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  3. The purpose of the MaxT algorithm is to provide a significance test algorithm that controls the family-wise error rate (FWER) during simultaneous hypothesis testing. However, the requirements in terms of compu...

    Authors: François Van Lishout, Francesco Gadaleta, Jason H. Moore, Louis Wehenkel and Kristel Van Steen
    Citation: BioData Mining 2015 8:36
    Content type: SOFTWARE ARTICLE Published on:

  4. Racial/ethnic differences for commonly measured clinical variables are well documented, and it has been postulated that population-specific genetic factors may play a role. The genetic heterogeneity of admixed...

    Authors: Logan Dumitrescu, Nicole A. Restrepo, Robert Goodloe, Jonathan Boston, Eric Farber-Eger, Sarah A. Pendergrass, William S. Bush and Dana C. Crawford
    Citation: BioData Mining 2015 8:35
    Content type: Research Published on:

  6. Connectivity networks, which reflect multiple interactions between genes and proteins, possess not only a descriptive but also a predictive value, as new connections can be extrapolated and tested by means of ...

    Authors: Olga V. Valba, Sergei K. Nechaev, Mark G. Sterken, L. Basten Snoek, Jan E. Kammenga and Olga O. Vasieva
    Citation: BioData Mining 2015 8:33
    Content type: Research Published on:

  7. In cancer, large-scale technologies such as next-generation sequencing and microarrays have produced a wide number of genomic features such as DNA copy number alterations (CNA), mRNA expression (EXPR), microRN...

    Authors: Hugo Gómez-Rueda, Emmanuel Martínez-Ledesma, Antonio Martínez-Torteya, Rebeca Palacios-Corona and Victor Trevino
    Citation: BioData Mining 2015 8:32
    Content type: Research Published on:

  8. Diverse types of biological data, primary as well as derived, are available in various formats and are stored in heterogeneous resources. Database-specific as well as integrated search engines are available fo...

    Authors: Rajiv Karbhal, Sangeeta Sawant and Urmila Kulkarni-Kale
    Citation: BioData Mining 2015 8:31
    Content type: Research Published on:

    The Erratum to this article has been published in BioData Mining 2016 9:8

  9. The identification of interaction networks between proteins and complexes holds the promise of offering novel insights into the molecular mechanisms that regulate many biological processes. With increasing vol...

    Authors: Syed Haider, Zoltan Lipinszki, Marcin R. Przewloka, Yaseen Ladak, Pier Paolo D’Avino, Yuu Kimata, Pietro Lio’ and David M. Glover
    Citation: BioData Mining 2015 8:30
    Content type: Software article Published on:

  11. Modeling of the immune system – a highly non-linear and complex system – requires practical and efficient data analytic approaches. The immune system is composed of heterogeneous cell populations and hundreds ...

    Authors: Pinyi Lu, Vida Abedi, Yongguo Mei, Raquel Hontecillas, Stefan Hoops, Adria Carbo and Josep Bassaganya-Riera
    Citation: BioData Mining 2015 8:27
    Content type: Research Published on:

  12. Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static netw...

    Authors: Yuji Zhang
    Citation: BioData Mining 2015 8:26
    Content type: Research Published on:

  13. Although principal component analysis (PCA) is widely used for the dimensional reduction of biomedical data, interpretation of PCA results remains daunting. Most existing interpretation methods attempt to expl...

    Authors: H. Robert Frost, Zhigang Li and Jason H. Moore
    Citation: BioData Mining 2015 8:25
    Content type: Methodology Published on:

  16. Biological data mining is a powerful tool that can provide a wealth of information about patterns of genetic and genomic biomarkers of health and disease. A potential disadvantage of data mining is volume and ...

    Authors: Talia L. Weiss, Amanda Zieselman, Douglas P. Hill, Solomon G. Diamond, Li Shen, Andrew J. Saykin and Jason H. Moore
    Citation: BioData Mining 2015 8:22
    Content type: Review Published on:

  17. Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties tha...

    Authors: Magnus Bosse, Alexander Heuwieser, Andreas Heinzel, Ivan Nancucheo, Hivana Melo Barbosa Dall’Agnol, Arno Lukas, George Tzotzos and Bernd Mayer
    Citation: BioData Mining 2015 8:21
    Content type: Research Published on:

  19. Taxanes are naturally occurring compounds which belong to a powerful group of chemotherapeutic drugs with anticancer properties. Their current use, clinical efficacy, and unique mechanism of action indicate th...

    Authors: Kasi Murugan, Sangeetha Shanmugasamy, Saleh Al-Sohaibani, Naga Vignesh, Kandavel Palanikannan, Antonydhason Vimala and Gopal Ramesh Kumar
    Citation: BioData Mining 2015 8:19
    Content type: Methodology Published on:

  20. The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray ...

    Authors: Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar and Wiktor Jurkowski
    Citation: BioData Mining 2015 8:18
    Content type: Software article Published on:

  21. In genome-wide studies, hundreds of thousands of hypothesis tests are performed simultaneously. Bonferroni correction and False Discovery Rate (FDR) can effectively control type I error but often yield a high ...

    Authors: Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore and Carol Kim
    Citation: BioData Mining 2015 8:17
    Content type: Methodology Published on:

  23. Biorepositories linked to de-identified electronic medical records (EMRs) have the potential to complement traditional epidemiologic studies in genotype-phenotype studies of complex human diseases and traits. ...

    Authors: Logan Dumitrescu, Robert Goodloe, Yukiko Bradford, Eric Farber-Eger, Jonathan Boston and Dana C Crawford
    Citation: BioData Mining 2015 8:15
    Content type: Research Published on:

  24. Accurate identification of linear B-cell epitopes plays an important role in peptide vaccine designs, immunodiagnosis, and antibody productions. Although several prediction methods have been reported, unsatisf...

    Authors: Weike Shen, Yuan Cao, Lei Cha, Xufei Zhang, Xiaomin Ying, Wei Zhang, Kun Ge, Wuju Li and Li Zhong
    Citation: BioData Mining 2015 8:14
    Content type: Research Published on:

  27. To facilitate the implementation of the Family Smoking Prevention and Tobacco Control Act of 2009, the Federal Drug Agency (FDA) Center for Tobacco Products (CTP) has identified research priorities under the u...

    Authors: Dingcheng Li, Janet Okamoto, Hongfang Liu and Scott Leischow
    Citation: BioData Mining 2015 8:11
    Content type: Research Published on:

  28. One of the most challenging tasks in genomic analysis nowadays is metagenomics. Biomedical applications of metagenomics give rise to datasets containing hundreds and thousands of samples from various body site...

    Authors: Dmitry Alexeev, Tanya Bibikova, Boris Kovarsky, Damir Melnikov, Alexander Tyakht and Vadim Govorun
    Citation: BioData Mining 2015 8:10
    Content type: Methodology Published on:

  29. Pharmacogenomics (PGx) as an emerging field, is poised to change the way we practice medicine and deliver health care by customizing drug therapies on the basis of each patient’s genetic makeup. A large volume...

    Authors: Liwei Wang, Hongfang Liu, Christopher G Chute and Qian Zhu
    Citation: BioData Mining 2015 8:9
    Content type: Research Published on:

  31. Whether your interests lie in scientific arenas, the corporate world, or in government, you have certainly heard the praises of big data: Big data will give you new insights, allow you to become more efficient...

    Authors: Xiuzhen Huang, Steven F Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L Cramer, Weihua Guan, Uwe KK Hilgert, Hongmei Jiang, Zenglu Li, Gail McClure, Donald F McMullen, Bindu Nanduri, Andy Perkins, Bhanu Rekepalli…
    Citation: BioData Mining 2015 8:7
    Content type: Editorial Published on:

  33. Biological insights into group differences, such as disease status, have been achieved through differential co-expression analysis of microarray data. Additional understanding of group differences may be achie...

    Authors: Caleb A Lareau, Bill C White, Ann L Oberg and Brett A McKinney
    Citation: BioData Mining 2015 8:5
    Content type: Research Published on:

  35. The prediction of solvent accessibility could provide valuable clues for analyzing protein structure and functions, such as protein 3-Dimensional structure and B-cell epitope prediction. To fully decipher the ...

    Authors: Jian Zhang, Wenhan Chen, Pingping Sun, Xiaowei Zhao and Zhiqiang Ma
    Citation: BioData Mining 2015 8:3
    Content type: Research Published on:

  36. We develop a new concept that reflects how genes are connected based on microarray data using the coefficient of determination (the squared Pearson correlation coefficient). Our gene rank combines a priori kno...

    Authors: Eugene Demidenko
    Citation: BioData Mining 2015 8:2
    Content type: Research Published on:

  39. The discovery of breast cancer subtypes and subsequent development of treatments aimed at them has allowed for a great reduction in the mortality of breast cancer. But despite this progress, tumors with simila...

    Authors: Nima Pouladi, Richard Cowper-Sallari and Jason H Moore
    Citation: BioData Mining 2014 7:27
    Content type: Research Published on:

  40. Identifying genetic interactions in data obtained from genome-wide association studies (GWASs) can help in understanding the genetic basis of complex diseases. The large number of single nucleotide polymorphis...

    Authors: Charalampos S Floudas, Nara Um, M Ilyas Kamboh, Michael M Barmada and Shyam Visweswaran
    Citation: BioData Mining 2014 7:35
    Content type: Methodology Published on:

  41. Using a collection of different terminal nodesize constructed random forests, each generating a synthetic feature, a synthetic random forest is defined as a kind of hyperforest, calculated using the new input ...

    Authors: Hemant Ishwaran and James D Malley
    Citation: BioData Mining 2014 7:28
    Content type: Methodology Published on:

  42. Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Se...

    Authors: Kirsti Laurila, Reija Autio, Lingjia Kong, Elisa Närvä, Samer Hussein, Timo Otonkoski, Riitta Lahesmaa and Harri Lähdesmäki
    Citation: BioData Mining 2014 7:32
    Content type: Research Published on:

  44. A network motif is a recurring subnetwork within a network, and it takes on certain functions in practical biological macromolecule applications. Previous algorithms have focused on the computational efficienc...

    Authors: Qiang Zhang and Yuan Xu
    Citation: BioData Mining 2014 8:29
    Content type: Methodology Published on:

  47. PGxClean is a new web application that performs quality control analyses for data produced by the Affymetrix DMET chip or other candidate gene technologies. Importantly, the software does not assume that varia...

    Authors: Daniel Rotroff, John Jack, Nathan Campbell, Scott Clark and Alison A Motsinger-Reif
    Citation: BioData Mining 2014 7:24
    Content type: Short report Published on:

  48. The major histocompatibility complex (MHC) is responsible for presenting antigens (epitopes) on the surface of antigen-presenting cells (APCs). When pathogen-derived epitopes are presented by MHC class II on a...

    Authors: Clemente Aguilar-Bonavides, Reinaldo Sanchez-Arias and Cristina Lanzas
    Citation: BioData Mining 2014 7:23
    Content type: Research Published on:

  49. The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called “big data” challenges traditional analytic tools and will increas...

    Authors: Emad A Mohammed, Behrouz H Far and Christopher Naugler
    Citation: BioData Mining 2014 7:22
    Content type: Review Published on:

  50. Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions ...

    Authors: Laurence D Parnell, Britt A Blokker, Hassan S Dashti, Paula-Dene Nesbeth, Brittany Elle Cooper, Yiyi Ma, Yu-Chi Lee, Ruixue Hou, Chao-Qiang Lai, Kris Richardson and José M Ordovás
    Citation: BioData Mining 2014 7:21
    Content type: Research Published on:
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BioData Mining

ISSN: 1756-0381