Volume 32; Issue 17

Main
Bioinformatics
Volume 32; Issue 17

Bioinformatics

Volume 32; Issue 17

1

Gene-set association tests for next-generation sequencing data

Lee, Jaehoon, Kim, Young Jin, Lee, Juyoung, Kim, Bong-Jo, Lee, Seungyeoun, Park, Taesung

Journal:

Year:

2016

Language:

english

File:

PDF, 412 KB

english, 2016

2

ModuleAlign: module-based global alignment of protein–protein interaction networks

Hashemifar, Somaye, Ma, Jianzhu, Naveed, Hammad, Canzar, Stefan, Xu, Jinbo

Journal:

Year:

2016

Language:

english

File:

PDF, 561 KB

english, 2016

3

PanTools: representation, storage and exploration of pan-genomic data

Sheikhizadeh, Siavash, Schranz, M. Eric, Akdel, Mehmet, de Ridder, Dick, Smit, Sandra

Journal:

Year:

2016

Language:

english

File:

PDF, 798 KB

english, 2016

4

Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach

Koutroumpas, Konstantinos, Ballarini, Paolo, Votsi, Irene, Cournède, Paul-Henry

Journal:

Year:

2016

Language:

english

File:

PDF, 2.90 MB

english, 2016

5

Assemble CRISPRs from metagenomic sequencing data

Lei, Jikai, Sun, Yanni

Journal:

Year:

2016

Language:

english

File:

PDF, 808 KB

english, 2016

6

CoLoRMap: Correcting Long Reads by Mapping short reads

Haghshenas, Ehsan, Hach, Faraz, Sahinalp, S. Cenk, Chauve, Cedric

Journal:

Year:

2016

Language:

english

File:

PDF, 208 KB

english, 2016

7

Patterns of amino acid conservation in human and animal immunodeficiency viruses

Voitenko, Olga S., Dhroso, Andi, Feldmann, Anna, Korkin, Dmitry, Kalinina, Olga V.

Journal:

Year:

2016

Language:

english

File:

PDF, 579 KB

english, 2016

8

Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data

Ben-Elazar, Shay, Chor, Benny, Yakhini, Zohar

Journal:

Year:

2016

Language:

english

File:

PDF, 1.12 MB

english, 2016

9

Fast genotyping of known SNPs through approximate k -mer matching

Shajii, Ariya, Yorukoglu, Deniz, William Yu, Yun, Berger, Bonnie

Journal:

Year:

2016

Language:

english

File:

PDF, 2.25 MB

english, 2016

10

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures

Girotto, Samuele, Pizzi, Cinzia, Comin, Matteo

Journal:

Year:

2016

Language:

english

File:

PDF, 317 KB

english, 2016

11

Benchmarking the next generation of homology inference tools

Saripella, Ganapathi Varma, Sonnhammer, Erik L. L., Forslund, Kristoffer

Journal:

Year:

2016

Language:

english

File:

PDF, 698 KB

english, 2016

12

Snowball : strain aware gene assembly of metagenomes

Gregor, I., Schönhuth, A., McHardy, A. C.

Journal:

Year:

2016

Language:

english

File:

PDF, 631 KB

english, 2016

13

AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields

Wang, Sheng, Ma, Jianzhu, Xu, Jinbo

Journal:

Year:

2016

Language:

english

File:

PDF, 254 KB

english, 2016

14

Complementary feature selection from alternative splicing events and gene expression for phenotype prediction

Labuzzetta, Charles J., Antonio, Margaret L., Watson, Patricia M., Wilson, Robert C., Laboissonniere, Lauren A., Trimarchi, Jeffrey M., Genc, Baris, Ozdinler, P. Hande, Watson, Dennis K., Anderson, Pa

Journal:

Year:

2016

Language:

english

File:

PDF, 324 KB

english, 2016

15

Higher order methylation features for clustering and prediction in epigenomic studies

Kapourani, Chantriolnt-Andreas, Sanguinetti, Guido

Journal:

Year:

2016

Language:

english

File:

PDF, 835 KB

english, 2016

16

Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

Ammad-ud-din, Muhammad, Khan, Suleiman A., Malani, Disha, Murumägi, Astrid, Kallioniemi, Olli, Aittokallio, Tero, Kaski, Samuel

Journal:

Year:

2016

Language:

english

File:

PDF, 856 KB

english, 2016

17

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration

Le Van, Thanh, van Leeuwen, Matthijs, Carolina Fierro, Ana, De Maeyer, Dries, Van den Eynden, Jimmy, Verbeke, Lieven, De Raedt, Luc, Marchal, Kathleen, Nijssen, Siegfried

Journal:

Year:

2016

Language:

english

File:

PDF, 1.63 MB

english, 2016

18

The Network Library: a framework to rapidly integrate network biology resources

Summer, Georg, Kelder, Thomas, Radonjic, Marijana, van Bilsen, Marc, Wopereis, Suzan, Heymans, Stephane

Journal:

Year:

2016

Language:

english

File:

PDF, 485 KB

english, 2016

19

GTRAC: fast retrieval from compressed collections of genomic variants

Tatwawadi, Kedar, Hernaez, Mikel, Ochoa, Idoia, Weissman, Tsachy

Journal:

Year:

2016

Language:

english

File:

PDF, 818 KB

english, 2016

20

Combining dependent P- values with an empirical adaptation of Brown’s method

Poole, William, Gibbs, David L., Shmulevich, Ilya, Bernard, Brady, Knijnenburg, Theo A.

Journal:

Year:

2016

Language:

english

File:

PDF, 456 KB

english, 2016

21

Causality modeling for directed disease network

Bang, Sunjoo, Kim, Jae-Hoon, Shin, Hyunjung

Journal:

Year:

2016

Language:

english

File:

PDF, 810 KB

english, 2016

22

Information-optimal genome assembly via sparse read-overlap graphs

Shomorony, Ilan, Kim, Samuel H., Courtade, Thomas A., Tse, David N. C.

Journal:

Year:

2016

Language:

english

File:

PDF, 878 KB

english, 2016

23

Optimization of signal-to-noise ratio for efficient microarray probe design

Matveeva, Olga V., Nechipurenko, Yury D., Riabenko, Evgeniy, Ragan, Chikako, Nazipova, Nafisa N., Ogurtsov, Aleksey Y., Shabalina, Svetlana A.

Journal:

Year:

2016

Language:

english

File:

PDF, 707 KB

english, 2016

24

Characterizing leader sequences of CRISPR loci

Alkhnbashi, Omer S., Shah, Shiraz A., Garrett, Roger A., Saunders, Sita J., Costa, Fabrizio, Backofen, Rolf

Journal:

Year:

2016

Language:

english

File:

PDF, 979 KB

english, 2016

25

A program for verification of phylogenetic network models

Gunawan, Andreas D.M., Lu, Bingxin, Zhang, Louxin

Journal:

Year:

2016

Language:

english

File:

PDF, 564 KB

english, 2016

26

ECCB 2016 ORGANIZATION

Journal:

Year:

2016

Language:

english

File:

PDF, 55 KB

english, 2016

27

ECCB 2016: The 15th European Conference on Computational Biology

Journal:

Year:

2016

Language:

english

File:

PDF, 92 KB

english, 2016

28

Improve homology search sensitivity of PacBio data by correcting frameshifts

Du, Nan, Sun, Yanni

Journal:

Year:

2016

Language:

english

File:

PDF, 1.09 MB

english, 2016

29

Large-scale inference of conjunctive Bayesian networks

Montazeri, Hesam, Kuipers, Jack, Kouyos, Roger, Böni, Jürg, Yerly, Sabine, Klimkait, Thomas, Aubert, Vincent, Günthard, Huldrych F., Beerenwinkel, Niko

Journal:

Year:

2016

Language:

english

File:

PDF, 402 KB

english, 2016

30

Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation

Traynard, Pauline, Fauré, Adrien, Fages, François, Thieffry, Denis

Journal:

Year:

2016

Language:

english

File:

PDF, 328 KB

english, 2016

31

DeepChrome: deep-learning for predicting gene expression from histone modifications

Singh, Ritambhara, Lanchantin, Jack, Robins, Gabriel, Qi, Yanjun

Journal:

Year:

2016

Language:

english

File:

PDF, 618 KB

english, 2016

32

Pathway-based approach using hierarchical components of collapsed rare variants

Lee, Sungyoung, Choi, Sungkyoung, Kim, Young Jin, Kim, Bong-Jo, Hwang, Heungsun, Park, Taesung

Journal:

Year:

2016

Language:

english

File:

PDF, 513 KB

english, 2016

33

Genome wide predictions of miRNA regulation by transcription factors

Ruffalo, Matthew, Bar-Joseph, Ziv

Journal:

Year:

2016

Language:

english

File:

PDF, 989 KB

english, 2016

34

PEPSI-Dock: a detailed data-driven protein–protein interaction potential accelerated by polar Fourier correlation

Neveu, Emilie, Ritchie, David W., Popov, Petr, Grudinin, Sergei

Journal:

Year:

2016

Language:

english

File:

PDF, 802 KB

english, 2016

35

A unified model based multifactor dimensionality reduction framework for detecting gene–gene interactions

Yu, Wenbao, Lee, Seungyeoun, Park, Taesung

Journal:

Year:

2016

Language:

english

File:

PDF, 321 KB

english, 2016

36

On cross-conditional and fluctuation correlations in competitive RNA networks

Sánchez-Taltavull, Daniel, MacLeod, Matthew, Perkins, Theodore J.

Journal:

Year:

2016

Language:

english

File:

PDF, 654 KB

english, 2016

37

LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs

Äijö, Tarmo, Yue, Xiaojing, Rao, Anjana, Lähdesmäki, Harri

Journal:

Year:

2016

Language:

english

File:

PDF, 616 KB

english, 2016

38

iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models

Sajitz-Hermstein, Max, Töpfer, Nadine, Kleessen, Sabrina, Fernie, Alisdair R., Nikoloski, Zoran

Journal:

Year:

2016

Language:

english

File:

PDF, 359 KB

english, 2016

39

A weighted exact test for mutually exclusive mutations in cancer

Leiserson, Mark D.M., Reyna, Matthew A., Raphael, Benjamin J.

Journal:

Year:

2016

Language:

english

File:

PDF, 670 KB

english, 2016

40

Edge-based sensitivity analysis of signaling networks by using Boolean dynamics

Trinh, Hung-Cuong, Kwon, Yung-Keun

Journal:

Year:

2016

Language:

english

File:

PDF, 936 KB

english, 2016

41

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries

Trappe, Kathrin, Marschall, Tobias, Renard, Bernhard Y.

Journal:

Year:

2016

Language:

english

File:

PDF, 414 KB

english, 2016

42

Estimating real cell size distribution from cross-section microscopy imaging

Lenz, Michael, Roumans, Nadia J.T., Vink, Roel G., van Baak, Marleen A., Mariman, Edwin C.M., Arts, Ilja C.W., de Kok, Theo M., Ertaylan, Gökhan

Journal:

Year:

2016

Language:

english

File:

PDF, 594 KB

english, 2016

43

XGSA: A statistical method for cross-species gene set analysis

Djordjevic, Djordje, Kusumi, Kenro, Ho, Joshua W. K.

Journal:

Year:

2016

Language:

english

File:

PDF, 765 KB

english, 2016

44

PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins

Tsirigos, Konstantinos D., Elofsson, Arne, Bagos, Pantelis G.

Journal:

Year:

2016

Language:

english

File:

PDF, 238 KB

english, 2016

45

4DGenome: a comprehensive database of chromatin interactions

Teng, Li, He, Bing, Wang, Jiahui, Tan, Kai

Journal:

Year:

2016

File:

PDF, 68 KB

2016

46

PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments

Hartonen, Tuomo, Sahu, Biswajyoti, Dave, Kashyap, Kivioja, Teemu, Taipale, Jussi

Journal:

Year:

2016

Language:

english

File:

PDF, 932 KB

english, 2016

47

Simulated linear test applied to quantitative proteomics

Pham, T.V., Jimenez, C.R.

Journal:

Year:

2016

Language:

english

File:

PDF, 763 KB

english, 2016

48

L 1 regularization facilitates detection of cell type-specific parameters in dynamical systems

Steiert, Bernhard, Timmer, Jens, Kreutz, Clemens

Journal:

Year:

2016

Language:

english

File:

PDF, 634 KB

english, 2016

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