Volume 40(6); 2024 Jun

Applications Note

Data and Text Mining

Bigtools: a high-performance BigWig and BigBed library in Rust

Jack D Huey, Nezar Abdennur

Bioinformatics. 2024 Jun; 40(6): btae350. Published online 2024 Jun 11. doi: 10.1093/bioinformatics/btae350

PMCID:: PMC11167208

Abstract Article PDF–606K

biotextgraph: graphical summarization of functional similarities from textual information

Noriaki Sato, Yao-zhong Zhang, Zuguang Gu, Seiya Imoto

Bioinformatics. 2024 Jun; 40(6): btae357. Published online 2024 Jun 8. doi: 10.1093/bioinformatics/btae357

PMCID:: PMC11198732

Abstract Article PDF–1.8M

Databases and Ontologies

KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models

Nicholas Matsumoto, Jay Moran, Hyunjun Choi, Miguel E Hernandez, Mythreye Venkatesan, Paul Wang, Jason H Moore

Bioinformatics. 2024 Jun; 40(6): btae353. Published online 2024 Jun 3. doi: 10.1093/bioinformatics/btae353

PMCID:: PMC11164829

Abstract Article PDF–1.2M

Gene Expression

RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution

Jonathan Chacko, Hakan Ozadam, Can Cenik

Bioinformatics. 2024 Jun; 40(6): btae369. Published online 2024 Jun 19. doi: 10.1093/bioinformatics/btae369

PMCID:: PMC11197854

Abstract Article PDF–1.4M

Genetics and Population Analysis

snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics

Kim L Vertacnik, Oksana V Vernygora, Julian R Dupuis

Bioinformatics. 2024 Jun; 40(6): btae377. Published online 2024 Jun 17. doi: 10.1093/bioinformatics/btae377

PMCID:: PMC11194479

Abstract Article PDF–1.1M

Genome Analysis

SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models

Ketrin Gjoni, Katherine S Pollard

Bioinformatics. 2024 Jun; 40(6): btae340. Published online 2024 May 25. doi: 10.1093/bioinformatics/btae340

PMCID:: PMC11153836

Abstract Article PDF–3.9M

Mariner: explore the Hi-Cs

Eric S Davis, Sarah M Parker, Nicole E Kramer, J P Flores, Manjari Kiran, Douglas H Phanstiel

Bioinformatics. 2024 Jun; 40(6): btae352. Published online 2024 May 30. doi: 10.1093/bioinformatics/btae352

PMCID:: PMC11176088

Abstract Article PDF–436K

Figeno: multi-region genomic figures with long-read support

Etienne Sollier, Jessica Heilmann, Clarissa Gerhauser, Michael Scherer, Christoph Plass, Pavlo Lutsik

Bioinformatics. 2024 Jun; 40(6): btae354. Published online 2024 Jun 10. doi: 10.1093/bioinformatics/btae354

PMCID:: PMC11184262

Abstract Article PDF–1.7M

Sequence Analysis

Flexible parsing, interpretation, and editing of technical sequences with splitcode

Delaney K Sullivan, Lior Pachter

Bioinformatics. 2024 Jun; 40(6): btae331. Published online 2024 Jun 14. doi: 10.1093/bioinformatics/btae331

PMCID:: PMC11193061

Abstract Article PDF–1.4M

SWGTS—a platform for stream-based host DNA depletion

Philipp Spohr, Max Ried, Laura Kühle, Alexander Dilthey

Bioinformatics. 2024 Jun; 40(6): btae332. Published online 2024 May 24. doi: 10.1093/bioinformatics/btae332

PMCID:: PMC11167210

Abstract Article PDF–1.8M

Structural Bioinformatics

MolDy: molecular dynamics simulation made easy

Mohd Imran Khan, Sheetal Pathania, Mohammed W Al-Rabia, Abdul S Ethayathulla, Mohammad Imran Khan, Khaled S Allemailem, Mohd Azam, Gururao Hariprasad, Mohammad Azhar Imran

Bioinformatics. 2024 Jun; 40(6): btae313. Published online 2024 Jun 12. doi: 10.1093/bioinformatics/btae313

PMCID:: PMC11187490

Abstract Article PDF–2.0M

MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2

Ho Yeung Chim, Arne Elofsson

Bioinformatics. 2024 Jun; 40(6): btae329. Published online 2024 May 23. doi: 10.1093/bioinformatics/btae329

PMCID:: PMC11194477

Abstract Article PDF–2.4M

Systems Biology

PathwayNexus: a tool for interactive metabolic data analysis

Philipp Eberhard, Martin Kern, Michael Aichem, Hanna Borlinghaus, Karsten Klein, Johannes Delp, Ilinca Suciu, Benjamin Moser, Daniel Dietrich, Marcel Leist, Falk Schreiber

Bioinformatics. 2024 Jun; 40(6): btae310. Published online 2024 May 9. doi: 10.1093/bioinformatics/btae310

PMCID:: PMC11153943

Abstract Article PDF–2.8M

ReactomeGSA: new features to simplify public data reuse

Alexander Grentner, Eliot Ragueneau, Chuqiao Gong, Adrian Prinz, Sabina Gansberger, Inigo Oyarzun, Henning Hermjakob, Johannes Griss

Bioinformatics. 2024 Jun; 40(6): btae338. Published online 2024 May 28. doi: 10.1093/bioinformatics/btae338

PMCID:: PMC11147800

Abstract Article PDF–918K

bnglViz: online visualization of rule-based models

Noah Liguori-Bills, Michael L Blinov

Bioinformatics. 2024 Jun; 40(6): btae351. Published online 2024 May 30. doi: 10.1093/bioinformatics/btae351

PMCID:: PMC11176710

Abstract Article PDF–801K

Original Papers

Bioimage Informatics

CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm

Teng-Yu Lin, Szu-Chi Chung

Bioinformatics. 2024 Jun; 40(6): btae345. Published online 2024 Jun 5. doi: 10.1093/bioinformatics/btae345

PMCID:: PMC11167209

Abstract Article PDF–3.6M

GammaGateR: semi-automated marker gating for single-cell multiplexed imaging

Jiangmei Xiong, Harsimran Kaur, Cody N Heiser, Eliot T McKinley, Joseph T Roland, Robert J Coffey, Martha J Shrubsole, Julia Wrobel, Siyuan Ma, Ken S Lau, Simon Vandekar

Bioinformatics. 2024 Jun; 40(6): btae356. Published online 2024 Jun 4. doi: 10.1093/bioinformatics/btae356

PMCID:: PMC11193056

Abstract Article PDF–4.3M

Data and Text Mining

DEAttentionDTA: protein–ligand binding affinity prediction based on dynamic embedding and self-attention

Xiying Chen, Jinsha Huang, Tianqiao Shen, Houjin Zhang, Li Xu, Min Yang, Xiaoman Xie, Yunjun Yan, Jinyong Yan

Bioinformatics. 2024 Jun; 40(6): btae319. Published online 2024 Jun 19. doi: 10.1093/bioinformatics/btae319

PMCID:: PMC11193059

Abstract Article PDF–2.8M

TARO: tree-aggregated factor regression for microbiome data integration

Aditya K Mishra, Iqbal Mahmud, Philip L Lorenzi, Robert R Jenq, Jennifer A Wargo, Nadim J Ajami, Christine B Peterson

Bioinformatics. 2024 Jun; 40(6): btae321. Published online 2024 May 24. doi: 10.1093/bioinformatics/btae321

PMCID:: PMC11193058

Abstract Article PDF–3.6M

Improving the performance and interpretability on medical datasets using graphical ensemble feature selection

Enzo Battistella, Dina Ghiassian, Albert-László Barabási

Bioinformatics. 2024 Jun; 40(6): btae341. Published online 2024 Jun 5. doi: 10.1093/bioinformatics/btae341

PMCID:: PMC11187494

Abstract Article PDF–1.0M

Gene Expression

HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data

Xingjian Chen, Jiecong Lin, Yuchen Wang, Weitong Zhang, Weidun Xie, Zetian Zheng, Ka-Chun Wong

Bioinformatics. 2024 Jun; 40(6): btae343. Published online 2024 Jun 5. doi: 10.1093/bioinformatics/btae343

PMCID:: PMC11164830

Abstract Article PDF–3.0M

Genetics and Population Analysis

SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts

Nianqiao Ju, Jiawei Liu, Qixin He

Bioinformatics. 2024 Jun; 40(6): btae344. Published online 2024 Jun 17. doi: 10.1093/bioinformatics/btae344

PMCID:: PMC11187496

Abstract Article PDF–12M

Genome Analysis

AmplificationTimeR: an R package for timing sequential amplification events

G Maria Jakobsdottir, Stefan C Dentro, Robert G Bristow, David C Wedge

Bioinformatics. 2024 Jun; 40(6): btae281. Published online 2024 Apr 24. doi: 10.1093/bioinformatics/btae281

PMCID:: PMC11153944

Abstract Article PDF–11M

SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings

Aysun Urhan, Bianca-Maria Cosma, Ashlee M Earl, Abigail L Manson, Thomas Abeel

Bioinformatics. 2024 Jun; 40(6): btae328. Published online 2024 May 22. doi: 10.1093/bioinformatics/btae328

PMCID:: PMC11147799

Abstract Article PDF–1.3M

Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation

Minzhu Xie, Yabin Kuang, Mengyun Song, Ergude Bao

Bioinformatics. 2024 Jun; 40(6): btae360. Published online 2024 Jun 10. doi: 10.1093/bioinformatics/btae360

PMCID:: PMC11194476

Abstract Article PDF–1.1M

Phylogenetics

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach

Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab

Bioinformatics. 2024 Jun; 40(6): btae361. Published online 2024 Jun 13. doi: 10.1093/bioinformatics/btae361

PMCID:: PMC11193062

Abstract Article PDF–2.9M

Sequence Analysis

Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy’s outcome for HIV-1

Giulia Di Teodoro, Martin Pirkl, Francesca Incardona, Ilaria Vicenti, Anders Sönnerborg, Rolf Kaiser, Laura Palagi, Maurizio Zazzi, Thomas Lengauer

Bioinformatics. 2024 Jun; 40(6): btae327. Published online 2024 May 22. doi: 10.1093/bioinformatics/btae327

PMCID:: PMC11153833

Abstract Article PDF–2.1M

MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data

Marjan Faizi, Ryan T Fellers, Dan Lu, Bryon S Drown, Ashwini Jambhekar, Galit Lahav, Neil L Kelleher, Jeremy Gunawardena

Bioinformatics. 2024 Jun; 40(6): btae335. Published online 2024 May 25. doi: 10.1093/bioinformatics/btae335

PMCID:: PMC11157153

Abstract Article PDF–1.8M

Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data

Siang Chen, Hao Wang, Dongdong Zhang, Runsheng Chen, Jianjun Luo

Bioinformatics. 2024 Jun; 40(6): btae336. Published online 2024 May 28. doi: 10.1093/bioinformatics/btae336

PMCID:: PMC11162696

Abstract Article PDF–3.7M

Systems Biology

spillR: spillover compensation in mass cytometry data

Marco Guazzini, Alexander G Reisach, Sebastian Weichwald, Christof Seiler

Bioinformatics. 2024 Jun; 40(6): btae337. Published online 2024 Jun 6. doi: 10.1093/bioinformatics/btae337

PMCID:: PMC11189660

Abstract Article PDF–1.3M

Drug–target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism

Wei Song, Lewen Xu, Chenguang Han, Zhen Tian, Quan Zou

Bioinformatics. 2024 Jun; 40(6): btae346. Published online 2024 Jun 5. doi: 10.1093/bioinformatics/btae346

PMCID:: PMC11164831

Abstract Article PDF–5.4M

Correction

Correction to: For antibody sequence generative modeling, mixture models may be all you need

Bioinformatics. 2024 Jun; 40(6): btae407. Published online 2024 Jun 24. doi: 10.1093/bioinformatics/btae407

Corrects:: Bioinformatics. 2024 May; 40(5): btae278.

PMCID:: PMC11194480

Correction PDF–184K

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