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Briefings in Functional Genomics

Tsukasa Fukunaga, Michiaki Hamada
Transient and alternative structures of ribonucleic acids (RNAs) play essential roles in various regulatory processes, such as translation regulation in living cells. Because experimental analyses for RNA structures are difficult and time-consuming, computational approaches based on RNA secondary structures are promising. In this article, we review computational methods for detecting and analyzing transient/alternative secondary structures of RNAs, including static approaches based on probabilistic distributions of RNA secondary structures and dynamic approaches such as kinetic folding and folding pathway predictions...
January 28, 2019: Briefings in Functional Genomics
Denis Awany, Imane Allali, Emile R Chimusa
Over the past decade, human host genome-wide association studies (GWASs) have contributed greatly to our understanding of the impact of host genetics on phenotypes. Recently, the microbiome has been recognized as a complex trait in host genetic variation, leading to microbiome GWAS (mGWASs). For these, many different statistical methods and software tools have been developed for association mapping. Applications of these methods and tools have revealed several important findings; however, the establishment of causal factors and the direction of causality in the interactive role between human genetic polymorphisms, the microbiome and the host phenotypes are still a huge challenge...
January 3, 2019: Briefings in Functional Genomics
Yan Guo, Hui Yu, David C Samuels, Wei Yue, Scott Ness, Ying-Yong Zhao
No abstract text is available yet for this article.
December 28, 2018: Briefings in Functional Genomics
Wenying He, Leyi Wei, Quan Zou
Posttranslational modifications (PTMs) play an important role in regulating protein folding, activity and function and are involved in almost all cellular processes. Identification of PTMs of proteins is the basis for elucidating the mechanisms of cell biology and disease treatments. Compared with the laboriousness of equivalent experimental work, PTM prediction using various machine-learning methods can provide accurate, simple and rapid research solutions and generate valuable information for further laboratory studies...
December 20, 2018: Briefings in Functional Genomics
Subhadip Basu, Dariusz Plewczynski
No abstract text is available yet for this article.
November 26, 2018: Briefings in Functional Genomics
Sagnik Sen, Ujjwal Maulik
In the current era of epigenetics research, we have observed many examples of epigenetic modifications, like histone modification and DNA methylation, in various fatal diseases. These include solid tumors, hematological malignancies and viral infections with DNA or RNA viruses. The purpose of this review is to summarize the role of epigenetic modifications during the abovementioned viral infections, viral-associated and independent malignancies. In this article, the essential biological aspects of DNA methylation are discussed...
November 26, 2018: Briefings in Functional Genomics
Dariusz Izak, Joanna Klim, Szymon Kaczanowski
Malaria remains one of the highest mortality infectious diseases. Malaria is caused by parasites from the genus Plasmodium. Most deaths are caused by infections involving Plasmodium falciparum, which has a complex life cycle. Malaria parasites are extremely well adapted for interactions with their host and their host's immune system and are able to suppress the human immune system, erase immunological memory and rapidly alter exposed antigens. Owing to this rapid evolution, parasites develop drug resistance and express novel forms of antigenic proteins that are not recognized by the host immune system...
November 26, 2018: Briefings in Functional Genomics
Michal Lazniewski, Wayne K Dawson, Teresa Szczepinska, Dariusz Plewczynski
Hemagglutinin (HA) is a transmembrane protein of the influenza A virus and a key component in its life cycle. The protein allows the virus to enter a host cell by recognizing specific glycans attached to transmembrane proteins of the host, which leads to viral endocytosis. In recent years, significant progress has been made in understanding the structural relationship between changes in the HA receptor-binding site (RBS) and the sialylated glycans that bind them. Several mutations were identified in the HA RBS that allows the virus to change host tropism...
November 26, 2018: Briefings in Functional Genomics
Sumanta Ray, Ujjwal Maulik, Anirban Mukhopadhyay
Chronic infection of hepatitis C virus (HCV) leads to severe life-threatening liver diseases such as cirrhosis of liver, fibrosis and hepatocellular carcinoma (HCC). Severity of the disease infects >180 million people worldwide. In recent years, many computational approaches have been proposed to study and analyze the progression of liver fibrosis, HCC and other liver diseases developed from chronic HCV infection. In this article, we review the literature published in this area of study. Here we categorize all the approaches into two basic groups: analyzing gene expression and studying protein-protein interaction network among HCV-infected human proteins...
November 26, 2018: Briefings in Functional Genomics
Anupam Banerjee, Abantika Pal, Debnath Pal, Pralay Mitra
Zaire ebolavirus, one of the most pathogenic species of Ebolavirus, is a significant threat to the human community being both highly infectious and lethal. The viral proteins (VPs), specifically VP24 and VP35, antagonize the interferon (IFN) proteins accountable for human immune response. Several efforts have been made to design vaccines and therapeutics drugs. However, the success is not encouraging because of limited knowledge about the binding site information of the VPs. Such limitations stem largely from the highly infectious nature of the virus that requires specialized personnel and biosafety laboratories...
November 26, 2018: Briefings in Functional Genomics
Tomasz Wolkowicz
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e...
November 26, 2018: Briefings in Functional Genomics
Wayne K Dawson, Michal Lazniewski, Dariusz Plewczynski
In one more years, we will 'celebrate' an exact centenary of the Spanish flu pandemic. With the rapid evolution of the influenza virus, the possibility of novel pandemic remains ever a concern. This review covers our current knowledge of the influenza A virus: on the role of RNA in translation, replication, what is known of the expressed proteins and the protein products generated from alternative splicing, and on the role of base pairing in RNA structure. We highlight the main events associated with viral entry into the cell, the transcription and replication process, an export of the viral genetic material from the nucleus and the final release of the virus...
November 26, 2018: Briefings in Functional Genomics
Sovan Saha, Kaustav Sengupta, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri
Infection and disease progression is the outcome of protein interactions between pathogen and host. Pathogen, the role player of Infection, is becoming a severe threat to life as because of its adaptability toward drugs and evolutionary dynamism in nature. Identifying protein targets by analyzing protein interactions between host and pathogen is the key point. Proteins with higher degree and possessing some topologically significant graph theoretical measures are found to be drug targets. On the other hand, exceptional nodes may be involved in infection mechanism because of some pathway process and biologically unknown factors...
November 26, 2018: Briefings in Functional Genomics
Anup Kumar Halder, Pritha Dutta, Mahantapas Kundu, Subhadip Basu, Mita Nasipuri
Identification of potential virus-host interactions is useful and vital to control the highly infectious virus-caused diseases. This may contribute toward development of new drugs to treat the viral infections. Recently, database records of clinically and experimentally validated interactions between a small set of human proteins and Ebola virus (EBOV) have been published. Using the information of the known human interaction partners of EBOV, our main objective is to identify a set of proteins that may interact with EBOV proteins...
November 26, 2018: Briefings in Functional Genomics
Pritha Dutta, Anup Kumar Halder, Subhadip Basu, Mahantapas Kundu
A detailed understanding of the Ebola virus (EBOV) pathogenesis has not been possible because of safety concerns, which arise while handling the live EBOV. Understanding the mechanisms involved in EBOV entry, replication and inhibition of the antiviral response in the host cell are crucial for the development of effective therapeutic measures. In this article, we provide a description of the EBOV genome and the role of each EBOV protein in spreading infection in the host cell. We also discuss some of the major computational works done on EBOV for the purpose of developing effective vaccines and drugs...
November 26, 2018: Briefings in Functional Genomics
YongKiat Wee, Salma Begum Bhyan, Yining Liu, Jiachun Lu, Xiaoyan Li, Min Zhao
The application of third-generation sequencing (TGS) technology in genetics and genomics have provided opportunities to categorize and explore the individual genomic landscapes and mutations relevant for diagnosis and therapy using whole genome sequencing and de novo genome assembly. In general, the emerging TGS technology can produce high quality long reads for the determination of overlapping reads and transcript isoforms. However, this technology still faces challenges such as the accuracy for the identification of nucleotide bases and high error rates...
November 21, 2018: Briefings in Functional Genomics
Rashmi K Ambasta, Rohan Gupta, Dhiraj Kumar, Saurabh Bhattacharya, Aditi Sarkar, Pravir Kumar
Diabetes and colon cancer are the leading cause of mortality worldwide. According to World Health Organization, the number of patients with diabetes and cancer is going to be elevated by 50% in 2020. However, several flavonoids have been known to be useful in reducing the chance of cancer/diabetes but the hunt of a single biomolecule that can act as therapeutic and preventive molecules for future epidemic continues. In this review, we aim to perform an illustration of all researches done that target molecular signaling using luteolin in cancer/diabetes and predicted target protein using PharmMapper...
November 21, 2018: Briefings in Functional Genomics
Koichi Nishigaki
The structure and function of unstable single-stranded DNA (ssDNA) have not been widely examined. While numerous studies have investigated DNA as an information molecule, the different potentials of DNA, particularly those of ssDNA, remain unclear. For polypeptides, the significance of denatured structures has been established in the past two decades. Polynucleotides have chemically distinct properties from polypeptides, but their behaviours have not been thoroughly studied. In this review, three different phenomena related to unstable ssDNA are discussed: i) ssDNA cleavage of restriction enzymes; ii) single-stranded conformation polymorphism, which can be theoretically explained by single-stranded conformation dynamics; and iii) random PCR (Polymerase Chain Reaction)...
November 15, 2018: Briefings in Functional Genomics
Qingfang Zhao, Liang Cao, Lulu Guan, Liangyu Bie, Saiqi Wang, Bojian Xie, Xiaobing Chen, Xiaokun Shen, Feiling Cao
Gastric cancer remains the second most common cause of cancer-related death worldwide. Because of the poor prognosis of late-stage gastric cancer patients, it is imperative to develop new strategies to improve the survival rate of this disease. Currently, immunotherapy is considered as an innovative approach for cancers such as lung cancer, gastric cancer and breast cancer. In fact, previous works have revealed promising results in this field. With further understanding of immunogenomics of gastric cancer, new immune checkpoint regulators could become more important...
November 2, 2018: Briefings in Functional Genomics
Kamalakshi Devi, Kuntal Kumar Dey, Sanjay Singh, Surajit Kumar Mishra, Mahendra Kumar Modi, Priyabrata Sen
miRNAs are class of endogenously initiated noncoding RNAs, which are most critical in gene expression and regulation at posttranscriptional level. They do so either by cleavage of the target mRNA or by translational repression. miRNAs are being given enough attention in recent years because of its role in myriad developmental processes including tumorogenesis and host-pathogen interaction. Advent of Next Generation Sequencing (NGS) technology and computational approach made it possible to pinpoint the precise role of miRNA and their target...
October 18, 2018: Briefings in Functional Genomics
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