MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate.
- A. Ireland, Alexi M. Micinski, T. Oliver
- Biology, MedicineCancer Cell
- 30 May 2020
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
- Steven Flygare, K. Simmon, R. Schlaberg
- BiologyGenome Biology
- 26 May 2016
It is shown that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles and enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.
SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization
- Y. Qiao, A. Quinlan, A. Jazaeri, R. Verhaak, D. Wheeler, G. Marth
- BiologyGenome Biology
- 26 August 2014
It is demonstrated how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient.
A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology
- Katrin P. Guillen, Maihi Fujita, A. Welm
- Medicine, BiologyNature Cancer
- 1 February 2022
A biobank of human-derived xenografts and organoids is presented and its value for high-throughput drug screening and applied precision medicine and a Food and Drug Administration (FDA)-approved drug with high efficacy against the models is uncovered.
Combating subclonal evolution of resistant cancer phenotypes
- Samuel W. Brady, J. McQuerry, A. Bild
- Biology, MedicineNature Communications
- 1 November 2017
The genetic and phenotypic subclonal evolution of four breast cancers through years of treatment is tracked to better understand how breast cancers become drug-resistant and suggest a phenotype-targeted treatment strategy to adapt to cancer as it evolves.
Mobile element insertions and associated structural variants in longitudinal breast cancer samples
- C. Steely, Kristi L. Russell, L. Jorde
- BiologyScientific Reports
- 11 February 2020
Overall, using a unique longitudinal dataset, it is found that most variants are likely passenger mutations in the four patients the authors examined, but some variants impact tumor progression.
bam.iobio: a web-based, real-time, sequence alignment file inspector
- Chase A. Miller, Y. Qiao, Tonya DiSera, Brian D'Astous, G. Marth
- Biology, Computer ScienceNature Methods
- 25 November 2014
Although large, whole-genome computation will remain essential for many tasks, it is expected that web-based, visually driven, real-time tools will offer a powerful new analysis modality for bioinformatics experts and bench scientists alike.
A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology
- Katrin P. Guillen, Maihi Fujita, A. Welm
- Medicine, BiologybioRxiv
- 11 March 2021
Development and characterization of a large bank of patient-derived xenografts and matched organoid cultures from tumors that represent some of the greatest unmet needs in breast cancer research and treatment are reported, revealing consistency between drug screening results in organoids and drug responses in Breast cancer PDX.
Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer.
- S. Groves, Geena V. Ildefonso, V. Quaranta
- BiologyCell Systems
- 1 August 2022
Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization
- T. Di Sera, M. Velinder, G. Marth
- BiologyScientific Reports
- 13 October 2021
It is demonstrated that adoption of gene.iobio in clinical and research settings empowers clinical care providers to interact directly with patient genomic data both for establishing clinical diagnoses and informing patient care, using sophisticated genomic analyses that previously were only accessible via complex command line tools.
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