Works matching IS 13674803 AND DT 2022 AND VI 38 AND IP 8

Results: 45

PCIG: a web-based application to explore immune–genomics interactions across cancer types.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2374, doi. 10.1093/bioinformatics/btac111

By:

Pedrola, Anna;
Franch-Expósito, Sebastià;
Lahoz, Sara;
Esteban-Fabró, Roger;
Dienstmann, Rodrigo;
Bassaganyas, Laia;
Camps, Jordi

Publication type:

Article

Integrated Genome Browser App Store.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2348, doi. 10.1093/bioinformatics/btac109

By:

Shanbhag, Sameer;
Patil, Riddhi;
Zahara, Noor;
Shetty, Chirag;
Weidenhammer, Rachel;
Watharkar, Sneha;
Tambvekar, Pranav;
Badzuh, Philip P;
Dias, Chester;
Vankayala, Narendra;
Kulkarni, Prutha;
Vallapureddy, Charan;
Kulkarni, Shamika;
Nikhare, Pooja;
Freese, Nowlan H;
Loraine, Ann E

Publication type:

Article

NeuCA web server: a neural network-based cell annotation tool with web-app and GUI.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2361, doi. 10.1093/bioinformatics/btac108

By:

Duan, Daoyu;
He, Sijia;
Huang, Emina;
Li, Ziyi;
Feng, Hao

Publication type:

Article

PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2135, doi. 10.1093/bioinformatics/btac106

By:

Zhang, Jun;
Yan, Ke;
Chen, Qingcai;
Liu, Bin

Publication type:

Article

TransformerGO: predicting protein–protein interactions by modelling the attention between sets of gene ontology terms.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2269, doi. 10.1093/bioinformatics/btac104

By:

Ieremie, Ioan;
Ewing, Rob M;
Niranjan, Mahesan

Publication type:

Article

Fast and accurate gene regulatory network inference by normalized least squares regression.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2263, doi. 10.1093/bioinformatics/btac103

By:

Hillerton, Thomas;
Seçilmiş, Deniz;
Nelander, Sven;
Sonnhammer, Erik L L

Publication type:

Article

Pre-training graph neural networks for link prediction in biomedical networks.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2254, doi. 10.1093/bioinformatics/btac100

By:

Long, Yahui;
Wu, Min;
Liu, Yong;
Fang, Yuan;
Kwoh, Chee Keong;
Chen, Jinmiao;
Luo, Jiawei;
Li, Xiaoli

Publication type:

Article

scGAC: a graph attentional architecture for clustering single-cell RNA-seq data.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2187, doi. 10.1093/bioinformatics/btac099

By:

Cheng, Yi;
Ma, Xiuli

Publication type:

Article

mzMD: visualization-oriented MS data storage and retrieval.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2333, doi. 10.1093/bioinformatics/btac098

By:

Yang, Runmin;
Ma, Jingjing;
Zhang, Shu;
Zheng, Yu;
Wang, Lusheng;
Zhu, Daming

Publication type:

Article

SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2369, doi. 10.1093/bioinformatics/btac097

By:

Knapp, Adam C;
Vieira, Luis Sordo;
Laubenbacher, Reinhard;
Chifman, Julia

Publication type:

Article

CNGPLD: case–control copy-number analysis using Gaussian process latent difference.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2096, doi. 10.1093/bioinformatics/btac096

By:

Shih, David J H;
Li, Ruoxing;
Müller, Peter;
Zheng, W Jim;
Do, Kim-Anh;
Lin, Shiaw-Yih;
Carter, Scott L

Publication type:

Article

ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2194, doi. 10.1093/bioinformatics/btac095

By:

Heydari, A Ali;
Davalos, Oscar A;
Zhao, Lihong;
Hoyer, Katrina K;
Sindi, Suzanne S

Publication type:

Article

Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2315, doi. 10.1093/bioinformatics/btac094

By:

Yao, Junfeng;
Sun, Wen;
Jian, Zhongquan;
Wu, Qingqiang;
Wang, Xiaoli

Publication type:

Article

riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2358, doi. 10.1093/bioinformatics/btac093

By:

Cope, Alexander L;
Anderson, Felicity;
Favate, John;
Jackson, Michael;
Mok, Amanda;
Kurowska, Anna;
Liu, Junchen;
MacKenzie, Emma;
Shivakumar, Vikram;
Tilton, Peter;
Winterbourne, Sophie M;
Xue, Siyin;
Kavoussanakis, Kostas;
Lareau, Liana F;
Shah, Premal;
Wallace, Edward W J

Publication type:

Article

MetaMutationalSigs: comparison of mutational signature refitting results made easy.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2344, doi. 10.1093/bioinformatics/btac091

By:

Pandey, Palash;
Arora, Sanjeevani;
Rosen, Gail L

Publication type:

Article

HIV-1 drug resistance profiling using amino acid sequence space cartography.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2307, doi. 10.1093/bioinformatics/btac090

By:

Pikalyova, Karina;
Orlov, Alexey;
Lin, Arkadii;
Tarasova, Olga;
Marcou, MarcouGilles;
Horvath, Dragos;
Poroikov, Vladimir;
Varnek, Alexandre

Publication type:

Article

Reconstructing viral haplotypes using long reads.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2127, doi. 10.1093/bioinformatics/btac089

By:

Cai, Dehan;
Sun, Yanni

Publication type:

Article

Multi-level attention graph neural network based on co-expression gene modules for disease diagnosis and prognosis.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2178, doi. 10.1093/bioinformatics/btac088

By:

Xing, Xiaohan;
Yang, Fan;
Li, Hang;
Zhang, Jun;
Zhao, Yu;
Gao, Mingxuan;
Huang, Junzhou;
Yao, Jianhua

Publication type:

Article

Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2341, doi. 10.1093/bioinformatics/btac087

By:

Wagner, Naama;
Avram, Oren;
Gold-Binshtok, Dafna;
Zerah, Ben;
Teper, Doron;
Pupko, Tal

Publication type:

Article

Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2297, doi. 10.1093/bioinformatics/btac086

By:

Irlmeier, Rebecca;
Hughey, Jacob J;
Bastarache, Lisa;
Denny, Joshua C;
Chen, Qingxia

Publication type:

Article

Multimodal reasoning based on knowledge graph embedding for specific diseases.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2235, doi. 10.1093/bioinformatics/btac085

By:

Zhu, Chaoyu;
Yang, Zhihao;
Xia, Xiaoqiong;
Li, Nan;
Zhong, Fan;
Liu, Lei

Publication type:

Article

Optimal transport improves cell–cell similarity inference in single-cell omics data.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2169, doi. 10.1093/bioinformatics/btac084

By:

Huizing, Geert-Jan;
Peyré, Gabriel;
Cantini, Laura

Publication type:

Article

EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2119, doi. 10.1093/bioinformatics/btac083

By:

Kirchoff, Kathryn E;
Gomez, Shawn M

Publication type:

Article

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2367, doi. 10.1093/bioinformatics/btac082

By:

Heinken, Almut;
Thiele, Ines

Publication type:

Article

SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2088, doi. 10.1093/bioinformatics/btac081

By:

Medeiros, Jessie J F;
Capo-Chichi, Jose-Mario;
Shlush, Liran I;
Dick, John E;
Arruda, Andrea;
Minden, Mark D;
Abelson, Sagi

Publication type:

Article

MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2287, doi. 10.1093/bioinformatics/btac080

By:

Moon, Sehwan;
Lee, Hyunju

Publication type:

Article

GMNN2CD: identification of circRNA–disease associations based on variational inference and graph Markov neural networks.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2246, doi. 10.1093/bioinformatics/btac079

By:

Niu, Mengting;
Zou, Quan;
Wang, Chunyu

Publication type:

Article

PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2162, doi. 10.1093/bioinformatics/btac078

By:

Li, Pengpai;
Liu, Zhi-Ping

Publication type:

Article

PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2226, doi. 10.1093/bioinformatics/btac077

By:

Yan, Cheng;
Duan, Guihua;
Li, Na;
Zhang, Lishen;
Wu, Fang-Xiang;
Wang, Jianxin

Publication type:

Article

blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2356, doi. 10.1093/bioinformatics/btac076

By:

Lachmann, Alexander;
Xie, Zhuorui;
Ma'ayan, Avi

Publication type:

Article

RF-Net 2: fast inference of virus reassortment and hybridization networks.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2144, doi. 10.1093/bioinformatics/btac075

By:

Markin, Alexey;
Wagle, Sanket;
Anderson, Tavis K;
Eulenstein, Oliver

Publication type:

Article

Identify connectome between genotypes and brain network phenotypes via deep self-reconstruction sparse canonical correlation analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2323, doi. 10.1093/bioinformatics/btac074

By:

Wang, Meiling;
Shao, Wei;
Hao, Xiaoke;
Huang, Shuo;
Zhang, Daoqiang

Publication type:

Article

reinforcement learning framework for pooled oligonucleotide design.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2219, doi. 10.1093/bioinformatics/btac073

By:

David, Benjamin M;
Wyllie, Ryan M;
Harouaka, Ramdane;
Jensen, Paul A

Publication type:

Article

pyFoldX: enabling biomolecular analysis and engineering along structural ensembles.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2353, doi. 10.1093/bioinformatics/btac072

By:

Radusky, Leandro G;
Serrano, Luis

Publication type:

Article

PIPENN: protein interface prediction from sequence with an ensemble of neural nets.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2111, doi. 10.1093/bioinformatics/btac071

By:

Stringer, Bas;
Ferrante, Hans de;
Abeln, Sanne;
Heringa, Jaap;
Feenstra, K Anton;
Haydarlou, Reza

Publication type:

Article

Efficient privacy-preserving whole-genome variant queries.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2202, doi. 10.1093/bioinformatics/btac070

By:

Akgün, Mete;
Pfeifer, Nico;
Kohlbacher, Oliver

Publication type:

Article

UbE3-APA: a bioinformatic strategy to elucidate ubiquitin E3 ligase activities in quantitative proteomics study.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2211, doi. 10.1093/bioinformatics/btac069

By:

Gong, Yao;
Chen, Yue

Publication type:

Article

LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2371, doi. 10.1093/bioinformatics/btac068

By:

Ott, Simon;
Barbosa-Silva, Adriano;
Samwald, Matthias

Publication type:

Article

DOMINO web-server for active module identification analysis.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2364, doi. 10.1093/bioinformatics/btac067

By:

Levi, Hagai;
Rahmanian, Nima;
Elkon, Ran;
Shamir, Ron

Publication type:

Article

Performance optimization in DNA short-read alignment.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2081, doi. 10.1093/bioinformatics/btac066

By:

Wilton, Richard;
Szalay, Alexander S

Publication type:

Article

Federated Random Forests can improve local performance of predictive models for various healthcare applications.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2278, doi. 10.1093/bioinformatics/btac065

By:

Hauschild, Anne-Christin;
Lemanczyk, Marta;
Matschinske, Julian;
Frisch, Tobias;
Zolotareva, Olga;
Holzinger, Andreas;
Baumbach, Jan;
Heider, Dominik

Publication type:

Article

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2350, doi. 10.1093/bioinformatics/btac062

By:

Penel, Simon;
Menet, Hugo;
Tricou, Théo;
Daubin, Vincent;
Tannier, Eric

Publication type:

Article

CICLOP: a robust and accurate computational framework for protein inner cavity detection.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2153, doi. 10.1093/bioinformatics/btac061

By:

Garg, Parth;
Sacher, Sukriti;
Mrinal;
Atul;
Gautam, Prutyay;
Ray, Arjun

Publication type:

Article

Srinivasan (1962–2021) in Bioinformatics and beyond.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2377, doi. 10.1093/bioinformatics/btac054

By:

Gromiha, M Michael;
Orengo, Christine A;
Sowdhamini, Ramanathan;
Thornton, and Janet M

Publication type:

Article

ProteinBERT: a universal deep-learning model of protein sequence and function.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2102, doi. 10.1093/bioinformatics/btac020

By:

Brandes, Nadav;
Ofer, Dan;
Peleg, Yam;
Rappoport, Nadav;
Linial, Michal

Publication type:

Article