keyword
MENU ▼
Read by QxMD icon Read
search

Bioinformatics & Computational Biology

keyword
https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#1
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#2
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29126724/dual-or-multi-targeting-inhibitors-the-next-generation-anticancer-agents
#3
REVIEW
Nulgumnalli Manjunathaiah Raghavendra, Divya Pingili, Sundeep Kadasi, Akhila Mettu, S V U M Prasad
Dual-targeting/Multi-targeting of oncoproteins by a single drug molecule represents an efficient, logical and alternative approach to drug combinations. An increasing interest in this approach is indicated by a steady upsurge in the number of articles on targeting dual/multi proteins published in the last 5 years. Combining different inhibitors that destiny specific single target is the standard treatment for cancer. A new generation of dual or multi-targeting drugs is emerging, where a single chemical entity can act on multiple molecular targets...
October 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29118436/combining-membrane-proteomics-and-computational-three-way-pathway-analysis-revealed-signalling-pathways-preferentially-regulated-in-human-ipscs-and-human-escs
#4
Wei-Sheng Tien, Pei-Mien Chen, Ching-Yu Chuang, Shook-Mun Lui, Hung-Chih Kuo, Yu-Ju Chen, Kun-Pin Wu
Owing to the clinical potential of human induced pluripotent stem cells (hiPSCs) in regenerative medicine, a thorough examination of the similarities and differences between hiPSCs and human embryonic stem cells (hESCs) has become indispensable. Moreover, as the important roles of membrane proteins in biological signalling, functional analyses of membrane proteome are therefore promising. In this study, a pathway analysis by the bioinformatics tool GSEA was first performed to identify significant pathways associated with the three comparative membrane proteomics experiments: hiPSCs versus precursor human foreskin fibroblasts (HFF), hESCs versus precursor HFF, and hiPSCs versus hESCs...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29113454/modulators-of-redox-metabolism-in-head-and-neck-cancer
#5
Xiaofei Chen, Jade Mims, Xiumei Huang, Naveen Singh, Edward A Motea, Sarah M Planchon, Muhammad Beg, Allen W Tsang, Mercedes Porosnicu, Melissa L Kemp, David A Boothman, Cristina Furdui
SIGNIFICANCE: Head and Neck Squamous Cell Cancer (HNSCC) is a complex disease characterized by high genetic and metabolic heterogeneity. Radiation therapy (RT) alone or combined with systemic chemotherapy is widely used for treatment of HNSCC as definitive treatment or as adjuvant treatment after surgery. Antibodies against Epidermal Growth Factor Receptor (EGFR) are used in definitive or palliative treatment. Recent Advances. Emerging targeted therapies against other proteins of interest as well as programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) immunotherapies are being explored in clinical trials...
November 7, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29110697/exutr-a-novel-pipeline-for-large-scale-prediction-of-3-utr-sequences-from-ngs-data
#6
Zixia Huang, Emma C Teeling
BACKGROUND: The three prime untranslated region (3'-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA. Many crucial developmental events, such as mammalian spermatogenesis, tissue patterning, sex determination and neurogenesis, rely heavily on post-transcriptional regulation by the 3'-UTR. However, 3'-UTR biology seems to be a relatively untapped field, with only limited tools and 3'-UTR resources available. To elucidate the regulatory mechanisms of the 3'-UTR on gene expression, firstly the 3'-UTR sequences must be identified...
November 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29095952/computer-simulation-models-as-a-tool-to-investigate-the-role-of-micrornas-in-osteoarthritis
#7
Carole J Proctor, Graham R Smith
The aim of this study was to show how computational models can be used to increase our understanding of the role of microRNAs in osteoarthritis (OA) using miR-140 as an example. Bioinformatics analysis and experimental results from the literature were used to create and calibrate models of gene regulatory networks in OA involving miR-140 along with key regulators such as NF-κB, SMAD3, and RUNX2. The individual models were created with the modelling standard, Systems Biology Markup Language, and integrated to examine the overall effect of miR-140 on cartilage homeostasis...
2017: PloS One
https://www.readbyqxmd.com/read/29095940/expressiondb-an-open-source-platform-for-distributing-genome-scale-datasets
#8
Laura D Hughes, Scott A Lewis, Michael E Hughes
RNA-sequencing (RNA-seq) and microarrays are methods for measuring gene expression across the entire transcriptome. Recent advances have made these techniques practical and affordable for essentially any laboratory with experience in molecular biology. A variety of computational methods have been developed to decrease the amount of bioinformatics expertise necessary to analyze these data. Nevertheless, many barriers persist which discourage new labs from using functional genomics approaches. Since high-quality gene expression studies have enduring value as resources to the entire research community, it is of particular importance that small labs have the capacity to share their analyzed datasets with the research community...
2017: PloS One
https://www.readbyqxmd.com/read/29092932/a-galaxy-implementation-of-next-generation-clustered-heatmaps-for-interactive-exploration-of-molecular-profiling-data
#9
Bradley M Broom, Michael C Ryan, Robert E Brown, Futa Ikeda, Mark Stucky, David W Kane, James Melott, Chris Wakefield, Tod D Casasent, Rehan Akbani, John N Weinstein
Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29077790/precision-medicine-needs-pioneering-clinical-bioinformaticians
#10
Gonzalo Gómez-López, Joaquín Dopazo, Juan C Cigudosa, Alfonso Valencia, Fátima Al-Shahrour
Success in precision medicine depends on accessing high-quality genetic and molecular data from large, well-annotated patient cohorts that couple biological samples to comprehensive clinical data, which in conjunction can lead to effective therapies. From such a scenario emerges the need for a new professional profile, an expert bioinformatician with training in clinical areas who can make sense of multi-omics data to improve therapeutic interventions in patients, and the design of optimized basket trials. In this review, we first describe the main policies and international initiatives that focus on precision medicine...
October 25, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29069296/xmwas-a-data-driven-integration-and-differential-network-analysis-tool
#11
Karan Uppal, Chunyu Ma, Young-Mi Go, Dean P Jones
Summary: Integrative omics is a central component of most systems biology studies. Computational methods are required for extracting meaningful relationships across different omics layers. Various tools have been developed to facilitate integration of paired heterogenous omics data; however most existing tools allow integration of only two omics datasets. Furthermore, existing data integration tools do not incorporate additional steps of identifying sub-networks or communities of highly connected entities and evaluating the topology of the integrative network under different conditions...
October 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29069283/bayesian-data-integration-for-quantifying-the-contribution-of-diverse-measurements-to-parameter-estimates
#12
Bram Thijssen, Tjeerd M H Dijkstra, Tom Heskes, Lodewyk F A Wessels
Motivation: Computational models in biology are frequently underdetermined, due to limits in our capacity to measure biological systems. In particular, mechanistic models often contain parameters whose values are not constrained by a single type of measurement. It may be possible to achieve better model determination by combining the information contained in different types of measurements. Bayesian statistics provides a convenient framework for this, allowing a quantification of the reduction in uncertainty with each additional measurement type...
October 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29069282/chromatin-accessibility-prediction-via-a-hybrid-deep-convolutional-neural-network
#13
Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang
Motivation: A majority of known genetic variants associated with human inherited diseases lie in non-coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and precisely decipher their implications in a comprehensive manner. Although computational approaches have been complementing high-throughput biological experiments towards the annotation of the human genome, it still remains a big challenge to accurately annotate regulatory elements in the context of a specific cell type via automatic learning of the DNA sequence code from large-scale sequencing data...
October 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29065609/molecular-skin-surface-based-transformation-visualization-between-biological-macromolecules
#14
Ke Yan, Bing Wang, Holun Cheng, Zhiwei Ji, Jing Huang, Zhigang Gao
Molecular skin surface (MSS), proposed by Edelsbrunner, is a C(2) continuous smooth surface modeling approach of biological macromolecules. Compared to the traditional methods of molecular surface representations (e.g., the solvent exclusive surface), MSS has distinctive advantages including having no self-intersection and being decomposable and transformable. For further promoting MSS to the field of bioinformatics, transformation between different MSS representations mimicking the macromolecular dynamics is demanded...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29062170/diseases-and-molecular-diagnostics-a-step-closer-to-precision-medicine
#15
EDITORIAL
Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Puneet Pareek, Apul Goel, Sanjay Khattri, Kamlesh Kumar Pant, Sanjeev Misra, Praveen Sharma
The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc...
October 2017: Indian Journal of Clinical Biochemistry: IJCB
https://www.readbyqxmd.com/read/29061110/a-rapid-and-accurate-approach-for-prediction-of-interactomes-from-co-elution-data-prince
#16
R Greg Stacey, Michael A Skinnider, Nichollas E Scott, Leonard J Foster
BACKGROUND: An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes...
October 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29060839/a-new-alignment-free-genome-comparison-algorithm-based-on-statistically-estimated-feature-frequency-profile
#17
Hyein Seo, Dong-Ho Cho
The sequence comparison is an important part in bioinformatics to understand the biological property of genome. Although the alignment based sequence comparison is traditional and reliable algorithm, alignment free methods have been actively researched because of their advantage in terms of computational complexity. In this paper, we suggest a new alignment free genome comparison scheme based on statistical approach. From sequence components, word frequency information of the sequence is estimated. By investigating the relationship between estimated frequency information and actual word frequency, the characteristics of the sequence are numerically represented...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29059639/-complexity-of-the-phenomenon-of-life-the-challenge-for-medicine
#18
Mieczysław Chorąży
The human organism presents a complex biological system that has hierarchical organization. The lowest, basal hierarchical level is composed of chemical molecules. The system's structure as "the whole" is maintained by complex interactions of its parts (molecules). New forms and functions, not present in molecules themselves emerge from their orchestrated and coordinated interaction, creating the novel "whole". The "whole" is not a simple summation of its parts. Therefore, on the basis of reductionist analysis and solely on the list of component elements of biological systems it is not possible to predict the future form and function of the "whole"...
2017: Wiadomości Lekarskie: Organ Polskiego Towarzystwa Lekarskiego
https://www.readbyqxmd.com/read/29049281/unmet-needs-for-analyzing-biological-big-data-a-survey-of-704-nsf-principal-investigators
#19
Lindsay Barone, Jason Williams, David Micklos
In a 2016 survey of 704 National Science Foundation (NSF) Biological Sciences Directorate principal investigators (BIO PIs), nearly 90% indicated they are currently or will soon be analyzing large data sets. BIO PIs considered a range of computational needs important to their work, including high performance computing (HPC), bioinformatics support, multistep workflows, updated analysis software, and the ability to store, share, and publish data. Previous studies in the United States and Canada emphasized infrastructure needs...
October 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29048466/pybel-a-computational-framework-for-biological-expression-language
#20
Charles Tapley Hoyt, Andrej Konotopez, Christian Ebeling
Summary: Biological Expression Language (BEL) assembles knowledge networks from biological relations across multiple modes and scales. Here, we present PyBEL; a software package for parsing, validating, converting, storing, querying, and visualizing networks encoded in BEL. Availability: PyBEL is implemented in platform-independent, universal Python code. Its source is distributed under the Apache 2.0 License at https://github.com/pybel. Contact: charles...
October 18, 2017: Bioinformatics
keyword
keyword
45746
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"