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Jan 13, 2025 | 
nature.com | Lin Tang
Inspired by the booming wave of large language models, hopes of reading and understanding the language of biomolecules have been fueled by the development of similar large-scale foundation models. “There has been tremendous progress in machine learning for protein design, but most important biological functions are accomplished by more than just a single monomeric protein scaffold,” says Patrick Hsu at the Arc Institute and the University of California, Berkeley.
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Dec 26, 2024 | 
mdpi.com | Lin Tang
1. IntroductionSoil fertility refers to the ability of soil to sustain agricultural plant growth; fertile soil provides a habitat with essential nutrients and favorable chemical, physical and biological characteristics to sustain plant growth [1], without toxic substances that inhibit plant development [2]. Essential plant nutrients are critical for plant growth and reproduction, a deficiency of them causes the plant growth cycle to fail [3].
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Dec 21, 2024 | 
4spepublications.onlinelibrary.wiley.com | Lin Tang |Qingyi Hu |Lizhi Li |Jing Jiang |Derun Chen |Pengcheng Zhou | +1 more
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Dec 6, 2024 | 
nature.com | Lin Tang
New experimental and computational methods illuminate the history of cell differentiation and its molecular underpinnings.
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Oct 9, 2024 | 
nature.com | Lin Tang
For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal. My fascination with how innovative and how powerful computational methods can be when analyzing genomics data is a gift for me as an editor at Nature Methods.
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Sep 9, 2024 | 
nature.com | Lin Tang
AbstractRituximab occasionally induces reactivation of hepatitis C virus (HCV) in patients with resolved HCV infection, sometimes with fatal consequences. As rituximab has become one of the first-line therapies for the treatment of phospholipase A2 receptor (PLA2R)-associated membranous nephropathy (MN) and is more widely used, there is a lack of studies reporting the effectiveness and safety of rituximab in patients with PLA2R-associated MN and resolved HCV infection.
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Jun 12, 2024 | 
nature.com | Lin Tang
Enhancers are one of the main players driving spatiotemporal gene expression patterns, and they could harbor genetic variants underlying complex traits and diseases. Despite being paramount to our understanding of gene regulation, “enhancer–gene maps are challenging to build experimentally.
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Apr 12, 2024 | 
nature.com | Lin Tang
The prowess of protein language models (PLMs) has been demonstrated in handling various tasks, such as protein structure prediction, function analysis and engineering, and novel protein design.
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Feb 12, 2024 | 
nature.com | Lin Tang
Boosted by the power of long-read sequencing, the frontiers of structural variation (SV) detection are advancing quickly. Accompanying and facilitating this progress, the toolbox of computational methods keeps expanding — although it is still far from being perfected. In 2018, Fritz Sedlazeck at Baylor College of Medicine and colleagues presented ‘Sniffles1’, which has since become a widely used tool for detecting SV using long-read sequencing data.
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Dec 6, 2023 | 
nature.com | Lin Tang
Large language models are learning the language of genomics. Protein science has been one of the pioneering areas adopting the use of LLMs. Using diverse protein sequence datasets compiled throughout the tree of life, protein language models with hundreds of millions to billions of parameters (Proc. Natl Acad. Sci. USA 118, e2016239118, 2021; Nat. Biotechnol.
