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92 result(s) for 'prep modell' within BMC Bioinformatics

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  1. For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress ...

    Authors: Rob Smith, Andrew D Mathis, Dan Ventura and John T Prince
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  2. Assessing the reproducibility of measurements is an important first step for improving the reliability of downstream analyses of high-throughput metabolomics experiments. We define a metabolite to be reproduci...

    Authors: Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina Kechris and Debashis Ghosh
    Citation: BMC Bioinformatics 2021 22:423
    Content type: Research Published on:

  3. Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via c...

    Authors: Shweta S Chavan, Michael A Bauer, Erich A Peterson, Christoph J Heuck and Donald J Johann Jr
    Citation: BMC Bioinformatics 2013 14(Suppl 14):S4
    Content type: Proceedings Published on:

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

  4. Correct segmentation is critical to many applications within automated microscopy image analysis. Despite the availability of advanced segmentation algorithms, variations in cell morphology, sample preparation...

    Authors: William J Cukierski, Kaustav Nandy, Prabhakar Gudla, Karen J Meaburn, Tom Misteli, David J Foran and Stephen J Lockett
    Citation: BMC Bioinformatics 2012 13:232
    Content type: Research article Published on:

  5. The central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation. Understanding gene regulatory relationships is crucial for unravelling t...

    Authors: Shuwen Hu, Yi Jing, Tao Li, You-Gan Wang, Zhenyu Liu, Jing Gao and Yu-Chu Tian
    Citation: BMC Bioinformatics 2023 24:362
    Content type: Research Published on:

  6. Allele specific expression (ASE) has become an important phenotype, being utilized for the detection of cis-regulatory variation, nonsense mediated decay and imprinting in the personal genome, and has been used t...

    Authors: Alan Hodgkinson, Jean-Christophe Grenier, Elias Gbeha and Philip Awadalla
    Citation: BMC Bioinformatics 2016 17:364
    Content type: Methodology article Published on:

  7. RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error...

    Authors: Zachary B. Abrams, Travis S. Johnson, Kun Huang, Philip R. O. Payne and Kevin Coombes
    Citation: BMC Bioinformatics 2019 20(Suppl 24):679
    Content type: Research Published on:

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

  8. Structural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exa...

    Authors: Jan Geryk, Alzbeta Zinkova, Iveta Zedníková, Halina Simková, Vlastimil Stenzl and Marie Korabecna
    Citation: BMC Bioinformatics 2021 22:464
    Content type: Research Published on:

  9. Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. However, the scientific discovery offered by NGS also include...

    Authors: Michael A Bauer, Shweta S Chavan, Erich A Peterson, Christoph J Heuck and Donald J Johann Jr
    Citation: BMC Bioinformatics 2014 15(Suppl 11):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 11

  10. The Turku Event Extraction System (TEES) is a text mining program developed for the extraction of events, complex biomedical relationships, from scientific literature. Based on a graph-generation approach, the...

    Authors: Jari Björne and Tapio Salakoski
    Citation: BMC Bioinformatics 2015 16(Suppl 16):S4
    Content type: Research Published on:

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

  12. Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event ext...

    Authors: Ngan Nguyen, Jin-Dong Kim, Makoto Miwa, Takuya Matsuzaki and Junichi Tsujii
    Citation: BMC Bioinformatics 2012 13:304
    Content type: Research article Published on:

  13. Computational methods for structural gene annotation have propelled gene discovery but face certain drawbacks with regards to prokaryotic genome annotation. Identification of transcriptional start sites, demar...

    Authors: Joseph S Reddy, Ranjit Kumar, James M Watt, Mark L Lawrence, Shane C Burgess and Bindu Nanduri
    Citation: BMC Bioinformatics 2012 13(Suppl 15):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 15

  14. In the era of information overload, natural language processing (NLP) techniques are increasingly needed to support advanced biomedical information management and discovery applications. In this paper, we pres...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Dongwook Shin
    Citation: BMC Bioinformatics 2020 21:188
    Content type: Software Published on:

  15. Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is re...

    Authors: Yifan Peng, Manabu Torii, Cathy H Wu and K Vijay-Shanker
    Citation: BMC Bioinformatics 2014 15:285
    Content type: Research article Published on:

  16. Genes that are determined to be significantly differentially regulated in microarray analyses often appear to have functional commonalities, such as being components of the same biochemical pathway. This resul...

    Authors: Charles C Kim and Stanley Falkow
    Citation: BMC Bioinformatics 2003 4:12
    Content type: Methodology article Published on:

  17. In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a f...

    Authors: Casey W Dunn, Mark Howison and Felipe Zapata
    Citation: BMC Bioinformatics 2013 14:330
    Content type: Software Published on:

  19. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from meta...

    Authors: Irena Spasić, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B Kell and Norman W Paton
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  20. Maize, a crop of global significance, is vulnerable to a variety of biotic stresses resulting in economic losses. Fusarium verticillioides (teleomorph Gibberella moniliformis) is one of the key fungal pathogens o...

    Authors: Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S12
    Content type: Proceedings Published on:

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

  21. Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. Ho...

    Authors: Tom R Gaunt, Santiago Rodriguez, Carlos Zapata and Ian NM Day
    Citation: BMC Bioinformatics 2006 7:227
    Content type: Software Published on:

  22. High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolut...

    Authors: Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin and Jun Zhang
    Citation: BMC Bioinformatics 2019 20:163
    Content type: Methodology article Published on:

  23. Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is...

    Authors: Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li and Xinchun Lin
    Citation: BMC Bioinformatics 2019 20(Suppl 25):687
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  24. Cancer associated copy number variation (CNV) events provide important information for identifying patient subgroups and suggesting treatment strategies. Technical and logistical issues, however, make it chall...

    Authors: David Soong, Jeran Stratford, Herve Avet-Loiseau, Nizar Bahlis, Faith Davies, Angela Dispenzieri, A. Kate Sasser, Jordan M. Schecter, Ming Qi, Chad Brown, Wendell Jones, Jonathan J. Keats, Daniel Auclair, Christopher Chiu, Jason Powers and Michael Schaffer
    Citation: BMC Bioinformatics 2020 21:98
    Content type: Methodology article Published on:

  25. Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut...

    Authors: Aaron Y. Lee, Cecilia S. Lee and Russell N. Van Gelder
    Citation: BMC Bioinformatics 2016 17:292
    Content type: Software Published on:

  26. Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging ...

    Authors: M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement and Seth M. Bybee
    Citation: BMC Bioinformatics 2016 17:101
    Content type: Methodology article Published on:

  27. All proteins associate with other molecules. These associated molecules are highly predictive of the potential functions of proteins. The association of a protein and a molecule can be determined from their co...

    Authors: Kamal Taha and Paul D. Yoo
    Citation: BMC Bioinformatics 2016 17:34
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:105

  28. Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use ...

    Authors: David E. Condon, Phu V. Tran, Yu-Chin Lien, Jonathan Schug, Michael K. Georgieff, Rebecca A. Simmons and Kyoung-Jae Won
    Citation: BMC Bioinformatics 2018 19:31
    Content type: Software Published on:

  29. Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based o...

    Authors: Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert D. Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe Jr. and Denise M. Scholtens
    Citation: BMC Bioinformatics 2017 18:84
    Content type: Methodology article Published on:

  30. Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

    Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts
    Citation: BMC Bioinformatics 2018 19:236
    Content type: Methodology article Published on:

  31. Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantit...

    Authors: Špela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe-Novak and Kristina Gruden
    Citation: BMC Bioinformatics 2017 18:276
    Content type: Software Published on:

  32. Stored biological samples with pathology information and medical records are invaluable resources for translational medical research. However, RNAs extracted from the archived clinical tissues are often substa...

    Authors: Liguo Wang, Jinfu Nie, Hugues Sicotte, Ying Li, Jeanette E. Eckel-Passow, Surendra Dasari, Peter T. Vedell, Poulami Barman, Liewei Wang, Richard Weinshiboum, Jin Jen, Haojie Huang, Manish Kohli and Jean-Pierre A. Kocher
    Citation: BMC Bioinformatics 2016 17:58
    Content type: Methodology article Published on:

  33. Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretati...

    Authors: Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres and Philipp Rescheneder
    Citation: BMC Bioinformatics 2019 20:258
    Content type: Research article Published on:

  34. Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called “microbial dark matter” (microbes that until now have ...

    Authors: Bertjan Broeksema, Magdalena Calusinska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse and Mohammad Ghoniem
    Citation: BMC Bioinformatics 2017 18:233
    Content type: Software Published on:

  35. Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion predict...

    Authors: Krutika S. Gaonkar, Federico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel A. Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam C. Resnick, Konstantin Strauch, Jaclyn N. Taroni and Jo Lynne Rokita
    Citation: BMC Bioinformatics 2020 21:577
    Content type: Software Published on:

  36. Data from biomedical domains often have an inherit hierarchical structure. As this structure is usually implicit, its existence can be overlooked by practitioners interested in constructing and evaluating pred...

    Authors: Dusan Popovic, Alejandro Sifrim, Jesse Davis, Yves Moreau and Bart De Moor
    Citation: BMC Bioinformatics 2015 16(Suppl 4):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 4

  37. Protein kinases are among the largest druggable family of signaling proteins, involved in various human diseases, including cancers and neurodegenerative disorders. Despite their clinical relevance, nearly 30%...

    Authors: Liang-Chin Huang, Rahil Taujale, Nathan Gravel, Aarya Venkat, Wayland Yeung, Dominic P. Byrne, Patrick A. Eyers and Natarajan Kannan
    Citation: BMC Bioinformatics 2021 22:446
    Content type: Methodology article Published on:

  40. DNA microarrays are potentially powerful technology for improving diagnostic classification, treatment selection, and prognostic assessment. The use of this technology to predict cancer outcome has a history o...

    Authors: Minta Thomas, Kris De Brabanter and Bart De Moor
    Citation: BMC Bioinformatics 2014 15:137
    Content type: Methodology article Published on:

  41. Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools an...

    Authors: Gwenna Breton, Anna C. V. Johansson, Per Sjödin, Carina M. Schlebusch and Mattias Jakobsson
    Citation: BMC Bioinformatics 2021 22:488
    Content type: Research article Published on:

  42. Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selec...

    Authors: Vinayak Kulkarni, Mounir Errami, Robert Barber and Harold R Garner
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S3
    Content type: Proceedings Published on:

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

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