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https://www.readbyqxmd.com/read/28803038/srsf-shape-analysis-for-sequencing-data-reveal-new-differentiating-patterns
#1
Sergiusz Wesolowski, Daniel Vera, Wei Wu
MOTIVATION: Sequencing-based methods to examine fundamental features of the genome, such as gene expression and chromatin structure, rely on inferences from the abundance and distribution of reads derived from Illumina sequencing. Drawing sound inferences from such experiments relies on appropriate mathematical methods to model the distribution of reads along the genome, which has been challenging due to the scale and nature of these data. RESULTS: We propose a new framework (SRSFseq) based on square root slope functions shape analysis to analyse Illumina sequencing data...
July 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28794899/an-extended-model-for-culture-dependent-heterogenous-gene-expression-and-proliferation-dynamics-in-mouse-embryonic-stem-cells
#2
Simon Godwin, Daniel Ward, Elisa Pedone, Martin Homer, Alexander G Fletcher, Lucia Marucci
During development, pluripotency is a transient state describing a cell's ability to give rise to all three germ layers and germline. Recent studies have shown that, in vitro, pluripotency is highly dynamic: exogenous stimuli provided to cultures of mouse embryonic stem cells, isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mouse embryonic stem cells into a ground-state of pluripotency, while serum/LIF cultures promote the co-existence of ground-like and primed-like mouse embryonic stem cell subpopulations...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28792517/comparison-of-alternative-approaches-for-analysing-multi-level-rna-seq-data
#3
Irina Mohorianu, Amanda Bretman, Damian T Smith, Emily K Fowler, Tamas Dalmay, Tracey Chapman
RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D...
2017: PloS One
https://www.readbyqxmd.com/read/28791781/many-transcription-factors-contribute-to-c-%C3%A2-elegans-growth-and-fat-storage
#4
Akihiro Mori, Amy D Holdorf, Albertha J M Walhout
Reverse genetic screens by RNA interference (RNAi) in model organisms such as the nematode Caenorhabditis elegans have provided numerous insights into gene function, thereby connecting genotype to phenotype. However, genes that contribute only subtly are often missed because relatively large numbers of measurements and reliable quantification are required to overcome experimental and biological noise that may mask subtle phenotypic effects. Here, we address this challenge by focusing on two phenotypes in C...
August 8, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28781712/trom-a-testing-based-method-for-finding-transcriptomic-similarity-of-biological-samples
#5
Wei Vivian Li, Yiling Chen, Jingyi Jessica Li
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and divergence of biological processes in different species. We propose a testing-based method TROM (Transcriptome Overlap Measure) for comparing transcriptomes within or between different species, and provide a different perspective, in contrast to traditional correlation analyses, about capturing transcriptomic similarity...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28781237/heterogeneity-of-stop-codon-readthrough-in-single-bacterial-cells-and-implications-for-population-fitness
#6
Yongqiang Fan, Christopher R Evans, Karl W Barber, Kinshuk Banerjee, Kalyn J Weiss, William Margolin, Oleg A Igoshin, Jesse Rinehart, Jiqiang Ling
Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase...
August 1, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28764663/erratum-to-detection-of-gene-environment-interactions-in-the-presence-of-linkage-disequilibrium-and-noise-by-using-genetic-risk-scores-with-internal-weights-from-elastic-net-regression
#7
Anke Hüls, Katja Ickstadt, Tamara Schikowski, Ursula Krämer
No abstract text is available yet for this article.
August 1, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28740089/effects-of-growth-rate-and-promoter-activity-on-single-cell-protein-expression
#8
Niclas Nordholt, Johan van Heerden, Remco Kort, Frank J Bruggeman
Protein expression in a single cell depends on its global physiological state. Moreover, genetically-identical cells exhibit variability (noise) in protein expression, arising from the stochastic nature of biochemical processes, cell growth and division. While it is well understood how cellular growth rate influences mean protein expression, little is known about the relationship between growth rate and noise in protein expression. Here we quantify this relationship in Bacillus subtilis by a novel combination of experiments and theory...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28738811/associations-of-genetic-variation-in-casp3-gene-with-noise-induced-hearing-loss-in-a-chinese-population-a-case-control-study
#9
Yinyin Wu, Juntao Ni, Mingjian Qi, Chengjian Cao, Yuxian Shao, Liangwen Xu, Haiyan Ma, Lei Yang
BACKGROUND: Noise-induced hearing loss (NIHL) is a complex disease caused by environmental and genetic risk factors. This study explored the relationship between the genetic variations in the CASP gene and the risk of developing NIHL among Chinese workers exposed to occupational noise. METHODS: A case-control study of 272 NIHL workers and 272 normal-hearing workers matched for age, sex and years of noise exposure was conducted. Fifteen single-nucleotide polymorphisms (SNP) in the CASP1, CASP3, CASP4, CASP5, CASP6, CASP8, CASP9, CASP10 and CASP14 genes were genotyped using the polymerase chain reaction-ligase detection reaction method...
July 24, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28734797/the-effects-of-continuously-acoustical-stress-on-cortisol-in-milkfish-chanos-chanos
#10
Chih An Wei, Tzu Hao Lin, Ruo Dong Chen, Yung-Che Tseng, Yi Ta Shao
Strong underwater acoustic noise has been known that may cause hearing loss and actual stress in teleost. However, the long-term physiological effects of relatively quiet but continuously noise on fish were less understood. In present study, milkfish, Chanos chanos, were exposed to the simulated-wind farm noise either quiet (109dB re 1μPa/125.4Hz; approx. 10-100m distant from the wind farm) or noisy (138dB re 1μPa/125.4Hz; nearby the wind farm) conditions for 24h, 3days and 1week. Comparing to the control group (80dB re 1μPa/125...
July 19, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28711280/unsupervised-extraction-of-stable-expression-signatures-from-public-compendia-with-an-ensemble-of-neural-networks
#11
Jie Tan, Georgia Doing, Kimberley A Lewis, Courtney E Price, Kathleen M Chen, Kyle C Cady, Barret Perchuk, Michael T Laub, Deborah A Hogan, Casey S Greene
Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models...
July 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28709943/propagation-and-control-of-gene-expression-noise-with-non-linear-translation-kinetics
#12
J David Van Dyken
Gene expression is a stochastic process involving small numbers of molecules. As a consequence, cells in a clonal population vary randomly and sometimes substantially from one another in the concentration of mRNA and protein species, a phenomenon known as gene expression noise. Previous theoretical models of gene expression noise assumed that translation is first-order (linear) in mRNA concentration, leading to unfiltered propagation of mRNA noise to the protein level. Here I consider the biological ramifications of relaxing this assumption...
July 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28709241/careful-accounting-of-extrinsic-noise-in-protein-expression-reveals-correlations-among-its-sources
#13
John A Cole, Zaida Luthey-Schulten
In order to grow and replicate, living cells must express a diverse array of proteins, but the process by which proteins are made includes a great deal of inherent randomness. Understanding this randomness-whether it arises from the discrete stochastic nature of chemical reactivity ("intrinsic" noise), or from cell-to-cell variability in the concentrations of molecules involved in gene expression, or from the timings of important cell-cycle events like DNA replication and cell division ("extrinsic" noise)-remains a challenge...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28698882/excnvss-a-noise-robust-method-for-copy-number-variation-detection-in-whole-exome-sequencing-data
#14
Jinhwa Kong, Jaemoon Shin, Jungim Won, Keonbae Lee, Unjoo Lee, Jeehee Yoon
Copy number variations (CNVs) are structural variants associated with human diseases. Recent studies verified that disease-related genes are based on the extraction of rare de novo and transmitted CNVs from exome sequencing data. The need for more efficient and accurate methods has increased, which still remains a challenging problem due to coverage biases, as well as the sparse, small-sized, and noncontinuous nature of exome sequencing. In this study, we developed a new CNV detection method, ExCNVSS, based on read coverage depth evaluation and scale-space filtering to resolve these problems...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28695665/analysis-of-large-16s-rrna-illumina-data-sets-impact-of-singleton-read-filtering-on-microbial-community-description
#15
Lucas Auer, Mahendra Mariadassou, Michael O'Donohue, Christophe Klopp, Guillermina Hernandez-Raquet
Next-generation sequencing technologies give access to large sets of data, which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large data sets is not only marred by technical biases and sequencing noise but also increases computation time and disc space use. To improve the accuracy of OTU predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise...
July 11, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28686713/transcriptome-wide-comparison-of-the-impact-of-atoh1-and-mir-183-family-on-pluripotent-stem-cells-and-multipotent-otic-progenitor-cells
#16
Michael Ebeid, Prashanth Sripal, Jason Pecka, Kirk W Beisel, Kelvin Kwan, Garrett A Soukup
Over 5% of the global population suffers from disabling hearing loss caused by multiple factors including aging, noise exposure, genetic predisposition, or use of ototoxic drugs. Sensorineural hearing loss is often caused by the loss of sensory hair cells (HCs) of the inner ear. A barrier to hearing restoration after HC loss is the limited ability of mammalian auditory HCs to spontaneously regenerate. Understanding the molecular mechanisms orchestrating HC development is expected to facilitate cell replacement therapies...
2017: PloS One
https://www.readbyqxmd.com/read/28685099/integrative-analysis-of-pathway-deregulation-in-obesity
#17
Francesc Font-Clos, Stefano Zapperi, Caterina A M La Porta
Obesity is a pandemic disease, linked to the onset of type 2 diabetes and cancer. Transcriptomic data provides a picture of the alterations in regulatory and metabolic activities associated with obesity, but its interpretation is typically blurred by noise. Here, we solve this problem by collecting publicly available transcriptomic data from adipocytes and removing batch effects using singular value decomposition. In this way we obtain a gene expression signature of 38 genes associated to obesity and identify the main pathways involved...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28680655/a-deterministic-method-for-estimating-free-energy-genetic-network-landscapes-with-applications-to-cell-commitment-and-reprogramming-paths
#18
Victor Olariu, Erica Manesso, Carsten Peterson
Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis-Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets...
June 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28679222/information-based-measures-for-logical-stochastic-resonance-in-a-synthetic-gene-network-under-l%C3%A3-vy-flight-superdiffusion
#19
Juan Wu, Yong Xu, Haiyan Wang, Jürgen Kurths
We investigate the logical information transmission of a synthetic gene network under Lévy flight superdiffusion by an information-based methodology. We first present the stochastic synthetic gene network model driven by a square wave signal under Lévy noise caused by Lévy flight superdiffusion. Then, to quantify the potential of logical information transmission and logical stochastic resonance, we theoretically obtain an information-based methodology of the symbol error rate, the noise entropy, and the mutual information of the logical information transmission...
June 2017: Chaos
https://www.readbyqxmd.com/read/28667253/inhibitors-alter-the-stochasticity-of-regulatory-proteins-to-force-cells-to-switch-to-the-other-state-in-the-bistable-system
#20
Wun-Sin Jhang, Shih-Chiang Lo, Chen-Chao Yeh, Che-Chi Shu
The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins. For a bistable system of a mutually inhibitory network, such a change of noise led to the migration of cells in the bimodal distribution...
June 30, 2017: Scientific Reports
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