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  1. 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

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  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. 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

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  8. 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

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  9. 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

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  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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

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  18. 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

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  19. 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

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

  20. 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

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  21. 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

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  22. 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

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  23. 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

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  24. 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

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  25. 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

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  26. 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

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  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

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  36. 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

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