467 results match your criteria Briefings in functional genomics[Journal]


Functional genomics in the era of cancer immunotherapy: challenges and clinical implications.

Brief Funct Genomics 2019 03;18(2):83-85

Department of General Surgery, Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/article/18/2/83/5416569
Publisher Site
http://dx.doi.org/10.1093/bfgp/elz003DOI Listing
March 2019
4 Reads

Interplay between miRNAs and host genes and their role in cancer.

Brief Funct Genomics 2019 Feb 20. Epub 2019 Feb 20.

Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.

MicroRNAs (miRNAs) are small endogenous non-coding functional RNAs that post-transcriptionally regulate gene expression. They play essential roles in nearly all biological processes including cell development and differentiation, DNA damage repair, cell death as well as intercellular communication. They are highly involved in cancer, acting as tumor suppressors and/or promoters to modulate cell proliferation, epithelial-mesenchymal transition and tumor invasion and metastasis. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
Publisher Site
http://dx.doi.org/10.1093/bfgp/elz002DOI Listing
February 2019
5 Reads

The expanding roles of APETALA2/Ethylene Responsive Factors and their potential applications in crop improvement.

Brief Funct Genomics 2019 Feb 20. Epub 2019 Feb 20.

Plant Translational Research Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India.

Understanding the molecular basis of the gene-regulatory networks underlying agronomic traits or plant responses to abiotic/biotic stresses is very important for crop improvement. In this context, transcription factors, which either singularly or in conjugation directly control the expression of many target genes, are suitable candidates for improving agronomic traits via genetic engineering. In this regard, members of one of the largest class of plant-specific APETALA2/Ethylene Response Factor (AP2/ERF) superfamily, which is implicated in various aspects of development and plant stress adaptation responses, are considered high-value targets for crop improvement. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/elz001DOI Listing
February 2019

Computational approaches for alternative and transient secondary structures of ribonucleic acids.

Brief Funct Genomics 2019 Jan 28. Epub 2019 Jan 28.

Waseda University.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely042DOI Listing
January 2019

Tantalizing dilemma in risk prediction from disease scoring statistics.

Brief Funct Genomics 2019 Jan 3. Epub 2019 Jan 3.

Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely040DOI Listing
January 2019
4 Reads

Corrigendum to: Single-nucleotide variants in human RNA: RNA editing and beyond.

Brief Funct Genomics 2018 Dec 28. Epub 2018 Dec 28.

Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University,Xi'an, Shaanxi, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely041DOI Listing
December 2018
3.670 Impact Factor

Research progress in protein posttranslational modification site prediction.

Brief Funct Genomics 2018 Dec 20. Epub 2018 Dec 20.

School of Computer Science and Technology, Tianjin University, Tianjin, China.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely039DOI Listing
December 2018

Emerging and threatening infectious diseases.

Brief Funct Genomics 2018 11;17(6):372-373

Center of New Technologies, University of Warsaw, Warsaw, Poland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely038DOI Listing
November 2018

The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing.

Brief Funct Genomics 2018 Nov 21. Epub 2018 Nov 21.

School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland, Australia.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely037DOI Listing
November 2018
16 Reads

Can luteolin be a therapeutic molecule for both colon cancer and diabetes?

Brief Funct Genomics 2018 Nov 21. Epub 2018 Nov 21.

Department of Biotechnology, Delhi Technological University (Former Delhi College of Engineering), Delhi, India.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely036DOI Listing
November 2018
12 Reads
3.670 Impact Factor

Short lifetime structures appearing in RNA and DNA.

Authors:
Koichi Nishigaki

Brief Funct Genomics 2018 Nov 15. Epub 2018 Nov 15.

Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely035DOI Listing
November 2018

Immunotherapy for gastric cancer: dilemmas and prospect.

Brief Funct Genomics 2019 03;18(2):107-112

Department of Surgical Oncology, Taizhou Hospital, Wenzhou Medical University, Taizhou, China.

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. Read More

View Article

Download full-text PDF

Source
http://fdslive.oup.com/www.oup.com/pdf/production_in_progres
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely019DOI Listing
March 2019
3 Reads

Identification and validation of plant miRNA from NGS data-an experimental approach.

Brief Funct Genomics 2018 Oct 18. Epub 2018 Oct 18.

Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India.

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. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely034DOI Listing
October 2018
10 Reads

Single-nucleotide variants in human RNA: RNA editing and beyond.

Brief Funct Genomics 2018 Oct 12. Epub 2018 Oct 12.

Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University,Xi'an, Shaanxi, China.

Through analysis of paired high-throughput DNA-Seq and RNA-Seq data, researchers quickly recognized that RNA-Seq can be used for more than just gene expression quantification. The alternative applications of RNA-Seq data are abundant, and we are particularly interested in its usefulness for detecting single-nucleotide variants, which arise from RNA editing, genomic variants and other RNA modifications. A stunning discovery made from RNA-Seq analyses is the unexpectedly high prevalence of RNA-editing events, many of which cannot be explained by known RNA-editing mechanisms. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely032DOI Listing
October 2018
1 Read
3.670 Impact Factor

Gene-specific metrics to facilitate identification of disease genes for molecular diagnosis in patient genomes: a systematic review.

Brief Funct Genomics 2018 Oct 12. Epub 2018 Oct 12.

Genetic Epidemiology and Bioinformatics Research Group, Human Development and Health, Faculty of Medicine, University of Southampton, UK.

The evolution of next-generation sequencing technologies has facilitated the detection of causal genetic variants in diseases previously undiagnosed at a molecular level. However, in genome sequencing studies, the identification of disease genes among a candidate gene list is often difficult because of the large number of apparently damaging (but usually neutral) variants. A number of variant prioritization tools have been developed to help detect disease-causal sites. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely033DOI Listing
October 2018
3.670 Impact Factor

Deep learning in omics: a survey and guideline.

Brief Funct Genomics 2018 Sep 26. Epub 2018 Sep 26.

School of Computer Science, National University of Defense Technology, Changsha, China.

Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big data. A huge amount of high dimensional and complex structured data has made it no longer applicable for conventional machine learning algorithms. Fortunately, deep learning technology can contribute toward resolving these challenges. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely030DOI Listing
September 2018
1 Read

III. Functions of short lifetime structures at large 9: case of nucleic acids.

Authors:
Koichi Nishigaki

Brief Funct Genomics 2018 Sep 24. Epub 2018 Sep 24.

Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology,1-1 Asahidai, Nomi, Ishikaw, Japan.

The short lifetime structures of nucleic acids are not well studied because of the poor recognition of their importance and the methodological difficulty. In case of proteins, which are a type of single-stranded biopolymers, the essential roles of their transient structures are well established. Therefore, the role of transient structures of nucleic acids is, naturally, of great interest. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely028DOI Listing
September 2018

Immune checkpoint inhibitors in non-small-cell lung cancer: current status and future directions.

Brief Funct Genomics 2019 03;18(2):147-156

Center of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, People's Republic of China.

Since 2015, immunotherapies, especially immune checkpoint inhibitors (ICIs), have made great breakthroughs in non-small-cell lung cancer (NSCLC). Among them, nivolumab, pembrolizumab and atezolizumab have been granted US Food and Drug Administration approval for NSCLC. It is imperative to combine ICIs with chemotherapy, radiotherapy, antivascular therapy and targeted therapy. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely029DOI Listing
March 2019
1 Read

Computational models for lncRNA function prediction and functional similarity calculation.

Brief Funct Genomics 2018 Sep 21. Epub 2018 Sep 21.

College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.

From transcriptional noise to dark matter of biology, the rapidly changing view of long non-coding RNA (lncRNA) leads to deep understanding of human complex diseases induced by abnormal expression of lncRNAs. There is urgent need to discern potential functional roles of lncRNAs for further study of pathology, diagnosis, therapy, prognosis, prevention of human complex disease and disease biomarker detection at lncRNA level. Computational models are anticipated to be an effective way to combine current related databases for predicting most potential lncRNA functions and calculating lncRNA functional similarity on the large scale. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely031DOI Listing
September 2018

Immune checkpoints and cancer in the immunogenomics era.

Brief Funct Genomics 2019 03;18(2):133-139

University of Hawaii Cancer Center and studies the mechanisms of chronic inflammation-associated cancer.

Immune checkpoints have been the subject of a wave of new studies. Among these checkpoints are tytotoxic T-lymphocyte-associated antigen 4, checkpoints programmed death-1 and programmed death-ligand 1; their blockades have been approved by the Food and Drug Administration for therapy of melanoma and other types of cancers. Immunogenomics, which combines the latest nucleic acid sequencing strategy with immunotherapy, provides precise information about genomic alterations (e. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely027DOI Listing

Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies.

Brief Funct Genomics 2018 Aug 8. Epub 2018 Aug 8.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely026DOI Listing

Single-cell genomics.

Authors:
Martin Hemberg

Brief Funct Genomics 2018 07;17(4):207-208

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063269PMC
July 2018
1 Read

RNA/DNA structures recognized by RNase H2.

Brief Funct Genomics 2018 Jul 12. Epub 2018 Jul 12.

Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Ribonuclease H (RNase H) [EC 3.1.26. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely024DOI Listing
July 2018
19 Reads

Recent advancement toward significant association between disordered transcripts and virus-infected diseases: a survey.

Brief Funct Genomics 2018 11;17(6):458-470

Department of Computer Science and Engineering, Jadavpur University, Kolkata, India.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely021DOI Listing
November 2018
3 Reads
3.670 Impact Factor

Cancer immunotherapy for metastasis: past, present and future.

Brief Funct Genomics 2019 03;18(2):140-146

Department of Orthopaedics, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Second Road, Guangzhou, P.R. China.

Cancer is a complex and refractory disease, which can disseminate from primary site to a different site even at an early stage. Cancer immunotherapy harnesses host immune system to battle against cancer, but only a minority of patients benefit from it. Genetic-based technologies have significantly promoted the development of cancer immunotherapy. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely022DOI Listing
March 2019
16 Reads
3.670 Impact Factor

Vaccine and antibody production in plants: developments and computational tools.

Brief Funct Genomics 2018 09;17(5):295-307

Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.

Plants as bioreactors have been widely used to express efficient vaccine antigens against viral, bacterial and protozoan infections. To date, many different plant-based expression systems have been analyzed, with a growing preference for transient expression systems. Antibody expression in diverse plant species for therapeutic applications is well known, and this review provides an overview of various aspects of plant-based biopharmaceutical production. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely020DOI Listing
September 2018
3.670 Impact Factor

Next-generation sequencing technologies accelerate advances in T-cell therapy for cancer.

Brief Funct Genomics 2019 03;18(2):119-128

Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, China.

Next-generation sequencing has produced a large quantity of DNA or RNA sequences related to the processes occurring within tumors and their microenvironment in a reasonable time and cost. These data have been used to guide the identification of neoantigens and to determine their specific T-cell receptors. Furthermore, adoptive T-cell therapy targeting neoantigens is under development for cancer treatment. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely018DOI Listing
March 2019
1 Read

Functions of short lifetime biological structures at large: the case of intrinsically disordered proteins.

Brief Funct Genomics 2018 Jul 3. Epub 2018 Jul 3.

Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.

Although for more than a century a protein function was intimately associated with the presence of unique structure in a protein molecule, recent years witnessed a skyrocket rise of the appreciation of protein intrinsic disorder concept that emphasizes the importance of the biologically active proteins without ordered structures. In different proteins, the depth and breadth of disorder penetrance are different, generating an amusing spatiotemporal heterogeneity of intrinsically disordered proteins (IDPs) and intrinsically disordered protein region regions (IDPRs), which are typically described as highly dynamic ensembles of rapidly interconverting conformations (or a multitude of short lifetime structures). IDPs/IDPRs constitute a substantial part of protein kingdom and have unique functions complementary to functional repertoires of ordered proteins. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely023DOI Listing
July 2018
7 Reads

CRISPR/Cas9 in plants: at play in the genome and at work for crop improvement.

Brief Funct Genomics 2018 09;17(5):319-328

Department of Plant Sciences and Plant Pathology, Montana State University, MT, USA.

The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system uses single-guide RNAs for genome editing, making it a simple, robust, powerful tool for targeted gene mutagenesis, knockout and knock-in/replacement, as well as transcriptional regulation. Here, we review the working principles, components and potential modifications of CRISPR/Cas9 for efficient single and multiplex gene editing in plants. We also describe recent work that has used CRISPR/Cas9 to improve economically important traits in crop plants. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely016DOI Listing
September 2018
15 Reads

Functional genomics: paving the way for more successful cancer immunotherapy.

Brief Funct Genomics 2019 03;18(2):86-98

Georgetown University.

Immunotherapies have revolutionized cancer treatment. Immunotherapy is effective for the treatment of a wide range of cancer types and can mediate complete and durable tumor regression. Nonetheless, the field still faces many significant challenges, such as the need for personalized therapeutic strategies and better biomarkers, the difficulty of selecting the right combination therapy, and resistance to currently available immunotherapies. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6430032PMC

Translating GWAS in rheumatic disease: approaches to establishing mechanism and function for genetic associations with ankylosing spondylitis.

Brief Funct Genomics 2018 09;17(5):308-318

Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.

Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158798PMC
September 2018
1 Read

Host-parasite interactions and ecology of the malaria parasite-a bioinformatics approach.

Brief Funct Genomics 2018 11;17(6):451-457

Department of Bioinformatics at the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely013DOI Listing
November 2018

Role of genomics in promoting the utilization of plant genetic resources in genebanks.

Brief Funct Genomics 2018 05;17(3):198-206

Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967547PMC
May 2018
1 Read

A decade of ChIP-seq.

Authors:
Georgi K Marinov

Brief Funct Genomics 2018 03;17(2):77-79

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5101.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely012DOI Listing

Integrating ChIP-seq with other functional genomics data.

Brief Funct Genomics 2018 03;17(2):104-115

Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIP-seq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can be used to test hypotheses about the mechanisms of gene regulation. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/article/17/2/104/4944665
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888983PMC
March 2018
5 Reads

Cas9/sgRNA-based genome editing and other reverse genetic approaches for functional genomic studies in rice.

Brief Funct Genomics 2018 09;17(5):339-351

Department of Plant Sciences, University of Hyderabad, Hyderabad, India.

One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/article/17/5/339/4951520
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely010DOI Listing
September 2018
1 Read

The application of CRISPR-Cas9 genome editing tool in cancer immunotherapy.

Brief Funct Genomics 2019 03;18(2):129-132

Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, Medical College, China Three Gorges University.

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system was originally discovered in prokaryotes functioned as a part of the adaptive immune system. Because of its high efficiency and easy operability, CRISPR-Cas9 system has been developed to be a powerful and versatile gene editing tool shortly after its discovery. Given that multiple genetic alterations are the main factors that drive genesis and development of tumor, CRISPR-Cas9 system has been applied to correct cancer-causing gene mutations and deletions and to engineer immune cells, such as chimeric antigen receptor T (CAR T) cells, for cancer immunotherapeutic applications. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/article/18/2/129/4951574
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely011DOI Listing
March 2019
6 Reads

Quantitative single-cell transcriptomics.

Brief Funct Genomics 2018 07;17(4):220-232

Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany.

Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over 50 protocols have been developed in recent years and also data processing and analyzes tools are evolving fast. Here, we review the basic principles underlying the different experimental protocols and how to benchmark them. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063296PMC
July 2018
1 Read

Significance of whole-genome duplications on the emergence of evolutionary novelties.

Brief Funct Genomics 2018 09;17(5):329-338

Department of Applied Biosciences, Toyo University, Tokyo, Japan.

Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/article/17/5/329/4951518
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely007DOI Listing
September 2018
4 Reads

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

Brief Funct Genomics 2018 09;17(5):352-361

RIKEN Center for Life Science Technologies, Kobe, Hyogo Japan.

Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158797PMC
September 2018
1 Read

CD8+ T-cell exhaustion in cancer: mechanisms and new area for cancer immunotherapy.

Brief Funct Genomics 2019 03;18(2):99-106

Nanjing Medical University.

Immunotherapies have emerged as the most promising area in cancer treatments in recent years. CD8+ T cells, as one of the primary effector cells of anticancer immunity, however, when infiltrating in cancer tissues, are generally in dysfunctional states termed T-cell exhaustion. Exhausted CD8+ T cells are characterized by impaired activity and proliferative ability, increased apoptotic rate and reduced production of effector cytokines. Read More

View Article

Download full-text PDF

Source
https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
Publisher Site
http://dx.doi.org/10.1093/bfgp/ely006DOI Listing
March 2019
6 Reads

The impact of single-cell RNA sequencing on understanding the functional organization of the immune system.

Brief Funct Genomics 2018 07;17(4):265-272

Department of Dermatology, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK.

Application of single-cell genomics technologies has revolutionized our approach to study the immune system. Unravelling the functional diversity of immune cells and their coordinated response is key to understanding immunity. Single-cell transcriptomics technologies provide high-dimensional assessment of the transcriptional states of immune cells and have been successfully applied to discover new immune cell types, reveal haematopoietic lineages, identify gene modules dictating immune responses and investigate lymphocyte antigen receptor diversity. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063276PMC

ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation.

Brief Funct Genomics 2018 03;17(2):116-137

Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889016PMC
March 2018
1 Read

Genomic and epigenomic perspectives of T-cell exhaustion in cancer.

Brief Funct Genomics 2019 03;18(2):113-118

Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China.

In chronic infection and cancer, T cells gradually become exhausted because of the persistent stimulation by antigens. In this process, the overexpression of multiple inhibitory receptors is induced, the production of effective cytokines decreases and the cytotoxicity and proliferation of T cells impairs, all contributing to the failure of T cells in fighting against cancer. Reversing T-cell exhaustion is a promising immunotherapy for cancer that has yielded encouraging results. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely005DOI Listing
March 2019
3 Reads

Genetic transformation of cell-walled plant and algae cells: delivering DNA through the cell wall.

Brief Funct Genomics 2018 01;17(1):26-33

Transformation techniques are a fundamental tool for functional genomics studies. These techniques are routinely used in many prokaryotic and eukaryotic organisms, but in eukaryotes that are surrounded by a cell wall, these protocols have proven difficult to successfully deliver heterologous or homologous DNA within their cytoplasm and nucleus. Such cell-walled organisms represent a challenge that requires the development of genetic transformation techniques that are able to overcome their natural barrier, to achieve targeted gene expression. Read More

View Article

Download full-text PDF

Source
http://academic.oup.com/bfg/article/17/1/26/3896135
Publisher Site
http://dx.doi.org/10.1093/bfgp/elx014DOI Listing
January 2018
11 Reads

Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data.

Authors:
Vilas Menon

Brief Funct Genomics 2018 Jan 16. Epub 2018 Jan 16.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/ely001DOI Listing
January 2018

Mapping gene regulatory networks from single-cell omics data.

Brief Funct Genomics 2018 07;17(4):246-254

VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium.

Single-cell techniques are advancing rapidly and are yielding unprecedented insight into cellular heterogeneity. Mapping the gene regulatory networks (GRNs) underlying cell states provides attractive opportunities to mechanistically understand this heterogeneity. In this review, we discuss recently emerging methods to map GRNs from single-cell transcriptomics data, tackling the challenge of increased noise levels and data sparsity compared with bulk data, alongside increasing data volumes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/elx046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063279PMC
July 2018
1 Read

The structural variability of the influenza A hemagglutinin receptor-binding site.

Brief Funct Genomics 2018 11;17(6):415-427

University of Warsaw, Center of New Technologies (CeNT), Warsaw, Poland.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/elx042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6252403PMC
November 2018
2 Reads

The expanding roles of Argonautes: RNA interference, splicing and beyond.

Brief Funct Genomics 2018 05;17(3):191-197

Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/elx045DOI Listing
May 2018
7 Reads

Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data.

Authors:
Vilas Menon

Brief Funct Genomics 2018 07;17(4):240-245

Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA, USA.

Advances in single-cell RNA-sequencing technology have resulted in a wealth of studies aiming to identify transcriptomic cell types in various biological systems. There are multiple experimental approaches to isolate and profile single cells, which provide different levels of cellular and tissue coverage. In addition, multiple computational strategies have been proposed to identify putative cell types from single-cell data. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bfgp/elx044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063268PMC