Volume 8; Issue 1

Main
BioData Mining
Volume 8; Issue 1

BioData Mining

Volume 8; Issue 1

1

Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm

Huang, Xiuzhen, Jennings, Steven F, Bruce, Barry, Buchan, Alison, Cai, Liming, Chen, Pengyin, Cramer, Carole L, Guan, Weihua, Hilgert, Uwe, Jiang, Hongmei, Li, Zenglu, McClure, Gail, McMullen, Donald

Journal:

Year:

2015

Language:

english

File:

PDF, 323 KB

english, 2015

2

Motif mining based on network space compression

Zhang, Qiang, Xu, Yuan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

3

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

Journal:

Year:

2015

Language:

english

File:

PDF, 391 KB

english, 2015

4

Microarray enriched gene rank

Demidenko, Eugene

Journal:

Year:

2015

Language:

english

File:

PDF, 1.71 MB

english, 2015

5

Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns

Meysman, Pieter, Zhou, Cheng, Cule, Boris, Goethals, Bart, Laukens, Kris

Journal:

Year:

2015

Language:

english

File:

PDF, 1.68 MB

english, 2015

6

An investigation of gene-gene interactions in dose-response studies with Bayesian nonparametrics

Beam, Andrew L, Motsinger-Reif, Alison A, Doyle, Jon

Journal:

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

7

Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure

Lareau, Caleb A, White, Bill C, Oberg, Ann L, McKinney, Brett A

Journal:

Year:

2015

Language:

english

File:

PDF, 1.24 MB

english, 2015

8

Visualisation of quadratic discriminant analysis and its application in exploration of microbial interactions

Gardner-Lubbe, Sugnet, Dube, Felix S

Journal:

Year:

2015

Language:

english

File:

PDF, 458 KB

english, 2015

9

Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing

Wang, Liwei, Liu, Hongfang, Chute, Christopher G, Zhu, Qian

Journal:

Year:

2015

Language:

english

File:

PDF, 963 KB

english, 2015

10

Mining severe drug-drug interaction adverse events using Semantic Web technologies: a case study

Jiang, Guoqian, Liu, Hongfang, Solbrig, Harold R, Chute, Christopher G

Journal:

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

11

Bacterial rose garden for metagenomic SNP-based phylogeny visualization

Alexeev, Dmitry, Bibikova, Tanya, Kovarsky, Boris, Melnikov, Damir, Tyakht, Alexander, Govorun, Vadim

Journal:

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

12

The effects of electronic medical record phenotyping details on genetic association studies: HDL-C as a case study

Dumitrescu, Logan, Goodloe, Robert, Bradford, Yukiko, Farber-Eger, Eric, Boston, Jonathan, Crawford, Dana C

Journal:

Year:

2015

Language:

english

File:

PDF, 507 KB

english, 2015

13

A bibliometric analysis on tobacco regulation investigators

Li, Dingcheng, Okamoto, Janet, Liu, Hongfang, Leischow, Scott

Journal:

Year:

2015

Language:

english

File:

PDF, 2.95 MB

english, 2015

14

Mining causal relationships among clinical variables for cancer diagnosis based on Bayesian analysis

Journal:

Year:

2015

Language:

english

File:

PDF, 1.81 MB

english, 2015

15

Prediction of protein solvent accessibility using PSO-SVR with multiple sequence-derived features and weighted sliding window scheme

Zhang, Jian, Chen, Wenhan, Sun, Pingping, Zhao, Xiaowei, Ma, Zhiqiang

Journal:

Year:

2015

Language:

english

File:

PDF, 858 KB

english, 2015

16

Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform

Madrigal, Pedro, Krajewski, Paweł

Journal:

Year:

2015

Language:

english

File:

PDF, 2.44 MB

english, 2015

17

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge

Journal:

Year:

2015

Language:

english

File:

PDF, 2.25 MB

english, 2015

18

Supervised learning methods in modeling of CD4+ T cell heterogeneity

Lu, Pinyi, Abedi, Vida, Mei, Yongguo, Hontecillas, Raquel, Hoops, Stefan, Carbo, Adria, Bassaganya-Riera, Josep

Journal:

Year:

2015

Language:

english

File:

PDF, 1.43 MB

english, 2015

19

Network construction and structure detection with metagenomic count data

Liu, Zhenqiu, Lin, Shili, Piantadosi, Steven

Journal:

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

20

Integration and comparison of different genomic data for outcome prediction in cancer

Gómez-Rueda, Hugo, Martínez-Ledesma, Emmanuel, Martínez-Torteya, Antonio, Palacios-Corona, Rebeca, Trevino, Victor

Journal:

Year:

2015

Language:

english

File:

PDF, 1.40 MB

english, 2015

21

Predicting linear B-cell epitopes using amino acid anchoring pair composition

Shen, Weike, Cao, Yuan, Cha, Lei, Zhang, Xufei, Ying, Xiaomin, Zhang, Wei, Ge, Kun, Li, Wuju, Zhong, Li

Journal:

Year:

2015

Language:

english

File:

PDF, 858 KB

english, 2015

22

Lumping versus splitting: the need for biological data mining in precision medicine

Williams, Scott M., Moore, Jason H.

Journal:

Year:

2015

Language:

english

File:

PDF, 328 KB

english, 2015

23

DNA microarray integromics analysis platform

Waller, Tomasz, Gubała, Tomasz, Sarapata, Krzysztof, Piwowar, Monika, Jurkowski, Wiktor

Journal:

Year:

2015

Language:

english

File:

PDF, 3.30 MB

english, 2015

24

TaxKB: a knowledge base for new taxane-related drug discovery

Murugan, Kasi, Shanmugasamy, Sangeetha, Al-Sohaibani, Saleh, Vignesh, Naga, Palanikannan, Kandavel, Vimala, Antonydhason, Kumar, Gopal Ramesh

Journal:

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

25

Interaction networks for identifying coupled molecular processes in microbial communities

Bosse, Magnus, Heuwieser, Alexander, Heinzel, Andreas, Nancucheo, Ivan, Melo Barbosa Dall’Agnol, Hivana, Lukas, Arno, Tzotzos, George, Mayer, Bernd

Journal:

Year:

2015

Language:

english

File:

PDF, 1.40 MB

english, 2015

26

Informative gene network for chemotherapy-induced peripheral neuropathy

Reyes-Gibby, Cielito C., Wang, Jian, Yeung, Sai-Ching J., Shete, Sanjay

Journal:

Year:

2015

Language:

english

File:

PDF, 1.88 MB

english, 2015

27

Principal component gene set enrichment (PCGSE)

Frost, H. Robert, Li, Zhigang, Moore, Jason H.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.14 MB

english, 2015

28

Prediction of relevant biomedical documents: a human microbiome case study

Thompson, Paul, Madan, Juliette C., Moore, Jason H.

Journal:

Year:

2015

Language:

english

File:

PDF, 453 KB

english, 2015

29

Functional dyadicity and heterophilicity of gene-gene interactions in statistical epistasis networks

Hu, Ting, Andrew, Angeline S., Karagas, Margaret R., Moore, Jason H.

Journal:

Year:

2015

Language:

english

File:

PDF, 700 KB

english, 2015

30

DAPPER: a data-mining resource for protein-protein interactions

Haider, Syed, Lipinszki, Zoltan, Przewloka, Marcin R., Ladak, Yaseen, D’Avino, Pier Paolo, Kimata, Yuu, Lio’, Pietro, Glover, David M.

Journal:

Year:

2015

Language:

english

File:

PDF, 580 KB

english, 2015

31

Next generation informatics for big data in precision medicine era

Zhang, Yuji, Zhu, Qian, Liu, Hongfang

Journal:

Year:

2015

Language:

english

File:

PDF, 309 KB

english, 2015

32

On predicting regulatory genes by analysis of functional networks in C. elegans

Valba, Olga V., Nechaev, Sergei K., Sterken, Mark G., Snoek, L. Basten, Kammenga, Jan E., Vasieva, Olga O.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.47 MB

english, 2015

33

BioDB extractor: customized data extraction system for commonly used bioinformatics databases

Karbhal, Rajiv, Sawant, Sangeeta, Kulkarni-Kale, Urmila

Journal:

Year:

2015

Language:

english

File:

PDF, 3.33 MB

english, 2015

34

Towards a phenome-wide catalog of human clinical traits impacted by genetic ancestry

Dumitrescu, Logan, Restrepo, Nicole A., Goodloe, Robert, Boston, Jonathan, Farber-Eger, Eric, Pendergrass, Sarah A., Bush, William S., Crawford, Dana C.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.24 MB

english, 2015

35

Genome-wide predictors of NF-κB recruitment and transcriptional activity

Cieślik, Marcin, Bekiranov, Stefan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

36

LAF: Logic Alignment Free and its application to bacterial genomes classification

Weitschek, Emanuel, Cunial, Fabio, Felici, Giovanni

Journal:

Year:

2015

Language:

english

File:

PDF, 680 KB

english, 2015

37

Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

De, Rishika, Verma, Shefali S., Drenos, Fotios, Holzinger, Emily R., Holmes, Michael V., Hall, Molly A., Crosslin, David R., Carrell, David S., Hakonarson, Hakon, Jarvik, Gail, Larson, Eric, Pacheco,

Journal:

Year:

2015

Language:

english

File:

PDF, 982 KB

english, 2015

38

Non-coding yet non-trivial: a review on the computational genomics of lincRNAs

Ching, Travers, Masaki, Jayson, Weirather, Jason, Garmire, Lana X.

Journal:

Year:

2015

Language:

english

File:

PDF, 487 KB

english, 2015

39

Characterizing gene-gene interactions in a statistical epistasis network of twelve candidate genes for obesity

De, Rishika, Hu, Ting, Moore, Jason H., Gilbert-Diamond, Diane

Journal:

Year:

2015

Language:

english

File:

PDF, 2.35 MB

english, 2015

40

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis

Beck, Daniel, Foster, James A.

Journal:

Year:

2015

Language:

english

File:

PDF, 672 KB

english, 2015

41

A novel biclustering algorithm of binary microarray data: BiBinCons and BiBinAlter

Saber, Haifa Ben, Elloumi, Mourad

Journal:

Year:

2015

Language:

english

File:

PDF, 1.01 MB

english, 2015

42

Testing multiple hypotheses through IMP weighted FDR based on a genetic functional network with application to a new zebrafish transcriptome study

Gui, Jiang, Greene, Casey S., Sullivan, Con, Taylor, Walter, Moore, Jason H., Kim, Carol

Journal:

Year:

2015

Language:

english

File:

PDF, 1.09 MB

english, 2015

43

The role of visualization and 3-D printing in biological data mining

Weiss, Talia L., Zieselman, Amanda, Hill, Douglas P., Diamond, Solomon G., Shen, Li, Saykin, Andrew J., Moore, Jason H.

Journal:

Year:

2015

Language:

english

File:

PDF, 553 KB

english, 2015

44

gammaMAXT: a fast multiple-testing correction algorithm

Lishout, François Van, Gadaleta, Francesco, Moore, Jason H., Wehenkel, Louis, Steen, Kristel Van

Journal:

Year:

2015

Language:

english

File:

PDF, 933 KB

english, 2015

45

A significant risk locus on 19q13 for bipolar disorder identified using a combined genome-wide linkage and copy number variation analysis

Lekman, Magnus, Karlsson, Robert, Graae, Lisette, Hössjer, Ola, Kockum, Ingrid

Journal:

Year:

2015

Language:

english

File:

PDF, 2.68 MB

english, 2015