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Source Code for Biology and Medicine

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https://www.readbyqxmd.com/read/28413437/gostag-gene-ontology-subtrees-to-tag-and-annotate-genes-within-a-set
#1
Brian D Bennett, Pierre R Bushel
BACKGROUND: Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times there are hundreds of statistically significant GO terms per gene set. Comparing enriched categories between a large number of analyses and identifying the term within the GO hierarchy with the most connections is challenging. Furthermore, ascertaining biological themes representative of the samples can be highly subjective from the interpretation of the enriched categories...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28344641/litdb-keeping-track-of-research-papers-from-your-institute-made-simple
#2
Jörn Bethune, Lars Kraemer, Ingo Thomsen, Andreas Keller, David Ellinghaus, Andre Franke
BACKGROUND: In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28194225/net-a-new-framework-for-the-vectorization-and-examination-of-network-data
#3
Jana Lasser, Eleni Katifori
BACKGROUND: The analysis of complex networks both in general and in particular as pertaining to real biological systems has been the focus of intense scientific attention in the past and present. In this paper we introduce two tools that provide fast and efficient means for the processing and quantification of biological networks like Drosophila tracheoles or leaf venation patterns: the Network Extraction Tool (NET) to extract data and the Graph-edit-GUI (GeGUI) to visualize and modify networks...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28191033/algorithm-and-software-to-automatically-identify-latency-and-amplitude-features-of-local-field-potentials-recorded-in-electrophysiological-investigation
#4
Maria Rubega, Claudia Cecchetto, Stefano Vassanelli, Giovanni Sparacino
BACKGROUND: Local field potentials (LFPs) evoked by sensory stimulation are particularly useful in electrophysiological research. For instance, spike timing and current transmembrane current flow estimated from LFPs recorded in the barrel cortex in rats and mice are exploited to investigate how the brain represents sensory stimuli. Recent improvements in microelectrodes technology enable neuroscientists to acquire a great amount of LFPs during the same experimental session, calling for algorithms for their quantitative automatic analysis...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28174599/deapp-an-interactive-web-interface-for-differential-expression-analysis-of-next-generation-sequence-data
#5
Yan Li, Jorge Andrade
BACKGROUND: A growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is however still challenging, as it requires sufficient computer programing and command-line knowledge. Furthermore, researchers often need to evaluate and visualize interactively the effect of using differential statistical and error models, assess the impact of selecting different parameters and cutoffs, and finally explore the overlapping consensus of cross-validated results obtained with different methods...
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/28077964/erratum-to-a-bedr-way-of-genomic-interval-processing
#6
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C Boutros
[This corrects the article DOI: 10.1186/s13029-016-0059-5.].
2017: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27999613/a-bedr-way-of-genomic-interval-processing
#7
Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, Paul C Boutros
BACKGROUND: Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annotation, merging multiple experiments together and subsequently quantifying and visualizing the overlap. The most widely-used tools for these tasks work at the command-line (e.g. BEDTools) and the small number of available R packages are either slow or have distinct semantics and features from command-line interfaces...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27999612/purecn-copy-number-calling-and-snv-classification-using-targeted-short-read-sequencing
#8
Markus Riester, Angad P Singh, A Rose Brannon, Kun Yu, Catarina D Campbell, Derek Y Chiang, Michael P Morrissey
BACKGROUND: Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known somatic alterations in cancer genes and often only sequence tumors. Therefore, an algorithm that reliably classifies variants would be helpful for retrospective exploratory analyses. Contamination of tumor samples with normal cells results in differences in expected allelic fractions of germline and somatic variants, which can be exploited to accurately infer genotypes after adjusting for local copy number...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27536334/cljam-a-library-for-handling-dna-sequence-alignment-map-sam-with-parallel-processing
#9
Toshiki Takeuchi, Atsuo Yamada, Takashi Aoki, Kunihiro Nishimura
BACKGROUND: Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27408618/tagdigger-user-friendly-extraction-of-read-counts-from-gbs-and-rad-seq-data
#10
Lindsay V Clark, Erik J Sacks
BACKGROUND: In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27375772/a-new-tool-for-prioritization-of-sequence-variants-from-whole-exome-sequencing-data
#11
Brigitte Glanzmann, Hendri Herbst, Craig J Kinnear, Marlo Möller, Junaid Gamieldien, Soraya Bardien
BACKGROUND: Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly provide important insights into disease mechanisms. In developing countries, bioinformatics capacity and expertise is severely limited and wet bench scientists are required to take on the challenging task of understanding and implementing the barrage of bioinformatics tools that are available to them...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27347003/log-programinfo-a-perl-module-to-collect-and-log-data-for-bioinformatics-pipelines
#12
John M Macdonald, Paul C Boutros
BACKGROUND: To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results. RESULTS: Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27330550/sv-stat-accurately-detects-structural-variation-via-alignment-to-reference-based-assemblies
#13
Caleb F Davis, Deborah I Ritter, David A Wheeler, Hongmei Wang, Yan Ding, Shannon P Dugan, Matthew N Bainbridge, Donna M Muzny, Pulivarthi H Rao, Tsz-Kwong Man, Sharon E Plon, Richard A Gibbs, Ching C Lau
BACKGROUND: Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich source of information in which to detect breakpoints of structural variations at base-pair resolution. However, accurate prediction of SVs remains challenging, and existing informatics tools predict rearrangements with significant rates of false positives or negatives. RESULTS: To address this challenge, we developed 'Structural Variation detection by STAck and Tail' (SV-STAT) which implements a novel scoring metric...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27087834/implementation-and-clinical-application-of-a-deformation-method-for-fast-simulation-of-biological-tissue-formed-by-fibers-and-fluid
#14
Ana Gabriella de Oliveira Sardinha, Ceres Nunes de Resende Oyama, Armando de Mendonça Maroja, Ivan F Costa
BACKGROUND: The aim of this paper is to provide a general discussion, algorithm, and actual working programs of the deformation method for fast simulation of biological tissue formed by fibers and fluid. In order to demonstrate the benefit of the clinical applications software, we successfully used our computational program to deform a 3D breast image acquired from patients, using a 3D scanner, in a real hospital environment. RESULTS: The method implements a quasi-static solution for elastic global deformations of objects...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27069505/mm2s-personalized-diagnosis-of-medulloblastoma-patients-and-model-systems
#15
Deena M A Gendoo, Benjamin Haibe-Kains
BACKGROUND: Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had resulted in improvement of human subtype classification methods, and the parallel development of MB mouse models towards identification of subtype-specific disease origins and signaling pathways. Despite these advances, MB classification schemes remained inadequate for personalized prediction of MB subtypes for individual patient samples and across model systems...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27042203/a-flexible-tool-to-plot-a-genomic-map-for-single-nucleotide-polymorphisms
#16
Fuquan Zhang
BACKGROUND: Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. However, resources to visualize the genomic map of candidate SNPs in a programming manner are limited. We have previously created an R package, mapsnp v0.1, to plot the genomic map for a panel of SNPs within a genomic region of interest. It failed to work under the latest version of Gviz package. RESULTS: We updated the mapsnp package to keep up with the latest package environment and improved its functionality by adding more parameters to fine tune plotting outputs...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27022408/a-generic-schema-and-data-collection-forms-applicable-to-diverse-entomological-studies-of-mosquitoes
#17
Samson S Kiware, Tanya L Russell, Zacharia J Mtema, Alpha D Malishee, Prosper Chaki, Dickson Lwetoijera, Javan Chanda, Dingani Chinula, Silas Majambere, John E Gimnig, Thomas A Smith, Gerry F Killeen
BACKGROUND: Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often in resource-limited tropical settings lacking specialized software or informatics support. RESULTS: Data from the majority of mosquito studies conformed to a generic schema, with data collection forms recording the experimental design, sorting of collections, details of sample pooling or subdivision, and additional observations...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/26962326/conserved-antigenic-sites-between-mers-cov-and-bat-coronavirus-are-revealed-through-sequence-analysis
#18
Refat Sharmin, Abul B M M K Islam
BACKGROUND: MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the degree of conserved antigenic sites among them. It is of importance to elucidate the shared antigenic-sites and extent of conservation between them to understand the evolutionary dynamics of MERS-CoV. RESULTS: Multiple sequence alignment of the spike (S), membrane (M), enveloped (E) and nucleocapsid (N) proteins was employed to identify the sequence conservation among MERS and Bat (HKU4, HKU5) coronaviruses...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/26884809/implementation-of-the-rank-weighted-co-localization-rwc-algorithm-in-multiple-image-analysis-platforms-for-quantitative-analysis-of-microscopy-images
#19
Vasanth R Singan, Jeremy C Simpson
BACKGROUND: Quantitative co-localization studies strengthen the analysis of fluorescence microscopy-based assays and are essential for illustrating and understanding many cellular processes and interactions. In our earlier study, we presented a rank-based intensity weighting scheme for the quantification of co-localization between structures in fluorescence microscopy images. This method, which uses a combined pixel co-occurrence and intensity correlation approach, is superior to conventional algorithms and provides a more accurate quantification of co-localization...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/26788121/symmetrical-treatment-of-diagnostic-and-statistical-manual-of-mental-disorders-fifth-edition-for-major-depressive-disorders
#20
Jitsuki Sawamura, Shigeru Morishita, Jun Ishigooka
BACKGROUND: We previously presented a group theoretical model that describes psychiatric patient states or clinical data in a graded vector-like format based on modulo groups. Meanwhile, the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5, the current version), is frequently used for diagnosis in daily psychiatric treatments and biological research. The diagnostic criteria of DSM-5 contain simple binominal items relating to the presence or absence of specific symptoms...
2016: Source Code for Biology and Medicine
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