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


Machine learning-based approaches for disease gene prediction.

Authors:
Duc-Hau Le

Brief Funct Genomics 2020 Jun 22. Epub 2020 Jun 22.

Department of Computational Biomedicine, Vingroup Big Data Institute, Hanoi, Vietnam.

Disease gene prediction is an essential issue in biomedical research. In the early days, annotation-based approaches were proposed for this problem. With the development of high-throughput technologies, interaction data between genes/proteins have grown quickly and covered almost genome and proteome; thus, network-based methods for the problem become prominent. Read More

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http://dx.doi.org/10.1093/bfgp/elaa013DOI Listing

CRISPR in medicine: applications and challenges.

Brief Funct Genomics 2020 May;19(3):151-153

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http://dx.doi.org/10.1093/bfgp/elaa011DOI Listing

Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data.

Brief Funct Genomics 2020 May 16. Epub 2020 May 16.

RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA library construction. Here, we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing reads to reference genomes and subsequent determination of transcript abundance. Read More

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http://dx.doi.org/10.1093/bfgp/elaa010DOI Listing

Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies.

Brief Funct Genomics 2020 May 12. Epub 2020 May 12.

Next generation sequencing (NGS) has revolutionised rare disease diagnostics. Concomitant with advancing technologies has been a rise in the number of new gene disorders discovered and diagnoses made for patients and their families. However, despite the trend towards whole exome and whole genome sequencing, diagnostic rates remain suboptimal. Read More

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http://dx.doi.org/10.1093/bfgp/elaa009DOI Listing

Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present.

Brief Funct Genomics 2020 May 12. Epub 2020 May 12.

Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Read More

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http://dx.doi.org/10.1093/bfgp/elaa008DOI Listing
May 2020
3.670 Impact Factor

Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.

Brief Funct Genomics 2020 Apr 29. Epub 2020 Apr 29.

Department of Computer Science, University of Saskatchewan.

The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure-function relationship of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assays to predict 3D genome organization (the 3D genome reconstruction problem). Many computational tools have been developed that answer this need, but a comprehensive comparison of their underlying algorithmic approaches has not been conducted. Read More

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http://dx.doi.org/10.1093/bfgp/elaa004DOI Listing

A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains.

Brief Funct Genomics 2020 Apr 2. Epub 2020 Apr 2.

Department of Botany, North-Eastern Hill University, Shillong 793022, India.

Carotenoids are mostly C40 terpenoids that participate in several important functions in plants including photosynthesis, responses to various forms of stress, signal transduction and photoprotection. While the antioxidant potential of carotenoids is of particular importance for human health, equally important is the role of β-carotene as the precursor for vitamin A in the human diet. Rice, which contributes upto 40% of dietary energy for mankind, contains very low level of β-carotene, thereby making it an important crop for enhancing β-carotene accumulation in its grains and consequently targeting vitamin A deficiency. Read More

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http://dx.doi.org/10.1093/bfgp/elaa007DOI Listing

3D genome organization: setting the stage and introducing its players.

Authors:
Daan Noordermeer

Brief Funct Genomics 2020 03;19(2):69-70

Chromatin Dynamics Group, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France

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http://dx.doi.org/10.1093/bfgp/elaa006DOI Listing
March 2020
3.670 Impact Factor

Identifying cell types to interpret scRNA-seq data: how, why and more possibilities.

Brief Funct Genomics 2020 Mar 31. Epub 2020 Mar 31.

Single-cell RNA sequencing (scRNA-seq) has generated numerous data and renewed our understanding of biological phenomena at the cellular scale. Identification of cell types has been one of the most prevalent means for interpreting scRNA-seq data, based upon which connections are made between the transcriptome and phenotype. Herein, we attempt to review the methods and tools that dedicate to the task regarding their feature and usage and look at the possibilities for scRNA-seq development in the near future. Read More

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http://dx.doi.org/10.1093/bfgp/elaa003DOI Listing

Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions.

Brief Funct Genomics 2020 Mar 27. Epub 2020 Mar 27.

RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster (D. Read More

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http://dx.doi.org/10.1093/bfgp/elaa005DOI Listing
March 2020
3.670 Impact Factor

Applications and advances of CRISPR/Cas9 in animal cancer model.

Brief Funct Genomics 2020 May;19(3):235-241

The recent developments of clustered regularly interspaced short palindromic repeats(CRISPR)/-associate protein 9 (CRISPR/Cas9) have got scientific interests due to the straightforward, efficient and versatile talents of it. Furthermore, the CRISPR/Cas9 system has democratized access to gene editing in many biological fields, including cancer. Cancer development is a multistep process caused by innate and acquired mutations and leads to the initiation and progression of tumorigenesis. Read More

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http://dx.doi.org/10.1093/bfgp/elaa002DOI Listing

Human embryo gene editing: God's scalpel or Pandora's box?

Brief Funct Genomics 2020 May;19(3):154-163

Department of Reproductive Center, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang, Wuhan, Hubei 430060, P.R. China.

Gene editing refers to the site-specific modification of the genome, which mainly focuses on basic research, model organism construction and treatment and prevention of disease. Since the first application of CRISPR/Cas9 on the human embryo genome in 2015, the controversy over embryo gene editing (abbreviated as EGE in the following text) has never stopped. At present, the main contradictions focus on (1) ideal application prospects and immature technologies; (2) scientific progress and ethical supervision; and (3) definition of reasonable application scope. Read More

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http://dx.doi.org/10.1093/bfgp/elz025DOI Listing
May 2020
3.670 Impact Factor

Application of CRISPR/Cas9 technology in sepsis research.

Brief Funct Genomics 2020 May;19(3):229-234

CRISPR/Cas9, as a new genome-editing tool, offers new approaches to understand and treat diseases, which is being rapidly applied in various areas of biomedical research including sepsis field. The type II prokaryotic CRISPR/Cas system uses a single-guide RNA (sgRNA) to target the Cas9 nuclease to a specific genomic sequence, which is introduced into disease models for functional characterization and for testing of therapeutic strategies. This incredibly precise technology can be used for therapeutic research of gene-related diseases and to program any sequence in a target cell. Read More

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http://dx.doi.org/10.1093/bfgp/elz040DOI Listing

CRISPR/Cas9 for cancer treatment: technology, clinical applications and challenges.

Brief Funct Genomics 2020 May;19(3):209-214

Department of Orthopaedics, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.

Clustered regularly interspaced short palindromic repeats (CRISPR) is described as RNA mediated adaptive immune system defense, which is naturally found in bacteria and archaea. CRISPR-Cas9 has shown great promise for cancer treatment in cancer immunotherapy, manipulation of cancer genome and epigenome and elimination or inactivation of carcinogenic viral infections. However, many challenges remain to be addressed to increase its efficacy, including off-target effects, editing efficiency, fitness of edited cells, immune response and delivery methods. Read More

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http://dx.doi.org/10.1093/bfgp/elaa001DOI Listing

Genome anchoring to nuclear landmarks drives functional compartmentalization of the nuclear space.

Brief Funct Genomics 2020 Mar;19(2):101-110

Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France.

The spatial organization of the genome contributes to essential functions such as transcription and chromosome integrity maintenance. The principles governing nuclear compartmentalization have been the focus of considerable research over the last decade. In these studies, the genome-nuclear structure interactions emerged as a main driver of this particular 3D genome organization. Read More

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http://dx.doi.org/10.1093/bfgp/elz034DOI Listing

Order and disorder: abnormal 3D chromatin organization in human disease.

Brief Funct Genomics 2020 Mar;19(2):128-138

Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

A precise three-dimensional (3D) organization of chromatin is central to achieve the intricate transcriptional patterns that are required to form complex organisms. Growing evidence supports an important role of 3D chromatin architecture in development and delineates its alterations as prominent causes of disease. In this review, we discuss emerging concepts on the fundamental forces shaping genomes in space and on how their disruption can lead to pathogenic phenotypes. Read More

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http://dx.doi.org/10.1093/bfgp/elz028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115703PMC

Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions.

Brief Funct Genomics 2020 Mar;19(2):111-118

We review the mechanism and consequences of the 'bridging-induced attraction', a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis of nuclear bodies and transcription factories via microphase separation. Including post-translational modification reactions involving these multivalent proteins can account for the fast dynamics of the ensuing clusters, as is observed via microscopy and photobleaching experiments. Read More

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http://dx.doi.org/10.1093/bfgp/elz032DOI Listing

Applications and explorations of CRISPR/Cas9 in CAR T-cell therapy.

Brief Funct Genomics 2020 May;19(3):175-182

Chimeric antigen receptor(CAR) T-cell therapy has shown remarkable effects and promising prospects in patients with refractory or relapsed malignancies, pending further progress in the next-generation CAR T cells with more optimized structure, enhanced efficacy and reduced toxicities. The clustered regulatory interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology holds immense promise for advancing the field owing to its flexibility, simplicity, high efficiency and multiplexing in precise genome editing. Herein, we review the applications and explorations of CRISPR/Cas9 technology in constructing allogenic universal CAR T cells, disrupting inhibitory signaling to enhance potency and exploration of safer and more controllable novel CAR T cells. Read More

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http://dx.doi.org/10.1093/bfgp/elz042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239310PMC

Aberrant DNA methylation and miRNAs in coronary artery diseases and stroke: a systematic review.

Brief Funct Genomics 2020 Jan 17. Epub 2020 Jan 17.

Coronary artery disease (CAD) and ischemic stroke are the two most predominant forms of cardiovascular diseases (CVDs) caused by genetic, epigenetic and environmental risk factors. Although studies on the impact of 'epigenetics' in CVDs is not new, its effects are increasingly being realized as a key regulatory determinant that may drive predisposition, pathophysiology and therapeutic outcome. The most widely studied epigenetic risk factors are regulated by DNA methylation and miRNA expression. Read More

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http://dx.doi.org/10.1093/bfgp/elz043DOI Listing
January 2020
3.670 Impact Factor

Molecular breeding approaches for production of disease-resilient commercially important tobacco.

Brief Funct Genomics 2020 01;19(1):10-25

Tobacco is one of the most widely cultivated nonfood cash crops, a source of income, model organism for plant molecular research, a natural pesticide and of pharmaceutical importance. First domesticated in South Americas, the modern-day tobacco (Nicotiana tabacum) is now cultivated in more than 125 countries to generate revenues worth billions of dollars each year. However, the production of this crop is highly threatened by the global presence of devastating infectious agents, which cause huge fiscal loss. Read More

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http://dx.doi.org/10.1093/bfgp/elz038DOI Listing
January 2020

CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects.

Brief Funct Genomics 2020 01;19(1):26-39

Several plant pathogens severely affect crop yield and quality, thereby threatening global food security. In order to cope with this challenge, genetic improvement of plant disease resistance is required for sustainable agricultural production, for which conventional breeding is unlikely to do enough. Luckily, genome editing systems that particularly clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) has revolutionized crop improvement by enabling robust and precise targeted genome modifications. Read More

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http://dx.doi.org/10.1093/bfgp/elz041DOI Listing
January 2020

Plant carotenoid cleavage oxygenases: structure-function relationships and role in development and metabolism.

Brief Funct Genomics 2020 01;19(1):1-9

Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India.

A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of 'carotenoids and apocarotenoids' is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide representation among organisms. Read More

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http://dx.doi.org/10.1093/bfgp/elz037DOI Listing
January 2020

Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies.

Brief Funct Genomics 2020 Mar;19(2):139-150

Genomic analysis of individuals or organisms is predicated on the availability of high-quality reference and genotype information. With the rapidly dropping costs of high-throughput DNA sequencing, this is becoming readily available for diverse organisms and for increasingly large populations of individuals. Despite these advances, there are still aspects of genome sequencing that remain challenging for existing sequencing methods. Read More

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http://dx.doi.org/10.1093/bfgp/elz026DOI Listing

Machine learning and its applications in plant molecular studies.

Brief Funct Genomics 2020 01;19(1):40-48

Harbin Institute of Technology in China. He is a professor in the Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China.

The advent of high-throughput genomic technologies has resulted in the accumulation of massive amounts of genomic information. However, biologists are challenged with how to effectively analyze these data. Machine learning can provide tools for better and more efficient data analysis. Read More

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http://dx.doi.org/10.1093/bfgp/elz036DOI Listing
January 2020

A broad survey of DNA sequence data simulation tools.

Brief Funct Genomics 2020 01;19(1):49-59

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

In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model. Read More

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http://dx.doi.org/10.1093/bfgp/elz033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7030445PMC
January 2020

CRISPR/Cas9 technology: towards a new generation of improved CAR-T cells for anticancer therapies.

Brief Funct Genomics 2020 May;19(3):191-200

Chimeric antigen receptor (CAR)-modified T cells have raised among other immunotherapies for cancer treatment, being implemented against B-cell malignancies. Despite the promising outcomes of this innovative technology, CAR-T cells are not exempt from limitations that must yet to be overcome in order to provide reliable and more efficient treatments against other types of cancer. The purpose of this review is to shed light on the field of CAR-T cell gene editing for therapy universalization and further enhancement of antitumor function. Read More

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http://dx.doi.org/10.1093/bfgp/elz039DOI Listing

Epigenome editing by CRISPR/Cas9 in clinical settings: possibilities and challenges.

Brief Funct Genomics 2020 May;19(3):215-228

Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, 100191 China.

Epigenome editing is a promising approach for both basic research and clinical application. With the convergence of techniques from different fields, regulating gene expression artificially becomes possible. From a clinical point of view, targeted epigenome editing by CRISPR/Cas9 of disease-related genes offers novel therapeutic avenues for many diseases. Read More

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http://dx.doi.org/10.1093/bfgp/elz035DOI Listing

3D genome organization during lymphocyte development and activation.

Brief Funct Genomics 2020 Mar;19(2):71-82

Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.

Chromosomes have a complex three-dimensional (3D) architecture comprising A/B compartments, topologically associating domains and promoter-enhancer interactions. At all these levels, the 3D genome has functional consequences for gene transcription and therefore for cellular identity. The development and activation of lymphocytes involves strict control of gene expression by transcription factors (TFs) operating in a three-dimensionally organized chromatin landscape. Read More

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http://dx.doi.org/10.1093/bfgp/elz030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115705PMC

3D genome organisation in Drosophila.

Brief Funct Genomics 2020 Mar;19(2):92-100

Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France.

Ever since Thomas Hunt Morgan's discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However, these domains might be formed through a slightly different mechanism than in vertebrates due to the presence of a large and potentially redundant set of insulator proteins and the minor role of dCTCF in TAD boundary formation. Read More

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http://dx.doi.org/10.1093/bfgp/elz029DOI Listing

CRISPR-Cas9 genome editing for cancer immunotherapy: opportunities and challenges.

Brief Funct Genomics 2020 May;19(3):183-190

Department of Pharmacology, Minhang Hospital and School of Pharmacy, Fudan University, Shanghai, China 201203.

Cancer immunotherapy, consisting of antibodies, adoptive T-cell transfer, vaccines and cytokines, is a novel strategy for fighting cancer by artificially stimulating the immune system. It has developed rapidly in recent years, and its efficacy in hematological malignancies and solid tumors has been remarkable. It is regarded as one of the most promising methods for cancer therapy. Read More

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http://dx.doi.org/10.1093/bfgp/elz027DOI Listing

Advances in therapeutic application of CRISPR-Cas9.

Brief Funct Genomics 2020 May;19(3):164-174

Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China.

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has been widely applied in countless areas, including genome editing, gene function investigation and gene therapy both in vitro and in vivo. In this paper, we briefly introduce the mechanisms of CRISPR-Cas9 tool in genome editing. Read More

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http://dx.doi.org/10.1093/bfgp/elz031DOI Listing

CRISPR therapy towards an HIV cure.

Brief Funct Genomics 2020 May;19(3):201-208

Department of Medical Microbiology Laboratory of Experimental Virology Amsterdam UMC, AMC, University of Amsterdam, Amsterdam, the Netherlands.

Tools based on RNA interference (RNAi) and the recently developed clustered regularly short palindromic repeats (CRISPR) system enable the selective modification of gene expression, which also makes them attractive therapeutic reagents for combating HIV infection and other infectious diseases. Several parallels can be drawn between the RNAi and CRISPR-Cas9 platforms. An ideal RNAi or CRISPR-Cas9 therapeutic strategy for treating infectious or genetic diseases should exhibit potency, high specificity and safety. Read More

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http://dx.doi.org/10.1093/bfgp/elz021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239311PMC

Genome organization via loop extrusion, insights from polymer physics models.

Brief Funct Genomics 2020 Mar;19(2):119-127

Univ Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France.

Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Read More

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http://dx.doi.org/10.1093/bfgp/elz023DOI Listing

Plasmodium comparative genomics.

Brief Funct Genomics 2019 09;18(5):267-269

Institute of Parasitology and Biomedicine López-Neyra, Spanish National Research Council (CSIC), Spain.

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http://dx.doi.org/10.1093/bfgp/elz020DOI Listing
September 2019

Three-dimensional chromosome organization in flowering plants.

Authors:
Stefan Grob

Brief Funct Genomics 2020 Mar;19(2):83-91

Institute of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.

Research on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes reported to be vital for chromosome folding in animals. Read More

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http://dx.doi.org/10.1093/bfgp/elz024DOI Listing

Polycomb proteins as organizers of 3D genome architecture in embryonic stem cells.

Brief Funct Genomics 2019 11;18(6):358-366

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany.

Polycomb group proteins (PcGs) control the epigenetic and transcriptional state of developmental genes and regulatory elements during mammalian embryogenesis. Moreover, PcGs can also contribute to 3D genome organization, adding an additional layer of complexity to their regulatory functions. Understanding the mechanistic basis and the dynamics of PcG-dependent chromatin structures will help us untangle the full complexity of PcG function during development. Read More

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http://dx.doi.org/10.1093/bfgp/elz022DOI Listing
November 2019

A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae.

Brief Funct Genomics 2019 11;18(6):367-376

School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China.

N6-methyladenosine (m6A) modification, as one of the commonest post-transcription modifications in RNAs, has been reported to be highly related to many biological processes. Over the past decade, several tools for m6A sites prediction of Saccharomyces cerevisiae have been developed and are freely available online. However, the quality of predictions by these tools is difficult to quantify and compare. Read More

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http://dx.doi.org/10.1093/bfgp/elz018DOI Listing
November 2019

Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies.

Brief Funct Genomics 2019 11;18(6):377-394

Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia.

Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Read More

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http://dx.doi.org/10.1093/bfgp/elz017DOI Listing
November 2019
3.670 Impact Factor

Technologies to study spatial genome organization: beyond 3C.

Brief Funct Genomics 2019 11;18(6):395-401

Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany.

The way that chromatin is organized in three-dimensional nuclear space is now acknowledged as a factor critical for the major cell processes, like transcription, replication and cell division. Researchers have been armed with new molecular and imaging technologies to study this structure-to-function link of genomes, spearheaded by the introduction of the 'chromosome conformation capture' technology more than a decade ago. However, this technology is not without shortcomings, and novel variants and orthogonal approaches are being developed to overcome these. Read More

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http://dx.doi.org/10.1093/bfgp/elz019DOI Listing
November 2019

Human core duplicon gene families: game changers or game players?

Brief Funct Genomics 2019 11;18(6):402-411

Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany.

Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. Read More

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http://dx.doi.org/10.1093/bfgp/elz016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920530PMC
November 2019

Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium.

Brief Funct Genomics 2019 09;18(5):281-289

Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA.

CRISPR/Cas9 approaches are revolutionizing our ability to perform functional genomics across a wide range of organisms, including the Plasmodium parasites that cause malaria. The ability to deliver single point mutations, epitope tags and gene deletions at increased speed and scale is enabling our understanding of the biology of these complex parasites, and pointing to potential new therapeutic targets. In this review, we describe some of the biological and technical considerations for designing CRISPR-based experiments, and discuss potential future developments that broaden the applications for CRISPR/Cas9 interrogation of the malaria parasite genome. Read More

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http://dx.doi.org/10.1093/bfgp/elz012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859820PMC
September 2019
3 Reads

Emerging challenge: dynamic solution structures of nucleic acids.

Brief Funct Genomics 2019 06;18(3):157-158

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

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http://dx.doi.org/10.1093/bfgp/elz015DOI Listing
June 2019
1 Read

Functional genomics of simian malaria parasites and host-parasite interactions.

Authors:
Mary R Galinski

Brief Funct Genomics 2019 09;18(5):270-280

Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.

Two simian malaria parasite species, Plasmodium knowlesi and Plasmodium cynomolgi, cause zoonotic infections in Southeast Asia, and they have therefore gained recognition among scientists and public health officials. Notwithstanding, these species and others including Plasmodium coatneyi have served for decades as sources of knowledge on the biology, genetics and evolution of Plasmodium, and the diverse ramifications and outcomes of malaria in their monkey hosts. Experimental analysis of these species can help to fill gaps in knowledge beyond what may be possible studying the human malaria parasites or rodent parasite species. Read More

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http://dx.doi.org/10.1093/bfgp/elz013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859816PMC
September 2019
2 Reads

Bioinoculant capability enhancement through metabolomics and systems biology approaches.

Brief Funct Genomics 2018 06;18(3):159-168

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

Bioinoculants are eco-friendly microorganisms, and their products are utilized for improving the potential of soil and fulfill the nutrients requirement for the host plant. The agricultural yield has increased due to the use of bioinoculants over chemical-based fertilizers, and thus it generates interest in understanding the innovation process by various methods. By gene-editing tool, the desired gene product can be changed for engineered microbial inoculants. Read More

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http://dx.doi.org/10.1093/bfgp/elz011DOI Listing
June 2018
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What functional genomics has taught us about transcriptional regulation in malaria parasites.

Brief Funct Genomics 2019 09;18(5):290-301

Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands.

Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Read More

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http://dx.doi.org/10.1093/bfgp/elz004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859821PMC
September 2019
7 Reads

The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites.

Brief Funct Genomics 2019 09;18(5):302-313

Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.

Due to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Read More

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http://dx.doi.org/10.1093/bfgp/elz005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859822PMC
September 2019
13 Reads

Prediction of tumor metastasis from sequencing data in the era of genome sequencing.

Brief Funct Genomics 2019 11;18(6):412-418

Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.

Tumor metastasis is the key reason for the high mortality rate of tumor. Growing number of scholars have begun to pay attention to the research on tumor metastasis and have achieved satisfactory results in this field. The advent of the era of sequencing has enabled us to study cancer metastasis at the molecular level, which is essential for understanding the molecular mechanism of metastasis, identifying diagnostic markers and therapeutic targets and guiding clinical decision-making. Read More

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http://dx.doi.org/10.1093/bfgp/elz010DOI Listing
November 2019
19 Reads

The genomic architecture of antimalarial drug resistance.

Brief Funct Genomics 2019 09;18(5):314-328

Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, USA.

Plasmodium falciparum and Plasmodium vivax, the two protozoan parasite species that cause the majority of cases of human malaria, have developed resistance to nearly all known antimalarials. The ability of malaria parasites to develop resistance is primarily due to the high numbers of parasites in the infected person's bloodstream during the asexual blood stage of infection in conjunction with the mutability of their genomes. Identifying the genetic mutations that mediate antimalarial resistance has deepened our understanding of how the parasites evade our treatments and reveals molecular markers that can be used to track the emergence of resistance in clinical samples. Read More

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http://dx.doi.org/10.1093/bfgp/elz008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859814PMC
September 2019
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Transcriptional variation in malaria parasites: why and how.

Brief Funct Genomics 2019 09;18(5):329-341

ICREA, 08010 Barcelona, Catalonia, Spain.

Transcriptional differences enable the generation of alternative phenotypes from the same genome. In malaria parasites, transcriptional plasticity plays a major role in the process of adaptation to fluctuations in the environment. Multiple studies with culture-adapted parasites and field isolates are starting to unravel the different transcriptional alternatives available to Plasmodium falciparum and the underlying molecular mechanisms. Read More

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https://academic.oup.com/bfg/advance-article/doi/10.1093/bfg
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http://dx.doi.org/10.1093/bfgp/elz009DOI Listing
September 2019
2 Reads