Skip to main content

Articles

Page 5 of 10

  2. Machine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Mea...

    Authors: Sebastian Bittrich, Marika Kaden, Christoph Leberecht, Florian Kaiser, Thomas Villmann and Dirk Labudde
    Citation: BioData Mining 2019 12:1
    Content type: Methodology Published on:

  3. One strategy for addressing missing heritability in genome-wide association study is gene-gene interaction analysis, which, unlike a single gene approach, involves high-dimensionality. The multifactor dimensio...

    Authors: Seungyeoun Lee, Donghee Son, Yongkang Kim, Wenbao Yu and Taesung Park
    Citation: BioData Mining 2018 11:27
    Content type: Methodology Published on:

  5. Metagenomic surveys of human microbiota are becoming increasingly widespread in academic research as well as in food and pharmaceutical industries and clinical context. Intuitive tools for investigating experi...

    Authors: Daria Efimova, Alexander Tyakht, Anna Popenko, Anatoly Vasilyev, Ilya Altukhov, Nikita Dovidchenko, Vera Odintsova, Natalya Klimenko, Robert Loshkarev, Maria Pashkova, Anna Elizarova, Viktoriya Voroshilova, Sergei Slavskii, Yury Pekov, Ekaterina Filippova, Tatiana Shashkova…
    Citation: BioData Mining 2018 11:25
    Content type: Software article Published on:

  6. It is becoming increasingly clear that the quantification of mitochondria and synapses is of great significance to understand the function of biological nervous systems. Electron microscopy (EM), with the nece...

    Authors: Weifu Li, Jing Liu, Chi Xiao, Hao Deng, Qiwei Xie and Hua Han
    Citation: BioData Mining 2018 11:24
    Content type: Methodology Published on:

  7. ReliefF is a nearest-neighbor based feature selection algorithm that efficiently detects variants that are important due to statistical interactions or epistasis. For categorical predictors, like genotypes, th...

    Authors: M. Arabnejad, B. A. Dawkins, W. S. Bush, B. C. White, A. R. Harkness and B. A. McKinney
    Citation: BioData Mining 2018 11:23
    Content type: Methodology Published on:

  10. Searching for interesting common subgraphs in graph data is a well-studied problem in data mining. Subgraph mining techniques focus on the discovery of patterns in graphs that exhibit a specific network struct...

    Authors: Aida Mrzic, Pieter Meysman, Wout Bittremieux, Pieter Moris, Boris Cule, Bart Goethals and Kris Laukens
    Citation: BioData Mining 2018 11:20
    Content type: Review Published on:

  12. The redundancy of information is becoming a critical issue for epidemiologists. High-dimensional datasets require new effective variable selection methods to be developed. This study implements an advanced evo...

    Authors: Christina Brester, Jussi Kauhanen, Tomi-Pekka Tuomainen, Sari Voutilainen, Mauno Rönkkö, Kimmo Ronkainen, Eugene Semenkin and Mikko Kolehmainen
    Citation: BioData Mining 2018 11:18
    Content type: Research Published on:

  13. The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction ...

    Authors: Cheng-Hong Yang, Kuo-Chuan Wu, Yu-Shiun Lin, Li-Yeh Chuang and Hsueh-Wei Chang
    Citation: BioData Mining 2018 11:17
    Content type: Methodology Published on:

  14. Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information abou...

    Authors: Jorge Parraga-Alava, Marcio Dorn and Mario Inostroza-Ponta
    Citation: BioData Mining 2018 11:16
    Content type: Methodology Published on:

  15. Triclustering has shown to be a valuable tool for the analysis of microarray data since its appearance as an improvement of classical clustering and biclustering techniques. The standard for validation of tric...

    Authors: David Gutiérrez-Avilés, Raúl Giráldez, Francisco Javier Gil-Cumbreras and Cristina Rubio-Escudero
    Citation: BioData Mining 2018 11:15
    Content type: Research Published on:

  16. Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activit...

    Authors: Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan and Casey S. Greene
    Citation: BioData Mining 2018 11:14
    Content type: Software article Published on:

  18. Human microbiome studies in clinical settings generally focus on distinguishing the microbiota in health from that in disease at a specific point in time. However, microbiome samples may be associated with dis...

    Authors: Laura Tipton, Karen T. Cuenco, Laurence Huang, Ruth M. Greenblatt, Eric Kleerup, Frank Sciurba, Steven R. Duncan, Michael P. Donahoe, Alison Morris and Elodie Ghedin
    Citation: BioData Mining 2018 11:12
    Content type: Research Published on:

  19. In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organi...

    Authors: Jens Dörpinghaus, Sebastian Schaaf and Marc Jacobs
    Citation: BioData Mining 2018 11:11
    Content type: Methodology Published on:

  20. The Toxicological Priority Index (ToxPi) is a method for prioritization and profiling of chemicals that integrates data from diverse sources. However, individual data sources (“assays”), such as in vitro bioas...

    Authors: Kimberly T. To, Rebecca C. Fry and David M. Reif
    Citation: BioData Mining 2018 11:10
    Content type: Research Published on:

  22. Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have be...

    Authors: Ravi Mathur, Daniel Rotroff, Jun Ma, Ali Shojaie and Alison Motsinger-Reif
    Citation: BioData Mining 2018 11:8
    Content type: Research Published on:

  25. Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remai...

    Authors: Shefali S. Verma, Anastasia Lucas, Xinyuan Zhang, Yogasudha Veturi, Scott Dudek, Binglan Li, Ruowang Li, Ryan Urbanowicz, Jason H. Moore, Dokyoon Kim and Marylyn D. Ritchie
    Citation: BioData Mining 2018 11:5
    Content type: Research Published on:

  26. Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be use...

    Authors: Juan A. Nepomuceno, Alicia Troncoso, Isabel A. Nepomuceno-Chamorro and Jesús S. Aguilar-Ruiz
    Citation: BioData Mining 2018 11:4
    Content type: Research Published on:

  28. Evolutionary computation (EC) has been widely applied to biological and biomedical data. The practice of EC involves the tuning of many parameters, such as population size, generation count, selection size, an...

    Authors: Moshe Sipper, Weixuan Fu, Karuna Ahuja and Jason H. Moore
    Citation: BioData Mining 2018 11:2
    Content type: Research Published on:

    The Correction to this article has been published in BioData Mining 2019 12:22

  29. Survival analysis is a statistical technique widely used in many fields of science, in particular in the medical area, and which studies the time until an event of interest occurs. Outlier detection in this co...

    Authors: Eunice Carrasquinha, André Veríssimo, Marta B. Lopes and Susana Vinga
    Citation: BioData Mining 2018 11:1
    Content type: Research Published on:

  30. Matrix factorization is a well established pattern discovery tool that has seen numerous applications in biomedical data analytics, such as gene expression co-clustering, patient stratification, and gene-disea...

    Authors: Andrej Čopar, Marinka žitnik and Blaž Zupan
    Citation: BioData Mining 2017 10:41
    Content type: Research Published on:

  31. In the nervous system, the neurons communicate through synapses. The size, morphology, and connectivity of these synapses are significant in determining the functional properties of the neural network. Therefo...

    Authors: Qiwei Xie, Xi Chen, Hao Deng, Danqian Liu, Yingyu Sun, Xiaojuan Zhou, Yang Yang and Hua Han
    Citation: BioData Mining 2017 10:40
    Content type: Research Published on:

  33. Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve...

    Authors: J. Grey Monroe, Zachariah A. Allen, Paul Tanger, Jack L. Mullen, John T. Lovell, Brook T. Moyers, Darrell Whitley and John K. McKay
    Citation: BioData Mining 2017 10:38
    Content type: Software article Published on:

  34. Clustering plays a crucial role in several application domains, such as bioinformatics. In bioinformatics, clustering has been extensively used as an approach for detecting interesting patterns in genetic data...

    Authors: Luluah Alhusain and Alaaeldin M. Hafez
    Citation: BioData Mining 2017 10:37
    Content type: Methodology Published on:

  35. The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world ...

    Authors: Randal S. Olson, William La Cava, Patryk Orzechowski, Ryan J. Urbanowicz and Jason H. Moore
    Citation: BioData Mining 2017 10:36
    Content type: Research Published on:

  38. Obesity is a medical condition that is known for increased body mass index (BMI). It is also associated with chronic low level inflammation. Obesity disrupts the immune-metabolic homeostasis by changing the se...

    Authors: Indrani Ray, Anindya Bhattacharya and Rajat K. De
    Citation: BioData Mining 2017 10:33
    Content type: Research Published on:

  39. Detecting the differences in gene expression data is important for understanding the underlying molecular mechanisms. Although the differentially expressed genes are a large component, differences in correlati...

    Authors: Elpidio-Emmanuel Gonzalez-Valbuena and Víctor Treviño
    Citation: BioData Mining 2017 10:32
    Content type: Methodology Published on:

  40. The ability of external investigators to reproduce published scientific findings is critical for the evaluation and validation of biomedical research by the wider community. However, a substantial proportion o...

    Authors: Spiros Denaxas, Kenan Direk, Arturo Gonzalez-Izquierdo, Maria Pikoula, Aylin Cakiroglu, Jason Moore, Harry Hemingway and Liam Smeeth
    Citation: BioData Mining 2017 10:31
    Content type: Review Published on:

  41. Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess glo...

    Authors: Bork A. Berghoff, Torgny Karlsson, Thomas Källman, E. Gerhart H. Wagner and Manfred G. Grabherr
    Citation: BioData Mining 2017 10:30
    Content type: Research Published on:

  42. The modeling of genetic interactions within a cell is crucial for a basic understanding of physiology and for applied areas such as drug design. Interactions in gene regulatory networks (GRNs) include effects ...

    Authors: Mina Moradi Kordmahalleh, Mohammad Gorji Sefidmazgi, Scott H. Harrison and Abdollah Homaifar
    Citation: BioData Mining 2017 10:29
    Content type: Methodology Published on:

  43. BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised u...

    Authors: W. B. Langdon and Brian Yee Hong Lam
    Citation: BioData Mining 2017 10:28
    Content type: Short Report Published on:

  44. Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically...

    Authors: Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo and Alfonso Urso
    Citation: BioData Mining 2017 10:27
    Content type: Research Published on:

  46. The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits...

    Authors: Emily R. Holzinger, Shefali S. Verma, Carrie B. Moore, Molly Hall, Rishika De, Diane Gilbert-Diamond, Matthew B. Lanktree, Nathan Pankratz, Antoinette Amuzu, Amber Burt, Caroline Dale, Scott Dudek, Clement E. Furlong, Tom R. Gaunt, Daniel Seung Kim, Helene Riess…
    Citation: BioData Mining 2017 10:25
    Content type: Research Published on:

  47. Recently we surveyed the dark-proteome, i.e., regions of proteins never observed by experimental structure determination and inaccessible to homology modelling. Surprisingly, we found that most of the dark pro...

    Authors: Nelson Perdigão, Agostinho C. Rosa and Seán I. O’Donoghue
    Citation: BioData Mining 2017 10:24
    Content type: Software article Published on:

  49. Refinement of candidate gene lists to select the most promising candidates for further experimental verification remains an essential step between high-throughput exploratory analysis and the discovery of spec...

    Authors: Artem Lysenko, Keith Anthony Boroevich and Tatsuhiko Tsunoda
    Citation: BioData Mining 2017 10:22
    Content type: Software article Published on:
Submit manuscript

Follow

Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 4.0
    5-year Journal Impact Factor: 3.7
    Source Normalized Impact per Paper (SNIP): 1.413
    SCImago Journal Rank (SJR): 0.958

    Speed 2023
    Submission to first editorial decision (median days): 15
    Submission to acceptance (median days): 171

    Usage 2023
    Downloads: 400,374
    Altmetric mentions: 146
     

BioData Mining

ISSN: 1756-0381