Wuwei Tan

Protein structure-informed deep learning enables species-specific codon optimization

W. J. Jin, Wuwei Tan, Hui Li, Xiangyu Ji et autres

Abstract Codon usage bias is highly species-specific, posing a major challenge for heterologous protein expression. Existing deep learning approaches to codon optimization rely primarily on DNA or protein sequence information and largely neglect constraints imposed by protein structure and folding. Here, we …

cn (code pays fourni par la source)

Integrated antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy

Hannah F. Almubarak, Wuwei Tan, Andrew D. Hoffmann, Yuanfei Sun et autres

. AbLM outperformed other language models in predicting IgGs with low variant susceptibility. Our work advances artificial intelligence-based antibody discovery by synergizing data-driven language models and Kriging with physics-driven docking and design.

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

Jacob Schreiber, Carles A. Boix, Jin wook Lee, Hongyang Li et autres

Following publication of the original article [1], the authors identified that the affiliation 1 was incorrectly used for all authors. The correct affiliations are used in this correction article and the original article [1] has been corrected.

us, jp, de, gb, it, ch, hk (code pays fourni par la source)

CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs)

Maria Cristina Aspromonte, Alessio Del Conte, Shaowen Zhu, Wuwei Tan et autres

The Genetics of Neurodevelopmental Disorders Lab in Padua provided a new intellectual disability (ID) Panel challenge for computational methods to predict patient phenotypes and their causal variants in the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6). Eight …

it, us, hk, cn, sa, in (code pays fourni par la source)

Abstract PO3-29-03: An Emerging Class of ER mutations Enhances ER Dimerization and Promotes ER Activity

Seema Irani, Wuwei Tan, Qing Li, Weiyi Toy et autres

Abstract Physiological activation of estrogen receptor alpha (ERα) requires the binding of estradiol (E2) to the ligand binding domain (LBD) of the receptor. This interaction triggers a repositioning of helix 12 (H12), facilitating the recruitment of coactivator proteins to the unoccupied coactivator …

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Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project

Sarah L. Stenton, Melanie O’Leary, Gabrielle Lemire, Grace E. VanNoy et autres

BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and …

us, sa, it, be, gb, in, cn, vn (code pays fourni par la source)

Novel antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy

Hannah F. Almubarak, Wuwei Tan, Andrew D. Hoffmann, Yuanfei Sun et autres

Abstract Therapeutic antibodies have become one of the most influential therapeutics in modern medicine to fight against infectious pathogens, cancer, and many other diseases. However, experimental screening for highly efficacious targeting antibodies is labor-intensive and of high cost, which is exacerbated by …

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Somatic estrogen receptor α mutations that induce dimerization promote receptor activity and breast cancer proliferation

Seema Irani, Wuwei Tan, Qing Li, Weiyi Toy et autres

Physiologic activation of estrogen receptor α (ERα) is mediated by estradiol (E2) binding in the ligand-binding pocket of the receptor, repositioning helix 12 (H12) to facilitate binding of coactivator proteins in the unoccupied coactivator binding groove. In breast cancer, activation of ERα …

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Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

Wuwei Tan, Yang Shen

MOTIVATION: A growing amount of noncoding genetic variants, including single-nucleotide polymorphisms, are found to be associated with complex human traits and diseases. Their mechanistic interpretation is relatively limited and can use the help from computational prediction of their effects on epigenetic profiles. …

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Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project

Sarah L. Stenton, Melanie O’Leary, Gabrielle Lemire, Grace E. VanNoy et autres

ABSTRACT Background A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average “diagnostic odyssey” lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on …

us, sa, it, gb, in, cn, vn (code pays fourni par la source)

CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)

Maria Cristina Aspromonte, Alessio Del Conte, Shaowen Zhu, Wuwei Tan et autres

it, us, cn, hk, sa, in (code pays fourni par la source)

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

Wuwei Tan

ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 …

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