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157 result(s) for 'Quick Dash Interpretation' within BMC Bioinformatics

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  2. Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one pla...

    Authors: Khong-Loon Tiong and Chen-Hsiang Yeang
    Citation: BMC Bioinformatics 2019 20:145
    Content type: Methodology article Published on:

  5. This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear corresp...

    Authors: Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga-Llavori and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 10

  7. The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usu...

    Authors: Zhengdong Zhang, George W Jackson, George E Fox and Richard C Willson
    Citation: BMC Bioinformatics 2006 7:117
    Content type: Research article Published on:

  9. Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but requi...

    Authors: Arnaud Amzallag, Sridhar Ramaswamy and Cyril H. Benes
    Citation: BMC Bioinformatics 2019 20:83
    Content type: Methodology article Published on:

  10. DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.

    Authors: Jeff Skinner, Yuri Kotliarov, Sudhir Varma, Karina L Mine, Anatoly Yambartsev, Richard Simon, Yentram Huyen and Andrey Morgun
    Citation: BMC Bioinformatics 2011 12:286
    Content type: Software Published on:

  11. RNA-Sequencing analysis methods are rapidly evolving, and the tool choice for each step of one common workflow, differential expression analysis, which includes read alignment, expression modeling, and differe...

    Authors: Alyssa Baccarella, Claire R. Williams, Jay Z. Parrish and Charles C. Kim
    Citation: BMC Bioinformatics 2018 19:423
    Content type: Research article Published on:

  12. Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New me...

    Authors: Thorsteinn Rögnvaldsson, Terence A Etchells, Liwen You, Daniel Garwicz, Ian Jarman and Paulo JG Lisboa
    Citation: BMC Bioinformatics 2009 10:149
    Content type: Methodology article Published on:

  13. Ordinary differential equation systems are frequently utilized to model biological systems and to infer knowledge about underlying properties. For instance, the development of drugs requires the knowledge to w...

    Authors: Pascal Dolejsch, Helge Hass and Jens Timmer
    Citation: BMC Bioinformatics 2019 20:395
    Content type: Methodology article Published on:

  14. Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregula...

    Authors: Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson and Stephanie D. Byrum
    Citation: BMC Bioinformatics 2021 22:275
    Content type: Software Published on:

  15. In many approaches to the inference and modeling of regulatory interactions using microarray data, the expression of the gene coding for the transcription factor is considered to be an accurate surrogate for t...

    Authors: Simon Rogers, Raya Khanin and Mark Girolami
    Citation: BMC Bioinformatics 2007 8(Suppl 2):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 8 Supplement 2

  16. G-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM) domain. Because of their s...

    Authors: Marijn PA Sanders, Wilco WM Fleuren, Stefan Verhoeven, Sven van den Beld, Wynand Alkema, Jacob de Vlieg and Jan PG Klomp
    Citation: BMC Bioinformatics 2011 12:332
    Content type: Research article Published on:

  17. Meta-analysis is a statistical method that combines the results of multiple studies to increase statistical power. When multiple studies participating in a meta-analysis utilize the same public dataset as cont...

    Authors: Emma E. Kim, Chloe Soohyun Jang, Hakin Kim and Buhm Han
    Citation: BMC Bioinformatics 2024 25:24
    Content type: Research Published on:

  19. Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-opt...

    Authors: Stefan Janssen, Christian Schudoma, Gerhard Steger and Robert Giegerich
    Citation: BMC Bioinformatics 2011 12:429
    Content type: Research article Published on:

  20. Molecular database search tools need statistical models to assess the significance for the resulting hits. In the classical approach one asks the question how probable a certain score is observed by pure chanc...

    Authors: Stefan Wolfsheimer, Inke Herms, Sven Rahmann and Alexander K Hartmann
    Citation: BMC Bioinformatics 2011 12:47
    Content type: Research article Published on:

  21. Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanog...

    Authors: Nick W. Smith, Paul R. Shorten, Eric Altermann, Nicole C. Roy and Warren C. McNabb
    Citation: BMC Bioinformatics 2021 22:3
    Content type: Research article Published on:

  22. Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcodi...

    Authors: T. M. Porter and M. Hajibabaei
    Citation: BMC Bioinformatics 2021 22:256
    Content type: Methodology article Published on:

  23. Advances in high throughput technologies and growth of biomedical knowledge have contributed to an exponential increase in associative data. These data can be represented in the form of complex networks of bio...

    Authors: Ákos Tényi, Pedro de Atauri, David Gomez-Cabrero, Isaac Cano, Kim Clarke, Francesco Falciani, Marta Cascante, Josep Roca and Dieter Maier
    Citation: BMC Bioinformatics 2016 17:17
    Content type: Methodology article Published on:

  24. In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological d...

    Authors: Mozhgan Kabiri Chimeh, Peter Heywood, Marzio Pennisi, Francesco Pappalardo and Paul Richmond
    Citation: BMC Bioinformatics 2019 20(Suppl 6):579
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  25. Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapi...

    Authors: Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F Stadler and Sonja J Prohaska
    Citation: BMC Bioinformatics 2011 12:124
    Content type: Methodology article Published on:

  26. Genotypes generated in next generation sequencing studies contain errors which can significantly impact the power to detect signals in common and rare variant association tests. These genotyping errors are not...

    Authors: Andrew R Carson, Erin N Smith, Hiroko Matsui, Sigrid K Brækkan, Kristen Jepsen, John-Bjarne Hansen and Kelly A Frazer
    Citation: BMC Bioinformatics 2014 15:125
    Content type: Methodology article Published on:

  27. The interpretation of the results from genome-scale experiments is a challenging and important problem in contemporary biomedical research. Biological networks that integrate experimental results with existing...

    Authors: Corinna Vehlow, David P Kao, Michael R Bristow, Lawrence E Hunter, Daniel Weiskopf and Carsten Görg
    Citation: BMC Bioinformatics 2015 16:135
    Content type: Research Article Published on:

  28. Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of ind...

    Authors: Francisco Pina-Martins, Bruno M. Vieira, Sofia G. Seabra, Dora Batista and Octávio S. Paulo
    Citation: BMC Bioinformatics 2016 17:41
    Content type: Software Published on:

  29. To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potential...

    Authors: Mikołaj Rybiński, Simon Möller, Mikael Sunnåker, Claude Lormeau and Jörg Stelling
    Citation: BMC Bioinformatics 2020 21:34
    Content type: Software Published on:

  30. To integrate molecular features from multiple high-throughput platforms in prediction, a regression model that penalizes features from all platforms equally is commonly used. However, data from different platf...

    Authors: Jie Liu, Gangning Liang, Kimberly D Siegmund and Juan Pablo Lewinger
    Citation: BMC Bioinformatics 2018 19:369
    Content type: Methodology article Published on:

  31. Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While ther...

    Authors: Sarvesh Nikumbh and Nico Pfeifer
    Citation: BMC Bioinformatics 2017 18:218
    Content type: Research Article Published on:

  32. In many domains, scientists build complex simulators of natural phenomena that encode their hypotheses about the underlying processes. These simulators can be deterministic or stochastic, fast or slow, constra...

    Authors: Edward Meeds, Michael Chiang, Mary Lee, Olivier Cinquin, John Lowengrub and Max Welling
    Citation: BMC Bioinformatics 2015 16:264
    Content type: Methodology Article Published on:

  33. Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds)...

    Authors: Arne Kutzner, Pok-Son Kim and Markus Schmidt
    Citation: BMC Bioinformatics 2020 21:328
    Content type: Methodology article Published on:

  34. The application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaff...

    Authors: Sen Wang, Hengchao Wang, Fan Jiang, Anqi Wang, Hangwei Liu, Hanbo Zhao, Boyuan Yang, Dong Xu, Yan Zhang and Wei Fan
    Citation: BMC Bioinformatics 2022 23:528
    Content type: Software Published on:

  35. A challenging issue in designing computational methods for predicting the gene structure into exons and introns from a cluster of transcript (EST, mRNA) sequences, is guaranteeing accuracy as well as efficienc...

    Authors: Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova and Paola Bonizzoni
    Citation: BMC Bioinformatics 2012 13(Suppl 5):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  37. Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. Several existing methods have been presented...

    Authors: Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Truong, Jiuyong Li, Nini Rao and Thuc Duy Le
    Citation: BMC Bioinformatics 2019 20(Suppl 23):613
    Content type: Research Published on:

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

    The Correction to this article has been published in BMC Bioinformatics 2020 21:32

  38. Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic p...

    Authors: O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai and D. Szüts
    Citation: BMC Bioinformatics 2017 18:73
    Content type: Methodology article Published on:

  39. Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.

    Authors: Andrew Schoenrock, Bahram Samanfar, Sylvain Pitre, Mohsen Hooshyar, Ke Jin, Charles A Phillips, Hui Wang, Sadhna Phanse, Katayoun Omidi, Yuan Gui, Md Alamgir, Alex Wong, Fredrik Barrenäs, Mohan Babu, Mikael Benson, Michael A Langston…
    Citation: BMC Bioinformatics 2014 15:383
    Content type: Research article Published on:

  40. In molecular epidemiology, comparison of intra-host viral variants among infected persons is frequently used for tracing transmissions in human population and detecting viral infection outbreaks. Application o...

    Authors: David S. Campo and Yury Khudyakov
    Citation: BMC Bioinformatics 2020 21(Suppl 18):482
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 18

  41. In cancer research, robustness of a complex biochemical network is one of the most relevant properties to investigate for the development of novel targeted therapies. In cancer systems biology, biological netw...

    Authors: Fortunato Bianconi, Chiara Antonini, Lorenzo Tomassoni and Paolo Valigi
    Citation: BMC Bioinformatics 2019 20:385
    Content type: Software Published on:

  42. In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling t...

    Authors: Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li and Renxiao Wang
    Citation: BMC Bioinformatics 2017 18:343
    Content type: Methodology Article Published on:

  43. The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant ...

    Authors: Pedro Seoane, Marina Espigares, Rosario Carmona, Álvaro Polonio, Julia Quintana, Enrico Cretazzo, Josefina Bota, Alejandro Pérez-García, Juan de Dios Alché, Luis Gómez and M. Gonzalo Claros
    Citation: BMC Bioinformatics 2018 19(Suppl 14):416
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  44. Most dynamical models for genomic networks are built upon two current methodologies, one process-based and the other based on Boolean-type networks. Both are problematic when it comes to experimental design pu...

    Authors: Daniel N Mohsenizadeh, Jianping Hua, Michael Bittner and Edward R Dougherty
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 16 Supplement 13

  45. A cell exhibits a variety of responses to internal and external cues. These responses are possible, in part, due to the presence of an elaborate gene regulatory network (GRN) in every single cell. In the past ...

    Authors: Lior I. Shachaf, Elijah Roberts, Patrick Cahan and Jie Xiao
    Citation: BMC Bioinformatics 2023 24:84
    Content type: Research Published on:

  46. Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. Computation may become the bottleneck of genome ...

    Authors: Brendan A Veeneman, Matthew K Iyer and Arul M Chinnaiyan
    Citation: BMC Bioinformatics 2012 13:297
    Content type: Software Published on:

  47. Cellular memory is a ubiquitous function of biological systems. By generating a sustained response to a transient inductive stimulus, often due to bistability, memory is central to the robust control of many i...

    Authors: A. B. M. Shamim Ul Hasan, Hiroyuki Kurata and Sebastian Pechmann
    Citation: BMC Bioinformatics 2019 20:734
    Content type: Research article Published on:

  48. Mapping expression quantitative trait loci (eQTLs) has provided insight into gene regulation. Compared to cis-eQTLs, the regulatory mechanisms of trans-eQTLs are less known. Previous studies suggest that trans...

    Authors: Nayang Shan, Zuoheng Wang and Lin Hou
    Citation: BMC Bioinformatics 2019 20(Suppl 3):126
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  49. Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects ...

    Authors: Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin and Johan Trygg
    Citation: BMC Bioinformatics 2019 20:498
    Content type: Methodology article Published on:

  50. Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enab...

    Authors: Kiyoshi Ezawa
    Citation: BMC Bioinformatics 2016 17:304
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:457

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