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Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods

Ross G Murphy, Aideen C Roddy, Shambhavi Srivastava, Esther Baena, David J Waugh, Joe M. O'Sullivan, Darragh G McArt, Suneil Jain, Melissa J LaBonte
2020 NAR Genomics and Bioinformatics  
Another alignment-free method for calling single-nucleotide variants from raw next-generation sequencing samples has determined possible variants and genomic locations that may be able to characterize  ...  From multi-regional sampling divergent branching, we validated two different lesions within a patient's prostate.  ...  ACKNOWLEDGEMENTS The authors would like to thank Richard Marais for his role in data provision of the prostate cancer patient multiregional sampling cohort.  ... 
doi:10.1093/nargab/lqaa062 pmid:32856020 pmcid:PMC7440682 fatcat:tsy2bul2jzfgjcjtld5ntbmgha

Phylogeny and Patterns of Diversity of Goat mtDNA Haplogroup A Revealed by Resequencing Complete Mitogenomes

Maria Grazia Doro, Daniela Piras, Giovanni Giuseppe Leoni, Giuseppina Casu, Simona Vaccargiu, Debora Parracciani, Salvatore Naitana, Mario Pirastu, Andrea Novelletto, Yong-Gang Yao
2014 PLoS ONE  
However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected.  ...  Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny.  ...  Each circle represents a sequence. Branch length is proportional to the number of mutations.  ... 
doi:10.1371/journal.pone.0095969 pmid:24763315 pmcid:PMC3999278 fatcat:a3acpufyerh3fk3hzvehkt5z5a

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

Valentí Moncunill, Santi Gonzalez, Sílvia Beà, Lise O Andrieux, Itziar Salaverria, Cristina Royo, Laura Martinez, Montserrat Puiggròs, Maia Segura-Wang, Adrian M Stütz, Alba Navarro, Romina Royo (+8 others)
2014 Nature Biotechnology  
To define the complete catalog of somatic variation (SNVs and structural variants) for a given tumor still requires complex computational pipelines with combinations of different methods, each of them  ...  The characterization of somatic variation in tumor samples is, therefore, rapidly becoming a standard practice in biomedicine 2 .  ...  to generate mapped BAM files; (ii) the detection, in a single execution, of SNVs and structural variants, such as inter-and intrachromosomal translocations, inversions, insertions and deletions of any  ... 
doi:10.1038/nbt.3027 pmid:25344728 fatcat:dcryvmyee5b45klmucl3g7levu

Extraction of product evolution tree from source code of product variants

Tetsuya Kanda, Takashi Ishio, Katsuro Inoue
2013 Proceedings of the 17th International Software Product Line Conference on - SPLC '13  
We construct a Product Evolution Tree as a minimum spanning tree whose cost function is defined by the number of similar files between products.  ...  A large number of software products may be derived from an original single product.  ...  We calculate similarity for all pairs of files across different products, since a file may be renamed in a different product variant.  ... 
doi:10.1145/2491627.2491637 dblp:conf/splc/KandaII13 fatcat:suhlnhe3kbacfnp44nsmg4sybi

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines

Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele A Calogero
2018 BMC Bioinformatics  
Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application.  ...  One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository  ...  The transition between development and stable branch is done when a module (R function(s)/docker container(s)) fulfills the 10 rules suggested by Sandve [5] for the good bioinformatics practice ( Table  ... 
doi:10.1186/s12859-018-2296-x pmid:30367595 pmcid:PMC6191970 fatcat:svttxrofbndzla5lduo2ntozfy

DiscoSnp-RAD: de novo detection of small variants for population genomics [article]

Jeremy Gauthier, Charlotte Mouden, Tomasz Suchan, Nadir Alvarez, Nils Arrigo, Chloe Riou, Claire Lemaitre, Pierre Peterlongo
2017 bioRxiv   pre-print
We present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq).  ...  Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnpRad avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets  ...  Acknowledgments Authors thank Camille Marchet for her precious help on the clustering implementation. Computations have been made possible thanks to the resources of the Genouest infrastructures.  ... 
doi:10.1101/216747 fatcat:d7mvbnu6n5gv5fdw4oymhhhfsy

Enhancements of anatomical information in UMLS knowledge sources

C Rosse, M Ben Said, K R Eno, J F Brinkley
1995 Proceedings. Symposium on Computer Applications in Medical Care  
representing anatomical concepts in machine readable form.  ...  Although anatomical terminology forms a part of biomedical structured vocabularies, available sources lack the requisite granularity, semantic types and relationships for comprehensively and consistently  ...  Briggs for making SNOMED International available for our work.  ... 
pmid:8563417 pmcid:PMC2579218 fatcat:jnbwfm35ubgubhrqtlfo6jzbk4

The utility of multiple molecular methods including whole genome sequencing as tools to differentiateEscherichia coliO157:H7 outbreaks

Byron M Berenger, Chrystal Berry, Trevor Peterson, Patrick Fach, Sabine Delannoy, Vincent Li, Lorelee Tschetter, Celine Nadon, Lance Honish, Marie Louie, Linda Chui
2015 Eurosurveillance  
Alberta Health for patient demographic information.  ...  each of the variant call format files created by FreeBayes, complex variant calls were split into single variant calls to create new variant call format files.  ...  All variant calls were merged into a single alignment file. SAMtools v [22] was used to investigate positions where not every genome had a variant call.  ... 
doi:10.2807/ pmid:26625187 fatcat:zs54mnlryrfojaldon35mlf24m

Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Joanna Grzegorczyk, Artur Gurgul, Maria Oczkowicz, Tomasz Szmatoła, Agnieszka Fornal, Monika Bugno-Poniewierska
2021 Genes  
The GBS method allowed for the detection of 3833 common raw SNPs.  ...  Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs.  ...  From the practical point of view, the GBS method is based only on a few laboratory processes.  ... 
doi:10.3390/genes12071074 pmid:34356090 pmcid:PMC8307914 fatcat:nqpcvrlzmng7vdfzkvevrakv5a

Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

Alexandre De Bruyn, Mireille Harimalala, Innocent Zinga, Batsirai M. Mabvakure, Murielle Hoareau, Virginie Ravigné, Matthew Walters, Bernard Reynaud, Arvind Varsani, Gordon W. Harkins, Darren P. Martin, Jean-Michel Lett (+1 others)
2016 BMC Evolutionary Biology  
This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment.  ...  Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species.  ...  Consent for publication  ... 
doi:10.1186/s12862-016-0749-2 pmid:27600545 pmcid:PMC5012068 fatcat:spkduchbdvanbfpsjjax57ksgm

Supporting evolution of SDL-based systems: industrial experience [chapter]

B. Gulla, J. Gorman
1996 IFIP Advances in Information and Communication Technology  
A crucial issue for the success of the approach in this industrial context turns out to be efficient handling of system variants and evolution.  ...  Stentofon, a Norwegian company producing customized internal communication systems, uses SDL and automatic code generation for software development.  ...  acknowledge the contributions made by current and previous members of the project, and especially Arvid Strømme of Stentofon, Professor Reidar Conradi of NTH, Jacqueline Floch and Richard Sanders (DELAB) for  ... 
doi:10.1007/978-0-387-34945-9_18 fatcat:s7jqyw2yirgczpqhrn5zdbbgsi

Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks

Eric Garcia, Daniel Wright, Remy Gatins, May B. Roberts, Hudson T. Pinheiro, Eva Salas, Jei-Ying Chen, Jacob R. Winnikoff, Giacomo Bernardi, Jeffrey A. Eble
2021 PLoS ONE  
index called branch diversity.  ...  Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity.  ...  Acknowledgments We would like to thank Chris Bird for useful comments on the manuscript. HTP thanks the Hope for Reefs initiative of the California Academy of Sciences.  ... 
doi:10.1371/journal.pone.0251878 pmid:34191803 pmcid:PMC8244886 fatcat:bdj44wwrtnak7kpfubxxtx36qq

APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors

Nitin Roper, Shaojian Gao, Tapan K. Maity, A. Rouf Banday, Xu Zhang, Abhilash Venugopalan, Constance M. Cultraro, Rajesh Patidar, Sivasish Sindiri, Anna-Leigh Brown, Alexander Goncearenco, Anna R. Panchenko (+9 others)
2019 Cell Reports  
APOBEC mutagenesis, promoted by increased expression of APOBEC3 region transcripts and associated with a high-risk APOBEC3 germline variant, correlated with mutational tumor heterogeneity.  ...  Here, we elucidate mechanisms of tumor evolution and heterogeneity in metastatic thoracic tumors (lung adenocarcinoma and thymic carcinoma) using whole-exome and transcriptome sequencing, SNP array for  ...  Jennifer Cheng from the Pain and Palliative Care Team; Susan Perry and Emerson Padiernos; clinical and research nurses; and social work and spiritual care teams for their clinical care of the patients  ... 
doi:10.1016/j.celrep.2019.02.028 pmid:30840888 pmcid:PMC6461561 fatcat:b4by4tqwkrcebhh2q4p6z55o44

Rhizome: A Feature Modeling and Generation Platform

Guozheng Ge, E. James Whitehead Jr.
2008 2008 23rd IEEE/ACM International Conference on Automated Software Engineering  
These design choices can be automatically associated with code templates and interpreted as parameter values for code generation.  ...  Rhizome is an end-to-end feature modeling and code generation platform that includes a feature modeling language (FeatureML), a template language (MarkerML) and a template-based code generator.  ...  Pure::variants [5] is a commercial tool for variant management in software product lines.  ... 
doi:10.1109/ase.2008.52 dblp:conf/kbse/GeW08 fatcat:diqytj4lr5hehlwruwgbhdtfxe

Reliability of function points measurement: a field experiment

Chris F. Kemerer
1993 Communications of the ACM  
Measures of both inter-rater and inter-method reliability were developed and estimated for this sample.  ...  The very limited research that has been done in this area on individual programs has only been able to suggest a degree of agreement between two raters measuring the same program as +/-30%, and inter-method  ...  If true, this lack of inter-method reliability poses several practical problems.  ... 
doi:10.1145/151220.151230 fatcat:y6akdj2d5jdalh7uei7bhne6na
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