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Select item 119171541.

Validating a web application’s use of genetic distance to determine helminth species boundaries and aid in identification

Abigail Hui En Chan, Urusa Thaenkham, Tanaphum Wichaita, Sompob Saralamba

BMC Bioinformatics. 2025; 26: 85. Published online 2025 Mar 18. doi: 10.1186/s12859-025-06098-0

PMCID:: PMC11917154

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FPGA-based accelerator for adaptive banded event alignment in nanopore sequencing data analysis

Yilin Feng, Zheyu Li, Gulsum Gudukbay Akbulut, Vijaykrishnan Narayanan, Mahmut Taylan Kandemir, Chita R. Das

BMC Bioinformatics. 2025; 26: 83. Published online 2025 Mar 17. doi: 10.1186/s12859-024-06011-1

PMCID:: PMC11917103

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Transfer learning for accelerated failure time model with microarray data

Yan-Bo Pei, Zheng-Yang Yu, Jun-Shan Shen

BMC Bioinformatics. 2025; 26: 84. Published online 2025 Mar 17. doi: 10.1186/s12859-025-06056-w

PMCID:: PMC11917065

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A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions

Rohan Gnanaolivu, Gavin Oliver, Garrett Jenkinson, Emily Blake, Wenan Chen, Nicholas Chia, Eric W. Klee, Chen Wang

BMC Bioinformatics. 2025; 26: 82. Published online 2025 Mar 14. doi: 10.1186/s12859-025-06096-2

PMCID:: PMC11908102

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Constructing multilayer PPI networks based on homologous proteins and integrating multiple PageRank to identify essential proteins

He Zhao, Huan Xu, Tao Wang, Guixia Liu

BMC Bioinformatics. 2025; 26: 80. Published online 2025 Mar 10. doi: 10.1186/s12859-025-06093-5

PMCID:: PMC11892321

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UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline

Jordana Lindner, Bareket Dassa, Noa Wigoda, Gil Stelzer, Ester Feldmesser, Jaime Prilusky, Dena Leshkowitz

BMC Bioinformatics. 2025; 26: 79. Published online 2025 Mar 7. doi: 10.1186/s12859-025-06090-8

PMCID:: PMC11889741

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An alignment-free method for phylogeny estimation using maximum likelihood

Tasfia Zahin, Md. Hasin Abrar, Mizanur Rahman Jewel, Tahrina Tasnim, Md. Shamsuzzoha Bayzid, Atif Rahman

BMC Bioinformatics. 2025; 26: 77. Published online 2025 Mar 7. doi: 10.1186/s12859-025-06080-w

PMCID:: PMC11887328

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Select item 118872558.

TRain: T-cell receptor automated immunoinformatics

Austin Seamann, Maia Bennett-Boehm, Ryan Ehrlich, Anna Gil, Liisa Selin, Dario Ghersi

BMC Bioinformatics. 2025; 26: 76. Published online 2025 Mar 6. doi: 10.1186/s12859-025-06074-8

PMCID:: PMC11887255

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Select item 118839959.

Cross-validation for training and testing co-occurrence network inference algorithms

Daniel Agyapong, Jeffrey Ryan Propster, Jane Marks, Toby Dylan Hocking

BMC Bioinformatics. 2025; 26: 74. Published online 2025 Mar 6. doi: 10.1186/s12859-025-06083-7

PMCID:: PMC11883995

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Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data

Joshua Chuah, Carmalena V. Cordi, Juergen Hahn, Jennifer M. Hurley

BMC Bioinformatics. 2025; 26: 72. Published online 2025 Mar 4. doi: 10.1186/s12859-025-06089-1

PMCID:: PMC11881278

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ProToDeviseR: an automated protein topology scheme generator

Petar Petrov, Valerio Izzi

BMC Bioinformatics. 2025; 26: 71. Published online 2025 Mar 3. doi: 10.1186/s12859-025-06088-2

PMCID:: PMC11874827

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Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction

João Capela, Maria Zimmermann-Kogadeeva, Aalt D. J. van Dijk, Dick de Ridder, Oscar Dias, Miguel Rocha

BMC Bioinformatics. 2025; 26: 68. Published online 2025 Feb 27. doi: 10.1186/s12859-025-06081-9

PMCID:: PMC11866580

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GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs

Matheus Henrique Pimenta-Zanon, André Yoshiaki Kashiwabara, André Luís Laforga Vanzela, Fabricio Martins Lopes

BMC Bioinformatics. 2025; 26: 66. Published online 2025 Feb 25. doi: 10.1186/s12859-025-06037-z

PMCID:: PMC11863517

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Select item 1186349214.

Tisslet tissues-based learning estimation for transcriptomics

Ahmed Miloudi, Aisha Al-Qahtani, Thamanna Hashir, Mohamed Chikri, Halima Bensmail

BMC Bioinformatics. 2025; 26: 65. Published online 2025 Feb 25. doi: 10.1186/s12859-024-06025-9

PMCID:: PMC11863492

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goloco: a web application to create genome scale information from surprisingly small experiments

Sajid M. Hossain, Yiyun Rao, Jahid O. Hossain, Justin R. Pritchard, Boyang Zhao

BMC Bioinformatics. 2025; 26: 61. Published online 2025 Feb 25. doi: 10.1186/s12859-025-06070-y

PMCID:: PMC11854281

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MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism

Na Quan, Shicheng Ma, Kai Zhao, Xuehua Bi, Linlin Zhang

BMC Bioinformatics. 2025; 26: 57. Published online 2025 Feb 18. doi: 10.1186/s12859-025-06075-7

PMCID:: PMC11834641

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BHCox: Bayesian heredity-constrained Cox proportional hazards models for detecting gene-environment interactions

Na Sun, Qiang Han, Yu Wang, Mengtong Sun, Ziqing Sun, Hongpeng Sun, Yueping Shen

BMC Bioinformatics. 2025; 26: 58. Published online 2025 Feb 18. doi: 10.1186/s12859-025-06077-5

PMCID:: PMC11834309

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Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity

Jiashan Li, Xinqi Gong

BMC Bioinformatics. 2025; 26: 55. Published online 2025 Feb 17. doi: 10.1186/s12859-025-06064-w

PMCID:: PMC11834573

Article PDF–2.9M

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A novel weighted pseudo-labeling framework based on matrix factorization for adverse drug reaction prediction

Junheng Chen, Fangfang Han, Mingxiu He, Yiyang Shi, Yongming Cai

BMC Bioinformatics. 2025; 26: 54. Published online 2025 Feb 17. doi: 10.1186/s12859-025-06053-z

PMCID:: PMC11831795

Article PDF–3.4M

Select item 1182954620.

CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes

Peng Sun, Yu Yang, Mengjie Yuan, Qin Tang

BMC Bioinformatics. 2025; 26: 53. Published online 2025 Feb 14. doi: 10.1186/s12859-025-06034-2

PMCID:: PMC11829546

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"BMC Bioinformatics"[jour] (12611)
PMC
Homo sapiens glypican 3 (GPC3), transcript variant 2, mRNA
Homo sapiens glypican 3 (GPC3), transcript variant 2, mRNA
gi|257471004|ref|NM_004484.3|

Nucleotide
RecName: Full=Zinc finger protein PLAG1; AltName: Full=Pleiomorphic adenoma gene...
RecName: Full=Zinc finger protein PLAG1; AltName: Full=Pleiomorphic adenoma gene 1 protein
gi|74757442|sp|Q6DJT9.1|PLAG1_HUMAN

Protein
Homo sapiens PLAG1 zinc finger (PLAG1), transcript variant 1, mRNA
Homo sapiens PLAG1 zinc finger (PLAG1), transcript variant 1, mRNA
gi|1519246549|ref|NM_002655.3|

Nucleotide
thiamine biosynthesis protein ThiS [Nonomuraea glycinis]
thiamine biosynthesis protein ThiS [Nonomuraea glycinis]
gi|1904102060|dbj|GGP15131.1||gnl|W NK|GGP15131

Protein

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