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Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ERBB receptors in breast cancer cellsThe analysis of CAGE (Cap Analysis of Gene Expression) time-courses has been applied to examine the dynamics of enhancer and promoter by sequentially...
Research
Tumour draining lymph node-generated CD8 T cells play a role in controlling lung metastases after a primary tumour is removed but not when adjuvant immunotherapy is usedSurgical resection of cancer remains the frontline therapy for millions of patients annually, but post-operative recurrence is common, with a relapse rate of around 45% for non-small cell lung cancer. The tumour draining lymph nodes (dLN) are resected at the time of surgery for staging purposes, and this cannot be a null event for patient survival and future response to immune checkpoint blockade treatment. This project investigates cancer surgery, lymphadenectomy, onset of metastatic disease, and response to immunotherapy in a novel model that closely reflects the clinical setting. In a murine metastatic lung cancer model, primary subcutaneous tumours were resected with associated dLNs remaining intact, completely resected or partially resected.
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Timo LassmannFeilman Fellow; Program Head, Precision Health and Team Lead, Computational Biology
Research
CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural inductionAn estimated 3.5%-5.9% of the global population live with rare diseases, and approximately 80% of these diseases have a genetic cause. Rare genetic diseases are difficult to diagnose, with some affected individuals experiencing diagnostic delays of 5-30 years. Next-generation sequencing has improved clinical diagnostic rates to 33%-48%. In a majority of cases, novel variants potentially causing the disease are discovered.
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SAMStat 2: quality control for next generation sequencing dataSAMStat is an efficient program to extract quality control metrics from fastq and SAM/BAM files. A distinguishing feature is that it displays sequence composition, base quality composition and mapping error profiles split by mapping quality. This allows users to rapidly identify reasons for poor mapping including the presence of untrimmed adapters or poor sequencing quality at individual read positions.
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Electrostatic Filters to Reduce COVID-19 Spread in Bubble CPAP: An in vitro Study of Safety and EfficacyBubble CPAP may be used in infants with suspected or confirmed COVID-19. Electrostatic filters may reduce cross infection. This study aims to determine if including a filter in the bubble CPAP circuit impacts stability of pressure delivery. A new electrostatic filter was placed before (pre) or after (post) the bubble CPAP generator, or with no filter (control) in an in vitro study. Pressure was recorded at the nasal interface for 18 h (6 L/min; 7 cm H2O) on 3 occasions for each configuration. Filter failure was defined as pressure >9 cm H2O for 60 continuous minutes. The filter was weighed before and after each experiment.
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Bilateral murine tumor models for characterizing the response to immune checkpoint blockadeThis protocol describes bilateral murine tumor models that display a symmetrical yet dichotomous response to immune checkpoint blockade
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Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted TherapeuticsWe investigated the relationship between the sensitivity of hundreds of cell lines to hundreds of drugs, and the relative expression levels of the targets
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Identification of novel cerebellar developmental transcriptional regulators with motif activity analysisThe FANTOM5 cerebellum time series is a high-quality transcriptome database for functional investigation of gene regulatory networks in cerebellar development
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Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuliWe obtain a set of 57 candidate immediate early genes possessing promoters that consistently drive a rapid but transient increase in expression over time