Scientific large language models: A survey on biological & chemical domains

Q Zhang, K Ding, T Lv, X Wang, Q Yin, Y Zhang… - ACM Computing …, 2024 - dl.acm.org
Large Language Models (LLMs) have emerged as a transformative power in enhancing
natural language comprehension, representing a significant stride toward artificial general …

kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq

DK Sullivan, KH Min, KE Hjörleifsson, L Luebbert… - Nature …, 2024 - nature.com
The term 'RNA-seq'refers to a collection of assays based on sequencing experiments that
involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto …

COSMIC: a curated database of somatic variants and clinical data for cancer

Z Sondka, NB Dhir, D Carvalho-Silva… - Nucleic Acids …, 2024 - academic.oup.com
Abstract The Catalogue Of Somatic Mutations In Cancer (COSMIC), https://cancer. sanger.
ac. uk/cosmic, is an expert-curated knowledgebase providing data on somatic variants in …

CADD v1. 7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions

M Schubach, T Maass, L Nazaretyan… - Nucleic acids …, 2024 - academic.oup.com
Abstract Machine Learning-based scoring and classification of genetic variants aids the
assessment of clinical findings and is employed to prioritize variants in diverse genetic …

A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction

PY Ting, S Borikar, JR Kerrigan, NM Thomsen… - Science, 2024 - science.org
Sickle cell disease (SCD) is a prevalent, life-threatening condition attributable to a heritable
mutation in β-hemoglobin. Therapeutic induction of fetal hemoglobin (HbF) can ameliorate …

Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity

MJ Wu, H Kondo, AV Kammula, L Shi, Y **ao, S Dhiab… - Science, 2024 - science.org
Isocitrate dehydrogenase 1 (IDH1) is the most commonly mutated metabolic gene across
human cancers. Mutant IDH1 (mIDH1) generates the oncometabolite (R)-2 …

VARIDT 3.0: the phenotypic and regulatory variability of drug transporter

J Yin, Z Chen, N You, F Li, H Zhang, J Xue… - Nucleic acids …, 2024 - academic.oup.com
The phenotypic and regulatory variability of drug transporter (DT) are vital for the
understanding of drug responses, drug-drug interactions, multidrug resistances, and so on …

Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation

F Yilmaz, C Karageorgiou, K Kim, P Pajic, K Scheer… - Science, 2024 - science.org
Previous studies suggested that the copy number of the human salivary amylase gene,
AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by …

Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma

R Culliford, SED Lawrence, C Mills, Z Tippu… - Nature …, 2024 - nature.com
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a
comprehensive description of its genomic landscape is lacking. We report the whole …

Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources

I Diamant, DJB Clarke, JE Evangelista… - Nucleic Acids …, 2025 - academic.oup.com
By processing and abstracting diverse omics datasets into associations between genes and
their attributes, the Harmonizome database enables researchers to explore and integrate …