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Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition.

Authors : Yousefian, Maryam¹ (AUTHOR); Frank, Anna-Simone¹ (AUTHOR); Weber, Marcus² (AUTHOR)

Source: BMC Bioinformatics. 6/2/2025, Vol. 26 Issue 1, p1-23. 23p.

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

Authors : Capela, João¹ (AUTHOR) ; Zimmermann-Kogadeeva, Maria² (AUTHOR); Dijk, Aalt D. J. van^3,4 (AUTHOR)

Source: BMC Bioinformatics. 2/27/2025, Vol. 26 Issue 1, p1-21. 21p.

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Academic Journal

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

Authors : Sun, Na^1,2 (AUTHOR); Han, Qiang¹ (AUTHOR); Wang, Yu¹ (AUTHOR)

Source: BMC Bioinformatics. 2/18/2025, Vol. 26 Issue 1, p1-16. 16p.

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Academic Journal

Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models.

Authors : Edelman, Brice¹ (AUTHOR); Skolnick, Jeffrey¹ (AUTHOR)

Source: BMC Bioinformatics. 5/28/2025, Vol. 26 Issue 1, p1-25. 25p.

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Academic Journal

PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models.

Authors : Xie, Jun^1,2,3 (AUTHOR) ; Zhang, Youli^2,3 (AUTHOR) ; Wang, Ziyang^1,2,3 (AUTHOR)

Source: BMC Bioinformatics. 4/29/2025, Vol. 26 Issue 1, p1-15. 15p.

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Academic Journal

Distinguishing word identity and sequence context in DNA language models.

Authors : Sanabria, Melissa¹ (AUTHOR); Hirsch, Jonas¹ (AUTHOR); Poetsch, Anna R.^1,2 (AUTHOR)

Source: BMC Bioinformatics. 9/13/2024, Vol. 25 Issue 1, p1-12. 12p.

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Academic Journal

Can large language models understand molecules?

Authors : Sadeghi, Shaghayegh¹ (AUTHOR) ; Bui, Alan¹ (AUTHOR); Forooghi, Ali¹ (AUTHOR)

Source: BMC Bioinformatics. 6/26/2024, Vol. 25 Issue 1, p1-17. 17p.

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Academic Journal

Improvements in viral gene annotation using large language models and soft alignments.

Authors : Harrigan, William L.¹ (AUTHOR); Ferrell, Barbra D.² (AUTHOR); Wommack, K. Eric² (AUTHOR)

Source: BMC Bioinformatics. 4/25/2024, Vol. 25 Issue 1, p1-19. 19p.

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Academic Journal

Bayesian compositional generalized linear mixed models for disease prediction using microbiome data.

Authors : Zhang, Li¹ (AUTHOR) ; Zhang, Xinyan² (AUTHOR); Leach, Justin M.³ (AUTHOR)

Source: BMC Bioinformatics. 4/5/2025, Vol. 26 Issue 1, p1-14. 14p.

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Academic Journal

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques.

Authors : Fresnais, Louison^1,2 (AUTHOR) ; Perin, Olivier² (AUTHOR); Riu, Anne² (AUTHOR)

Source: BMC Bioinformatics. 7/11/2024, Vol. 25 Issue 1, p1-32. 32p.

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Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition.

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

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

Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models.

PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models.

Distinguishing word identity and sequence context in DNA language models.

Can large language models understand molecules?

Improvements in viral gene annotation using large language models and soft alignments.

Bayesian compositional generalized linear mixed models for disease prediction using microbiome data.

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques.

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