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  2. Of late, high-throughput microarray and sequencing data have been extensively used to monitor biomarkers and biological processes related to many diseases. Under this circumstance, the support vector machine (...

    Authors: SungHwan Kim, Jae-Hwan Jhong, JungJun Lee and Ja-Yong Koo
    Citation: BioData Mining 2017 10:2
    Content type: Methodology Published on:

    The Erratum to this article has been published in BioData Mining 2017 10:8

  4. The Interaction Network Ontology (INO) logically represents biological interactions, pathways, and networks. INO has been demonstrated to be valuable in providing a set of structured ontological terms and asso...

    Authors: Arzucan Özgür, Junguk Hur and Yongqun He
    Citation: BioData Mining 2016 9:41
    Content type: Research Published on:

  5. Bladder cancer is common disease with a complex etiology that is likely due to many different genetic and environmental factors. The goal of this study was to embrace this complexity using a bioinformatics ana...

    Authors: Samantha Cheng, Angeline S. Andrew, Peter C. Andrews and Jason H. Moore
    Citation: BioData Mining 2016 9:40
    Content type: Short report Published on:

  7. Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires h...

    Authors: Giulia Fiscon, Emanuel Weitschek, Eleonora Cella, Alessandra Lo Presti, Marta Giovanetti, Muhammed Babakir-Mina, Marco Ciotti, Massimo Ciccozzi, Alessandra Pierangeli, Paola Bertolazzi and Giovanni Felici
    Citation: BioData Mining 2016 9:38
    Content type: Research Published on:

  8. An imbalanced dataset is defined as a training dataset that has imbalanced proportions of data in both interesting and uninteresting classes. Often in biomedical applications, samples from the stimulating clas...

    Authors: Jinyan Li, Simon Fong, Yunsick Sung, Kyungeun Cho, Raymond Wong and Kelvin K. L. Wong
    Citation: BioData Mining 2016 9:37
    Content type: Research Published on:

  9. Biomarker discovery methods are essential to identify a minimal subset of features (e.g., serum markers in predictive medicine) that are relevant to develop prediction models with high accuracy. By now, there ...

    Authors: Ursula Neumann, Mona Riemenschneider, Jan-Peter Sowa, Theodor Baars, Julia Kälsch, Ali Canbay and Dominik Heider
    Citation: BioData Mining 2016 9:36
    Content type: Research Published on:

  11. High-throughput sequencing technology and bioinformatics have identified chimeric RNAs (chRNAs), raising the possibility of chRNAs expressing particularly in diseases can be used as potential biomarkers in bot...

    Authors: Sacha Beaumeunier, Jérôme Audoux, Anthony Boureux, Florence Ruffle, Thérèse Commes, Nicolas Philippe and Ronnie Alves
    Citation: BioData Mining 2016 9:34
    Content type: Research Published on:

  13. A low-mass-ion discriminant equation (LOME) was constructed to investigate whether systematic low-mass-ion (LMI) profiling could be applied to ovarian cancer (OVC) screening.

    Authors: Jun Hwa Lee, Byong Chul Yoo, Yun Hwan Kim, Sun-A Ahn, Seung-Gu Yeo, Jae Youl Cho, Kyung-Hee Kim and Seung Cheol Kim
    Citation: BioData Mining 2016 9:32
    Content type: Research Published on:

  14. Redundant hierarchical relations refer to such patterns as two paths from one concept to another, one with length one (direct) and the other with length greater than one (indirect). Each redundant relation rep...

    Authors: Guangming Xing, Guo-Qiang Zhang and Licong Cui
    Citation: BioData Mining 2016 9:31
    Content type: Research Published on:

  16. Modern cohort studies include self-reported measures on disease, behavior and lifestyle, sensor-based observations from mobile phones and wearables, and rich -omics data. Follow-up is often achieved through el...

    Authors: Spiros C. Denaxas, Folkert W. Asselbergs and Jason H. Moore
    Citation: BioData Mining 2016 9:29
    Content type: Editorial Published on:

  17. Functional networks play an important role in the analysis of biological processes and systems. The inference of these networks from high-throughput (-omics) data is an area of intense research. So far, the si...

    Authors: Nicola Lazzarini, Paweł Widera, Stuart Williamson, Rakesh Heer, Natalio Krasnogor and Jaume Bacardit
    Citation: BioData Mining 2016 9:28
    Content type: Methodology Published on:

  18. BioBin is a bioinformatics software package developed to automate the process of binning rare variants into groups for statistical association analysis using a biological knowledge-driven framework. BioBin col...

    Authors: Carrie Colleen Buchanan Moore, Anna Okula Basile, John Robert Wallace, Alex Thomas Frase and Marylyn DeRiggi Ritchie
    Citation: BioData Mining 2016 9:27
    Content type: Software article Published on:

  19. Mass spectrometry (MS) are a group of a high-throughput techniques used to increase knowledge about biomolecules. They produce a large amount of data which is presented as a list of hundreds or thousands of pr...

    Authors: Pau M. Muñoz-Torres, Filip Rokć, Robert Belužic, Ivana Grbeša and Oliver Vugrek
    Citation: BioData Mining 2016 9:26
    Content type: SOFTWARE ARTICLE Published on:

  20. Heterogeneous biological data such as sequence matches, gene expression correlations, protein-protein interactions, and biochemical pathways can be merged and analyzed via graphs, or networks. Existing softwar...

    Authors: Jennifer Chang, Hyejin Cho and Hui-Hsien Chou
    Citation: BioData Mining 2016 9:25
    Content type: SOFTWARE ARTICLE Published on:

  21. Technological advances enable the cost-effective acquisition of Multi-Modal Data Sets (MMDS) composed of measurements for multiple, high-dimensional data types obtained from a common set of bio-samples. The joint...

    Authors: Gordon Okimoto, Ashkan Zeinalzadeh, Tom Wenska, Michael Loomis, James B. Nation, Tiphaine Fabre, Maarit Tiirikainen, Brenda Hernandez, Owen Chan, Linda Wong and Sandi Kwee
    Citation: BioData Mining 2016 9:24
    Content type: Methodology Published on:

  22. Systems biology experiments generate large volumes of data of multiple modalities and this information presents a challenge for integration due to a mix of complexity together with rich semantics. Here, we des...

    Authors: Artem Lysenko, Irina A. Roznovăţ, Mansoor Saqi, Alexander Mazein, Christopher J Rawlings and Charles Auffray
    Citation: BioData Mining 2016 9:23
    Content type: Review Published on:

  24. Genomic alterations affecting drug target proteins occur in several tumor types and are prime candidates for patient-specific tailored treatments. Increasingly, patients likely to benefit from targeted cancer ...

    Authors: Riku Louhimo, Marko Laakso, Denis Belitskin, Juha Klefström, Rainer Lehtonen and Sampsa Hautaniemi
    Citation: BioData Mining 2016 9:21
    Content type: Research Published on:

  25. Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual ...

    Authors: Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen and Sampsa Hautaniemi
    Citation: BioData Mining 2016 9:20
    Content type: SOFTWARE ARTICLE Published on:

  26. Real Time Cell Analysis (RTCA) technology is used to monitor cellular changes continuously over the entire exposure period. Combining with different testing concentrations, the profiles have potential in probi...

    Authors: Yile Zhang, Yau Shu Wong, Jian Deng, Cristina Anton, Stephan Gabos, Weiping Zhang, Dorothy Yu Huang and Can Jin
    Citation: BioData Mining 2016 9:19
    Content type: Research Published on:

  27. The future of medicine is moving towards the phase of precision medicine, with the goal to prevent and treat diseases by taking inter-individual variability into account. A large part of the variability lies i...

    Authors: Ruowang Li, Scott M. Dudek, Dokyoon Kim, Molly A. Hall, Yuki Bradford, Peggy L. Peissig, Murray H. Brilliant, James G. Linneman, Catherine A. McCarty, Le Bao and Marylyn D. Ritchie
    Citation: BioData Mining 2016 9:18
    Content type: Methodology Published on:

  29. High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Pr...

    Authors: Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min and Mattia Prosperi
    Citation: BioData Mining 2016 9:16
    Content type: Review Published on:

  30. Biomedical informatics has become a central focus for many academic medical centers and universities as biomedical research because increasingly reliant on the processing, analysis, and interpretation of large...

    Authors: Jason H. Moore and John H. Holmes
    Citation: BioData Mining 2016 9:15
    Content type: Editorial Published on:

  32. Gene isoforms are commonly found in both prokaryotes and eukaryotes. Since each isoform may perform a specific function in response to changing environmental conditions, studying the dynamics of gene isoforms ...

    Authors: Ma Liang, Castle Raley, Xin Zheng, Geetha Kutty, Emile Gogineni, Brad T. Sherman, Qiang Sun, Xiongfong Chen, Thomas Skelly, Kristine Jones, Robert Stephens, Bin Zhou, William Lau, Calvin Johnson, Tomozumi Imamichi, Minkang Jiang…
    Citation: BioData Mining 2016 9:13
    Content type: Methodology Published on:

  33. Genetic studies of human diseases have identified many variants associated with pathogenesis and severity. However, most studies have used only statistical association to assess putative relationships to disea...

    Authors: Minjun Huang, Britney E. Graham, Ge Zhang, Reed Harder, Nuri Kodaman, Jason H. Moore, Louis Muglia and Scott M. Williams
    Citation: BioData Mining 2016 9:12
    Content type: Methodology Published on:

  34. study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to us...

    Authors: Shan E Ahmed Raza, Daniel Langenkämper, Korsuk Sirinukunwattana, David Epstein, Tim W. Nattkemper and Nasir M. Rajpoot
    Citation: BioData Mining 2016 9:11
    Content type: Research Published on:

  35. Antiretroviral therapy is essential for human immunodeficiency virus (HIV) infected patients to inhibit viral replication and therewith to slow progression of disease and prolong a patient’s life. However, the...

    Authors: Mona Riemenschneider, Robin Senge, Ursula Neumann, Eyke Hüllermeier and Dominik Heider
    Citation: BioData Mining 2016 9:10
    Content type: SHORT REPORT Published on:

  38. Machine learning methods and in particular random forests (RFs) are a promising alternative to standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable importance measures (...

    Authors: Silke Szymczak, Emily Holzinger, Abhijit Dasgupta, James D. Malley, Anne M. Molloy, James L. Mills, Lawrence C. Brody, Dwight Stambolian and Joan E. Bailey-Wilson
    Citation: BioData Mining 2016 9:7
    Content type: Methodology Published on:

  39. To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasi...

    Authors: Florian Heinke, Sebastian Bittrich, Florian Kaiser and Dirk Labudde
    Citation: BioData Mining 2016 9:6
    Content type: SOFTWARE ARTICLE Published on:

  42. Alzheimer’s disease (AD) is a neurodegenerative disease that causes dementia. While molecular basis of AD is not fully understood, genetic factors are expected to participate in the development and progression...

    Authors: Ailin Song, Jingwen Yan, Sungeun Kim, Shannon Leigh Risacher, Aaron K. Wong, Andrew J. Saykin, Li Shen and Casey S. Greene
    Citation: BioData Mining 2016 9:3
    Content type: Short report Published on:

  43. Multi-gene lists and single sample predictor models have been currently used to reduce the multidimensional complexity of breast cancers, and to identify intrinsic subtypes. The perceived inability of some mod...

    Authors: Heloisa H. Milioli, Renato Vimieiro, Inna Tishchenko, Carlos Riveros, Regina Berretta and Pablo Moscato
    Citation: BioData Mining 2016 9:2
    Content type: SHORT REPORT Published on:

  45. Recent findings have reemphasized the importance of epistasis, or gene-gene interactions, as a contributing factor to the unexplained heritability of obesity. Network-based methods such as statistical epistasis n...

    Authors: Rishika De, Ting Hu, Jason H. Moore and Diane Gilbert-Diamond
    Citation: BioData Mining 2015 8:45
    Content type: Research Published on:

  47. The interaction effect among multiple genetic factors, i.e. epistasis, plays an important role in explaining susceptibility on common human diseases and phenotypic traits. The uncertainty over the number of ge...

    Authors: Ting Hu, Angeline S. Andrew, Margaret R. Karagas and Jason H. Moore
    Citation: BioData Mining 2015 8:43
    Content type: Research Published on:

  48. The genetic background to bipolar disorder (BPD) has been attributed to different genetic and genomic risk factors. In the present study we hypothesized that inherited copy number variations (CNVs) contribute ...

    Authors: Magnus Lekman, Robert Karlsson, Lisette Graae, Ola Hössjer and Ingrid Kockum
    Citation: BioData Mining 2015 8:42
    Content type: Research Published on:

  49. Despite heritability estimates of 40–70 % for obesity, less than 2 % of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions a...

    Authors: Rishika De, Shefali S. Verma, Fotios Drenos, Emily R. Holzinger, Michael V. Holmes, Molly A. Hall, David R. Crosslin, David S. Carrell, Hakon Hakonarson, Gail Jarvik, Eric Larson, Jennifer A. Pacheco, Laura J. Rasmussen-Torvik, Carrie B. Moore, Folkert W. Asselbergs, Jason H. Moore…
    Citation: BioData Mining 2015 8:41
    Content type: Research Published on:
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BioData Mining

ISSN: 1756-0381