Works matching IS 13674803 AND DT 2023 AND VI 39 AND IP 11

Results: 70

pyPESTO: a modular and scalable tool for parameter estimation for dynamic models.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad711

By:

Schälte, Yannik;
Fröhlich, Fabian;
Jost, Paul J;
Vanhoefer, Jakob;
Pathirana, Dilan;
Stapor, Paul;
Lakrisenko, Polina;
Wang, Dantong;
Raimúndez, Elba;
Merkt, Simon;
Schmiester, Leonard;
Städter, Philipp;
Grein, Stephan;
Dudkin, Erika;
Doresic, Domagoj;
Weindl, Daniel;
Hasenauer, Jan

Publication type:

Article

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

Published in:: 2023
Publication type:: Correction Notice

regioneReloaded: evaluating the association of multiple genomic region sets.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad704

By:

Malinverni, Roberto;
Corujo, David;
Gel, Bernat;
Buschbeck, Marcus

Publication type:

Article

Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad703

By:

Pfeifer, Bastian;
Chereda, Hryhorii;
Martin, Roman;
Saranti, Anna;
Clemens, Sandra;
Hauschild, Anne-Christin;
Beißbarth, Tim;
Holzinger, Andreas;
Heider, Dominik

Publication type:

Article

Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad702

By:

Konanov, Dmitry N;
Babenko, Vladislav V;
Belova, Aleksandra M;
Madan, Arina G;
Boldyreva, Daria I;
Glushenko, Oksana E;
Butenko, Ivan O;
Fedorov, Dmitry E;
Manolov, Alexander I;
Krivonos, Danil V;
Lazarev, Vassilii N;
Govorun, Vadim M;
Ilina, Elena N

Publication type:

Article

gmcoda: Graphical model for multiple compositional vectors in microbiome studies.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad700

By:

Fang, Huaying

Publication type:

Article

Examining DNA breathing with pyDNA-EPBD.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad699

By:

Kabir, Anowarul;
Bhattarai, Manish;
Rasmussen, Kim Ø;
Shehu, Amarda;
Usheva, Anny;
Bishop, Alan R;
Alexandrov, Boian

Publication type:

Article

BELB: a biomedical entity linking benchmark.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad698

By:

Garda, Samuele;
Weber-Genzel, Leon;
Martin, Robert;
Leser, Ulf

Publication type:

Article

Correction to: Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads.

Published in:: 2023
Publication type:: Correction Notice

Modified RNAs and predictions with the ViennaRNA Package.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad696

By:

Varenyk, Yuliia;
Spicher, Thomas;
Hofacker, Ivo L;
Lorenz, Ronny

Publication type:

Article

RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad695

By:

Xu, Xiaoming;
Yin, Zekun;
Yan, Lifeng;
Yi, Huiguang;
Wang, Hua;
Schmidt, Bertil;
Liu, Weiguo

Publication type:

Article

Molecular generation strategy and optimization based on A2C reinforcement learning in de novo drug design.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad693

By:

Wang, Qian;
Wei, Zhiqiang;
Hu, Xiaotong;
Wang, Zhuoya;
Dong, Yujie;
Liu, Hao

Publication type:

Article

PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad690

By:

Wu, Jun;
Ouyang, Jian;
Qin, Haipeng;
Zhou, Jiajia;
Roberts, Ruth;
Siam, Rania;
Wang, Lan;
Tong, Weida;
Liu, Zhichao;
Shi, Tieliu

Publication type:

Article

Integration of multiple terminology bases: a multi-view alignment method using the hierarchical structure.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad689

By:

Hu, Peihong;
Ye, Qi;
Zhang, Weiyan;
Liu, Jingping;
Ruan, Tong

Publication type:

Article

Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad678

By:

Fontanesi, Michele;
Micheli, Alessio;
Milazzo, Paolo;
Podda, Marco

Publication type:

Article

CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad687

By:

Rapakoulia, Trisevgeni;
Vargas, Sara Lopez Ruiz De;
Omgba, Persia Akbari;
Laupert, Verena;
Ulitsky, Igor;
Vingron, Martin

Publication type:

Article

PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad684

By:

Kaynar, Gun;
Cakmakci, Doruk;
Bund, Caroline;
Todeschi, Julien;
Namer, Izzie Jacques;
Cicek, A Ercument

Publication type:

Article

DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad683

By:

Wang, Junmin;
Novick, Steven

Publication type:

Article

IDESS: a toolbox for identification and automated design of stochastic gene circuits.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad682

By:

Sequeiros, Carlos;
Pájaro, Manuel;
Vázquez, Carlos;
Banga, Julio R;
Otero-Muras, Irene

Publication type:

Article

ReGeNNe: genetic pathway-based deep neural network using canonical correlation regularizer for disease prediction.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad679

By:

Sharma, Divya;
Xu, Wei

Publication type:

Article

BELMM: Bayesian model selection and random walk smoothing in time-series clustering.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad686

By:

Sarala, Olli;
Pyhäjärvi, Tanja;
Sillanpää, Mikko J

Publication type:

Article

AFRbase: a database of protein mutations responsible for antifungal resistance.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad677

By:

Jain, Aakriti;
Singhal, Neelja;
Kumar, Manish

Publication type:

Article

PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad676

By:

Feng, Zerong;
Feng, Jiejie;
Zhang, Baoyi;
Fei, Yuhan;
Zhang, Hongsheng;
Huang, Ji

Publication type:

Article

PyPCN: protein contact networks in PyMOL.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad675

By:

Rosignoli, Serena;
Paola, Luisa di;
Paiardini, Alessandro

Publication type:

Article

FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad674

By:

Alamoudi, Emad;
Schälte, Yannik;
Müller, Robert;
Starruß, Jörn;
Bundgaard, Nils;
Graw, Frederik;
Brusch, Lutz;
Hasenauer, Jan

Publication type:

Article

hipFG: high-throughput harmonization and integration pipeline for functional genomics data.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad673

By:

Cifello, Jeffrey;
Kuksa, Pavel P;
Saravanan, Naveensri;
Valladares, Otto;
Wang, Li-San;
Leung, Yuk Yee

Publication type:

Article

Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID).

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad661

By:

Gomez, Javier D;
Wall, Martha L;
Rahim, Mohsin;
Kambhampati, Shrikaar;
Evans, Bradley S;
Allen, Doug K;
Antoniewicz, Maciek R;
Young, Jamey D

Publication type:

Article

PROSTATA: a framework for protein stability assessment using transformers.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad671

By:

Umerenkov, Dmitriy;
Nikolaev, Fedor;
Shashkova, Tatiana I;
Strashnov, Pavel V;
Sindeeva, Maria;
Shevtsov, Andrey;
Ivanisenko, Nikita V;
Kardymon, Olga L

Publication type:

Article

aPEAR: an R package for autonomous visualization of pathway enrichment networks.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad672

By:

Kerseviciute, Ieva;
Gordevicius, Juozas

Publication type:

Article

RNA interaction format: a general data format for RNA interactions.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad665

By:

Schäfer, Richard A;
Rabsch, Dominik;
Scholz, Guillaume E;
Stadler, Peter F;
Hess, Wolfgang R;
Backofen, Rolf;
Fallmann, Jörg;
Voß, Björn

Publication type:

Article

SSLpheno: a self-supervised learning approach for gene–phenotype association prediction using protein–protein interactions and gene ontology data.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad662

By:

Bi, Xuehua;
Liang, Weiyang;
Zhao, Qichang;
Wang, Jianxin

Publication type:

Article

Correction to: CITEdb: a manually curated database of cell–cell interactions in human.

Published in:: 2023
Publication type:: Correction Notice

ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad659

By:

Schäfer, Richard A;
Guo, Qingxiang;
Yang, Rendong

Publication type:

Article

Inferring delays in partially observed gene regulation processes.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad670

By:

Hong, Hyukpyo;
Cortez, Mark Jayson;
Cheng, Yu-Yu;
Kim, Hang Joon;
Choi, Boseung;
Josić, Krešimir;
Kim, Jae Kyoung

Publication type:

Article

TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad663

By:

Sledzieski, Samuel;
Devkota, Kapil;
Singh, Rohit;
Cowen, Lenore;
Berger, Bonnie

Publication type:

Article

Compositional analysis of microbiome data using the linear decomposition model (LDM).

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad668

By:

Hu, Yi-Juan;
Satten, Glen A

Publication type:

Article

An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad667

By:

Nguyen, Dat Thanh

Publication type:

Article

Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad666

By:

Liao, Xinmeng;
Ozcan, Mehmet;
Shi, Mengnan;
Kim, Woonghee;
Jin, Han;
Li, Xiangyu;
Turkez, Hasan;
Achour, Adnane;
Uhlén, Mathias;
Mardinoglu, Adil;
Zhang, Cheng

Publication type:

Article

An evolution strategy approach for the balanced minimum evolution problem.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad660

By:

Gasparin, Andrea;
Verdù, Federico Julian Camerota;
Catanzaro, Daniele;
Castelli, Lorenzo

Publication type:

Article

ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad664

By:

Abbas, Zeeshan;
Rehman, Mobeen Ur;
Tayara, Hilal;
Chong, Kil To

Publication type:

Article

An automated model annotation system (AMAS) for SBML models.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad658

By:

Shin, Woosub;
Gennari, John H;
Hellerstein, Joseph L;
Sauro, Herbert M

Publication type:

Article

oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad657

By:

Ullrich, Kristian K;
Glytnasi, Nikoleta E

Publication type:

Article

Expanded utility of the R package, qgg, with applications within genomic medicine.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad656

By:

Rohde, Palle Duun;
Sørensen, Izel Fourie;
Sørensen, Peter

Publication type:

Article

EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad650

By:

Hou, Xiaoyang;
Wang, Yu;
Bu, Dongbo;
Wang, Yaojun;
Sun, Shiwei

Publication type:

Article

Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad655

By:

Shuey, Megan M;
Stead, William W;
Aka, Ida;
Barnado, April L;
Bastarache, Julie A;
Brokamp, Elly;
Campbell, Meredith;
Carroll, Robert J;
Goldstein, Jeffrey A;
Lewis, Adam;
Malow, Beth A;
Mosley, Jonathan D;
Osterman, Travis;
Padovani-Claudio, Dolly A;
Ramirez, Andrea;
Roden, Dan M;
Schuler, Bryce A;
Siew, Edward;
Sucre, Jennifer;
Thomsen, Isaac

Publication type:

Article

Hunting down zinc(II)-binding sites in proteins with distance matrices.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad653

By:

Laveglia, Vincenzo;
Bazayeva, Milana;
Andreini, Claudia;
Rosato, Antonio

Publication type:

Article

LexicHash: sequence similarity estimation via lexicographic comparison of hashes.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad652

By:

Greenberg, Grant;
Ravi, Aditya Narayan;
Shomorony, Ilan

Publication type:

Article

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad651

By:

Jin, Qiao;
Kim, Won;
Chen, Qingyu;
Comeau, Donald C;
Yeganova, Lana;
Wilbur, W John;
Lu, Zhiyong

Publication type:

Article

Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad644

By:

Oubounyt, Mhaned;
Adlung, Lorenz;
Patroni, Fabio;
Wenke, Nina Kerstin;
Maier, Andreas;
Hartung, Michael;
Baumbach, Jan;
Elkjaer, Maria L

Publication type:

Article

Automated exploitation of deep learning for cancer patient stratification across multiple types.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad654

By:

Sun, Pingping;
Fan, Shijie;
Li, Shaochuan;
Zhao, Yingwei;
Lu, Chang;
Wong, Ka-Chun;
Li, Xiangtao

Publication type:

Article