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Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
TLDR
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. Expand
SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization
TLDR
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. Expand
Combating subclonal evolution of resistant cancer phenotypes
TLDR
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. Expand
MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate.
TLDR
It is revealed that mouse and human models with a time-series single-cell transcriptome analysis reveal that MYC drives dynamic evolution of SCLC subtypes, suggesting that genetics, cell of origin, and tumor cell plasticity determine SclC subtype. Expand
bam.iobio: a web-based, real-time, sequence alignment file inspector
TLDR
The first complete iobio web app, bam.iobio, is reported, an open-source dashboard web application providing an insightful overview of the contents of these large, non–humanreadable BAM files and enabling users to further analyze their alignments, all in real time. Expand
A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology
TLDR
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. Expand
Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools
TLDR
The use of iobio, a web-based tool suite for intuitive, real-time genome diagnostic analyses, is described to identify the disease-causing variant in a patient with early infantile epileptic encephalopathy with prior nondiagnostic genetic testing. Expand
Ongoing Clonal Evolution in Chronic Myelomonocytic Leukemia on Hypomethylating Agents: A Computational Perspective
TLDR
SubcloneSeeker computational analysis algorithm is applied to whole exome sequencing (WES) and single nucleotide polymorphism (SNP) array data to uncover clonal architecture and evolution in CMML patients treated with 5-Aza on a prospective trial. Expand
RAPID CONVERSION OF CHRONIC MYELOID LEUKEMIA TO CHRONIC MYELOMONOCYTIC LEUKEMIA IN A PATIENT ON IMATINIB THERAPY
TLDR
Rapid conversion of chronic myeloid leukemia to chronicMyelomonocytic leukemia in a patient on imatinib therapy is shown to be a positive trend. Expand
OncoGEMINI: Software for Investigating Tumor Variants From Multiple Biopsies With Integrated Cancer Annotations
TLDR
OncoGEMINI is described, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course of treatment, and enables rapid searches for mutations that may be driving subclonal evolution. Expand
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