Works matching IS 13674803 AND DT 2021 AND VI 37 AND IP 17

Results: 51

COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2691, doi. 10.1093/bioinformatics/btab163

By:

Draghici, Sorin;
Nguyen, Tuan-Minh;
Sonna, Larry A.;
Ziraldo, Cordelia;
Vanciu, Radu;
Fadel, Raef;
Morrison, Austin;
Kenney, Rachel M.;
Alangaden, George;
Ramesh, Mayur;
Mor, Gil

Publication type:

Article

Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2659, doi. 10.1093/bioinformatics/btab171

By:

Alkan, Ferhat;
Silva, Joana;
Barberà, Eric Pintó;
Faller, William J.

Publication type:

Article

MUFFIN: multi-scale feature fusion for drug–drug interaction prediction.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2651, doi. 10.1093/bioinformatics/btab169

By:

Chen, Yujie;
Ma, Tengfei;
Yang, Xixi;
Wang, Jianmin;
Song, Bosheng;
Zeng, Xiangxiang

Publication type:

Article

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2589, doi. 10.1093/bioinformatics/btab165

By:

Singh, Jaswinder;
Paliwal, Kuldip;
Zhang, Tongchuan;
Singh, Jaspreet;
Litfin, Thomas;
Zhou, Yaoqi

Publication type:

Article

sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2644, doi. 10.1093/bioinformatics/btab164

By:

Andersson, Alma;
Lundeberg, Joakim

Publication type:

Article

MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2637, doi. 10.1093/bioinformatics/btab162

By:

Zheng, Zihao;
Mergaert, Aisha M.;
Ong, Irene M.;
Shelef, Miriam A.;
Newton, Michael A.

Publication type:

Article

Hummingbird: efficient performance prediction for executing genomic applications in the cloud.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2537, doi. 10.1093/bioinformatics/btab161

By:

Bahmani, Amir;
Xing, Ziye;
Krishnan, Vandhana;
Ray, Utsab;
Mueller, Frank;
Alavi, Amir;
Tsao, Philip S.;
Snyder, Michael P.;
Pan, Cuiping

Publication type:

Article

Conditional canonical correlation estimation based on covariates with random forests.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2714, doi. 10.1093/bioinformatics/btab158

By:

Alakuş, Cansu;
Larocque, Denis;
Jacquemont, Sébastien;
Barlaam, Fanny;
Martin, Charles-Olivier;
Agbogba, Kristian;
Lippé, Sarah;
Labbe, Aurélie

Publication type:

Article

KibioR & Kibio: a new architecture for next-generation data querying and sharing in big biology.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2706, doi. 10.1093/bioinformatics/btab157

By:

Ongaro-Carcy, Régis;
Scott-Boyer, Marie-Pier;
Dessemond, Adrien;
Belleau, François;
Leclercq, Mickael;
Périn, Olivier;
Droit, Arnaud

Publication type:

Article

Compact and evenly distributed k-mer binning for genomic sequences.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2563, doi. 10.1093/bioinformatics/btab156

By:

Nyström-Persson, Johan;
Keeble-Gagnère, Gabriel;
Zawad, Niamat

Publication type:

Article

Super-delta2: an enhanced differential expression analysis procedure for multi-group comparisons of RNA-seq data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2627, doi. 10.1093/bioinformatics/btab155

By:

Cui, Zihan;
Liu, Yuhang;
Zhang, Jinfeng;
Qiu, Xing

Publication type:

Article

Protein interaction interface region prediction by geometric deep learning.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2580, doi. 10.1093/bioinformatics/btab154

By:

Dai, Bowen;
Bailey-Kellogg, Chris

Publication type:

Article

Knowledge enhanced LSTM for coreference resolution on biomedical texts.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2699, doi. 10.1093/bioinformatics/btab153

By:

Li, Yufei;
Ma, Xiaoyong;
Zhou, Xiangyu;
Cheng, Pengzhen;
He, Kai;
Li, Chen

Publication type:

Article

DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2722, doi. 10.1093/bioinformatics/btab147

By:

Liu-Wei, Wang;
Kafkas, Şenay;
Chen, Jun;
Dimonaco, Nicholas J.;
Tegnér, Jesper;
Hoehndorf, Robert

Publication type:

Article

MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2757, doi. 10.1093/bioinformatics/btab078

By:

Hu, Kang;
Huang, Neng;
Zou, You;
Liao, Xingyu;
Wang, Jianxin

Publication type:

Article

BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2556, doi. 10.1093/bioinformatics/btab133

By:

Charoenkwan, Phasit;
Nantasenamat, Chanin;
Hasan, Md Mehedi;
Manavalan, Balachandran;
Shoombuatong, Watshara

Publication type:

Article

Proteo-chemometrics interaction fingerprints of protein–ligand complexes predict binding affinity.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2570, doi. 10.1093/bioinformatics/btab132

By:

Wang, Debby D.;
Xie, Haoran;
Yan, Hong

Publication type:

Article

ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2529, doi. 10.1093/bioinformatics/btab146

By:

Panta, Manisha;
Mishra, Avdesh;
Hoque, Md Tamjidul;
Atallah, Joel

Publication type:

Article

NIBNA: a network-based node importance approach for identifying breast cancer drivers.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2521, doi. 10.1093/bioinformatics/btab145

By:

Chaudhary, Mandar S.;
Pham, Vu V.H.;
Le, Thuc D.

Publication type:

Article

A modeling framework for embedding-based predictions for compound–viral protein activity.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2544, doi. 10.1093/bioinformatics/btab130

By:

Mall, Raghvendra;
Elbasir, Abdurrahman;
Almeer, Hossam;
Islam, Zeyaul;
Kolatkar, Prasanna R.;
Chawla, Sanjay;
Ullah, Ehsan

Publication type:

Article

Bipartite graph-based approach for clustering of cell lines by gene expression–drug response associations.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2617, doi. 10.1093/bioinformatics/btab143

By:

Chi, Calvin;
Ye, Yuting;
Chen, Bin;
Huang, Haiyan

Publication type:

Article

ASpli: integrative analysis of splicing landscapes through RNA-Seq assays.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2609, doi. 10.1093/bioinformatics/btab141

By:

Mancini, Estefania;
Rabinovich, Andres;
Iserte, Javier;
Yanovsky, Marcelo;
Chernomoretz, Ariel

Publication type:

Article

Integrative survival analysis of breast cancer with gene expression and DNA methylation data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2601, doi. 10.1093/bioinformatics/btab140

By:

Bichindaritz, Isabelle;
Liu, Guanghui;
Bartlett, Christopher

Publication type:

Article

CCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2513, doi. 10.1093/bioinformatics/btab139

By:

Yang, Fan;
Gleason, Kevin J.;
Wang, Jiebiao;
Duan, Jubao;
He, Xin;
Pierce, Brandon L.;
Chen, Lin S.

Publication type:

Article

Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2682, doi. 10.1093/bioinformatics/btab138

By:

Liu, Wen;
Li, Xiang;
Qi, Hong;
Wu, Yuning;
Qu, Jing;
Yin, Zhiyong;
Gao, Xuejuan;
Han, Aidong;
Shuai, Jianwei

Publication type:

Article

Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM).

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2730, doi. 10.1093/bioinformatics/btab136

By:

Patel, Lekha;
Williamson, David;
Owen, Dylan M.;
Cohen, Edward A. K.

Publication type:

Article

Using interpretable deep learning to model cancer dependencies.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2675, doi. 10.1093/bioinformatics/btab137

By:

Lin, Chih-Hsu;
Lichtarge, Olivier

Publication type:

Article

WgLink: reconstructing whole-genome viral haplotypes using L<sub>0</sub>+L<sub>1</sub>-regularization.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2744, doi. 10.1093/bioinformatics/btab076

By:

Cao, Chen;
Greenberg, Matthew;
Long, Quan

Publication type:

Article

Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2668, doi. 10.1093/bioinformatics/btab128

By:

Öksüz, Abdullah Çağlar;
Ayday, Erman;
Güdükbay, Uğur

Publication type:

Article

Crypt4GH: a file format standard enabling native access to encrypted data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2753, doi. 10.1093/bioinformatics/btab087

By:

Senf, Alexander;
Davies, Robert;
Haziza, Frédéric;
Marshall, John;
Troncoso-Pastoriza, Juan;
Hofmann, Oliver;
Keane, Thomas M.

Publication type:

Article

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2750, doi. 10.1093/bioinformatics/btab082

By:

Hepp, Benjamin;
Cunha, Violette Da;
Lorieux, Florence;
Oberto, Jacques

Publication type:

Article

Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2747, doi. 10.1093/bioinformatics/btab079

By:

Dérozier, Sandra;
Nicolas, Pierre;
Mäder, Ulrike;
Guérin, Cyprien

Publication type:

Article

RAD: a web application to identify region associated differentially expressed genes.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2741, doi. 10.1093/bioinformatics/btab075

By:

Guo, Yixin;
Xue, Ziwei;
Yuan, Ruihong;
Li, Jingyi Jessica;
Pastor, William A.;
Liu, Wanlu

Publication type:

Article

rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2755, doi. 10.1093/bioinformatics/btab073

By:

Schwarz, Marek;
Vohradský, Jiří;
Pánek, Josef

Publication type:

Article

Viral Host Range database, an online tool for recording, analyzing and disseminating virus–host interactions.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2798, doi. 10.1093/bioinformatics/btab070

By:

Lamy-Besnier, Quentin;
Brancotte, Bryan;
Brancotte;
Ménager, Hervé;
Ménager;
Debarbieux, Laurent

Publication type:

Article

Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2770, doi. 10.1093/bioinformatics/btab065

By:

Borges, Hélène;
Hesse, Anne-Marie;
Kraut, Alexandra;
Couté, Yohann;
Brun, Virginie;
Burger, Thomas

Publication type:

Article

BioCommons: a robust java library for RNA structural bioinformatics.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2766, doi. 10.1093/bioinformatics/btab069

By:

Zok, Tomasz

Publication type:

Article

Epidemiological modeling in StochSS Live!

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2787, doi. 10.1093/bioinformatics/btab061

By:

Jiang, Richard;
Jacob, Bruno;
Geiger, Matthew;
Matthew, Sean;
Rumsey, Bryan;
Singh, Prashant;
Wrede, Fredrik;
Yi, Tau-Mu;
Drawert, Brian;
Hellander, Andreas;
Petzold, Linda

Publication type:

Article

M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2785, doi. 10.1093/bioinformatics/btab060

By:

Weglarz-Tomczak, Ewelina;
Tomczak, Jakub M.;
Brul, Stanley

Publication type:

Article

wiSDOM: a visual and statistical analytics for interrogating microbiome.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2795, doi. 10.1093/bioinformatics/btab057

By:

Su, Shih-Chi;
Galvin, James E.;
Yang, Shun-Fa;
Chung, Wen-Hung;
Chang, Lun-Ching

Publication type:

Article

Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2782, doi. 10.1093/bioinformatics/btab058

By:

Pietzsch, Tobias;
Duso, Lorenzo;
Zechner, Christoph

Publication type:

Article

ConPlot: web-based application for the visualization of protein contact maps integrated with other data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2763, doi. 10.1093/bioinformatics/btab049

By:

Rodríguez, Filomeno Sánchez;
Mesdaghi, Shahram;
Simpkin, Adam J.;
Burgos-Mármol, J. Javier;
Murphy, David L.;
Uski, Ville;
Keegan, Ronan M.;
Rigden, Daniel J.

Publication type:

Article

mzRecal: universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2768, doi. 10.1093/bioinformatics/btab056

By:

Marissen, Rob;
Palmblad, Magnus

Publication type:

Article

HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2792, doi. 10.1093/bioinformatics/btab042

By:

Weber, Leon;
Sänger, Mario;
Münchmeyer, Jannes;
Habibi, Maryam;
Leser, Ulf;
Akbik, Alan

Publication type:

Article

Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2772, doi. 10.1093/bioinformatics/btab046

By:

Wang, Di;
Jing, Zheng;
He, Kevin;
Garmire, Lana X.

Publication type:

Article

Mercator: a pipeline for multi-method, unsupervised visualization and distance generation.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2780, doi. 10.1093/bioinformatics/btab037

By:

Abrams, Zachary B.;
Coombes, Caitlin E.;
Li, Suli;
Coombes, Kevin R.

Publication type:

Article

mlr3proba: an R package for machine learning in survival analysis.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2789, doi. 10.1093/bioinformatics/btab039

By:

Sonabend, Raphael;
Király, Franz J.;
Bender, Andreas;
Bischl, Bernd;
Lang, Michel

Publication type:

Article

DNAModAnnot: a R toolbox for DNA modification filtering and annotation.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2738, doi. 10.1093/bioinformatics/btab032

By:

Hardy, Alexis;
Matelot, Mélody;
Touzeau, Amandine;
Klopp, Christophe;
Lopez-Roques, Céline;
Duharcourt, Sandra;
Defrance, Matthieu

Publication type:

Article

CoRC: the COPASI R Connector.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2778, doi. 10.1093/bioinformatics/btab033

By:

Förster, Jonas;
Bergmann, Frank T.;
Pahle, Jürgen

Publication type:

Article

PrInCE: an R/Bioconductor package for protein–protein interaction network inference from co-fractionation mass spectrometry data.

Published in:

Bioinformatics, 2021, v. 37, n. 17, p. 2775, doi. 10.1093/bioinformatics/btab022

By:

Skinnider, Michael A.;
Cai, Charley;
Stacey, R. Greg;
Foster, Leonard J.

Publication type:

Article