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 …

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 …

Comprehensive outline of whole exome sequencing data analysis tools available in clinical oncology

Á Bartha, B Győrffy - Cancers, 2019 - mdpi.com
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 …

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 …

[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 …

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 …

[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 …

Music of metagenomics—A review of its applications, analysis pipeline, and associated tools

B Wajid, F Anwar, I Wajid, H Nisar, S Meraj… - Functional & integrative …, 2022 - Springer
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 …

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 …

Spatial distribution of private gene mutations in clear cell renal cell carcinoma

AL Moore, AA Batavia, J Kuipers, J Singer, E Burcklen… - Cancers, 2021 - mdpi.com
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 …