A5057577882- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- RNA modifications and cancer
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Genetic factors in colorectal cancer
- Plant Virus Research Studies
- Nanopore and Nanochannel Transport Studies
- RNA Research and Splicing
- Lung Cancer Treatments and Mutations
- Advanced Computational Techniques and Applications
- Epigenetics and DNA Methylation
- Protein Structure and Dynamics
- Hedgehog Signaling Pathway Studies
- Cancer Cells and Metastasis
- Advanced Algorithms and Applications
- Occupational and environmental lung diseases
- DNA and Nucleic Acid Chemistry
- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- TGF-β signaling in diseases
- Financial Distress and Bankruptcy Prediction
Freenome (United States)
2023
HealthPoint Communications
2022
Ankang City Central Hospital
2018
University of California, Irvine
2018
University of California, San Francisco
2011-2017
UCSF Helen Diller Family Comprehensive Cancer Center
2013-2016
Sun Yat-sen University
2013
Third Affiliated Hospital of Sun Yat-sen University
2013
Hebrew University of Jerusalem
2011
University of California, Los Angeles
2007-2011
The precisionFDA Truth Challenge V2 aimed to assess the state of art variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 call sets for one or more sequencing technologies (Illumina, PacBio HiFi, Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants updated Genome a Bottle benchmark genome stratifications. submissions included numerous...
SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly calls for both single nucleotide variants and small insertions deletions. The workflow currently incorporates five state-of-the-art callers, extracts over 70 individual genomic sequencing features each candidate site. A training set provided adaptively boosted decision tree learner create classifier predicting statuses. We validate our results with synthetic real data....
Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA $d$ spacings in bacteriophage $\ensuremath{\lambda}$ with mono-, di-, and polyvalent salt concentrations, for wild-type [$48.5\ifmmode\times\else\texttimes\fi{}{10}^{3}$ base pairs (bp)] short-genome-mutant (37.8 kbp) strains. From decrease increasing salt, deduce relative contributions DNA self-repulsion bending to energetics packaged phage genomes. We quantify interaction energies within intact by combining...
Molecular biomarkers hold promise for personalization of cancer treatment. However, a typical tumor biopsy may be difficult to acquire and not capture genetic variations within or across tumors. Given these limitations, genotyping using next-generation sequencing plasma-derived circulating (ct)-DNA has the potential transform non–small cell lung (NSCLC) management. Importantly, mutations detected in biopsied tissue must also ctDNA at different disease stages. Using AVENIO Surveillance kit...
// Hio Chung Kang 1, 2, * , Hong Kwan Kim 3, Sharon Lee 4 Pedro Mendez 1 James Wansoo Gavitt Woodard Jun-Hee Yoon Kuang-Yu Jen 5 Li Tai Fang Kirk Jones David M. Jablons 2 Il-Jin Thoracic Oncology Laboratory, Department of Surgery, University California San Francisco, CA, USA Comprehensive Cancer Center, 3 and Cardiovascular Samsung Medical Sungkyunkwan School Medicine, Seoul, Korea CureSeq Inc, Brisbane, Pathology, These authors have contributed equally to this work Correspondence to: Kim,...
Summary The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their pipelines submitted 64 callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants new GIAB benchmark sets genome...
Abstract With the rapid advancement of sequencing technologies, next generation (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS adopted clinical oncology to advance personalized medicine. Clinical applications precision require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during processes or data analysis. Therefore, there is an urgent need develop best practices mutation detection using and for standard...
Abstract Background The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, variant (SV) characterization plays a paramount role in target identification, oncology diagnostics, personalized medicine. As part the SEQC2 Consortium effort, present study established evaluated consensus SV call set using breast reference cell line matched normal control derived...
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Background Gremlin, a member of the Dan family BMP antagonists, is glycosylated extracellular protein. Previously Gremlin has been shown to play role in dorsal-ventral patterning, tissue remodeling, and recently angiogenesis. Evidence previously presented showing both over- under-expression different tumor tissues. Here, we sought quantify expression cancers lung performed vitro experiments check whether promotes cell growth proliferation. Methodology/Principal Findings Expression 161...
Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based mutation approach, demonstrated performance advantages on silico data.
Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) same sequence monomers. To elucidate dependence compactness on nature and extent branching, we represent ssRNA secondary structures as tree graphs which treat ideal branched polymers, use a theorem Kramers for evaluating their root-mean-square radius gyration, $\hat R_g = \sqrt {\langle {R_g^2 } \rangle...
We performed whole exome sequencing and gene expression analysis on a metastatic colon cancer to the lung, along with adjacent normal tissue of lung. Whole uncovered 71 high-confidence non‑synonymous mutations. selected 16 mutation candidates, 13 out mutations were validated by targeted deep using Ion Torrent PGM customized AmpliSeq panel. By integrating mutation, copy number microarray data, we identified JAZF1 gain-of-copy, suggesting its oncogenic potential for lung metastasis from...
The Hedgehog (Hh) signaling pathway has been implicated in stem cell maintenance and its activation is aberrant several types of cancer including mesothelioma. Protein kinase CK2 affects pathways through the mechanism phosphorylation. mRNA levels CK2α Gli1 were tested by quantitative RT-PCR immunohistochemistry staining mesothelioma samples lines. Down-regulated expression transcriptional activity demonstrated RT-PCR, Western blot luciferase reporter assay. In this study, we show that...
Despite recent advances, many cancers are still detected too late for curative treatment. There is, therefore, a need the development of new diagnostic methods and biomarkers. One approach may arise from detection extrachromosomal circular DNA (eccDNA), which is part cell-free in human plasma.First, we assessed compared two purification eccDNA plasma. Second, tested an easy application liquid biopsy-based assays.For comparison solid-phase silica method phenol/chloroform with salt...
Cullin4A (Cul4A) is a scaffold protein that assembles cullin-RING ubiquitin ligase (E3) complexes and regulates many cellular events, including cell survival, development, growth cycle control. Our previous study suggested Cul4A oncogenic in vitro, but its role vivo has not been studied. Here, we used transgenic mouse model to the potential of lung tumour development. After over-expression was induced lungs for 32 weeks, atypical epithelial cells were observed. 40 tumours visible...
LongISLND is a software package designed to simulate sequencing data according the characteristics of third generation, single-molecule technologies. The general architecture easily extendable, as demonstrated by emulation Pacific Biosciences (PacBio) multi-pass with P5 and P6 chemistries, producing in FASTQ, H5, latest PacBio BAM format. We demonstrate its utility downstream processing consensus building variant calling.LongISLND implemented Java available at...
AIM:To evaluate the role of mitochondrial microsatellite instability (mtMSI) in gastric carcinogenesis. METHODS:MtMSI was measured with PCR-single strand conformation polymophism (PCR-SSCP) 68 cases advanced cancer, 40 chronic gastritis, 30 intestinal metaplasia and 20 dysplasia. RESULTS:MtMSI observed 12.5% (5 40) 20.0% (6 30) metaplasia, 25.0% 20) dysplasia 38.2% (26 68) cancer.These findings showed a sequential accumulation mtMSI histological progression from chonic gastritis to cancer.An...
Among patients with vasodilatory shock, gene expression scores may identify different immune states. We aimed to test whether such are robust in identifying patients' state and predicting response hydrocortisone treatment shock.We selected genes generate continuous define previously established subclasses of sepsis. used these a patient's state. evaluated the potential for states assess differential effect two randomized clinical trials versus placebo initially identified associated...
We introduce a simple model for folding random-sequence RNA molecules, arguing that it provides direct route to predicting and rationalizing several average properties of secondary structures. The first step involves identifying the longest possible duplex, thereby dividing molecule into pair daughter loops. Successive steps involve similarly duplex in each new loops, with this process proceeding sequentially until loops are too small viable form. Approximate analytical solutions found...