Brickelmaier M, Chen LL, Jin P, Weinreb PH, Sidhu SS. Synthetic antibodies and peptides recognizing progressive multifocal leukoencephalopathy-specific point mutations in polyomavirus JC capsid viral protein 1. Mabs. 7: 681-92. PMID 25879139 DOI: 10.1080/19420862.2015.1038447  1
2015 Hu SB, Xiang JF, Li X, Xu Y, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D, Chen LL. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes & Development. 29: 630-45. PMID 25792598 DOI: 10.1101/Gad.257048.114  1
2015 Chen LL, Yang L. Regulation of circRNA biogenesis. Rna Biology. 12: 381-8. PMID 25746834 DOI: 10.1080/15476286.2015.1020271  1
2015 Chen T, Xiang JF, Zhu S, Chen S, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L, Chen LL. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Research. 25: 459-76. PMID 25708366 DOI: 10.1038/cr.2015.24  1
2015 Wang C, Deng ZL, Xie ZM, Chu XY, Chang JW, Kong DX, Li BJ, Zhang HY, Chen LL. Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery. Febs Letters. 589: 285-94. PMID 25535697 DOI: 10.1016/j.febslet.2014.12.010  1
2015 Liu AC, Chou CY, Chen LL, Kuo CH. Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis. Journal of Biotechnology. 194: 124-31. PMID 25500375 DOI: 10.1016/J.Jbiotec.2014.11.026  1
2015 Yin QF, Hu SB, Xu YF, Yang L, Carmichael GG, Chen LL. SnoVectors for nuclear expression of RNA. Nucleic Acids Research. 43: e5. PMID 25378317 DOI: 10.1093/Nar/Gku1050  1
2015 Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Research. 43: D1018-22. PMID 25274737 DOI: 10.1093/Nar/Gku894  1
2015 Yin QF, Chen LL, Yang L. Fractionation of non-polyadenylated and ribosomal-free RNAs from mammalian cells. Methods in Molecular Biology (Clifton, N.J.). 1206: 69-80. PMID 25240887 DOI: 10.1007/978-1-4939-1369-5_6  1
2014 Zhang XO, Yin QF, Chen LL, Yang L. Gene expression profiling of non-polyadenylated RNA-seq across species. Genomics Data. 2: 237-41. PMID 26484100 DOI: 10.1016/J.Gdata.2014.07.005  1
2014 Yang L, Chen LL. Microexons go big. Cell. 159: 1488-9. PMID 25525868 DOI: 10.1016/J.Cell.2014.12.004  1
2014 Yang L, Chen LL. Competition of RNA splicing: line in or circle up. Science China. Life Sciences. 57: 1232-3. PMID 25398364 DOI: 10.1007/S11427-014-4770-7  1
2014 Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL, Yang L. Complementary sequence-mediated exon circularization. Cell. 159: 134-47. PMID 25242744 DOI: 10.1016/J.Cell.2014.09.001  1
2014 Chen LL, Zhao JC. Functional analysis of long noncoding RNAs in development and disease. Advances in Experimental Medicine and Biology. 825: 129-58. PMID 25201105 DOI: 10.1007/978-1-4939-1221-6_4  1
2014 Ding YD, Chang JW, Guo J, Chen D, Li S, Xu Q, Deng XX, Cheng YJ, Chen LL. Prediction and functional analysis of the sweet orange protein-protein interaction network. Bmc Plant Biology. 14: 213. PMID 25091279 DOI: 10.1186/s12870-014-0213-7  1
2014 Chen LL. Scientific migration of junior scientists to China. Genome Biology. 15: 119. PMID 25001910 DOI: 10.1186/Gb4180  1
2014 Zhang XO, Yin QF, Wang HB, Zhang Y, Chen T, Zheng P, Lu X, Chen LL, Yang L. Species-specific alternative splicing leads to unique expression of sno-lncRNAs. Bmc Genomics. 15: 287. PMID 24734784 DOI: 10.1186/1471-2164-15-287  1
2014 Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL. CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. Molecular Plant. 7: 1494-6. PMID 24719468 DOI: 10.1093/mp/ssu044  1
2014 Quan QM, Chen LL, Wang X, Li S, Yang XL, Zhu YG, Wang M, Cheng Z. Genetic diversity and distribution patterns of host insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau. Plos One. 9: e92293. PMID 24667533 DOI: 10.1371/journal.pone.0092293  1
2014 Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wu Z, Zhang S, Wang HB, Ge J, Lu X, Yang L, Chen LL. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Research. 24: 513-31. PMID 24662484 DOI: 10.1038/Cr.2014.35  1
2014 Chang TH, Lo WS, Ku C, Chen LL, Kuo CH. Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biology and Evolution. 6: 500-9. PMID 24534435 DOI: 10.1093/Gbe/Evu033  1
2014 Zhang Y, Yang L, Chen LL. Life without A tail: new formats of long noncoding RNAs. The International Journal of Biochemistry & Cell Biology. 54: 338-49. PMID 24513732 DOI: 10.1016/J.Biocel.2013.10.009  1
2014 Wang J, Chen D, Lei Y, Chang JW, Hao BH, Xing F, Li S, Xu Q, Deng XX, Chen LL. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. Plos One. 9: e87723. PMID 24489955 DOI: 10.1371/journal.pone.0087723  1
2014 Ku C, Lo WS, Chen LL, Kuo CH. Complete Genome Sequence of Spiroplasma apis B31T (ATCC 33834), a Bacterium Associated with May Disease of Honeybees (Apis mellifera). Genome Announcements. 2. PMID 24407648 DOI: 10.1128/Genomea.01151-13  1
2014 Chen D, Fu LY, Zhang Z, Li G, Zhang H, Jiang L, Harrison AP, Shanahan HP, Klukas C, Zhang HY, Ruan Y, Chen LL, Chen M. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Research. 42: 3028-43. PMID 24357409 DOI: 10.1093/Nar/Gkt1294  1
2014 Zhang Z, Sang J, Ma L, Wu G, Wu H, Huang D, Zou D, Liu S, Li A, Hao L, Tian M, Xu C, Wang X, Wu J, Xiao J, ... Chen LL, et al. RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Research. 42: D1222-8. PMID 24136999 DOI: 10.1093/Nar/Gkt926  1
2014 Hanf KJ, Arndt JW, Chen LL, Jarpe M, Boriack-Sjodin PA, Li Y, van Vlijmen HW, Pepinsky RB, Simon KJ, Lugovskoy A. Antibody humanization by redesign of complementarity-determining region residues proximate to the acceptor framework. Methods (San Diego, Calif.). 65: 68-76. PMID 23816785 DOI: 10.1016/J.Ymeth.2013.06.024  1
2013 Guo J, Li H, Chang JW, Lei Y, Li S, Chen LL. Prediction and characterization of protein-protein interaction network in Xanthomonas oryzae pv. oryzae PXO99 A. Research in Microbiology. 164: 1035-44. PMID 24113387 DOI: 10.1016/j.resmic.2013.09.001  1
2013 Zhang Y, Zhang XO, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L, Chen LL. Circular intronic long noncoding RNAs. Molecular Cell. 51: 792-806. PMID 24035497 DOI: 10.1016/J.Molcel.2013.08.017  1
2013 Lo WS, Ku C, Chen LL, Chang TH, Kuo CH. Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biology and Evolution. 5: 1512-23. PMID 23873917 DOI: 10.1093/Gbe/Evt108  1
2013 Ku C, Chung WC, Chen LL, Kuo CH. The Complete Plastid Genome Sequence of Madagascar Periwinkle Catharanthus roseus (L.) G. Don: Plastid Genome Evolution, Molecular Marker Identification, and Phylogenetic Implications in Asterids. Plos One. 8: e68518. PMID 23825699 DOI: 10.1371/Journal.Pone.0068518  1
2013 Jiao WB, Huang D, Xing F, Hu Y, Deng XX, Xu Q, Chen LL. Genome-wide characterization and expression analysis of genetic variants in sweet orange. The Plant Journal : For Cell and Molecular Biology. 75: 954-64. PMID 23738603 DOI: 10.1111/tpj.12254  1
2013 Ku C, Lo WS, Chen LL, Kuo CH. Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma. Genome Biology and Evolution. 5: 1151-64. PMID 23711669 DOI: 10.1093/Gbe/Evt084  1
2013 Chung WC, Chen LL, Lo WS, Lin CP, Kuo CH. Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. Plos One. 8: e62770. PMID 23626855 DOI: 10.1371/Journal.Pone.0062770  1
2013 Chung WC, Chen LL, Lo WS, Kuo PA, Tu J, Kuo CH. Complete Genome Sequence of Serratia marcescens WW4. Genome Announcements. 1: e0012613. PMID 23558532 DOI: 10.1128/Genomea.00126-13  1
2013 He H, Liu XL, Zhang HL, Yang J, Niu FB, Li ZX, Liu Y, Chen L. SNV and haplotype analysis reveals new CSRP1 variants associated with growth and carcass traits. Gene. 522: 206-13. PMID 23537997 DOI: 10.1016/j.gene.2013.03.030  1
2013 Zhu S, Xiang JF, Chen T, Chen LL, Yang L. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. Bmc Genomics. 14: 206. PMID 23537002 DOI: 10.1186/1471-2164-14-206  1
2013 Lu X, Chen D, Shu D, Zhang Z, Wang W, Klukas C, Chen LL, Fan Y, Chen M, Zhang C. The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiology. 162: 440-55. PMID 23478895 DOI: 10.1104/Pp.113.214874  1
2013 Lo WS, Chen LL, Chung WC, Gasparich GE, Kuo CH. Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. Bmc Genomics. 14: 22. PMID 23324436 DOI: 10.1186/1471-2164-14-22  1
2013 Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, et al. The draft genome of sweet orange (Citrus sinensis). Nature Genetics. 45: 59-66. PMID 23179022 DOI: 10.1038/ng.2472  1
2013 Lei Y, Kang SK, Gao J, Jia XS, Chen LL. Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A. Journal of Biomolecular Structure & Dynamics. 31: 342-50. PMID 22849520 DOI: 10.1080/07391102.2012.698218  1
2012 Sun YY, Lu M, Xi XW, Qiao QQ, Chen LL, Xu XM, Feng YJ. Response to Letter to the Editor. Reproductive Sciences (Thousand Oaks, Calif.). 19: NP2. PMID 29667862 DOI: 10.1177/1933719112451795  1
2012 Sun E, Chen LL, Jia XB, Qian Q, Cui L. [Affect regularity of medicinal species and heating time on flavonoids contents in Epimedium cut crude drug]. Zhong Yao Cai = Zhongyaocai = Journal of Chinese Medicinal Materials. 35: 1402-7. PMID 23451493  0.2
2012 Chen XJ, Chen LL, Shi X, Xie LX, Leng H, Ji J, Lu DD. The effect of desloratadine on patch test reactions in Chinese patients. Asian Pacific Journal of Allergy and Immunology / Launched by the Allergy and Immunology Society of Thailand. 30: 209-13. PMID 23156851  1
2012 Wang Q, Lei Y, Xu X, Wang G, Chen LL. Theoretical prediction and experimental verification of protein-coding genes in plant pathogen genome Agrobacterium tumefaciens strain C58. Plos One. 7: e43176. PMID 22984411 DOI: 10.1371/journal.pone.0043176  1
2012 Yin QF, Yang L, Zhang Y, Xiang JF, Wu YW, Carmichael GG, Chen LL. Long noncoding RNAs with snoRNA ends. Molecular Cell. 48: 219-30. PMID 22959273 DOI: 10.1016/J.Molcel.2012.07.033  1
2012 Fan XL, Barrett SC, Lin H, Chen LL, Zhou X, Gao JY. Rain pollination provides reproductive assurance in a deceptive orchid. Annals of Botany. 110: 953-8. PMID 22851311 DOI: 10.1093/Aob/Mcs165  1
2012 Chen LL, Cheng YG, Chen ZM, Li SX, Li XJ, Wang YS. [Mixed infections in children with Mycoplasma pneumoniae pneumonia]. Zhonghua Er Ke Za Zhi. Chinese Journal of Pediatrics. 50: 211-5. PMID 22801206  1
2012 Wang D, Su LY, Zhang AM, Li YY, Li XA, Chen LL, Long H, Yao YG. Mitochondrial DNA copy number, but not haplogroup, confers a genetic susceptibility to leprosy in Han Chinese from Southwest China. Plos One. 7: e38848. PMID 22719964 DOI: 10.1371/Journal.Pone.0038848  1
2012 Zhang F, Lin QY, Chen LL, Ke JG. Bis(2-amino-1,3-benzothia-zol-3-ium) bis-(7-oxabicyclo-[2.2.1]heptane-2,3-dicarboxyl-ato)cadmate hexa-hydrate. Acta Crystallographica. Section E, Structure Reports Online. 68: m818. PMID 22719361 DOI: 10.1107/S1600536812022593  0.01
2012 Chen LL, Chung WC, Lin CP, Kuo CH. Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. Plos One. 7: e34407. PMID 22479625 DOI: 10.1371/Journal.Pone.0034407  1
2012 Wu YQ, Chen DJ, He HB, Chen DS, Chen LL, Chen HC, Liu ZF. Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs. Plos One. 7: e30988. PMID 22292087 DOI: 10.1371/journal.pone.0030988  0.01
2012 Kim KM, Qin T, Jiang YY, Chen LL, Xiong M, Caetano-Anollés D, Zhang HY, Caetano-Anollés G. Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. Structure (London, England : 1993). 20: 67-76. PMID 22244756 DOI: 10.1016/J.Str.2011.11.003  1
2012 Chen D, Yuan C, Zhang J, Zhang Z, Bai L, Meng Y, Chen LL, Chen M. PlantNATsDB: a comprehensive database of plant natural antisense transcripts. Nucleic Acids Research. 40: D1187-93. PMID 22058132 DOI: 10.1093/Nar/Gkr823  1
2012 Chen LL, Carmichael GG. Nuclear Editing of mRNA 3'-UTRs. Current Topics in Microbiology and Immunology. 353: 111-21. PMID 21725897 DOI: 10.1007/82_2011_149  1
2011 Kong DX, Guo MY, Xiao ZH, Chen LL, Zhang HY. Historical variation of structural novelty in a natural product library. Chemistry & Biodiversity. 8: 1968-77. PMID 22083910 DOI: 10.1002/cbdv.201100156  1
2011 Sun YY, Lu M, Xi XW, Qiao QQ, Chen LL, Xu XM, Feng YJ. Regulation of epithelial-mesenchymal transition by homeobox gene DLX4 in JEG-3 trophoblast cells: a role in preeclampsia. Reproductive Sciences (Thousand Oaks, Calif.). 18: 1138-45. PMID 21602546 DOI: 10.1177/1933719111408112  1
2011 Chen D, Meng Y, Yuan C, Bai L, Huang D, Lv S, Wu P, Chen LL, Chen M. Plant siRNAs from introns mediate DNA methylation of host genes. Rna (New York, N.Y.). 17: 1012-24. PMID 21518803 DOI: 10.1261/Rna.2589011  1
2011 Peng S, Chen LL, Lei XX, Yang L, Lin H, Carmichael GG, Huang Y. Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells. Stem Cells (Dayton, Ohio). 29: 496-504. PMID 21425412 DOI: 10.1002/Stem.591  1
2011 Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL. Genomewide characterization of non-polyadenylated RNAs. Genome Biology. 12: R16. PMID 21324177 DOI: 10.1186/Gb-2011-12-2-R16  1
2011 Lin SM, Chen FA, Huang YF, Hsing LL, Chen LL, Wu LS, Liu TS, Chang-Chien GP, Chen KC, Chao HR. Negative associations between PBDE levels and thyroid hormones in cord blood. International Journal of Hygiene and Environmental Health. 214: 115-20. PMID 21106438 DOI: 10.1016/J.Ijheh.2010.10.002  1
2010 Chen LL, Carmichael GG. Long noncoding RNAs in mammalian cells: what, where, and why? Wiley Interdisciplinary Reviews. Rna. 1: 2-21. PMID 21956903 DOI: 10.1002/Wrna.5  1
2010 Chen LL, Yang L, Carmichael GG. Molecular basis for an attenuated cytoplasmic dsRNA response in human embryonic stem cells. Cell Cycle (Georgetown, Tex.). 9: 3552-64. PMID 20814227 DOI: 10.4161/Cc.9.17.12792  1
2010 Gorelik L, Lerner M, Bixler S, Crossman M, Schlain B, Simon K, Pace A, Cheung A, Chen LL, Berman M, Zein F, Wilson E, Yednock T, Sandrock A, Goelz SE, et al. Anti-JC virus antibodies: implications for PML risk stratification. Annals of Neurology. 68: 295-303. PMID 20737510 DOI: 10.1002/ana.22128  1
2010 Zhang HY, Chen LL, Li XJ, Zhang J. Evolutionary inspirations for drug discovery. Trends in Pharmacological Sciences. 31: 443-8. PMID 20724009 DOI: 10.1016/j.tips.2010.07.003  1
2010 Chen LL, Carmichael GG. Decoding the function of nuclear long non-coding RNAs. Current Opinion in Cell Biology. 22: 357-64. PMID 20356723 DOI: 10.1016/J.Ceb.2010.03.003  1
2010 Gao N, Chen LL, Ji HF, Wang W, Chang JW, Gao B, Zhang L, Zhang SC, Zhang HY. DIGA--a database of improved gene annotation for phytopathogens. Bmc Genomics. 11: 54. PMID 20089203 DOI: 10.1186/1471-2164-11-54  1
2010 Gabarra V, Cho S, Ramirez M, Ren Y, Chen LL, Cheung A, Cao X, Rennard R, Unruh KR, Graff CP, Browning B, Huet HA, McLachlan K. Antibodies directed to alpha6beta4 highlight the adhesive and signaling functions of the integrin in breast cancer cell lines. Cancer Biology & Therapy. 9: 437-45. PMID 20061819  1
2010 Gao J, Chen LL. Theoretical methods for identifying important functional genes in bacterial genomes. Research in Microbiology. 161: 1-8. PMID 19900539 DOI: 10.1016/j.resmic.2009.10.007  1
2009 Gao N, Ma BG, Zhang YS, Song Q, Chen LL, Zhang HY. Gene Expression Analysis of Four Radiation-resistant Bacteria. Genomics Insights. 2: 11-22. PMID 26244019  1
2009 Zhao JN, Wang Y, Zhao BS, Chen LL. Analyzing S-adenosylhomocysteine hydrolase gene sequences in deuterostome genomes. Journal of Biomolecular Structure & Dynamics. 27: 371-80. PMID 19795919 DOI: 10.1080/07391102.2009.10507323  1
2009 Chen LL, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Molecular Cell. 35: 467-78. PMID 19716791 DOI: 10.1016/J.Molcel.2009.06.027  1
2009 Qu G, Wang W, Chen LL, Qian SS, Zhang HY. tRNA-dependent cysteine biosynthetic pathway represents a strategy to increase cysteine contents by preventing it from thermal degradation: thermal adaptation of methanogenic archaea ancestor. Journal of Biomolecular Structure & Dynamics. 27: 111-4. PMID 19583437 DOI: 10.1080/07391102.2009.10507301  1
2009 Chen LL, Hui C, Lin ZS. Habitat destruction and the extinction debt revisited: the Allee effect. Mathematical Biosciences. 221: 26-32. PMID 19559716 DOI: 10.1016/j.mbs.2009.06.003  1
2009 Zhang HY, Li XJ, Gao N, Chen LL. Antioxidants used by Deinococcus radiodurans and implications for antioxidant drug discovery. Nature Reviews. Microbiology. 7: 476; author reply 47. PMID 19444250 DOI: 10.1038/nrmicro2073-c1  1
2008 Chen LL, Gabarra V, Cho S, Browning B, Cao X, Huet H, Cheung A, Morena R, Ramirez M, Shields M, Blake Pepinsky R, McLachlan K. Functional characterization of integrin alpha6beta4 adhesion interactions using soluble integrin constructs reveals the involvement of different functional domains in the beta4 subunit. Cell Communication & Adhesion. 15: 317-31. PMID 18979297 DOI: 10.1080/15419060802428356  1
2008 Chen LL, Carmichael GG. Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle (Georgetown, Tex.). 7: 3294-301. PMID 18948735 DOI: 10.4161/Cc.7.21.6927  1
2008 Huang XQ, Huang XJ, Zhang LH, Chen LL, Lu YB, Zhang WP, Wei EQ. [5-Lipoxygenase/cysteinyl leukotriene pathway is not involved in injury of rat C6 glioma cells induced by oxygen-glucose deprivation]. Zhejiang Da Xue Xue Bao. Yi Xue Ban = Journal of Zhejiang University. Medical Sciences. 37: 456-62. PMID 18925711  0.01
2008 Zhou J, Wang Q, Chen LL, Carmichael GG. On the mechanism of induction of heterochromatin by the RNA-binding protein vigilin. Rna (New York, N.Y.). 14: 1773-81. PMID 18648073 DOI: 10.1261/Rna.1036308  1
2008 Wang J, Ma BG, Zhang HY, Chen LL, Zhang SC. How does gene expression level contribute to thermophilic adaptation of prokaryotes? An exploration based on predictors. Gene. 421: 32-6. PMID 18621118 DOI: 10.1016/j.gene.2008.06.020  1
2008 Chen LL, DeCerbo JN, Carmichael GG. Alu element-mediated gene silencing. The Embo Journal. 27: 1694-705. PMID 18497743 DOI: 10.1038/Emboj.2008.94  1
2008 Rushe M, Silvian L, Bixler S, Chen LL, Cheung A, Bowes S, Cuervo H, Berkowitz S, Zheng T, Guckian K, Pellegrini M, Lugovskoy A. Structure of a NEMO/IKK-associating domain reveals architecture of the interaction site. Structure (London, England : 1993). 16: 798-808. PMID 18462684 DOI: 10.1016/J.Str.2008.02.012  1
2008 Chen LL, Ma BG, Gao N. Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043. The Febs Journal. 275: 198-206. PMID 18067578 DOI: 10.1111/j.1742-4658.2007.06190.x  1
2007 Chen LL, Wang GZ, Zhang HY. Sterol biosynthesis and prokaryotes-to-eukaryotes evolution. Biochemical and Biophysical Research Communications. 363: 885-8. PMID 17923113 DOI: 10.1016/j.bbrc.2007.09.093  1
2007 Ji HF, Kong DX, Shen L, Chen LL, Ma BG, Zhang HY. Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biology. 8: R176. PMID 17727706 DOI: 10.1186/gb-2007-8-8-r176  1
2007 Ma BG, Chen LL, Zhang HY. What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms. Journal of Molecular Biology. 370: 439-48. PMID 17524416 DOI: 10.1016/j.jmb.2007.04.051  1
2007 Ji HF, Zhang HY, Chen LL. Why are prion diseases precluded by non-mammals? Trends in Biochemical Sciences. 32: 206-8; discussion 20. PMID 17419063 DOI: 10.1016/j.tibs.2007.03.004  1
2007 Wang GZ, Chen LL, Zhang HY. Phase-dependent nucleotide substitution in protein-coding sequences. Biochemical and Biophysical Research Communications. 355: 599-602. PMID 17300744 DOI: 10.1016/j.bbrc.2007.01.006  1
2007 Wang GZ, Chen LL, Zhang HY. Neighboring-site effects of amino acid mutation. Biochemical and Biophysical Research Communications. 353: 531-4. PMID 17198679 DOI: 10.1016/j.bbrc.2006.12.089  1
2006 Peng GZ, Chen LL, Tian DC. [Progress in the study of gene duplication]. Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. 28: 886-92. PMID 16825179  1
2006 Chen LL, Peng GZ, Zhang WL, Tian DC. [The significance of mutations in genomic evolution]. Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. 28: 631-8. PMID 16735247  1
2006 Chen LL. Identification of genomic islands in six plant pathogens. Gene. 374: 134-41. PMID 16581205 DOI: 10.1016/j.gene.2006.01.029  1
2006 Baker DP, Lin EY, Lin K, Pellegrini M, Petter RC, Chen LL, Arduini RM, Brickelmaier M, Wen D, Hess DM, Chen L, Grant D, Whitty A, Gill A, Lindner DJ, et al. N-terminally PEGylated human interferon-beta-1a with improved pharmacokinetic properties and in vivo efficacy in a melanoma angiogenesis model. Bioconjugate Chemistry. 17: 179-88. PMID 16417267 DOI: 10.1021/Bc050237Q  1
2006 Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR, Rajakumar K. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Research. 34: e3. PMID 16414954 DOI: 10.1093/nar/gnj005  1
2005 Wu H, Yang Y, Jiang SJ, Chen LL, Gao HX, Fu QS, Li F, Ma BG, Zhang HY. DCCP and DICP: construction and analyses of databases for copper- and iron-chelating proteins. Genomics, Proteomics & Bioinformatics. 3: 52-7. PMID 16144523 DOI: 10.1016/S1672-0229(05)03008-1  1
2005 Ma BG, Chen LL. The most deviated codon position in AT-rich bacterial genomes: a function related analysis. Journal of Biomolecular Structure & Dynamics. 23: 143-9. PMID 16060688 DOI: 10.1080/07391102.2005.10507055  1
2005 Cui YM, Huang QQ, Xu J, Chen LL, Li JY, Ye QZ, Li J, Nan FJ. Identification of potent type I MetAPs inhibitors by simple bioisosteric replacement. Part 2: SAR studies of 5-heteroalkyl substituted TCAT derivatives. Bioorganic & Medicinal Chemistry Letters. 15: 4130-5. PMID 16005224 DOI: 10.1016/j.bmcl.2005.06.005  1
2005 Cui YM, Huang QQ, Xu J, Chen LL, Li JY, Ye QZ, Li J, Nan FJ. Identification of potent type I MetAP inhibitors by simple bioisosteric replacement. Part 1: Synthesis and preliminary SAR studies of thiazole-4-carboxylic acid thiazol-2-ylamide derivatives. Bioorganic & Medicinal Chemistry Letters. 15: 3732-6. PMID 15993057 DOI: 10.1016/j.bmcl.2005.05.055  1
2005 Chen LL, Gao F. Detection of nucleolar organizer and mitochondrial DNA insertion regions based on the isochore map of Arabidopsis thaliana. The Febs Journal. 272: 3328-36. PMID 15978039 DOI: 10.1111/j.1742-4658.2005.04748.x  1
2005 Fu QS, Li F, Chen LL. Gene expression analysis of six GC-rich Gram-negative phytopathogens. Biochemical and Biophysical Research Communications. 332: 380-7. PMID 15910748 DOI: 10.1016/j.bbrc.2005.04.128  1
2005 Zheng WX, Chen LL, Ou HY, Gao F, Zhang CT. Coronavirus phylogeny based on a geometric approach. Molecular Phylogenetics and Evolution. 36: 224-32. PMID 15890535 DOI: 10.1016/j.ympev.2005.03.030  1
2003 Chen LL, Zhang CT. Gene recognition from questionable ORFs in bacterial and archaeal genomes Journal of Biomolecular Structure and Dynamics. 21: 99-109. PMID 12854962 DOI: 10.1080/07391102.2003.10506908  1
2003 Chen LL, Zhang CT. Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages Biochemical and Biophysical Research Communications. 306: 310-317. PMID 12788106 DOI: 10.1016/S0006-291X(03)00973-2  1
1993 Chen LL, Clawson ML, Bilgrami S, Carmichael G. A sequence-specific single-stranded DNA-binding protein that is responsive to epidermal growth factor recognizes an S1 nuclease-sensitive region in the epidermal growth factor receptor promoter. Cell Growth & Differentiation : the Molecular Biology Journal of the American Association For Cancer Research. 4: 975-83. PMID 8117624  0.2
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