Volume 32; Issue 12

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Bioinformatics
Volume 32; Issue 12

Bioinformatics

Volume 32; Issue 12

1

Fast metabolite identification with Input Output Kernel Regression

Brouard, Céline, Shen, Huibin, Dührkop, Kai, d'Alché-Buc, Florence, Böcker, Sebastian, Rousu, Juho

Journal:

Year:

2016

Language:

english

File:

PDF, 524 KB

english, 2016

2

Classifying and segmenting microscopy images with deep multiple instance learning

Kraus, Oren Z., Ba, Jimmy Lei, Frey, Brendan J.

Journal:

Year:

2016

Language:

english

File:

PDF, 970 KB

english, 2016

3

An integer programming framework for inferring disease complexes from network data

Mazza, Arnon, Klockmeier, Konrad, Wanker, Erich, Sharan, Roded

Journal:

Year:

2016

Language:

english

File:

PDF, 1.64 MB

english, 2016

4

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

Glicksberg, Benjamin S., Li, Li, Badgeley, Marcus A., Shameer, Khader, Kosoy, Roman, Beckmann, Noam D., Pho, Nam, Hakenberg, Jörg, Ma, Meng, Ayers, Kristin L., Hoffman, Gabriel E., Dan Li, Shuyu, Scha

Journal:

Year:

2016

Language:

english

File:

PDF, 4.46 MB

english, 2016

5

A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps

Hu, Xihao, Shi, Christina Huan, Yip, Kevin Y.

Journal:

Year:

2016

Language:

english

File:

PDF, 671 KB

english, 2016

6

DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

Yuan, Qingjun, Gao, Junning, Wu, Dongliang, Zhang, Shihua, Mamitsuka, Hiroshi, Zhu, Shanfeng

Journal:

Year:

2016

Language:

english

File:

PDF, 583 KB

english, 2016

7

Reconstructing the temporal progression of HIV-1 immune response pathways

Jain, Siddhartha, Arrais, Joel, Venkatachari, Narasimhan J., Ayyavoo, Velpandi, Bar-Joseph, Ziv

Journal:

Year:

2016

Language:

english

File:

PDF, 3.28 MB

english, 2016

8

Linear effects models of signaling pathways from combinatorial perturbation data

Szczurek, Ewa, Beerenwinkel, Niko

Journal:

Year:

2016

Language:

english

File:

PDF, 1.03 MB

english, 2016

9

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

Srivastava, Avi, Sarkar, Hirak, Gupta, Nitish, Patro, Rob

Journal:

Year:

2016

Language:

english

File:

PDF, 373 KB

english, 2016

10

What time is it? Deep learning approaches for circadian rhythms

Agostinelli, Forest, Ceglia, Nicholas, Shahbaba, Babak, Sassone-Corsi, Paolo, Baldi, Pierre

Journal:

Year:

2016

Language:

english

File:

PDF, 1.07 MB

english, 2016

11

Analysis of aggregated cell–cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells

Schissler, A. Grant, Li, Qike, Chen, James L., Kenost, Colleen, Achour, Ikbel, Billheimer, D. Dean, Li, Haiquan, Piegorsch, Walter W., Lussier, Yves A.

Journal:

Year:

2016

Language:

english

File:

PDF, 748 KB

english, 2016

12

Convolutional neural network architectures for predicting DNA–protein binding

Zeng, Haoyang, Edwards, Matthew D., Liu, Ge, Gifford, David K.

Journal:

Year:

2016

Language:

english

File:

PDF, 477 KB

english, 2016

13

Prediction of ribosome footprint profile shapes from transcript sequences

Liu, Tzu-Yu, Song, Yun S.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.14 MB

english, 2016

14

Faster and more accurate graphical model identification of tandem mass spectra using trellises

Wang, Shengjie, Halloran, John T., Bilmes, Jeff A., Noble, William S.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.98 MB

english, 2016

15

A novel algorithm for calling mRNA m 6 A peaks by modeling biological variances in MeRIP-seq data

Cui, Xiaodong, Meng, Jia, Zhang, Shaowu, Chen, Yidong, Huang, Yufei

Journal:

Year:

2016

Language:

english

File:

PDF, 800 KB

english, 2016

16

Analysis of differential splicing suggests different modes of short-term splicing regulation

Topa, Hande, Honkela, Antti

Journal:

Year:

2016

Language:

english

File:

PDF, 3.09 MB

english, 2016

17

RCK: accurate and efficient inference of sequence- and structure-based protein–RNA binding models from RNAcompete data

Orenstein, Yaron, Wang, Yuhao, Berger, Bonnie

Journal:

Year:

2016

Language:

english

File:

PDF, 1017 KB

english, 2016

18

Read-based phasing of related individuals

Garg, Shilpa, Martin, Marcel, Marschall, Tobias

Journal:

Year:

2016

Language:

english

File:

PDF, 385 KB

english, 2016

19

DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences

Meng, Fanchi, Kurgan, Lukasz

Journal:

Year:

2016

Language:

english

File:

PDF, 938 KB

english, 2016

20

DeepMeSH: deep semantic representation for improving large-scale MeSH indexing

Peng, Shengwen, You, Ronghui, Wang, Hongning, Zhai, Chengxiang, Mamitsuka, Hiroshi, Zhu, Shanfeng

Journal:

Year:

2016

Language:

english

File:

PDF, 417 KB

english, 2016

21

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

Jo, Kyuri, Jung, Inuk, Moon, Ji Hwan, Kim, Sun

Journal:

Year:

2016

Language:

english

File:

PDF, 576 KB

english, 2016

22

RNAiFold2T: Constraint Programming design of thermo-IRES switches

Garcia-Martin, Juan Antonio, Dotu, Ivan, Fernandez-Chamorro, Javier, Lozano, Gloria, Ramajo, Jorge, Martinez-Salas, Encarnacion, Clote, Peter

Journal:

Year:

2016

Language:

english

File:

PDF, 661 KB

english, 2016

23

A network-driven approach for genome-wide association mapping

Lee, Seunghak, Kong, Soonho, Xing, Eric P.

Journal:

Year:

2016

Language:

english

File:

PDF, 993 KB

english, 2016

24

A cross-species bi-clustering approach to identifying conserved co-regulated genes

Sun, Jiangwen, Jiang, Zongliang, Tian, Xiuchun, Bi, Jinbo

Journal:

Year:

2016

Language:

english

File:

PDF, 482 KB

english, 2016

25

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction

He, Dan, Kuhn, David, Parida, Laxmi

Journal:

Year:

2016

Language:

english

File:

PDF, 467 KB

english, 2016

26

A convex optimization approach for identification of human tissue-specific interactomes

Mohammadi, Shahin, Grama, Ananth

Journal:

Year:

2016

Language:

english

File:

PDF, 1.59 MB

english, 2016

27

deBWT: parallel construction of Burrows–Wheeler Transform for large collection of genomes with de Bruijn-branch encoding

Liu, Bo, Zhu, Dixian, Wang, Yadong

Journal:

Year:

2016

Language:

english

File:

PDF, 416 KB

english, 2016

28

Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction

Tabei, Yasuo, Yamanishi, Yoshihiro, Kotera, Masaaki

Journal:

Year:

2016

Language:

english

File:

PDF, 852 KB

english, 2016

29

Jumping across biomedical contexts using compressive data fusion

Zitnik, Marinka, Zupan, Blaz

Journal:

Year:

2016

Language:

english

File:

PDF, 1.41 MB

english, 2016

30

BioASF: a framework for automatically generating executable pathway models specified in BioPAX

Haydarlou, Reza, Jacobsen, Annika, Bonzanni, Nicola, Feenstra, K. Anton, Abeln, Sanne, Heringa, Jaap

Journal:

Year:

2016

Language:

english

File:

PDF, 1.09 MB

english, 2016

31

PHOCOS: inferring multi-feature phenotypic crosstalk networks

Deng, Yue, Altschuler, Steven J., Wu, Lani F.

Journal:

Year:

2016

Language:

english

File:

PDF, 826 KB

english, 2016

32

Finding correct protein–protein docking models using ProQDock

Basu, Sankar, Wallner, Björn

Journal:

Year:

2016

Language:

english

File:

PDF, 719 KB

english, 2016

33

phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats

Schaeffer, Carly E., Figueroa, Nathaniel D., Liu, Xiaolin, Karro, John E.

Journal:

Year:

2016

Language:

english

File:

PDF, 257 KB

english, 2016

34

An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree

Journal:

Year:

2016

Language:

english

File:

PDF, 250 KB

english, 2016

35

Structure-based prediction of transcription factor binding specificity using an integrative energy function

Farrel, Alvin, Murphy, Jonathan, Guo, Jun-tao

Journal:

Year:

2016

Language:

english

File:

PDF, 914 KB

english, 2016

36

Genome assembly from synthetic long read clouds

Kuleshov, Volodymyr, Snyder, Michael P., Batzoglou, Serafim

Journal:

Year:

2016

Language:

english

File:

PDF, 296 KB

english, 2016

37

CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

Cui, Xuefeng, Lu, Zhiwu, Wang, Sheng, Jing-Yan Wang, Jim, Gao, Xin

Journal:

Year:

2016

Language:

english

File:

PDF, 638 KB

english, 2016

38

Using genomic annotations increases statistical power to detect eGenes

Duong, Dat, Zou, Jennifer, Hormozdiari, Farhad, Sul, Jae Hoon, Ernst, Jason, Han, Buhm, Eskin, Eleazar

Journal:

Year:

2016

Language:

english

File:

PDF, 457 KB

english, 2016

39

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing

Tsuchiya, Mariko, Amano, Kojiro, Abe, Masaya, Seki, Misato, Hase, Sumitaka, Sato, Kengo, Sakakibara, Yasubumi

Journal:

Year:

2016

Language:

english

File:

PDF, 479 KB

english, 2016

40

Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

Intosalmi, Jukka, Nousiainen, Kari, Ahlfors, Helena, Lähdesmäki, Harri

Journal:

Year:

2016

Language:

english

File:

PDF, 584 KB

english, 2016

41

Compacting de Bruijn graphs from sequencing data quickly and in low memory

Chikhi, Rayan, Limasset, Antoine, Medvedev, Paul

Journal:

Year:

2016

Language:

english

File:

PDF, 384 KB

english, 2016

42

ISMB 2016 Proceedings Papers Committee

Journal:

Year:

2016

Language:

english

File:

PDF, 68 KB

english, 2016

43

Author Index

Journal:

Year:

2016

Language:

english

File:

PDF, 43 KB

english, 2016

44

ISMB 2016 Proceedings

Baldi, Pierre, Przytycka, Teresa

Journal:

Year:

2016

Language:

english

File:

PDF, 58 KB

english, 2016