Works matching IS 13674803 AND DT 2019 AND VI 35 AND IP 14

Results: 105

ISMB/ECCB 2019 PROCEEDINGS PAPERS COMMITTEE.

Published in:: Bioinformatics, 2019, v. 35, n. 14, p. i3, doi. 10.1093/bioinformatics/btz494
Publication type:: Article

Author Index.

Published in:: Bioinformatics, 2019, v. 35, n. 14, p. i643, doi. 10.1093/bioinformatics/btz510
Publication type:: Article

ISMB/ECCB 2019 Proceedings.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i1, doi. 10.1093/bioinformatics/btz439

By:

Bromberg, Yana;
El-Mabrouk, Nadia;
Radivojac, Predrag

Publication type:

Article

ShaKer: RNA SHAPE prediction using graph kernel.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i354, doi. 10.1093/bioinformatics/btz395

By:

Mautner, Stefan;
Montaseri, Soheila;
Miladi, Milad;
Raden, Martin;
Costa, Fabrizio;
Backofen, Rolf

Publication type:

Article

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i31, doi. 10.1093/bioinformatics/btz394

By:

Sayyari, Erfan;
Kawas, Ban;
Mirarab, Siavash

Publication type:

Article

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i436, doi. 10.1093/bioinformatics/btz363

By:

Sturm, Gregor;
Finotello, Francesca;
Petitprez, Florent;
Zhang, Jitao David;
Baumbach, Jan;
Fridman, Wolf H;
List, Markus;
Aneichyk, Tatsiana

Publication type:

Article

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i538, doi. 10.1093/bioinformatics/btz369

By:

Yin, Bojian;
Balvert, Marleen;
Spek, Rick A A van der;
Dutilh, Bas E;
Bohté, Sander;
Veldink, Jan;
Schönhuth, Alexander

Publication type:

Article

Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i360, doi. 10.1093/bioinformatics/btz368

By:

Sumanaweera, Dinithi;
Allison, Lloyd;
Konagurthu, Arun S

Publication type:

Article

Selfish: discovery of differential chromatin interactions via a self-similarity measure.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i145, doi. 10.1093/bioinformatics/btz362

By:

Ardakany, Abbas Roayaei;
Ay, Ferhat;
Lonardi, Stefano

Publication type:

Article

Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i324, doi. 10.1093/bioinformatics/btz336

By:

Wu, Jiansheng;
Liu, Ben;
Chan, Wallace K B;
Wu, Weijian;
Pang, Tao;
Hu, Haifeng;
Yan, Shancheng;
Ke, Xiaoyan;
Zhang, Yang

Publication type:

Article

MCS 2 : minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i615, doi. 10.1093/bioinformatics/btz393

By:

Miraskarshahi, Reza;
Zabeti, Hooman;
Stephen, Tamon;
Chindelevitch, Leonid

Publication type:

Article

Inference of clonal selection in cancer populations using single-cell sequencing data.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i398, doi. 10.1093/bioinformatics/btz392

By:

Skums, Pavel;
Tsyvina, Viachaslau;
Zelikovsky, Alex

Publication type:

Article

Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i586, doi. 10.1093/bioinformatics/btz378

By:

Marguet, Aline;
Lavielle, Marc;
Cinquemani, Eugenio

Publication type:

Article

Efficient merging of genome profile alignments.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i71, doi. 10.1093/bioinformatics/btz377

By:

Hennig, André;
Nieselt, Kay

Publication type:

Article

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i200, doi. 10.1093/bioinformatics/btz376

By:

Gao, Yan;
Liu, Bo;
Wang, Yadong;
Xing, Yi

Publication type:

Article

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i295, doi. 10.1093/bioinformatics/btz375

By:

Huang, Liang;
Zhang, He;
Deng, Dezhong;
Zhao, Kai;
Liu, Kaibo;
Hendrix, David A;
Mathews, David H

Publication type:

Article

NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i315, doi. 10.1093/bioinformatics/btz374

By:

Tagirdzhanov, Azat M;
Shlemov, Alexander;
Gurevich, Alexey

Publication type:

Article

Representation transfer for differentially private drug sensitivity prediction.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i218, doi. 10.1093/bioinformatics/btz373

By:

Niinimäki, Teppo;
Heikkilä, Mikko A;
Honkela, Antti;
Kaski, Samuel

Publication type:

Article

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i510, doi. 10.1093/bioinformatics/btz372

By:

Mourragui, Soufiane;
Loog, Marco;
Wiel, Mark A van de;
Reinders, Marcel J T;
Wessels, Lodewyk F A

Publication type:

Article

Controlling large Boolean networks with single-step perturbations.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i558, doi. 10.1093/bioinformatics/btz371

By:

Baudin, Alexis;
Paul, Soumya;
Su, Cui;
Pang, Jun

Publication type:

Article

Learning a mixture of microbial networks using minorization–maximization.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i23, doi. 10.1093/bioinformatics/btz370

By:

Tavakoli, Sahar;
Yooseph, Shibu

Publication type:

Article

DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i284, doi. 10.1093/bioinformatics/btz367

By:

Chen, Hao;
Shaw, Dipan;
Zeng, Jianyang;
Bu, Dongbo;
Jiang, Tao

Publication type:

Article

Model-based optimization of subgroup weights for survival analysis.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i484, doi. 10.1093/bioinformatics/btz361

By:

Richter, Jakob;
Madjar, Katrin;
Rahnenführer, Jörg

Publication type:

Article

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i183, doi. 10.1093/bioinformatics/btz366

By:

Yang, Hao;
Chi, Hao;
Zeng, Wen-Feng;
Zhou, Wen-Jing;
He, Si-Min

Publication type:

Article

Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i568, doi. 10.1093/bioinformatics/btz365

By:

Mukherjee, Sumit;
Perumal, Thanneer M;
Daily, Kenneth;
Sieberts, Solveig K;
Omberg, Larsson;
Preuss, Christoph;
Carter, Gregory W;
Mangravite, Lara M;
Logsdon, Benjamin A

Publication type:

Article

Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i260, doi. 10.1093/bioinformatics/btz364

By:

Lin, Ruogu;
Zeng, Xiangrui;
Kitani, Kris;
Xu, Min

Publication type:

Article

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i108, doi. 10.1093/bioinformatics/btz352

By:

Nair, Surag;
Kim, Daniel S;
Perricone, Jacob;
Kundaje, Anshul

Publication type:

Article

Modeling clinical and molecular covariates of mutational process activity in cancer.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i492, doi. 10.1093/bioinformatics/btz340

By:

Robinson, Welles;
Sharan, Roded;
Leiserson, Mark D M

Publication type:

Article

Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i154, doi. 10.1093/bioinformatics/btz338

By:

Handl, Lisa;
Jalali, Adrin;
Scherer, Michael;
Eggeling, Ralf;
Pfeifer, Nico

Publication type:

Article

Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i269, doi. 10.1093/bioinformatics/btz339

By:

Trabelsi, Ameni;
Chaabane, Mohamed;
Ben-Hur, Asa

Publication type:

Article

Reconstructing signaling pathways using regular language constrained paths.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i624, doi. 10.1093/bioinformatics/btz360

By:

Wagner, Mitchell J;
Pratapa, Aditya;
Murali, T M

Publication type:

Article

divide-and-conquer method for scalable phylogenetic network inference from multilocus data.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i370, doi. 10.1093/bioinformatics/btz359

By:

Zhu, Jiafan;
Liu, Xinhao;
Ogilvie, Huw A;
Nakhleh, Luay K

Publication type:

Article

Large scale microbiome profiling in the cloud.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i13, doi. 10.1093/bioinformatics/btz356

By:

Valdes, Camilo;
Stebliankin, Vitalii;
Narasimhan, Giri

Publication type:

Article

Collaborative intra-tumor heterogeneity detection.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i379, doi. 10.1093/bioinformatics/btz355

By:

Khakabimamaghani, Sahand;
Malikic, Salem;
Tang, Jeffrey;
Ding, Dujian;
Morin, Ryan;
Chindelevitch, Leonid;
Ester, Martin

Publication type:

Article

Locality-sensitive hashing for the edit distance.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i127, doi. 10.1093/bioinformatics/btz354

By:

Marçais, Guillaume;
DeBlasio, Dan;
Pandey, Prashant;
Kingsford, Carl

Publication type:

Article

Rotation equivariant and invariant neural networks for microscopy image analysis.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i530, doi. 10.1093/bioinformatics/btz353

By:

Chidester, Benjamin;
Zhou, Tianming;
Do, Minh N;
Ma, Jian

Publication type:

Article

Prediction of mRNA subcellular localization using deep recurrent neural networks.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i333, doi. 10.1093/bioinformatics/btz337

By:

Yan, Zichao;
Lécuyer, Eric;
Blanchette, Mathieu

Publication type:

Article

Minnow : a principled framework for rapid simulation of dscRNA-seq data at the read level.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i136, doi. 10.1093/bioinformatics/btz351

By:

Sarkar, Hirak;
Srivastava, Avi;
Patro, Rob

Publication type:

Article

Building large updatable colored de Bruijn graphs via merging.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i51, doi. 10.1093/bioinformatics/btz350

By:

Muggli, Martin D;
Alipanahi, Bahar;
Boucher, Christina

Publication type:

Article

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i61, doi. 10.1093/bioinformatics/btz349

By:

Tolstoganov, Ivan;
Bankevich, Anton;
Chen, Zhoutao;
Pevzner, Pavel A

Publication type:

Article

scOrange—a tool for hands-on training of concepts from single-cell data analytics.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i4, doi. 10.1093/bioinformatics/btz348

By:

Stražar, Martin;
Žagar, Lan;
Kokošar, Jaka;
Tanko, Vesna;
Erjavec, Aleš;
Poličar, Pavlin G;
Starič, Anže;
Demšar, Janez;
Shaulsky, Gad;
Menon, Vilas;
Lemire, Andrew;
Parikh, Anup;
Zupan, Blaž

Publication type:

Article

Efficient haplotype matching between a query and a panel for genealogical search.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i233, doi. 10.1093/bioinformatics/btz347

By:

Naseri, Ardalan;
Holzhauser, Erwin;
Zhi, Degui;
Zhang, Shaojie

Publication type:

Article

Alignment-free filtering for cfNA fusion fragments.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i225, doi. 10.1093/bioinformatics/btz346

By:

Yang, Xiao;
Saito, Yasushi;
Rao, Arjun;
Kim, Hyunsung John;
Singh, Pranav;
Scott, Eric;
Larson, Matthew;
Pan, Wenying;
Desai, Mohini;
Hubbell, Earl

Publication type:

Article

Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i208, doi. 10.1093/bioinformatics/btz345

By:

Guo, Dan;
Bemis, Kylie;
Rawlins, Catherine;
Agar, Jeffrey;
Vitek, Olga

Publication type:

Article

TreeMerge: a new method for improving the scalability of species tree estimation methods.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i417, doi. 10.1093/bioinformatics/btz344

By:

Molloy, Erin K;
Warnow, Tandy

Publication type:

Article

Large-scale mammalian genome rearrangements coincide with chromatin interactions.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i117, doi. 10.1093/bioinformatics/btz343

By:

Swenson, Krister M;
Blanchette, Mathieu

Publication type:

Article

Deep learning with multimodal representation for pancancer prognosis prediction.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i446, doi. 10.1093/bioinformatics/btz342

By:

Cheerla, Anika;
Gevaert, Olivier

Publication type:

Article

Fully-sensitive seed finding in sequence graphs using a hybrid index.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i81, doi. 10.1093/bioinformatics/btz341

By:

Ghaffaari, Ali;
Marschall, Tobias

Publication type:

Article

Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose–response experiments.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i464, doi. 10.1093/bioinformatics/btz335

By:

Labelle, Caroline;
Marinier, Anne;
Lemieux, Sébastien

Publication type:

Article

Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i605, doi. 10.1093/bioinformatics/btz334

By:

Tiuryn, Jerzy;
Szczurek, Ewa

Publication type:

Article