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  1. 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:

  2. 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:

  4. 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:

  7. 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:

  8. 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:

  10. 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

  11. 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:

  12. 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:

  13. 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:

  15. 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:

  16. 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:

  17. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  28. 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:

  29. 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:

  31. 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:

  34. Large-scale genetic studies of common human diseases have focused almost exclusively on the independent main effects of single-nucleotide polymorphisms (SNPs) on disease susceptibility. These studies have had ...

    Authors: Jason H. Moore, Peter C. Andrews, Randal S. Olson, Sarah E. Carlson, Curt R. Larock, Mario J. Bulhoes, James P. O’Connor, Ellen M. Greytak and Steven L. Armentrout
    Citation: BioData Mining 2017 10:19
    Content type: Methodology Published on:

  35. Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Ana...

    Authors: Vinicius Tragante, Johannes M. I. H. Gho, Janine F. Felix, Ramachandran S. Vasan, Nicholas L. Smith, Benjamin F. Voight, Colin Palmer, Pim van der Harst, Jason H. Moore and Folkert W. Asselbergs
    Citation: BioData Mining 2017 10:18
    Content type: Methodology Published on:

  36. Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management...

    Authors: Lucas P. P. Braga, Rafael F. Alves, Marina T. F. Dellias, Acacio A. Navarrete, Thiago O. Basso and Siu M. Tsai
    Citation: BioData Mining 2017 10:17
    Content type: Short report Published on:

  37. Any family of learning machines can be combined into a single learning machine using various methods with myriad degrees of usefulness.

    Authors: Bilguunzaya Battogtokh, Majid Mojirsheibani and James Malley
    Citation: BioData Mining 2017 10:16
    Content type: Research Published on:

  38. Reverse engineering of gene regulatory networks (GRNs) from gene expression data is a classical challenge in systems biology. Thanks to high-throughput technologies, a massive amount of gene-expression data ha...

    Authors: Ngoc C. Pham, Benjamin Haibe-Kains, Pau Bellot, Gianluca Bontempi and Patrick E. Meyer
    Citation: BioData Mining 2017 10:15
    Content type: Methodology Published on:

  39. Large number of features are extracted from protein crystallization trial images to improve the accuracy of classifiers for predicting the presence of crystals or phases of the crystallization process. The exc...

    Authors: Madhav Sigdel, Imren Dinc, Madhu S. Sigdel, Semih Dinc, Marc L. Pusey and Ramazan S. Aygun
    Citation: BioData Mining 2017 10:14
    Content type: Research Published on:

  40. A computational evolution system (CES) is a knowledge discovery engine that can identify subtle, synergistic relationships in large datasets. Pareto optimization allows CESs to balance accuracy with model comp...

    Authors: Nathaniel M. Crabtree, Jason H. Moore, John F. Bowyer and Nysia I. George
    Citation: BioData Mining 2017 10:13
    Content type: Methodology Published on:

  43. In metabolomics, thousands of substances can be detected in a single assay. This capacity motivates the development of metabolomics testing, which is currently a very promising option for improving laboratory ...

    Authors: Petr G. Lokhov, Dmitri L. Maslov, Oleg N. Kharibin, Elena E. Balashova and Alexander I. Archakov
    Citation: BioData Mining 2017 10:10
    Content type: Methodology Published on:

  44. Genetic predispositions to diseases populate the noncoding regions of the human genome. Delineating their functional basis can inform on the mechanisms contributing to disease development. However, this remain...

    Authors: Musaddeque Ahmed, Richard C. Sallari, Haiyang Guo, Jason H. Moore, Housheng Hansen He and Mathieu Lupien
    Citation: BioData Mining 2017 10:9
    Content type: Methodology Published on:

  46. Capturing complete medical knowledge is challenging-often due to incomplete patient Electronic Health Records (EHR), but also because of valuable, tacit medical knowledge hidden away in physicians’ experiences...

    Authors: Hossein Mohammadhassanzadeh, William Van Woensel, Samina Raza Abidi and Syed Sibte Raza Abidi
    Citation: BioData Mining 2017 10:7
    Content type: Methodology Published on:

  47. Aldolase A (ALDOA) is one of the glycolytic enzymes primarily found in the developing embryo and adult muscle. Recently, a new role of ALDOA in several cancers has been proposed. However, the underlying mechan...

    Authors: Fan Zhang, Jie-Diao Lin, Xiao-Yu Zuo, Yi-Xuan Zhuang, Chao-Qun Hong, Guo-Jun Zhang, Xiao-Jiang Cui and Yu-Kun Cui
    Citation: BioData Mining 2017 10:6
    Content type: Research Published on:

  48. In gene set analysis, the researchers are interested in determining the gene sets that are significantly correlated with an outcome, e.g. disease status or treatment. With the rapid development of high through...

    Authors: Xing Ren, Qiang Hu, Song Liu, Jianmin Wang and Jeffrey C. Miecznikowski
    Citation: BioData Mining 2017 10:5
    Content type: Methodology Published on:

  49. With the development of high-throughput technology, the researchers can acquire large number of expression data with different types from several public databases. Because most of these data have small number ...

    Authors: Wei Du, Zhongbo Cao, Tianci Song, Ying Li and Yanchun Liang
    Citation: BioData Mining 2017 10:4
    Content type: Methodology Published on:
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BioData Mining

ISSN: 1756-0381