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

Page 3 of 9

  2. In this paper, we analysed an extensive collection of full genome gene-expression data (RNA-seq) and DNA methylation data of genomic CpG islands (using Illumina methylation arrays) generated from a sample of tumo...

    Authors: Alexander Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor Kolpakov, Maxim Filipenko…
    Citation: BMC Bioinformatics 2019 20(Suppl 4):119
    Content type: Research Published on:

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

  3. Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), ...

    Authors: Fang-Dong Li, Wei Tong, En-Hua Xia and Chao-Ling Wei
    Citation: BMC Bioinformatics 2019 20:553
    Content type: Research article Published on:

  4. Flow cytometry (FCM) is a powerful single-cell based measurement method to ascertain multidimensional optical properties of millions of cells. FCM is widely used in medical diagnostics and health research. The...

    Authors: Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler and Susann Müller
    Citation: BMC Bioinformatics 2019 20:643
    Content type: Software Published on:

  5. Quantitative areas is of great measurement of wound significance in clinical trials, wound pathological analysis, and daily patient care. 2D methods cannot solve the problems caused by human body curvatures an...

    Authors: Chunhui Liu, Xingyu Fan, Zhizhi Guo, Zhongjun Mo, Eric I-Chao Chang and Yan Xu
    Citation: BMC Bioinformatics 2019 20:724
    Content type: Methodology Article Published on:

  6. A lack of reproducibility has been repeatedly criticized in computational research. High throughput sequencing (HTS) data analysis is a complex multi-step process. For most of the steps a range of bioinformati...

    Authors: Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor and Jörg Hackermüller
    Citation: BMC Bioinformatics 2019 20:664
    Content type: Software Published on:

  8. Our VIO modeling identified many variables related to data processing and analysis such as normalization method, cut-off criteria, software settings including software version. The datasets from two previous stud...

    Authors: Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu and Yongqun He
    Citation: BMC Bioinformatics 2019 20(Suppl 21):704
    Content type: Research Published on:

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

  10. The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of ...

    Authors: Anh Nhat Tran, Alex M. Dussaq, Timothy Kennell Jr, Christopher D. Willey and Anita B. Hjelmeland
    Citation: BMC Bioinformatics 2019 20:463
    Content type: Software Published on:

  11. In this paper, we present BAMSE (BAyesian Model Selection for tumor Evolution), a new probabilistic method for inferring subclonal history and lineage tree reconstruction of heterogeneous tumor samples. BAMSE use...

    Authors: Hosein Toosi, Ali Moeini and Iman Hajirasouliha
    Citation: BMC Bioinformatics 2019 20(Suppl 11):282
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  12. We adapted our previously developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementation Read-SpaM.

    Authors: Anna-Katharina Lau, Svenja Dörrer, Chris-André Leimeister, Christoph Bleidorn and Burkhard Morgenstern
    Citation: BMC Bioinformatics 2019 20(Suppl 20):638
    Content type: Research Published on:

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

  13. The rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene ampli...

    Authors: Nhan Thi Ho, Fan Li, Shuang Wang and Louise Kuhn
    Citation: BMC Bioinformatics 2019 20:188
    Content type: Software Published on:

  14. In this paper we study the stable behaviours of phage λ...via a hybrid system based model. We identify wild type and mutant behaviours that arise for various orderings of binding site affinities. We propose exper...

    Authors: Dace Ruklisa, Alvis Brazma, Karlis Cerans, Thomas Schlitt and Juris Viksna
    Citation: BMC Bioinformatics 2019 20:296
    Content type: Research article Published on:

  15. In this paper, we developed a proximal gradient algorithm for differential network (ProGAdNet) inference, that jointly infers two gene networks under different conditions and then identifies changes in the networ...

    Authors: Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D’Urso and Xiaodong Cai
    Citation: BMC Bioinformatics 2019 20:224
    Content type: Methodology article Published on:

  16. PaperBot may operate stand-alone or it can be easily integrated with other software platforms and knowledge bases. Without user interactions ... to be integrated with or replaced by additional software. All metad...

    Authors: Patricia Maraver, Rubén Armañanzas, Todd A. Gillette and Giorgio A. Ascoli
    Citation: BMC Bioinformatics 2019 20:50
    Content type: Software Published on:

  17. Following publication of the original article [1], the author noticed that the following lines were missing from the published article. The original article has been corrected.

    Authors: Mai Anh BUI T, Nick Papoulias, Serge Stinckwich, Mikal Ziane and Benjamin Roche
    Citation: BMC Bioinformatics 2019 20:439
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2019 20:312

  18. High-throughput technologies have brought tremendous changes to biological domains, and the resulting high-dimensional data has also posed enormous challenges to computational science. A Bayesian network is a ...

    Authors: Jiajin Chen, Ruyang Zhang, Xuesi Dong, Lijuan Lin, Ying Zhu, Jieyu He, David C. Christiani, Yongyue Wei and Feng Chen
    Citation: BMC Bioinformatics 2019 20:711
    Content type: Software Published on:

  19. Haemorrhagic stroke accounts for approximately 31.52% of all stroke cases, and the most common origin is hypertension. However, little is known about the method to identify high-risk populations of hypertensiv...

    Authors: Le Zhang, Jin Li, Kaikai Yin, Zhouyang Jiang, Tingting Li, Rong Hu, Zheng Yu, Hua Feng and Yujie Chen
    Citation: BMC Bioinformatics 2019 20(Suppl 7):193
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  20. Emerging evidence suggests retroviruses play a role in the pathophysiology of amyotrophic lateral sclerosis (ALS). Specifically, activation of ancient viral genes embedded in the human genome is theorized to lead...

    Authors: Jon P. Klein, Zhifu Sun and Nathan P. Staff
    Citation: BMC Bioinformatics 2019 20(Suppl 24):680
    Content type: Research Published on:

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

  21. The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification ...

    Authors: Jungmin Ha, Ho Hwi Jeon, Dong U. Woo, Yejin Lee, Halim Park, Joohyeong Lee and Yang Jae Kang
    Citation: BMC Bioinformatics 2019 20(Suppl 13):384
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  23. We show that for single-cell RNA-Seq circularization improves the recovery of accurate single-cell transcriptome estimates, especially when there are a high number of errors per read. This approach is robust to t...

    Authors: Akshay Tambe and Lior Pachter
    Citation: BMC Bioinformatics 2019 20:32
    Content type: Software Published on:

  24. Here, we present the rstoolbox, a Python library for the analysis of large-scale structural data tailored for CPD applications. rstoolbox is oriented towards both CPD software users and developers, being easily i...

    Authors: Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck and Bruno E. Correia
    Citation: BMC Bioinformatics 2019 20:240
    Content type: Software Published on:

  26. Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods f...

    Authors: Hasiba Asma and Marc S. Halfon
    Citation: BMC Bioinformatics 2019 20:174
    Content type: Methodology article Published on:

  29. Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA se...

    Authors: Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah and Jeffrey Fillingham
    Citation: BMC Bioinformatics 2019 20:533
    Content type: Methodology Article Published on:

  30. We present a computational tool for processing single cell RNA-seq data that uses a voting algorithm to automatically identify cells based on approval votes received by known molecular markers. Using a stochastic...

    Authors: Sergii Domanskyi, Anthony Szedlak, Nathaniel T Hawkins, Jiayin Wang, Giovanni Paternostro and Carlo Piermarocchi
    Citation: BMC Bioinformatics 2019 20:369
    Content type: Methodology article Published on:

  32. MIPRIP 2.0 identified common as well as tumor type specific regulators of TERT. The software can be easily applied to transcriptome datasets...

    Authors: Alexandra M. Poos, Theresa Kordaß, Amol Kolte, Volker Ast, Marcus Oswald, Karsten Rippe and Rainer König
    Citation: BMC Bioinformatics 2019 20:737
    Content type: Methodology article Published on:

  33. The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The eff...

    Authors: Yulia Panina, Arno Germond, Brit G. David and Tomonobu M. Watanabe
    Citation: BMC Bioinformatics 2019 20:295
    Content type: Methodology article Published on:

  34. Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant da...

    Authors: Hamid Bagheri, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin and Hridesh Rajan
    Citation: BMC Bioinformatics 2019 20:436
    Content type: Research article Published on:

  35. Multiplexed in-situ fluorescent imaging offers several advantages over single-cell assays that do not preserve the spatial characteristics of biological samples. This spatial information, in addition to morpholog...

    Authors: Eric Czech, Bulent Arman Aksoy, Pinar Aksoy and Jeff Hammerbacher
    Citation: BMC Bioinformatics 2019 20:448
    Content type: Software Published on:

  36. Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorith...

    Authors: Minzhe Zhang, Qiwei Li, Donghyeon Yu, Bo Yao, Wei Guo, Yang Xie and Guanghua Xiao
    Citation: BMC Bioinformatics 2019 20:12
    Content type: Software Published on:

  37. The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typical...

    Authors: Ya-Chi Lin, Yueh-Chun Lee, Kai-Li Chang and Kuei-Yang Hsiao
    Citation: BMC Bioinformatics 2019 20:372
    Content type: Software Published on:

  40. The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and software

    Authors: Ismael Navas-Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybinski, Rocio Lavado, Miguel Ángel Berciano Guerrero and José F. Aldana-Montes
    Citation: BMC Bioinformatics 2019 20(Suppl 4):150
    Content type: Software Published on:

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

  41. This preface introduces the content of the BioMed Central Bioinformatics journal Supplement related to the 15th annual meeting of the Bioinformatics Italian Society, BITS2018. The Conference was held in Torino...

    Authors: Francesca Cordero, Raffaele A. Calogero and Michele Caselle
    Citation: BMC Bioinformatics 2019 20(Suppl 9):562
    Content type: Introduction Published on:

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

  42. Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies...

    Authors: Leandro Gabriel Roser, Fernán Agüero and Daniel Oscar Sánchez
    Citation: BMC Bioinformatics 2019 20:361
    Content type: Software Published on:

  44. RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such ...

    Authors: Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran and Dena Leshkowitz
    Citation: BMC Bioinformatics 2019 20:154
    Content type: Software Published on:

  45. The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs...

    Authors: Tobias Paczian, William L. Trimble, Wolfgang Gerlach, Travis Harrison, Andreas Wilke and Folker Meyer
    Citation: BMC Bioinformatics 2019 20:561
    Content type: Software Published on:

  46. Modern flow cytometry technology has enabled the simultaneous analysis of multiple cell markers at the single-cell level, and it is widely used in a broad field of research. The detection of cell populations in f...

    Authors: Kodai Minoura, Ko Abe, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura
    Citation: BMC Bioinformatics 2019 20(Suppl 23):633
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  47. Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content..., in surveillance and outbreak detection, assembling each genome can become a redundant an...

    Authors: Hatice Akarsu, Lisandra Aguilar-Bultet and Laurent Falquet
    Citation: BMC Bioinformatics 2019 20:621
    Content type: Software Published on:

  50. Image segmentation and quantification are essential steps in quantitative cellular analysis. In this work, we present a fast, customizable, and unsupervised cell segmentation method that is based solely on Fiji (...

    Authors: Mischa Schwendy, Ronald E. Unger, Mischa Bonn and Sapun H. Parekh
    Citation: BMC Bioinformatics 2019 20:39
    Content type: Methodology article Published on:

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