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Bioinformatics

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https://www.readbyqxmd.com/read/28379466/mackinac-a-bridge-between-modelseed-and-cobrapy-to-generate-and-analyze-genome-scale-metabolic-models
#1
Michael Mundy, Helena Mendes-Soares, Nicholas Chia
Summary: Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms...
August 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633445/bpp-a-sequence-based-algorithm-for-branch-point-prediction
#2
Qing Zhang, Xiaodan Fan, Yejun Wang, Mingan Sun, Jianlin Shao, Dianjing Guo
Motivation: Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results: We here propose a novel branch point prediction algorithm that utilises information on the branch point sequence and the polypyrimidine tract...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633441/bioqueue-a-novel-pipeline-framework-to-accelerate-bioinformatics-analysis
#3
Li Yao, Heming Wang, Yuanyuan Song, Guangchao Sui
Motivation: With the rapid development of Next-Generation Sequencing, a large amount of data is now available for bioinformatics research. Meanwhile, the presence of many pipeline frameworks makes it possible to analyse these data. However, these tools concentrate mainly on their syntax and design paradigms, and dispatch jobs based on users' experience about the resources needed by the execution of a certain step in a protocol. As a result, it is difficult for these tools to maximize the potential of computing resources, and avoid errors caused by overload, such as memory overflow...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633438/sandpuma-ensemble-predictions-of-nonribosomal-peptide-chemistry-reveals-biosynthetic-diversity-across-actinobacteria
#4
Marc G Chevrette, Fabian Aicheler, Oliver Kohlbacher, Cameron R Currie, Marnix H Medema
Summary: Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633433/the-international-society-for-computational-biology-and-wikiproject-computational-biology-celebrating-ten-years-of-collaboration-towards-open-access
#5
Kieran O'Neill, Vivek Rai, Alastair M Kilpatrick
No abstract text is available yet for this article.
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633423/rqt-an-r-package-for-gene-level-meta-analysis
#6
Ilya Y Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin
Motivation: Despite recent advances of modern GWAS methods, it is still remains an important problem of addressing calculation an effect size and corresponding p -value for the whole gene rather than for single variant. Results: We developed an R package rqt , which offers gene-level GWAS meta-analysis. The package can be easily included into bioinformatics pipeline or used stand-alone. We applied this tool to the analysis of Alzheimer's disease data from three datasets CHS, FHS, and LOADFS...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633418/detecting-and-removing-multiplicative-spatial-bias-in-high-throughput-screening-technologies
#7
Iurie Caraus, Bogdan Mazoure, Robert Nadon, Vladimir Makarenkov
Motivation: Considerable attention has been paid recently to improve data quality in high-throughput screening (HTS) and high-content screening (HCS) technologies widely used in drug development and chemical toxicity research. However, several environmentally- and procedurally-induced spatial biases in these screens decrease measurement accuracy, leading to increased numbers of false positives and false negatives in hit selection. Although effective bias correction methods and software have been developed over the past decades, almost all of these tools have been designed to reduce the effect of additive bias only...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633399/the-interfacial-character-of-antibody-paratopes-analysis-of-antibody-antigen-structures
#8
Minh N Nguyen, Mohan R Pradhan, Chandra Verma, Pingyu Zhong
Summary: In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen-antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633391/kmerpyramid-an-interactive-visualization-tool-for-nucleobase-and-k-mer-frequencies
#9
Jochen Kruppa, Erhard van der Vries, Wendy K Jo, Alexander Postel, Paul Becher, Albert Osterhaus, Klaus Jung
Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k -mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k -mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633385/timiner-ngs-data-mining-pipeline-for-cancer-immunology-and-immunotherapy
#10
Elias Tappeiner, Francesca Finotello, Pornpimol Charoentong, Clemens Mayer, Dietmar Rieder, Zlatko Trajanoski
Summary: Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing (NGS) data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from NGS data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates, and quantification of tumor immunogenicity...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633357/matter-an-r-package-for-rapid-prototyping-with-larger-than-memory-datasets-on-disk
#11
Kylie A Bemis, Olga Vitek
Summary: We introduce matter , an R package for direct interactions with larger-than-memory datasets, stored in an arbitrary number of files of any size. matter is primarily designed for datasets in new and rapidly evolving file formats, which may lack extensive software support. matter enables a wide variety of data exploration and manipulation steps, and is extensible to many bioinformatics applications. It supports reproducible research by minimizing the need of converting and storing data in multiple formats...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#12
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633280/motifhyades-expectation-maximization-for-de-novo-dna-motif-pair-discovery-on-paired-sequences
#13
Ka-Chun Wong
Motivation: In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter-enhancer pairs) systematically. Results: To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences...
June 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605519/cancersubtypes-an-r-bioconductor-package-for-molecular-cancer-subtype-identification-validation-and-visualization
#14
Taosheng Xu, Thuc Duy Le, Lin Liu, Ning Su, Rujing Wang, Bingyu Sun, Antonio Colaprico, Gianluca Bontempi, Jiuyong Li
Summary: Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes , an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization...
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605406/cloudneo-a-cloud-pipeline-for-identifying-patient-specific-tumor-neoantigens
#15
Preeti Bais, Sandeep Namburi, Daniel M Gatti, Xinyu Zhang, Jeffrey H Chuang
Availability: The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo . For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform ( htps://cgc.sbgenomics.com/ , recommended version) can be obtained by contacting the authors. Contact: jeff.chuang@jax.org.
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605402/sparse-redundancy-analysis-of-high-dimensional-genetic-and-genomic-data
#16
Attila Csala, Frans P J M Voorbraak, Aeilko H Zwinderman, Michel H Hof
Motivation: Recent technological developments have enabled the possibility of genetic and genomic integrated data analysis approaches, where multiple omics data sets from various biological levels are combined and used to describe (disease) phenotypic variations. The main goal is to explain and ultimately predict phenotypic variations by understanding their genetic basis and the interaction of the associated genetic factors. Therefore, understanding the underlying geneticmechanisms of phenotypic variations is an ever increasing research interest in biomedical sciences...
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605508/message-from-the-iscb-2017-iscb-overton-prize-awarded-to-christoph-bock
#17
Christiana N Fogg, Diane E Kovats, Bonnie Berger
No abstract text is available yet for this article.
June 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605502/fast-bootstrapping-based-estimation-of-confidence-intervals-of-expression-levels-and-differential-expression-from-rna-seq-data
#18
Igor Mandric, Yvette Temate-Tiagueu, Tatiana Shcheglova, Sahar Al Seesi, Alex Zelikovsky, Ion I Mandoiu
Summary: This note presents IsoEM2 and IsoDE2, new versions with enhanced features and faster runtime of the IsoEM and IsoDE packages for expression level estimation and differential expression. IsoEM2 estimates FPKM and TPM levels for genes and isoforms with confidence intervals through bootstrapping, while IsoDE2 performs differential expression (DE) analysis using the bootstrap samples generated by IsoEM2. Both tools are available with a command line interface as well as a graphical user interface through wrappers for the Galaxy platform...
June 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605497/message-from-the-iscb-2017-outstanding-contributions-to-iscb-award-given-to-fran-lewitter
#19
Christiana N Fogg, Diane E Kovats, Bonnie Berger
No abstract text is available yet for this article.
June 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28605489/message-from-the-iscb-2017-iscb-accomplishment-by-a-senior-scientist-award-given-to-pavel-pevzner
#20
Christiana N Fogg, Diane E Kovats, Bonnie Berger
No abstract text is available yet for this article.
June 10, 2017: Bioinformatics
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