personalized-peptide-arrays-for-detection-hla-alloantibodies-organ

Personalized Peptide Arrays for Detection of HLA Alloantibodies in Organ Transplantation

In organ transplantation, the function and longevity of the graft critically rely on the success of controlling immunological rejection reactivity against ...

Southeast University

Modular protein domains are functional units that can be modified through the acquisition of new intrinsic activities or by the formation of novel domain combinations, thereby contributing to the evolution of proteins with new biological properties. Here, we assign proteins to groups with related domain compositions and functional properties, termed "domain clubs," which we use to compare multiple eukaryotic proteomes. This analysis shows that different domain types can take distinct evolutionary trajectories, which correlate with the conservation, gain, expansion, or decay of particular biological processes. Evolutionary jumps are associated with a domain that coordinately acquires a new intrinsic function and enters new domain clubs, thereby providing the modified domain with access to a new cellular microenvironment. We also coordinately analyzed the covalent and noncovalent interactions of different domain types to assess the molecular compartment occupied by each domain. This reveals that specific subsets of domains demarcate particular cellular processes, such as growth factor signaling, chromatin remodeling, apoptotic and inflammatory responses, or vesicular trafficking. We suggest that domains, and the proteins in which they reside, are selected during evolution through reciprocal interactions with protein domains in their local microenvironment. Based on this scheme, we propose a mechanism by which Tudor domains may have evolved to support different modes of epigenetic regulation and suggest a role for the germline group of mammalian Tudor domains in Piwi-regulated RNA biology.

Eukaryotic protein domains as functional units of cellular evolution.

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

The sequence and de novo assembly of the giant panda genome.

Early growth response gene 1 (EGR1) has been implicated in megakaryocyte differentiation induced by phorbol ester. But the molecule mechanism of EGR1 in this process has not been widely investigated. The identification of direct EGR1 target genes in a global scale is critical for our understanding of how EGR1 contributes to this process. In this study, we provide a global survey on the binding location of EGR1 in the K562 cells using chromatin immunoprecipitation and massively parallel sequencing. Over 14 000 highly confident in vivo EGR1 binding sites were identified in phorbol 12-myristate 13-acetate-treated K562 cells. More than 70% of these genomic sites associated with EGR1 binding were located around annotated gene regions. Molecular functional classification of 6138 putative EGR1 target genes showed that the transcription factor class (695 of 6138; 11%) is the largest significantly enriched one. The results showed that a high coverage of the genome and a high positive rate achieve were achieved. This whole genome study on the EGR1 targets may provide a better understanding of the EGR1 regulated genes and the downstream pathway in megakaryocyte differentiation.

Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing.

Although much is known about microRNAs' regulation in gene expression and their contributions in cell fate, to date, globally lineage-(cell-) specific identification of the binding events between a transcription factor and its targeting microRNA genes is still waiting for elucidation. In this paper, we performed a ChIP-Seq experiment to find the targeting microRNA genes of a transcription factor, Egr1, in human erythroleukemia cell line K562. We found Egr1 binding sites near the promoters of 124 distinct microRNA genes, accounting for about 42% of the miRNAs which have high-confidence predicted promoters (294). We also found EGR1 bind to another 63 pre-miRNAs. We chose 12 of the 187 microRNAs with Egr1 binding sites to perform ChIP-PCR assays and the positive binding signal from ChIP-PCR confirmed the ChIP-Seq results. Our experiments provide the first global binding profile between Egr1 and its targeting microRNA genes in PMA-treated K562 cells, which may facilitate the understanding of pathways controlling microRNA biology in this specific cell line.

Global Egr1-miRNAs binding analysis in PMA-induced K562 cells using ChIP-Seq.

Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis.

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.

Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increased site accessibility around miRNA target sites in plants. Guanine-cytosine (GC)-poor codons are preferred in the flank region of miRNA target sites. Within-genome analyses show significant variation among miRNA targets in species. GC content of the target gene can partly explain the variation of site accessibility among miRNA targets. miRNA targets in GC-rich genes show stronger selection signals than those in GC-poor genes. Gene's codon usage bias and the conservation level of miRNA and its target also have some effects on site accessibility, but the expression level of miRNA or its target and the mechanism of miRNA activity do not contribute to site accessibility differences among miRNA targets. We suggest that synonymous codons near miRNA targets are selected for efficient miRNA binding and proper miRNA function. Our results present a new dimension of natural selection on synonymous codons near miRNA target sites in plants, which will have important implications of coding sequence evolution.

Selection on synonymous sites for increased accessibility around miRNA binding sites in plants.

Codons synonymes sont largement s&eacute;lectionn&eacute;s pour diff&eacute;rents m&eacute;canismes biologiques chez les procaryotes et les eucaryotes. R&eacute;centes indiquent que les microARN (miARN) fonction peut-&ecirc;tre affecter des choix de codons synonymes pr&egrave;s de sites cibles miRNA. Pour mieux comprendre cela, nous effectuons analyse G&eacute;nome-large sur l&#39;utilisation de codons synonymes autour des sites cibles miRNA dans quatre g&eacute;nomes de plantes. Nous avons observ&eacute; une tendance g&eacute;n&eacute;rale de l&#39;accessibilit&eacute; du site accrue autour des sites cibles miRNA chez les plantes. Guanine-cytosine (GC)-pauvres codons sont pr&eacute;f&eacute;r&eacute;s dans la r&eacute;gion du flanc des sites cibles de miRNA. Des analyses au sein du g&eacute;nome montrent une variation significative dans les cibles de miRNA en esp&egrave;ces. Contenu en GC du g&egrave;ne cible peut en partie expliquer la variation de l&#39;accessibilit&eacute; des sites dans les cibles de miRNA. miRNA cibles dans les g&egrave;nes riche en GC montrent des signaux de s&eacute;lection plus fortes que celles dans les g&egrave;nes de la GC-pauvres. Biais de son utilisation pour le codon du g&egrave;ne et le niveau de conservation de miRNA et sa cible ont &eacute;galement des effets sur l&#39;accessibilit&eacute; des sites, mais le niveau d&#39;expression de miRNA ou sa cible et le m&eacute;canisme de l&#39;activit&eacute; de miRNA ne contribuent pas &agrave; des diff&eacute;rences d&#39;accessibilit&eacute; site parmi les cibles de miRNA. Nous sugg&eacute;rons que les codons synonymes pr&egrave;s de miRNA cibles sont s&eacute;lectionn&eacute;s pour liaison efficace miRNA et miRNA bonne fonction. Nos r&eacute;sultats pr&eacute;sentent une nouvelle dimension de la s&eacute;lection naturelle sur des codons synonymes pr&egrave;s de miRNA sites cibles chez les plantes, ce qui auront des implications importantes de l&#39;&eacute;volution de la s&eacute;quence de codage.

S&eacute;lection sur les sites synonymes pour une accessibilit&eacute; accrue autour des sites de liaison du miARN chez les plantes.

Codoni sinonimi sono ampiamente selezionati per vari meccanismi biologici in sia procarioti ed eucarioti. Recenti evidenze suggeriscono che funzione di microRNA (miRNA) possa influenzare scelte codone sinonimo vicino miRNA siti di destinazione. Per comprendere meglio questo, effettuiamo analisi genome-wide su uso del codone sinonimo intorno a siti bersaglio miRNA in quattro genomi vegetali. Abbiamo osservato una tendenza generale di accessibilit&agrave; sito aumento intorno a siti bersaglio miRNA nelle piante. Guanina-citosina (GC)-poveri codoni sono preferiti nella regione del fianco di miRNA siti di destinazione. All&#39;interno del genoma analisi mostrano variazione significativa tra obiettivi di miRNA in specie. Contenuto GC del gene dell&#39;obiettivo pu&ograve; parzialmente spiegare la variazione dell&#39;accessibilit&agrave; del sito tra gli obiettivi di miRNA. obiettivi di miRNA in geni GC-ricchi mostrano segnali di selezione pi&ugrave; forte rispetto a quelli dei geni GC-poveri. Bias di utilizzo codone di gene e il livello di conservazione di miRNA e la sua destinazione anche avere alcuni effetti sull&#39;accessibilit&agrave; del sito, ma il livello di espressione di miRNA o il bersaglio e il meccanismo di miRNA attivit&agrave; non contribuiscono alle differenze accessibilit&agrave; sito tra gli obiettivi di miRNA. Suggeriamo che codoni sinonimi vicino miRNA obiettivi sono selezionati per associazione efficiente miRNA e miRNA corretta funzione. I nostri risultati presentano una nuova dimensione della selezione naturale su codoni sinonimi vicino miRNA siti bersaglio nelle piante, che avranno importanti implicazioni di evoluzione della sequenza di codificazione.

Selezione siti sinonimo per maggiore accessibilit&agrave; intorno a siti di legame di miRNA in piante.

With respect to upstream regions of microRNA (miRNA) target sites located in protein coding sequences, experimental studies have suggested rare codons, rather than frequent codons, are important for miRNA function, because they slow down the local translational process. But, whether there is a trend of reduced translation efficiency near miRNA targets is still unknown. Using Arabidopsis thaliana, we perform genome-wide analysis of synonymous codon usage in upstream regions of miRNA target sites. At the whole genome level, we find no significant selection signals for decreased translational efficiency. However, the same genome analyses do show substantial variations of translation efficiency reduction among miRNA targets. We find that miRNA conservation level, gene codon usage bias, and the mechanism of miRNA action can account for the differences in translation efficiency. But gene's GC content, gene expression level, and miRNA target's conservation level have no effect on local translation efficiency of miRNA targets. Although local translation efficiency in the upstream region of miRNA targets is related to miRNA function in A. thaliana, the selection signal of rare codon usage in that region is weak. We propose some other biological factors are more important than local translation efficiency in miRNA action when miRNA targets are located in protein coding sequences.

Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana.

En ce qui concerne les r&eacute;gions en amont des sites cibles de microARN (miARN) situ&eacute;s en prot&eacute;ines s&eacute;quences codantes, des &eacute;tudes exp&eacute;rimentales ont sugg&eacute;r&eacute; codons rares, plut&ocirc;t que des codons fr&eacute;quents, sont importants pour la fonction de miRNA, car ils ralentissent le processus traductionnel local. Mais, s&#39;il y a une tendance de l&#39;efficacit&eacute; de la traduction r&eacute;duite pr&egrave;s des cibles de miRNA est encore inconnue. &Agrave; l&#39;aide de Arabidopsis thaliana, nous effectuons analyse de G&eacute;nome-large d&#39;utilisation de codons synonymes dans les r&eacute;gions en amont des sites cibles de miRNA. Au niveau de l&#39;ensemble du g&eacute;nome, nous ne trouvons aucun signal de s&eacute;lection important pour une diminution efficacit&eacute; traductionnelle. Cependant, les analyses de g&eacute;nome m&ecirc;me montrent des variations importantes de r&eacute;duction de l&#39;efficacit&eacute; de traduction chez miRNA cibles. Nous trouvons que le niveau de conservation de miRNA, g&egrave;ne codon utilisation biais et le m&eacute;canisme d&#39;action de miRNA peuvent rendre compte des diff&eacute;rences dans l&#39;efficacit&eacute; de la traduction. Mais le contenu en GC de g&egrave;ne, niveau d&#39;expression de g&egrave;ne et le niveau de conservation de la cible de miRNA n&#39;ont aucun effet sur l&#39;efficacit&eacute; de la traduction locale des cibles de miRNA. Bien que l&#39;efficacit&eacute; de traduction locale dans la r&eacute;gion en amont de miRNA cibles est li&eacute;e &agrave; la fonction miRNA dans Arabidopsis, le signal de s&eacute;lection de l&#39;utilisation de codon rare dans cette r&eacute;gion est faible. Nous vous proposons que d&#39;autres facteurs biologiques sont plus importantes que l&#39;efficacit&eacute; de la traduction locale en action de miRNA quand miRNA cibles sont trouvent dans les prot&eacute;ines s&eacute;quences codantes.

Efficacit&eacute; de traduction dans la r&eacute;gion en amont de cibles de microARN chez Arabidopsis thaliana.

Per quanto riguarda le regioni a Monte dei microRNA (miRNA) siti di destinazione che si trova in sequenze di codificazione della proteina, studi sperimentali hanno suggerito codoni rari, piuttosto frequenti codoni, sono importanti per la funzione di miRNA, perch&eacute; rallentano il processo di traslazione locale. Ma, se c&#39;&egrave; una tendenza di efficienza ridotta traduzione vicino miRNA target &egrave; ancora sconosciuto. Utilizzando Arabidopsis thaliana, effettuiamo analisi genome-wide di utilizzo sinonimo codone in regioni a monte di miRNA siti di destinazione. A livello di intero genoma, non troviamo alcuna significativa selezione segnali per ridotta efficienza traslazionale. Tuttavia, l&#39;analisi del genoma stesso mostrano notevoli variazioni di riduzione di efficienza di traduzione tra obiettivi di miRNA. Troviamo che il livello di conservazione di miRNA, gene codone uso bias e il meccanismo d&#39;azione di miRNA pu&ograve; account per le differenze di efficienza di traduzione. Ma contenuto GC del gene, livello di espressione genica e livello di miRNA target di conservazione non hanno alcun effetto sull&#39;efficienza di traduzione locale di miRNA target. Anche se l&#39;efficienza di traduzione locale nella regione a monte di miRNA target &egrave; legata alla funzione di miRNA in a. thaliana, il segnale di selezione di uso raro codone in quella regione &egrave; debole. Vi proponiamo che alcuni altri fattori biologici sono pi&ugrave; importanti di efficienza locale traduzione in azione miRNA quando miRNA obiettivi si trovano in sequenze di codificazione della proteina.

Efficienza di traduzione nella regione a monte del microRNA bersagli in Arabidopsis thaliana.

Recent analyses have revealed many functional microRNA (miRNA) targets in mammalian protein coding regions. But, the mechanisms that ensure miRNA function when their target sites are located in protein coding regions of mammalian mRNA transcripts are largely unknown. In this paper, we investigate some potential biological factors, such as target site accessibility and local translation efficiency. We computationally analyze these two factors using experimentally identified miRNA targets in human protein coding region. We find site accessibility is significantly increased in miRNA target region to facilitate miRNA binding. At the mean time, local translation efficiency is also selectively decreased near miRNA target region. GC-poor codons are preferred in the flank region of miRNA target sites to ease the access of miRNA targets. Within-genome analysis shows substantial variations of site accessibility and local translation efficiency among different miRNA targets in the genome. Further analyses suggest target gene's GC content and conservation level could explain some of the differences in site accessibility. On the other hand, target gene's functional importance and conservation level can affect local translation efficiency near miRNA target region. We hence propose both site accessibility and local translation efficiency are important in miRNA action when miRNA target sites are located in mammalian protein coding regions.

Biological basis of miRNA action when their targets are located in human protein coding region.

Exosomes are small membrane-bound vesicles secreted by most cell types. Exosomes contain various functional proteins, mRNAs and microRNAs (miRNAs) that could be used for diagnostic and therapeutic purposes. How we should store the samples before RNA isolation and whether those long term stored samples could be used for circulating RNA investigation because of RNase is unknown. The aim of the study was to determine the stability of circulating miRNA in exosomes and plasma. Exosomes were isolated from plasma samples by using ExoQuick Precipitation methods. RNA was extracted from exosomes and the corresponding plasma samples with a Qiagen miRNeasy Mini kit. The concentration of RNA was measured by a Qubit® RNA HS Assay Kit, and quantitative PCR was used for individual miRNA expression level detection. Results showed that exosomal miRNA showed extra stability under different storage conditions and no significant influence on plasma miRNA, except for short term storage at 4 °C. It is thus indicated that exosome miRNAs can be good biomarkers based on their stability under various storage conditions.

miRNA in plasma exosome is stable under different storage conditions.

Recent studies have suggested that the secondary structure of the 5' untranslated region (5' UTR) of messenger RNA (mRNA) is important for microRNA (miRNA)-mediated gene regulation in humans. mRNAs that are targeted by miRNA tend to have a higher degree of local secondary structure in their 5' UTR; however, the general role of the 5' UTR in miRNA-mediated gene regulation remains unknown. We systematically surveyed the secondary structure of 5' UTRs in both plant and animal species and found a universal trend of increased mRNA stability near the 5' cap in mRNAs that are regulated by miRNA in animals, but not in plants. Intra-genome comparison showed that gene expression level, GC content of the 5' UTR, number of miRNA target sites, and 5' UTR length may influence mRNA structure near the 5' cap. Our results suggest that the 5' UTR secondary structure performs multiple functions in regulating post-transcriptional processes. Although the local structure immediately upstream of the start codon is involved in translation initiation, RNA structure near the 5' cap site, rather than the structure of the full-length 5' UTR sequences, plays an important role in miRNA-mediated gene regulation.

The role of RNA structure at 5' untranslated region in microRNA-mediated gene regulation.

Understanding miRNAs' regulatory networks and target genes could facilitate the development of therapies for human diseases such as cancer. Although much useful gene expression profiling data for tumor cell lines is available, microarray data for miRNAs and mRNAs in the human HepG2 cell line have only been compared with that of other cell lines separately. The relationship between miRNAs and mRNAs in integrated expression profiles for HepG2 cells is still unknown. To explore the miRNA-mRNA correlations in hepatocellular carcinoma (HCC) cells, we performed miRNA and mRNA expression profiling in HepG2 cells and normal liver HL-7702 cells at the genome scale using next-generation sequencing technology. We identified 193 miRNAs that are differentially expressed in these two cell lines. Of these, 89 miRNAs were down-regulated in HepG2 cells compared with HL-7702 cells, while 104 miRNAs were up-regulated. We also observed 3035 mRNAs that are significantly dys-regulated in HepG2 cells. We then performed an integrated analysis of the expression data for differentially expressed miRNAs and mRNAs and found several miRNA-mRNA pairs that are significantly correlated in HepG2 cells. Further analysis suggested that these differentially expressed genes were enriched in four tumorigenesis-related signaling pathways, namely, ErbB, JAK-STAT, mTOR, and WNT, which until now had not been fully reported. Our results could be helpful in understanding the mechanisms of HCC occurrence and development.

The RNA expression signature of the HepG2 cell line as determined by the integrated analysis of miRNA and mRNA expression profiles.

Macrosomia is associated with problems at birth and has life-long health implications for the infant. The aim of this study was to profile the plasma microRNAs (miRNAs or miRs) and evaluate the potential of circulating miRNAs to predict fetal macrosomia. The expression levels of miRNAs in plasma samples obtained from pregnant women with fetal macrosomia and from women with normal pregnancies (controls) were analyzed using TaqMan Low-Density Arrays (TLDAs) followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) validation and analysis. The TLDA data revealed that 143 miRNAs were differentially expressed in the plasma samples from pregnant women with fetal macrosomia compared with the controls (43 upregulated and 100 downregulated miRNAs). Twelve of these miRNAs were selected for RT-qPCR analysis. Receiver operational characteristic (ROC) curve analysis indicated that several miRNAs (e.g., miR‑141-3p and miR-200c-3p) were clearly distinguished between pregnancies with fetal macrosomia and other types of abnormal pregnancy and healthy pregnancies with high sensitivity and specificity (AUC >0.9). The expression of miRNA clusters also showed a similar trend in pregnancies with fetal macrosomia. This study provides a platform for profiling circulating miRNAs in maternal plasma. Our data also suggest that altered levels of maternal plasma miRNAs have great potential to serve as non-invasive biomarkers and as a mechanistic indicator of abnormal pregnancies.

Differential expression of circulating miRNAs in maternal plasma in pregnancies with fetal macrosomia.

Lung cancer is the leading cause of cancer deaths. Non-small-cell lung cancer (NSCLC) is the major type of lung cancer. The aim of this study was to characterize the expression profiles of miRNAs in adenocarcinoma (AC), one major subtype of NSCLC. In this study, the miRNAs were detected in normal, adjacent, and tumor tissues by next-generation sequencing. Then the expression levels of differential miRNAs were quantified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). In the results, 259, 401, and 389 miRNAs were detected in tumor, adjacent, and normal tissues of pooled AC samples, respectively. In addition, for the first time we have found that miR-21-5p and miR-196a-5p were gradually upregulated from normal to adjacent to tumor tissues; miR-218-5p was gradually downregulated with 2-fold or greater change in AC tissues. These 3 miRNAs were validated by qRT-PCR. Lastly, we predicted target genes of these 3 miRNAs and enriched the potential functions and regulatory pathways. The aberrant miR-21-5p, miR-196a-5p, and miR-218-5p may become biomarkers for diagnosis and prognosis of lung adenocarcinoma. This research may be useful for lung adenocarcinoma diagnosis and the study of pathology in lung cancer.

Differentially Expressed miRNAs in Tumor, Adjacent, and Normal Tissues of Lung Adenocarcinoma.

HLA mismatches are the primary cause of alloantibody-mediated rejection (AMR) in organ transplantation. To delineate antigenic and immunogenic potentials among individual HLA mismatches, information regarding antibody specificity at the epitope level, instead of the allelic level, is needed.

A Novel Method for Anti-HLA Antibody Detection Using Personalized Peptide Arrays.

Jujube (Ziziphus Jujuba Mill.) has been eaten as a fruit and nutraceutical food in China for thousands of years. Recent phytochemical and pharmacological studies have shown that the polysaccharides are one of major biologically active components of the jujube fruit and have various biological effects, including immunomodulatory, antioxidant, antitumor, hepatoprotective, and hypoglycemic activities, and gastrointestinal-protective effects. Although the extraction and purification of jujube polysaccharides are tedious processes, including different steps of liquid- and solid-phase separation, the polysaccharides have been structurally characterized. However, the relationships between the structures and activities of the jujube polysaccharides are not well established. The purpose of the present review is to appraise the previous and current literature on the extraction, purification, structural characterization, and biological activities of jujube polysaccharides. This review should provide a useful bibliography for the further investigation, production, and application of jujube polysaccharides in functional foods and therapeutic agents.

Isolation, structures and bioactivities of the polysaccharides from jujube fruit (Ziziphus jujuba Mill.): A review.

Circular RNAs (circRNAs) are a class of non-coding RNAs that are widely expressed in various cell lines and tissues of many organisms. Although the exact function of many circRNAs is largely unknown, the cell type- and tissue-specific circRNA expression has implicated their crucial functions in many biological processes. Hence, the quantification of circRNA expression from high-throughput RNA-seq data is becoming important to ascertain. Although many model-based methods have been developed to quantify linear RNA expression from RNA-seq data, these methods are not applicable to circRNA quantification.

Article	Year
Eukaryotic protein domains as functional units of cellular evolution. Science signaling\| PubMed ID: 19934434	2009
The sequence and de novo assembly of the giant panda genome. Nature\| PubMed ID: 20010809	2010
Global analysis of in vivo EGR1-binding sites in erythroleukemia cell using chromatin immunoprecipitation and massively parallel sequencing. Electrophoresis\| PubMed ID: 20690147	2010
Global Egr1-miRNAs binding analysis in PMA-induced K562 cells using ChIP-Seq. Journal of biomedicine & biotechnology\| PubMed ID: 20811575	2010
Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks. BMC evolutionary biology\| PubMed ID: 21849086	2011
Selection on synonymous sites for increased accessibility around miRNA binding sites in plants. Molecular biology and evolution\| PubMed ID: 22490819	2012
Translation Efficiency in Upstream Region of microRNA Targets in Arabidopsis thaliana. Evolutionary bioinformatics online\| PubMed ID: 23071387	2012
Biological basis of miRNA action when their targets are located in human protein coding region. PloS one\| PubMed ID: 23671676	2013
miRNA in plasma exosome is stable under different storage conditions. Molecules (Basel, Switzerland)\| PubMed ID: 24473213	2014
The role of RNA structure at 5' untranslated region in microRNA-mediated gene regulation. RNA (New York, N.Y.)\| PubMed ID: 25002673	2014
The RNA expression signature of the HepG2 cell line as determined by the integrated analysis of miRNA and mRNA expression profiles. Gene\| PubMed ID: 25014136	2014
Differential expression of circulating miRNAs in maternal plasma in pregnancies with fetal macrosomia. International journal of molecular medicine\| PubMed ID: 25370776	2015
Differentially Expressed miRNAs in Tumor, Adjacent, and Normal Tissues of Lung Adenocarcinoma. BioMed research international\| PubMed ID: 27247934	2016
A Novel Method for Anti-HLA Antibody Detection Using Personalized Peptide Arrays. Transplantation direct\| PubMed ID: 27826602	2016
Isolation, structures and bioactivities of the polysaccharides from jujube fruit (Ziziphus jujuba Mill.): A review. Food chemistry\| PubMed ID: 28274443	2017
Quantifying circular RNA expression from RNA-seq data using model-based framework. Bioinformatics (Oxford, England)\| PubMed ID: 28334396	2017

Xueying Xie

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