Analysis of Mutations in Precision Oncology using The Automated, Accurate, and User-Friendly Web Tool PredictONCO
RT Khan, P Pokorna, J Stourac, S Borko, A Dobias… - bioRxiv, 2024 - biorxiv.org
Next-generation sequencing technology has created many new opportunities for clinical
diagnostics, but it faces the challenge of functional annotation of identified mutations …
diagnostics, but it faces the challenge of functional annotation of identified mutations …
A computational workflow for analysis of missense mutations in precision oncology
RT Khan, P Pokorna, J Stourac, S Borko… - Journal of …, 2024 - Springer
Every year, more than 19 million cancer cases are diagnosed, and this number continues to
increase annually. Since standard treatment options have varying success rates for different …
increase annually. Since standard treatment options have varying success rates for different …
BayesPI-BAR2: a new python package for predicting functional non-coding mutations in cancer patient cohorts
K Batmanov, J Delabie, J Wang - Frontiers in genetics, 2019 - frontiersin.org
Most of somatic mutations in cancer occur outside of gene coding regions. These mutations
may disrupt the gene regulation by affecting protein-DNA interaction. A study of these …
may disrupt the gene regulation by affecting protein-DNA interaction. A study of these …
Applying expression profile similarity for discovery of patient-specific functional mutations
G Meng - High-throughput, 2018 - mdpi.com
The progress of cancer genome sequencing projects yields unprecedented information of
mutations for numerous patients. However, the complexity of mutation profiles of cancer …
mutations for numerous patients. However, the complexity of mutation profiles of cancer …
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine …
J Stourac, S Borko, RT Khan, P Pokorna… - Briefings in …, 2024 - academic.oup.com
PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins
frequently altered in various cancer types. The server can assess the impact of mutations on …
frequently altered in various cancer types. The server can assess the impact of mutations on …
Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep
K Tzavella, A Diaz, C Olsen, WF Vranken - bioRxiv, 2023 - biorxiv.org
Background: The mutations driving cancer are being increasingly exposed through tumor-
specific genomic data. However, differentiating between cancer-causing driver mutations …
specific genomic data. However, differentiating between cancer-causing driver mutations …
Computational structure prediction methods enable the systematic identification of oncogenic mutations
Oncogenic mutations are associated with the activation of key pathways necessary for the
initiation, progression and treatment-evasion of tumors. While large genomic studies provide …
initiation, progression and treatment-evasion of tumors. While large genomic studies provide …
CancerVar: An artificial intelligence–empowered platform for clinical interpretation of somatic mutations in cancer
Several knowledgebases are manually curated to support clinical interpretations of
thousands of hotspot somatic mutations in cancer. However, discrepancies or even …
thousands of hotspot somatic mutations in cancer. However, discrepancies or even …
Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks
M Nourbakhsh, K Degn, A Saksager… - Briefings in …, 2024 - academic.oup.com
The vast amount of available sequencing data allows the scientific community to explore
different genetic alterations that may drive cancer or favor cancer progression. Software …
different genetic alterations that may drive cancer or favor cancer progression. Software …
Comprehensive assessment of computational algorithms in predicting cancer driver mutations
Background The initiation and subsequent evolution of cancer are largely driven by a
relatively small number of somatic mutations with critical functional impacts, so-called driver …
relatively small number of somatic mutations with critical functional impacts, so-called driver …
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