Volume 33; Issue 14

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Bioinformatics
Volume 33; Issue 14

Bioinformatics

Volume 33; Issue 14

1

MaBoSS 2.0: an environment for stochastic Boolean modeling

Stoll, Gautier, Caron, Barthélémy, Viara, Eric, Dugourd, Aurélien, Zinovyev, Andrei, Naldi, Aurélien, Kroemer, Guido, Barillot, Emmanuel, Calzone, Laurence

Journal:

Year:

2017

Language:

english

File:

PDF, 204 KB

english, 2017

2

Stepwise inference of likely dynamic flux distributions from metabolic time series data

Faraji, Mojdeh, Voit, Eberhard O.

Journal:

Year:

2017

Language:

english

File:

PDF, 681 KB

english, 2017

3

Deep learning with word embeddings improves biomedical named entity recognition

Habibi, Maryam, Weber, Leon, Neves, Mariana, Wiegandt, David Luis, Leser, Ulf

Journal:

Year:

2017

Language:

english

File:

PDF, 528 KB

english, 2017

4

TITER: predicting translation initiation sites by deep learning

Zhang, Sai, Hu, Hailin, Jiang, Tao, Zhang, Lei, Zeng, Jianyang

Journal:

Year:

2017

Language:

english

File:

PDF, 1.03 MB

english, 2017

5

Predicting multicellular function through multi-layer tissue networks

Zitnik, Marinka, Leskovec, Jure

Journal:

Year:

2017

Language:

english

File:

PDF, 1.37 MB

english, 2017

6

Molecular signatures that can be transferred across different omics platforms

Altenbuchinger, M., Schwarzfischer, P., Rehberg, T., Reinders, J., Kohler, Ch. W., Gronwald, W., Richter, J., Szczepanowski, M., Masqué-Soler, N., Klapper, W., Oefner, P. J., Spang, R.

Journal:

Year:

2017

Language:

english

File:

PDF, 796 KB

english, 2017

7

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph

Pandey, Prashant, Bender, Michael A., Johnson, Rob, Patro, Rob

Journal:

Year:

2017

Language:

english

File:

PDF, 371 KB

english, 2017

8

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

Min, Xu, Zeng, Wanwen, Chen, Ning, Chen, Ting, Jiang, Rui

Journal:

Year:

2017

Language:

english

File:

PDF, 790 KB

english, 2017

9

Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev

Fogg, Christiana N., Kovats, Diane E., Berger, Bonnie

Journal:

Year:

2017

Language:

english

File:

PDF, 142 KB

english, 2017

10

Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner

Fogg, Christiana N., Kovats, Diane E., Berger, Bonnie

Journal:

Year:

2017

Language:

english

File:

PDF, 92 KB

english, 2017

11

Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter

Fogg, Christiana N., Kovats, Diane E., Berger, Bonnie

Journal:

Year:

2017

Language:

english

File:

PDF, 83 KB

english, 2017

12

ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE

Journal:

Year:

2017

Language:

english

File:

PDF, 50 KB

english, 2017

13

ISMB/ECCB 2017 proceedings

Beerenwinkel, Niko, Bromberg, Yana

Journal:

Year:

2017

Language:

english

File:

PDF, 60 KB

english, 2017

14

Denoising genome-wide histone ChIP-seq with convolutional neural networks

Koh, Pang Wei, Pierson, Emma, Kundaje, Anshul

Journal:

Year:

2017

Language:

english

File:

PDF, 692 KB

english, 2017

15

Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes

Duong, Dat, Gai, Lisa, Snir, Sagi, Kang, Eun Yong, Han, Buhm, Sul, Jae Hoon, Eskin, Eleazar

Journal:

Year:

2017

Language:

english

File:

PDF, 422 KB

english, 2017

16

Multiple network-constrained regressions expand insights into influenza vaccination responses

Avey, Stefan, Mohanty, Subhasis, Wilson, Jean, Zapata, Heidi, Joshi, Samit R., Siconolfi, Barbara, Tsang, Sui, Shaw, Albert C., Kleinstein, Steven H.

Journal:

Year:

2017

Language:

english

File:

PDF, 452 KB

english, 2017

17

Abundance estimation and differential testing on strain level in metagenomics data

Fischer, Martina, Strauch, Benjamin, Renard, Bernhard Y.

Journal:

Year:

2017

Language:

english

File:

PDF, 297 KB

english, 2017

18

BIOSSES: a semantic sentence similarity estimation system for the biomedical domain

Soğancıoğlu, Gizem, Öztürk, Hakime, Özgür, Arzucan

Journal:

Year:

2017

Language:

english

File:

PDF, 433 KB

english, 2017

19

Exploiting sequence-based features for predicting enhancer–promoter interactions

Yang, Yang, Zhang, Ruochi, Singh, Shashank, Ma, Jian

Journal:

Year:

2017

Language:

english

File:

PDF, 577 KB

english, 2017

20

Tumor phylogeny inference using tree-constrained importance sampling

Satas, Gryte, Raphael, Benjamin J.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.96 MB

english, 2017

21

Discovery and genotyping of novel sequence insertions in many sequenced individuals

Kavak, Pınar, Lin, Yen-Yi, Numanagić, Ibrahim, Asghari, Hossein, Güngör, Tunga, Alkan, Can, Hach, Faraz

Journal:

Year:

2017

Language:

english

File:

PDF, 677 KB

english, 2017

22

Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis

Hao, Xiaoke, Li, Chanxiu, Yan, Jingwen, Yao, Xiaohui, Risacher, Shannon L., Saykin, Andrew J., Shen, Li, Zhang, Daoqiang

Journal:

Year:

2017

Language:

english

File:

PDF, 944 KB

english, 2017

23

A new method to study the change of miRNA–mRNA interactions due to environmental exposures

Petralia, Francesca, Aushev, Vasily N., Gopalakrishnan, Kalpana, Kappil, Maya, W. Khin, Nyan, Chen, Jia, Teitelbaum, Susan L., Wang, Pei

Journal:

Year:

2017

Language:

english

File:

PDF, 4.06 MB

english, 2017

24

Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression

Ammad-ud-din, Muhammad, Khan, Suleiman A., Wennerberg, Krister, Aittokallio, Tero

Journal:

Year:

2017

Language:

english

File:

PDF, 5.17 MB

english, 2017

25

Rectified factor networks for biclustering of omics data

Clevert, Djork-Arné, Unterthiner, Thomas, Povysil, Gundula, Hochreiter, Sepp

Journal:

Year:

2017

Language:

english

File:

PDF, 404 KB

english, 2017

26

popFBA: tackling intratumour heterogeneity with Flux Balance Analysis

Damiani, Chiara, Di Filippo, Marzia, Pescini, Dario, Maspero, Davide, Colombo, Riccardo, Mauri, Giancarlo

Journal:

Year:

2017

Language:

english

File:

PDF, 548 KB

english, 2017

27

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants

Pagel, Kymberleigh A, Pejaver, Vikas, Lin, Guan Ning, Nam, Hyun-Jun, Mort, Matthew, Cooper, David N, Sebat, Jonathan, Iakoucheva, Lilia M, Mooney, Sean D, Radivojac, Predrag

Journal:

Year:

2017

Language:

english

File:

PDF, 550 KB

english, 2017

28

CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions

Hallen, Mark A, Donald, Bruce R

Journal:

Year:

2017

Language:

english

File:

PDF, 447 KB

english, 2017

29

Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes

Nakatani, Yoichiro, McLysaght, Aoife

Journal:

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

30

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems

Pischel, Dennis, Sundmacher, Kai, Flassig, Robert J

Journal:

Year:

2017

Language:

english

File:

PDF, 958 KB

english, 2017

31

Alignment of dynamic networks

Vijayan, V, Critchlow, D, Milenković, T

Journal:

Year:

2017

Language:

english

File:

PDF, 823 KB

english, 2017

32

DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields

Shao, Mingfu, Ma, Jianzhu, Wang, Sheng

Journal:

Year:

2017

Language:

english

File:

PDF, 615 KB

english, 2017

33

Integrative deep models for alternative splicing

Jha, Anupama, Gazzara, Matthew R, Barash, Yoseph

Journal:

Year:

2017

Language:

english

File:

PDF, 590 KB

english, 2017

34

Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields

Robinson, Sean, Nevalainen, Jaakko, Pinna, Guillaume, Campalans, Anna, Radicella, J Pablo, Guyon, Laurent

Journal:

Year:

2017

Language:

english

File:

PDF, 978 KB

english, 2017

35

A scalable moment-closure approximation for large-scale biochemical reaction networks

Kazeroonian, Atefeh, Theis, Fabian J, Hasenauer, Jan

Journal:

Year:

2017

Language:

english

File:

PDF, 1.84 MB

english, 2017

36

Modelling haplotypes with respect to reference cohort variation graphs

Rosen, Yohei, Eizenga, Jordan, Paten, Benedict

Journal:

Year:

2017

Language:

english

File:

PDF, 505 KB

english, 2017

37

Association testing of bisulfite-sequencing methylation data via a Laplace approximation

Weissbrod, Omer, Rahmani, Elior, Schweiger, Regev, Rosset, Saharon, Halperin, Eran

Journal:

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

38

SnapDock—template-based docking by Geometric Hashing

Estrin, Michael, Wolfson, Haim J

Journal:

Year:

2017

Language:

english

File:

PDF, 542 KB

english, 2017

39

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Train, Clément-Marie, Glover, Natasha M, Gonnet, Gaston H, Altenhoff, Adrian M, Dessimoz, Christophe

Journal:

Year:

2017

Language:

english

File:

PDF, 1.35 MB

english, 2017

40

Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression

Ding, Lei, McDonald, Daniel J

Journal:

Year:

2017

Language:

english

File:

PDF, 528 KB

english, 2017

41

HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington’s epigenetic landscape

Guo, Jing, Zheng, Jie

Journal:

Year:

2017

Language:

english

File:

PDF, 668 KB

english, 2017

42

Improved data-driven likelihood factorizations for transcript abundance estimation

Zakeri, Mohsen, Srivastava, Avi, Almodaresi, Fatemeh, Patro, Rob

Journal:

Year:

2017

Language:

english

File:

PDF, 542 KB

english, 2017

43

Improving the performance of minimizers and winnowing schemes

Marçais, Guillaume, Pellow, David, Bork, Daniel, Orenstein, Yaron, Shamir, Ron, Kingsford, Carl

Journal:

Year:

2017

Language:

english

File:

PDF, 249 KB

english, 2017

44

Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms

Xu, Min, Chai, Xiaoqi, Muthakana, Hariank, Liang, Xiaodan, Yang, Ge, Zeev-Ben-Mordehai, Tzviya, Xing, Eric P

Journal:

Year:

2017

Language:

english

File:

PDF, 844 KB

english, 2017

45

Large-scale structure prediction by improved contact predictions and model quality assessment

Michel, Mirco, Menéndez Hurtado, David, Uziela, Karolis, Elofsson, Arne

Journal:

Year:

2017

Language:

english

File:

PDF, 635 KB

english, 2017

46

Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects

Lee, C H, Eskin, E, Han, B

Journal:

Year:

2017

Language:

english

File:

PDF, 291 KB

english, 2017

47

Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data

Cinquemani, Eugenio, Laroute, Valérie, Cocaign-Bousquet, Muriel, de Jong, Hidde, Ropers, Delphine

Journal:

Year:

2017

Language:

english

File:

PDF, 669 KB

english, 2017

48

Image-based spatiotemporal causality inference for protein signaling networks

Ruan, Xiongtao, Wülfing, Christoph, Murphy, Robert F

Journal:

Year:

2017

Language:

english

File:

PDF, 623 KB

english, 2017

49

Efficient approximations of RNA kinetics landscape using non-redundant sampling

Michálik, Juraj, Touzet, Hélène, Ponty, Yann

Journal:

Year:

2017

Language:

english

File:

PDF, 1.06 MB

english, 2017

50

miniMDS: 3D structural inference from high-resolution Hi-C data

Rieber, Lila, Mahony, Shaun

Journal:

Year:

2017

Language:

english

File:

PDF, 694 KB

english, 2017

51

Author Index

Journal:

Year:

2017

File:

PDF, 73 KB

2017

52

DextMP: deep dive into text for predicting moonlighting proteins

Khan, Ishita K, Bhuiyan, Mansurul, Kihara, Daisuke

Journal:

Year:

2017

Language:

english

File:

PDF, 436 KB

english, 2017

53

Direct AUC optimization of regulatory motifs

Zhu, Lin, Zhang, Hong-Bo, Huang, De-Shuang

Journal:

Year:

2017

File:

PDF, 527 KB

2017

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