Bioinformatics for precision oncology
J Singer, A Irmisch, HJ Ruscheweyh… - Briefings in …, 2019 - academic.oup.com
Molecular profiling of tumor biopsies plays an increasingly important role not only in cancer
research, but also in the clinical management of cancer patients. Multi-omics approaches …
research, but also in the clinical management of cancer patients. Multi-omics approaches …
Acquired resistance to anti-PD1 therapy in patients with NSCLC associates with immunosuppressive T cell phenotype
S Hiltbrunner, L Cords, S Kasser, SN Freiberger… - Nature …, 2023 - nature.com
Immune checkpoint inhibitor treatment has the potential to prolong survival in non-small cell
lung cancer (NSCLC), however, some of the patients develop resistance following initial …
lung cancer (NSCLC), however, some of the patients develop resistance following initial …
Comprehensive outline of whole exome sequencing data analysis tools available in clinical oncology
Whole exome sequencing (WES) enables the analysis of all protein coding sequences in
the human genome. This technology enables the investigation of cancer-related genetic …
the human genome. This technology enables the investigation of cancer-related genetic …
grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads
L Czech, M Exposito-Alonso - Bioinformatics, 2022 - academic.oup.com
We developed grenepipe, an all-in-one Snakemake workflow to streamline the data
processing from raw high-throughput sequencing data of individuals or populations to …
processing from raw high-throughput sequencing data of individuals or populations to …
[HTML][HTML] Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize
P Liu, L Ma, S Jian, Y He, G Yuan, F Ge, Z Chen… - Journal of Integrative …, 2024 - Elsevier
Genetic transformation has been an effective technology for improving the agronomic traits
of maize. However, it is highly reliant on the use of embryonic callus (EC) and shows a …
of maize. However, it is highly reliant on the use of embryonic callus (EC) and shows a …
SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics
F Singer, A Irmisch, NC Toussaint, L Grob… - BMC medical informatics …, 2018 - Springer
Background Molecular precision oncology is an emerging practice to improve cancer
therapy by decreasing the risk of choosing treatments that lack efficacy or cause adverse …
therapy by decreasing the risk of choosing treatments that lack efficacy or cause adverse …
[HTML][HTML] PipeIT: a singularity container for molecular diagnostic somatic variant calling on the ion torrent next-generation sequencing platform
A Garofoli, V Paradiso, H Montazeri… - The Journal of Molecular …, 2019 - Elsevier
The accurate identification of somatic mutations has become a pivotal component of tumor
profiling and precision medicine. In molecular diagnostics laboratories, somatic mutation …
profiling and precision medicine. In molecular diagnostics laboratories, somatic mutation …
Music of metagenomics—A review of its applications, analysis pipeline, and associated tools
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and
rhythmic way. The paper enforces the significance of the research area, provides details …
rhythmic way. The paper enforces the significance of the research area, provides details …
iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data
A Anilkumar Sithara, DP Maripuri… - NAR Genomics and …, 2022 - academic.oup.com
Despite the tremendous increase in omics data generated by modern sequencing
technologies, their analysis can be tricky and often requires substantial expertise in …
technologies, their analysis can be tricky and often requires substantial expertise in …
Spatial distribution of private gene mutations in clear cell renal cell carcinoma
Simple Summary Tumours consist of multiple groups of similar cells resulting from differing
evolutionary trajectories, ie, subclones. These subclones are prevalent in clear cell renal cell …
evolutionary trajectories, ie, subclones. These subclones are prevalent in clear cell renal cell …