Genomics, Proteomics and Bioinformatics Genomics, Proteomics and Bioinformatics RSS feedThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Deep Learning and Its Applications in Biomedicine
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Chensi Cao, Feng Liu, Hai Tan, Deshou Song, Wenjie Shu, Weizhong Li, Yiming Zhou, Xiaochen Bo, Zhi XieAbstractAdvances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein sequences. Learning from these data facilitates the understanding of human health and disease. Developed from artificial neural networks, deep learning-based algorithms show great promise in extracting features and lea...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Human Gut Microbiota and Gastrointestinal Cancer
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Changting Meng, Chunmei Bai, Thomas D. Brown, Leroy E. Hood, Qiang TianAbstractHuman gut microbiota play an essential role in both healthy and diseased states of humans. In the past decade, the interactions between microorganisms and tumors have attracted much attention in the efforts to understand various features of the complex microbial communities, as well as the possible mechanisms through which the microbiota are involved in cancer prevention, carcinogenesis, and anti-cancer therapy. A large number of studies ha...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Microvesicles as Emerging Biomarkers and Therapeutic Targets in Cardiometabolic Diseases
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Yan Chen, Guangping Li, Ming-Lin LiuAbstractMicrovesicles (MVs, also known as microparticles) are small vesicles that originate from plasma membrane of almost all eukaryotic cells during apoptosis or activation. MVs can serve as extracellular vehicles to transport bioactive molecules from their parental cells to recipient target cells, thereby serving as novel mediators for intercellular communication. Importantly, more and more evidence indicates that MVs could play important roles in early pathogenesis and subsequen...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

GoldCLIP: Gel-omitted Ligation-dependent CLIP
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J. Hannon, Yang YuAbstractProtein–RNA interaction networks are essential to understand gene regulation control. Identifying binding sites of RNA-binding proteins (RBPs) by the UV-crosslinking and immunoprecipitation (CLIP) represents one of the most powerful methods to map protein–RNA interactions in vivo. However, the traditional CLIP protocol is technically challenging, which requires radioactive labeling and suffers from material l...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Junchao Shi, Eun-A Ko, Kenton M. Sanders, Qi Chen, Tong ZhouAbstractHigh-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since exist...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Corrigendum to “Pharmacogenomics of Drug Metabolizing Enzymes and Transporters: Relevance to Precision Medicine” [Genomics Proteomics Bioinformatics 14 (5) (2016) 298–313]
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Shabbir Ahmed, Zhan Zhou, Jie Zhou, Shu-Qing Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Structural Insights into N6-methyladenosine (m6A) Modification in the Transcriptome
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Jinbo Huang, Ping YinAbstractMore than 100 types of chemical modifications in RNA have been well documented. Recently, several modifications, such as N6-methyladenosine (m6A), have been detected in mRNA, opening the window into the realm of epitranscriptomics. The m6A modification is the most abundant modification in mRNA and non-coding RNA (ncRNA). At the molecular level, m6A affects almost all aspects of mRNA metabolism, including splicing, translation, and stability, as well as microRNA (miRNA) maturation, playing ess...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

YTH Domain: A Family of N6-methyladenosine (m6A) Readers
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Shanhui Liao, Hongbin Sun, Chao XuAbstractLike protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N6-methyladenosine (m6A) is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs (lncRNAs). In mammalian cells, m6A can be incorporated by...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Applications of RNA Indexes for Precision Oncology in Breast Cancer
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Liming Ma, Zirui Liang, Hui Zhou, Lianghu QuAbstractPrecision oncology aims to offer the most appropriate treatments to cancer patients mainly based on their individual genetic information. Genomics has provided numerous valuable data on driver mutations and risk loci; however, it remains a formidable challenge to transform these data into therapeutic agents. Transcriptomics describes the multifarious expression patterns of both mRNAs and non-coding RNAs (ncRNAs), which facilitates the deciphering of genomic codes. In th...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

The Role of Exportin-5 in MicroRNA Biogenesis and Cancer
Publication date: April 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 2Author(s): Ke Wu, Juan He, Wenchen Pu, Yong PengAbstractMicroRNAs (miRNAs) are conserved small non-coding RNAs that play an important role in the regulation of gene expression and participate in a variety of biological processes. The biogenesis of miRNAs is tightly controlled at multiple steps, such as transcription of miRNA genes, processing by Drosha and Dicer, and transportation of precursor miRNAs (pre-miRNAs) from the nucleus to the cytoplasm by exportin-5 (XPO5). Given the critical role of nuclear export of pre-miRNAs in miRN...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification
In this study, we performed a systems-level analysis of human genes frequently regulated by m6A modification (m6Afreq genes) and those occasionally regulated by m6A modification (m6Aocca genes). Compared to the m6Aocca genes, the m6Afreq genes exhibit gene importance-related features, such as lower dN/dS ratio, higher protein–protein interaction network degree, and reduced tissue expression specificity. Signaling network analysis indicates that the m6Afreq genes are associated with downstream components of signaling cascades, high-linked signaling adaptors, and specific network motifs like incoherent feed forward loops. ...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Tet2 Regulates Osteoclast Differentiation by Interacting with Runx1 and Maintaining Genomic 5-Hydroxymethylcytosine (5hmC)
Publication date: Available online 13 June 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yajing Chu, Zhigang Zhao, David Wayne Sant, Ganqian Zhu, Sarah M. Greenblatt, Lin Liu, Jinhuan Wang, Zeng Cao, Jeanette Cheng Tho, Shi Chen, Xiaochen Liu, Peng Zhang, Jaroslaw P. Maciejewski, Stephen Nimer, Gaofeng Wang, Weiping Yuan, Feng-Chun Yang, Mingjiang XuAbstractAs a dioxygenase, Ten-Eleven Translocation 2 (TET2) catalyzes subsequent steps of 5-methylcytosine (5mC) oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hematopoietic stem cells, but its impact on mature hem...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Reversible RNA Modification N1-methyladenosine (m1A) in mRNA and tRNA
Publication date: Available online 14 June 2018Source: Genomics, Proteomics & BioinformaticsAuthor(s): Chi Zhang, Guifang JiaAbstractMore than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6-methyladenosine (m6A), N1-methyladenosine (m1A) has been found as a reversible modification in tRNA and mRNA. m1A occurs at positions 9, 14, and 58 of tRNA, with m1A58 being critical for tRNA stability. Other than the hundreds of m1A sites in mRNA and long non-coding RNA transcripts, transc...
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research

Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development
In conclusion, we identified several miRNAs in blood of COPD patients, which could serve as candidates for biomarkers to help identify COPD patients at risk for developing cancer. (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 10, 2018 Category: Bioinformatics Source Type: research