Publications by authors named "M T Kircher"
PET/CT targeting fibroblast activation protein α (FAP) in cancer-associated fibroblasts shows promise in theranostics. Here, we report the case of a 31-year-old woman with hormone receptor-positive/human epidermal growth factor receptor 2-negative breast cancer who presented with rising CA15-3 for further diagnostic workup. Whereas [18F]FDG PET/CT was unremarkable, novel [68Ga]RTX-1363 PET/CT revealed intense tracer accumulation in thoracoabdominal lymph nodes and both ovaries.
View Article and Find Full Text PDFThe human genome contains millions of candidate cis-regulatory elements (cCREs) with cell-type-specific activities that shape both health and many disease states. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these cCREs. Here we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of more than 680,000 sequences, representing an extensive set of annotated cCREs among three cell types (HepG2, K562 and WTC11), and found that 41.
View Article and Find Full Text PDFArticle Synopsis
- Cell-free DNA (cfDNA) serves as an important biomarker from urine or blood, but lacks a standardized processing method, which hinders the integration of innovative analysis strategies.
- The cfDNA UniFlow is introduced as a comprehensive, standardized workflow for processing cfDNA samples, developed in Snakemake, and capable of working on both individual computers and larger clusters, with various built-in quality control methods.
- This automated pipeline includes functionalities like bias correction and signal extraction, aiming to facilitate future cfDNA research and clinical applications, with all resources available on GitHub for further access.
Objective: To evaluate cochlear implant speech perception among patients with sporadic inner ear schwannoma who underwent ipsilateral implantation.
Study Design: Retrospective multi-institutional cohort study.
Setting: Eleven tertiary academic medical centers across Germany, Denmark, and the United States.
LBFextract: Unveiling transcription factor dynamics from liquid biopsy data.
Comput Struct Biotechnol J
December 2024
Motivation: The analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation, but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns.
Results: We introduce Liquid Biopsy Feature extract (LBFextract), a comprehensive package designed to streamline feature extraction from cfDNA sequencing data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies.