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438 result(s) for 'Software' within Volume 20 of BMC Bioinformatics

Page 1 of 9

  2. Clustering methods are essential to partitioning biological samples being useful to minimize the information complexity in large datasets. Tools in this context usually generates data with greed algorithms tha...

    Authors: Bruno Thiago de Lima Nichio, Aryel Marlus Repula de Oliveira, Camilla Reginatto de Pierri, Leticia Graziela Costa Santos, Alexandre Quadros Lejambre, Ricardo Assunção Vialle, Nilson Antônio da Rocha Coimbra, Dieval Guizelini, Jeroniza Nunes Marchaukoski, Fabio de Oliveira Pedrosa and Roberto Tadeu Raittz
    Citation: BMC Bioinformatics 2019 20:392
    Content type: Software Published on:

  6. RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and t...

    Authors: Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi
    Citation: BMC Bioinformatics 2019 20(Suppl 4):124
    Content type: Software Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  7. Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct repr...

    Authors: Leijie Li, Dongxue Che, Xiaodan Wang, Peng Zhang, Siddiq Ur Rahman, Jianbang Zhao, Jiantao Yu, Shiheng Tao, Hui Lu and Mingzhi Liao
    Citation: BMC Bioinformatics 2019 20:111
    Content type: Software Published on:

  9. Log-linear and multinomial modeling offer a flexible framework for genetic association analyses of offspring (child), parent-of-origin and maternal effects, based on genotype data from a variety of child-parent c...

    Authors: Miriam Gjerdevik, Astanand Jugessur, Øystein A. Haaland, Julia Romanowska, Rolv T. Lie, Heather J. Cordell and Håkon K. Gjessing
    Citation: BMC Bioinformatics 2019 20:165
    Content type: Software Published on:

  11. LMN uses a ranking system (1–3) to assign lipid standards to target analytes. A ranking of 1 signifies that both the lipid class and adduct of the internal standard and target analyte match, while a ranking of 3 ...

    Authors: Jeremy P. Koelmel, Jason A. Cochran, Candice Z. Ulmer, Allison J. Levy, Rainey E. Patterson, Berkley C. Olsen, Richard A. Yost, John A. Bowden and Timothy J. Garrett
    Citation: BMC Bioinformatics 2019 20:217
    Content type: Software Published on:

  12. Over the last 10 years, there have been over 3300 genome-wide association studies (GWAS). Almost every GWAS study provides a Manhattan plot either as a main figure or in the supplement. Several software packages ...

    Authors: Christopher Grace, Martin Farrall, Hugh Watkins and Anuj Goel
    Citation: BMC Bioinformatics 2019 20:610
    Content type: Software Published on:

  13. We have developed an easy-to-use, interactive software tool for the analysis of multiple data ... bivariate data points. For each dataset, the software identifies the replicate data points from a...

    Authors: Andreas Hofmann, Sarah Preston, Megan Cross, H. M. P. Dilrukshi Herath, Anne Simon and Robin B. Gasser
    Citation: BMC Bioinformatics 2019 20:262
    Content type: Software Published on:

  14. Here we present an open source CirGO (Circular Gene Ontology) software that visualises non-redundant two-level hierarchically ... algorithm and grouped by hierarchical clustering. This software visualises the mos...

    Authors: Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham and Aleksandra Filipovska
    Citation: BMC Bioinformatics 2019 20:84
    Content type: Software Published on:

  15. We introduce LMAP_S (Lightweight Multigene Alignment and Phylogeny eStimation), a user-friendly command-line and interactive package, designed to handle an improved alignment and phylogeny estimation workflow: MS...

    Authors: Emanuel Maldonado and Agostinho Antunes
    Citation: BMC Bioinformatics 2019 20:739
    Content type: Software Published on:

  16. With the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aim...

    Authors: Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook and Carlos Flores
    Citation: BMC Bioinformatics 2019 20:234
    Content type: Software Published on:

  17. Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, ...

    Authors: Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi and Satoru Miyano
    Citation: BMC Bioinformatics 2019 20(Suppl 16):591
    Content type: Software Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  18. Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological in...

    Authors: Maarten W. Paul, H. Martijn de Gruiter, Zhanmin Lin, Willy M. Baarends, Wiggert A. van Cappellen, Adriaan B. Houtsmuller and Johan A. Slotman
    Citation: BMC Bioinformatics 2019 20:30
    Content type: Software Published on:

  19. High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PCR a...

    Authors: Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski and Tristan Cordier
    Citation: BMC Bioinformatics 2019 20:88
    Content type: Software Published on:

  20. With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for...

    Authors: Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun and Zhiqiang Lu
    Citation: BMC Bioinformatics 2019 20:75
    Content type: Software Published on:

  22. Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance im...

    Authors: Charlotte Debus, Ralf Floca, Michael Ingrisch, Ina Kompan, Klaus Maier-Hein, Amir Abdollahi and Marco Nolden
    Citation: BMC Bioinformatics 2019 20:31
    Content type: Software Published on:

  23. Here we present a software tool, ElemCor, to perform correction of...Saccharomyces cerevisiae. The tool is available at https://​github.​com/​4dsoftware/​elemcor

    Authors: Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su and Philip L. Lorenzi
    Citation: BMC Bioinformatics 2019 20:89
    Content type: Research article Published on:

  24. We present the tool mycelyso (MYCElium anaLYsis SOftware), an image analysis system tailored to...mycelyso, the developing hyphal streptomycete network is automatically segmented and tracked over the cultivation ...

    Authors: Christian Carsten Sachs, Joachim Koepff, Wolfgang Wiechert, Alexander Grünberger and Katharina Nöh
    Citation: BMC Bioinformatics 2019 20:452
    Content type: Software Published on:

  25. At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experime...

    Authors: S. Ha, E. Dimitrova, S. Hoops, D. Altarawy, M. Ansariola, D. Deb, J. Glazebrook, R. Hillmer, H. Shahin, F. Katagiri, J. McDowell, M. Megraw, J. Setubal, B. M. Tyler and R. Laubenbacher
    Citation: BMC Bioinformatics 2019 20:508
    Content type: Software Published on:

  26. Here we present RetSynth, software with a novel algorithm for determining all ... corpus of potential chassis organisms. Additionally, this software contains other features including the ability to ... using a bu...

    Authors: Leanne S. Whitmore, Bernard Nguyen, Ali Pinar, Anthe George and Corey M. Hudson
    Citation: BMC Bioinformatics 2019 20:461
    Content type: Software Published on:

  27. Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics suppo...

    Authors: Judit Kumuthini, Lyndon Zass, Sumir Panji, Samson P. Salifu, Jonathan K. Kayondo, Victoria Nembaware, Mamana Mbiyavanga, Ajayi Olabode, Ali Kishk, Gordon Wells and Nicola J. Mulder
    Citation: BMC Bioinformatics 2019 20:741
    Content type: Research article Published on:

  28. BPG provides a new approach for linking interactive and scripted data visualization and is available at ...http://labs.oicr.on.ca/boutros-lab/software/bpg

    Authors: Christine P’ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Denise Y. F. Mak, Felix Lam, Marco A. Albuquerque, Ying Wu, Esther H. Jung, Maud H. W. Starmans, Michelle A. Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang…
    Citation: BMC Bioinformatics 2019 20:42
    Content type: Software Published on:

  29. We previously reported that a sequence-independent chromatin signature identifies, with high sensitivity and specificity, genes subject to MAE in multiple tissue types using readily available ChIP-seq data. Here ...

    Authors: Svetlana Vinogradova, Sachit D. Saksena, Henry N. Ward, Sébastien Vigneau and Alexander A. Gimelbrant
    Citation: BMC Bioinformatics 2019 20:106
    Content type: Software Published on:

  30. The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio reri...

    Authors: Joseph Brown, Aaron R. Phillips, David A. Lewis, Michael-Andres Mans, Yvonne Chang, Robert L. Tanguay, Elena S. Peterson, Katrina M. Waters and Susan C. Tilton
    Citation: BMC Bioinformatics 2019 20:255
    Content type: Database Published on:

  31. Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representati...

    Authors: Ben C. Stöver, Sarah Wiechers and Kai F. Müller
    Citation: BMC Bioinformatics 2019 20:402
    Content type: Software Published on:

  33. The main objectives of this study were sequencing, assembling, and annotation of chloroplast genome of one of the main Siberian boreal forest tree conifer species Siberian larch (Larix sibirica Ledeb.) and detect...

    Authors: Eugeniya I. Bondar, Yuliya A. Putintseva, Nataliya V. Oreshkova and Konstantin V. Krutovsky
    Citation: BMC Bioinformatics 2019 20(Suppl 1):38
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 1

  34. This Editorial first introduces the background of the vaccine and drug relations and how biomedical terminologies and ontologies have been used to support their studies. The history of the seven workshops, ini...

    Authors: Junguk Hur, Cui Tao and Yongqun He
    Citation: BMC Bioinformatics 2019 20(Suppl 21):705
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  37. We designed a user-friendly software FitEllipsoid allowing to segment hundreds of ellipsoidal ... plugin to be used within the image analysis software Icy. We also provide a Matlab toolbox...

    Authors: Bastien Kovac, Jérôme Fehrenbach, Ludivine Guillaume and Pierre Weiss
    Citation: BMC Bioinformatics 2019 20:142
    Content type: Software Published on:

  38. Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST...

    Authors: Mattia Dalsass, Margherita Bodini, Christophe Lambert, Marie-Cécile Mortier, Marco Romanelli, Duccio Medini, Alessandro Muzzi and Alessandro Brozzi
    Citation: BMC Bioinformatics 2019 20(Suppl 9):347
    Content type: Software Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  40. Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently make a...

    Authors: Xiaoshuang Liu, Zhenhe Yan, Chao Wu, Yang Yang, Xiaomin Li and Guangxin Zhang
    Citation: BMC Bioinformatics 2019 20:345
    Content type: Software Published on:

  41. In biological experiments, comprehensive experimental metadata tracking – which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies – remains a challen...

    Authors: Elmar Bucher, Cheryl J. Claunch, Derrick Hee, Rebecca L. Smith, Kaylyn Devlin, Wallace Thompson, James E. Korkola and Laura M. Heiser
    Citation: BMC Bioinformatics 2019 20:542
    Content type: Software Published on:

  42. To associate enhancers with their target genes, we have previously developed and applied a method that tests for significant correlations between enhancer and gene expressions across a cohort of samples. To limit...

    Authors: Konstantin Okonechnikov, Serap Erkek, Jan O. Korbel, Stefan M. Pfister and Lukas Chavez
    Citation: BMC Bioinformatics 2019 20:60
    Content type: Software Published on:

  46. RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high...

    Authors: Venkat Sundar Gadepalli, Hatice Gulcin Ozer, Ayse Selen Yilmaz, Maciej Pietrzak and Amy Webb
    Citation: BMC Bioinformatics 2019 20(Suppl 24):670
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 24

  48. Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each ... o...

    Authors: Daniel J. Giguere, Jean M. Macklaim, Brandon Y. Lieng and Gregory B. Gloor
    Citation: BMC Bioinformatics 2019 20:580
    Content type: Software Published on:

  50. We present MS-Helios, an easy to use command line tool with multiple built-in data processing functions, allowing non-expert users to construct CPMs or in general terms circular plots with a non-genomic basis. MS...

    Authors: Harald Marx and Joshua J. Coon
    Citation: BMC Bioinformatics 2019 20:21
    Content type: Software Published on:

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