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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/28533025/enhancer-derived-rna-a-primer
#1
REVIEW
Feng Liu
Enhancer-derived RNAs (eRNAs) are a group of RNAs transcribed by RNA polymerase II from the domain of transcription enhancers, a major type of cis-regulatory elements in the genome. The correlation between eRNA production and enhancer activity has stimulated studies on the potential role of eRNAs in transcriptional regulation. Additionally, eRNA has also served as a marker for global identification of enhancers. Here I review the brief history and fascinating properties of eRNAs.
May 19, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28533024/epitranscriptomics-toward-a-better-understanding-of-rna-modifications
#2
Xushen Xiong, Chengqi Yi, Jinying Peng
No abstract text is available yet for this article.
May 19, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28533023/the-rna-modification-n-6-methyladenosine-and-its-implications-in-human-disease
#3
REVIEW
Pedro J Batista
Impaired gene regulation lies at the heart of many disorders, including developmental diseases and cancer. Furthermore, the molecular pathways that control gene expression are often the target of cellular parasites, such as viruses. Gene expression is controlled through multiple mechanisms that are coordinated to ensure the proper and timely expression of each gene. Many of these mechanisms target the life cycle of the RNA molecule, from transcription to translation. Recently, another layer of regulation at the RNA level involving RNA modifications has gained renewed interest of the scientific community...
May 19, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28529100/transcriptional-and-post-transcriptional-gene-regulation-by-long-non-coding-rna
#4
REVIEW
Iain Dykes, Costanza Emanueli
Advances in genomics technology over recent years have led to the surprising discovery that the genome is far more pervasively transcribed than was previously appreciated. Much of the newly-discovered transcriptome appears to represent long non-coding RNA (lncRNA), a heterogeneous group of largely uncharacterised transcripts. Understanding the biological function of these molecules represents a major challenge and in this review we discuss some of the progress made to date. One major theme of lncRNA biology seems to be the existence of a network of interactions with microRNA (miRNA) pathways...
May 18, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392481/protein-array-based-approaches-for-biomarker-discovery-in-cancer
#5
REVIEW
Yi Huang, Heng Zhu
Biomarkers are deemed to be potential tools in early diagnosis, therapeutic monitoring, and prognosis evaluation for cancer, with simplicity as well as economic advantages compared with computed tomography and biopsy. However, most of the current cancer biomarkers present insufficient sensitivity as well as specificity. Therefore, there is urgent requirement for the discovery of biomarkers for cancer. As one of the most exciting emerging technologies, protein array provides a versatile and robust platform in cancer proteomics research because it shows tremendous advantages of miniaturized features, high throughput, and sensitive detections in last decades...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392480/network-analysis-reveals-a-signaling-regulatory-loop-in-the-pik3ca-mutated-breast-cancer-predicting-survival-outcome
#6
Shauna R McGee, Chabane Tibiche, Mark Trifiro, Edwin Wang
Mutated genes are rarely common even in the same pathological type between cancer patients and as such, it has been very challenging to interpret genome sequencing data and difficult to predict clinical outcomes. PIK3CA is one of a few genes whose mutations are relatively popular in tumors. For example, more than 46.6% of luminal-A breast cancer samples have PIK3CA mutated, whereas only 35.5% of all breast cancer samples contain PIK3CA mutations. To understand the function of PIK3CA mutations in luminal A breast cancer, we applied our recently-proposed Cancer Hallmark Network Framework to investigate the network motifs in the PIK3CA-mutated luminal A tumors...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392479/circulating-tumor-dna-as-biomarkers-for-cancer-detection
#7
REVIEW
Xiao Han, Junyun Wang, Yingli Sun
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392478/disease-biomarkers-for-precision-medicine-challenges-and-future-opportunities
#8
EDITORIAL
Edwin Wang, William C S Cho, S C Cesar Wong, Siqi Liu
No abstract text is available yet for this article.
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28392477/lirex-a-package-for-identification-of-long-inverted-repeats-in-genomes
#9
Yong Wang, Jiao-Mei Huang
Long inverted repeats (LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer (Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28391009/the-promise-of-pharmacogenomics-in-reducing-toxicity-during-acute-lymphoblastic-leukemia-maintenance-treatment
#10
REVIEW
Shoshana Rudin, Marcus Marable, R Stephanie Huang
Pediatric acute lymphoblastic leukemia (ALL) affects a substantial number of children every year and requires a long and rigorous course of chemotherapy treatments in three stages, with the longest phase, the maintenance phase, lasting 2-3years. While the primary drugs used in the maintenance phase, 6-mercaptopurine (6-MP) and methotrexate (MTX), are necessary for decreasing risk of relapse, they also have potentially serious toxicities, including myelosuppression, which may be life-threatening, and gastrointestinal toxicity...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28391008/recent-5-year-findings-and-technological-advances-in-the-proteomic-study-of-hiv-associated-disorders
#11
REVIEW
Lijun Zhang, Xiaofang Jia, Jun-O Jin, Hongzhou Lu, Zhimi Tan
Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as well as subcellular proteomics and investigation of posttranslational modifications...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28389380/etumortype-an-algorithm-of-discriminating-cancer-types-for-circulating-tumor-cells-or-cell-free-dnas-in-blood
#12
Jinfeng Zou, Edwin Wang
With the technology development on detecting circulating tumor cells (CTCs) and cell-free DNAs (cfDNAs) in blood, serum, and plasma, non-invasive diagnosis of cancer becomes promising. A few studies reported good correlations between signals from tumor tissues and CTCs or cfDNAs, making it possible to detect cancers using CTCs and cfDNAs. However, the detection cannot tell which cancer types the person has. To meet these challenges, we developed an algorithm, eTumorType, to identify cancer types based on copy number variations (CNVs) of the cancer founding clone...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28377107/vitamin-pharmacogenomics-new-insight-into-individual-differences-in-diseases-and-drug-responses
#13
REVIEW
Hai-Yan He, Mou-Ze Liu, Yue-Li Zhang, Wei Zhang
Vitamins are vital to sustain normal physiological function, metabolism, and growth for all living organisms. Being an integral component of coenzyme, vitamins can affect the catalytic activities of many enzymes and the expression of drug transporters. Genetic variations in metabolism and/or transporter genes of drugs can influence the exposure of the human body to drugs and/or their active metabolites, thus contributing to the variations in drug responses and toxicities. Nonetheless, pharmacogenomics studies on nutrients have been rarely summarized...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28373027/omics-approaches-to-identify-potential-biomarkers-of-inflammatory-diseases-in-the-focal-adhesion-complex
#14
REVIEW
Johanne Brooks, Alastair Watson, Tamas Korcsmaros
Inflammatory diseases such as inflammatory bowel disease (IBD) require recurrent invasive tests, including blood tests, radiology, and endoscopic evaluation both to diagnose and assess disease activity, and to determine optimal therapeutic strategies. Simple 'bedside' biomarkers could be used in all phases of patient management to avoid unnecessary investigation and guide further management. The focal adhesion complex (FAC) has been implicated in the pathogenesis of multiple inflammatory diseases, including IBD, rheumatoid arthritis, and multiple sclerosis...
April 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28387199/gsa-genome-sequence-archive
#15
Yanqing Wang, Fuhai Song, Junwei Zhu, Sisi Zhang, Yadong Yang, Tingting Chen, Bixia Tang, Lili Dong, Nan Ding, Qian Zhang, Zhouxian Bai, Xunong Dong, Huanxin Chen, Mingyuan Sun, Shuang Zhai, Yubin Sun, Lei Yu, Li Lan, Jingfa Xiao, Xiangdong Fang, Hongxing Lei, Zhang Zhang, Wenming Zhao
With the rapid development of sequencing technologies towards higher throughput and lower cost, sequence data are generated at an unprecedentedly explosive rate. To provide an efficient and easy-to-use platform for managing huge sequence data, here we present Genome Sequence Archive (GSA; http://bigd.big.ac.cn/gsa or http://gsa.big.ac.cn), a data repository for archiving raw sequence data. In compliance with data standards and structures of the International Nucleotide Sequence Database Collaboration (INSDC), GSA adopts four data objects (BioProject, BioSample, Experiment, and Run) for data organization, accepts raw sequence reads produced by a variety of sequencing platforms, stores both sequence reads and metadata submitted from all over the world, and makes all these data publicly available to worldwide scientific communities...
February 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28235641/gsa-and-bigd-filling-the-gap-of-bioinformatics-resource-and-service-in-china-sup
#16
Jingchu Luo
No abstract text is available yet for this article.
February 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28188874/a-behind-the-scenes-story-of-precision-medicine-sup
#17
Maynard V Olson
No abstract text is available yet for this article.
February 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28185911/transcriptome-analysis-of-monozygotic-twin-brothers-with-childhood-primary-myelofibrosis
#18
Nan Ding, Zhaojun Zhang, Wenyu Yang, Lan Ren, Yingchi Zhang, Jingliao Zhang, Zhanqi Li, Peihong Zhang, Xiaofan Zhu, Xiaojuan Chen, Xiangdong Fang
Primary myelofibrosis (PMF) is a chronic myeloproliferative disorder in human bone marrow. Over 50% of patients with myelofibrosis have mutations in JAK2, MPL, or CALR. However, these mutations are rarely detected in children, suggesting a difference in the pathogenesis of childhood PMF. In this study, we investigated the response to drug treatment of a monozygotic twin pair with typical childhood PMF. The twin exhibited different clinical outcomes despite following the same treatment regimen. The transcriptomic profiles of patient samples after drug treatment (E2 and Y2) were significantly different between the twin pair, which is consistent with the observation that the drug treatment was effective only in the younger brother, despite the twin being genetically identical...
February 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28179121/a-piece-of-history-that-cannot-be-missed-for-precision-medicine
#19
EDITORIAL
Jun Yu
No abstract text is available yet for this article.
February 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28161493/lysine-acetylation-and-deacetylation-in-brain-development-and-neuropathies
#20
REVIEW
Alicia Tapias, Zhao-Qi Wang
Embryonic development is critical for the final functionality and maintenance of the adult brain. Brain development is tightly regulated by intracellular and extracellular signaling. Lysine acetylation and deacetylation are posttranslational modifications that are able to link extracellular signals to intracellular responses. A wealth of evidence indicates that lysine acetylation and deacetylation are critical for brain development and functionality. Indeed, mutations of the enzymes and cofactors responsible for these processes are often associated with neurodevelopmental and psychiatric disorders...
February 2017: Genomics, Proteomics & Bioinformatics
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