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Computational cell biology

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https://www.readbyqxmd.com/read/29045685/micrornas-and-complex-diseases-from-experimental-results-to-computational-models
#1
Xing Chen, Di Xie, Qi Zhao, Zhu-Hong You
Plenty of microRNAs (miRNAs) were discovered at a rapid pace in plants, green algae, viruses and animals. As one of the most important components in the cell, miRNAs play a growing important role in various essential and important biological processes. For the recent few decades, amounts of experimental methods and computational models have been designed and implemented to identify novel miRNA-disease associations. In this review, the functions of miRNAs, miRNA-target interactions, miRNA-disease associations and some important publicly available miRNA-related databases were discussed in detail...
October 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29045398/nonlatching-positive-feedback-enables-robust-bimodality-by-decoupling-expression-noise-from-the-mean
#2
Brandon S Razooky, Youfang Cao, Maike M K Hansen, Alan S Perelson, Michael L Simpson, Leor S Weinberger
Fundamental to biological decision-making is the ability to generate bimodal expression patterns where 2 alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV's fate decision between active replication and viral latency. We find that the HIV transactivator of transcription (Tat) protein manipulates the intrinsic toggling of HIV's promoter, the long terminal repeat (LTR), to generate bimodal ON-OFF expression and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality...
October 2017: PLoS Biology
https://www.readbyqxmd.com/read/29045032/aretrospective-review-of-six-hundred-nineteen-cases-to-determine-the-prevalence-and-factors-associated-with-revision-endoscopic-sinus-surgery-in-afrs-vs-non-afrs-patients
#3
Alykhan Rajwani, Jamil Manji, Andres Finkelstein-Kulka, Al-Rahim R Habib, Saad Alsaleh, Luis Macias-Valle, Amin R Javer
Patients undergoing revision functional endoscopic sinus surgery (rFESS) for refractory chronic rhinosinusitis (CRS) are more likely to be older, have worse pre-operative Lund-Mackay CT scores, and poorer quality-of-life scores than primary FESS patients. Patients with more aggressive forms of CRS such as CRS with nasal polyposis (CRSwNP) or allergic fungal rhinosinusitis (AFRS) may fare worse in the long term with residual disease and be more likely to seek out tertiary institutions for treatment including rFESS...
October 17, 2017: Clinical Otolaryngology
https://www.readbyqxmd.com/read/29044933/cross-tissue-identification-of-somatic-stem-and-progenitor-cells-using-a-single-cell-rna-seq-derived-gene-signature
#4
Petra C Schwalie, Paloma Ordonez Moran, Joerg Huelsken, Bart Deplancke
A long-standing question in biology is whether multipotent somatic stem and progenitor cells (SSPCs) feature molecular properties that could guide their system-independent identification. Population-based transcriptomic studies have so far not been able to provide a definite answer, given the rarity and heterogeneous nature of these cells. Here, we exploited the resolving power of single-cell RNA-sequencing to develop a computational model that is able to accurately distinguish SSPCs from differentiated cells across tissues...
October 16, 2017: Stem Cells
https://www.readbyqxmd.com/read/29044152/a-machine-learning-assisted-label-free-non-invasive-approach-for-somatic-reprogramming-in-induced-pluripotent-stem-cell-colony-formation-detection-and-prediction
#5
Ke Fan, Sheng Zhang, Ying Zhang, Jun Lu, Mike Holcombe, Xiao Zhang
During cellular reprogramming, the mesenchymal-to-epithelial transition is accompanied by changes in morphology, which occur prior to iPSC colony formation. The current approach for detecting morphological changes associated with reprogramming purely relies on human experiences, which involve intensive amounts of upfront training, human error with limited quality control and batch-to-batch variations. Here, we report a time-lapse-based bright-field imaging analysis system that allows us to implement a label-free, non-invasive approach to measure morphological dynamics...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044127/engineered-in-vitro-cell-line-mixtures-and-robust-evaluation-of-computational-methods-for-clonal-decomposition-and-longitudinal-dynamics-in-cancer
#6
Hossein Farahani, Camila P E de Souza, Raewyn Billings, Damian Yap, Karey Shumansky, Adrian Wan, Daniel Lai, Anne-Marie Mes-Masson, Samuel Aparicio, Sohrab P Shah
Characterization and quantification of tumour clonal populations over time via longitudinal sampling are essential components in understanding and predicting the response to therapeutic interventions. Computational methods for inferring tumour clonal composition from deep-targeted sequencing data are ubiquitous, however due to the lack of a ground truth biological data, evaluating their performance is difficult. In this work, we generate a benchmark data set that simulates tumour longitudinal growth and heterogeneity by in vitro mixing of cancer cell lines with known proportions...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29037894/indentation-mapping-reveals-poroelastic-but-not-viscoelastic-properties-spanning-native-zonal-articular-cartilage
#7
Joseph A Wahlquist, Frank W DelRio, Mark A Randolph, Aaron H Aziz, Chelsea M Heveran, Stephanie J Bryant, Corey P Neu, Virginia L Ferguson
Osteoarthrosis is a debilitating disease affecting millions, yet engineering materials for cartilage regeneration has proven difficult because of the complex microstructure of this tissue. Articular cartilage, like many biological tissues, produces a time-dependent response to mechanical load that is critical to cell's physiological function in part due to solid and fluid phase interactions and property variations across multiple length scales. Recreating the time-dependent strain and fluid flow may be critical for successfully engineering replacement tissues but thus far has largely been neglected...
October 13, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/29037750/environmental-toxicology-and-omics-a-question-of-sex
#8
Xuefang Liang, April Feswick, Denina Simmons, Christopher J Martyniuk
Molecular initiating events and downstream transcriptional/proteomic responses provide valuable information for adverse outcome pathways, which can be used predict the effects of chemicals on physiological systems. There has been a paucity of research that addresses sex-specific expression profiling in toxicology and due to cost, time, and logistical considerations, sex as a variable has not been widely considered. In response to this deficiency, federal agencies in the United States, Canada, and Europe have highlighted the importance of including sex as a variable in scientific investigations...
October 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29036714/accounting-for-technical-noise-in-differential-expression-analysis-of-single-cell-rna-sequencing-data
#9
Cheng Jia, Yu Hu, Derek Kelly, Junhyong Kim, Mingyao Li, Nancy R Zhang
Recent technological breakthroughs have made it possible to measure RNA expression at the single-cell level, thus paving the way for exploring expression heterogeneity among individual cells. Current single-cell RNA sequencing (scRNA-seq) protocols are complex and introduce technical biases that vary across cells, which can bias downstream analysis without proper adjustment. To account for cell-to-cell technical differences, we propose a statistical framework, TASC (Toolkit for Analysis of Single Cell RNA-seq), an empirical Bayes approach to reliably model the cell-specific dropout rates and amplification bias by use of external RNA spike-ins...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036374/gating-mass-cytometry-data-by-deep-learning
#10
Huamin Li, Uri Shaham, Kelly P Stanton, Yi Yao, Ruth R Montgomery, Yuval Kluger
Motivation: Mass cytometry or CyTOF is an emerging technology for high-dimensional multiparameter single cell analysis that overcomes many limitations of fluorescence-based flow cytometry. New methods for analyzing CyTOF data attempt to improve automation, scalability, performance and interpretation of data generated in large studies. Assigning individual cells into discrete groups of cell types (gating) involves time-consuming sequential manual steps, untenable for larger studies. Results: We introduce DeepCyTOF, a standardization approach for gating, based on deep learning techniques...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036318/dimm-sc-a-dirichlet-mixture-model-for-clustering-droplet-based-single-cell-transcriptomic-data
#11
Zhe Sun, Ting Wang, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu, Wei Chen
Motivation: Single cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct counting of transcript copies using Unique Molecular Identifier (UMI). Despite the technology advances, statistical methods and computational tools are still lacking for analyzing droplet-based scRNA-Seq data...
August 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29032150/functional-analysis-of-schizophrenia-genes-using-geneanalytics-program-and-integrated-databases
#12
Tharani Sundararajan, Ann M Manzardo, Merlin G Butler
Schizophrenia (SCZ) is a chronic debilitating neuropsychiatric disorder with multiple risk factors involving numerous complex genetic influences. We examined and updated a master list of clinically relevant and susceptibility genes associated with SCZ reported in the literature and genomic databases dedicated to gene discovery for characterization of SCZ genes. We used the commercially available GeneAnalytics computer-based gene analysis program and integrated genomic databases to create a molecular profile of the updated list of 608 SCZ genes to model their impact in select categories (tissues and cells, diseases, pathways, biological processes, molecular functions, phenotypes and compounds) using specialized GeneAnalytics algorithms...
October 12, 2017: Gene
https://www.readbyqxmd.com/read/29031966/bink-biological-binary-keypoint-descriptor
#13
Mário Saleiro, Kasim Terzić, J M F Rodrigues, J M H du Buf
Learning robust keypoint descriptors has become an active research area in the past decade. Matching local features is not only important for computational applications, but may also play an important role in early biological vision for disparity and motion processing. Although there were already some floating-point descriptors like SIFT and SURF that can yield high matching rates, the need for better and faster descriptors for real-time applications and embedded devices with low computational power led to the development of binary descriptors, which are usually much faster to compute and to match...
October 12, 2017: Bio Systems
https://www.readbyqxmd.com/read/29031516/growth-of-adult-spinal-cord-in-knifefish-development-and-parametrization-of-a-distributed-model
#14
Iulian Ilieş, Rifat Sipahi, Günther K H Zupanc
The study of indeterminate-growing organisms such as teleost fish presents a unique opportunity for improving our understanding of central nervous tissue growth during adulthood. Integrating the existing experimental data associated with this process into a theoretical framework through mathematical or computational modeling provides further research avenues through sensitivity analysis and optimization. While this type of approach has been used extensively in investigations of tumor growth, wound healing, and bone regeneration, the development of nervous tissue has been rarely studied within a modeling framework...
October 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29031098/stepwise-construction-of-a-metabolic-network-in-event-b-the-heat-shock-response
#15
Usman Sanwal, Luigia Petre, Ion Petre
There is a high interest in constructing large, detailed computational models for biological processes. This is often done by putting together existing submodels and adding to them extra details/knowledge. The result of such approaches is usually a model that can only answer questions on a very specific level of detail, and thus, ultimately, is of limited use. We focus instead on an approach to systematically add details to a model, with formal verification of its consistency at each step. In this way, one obtains a set of reusable models, at different levels of abstraction, to be used for different purposes depending on the question to address...
September 30, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29028065/a-bayesian-approach-for-estimating-protein-protein-interactions-by-integrating-structural-and-non-structural-biological-data
#16
Hafeez Ur Rehman, Inam Bari, Anwar Ali, Haroon Mahmood
Accurate elucidation of genome wide protein-protein interactions is crucial for understanding the regulatory processes of the cell. High-throughput techniques, such as the yeast-2-hybrid (Y2H) assay, co-immunoprecipitation (co-IP), mass spectrometric (MS) protein complex identification, affinity purification (AP) etc., are generally relied upon to determine protein interactions. Unfortunately, each type of method is inherently subject to different types of noise and results in false positive interactions. On the other hand, precise understanding of proteins, especially knowledge of their functional associations is necessary for understanding how complex molecular machines function...
October 13, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29026204/engineering-and-physical-sciences-in-oncology-challenges-and-opportunities
#17
REVIEW
Michael J Mitchell, Rakesh K Jain, Robert Langer
The principles of engineering and physics have been applied to oncology for nearly 50 years. Engineers and physical scientists have made contributions to all aspects of cancer biology, from quantitative understanding of tumour growth and progression to improved detection and treatment of cancer. Many early efforts focused on experimental and computational modelling of drug distribution, cell cycle kinetics and tumour growth dynamics. In the past decade, we have witnessed exponential growth at the interface of engineering, physics and oncology that has been fuelled by advances in fields including materials science, microfabrication, nanomedicine, microfluidics, imaging, and catalysed by new programmes at the National Institutes of Health (NIH), including the National Institute of Biomedical Imaging and Bioengineering (NIBIB), Physical Sciences in Oncology, and the National Cancer Institute (NCI) Alliance for Nanotechnology...
October 13, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29023190/effector-biology-in-focus-a-primer-for-computational-prediction-and-functional-characterization
#18
Ronaldo J D Dalio, John Herlihy, Tiago Silva Oliveira, John M McDowell, Marcos Antonio Antonio Machado
Plant-pathogen interactions are controlled by a multilayered immune system, which is activated by pathogen recognition in the host. Pathogens secrete effector molecules to interfere with the immune recognition/signaling network and reprogram cell structure or metabolism. Understanding the effector repertoires of diverse pathogens will contribute to unravelling the molecular mechanism of virulence and developing sustainable disease-control strategies for crops and natural ecosystems. Effector functionality has been investigated extensively only in a small number of pathogen species...
October 12, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29020802/recent-advances-in-the-systems-biology-of-aging
#19
Daniel Edward Lee Promislow, Mark A McCormick
<b><i>Significance</i></b>: Reductionist studies have contributed greatly to our understanding of the basic biology of aging in recent years but we still do not understand fundamental mechanisms for many identified drugs and pathways. Use of systems approaches will help us move forward in our understanding of aging. <b><i>Recent Advances</i></b>: Recent work described here has illustrated the power of systems biology to inform our understanding of aging through the study of 1) diet restriction; 2) neurodegenerative disease; and 3) biomarkers of aging...
October 12, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29019453/egonet-identifies-differential-ego-modules-and-pathways-related-to-prednisolone-resistance-in-childhood-acute-lymphoblastic-leukemia
#20
Jian Jiang, Xiang-Yun Yin, Xue-Wen Song, Dong Xie, Hui-Juan Xu, Jing Yang, Li-Rong Sun
PURPOSE: To extract feature ego-modules and pathways in childhood acute lymphoblastic leukemia (ALL) resistant to prednisolone treatment, and further to explore the mechanisms behind prednisolone resistance. MATERIALS AND METHODS: EgoNet algorithm was used to identify candidate ego-network modules, mainly via constructing differential co-expression network (DCN); selecting ego genes; collecting ego-network modules; refining candidate modules. Afterwards, statistical significance was calculated for these candidate modules...
October 11, 2017: Hematology (Amsterdam, Netherlands)
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