Works matching IS 13674803 AND DT 2024 AND VI 40 AND IP 9

Results: 42

Dynamic category-sensitive hypergraph inferring and homo-heterogeneous neighbor feature learning for drug-related microbe prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae562

By:

Xuan, Ping;
Xu, Zelong;
Cui, Hui;
Gu, Jing;
Liu, Cheng;
Zhang, Tiangang;
Wu, Peiliang

Publication type:

Article

Biomedical knowledge graph-optimized prompt generation for large language models.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae560

By:

Soman, Karthik;
Rose, Peter W;
Morris, John H;
Akbas, Rabia E;
Smith, Brett;
Peetoom, Braian;
Villouta-Reyes, Catalina;
Cerono, Gabriel;
Shi, Yongmei;
Rizk-Jackson, Angela;
Israni, Sharat;
Nelson, Charlotte A;
Huang, Sui;
Baranzini, Sergio E

Publication type:

Article

Accurate and efficient protein embedding using multi-teacher distillation learning.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae567

By:

Shang, Jiayu;
Peng, Cheng;
Ji, Yongxin;
Guan, Jiaojiao;
Cai, Dehan;
Tang, Xubo;
Sun, Yanni

Publication type:

Article

RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae561

By:

Liu, Xiaoyi;
Ai, Chengwei;
Yang, Hongpeng;
Dong, Ruihan;
Tang, Jijun;
Zheng, Shuangjia;
Guo, Fei

Publication type:

Article

MEHunter: transformer-based mobile element variant detection from long reads.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae557

By:

Jiang, Tao;
Zhou, Zuji;
Zhang, Zhendong;
Cao, Shuqi;
Wang, Yadong;
Liu, Yadong

Publication type:

Article

AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae555

By:

Fernández-Díaz, Raúl;
Cossio-Pérez, Rodrigo;
Agoni, Clement;
Lam, Hoang Thanh;
Lopez, Vanessa;
Shields, Denis C

Publication type:

Article

KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae538

By:

Khatri, Dhruv;
Yadav, Shivani A;
Athale, Chaitanya A

Publication type:

Article

mgikit: demultiplexing toolkit for MGI fastq files.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae554

By:

Bkhetan, Ziad Al;
Wang, Sen

Publication type:

Article

BenchStab: a tool for automated querying of web-based stability predictors.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae553

By:

Velecký, Jan;
Berezný, Matej;
Musil, Milos;
Damborsky, Jiri;
Bednar, David;
Mazurenko, Stanislav

Publication type:

Article

A distribution-free and analytic method for power and sample size calculation in single-cell differential expression.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae540

By:

Hsu, Chih-Yuan;
Liu, Qi;
Shyr, Yu

Publication type:

Article

STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae552

By:

Mehryary, Farrokh;
Nastou, Katerina;
Ohta, Tomoko;
Jensen, Lars Juhl;
Pyysalo, Sampo

Publication type:

Article

CSV-Filter: a deep learning-based comprehensive structural variant filtering method for both short and long reads.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae539

By:

Xia, Zeyu;
Xiang, Weiming;
Wang, Qingzhe;
Li, Xingze;
Li, Yilin;
Gao, Junyu;
Tang, Tao;
Yang, Canqun;
Cui, Yingbo

Publication type:

Article

Uncertainty quantification in high-dimensional linear models incorporating graphical structures with applications to gene set analysis.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae541

By:

Tan, Xiangyong;
Zhang, Xiao;
Cui, Yuehua;
Liu, Xu

Publication type:

Article

SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae537

By:

Lyu, Yue;
Lin, Steven H;
Wu, Hao;
Li, Ziyi

Publication type:

Article

Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae549

By:

Rijk, Peter De;
Watzeels, Tijs;
Küçükali, Fahri;
Dongen, Jasper Van;
Faura, Júlia;
Willems, Patrick;
Deyn, Lara De;
Duchateau, Lena;
Grones, Carolin;
Eekhout, Thomas;
Pooter, Tim De;
Joris, Geert;
Rombauts, Stephane;
Rybel, Bert De;
Rademakers, Rosa;
Breusegem, Frank Van;
Strazisar, Mojca;
Sleegers, Kristel;
Coster, Wouter De

Publication type:

Article

Feature selection by replicate reproducibility and non-redundancy.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae548

By:

Capraz, Tümay;
Huber, Wolfgang

Publication type:

Article

NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide–human leukocyte antigen complexes.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae547

By:

Jiang, Dawei;
Xi, Binbin;
Tan, Wenchong;
Chen, Zixi;
Wei, Jinfen;
Hu, Meiling;
Lu, Xiaoyun;
Chen, Dong;
Cai, Hongmin;
Du, Hongli

Publication type:

Article

Bin2cell reconstructs cells from high resolution Visium HD data.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae546

By:

Polański, Krzysztof;
Bartolomé-Casado, Raquel;
Sarropoulos, Ioannis;
Xu, Chuan;
England, Nick;
Jahnsen, Frode L;
Teichmann, Sarah A;
Yayon, Nadav

Publication type:

Article

SCMeTA: a pipeline for single-cell metabolic analysis data processing.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae545

By:

Pan, Xingyu;
Pan, Siyuan;
Du, Murong;
Yang, Jinlei;
Yao, Huan;
Zhang, Xinrong;
Zhang, Sichun

Publication type:

Article

SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae544

By:

Rimal, Prawin;
Panday, Shailesh Kumar;
Xu, Wang;
Peng, Yunhui;
Alexov, Emil

Publication type:

Article

bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae543

By:

Gavalda-Garcia, Jose;
Díaz, Adrián;
Vranken, Wim

Publication type:

Article

CELEBRIMBOR: core and accessory genes from metagenomes.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae542

By:

Hellewell, Joel;
Horsfield, Samuel T;
Wachsmann, Johanna von;
Gurbich, Tatiana A;
Finn, Robert D;
Iqbal, Zamin;
Roberts, Leah W;
Lees, John A

Publication type:

Article

Signature Search Polestar: a comprehensive drug repurposing method evaluation assistant for customized oncogenic signature.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae536

By:

Zhang, Jinbo;
Yuan, Shunling;
Cao, Wen;
Jiang, Xianrui;
Yang, Cheng;
Jiang, Chenchao;
Liu, Runhui;
Yang, Wei;
Tian, Saisai

Publication type:

Article

Guide assignment in single-cell CRISPR screens using crispat.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae535

By:

Braunger, Jana M;
Velten, Britta

Publication type:

Article

ChatMol: interactive molecular discovery with natural language.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae534

By:

Zeng, Zheni;
Yin, Bangchen;
Wang, Shipeng;
Liu, Jiarui;
Yang, Cheng;
Yao, Haishen;
Sun, Xingzhi;
Sun, Maosong;
Xie, Guotong;
Liu, Zhiyuan

Publication type:

Article

sparsesurv: a Python package for fitting sparse survival models via knowledge distillation.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae521

By:

Wissel, David;
Janakarajan, Nikita;
Schulte, Julius;
Rowson, Daniel;
Yuan, Xintian;
Boeva, Valentina

Publication type:

Article

Triangulating evidence in health sciences with Annotated Semantic Queries.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae519

By:

Liu, Yi;
Gaunt, Tom R

Publication type:

Article

scDiffusion: conditional generation of high-quality single-cell data using diffusion model.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae518

By:

Luo, Erpai;
Hao, Minsheng;
Wei, Lei;
Zhang, Xuegong

Publication type:

Article

DTI-LM: language model powered drug–target interaction prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae533

By:

Ahmed, Khandakar Tanvir;
Ansari, Md Istiaq;
Zhang, Wei

Publication type:

Article

SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae532

By:

Boulton, William;
Fidan, Fatma Rabia;
Denise, Hubert;
Maio, Nicola De;
Goldman, Nick

Publication type:

Article

Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae528

By:

Ma, Xin;
Thela, Sai Ritesh;
Zhao, Fengdi;
Yao, Bing;
Wen, Zhexing;
Jin, Peng;
Zhao, Jinying;
Chen, Li

Publication type:

Article

Higher-order correction of persistent batch effects in correlation networks.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae531

By:

Micheletti, Soel;
Schlauch, Daniel;
Quackenbush, John;
Guebila, Marouen Ben

Publication type:

Article

Are genomic language models all you need? Exploring genomic language models on protein downstream tasks.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae529

By:

Boshar, Sam;
Trop, Evan;
Almeida, Bernardo P de;
Copoiu, Liviu;
Pierrot, Thomas

Publication type:

Article

RCPedia: a global resource for studying and exploring retrocopies in diverse species.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae530

By:

Conceição, Helena B;
Mercuri, Rafael L V;
Castro, Matheus P M de;
Ohara, Daniel T;
Guardia, Gabriela D A;
Galante, Pedro A F

Publication type:

Article

Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae527

By:

Mohammad-Taheri, Sara;
Navada, Pruthvi Prakash;
Hoyt, Charles Tapley;
Zucker, Jeremy;
Sachs, Karen;
Gyori, Benjamin M;
Vitek, Olga

Publication type:

Article

MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae522

By:

Passemiers, Antoine;
Tuveri, Stefania;
Sudhakaran, Dhanya;
Jatsenko, Tatjana;
Laga, Tina;
Punie, Kevin;
Hatse, Sigrid;
Tejpar, Sabine;
Coosemans, An;
Nieuwenhuysen, Els Van;
Timmerman, Dirk;
Floris, Giuseppe;
Rompuy, Anne-Sophie Van;
Sagaert, Xavier;
Testa, Antonia;
Ficherova, Daniela;
Raimondi, Daniele;
Amant, Frederic;
Lenaerts, Liesbeth;
Moreau, Yves

Publication type:

Article

Multi-Omic Graph Diagnosis (MOGDx): a data integration tool to perform classification tasks for heterogeneous diseases.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae523

By:

Ryan, Barry;
Marioni, Riccardo E;
Simpson, T Ian

Publication type:

Article

Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae526

By:

Cannon, Steven B;
Lee, Hyun-Oh;
Weeks, Nathan T;
Berendzen, Joel

Publication type:

Article

FateNet: an integration of dynamical systems and deep learning for cell fate prediction.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae525

By:

Sadria, Mehrshad;
Bury, Thomas M

Publication type:

Article

GTAM: a molecular pretraining model with geometric triangle awareness.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae524

By:

Hou, Xiaoyang;
Zhu, Tian;
Ren, Milong;
Duan, Bo;
Zhang, Chunming;
Bu, Dongbo;
Sun, Shiwei

Publication type:

Article

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae512

By:

Marot-Lassauzaie, Valérie;
Beneyto-Calabuig, Sergi;
Obermayer, Benedikt;
Velten, Lars;
Beule, Dieter;
Haghverdi, Laleh

Publication type:

Article

SpatialOne: end-to-end analysis of visium data at scale.

Published in:

Bioinformatics, 2024, v. 40, n. 9, p. 1, doi. 10.1093/bioinformatics/btae509

By:

Kamel, Mena;
Sarangi, Amrut;
Senin, Pavel;
Villordo, Sergio;
Sunaal, Mathew;
Barot, Het;
Wang, Seqian;
Solbas, Ana;
Cano, Luis;
Classe, Marion;
Bar-Joseph, Ziv;
Planas, Albert Pla

Publication type:

Article