keyword
MENU ▼
Read by QxMD icon Read
search

Computational biology

keyword
https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#1
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28535294/hgva-the-human-genome-variation-archive
#2
Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28535263/gene-expression-variability-and-the-analysis-of-large-scale-rna-seq-studies-with-the-mdseq
#3
Di Ran, Z John Daye
Rapidly decreasing cost of next-generation sequencing has led to the recent availability of large-scale RNA-seq data, that empowers the analysis of gene expression variability, in addition to gene expression means. In this paper, we present the MDSeq, based on the coefficient of dispersion, to provide robust and computationally efficient analysis of both gene expression means and variability on RNA-seq counts. The MDSeq utilizes a novel reparametrization of the negative binomial to provide flexible generalized linear models (GLMs) on both the mean and dispersion...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28535149/quantitative-computational-models-of-molecular-self-assembly-in-systems-biology
#4
Marcus Thomas, Russell Schwartz
Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems...
May 23, 2017: Physical Biology
https://www.readbyqxmd.com/read/28534784/incorporation-of-solvent-effect-into-multi-objective-evolutionary-algorithm-for-improved-protein-structure-prediction
#5
Shangce Gao, Jiujun Cheng, Yuki Todo, Mengchu Zhou
The problem of predicting the three-dimensional structure of a protein from its one-dimensional sequence has been called the "holy grail of molecular biology", and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534781/reviving-the-two-state-markov-chain-approach
#6
Andrzej Mizera, Jun Pang, Qixia Yuan
Probabilistic Boolean networks (PBNs) is a well-established computational framework for modelling biological systems. The steady-state dynamics of PBNs is of crucial importance in the study of such systems. However, for large PBNs, which often arise in systems biology, obtaining the steady-state distribution poses a significant challenge. In this paper, we revive the two-state Markov chain approach to solve this problem. This paper contributes in three aspects. First, we identify a problem of generating biased results with the approach and we propose a few heuristics to avoid such a pitfall...
May 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534780/katzlgo-large-scale-prediction-of-lncrna-functions-by-using-the-katz-measure-based-on-multiple-networks
#7
Zuping Zhang, Jingpu Zhang, Chao Fan, Yongjun Tang, Lei Deng
Aggregating evidences have shown that long non-coding RNAs (lncRNAs) generally play key roles in cellular biological processes such as epigenetic regulation, gene expression regulation at transcriptional and post-transcriptional levels, cell differentiation and others. However, most lncRNAs have not been functionally characterized. There is an urgent need to develop computational approaches for function annotation of increasing available lncRNAs. In this article, we propose a global network-based method, KATZLGO, to predict the functions of human lncRNAs at large scale...
May 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534754/the-icvsie-a-general-purpose-integral-equation-method-for-bio-electromagnetic-analysis
#8
Luis J Gomez, Abdulkadir C Yucel, Eric Michielssen
An internally combined volume surface integral equation (ICVSIE) for analyzing electromagnetic (EM) interactions with biological tissue and wide ranging diagnostic, therapeutic, and research applications, is proposed. METHOD: The ICVSIE is a system of integral equations in terms of volume and surface equivalent currents in biological tissue subject to fields produced by externally or internally positioned devices. The system is created by using equivalence principles and solved numerically; the resulting current values are used to evaluate scattered and total electric fields, specific absorption rates, and related quantities...
May 16, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28534676/applications-of-raman-spectroscopy-in-biopharmaceutical-manufacturing-a-short-review
#9
Kevin Buckley, Alan G Ryder
The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc...
June 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28533757/multiscale-modeling-of-bone-healing-toward-a-systems-biology-approach
#10
REVIEW
Edoardo Borgiani, Georg N Duda, Sara Checa
Bone is a living part of the body that can, in most situations, heal itself after fracture. However, in some situations, healing may fail. Compromised conditions, such as large bone defects, aging, immuno-deficiency, or genetic disorders, might lead to delayed or non-unions. Treatment strategies for those conditions remain a clinical challenge, emphasizing the need to better understand the mechanisms behind endogenous bone regeneration. Bone healing is a complex process that involves the coordination of multiple events at different length and time scales...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28533466/cultural-evolution-of-military-camouflage
#11
Laszlo Talas, Roland J Baddeley, Innes C Cuthill
While one has evolved and the other been consciously created, animal and military camouflage are expected to show many similar design principles. Using a unique database of calibrated photographs of camouflage uniform patterns, processed using texture and colour analysis methods from computer vision, we show that the parallels with biology are deeper than design for effective concealment. Using two case studies we show that, like many animal colour patterns, military camouflage can serve multiple functions...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28533216/a-diverse-community-to-study-communities-integration-of-experiments-and-mathematical-models-to-study-microbial-consortia
#12
Antonella Succurro, Fiona Wanjiku Moejes, Oliver Ebenhöh
The last few years have seen the advancement of high-throughput experimental techniques produce an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from e.g. sequencing data, and often motivate further targeted experiments. The broad discipline of "computational biology" spans far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods like mathematical models are not yet as well integrated in the research studying microbial interactions...
May 22, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28532541/-analysis-of-growth-curve-type-in-pulmonary-nodules-with%C3%A2-different-characteristics
#13
Xinyue Wang, Rongcheng Han, Fangfang Guo, Xinling Li, Wensong Zheng, Qing Wang, Wenjing Song, Tielian Yu, Ying Wang
BACKGROUND: Background and objective Follow up by computed tomography (CT) and growth evaluation are routine methods for the differential diagnosis of indeterminate pulmonary nodules in clinical practice. Pulmonary nodules with diverse biological behaviors may show different growth patterns and velocities. The aim of this study is to identify the volume growth curve of both benign and malignant pulmonary nodules. This work also intends to determine these nodules' growth patterns and provide evidence for the establishment of a follow-up strategy...
May 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/28532357/visual-object-recognition-do-we-finally-know-more-now-than-we-did
#14
Isabel Gauthier, Michael J Tarr
How do we recognize objects despite changes in their appearance? The past three decades have been witness to intense debates regarding both whether objects are encoded invariantly with respect to viewing conditions and whether specialized, separable mechanisms are used for the recognition of different object categories. We argue that such dichotomous debates ask the wrong question. Much more important is the nature of object representations: What are features that enable invariance or differential processing between categories? Although the nature of object features is still an unanswered question, new methods for connecting data to models show significant potential for helping us to better understand neural codes for objects...
October 14, 2016: Annual Review of Vision Science
https://www.readbyqxmd.com/read/28532213/what-do-structures-tell-us-about-chemokine-receptor-function-and-antagonism
#15
Irina Kufareva, Martin Gustavsson, Yi Zheng, Bryan S Stephens, Tracy M Handel
Chemokines and their cell surface G protein-coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28531187/multi-scale-computational-study-of-the-mechanical-regulation-of-cell-mitotic-rounding-in-epithelia
#16
Ali Nematbakhsh, Wenzhao Sun, Pavel A Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J Zartman, Mark Alber
Mitotic rounding during cell division is critical for preventing daughter cells from inheriting an abnormal number of chromosomes, a condition that occurs frequently in cancer cells. Cells must significantly expand their apical area and transition from a polygonal to circular apical shape to achieve robust mitotic rounding in epithelial tissues, which is where most cancers initiate. However, how cells mechanically regulate robust mitotic rounding within packed tissues is unknown. Here, we analyze mitotic rounding using a newly developed multi-scale subcellular element computational model that is calibrated using experimental data...
May 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28531174/genome-partitioner-a-web-tool-for-multi-level-partitioning-of-large-scale-dna-constructs-for-synthetic-biology-applications
#17
Matthias Christen, Luca Del Medico, Heinz Christen, Beat Christen
Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs...
2017: PloS One
https://www.readbyqxmd.com/read/28530717/sparse-coding-with-memristor-networks
#18
Patrick M Sheridan, Fuxi Cai, Chao Du, Wen Ma, Zhengya Zhang, Wei D Lu
Sparse representation of information provides a powerful means to perform feature extraction on high-dimensional data and is of broad interest for applications in signal processing, computer vision, object recognition and neurobiology. Sparse coding is also believed to be a key mechanism by which biological neural systems can efficiently process a large amount of complex sensory data while consuming very little power. Here, we report the experimental implementation of sparse coding algorithms in a bio-inspired approach using a 32 × 32 crossbar array of analog memristors...
May 22, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28530546/the-role-of-qsar-and-virtual-screening-studies-in-type-2-diabetes-drug-discovery
#19
Simone Q Pantaleão, Drielli G V Fujji, Vinícius G Maltarollo, Danielle da C Silva, Gustavo H G Trossini, Karen C Weber, Luis P B Scott, Kathia M Honorio
BACKGROUND: Due to the increasing number of diabetes cases worldwide, there is an international concern to provide even more effective treatments to control this condition. METHODS: This review brings together a selection of studies that helped to broaden the comprehension of various biological targets and associated mechanisms involved in type 2 diabetes mellitus. RESULTS: Such studies demonstrated that QSAR techniques and virtual screenings have been successfully employed in drug design projects...
May 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28530232/tomographic-active-optical-trapping-of-arbitrarily-shaped-objects-by-exploiting-3d-refractive-index-maps
#20
Kyoohyun Kim, YongKeun Park
Optical trapping can manipulate the three-dimensional (3D) motion of spherical particles based on the simple prediction of optical forces and the responding motion of samples. However, controlling the 3D behaviour of non-spherical particles with arbitrary orientations is extremely challenging, due to experimental difficulties and extensive computations. Here, we achieve the real-time optical control of arbitrarily shaped particles by combining the wavefront shaping of a trapping beam and measurements of the 3D refractive index distribution of samples...
May 22, 2017: Nature Communications
keyword
keyword
20301
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"