delete extraneous refs

-@article{liQuantitativeNuclearHistomorphometric2019,

- title = {Quantitative Nuclear Histomorphometric Features Are Predictive of {{Oncotype DX}} Risk Categories in Ductal Carcinoma in Situ: Preliminary Findings},

- shorttitle = {Quantitative Nuclear Histomorphometric Features Are Predictive of {{Oncotype DX}} Risk Categories in Ductal Carcinoma in Situ},

- author = {Li, Haojia and Whitney, Jon and Bera, Kaustav and Gilmore, Hannah and Thorat, Mangesh A. and Badve, Sunil and Madabhushi, Anant},

- date = {2019-10-17},

- journaltitle = {Breast Cancer Research},

- shortjournal = {Breast Cancer Research},

- volume = {21},

- number = {1},

- pages = {114},

- issn = {1465-542X},

- doi = {10.1186/s13058-019-1200-6},

- url = {https://doi.org/10.1186/s13058-019-1200-6},

- urldate = {2020-02-04},

- abstract = {Oncotype DX (ODx) is a 12-gene assay assessing the recurrence risk (high, intermediate, and low) of ductal carcinoma in situ (pre-invasive breast cancer), which guides clinicians regarding prescription of radiotherapy. However, ODx is expensive, time-consuming, and tissue-destructive. In addition, the actual prognostic meaning for the intermediate ODx risk category remains unclear.}

-}

-@article{liuHnRNPA1SpecificallyRecognizes2018,

- title = {{{HnRNPA1 Specifically Recognizes}} the {{Base}} of {{Nucleotide}} at the {{Loop}} of {{RNA G-Quadruplex}}},

- author = {Liu, Xiao and Xu, Yan},

- date = {2018-01-22},

- journaltitle = {Molecules (Basel, Switzerland)},

- shortjournal = {Molecules},

- volume = {23},

- eprint = {29361764},

- eprinttype = {pmid},

- pages = {E237},

- issn = {1420-3049},

- doi = {10.3390/molecules23010237},

- abstract = {Human telomere RNA performs various cellular functions, such as telomere length regulation, heterochromatin formation, and end protection. We recently demonstrated that the loops in the RNA G-quadruplex are important in the interaction of telomere RNA with heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1). Here, we report on a detailed analysis of hnRNPA1 binding to telomere RNA G-quadruplexes with a group of loop variants using an electrophoretic mobility shift assay (EMSA) and circular dichroism (CD) spectroscopy. We found that the hnRNPA1 binds to RNA G-quadruplexes with the 2'-O-methyl and DNA loops, but fails to bind with the abasic RNA and DNA loops. These results suggested that hnRNPA1 binds to the loop of the RNA G-quadruplex by recognizing the base of the loop's nucleotides. The observation provides the first evidence that the base of the loop's nucleotides is a key factor for hnRNPA1 specifically recognizing the RNA G-quadruplex.},

- langid = {english},

- pmcid = {PMC6017123},

- keywords = {base,Circular Dichroism,Electrophoretic Mobility Shift Assay,G-Quadruplexes,Heterogeneous Nuclear Ribonucleoprotein A1,hnRNPA1,Humans,loop of RNA G-quadruplex,Nucleotides,Protein Binding,RNA,RNA G-quadruplex,Telomere,telomere RNA}

-}

-@article{liuHNRNPH1NovelRegulator2021,

- title = {{{HNRNPH1 Is}} a {{Novel Regulator Of Cellular Proliferation}} and {{Disease Progression}} in {{Chronic Myeloid Leukemia}}},

- author = {Liu, Menghan and Yang, Lin and Liu, Xiaojun and Nie, Ziyuan and Zhang, Xiaoyan and Lu, Yaqiong and Pan, Yuxia and Wang, Xingzhe and Luo, Jianmin},

- date = {2021-07-06},

- journaltitle = {Frontiers in Oncology},

- shortjournal = {Front Oncol},

- volume = {11},

- eprint = {34295818},

- eprinttype = {pmid},

- pages = {682859},

- issn = {2234-943X},

- doi = {10.3389/fonc.2021.682859},

- url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8290130/},

- urldate = {2023-01-10},

- abstract = {RNA binding proteins act as essential modulators in cancers by regulating biological cellular processes. Heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1), as a key member of the heterogeneous nuclear ribonucleoproteins family, is frequently upregulated in multiple cancer cells and involved in tumorigenesis. However, the function of HNRNPH1 in chronic myeloid leukemia (CML) remains unclear. In the present study, we revealed that HNRNPH1 expression level was upregulated in CML patients and cell lines. Moreover, the higher level of HNRNPH1 was correlated with disease progression of CML. In vivo and in vitro experiments showed that knockdown of HNRNPH1 inhibited cell proliferation and promoted cell apoptosis in CML cells. Importantly, knockdown of HNRNPH1 in CML cells enhanced sensitivity to imatinib. Mechanically, HNRNPH1 could bind to the mRNA of PTPN6 and negatively regulated its expression. PTPN6 mediated the regulation between HNRNPH1 and PI3K/AKT activation. Furthermore, the HNRNPH1–PTPN6–PI3K/AKT axis played a critical role in CML tumorigenesis and development. The present study first investigated the deregulated HNRNPH1–PTPN6–PI3K/AKT axis moderated cell growth and apoptosis in CML cells, whereby targeting this pathway may be a therapeutic CML treatment.},

- pmcid = {PMC8290130}

-}

-

-@article{liuMethyladenosinedependentRNAStructural2015,

- title = {N(6)-Methyladenosine-Dependent {{RNA}} Structural Switches Regulate {{RNA-protein}} Interactions},

- author = {Liu, Nian and Dai, Qing and Zheng, Guanqun and He, Chuan and Parisien, Marc and Pan, Tao},

- date = {2015-02-26},

- journaltitle = {Nature},

- shortjournal = {Nature},

- volume = {518},

- number = {7540},

- eprint = {25719671},

- eprinttype = {pmid},

- pages = {560--564},

- issn = {1476-4687},

- doi = {10.1038/nature14234},

- abstract = {RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBMs). However, RBMs can be buried within their local RNA structures, thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs, but how m(6)A achieves its wide-ranging physiological role needs further exploration. Here we show in human cells that m(6)A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism 'the m(6)A-switch'. We found that m(6)A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing. Combining photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and anti-m(6)A immunoprecipitation (MeRIP) approaches enabled us to identify 39,060 m(6)A-switches among HNRNPC-binding sites; and global m(6)A reduction decreased HNRNPC binding at 2,798 high-confidence m(6)A-switches. We determined that these m(6)A-switch-regulated HNRNPC-binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m(6)A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m(6)A-dependent RNA structural remodelling, and provide a new direction for investigating RNA-modification-coded cellular biology.},

- langid = {english},

- pmcid = {PMC4355918},

- keywords = {Adenosine,Alternative Splicing,Base Sequence,Cross-Linking Reagents,HEK293 Cells,HeLa Cells,Heterogeneous-Nuclear Ribonucleoprotein Group C,Humans,Immunoprecipitation,Nucleic Acid Conformation,Nucleotide Motifs,Protein Binding,RNA Messenger,Transcriptome}

-}

-

-@article{liuMuscleDevelopmentalDefects2017,

- title = {Muscle Developmental Defects in Heterogeneous Nuclear {{Ribonucleoprotein A1}} Knockout Mice},

- author = {Liu, Ting-Yuan and Chen, Yu-Chia and Jong, Yuh-Jyh and Tsai, Huai-Jen and Lee, Chien-Chin and Chang, Ya-Sian and Chang, Jan-Gowth and Chang, Yung-Fu},

- date = {2017-01-11},

- journaltitle = {Open Biology},

- shortjournal = {Open Biol},

- volume = {7},

- number = {1},

- eprint = {28077597},

- eprinttype = {pmid},

- pages = {160303},

- issn = {2046-2441},

- doi = {10.1098/rsob.160303},

- url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303281/},

- urldate = {2023-01-09},

- abstract = {Heterogeneous ribonucleoprotein A1 (hnRNP A1) is crucial for regulating alternative splicing. Its integrated function within an organism has not, however, been identified. We generated hnRNP A1 knockout mice to study the role of hnRNP A1 in vivo. The knockout mice, hnRNP A1−/−, showed embryonic lethality because of muscle developmental defects. The blood pressure and heart rate of the heterozygous mice were higher than those of the wild-type mice, indicating heart function defects. We performed mouse exon arrays to study the muscle development mechanism. The processes regulated by hnRNP A1 included cell adhesion and muscle contraction. The expression levels of muscle development-related genes in hnRNP A1+/− mice were significantly different from those in wild-type mice, as detected using qRT-PCR. We further confirmed the alternative splicing patterns of muscle development-related genes including mef2c, lrrfip1, usp28 and abcc9. Alternative mRNA isoforms of these genes were increased in hnRNP A1+/− mice compared with wild-type mice. Furthermore, we revealed that the functionally similar hnRNP A2/B1 did not compensate for the expression of hnRNP A1 in organisms. In summary, our study demonstrated that hnRNP A1 plays a critical and irreplaceable role in embryonic muscle development by regulating the expression and alternative splicing of muscle-related genes.},

- pmcid = {PMC5303281}

-}

-

-@article{liuN6methyladenosineAltersRNA2017,

- title = {N6-Methyladenosine Alters {{RNA}} Structure to Regulate Binding of a Low-Complexity Protein},

- author = {Liu, Nian and Zhou, Katherine I. and Parisien, Marc and Dai, Qing and Diatchenko, Luda and Pan, Tao},

- date = {2017-06-02},

- journaltitle = {Nucleic Acids Research},

- shortjournal = {Nucleic Acids Res},

- volume = {45},

- number = {10},

- eprint = {28334903},

- eprinttype = {pmid},

- pages = {6051--6063},

- issn = {1362-4962},

- doi = {10.1093/nar/gkx141},

- abstract = {N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m6A modification to control mRNA maturation, translation and decay. m6A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m6A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m6A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro. The Arg-Gly-Gly repeats within the low-complexity region are required for binding to the RNA motif exposed by m6A methylation. We identified 13,191 m6A sites in the transcriptome that regulate RNA-HNRNPG interaction and thereby alter the expression and alternative splicing pattern of target mRNAs. Low-complexity regions are pervasive among mRNA binding proteins. Our results show that m6A-dependent RNA structural alterations can promote direct binding of m6A-modified RNAs to low-complexity regions in RNA binding proteins.},

- langid = {english},

- pmcid = {PMC5449601},

- keywords = {Adenosine,Alternative Splicing,Conserved Sequence,Gene Knockdown Techniques,HEK293 Cells,HeLa Cells,Heterogeneous-Nuclear Ribonucleoproteins,Humans,Methyltransferases,Nucleic Acid Conformation,Oligoribonucleotides,Phylogeny,Protein Binding,RNA,RNA Interference,RNA Long Noncoding,RNA Small Interfering,Sequence Analysis RNA,Transcriptome}

-}

-

-@article{liuS1PR1EffectiveTarget2012,

- title = {{{S1PR1}} Is an Effective Target to Block {{STAT3}} Signaling in Activated {{B}} Cell-like Diffuse Large {{B-cell}} Lymphoma.},

- author = {Liu, Yong and Deng, Jiehui and Wang, Lin and Lee, Heehyoung and Armstrong, Brian and Scuto, Anna and Kowolik, Claudia and Weiss, Lawrence M and Forman, Stephen and Yu, Hua},

- date = {2012-08},

- journaltitle = {Blood},

- volume = {120},

- number = {7},

- pages = {1458--1465}

-}

- keywords = {Cancer genomics,Lymphocytes,Lymphoid tissues,Oncology},

- annotation = {Bandiera\_abtest: a\\

-Cc\_license\_type: cc\_by\\

-Cg\_type: Nature Research Journals\\

-Primary\_atype: Research\\

-Subject\_term: Cancer genomics;Lymphocytes;Lymphoid tissues;Oncology\\

-Subject\_term\_id: cancer-genomics;lymphocytes;lymphoid-tissues;oncology}