journal
MENU ▼
Read by QxMD icon Read
search

Current Genomics

journal
https://read.qxmd.com/read/31015793/catbnet-a-multi-network-analyzer-for-comparing-and-analyzing-the-topology-of-biological-networks
#1
Ehsan Pournoor, Naser Elmi, Ali Masoudi-Nejad
Background: Complexity and dynamicity of biological events is a reason to use comprehen-sive and holistic approaches to deal with their difficulty. Currently with advances in omics data genera-tion, network-based approaches are used frequently in different areas of computational biology and bio-informatics to solve problems in a systematic way. Also, there are many applications and tools for net-work data analysis and manipulation which their goal is to facilitate the way of improving our under-standings of inter/intra cellular interactions...
January 2019: Current Genomics
https://read.qxmd.com/read/31015792/profile-of-hbv-integration-in-the-plasma-dna-of-hepatocellular-carcinoma-patients
#2
Weiyang Li, Xiaofang Cui, Qing Huo, Yanwei Qi, Yuhui Sun, Meihua Tan, Qingsheng Kong
Background: Hepatitis B Viral (HBV) infection is one of the major causes of Hepatocellular Carcinoma (HCC). Mounting evidence had provided that the HBV integration might be a critical con-tributor of HCC carcinogenesis. Objective and Methods: To explore the profile of HBV integration in the plasma DNA, the method of next-generation sequencing, HBV capture and bioinformatics had been employed to screen for HBV in-tegration sites in the plasma samples. Results: In the initial experiment, a total of 87 breakpoints were detected in the 20 plasma samples...
January 2019: Current Genomics
https://read.qxmd.com/read/31015791/integrated-transcriptome-analysis-of-microrna-and-mrna-in-mouse-skin-derived-precursors-skps-and-skp-derived-fibroblast-sfbs-by-rna-seq
#3
Rongying Zhou, Yujie Mao, Lidan Xiong, Li Li
Background: Skin-derived precursors (SKPs) display the characteristics of self-renewal and multilineage differentiation. Objective: The study aimed to explore the molecular mechanisms of mouse SKPs differentiation into SKP-derived fibroblasts (SFBs). Methods: We compared the microRNA (miRNA) profile in mouse SKPs and SFBs by RNA sequenc-ing. Real-time quantitative reverse transcription PCR (qRT-PCR) was performed to validate the miRNA expression...
January 2019: Current Genomics
https://read.qxmd.com/read/31015790/prostate-cancer-gene-regulatory-network-inferred-from-rna-seq-data
#4
Daniel Moore, Ricardo de Matos Simoes, Matthias Dehmer, Frank Emmert-Streib
Background: Cancer is a complex disease with a lucid etiology and in understanding the causation, we need to appreciate this complexity. Objective: Here we are aiming to gain insights into the genetic associations of prostate cancer through a network-based systems approach using the BC3Net algorithm. Methods: Specifically, we infer a prostate cancer Gene Regulatory Network (GRN) from a large-scale gene expression data set of 333 patient RNA-seq profiles obtained from The Cancer Genome Atlas (TCGA) database...
January 2019: Current Genomics
https://read.qxmd.com/read/31015789/an-overview-about-the-biology-of-skeletal-muscle-satellite-cells
#5
REVIEW
Laura Forcina, Carmen Miano, Laura Pelosi, Antonio MusarĂ²
The peculiar ability of skeletal muscle tissue to operate adaptive changes during post-natal de-velopment and adulthood has been associated with the existence of adult somatic stem cells. Satellite cells, occupying an exclusive niche within the adult muscle tissue, are considered bona fide stem cells with both stem-like properties and myogenic activities. Indeed, satellite cells retain the capability to both maintain the quiescence in uninjured muscles and to be promptly activated in response to growth or re-generative signals, re-engaging the cell cycle...
January 2019: Current Genomics
https://read.qxmd.com/read/31015788/a-nonmathematical-review-of-optimal-operator-and-experimental-design-for-uncertain-scientific-models-with-application-to-genomics
#6
REVIEW
Edward R Dougherty
Introduction: The most basic aspect of modern engineering is the design of operators to act on physical systems in an optimal manner relative to a desired objective - for instance, designing a con-trol policy to autonomously direct a system or designing a classifier to make decisions regarding the sys-tem. These kinds of problems appear in biomedical science, where physical models are created with the intention of using them to design tools for diagnosis, prognosis, and therapy. Methods: In the classical paradigm, our knowledge regarding the model is certain; however, in practice, especially with complex systems, our knowledge is uncertain and operators must be designed while tak-ing this uncertainty into account...
January 2019: Current Genomics
https://read.qxmd.com/read/31015787/estimating-the-k-mer-coverage-frequencies-in-genomic-datasets-a-comparative-assessment-of-the-state-of-the-art
#7
Swati C Manekar, Shailesh R Sathe
Background: In bioinformatics, estimation of k-mer abundance histograms or just enumerat-ing the number of unique k-mers and the number of singletons are desirable in many genome sequence analysis applications. The applications include predicting genome sizes, data pre-processing for de Bruijn graph assembly methods (tune runtime parameters for analysis tools), repeat detection, sequenc-ing coverage estimation, measuring sequencing error rates, etc. Different methods for cardinality estima-tion in sequencing data have been developed in recent years...
January 2019: Current Genomics
https://read.qxmd.com/read/30532651/model-microbial-consortia-as-tools-for-understanding-complex-microbial-communities
#8
REVIEW
Shin Haruta, Kyosuke Yamamoto
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions...
December 2018: Current Genomics
https://read.qxmd.com/read/30532650/metabolic-modeling-of-microbial-community-interactions-for-health-environmental-and-biotechnological-applications
#9
REVIEW
Kok Siong Ang, Meiyappan Lakshmanan, Na-Rae Lee, Dong-Yup Lee
In nature, microbes do not exist in isolation but co-exist in a variety of ecological and biological environments and on various host organisms. Due to their close proximity, these microbes interact among themselves, and also with the hosts in both positive and negative manners. Moreover, these interactions may modulate dynamically upon external stimulus as well as internal community changes. This demands systematic techniques such as mathematical modeling to understand the intrinsic community behavior. Here, we reviewed various approaches for metabolic modeling of microbial communities...
December 2018: Current Genomics
https://read.qxmd.com/read/30532649/diverse-distribution-of-resistomes-in-the-human-and-environmental-microbiomes
#10
REVIEW
Mi Young Lim, Youna Cho, Mina Rho
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria...
December 2018: Current Genomics
https://read.qxmd.com/read/30532648/design-principles-of-microbial-communities-from-understanding-to-engineering
#11
EDITORIAL
Hyun-Seob Song
No abstract text is available yet for this article.
December 2018: Current Genomics
https://read.qxmd.com/read/30532647/epigenetic-changes-associated-with-early-life-experiences-saliva-a-biospecimen-for-dna-methylation-signatures
#12
Elaine L Bearer, Brianna S Mulligan
Background: Adverse Childhood Experiences (ACEs), which include traumatic injury, are associated with poor health outcomes in later life, yet the biological mechanisms mediating this association are unknown. Neurocircuitry, immune system and hormone regulation differ from normal in adults reporting ACEs. These systems could be affected by epigenetic changes, including methylation of cytosine (5mC) in genomic DNA, activated by ACEs. Since 5mC levels influence gene expression and can be long-lasting, altered 5mC status at specific sites or throughout the genome is hypothesized to influence mental and physical outcomes after ACE(s)...
December 2018: Current Genomics
https://read.qxmd.com/read/30532646/intergenerational-transmission-of-dna-methylation-signatures-associated-with-early-life-stress
#13
REVIEW
Ludwig Stenz, Daniel S Schechter, Sandra Rusconi Serpa, Ariane Paoloni-Giacobino
Early life stress in humans (i.e. maltreatment, violence exposure, loss of a loved one) and in rodents (i.e. disrupted attachment or nesting, electric shock, restraint, predator odor) occurs during critical steps of neural circuit formation. ELS in humans is associated with increased risk for developmental psychopathology, including anxious and depressive phenotypes. The biological mechanisms underlying these potentially persistent maladaptive changes involve long-term epigenetic modifications, which have been suggested to be potentially transmissible to subsequent generations...
December 2018: Current Genomics
https://read.qxmd.com/read/30532645/how-stress-gets-under-the-skin-early-life-adversity-and-glucocorticoid-receptor-epigenetic-regulation
#14
REVIEW
Patrick Z Liu, Robin Nusslock
Early life adversity is associated with both persistent disruptions in the hypothalamic-pituitary-adrenal (HPA) axis and psychiatric symptoms. Glucocorticoid receptors (GRs), which are encoded by the NR3C1 gene, bind to cortisol and other glucocorticoids to create a negative feedback loop within the HPA axis to regulate the body's neuroendocrine response to stress. Excess methylation of a promoter sequence within NR3C1 that attenuates GR expression, however, has been associated with both early life adversity and psychopathology...
December 2018: Current Genomics
https://read.qxmd.com/read/30532644/epigenetic-programming-effects-of-early-life-stress-a-dual-activation-hypothesis
#15
REVIEW
Vanessa Lux
Epigenetic processes during early brain development can function as 'developmental switches' that contribute to the stability of long-term effects of early environmental influences by programming central feedback mechanisms of the HPA axis and other neural networks. In this thematic review, we summarize accumulated evidence for a dual-activation of stress-related and sensory networks underlying the epigenetic programming effects of early life stress. We discuss findings indicating epigenetic programming of stress-related genes with impact on HPA axis function, the interaction of epigenetic mechanisms with neural activity in stress-related neural networks, epigenetic effects of glucocorticoid exposure, and the impact of stress on sensory development...
December 2018: Current Genomics
https://read.qxmd.com/read/30532643/a-genomic-and-epigenomic-approach-for-studying-neuropsychiatric-disorders-associated-to-early-life-stress-part-ii
#16
EDITORIAL
Xena Giada Pappalardo, Sebastiano Cavallaro
No abstract text is available yet for this article.
December 2018: Current Genomics
https://read.qxmd.com/read/30386174/a-network-biology-approach-for-assessing-the-role-of-pathologic-adipose-tissues-in-insulin-resistance-using-meta-analysis-of-microarray-datasets
#17
Aditya Saxena, Kumar Sachin
Background: The role of adipose tissue in Insulin resistance (IR) and Type 2 Diabetes (T2D) has well been received in the biomedical community; being a precursor of T2D, identification of the molecular basis of IR is therefore, vital to elucidate T2D- pathogenesis and meta-analysis of previously conducted microarray studies provides an inexpensive approach to achieve this end. Methods: In this study, we have carried out a statistical meta-analysis of 157 microarray datasets from five independent studies and identified a meta-signature of 1,511 genes; their functional meaning was elucidated by integrated pathways-analysis...
November 2018: Current Genomics
https://read.qxmd.com/read/30386173/interplay-between-micrornas-and-targeted-genes-in-cellular-homeostasis-of-adult-zebrafish-danio-rerio
#18
Ludivine Renaud, Willian A da Silveira, William B Glen, Edward S Hazard, Gary Hardiman
Background: Cellular homeostasis is regulated by the intricate interplay between a plethora of signaling pathways and "energetic sensors" in organs. In order to maintain energy balance, induction or repression of metabolic pathways must be regulated and act in concert with the energetic demands of the cell at a given point in time. A new class of small noncoding RNAs, the microRNAs (miRNAs), has added yet further complexity to the control of metabolic homeostasis. Objective: Understanding the damages induced by toxins in the liver and the intestine as well as the interplay between the miRNome and transcriptome first requires baseline characterization in these tissues in healthy animals under cellular homeostasis...
November 2018: Current Genomics
https://read.qxmd.com/read/30386172/parallel-algorithms-for-inferring-gene-regulatory-networks-a-review
#19
REVIEW
Omid Abbaszadeh, Ali Reza Khanteymoori, Ali Azarpeyvand
System biology problems such as whole-genome network construction from large-scale gene expression data are sophisticated and time-consuming. Therefore, using sequential algorithms are not feasible to obtain a solution in an acceptable amount of time. Today, by using massively parallel computing, it is possible to infer large-scale gene regulatory networks. Recently, establishing gene regulatory networks from large-scale datasets have drawn the noticeable attention of researchers in the field of parallel computing and system biology...
November 2018: Current Genomics
https://read.qxmd.com/read/30386171/early-life-stress-and-epigenetics-in-late-onset-alzheimer-s-dementia-a-systematic-review
#20
REVIEW
Erwin Lemche
Involvement of life stress in Late-Onset Alzheimer's Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have successfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper-phosphorylation and amyloidogenic processing...
November 2018: Current Genomics
journal
journal
35108
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"