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The Immunome of Colon Cancer: Functional In Silico Analysis of Antigenic Proteins Deduced from IgG Microarray Profiling
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Johana A. Luna Coronell, Khulan Sergelen, Philipp Hofer, István Gyurján, Stefanie Brezina, Peter Hettegger, Gernot Leeb, Karl Mach, Andrea Gsur, Andreas WeinhäuselAbstractCharacterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens (DIRAGs) could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer (CRC) pati...
Source: Genomics, Proteomics and Bioinformatics - July 5, 2018 Category: Bioinformatics Source Type: research

Acknowledgments to Peer Reviewers 2017
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 5, 2018 Category: Bioinformatics Source Type: research

Lessons Learned as President of the Institute for Systems Biology (2000–2018)
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Leroy E. Hood (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 5, 2018 Category: Bioinformatics Source Type: research

Genome Writing: Current Progress and Related Applications
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Yueqiang Wang, Yue Shen, Ying Gu, Shida Zhu, Ye YinAbstractThe ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome s...
Source: Genomics, Proteomics and Bioinformatics - July 5, 2018 Category: Bioinformatics Source Type: research

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 5, 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 5, 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 5, 2018 Category: Bioinformatics Source Type: research

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review
Publication date: February 2018Source: Genomics, Proteomics & Bioinformatics, Volume 16, Issue 1Author(s): Manuel Mauricio Goez, Maria Constanza Torres-Madroñero, Sarah Röthlisberger, Edilson Delgado-TrejosAbstractVarious methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background n...
Source: Genomics, Proteomics and Bioinformatics - July 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 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 5, 2018 Category: Bioinformatics Source Type: research