"Bioinformatics"[journal] - PMC

Ruipeng Lu, Tim Dumonceaux, Muhammad Anzar, Athanasios Zovoilis, Kym Antonation, Dillon Barker, Cindi Corbett, Celine Nadon, James Robertson, Shannon H C Eagle, Oliver Lung, Josip Rudar, Om Surujballi, Chad Laing

Bioinformatics. 2024 Oct; 40(10): btae601. Published online 2024 Oct 10. doi: 10.1093/bioinformatics/btae601

PMCID:: PMC11522871

Abstract Article PDF–2.2M

Select item 115204164.

DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs

Brad T Sherman, Ganesh Panzade, Tomozumi Imamichi, Weizhong Chang

Bioinformatics. 2024 Oct; 40(10): btae615. Published online 2024 Oct 16. doi: 10.1093/bioinformatics/btae615

PMCID:: PMC11520416

Abstract Article PDF–1.1M

Select item 115204135.

GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation

Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu

Bioinformatics. 2024 Sep; 40(Suppl 2): ii53–ii61. Published online 2024 Sep 4. doi: 10.1093/bioinformatics/btae401

PMCID:: PMC11520413

Abstract Article PDF–1.5M

Select item 115204106.

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

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

Bioinformatics. 2024 Sep; 40(9): btae561. Published online 2024 Sep 28. doi: 10.1093/bioinformatics/btae561

PMCID:: PMC11520410

Abstract Article PDF–2.5M

Select item 115204087.

Attention-based approach to predict drug–target interactions across seven target superfamilies

Aron Schulman, Juho Rousu, Tero Aittokallio, Ziaurrehman Tanoli

Bioinformatics. 2024 Aug; 40(8): btae496. Published online 2024 Aug 8. doi: 10.1093/bioinformatics/btae496

PMCID:: PMC11520408

Abstract Article PDF–5.0M

Select item 115203988.

ChatMol: interactive molecular discovery with natural language

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

Bioinformatics. 2024 Sep; 40(9): btae534. Published online 2024 Sep 2. doi: 10.1093/bioinformatics/btae534

PMCID:: PMC11520398

Abstract Article PDF–4.6M

Select item 115202309.

Multi-modal contrastive learning of subcellular organization using DICE

Rami Nasser, Leah V Schaffer, Trey Ideker, Roded Sharan

Bioinformatics. 2024 Sep; 40(Suppl 2): ii105–ii110. Published online 2024 Sep 4. doi: 10.1093/bioinformatics/btae387

PMCID:: PMC11520230

Abstract Article PDF–1.8M

Select item 1151301810.

scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering

Tianjiao Zhang, Hongfei Zhang, Jixiang Ren, Zhenao Wu, Zhongqian Zhao, Guohua Wang

Bioinformatics. 2024 Oct; 40(10): btae599. Published online 2024 Oct 15. doi: 10.1093/bioinformatics/btae599

PMCID:: PMC11513018

Abstract Article PDF–7.3M

Select item 1151259011.

Analysis of metadynamics simulations by metadynminer.py

Jan Beránek, Aleš Křenek, Vojtěch Spiwok

Bioinformatics. 2024 Oct; 40(10): btae614. Published online 2024 Oct 18. doi: 10.1093/bioinformatics/btae614

PMCID:: PMC11512590

Abstract Article PDF–1.4M

Select item 1150249812.

PocketDTA: an advanced multimodal architecture for enhanced prediction of drug−target affinity from 3D structural data of target binding pockets

Long Zhao, Hongmei Wang, Shaoping Shi

Bioinformatics. 2024 Oct; 40(10): btae594. Published online 2024 Oct 4. doi: 10.1093/bioinformatics/btae594

PMCID:: PMC11502498

Abstract Article PDF–7.9M

Select item 1149688813.

BEATRICE: Bayesian fine-mapping from summary data using deep variational inference

Sayan Ghosal, Michael C Schatz, Archana Venkataraman

Bioinformatics. 2024 Oct; 40(10): btae590. Published online 2024 Oct 3. doi: 10.1093/bioinformatics/btae590

PMCID:: PMC11496888

Abstract Article PDF–4.1M

Select item 1149567314.

Pair-EGRET: enhancing the prediction of protein–protein interaction sites through graph attention networks and protein language models

Ramisa Alam, Sazan Mahbub, Md Shamsuzzoha Bayzid

Bioinformatics. 2024 Oct; 40(10): btae588. Published online 2024 Oct 3. doi: 10.1093/bioinformatics/btae588

PMCID:: PMC11495673

Abstract Article PDF–3.4M

Select item 1149438015.

LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors

Koichiro Majima, Yasuhiro Kojima, Kodai Minoura, Ko Abe, Haruka Hirose, Teppei Shimamura

Bioinformatics. 2024 Oct; 40(10): btae520. Published online 2024 Aug 22. doi: 10.1093/bioinformatics/btae520

PMCID:: PMC11494380

Abstract Article PDF–7.8M

Select item 1148897416.

Correction to: AgIn: measuring the landscape of CpG methylation of individual repetitive elements

Bioinformatics. 2024 Oct; 40(10): btae600. Published online 2024 Oct 18. doi: 10.1093/bioinformatics/btae600

Corrects:: Bioinformatics. 2016 Oct 1; 32(19): 2911–2919.

PMCID:: PMC11488974

Correction PDF–167K

Select item 1148649917.

BatchFLEX: feature-level equalization of X-batch

Joshua T Davis, Alyssa N Obermayer, Alex C Soupir, Rebecca S Hesterberg, Thac Duong, Ching-Yao Yang, Ken Phong Dao, Brandon J Manley, G Daniel Grass, Dorina Avram, Paulo C Rodriguez, Brooke L Fridley, Xiaoqing Yu, Mingxiang Teng, Xuefeng Wang, Timothy I Shaw

Bioinformatics. 2024 Oct; 40(10): btae587. Published online 2024 Oct 3. doi: 10.1093/bioinformatics/btae587