A5100362117- Neurobiology and Insect Physiology Research
- Cancer, Hypoxia, and Metabolism
- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- RNA and protein synthesis mechanisms
- Gene expression and cancer classification
- Invertebrate Immune Response Mechanisms
- Single-cell and spatial transcriptomics
- Microtubule and mitosis dynamics
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Ion Transport and Channel Regulation
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Radiomics and Machine Learning in Medical Imaging
- Cancer-related molecular mechanisms research
- Cancer Cells and Metastasis
- Olfactory and Sensory Function Studies
- Protein Structure and Dynamics
- Viral Infectious Diseases and Gene Expression in Insects
- Diet and metabolism studies
- Metabolomics and Mass Spectrometry Studies
- ATP Synthase and ATPases Research
- Photosynthetic Processes and Mechanisms
Janelia Research Campus
2023-2025
University of Notre Dame
2016-2025
Chengdu Third People's Hospital
2025
Chongqing Medical University
2025
Southwest Jiaotong University
2025
National Institute of Biological Sciences, Beijing
2019-2025
Wenzhou Medical University
2010-2025
Qilu Hospital of Shandong University
2025
Stanford University
2011-2024
Howard Hughes Medical Institute
2015-2024
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical contain key features representing the democratized nature collection process. To ensure proper use this large dataset associated genomic features, we developed standardized named Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major outcome endpoints. In...
<h2>Summary</h2> DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 types. Mutations with accompanying loss heterozygosity were observed in over 1/3 genes, including <i>TP53</i> <i>BRCA1/2</i>. Other prevalent included epigenetic silencing the direct genes <i>EXO5</i>, <i>MGMT</i>, <i>ALKBH3</i> ∼20% samples. Homologous recombination (HRD) was...
For more than 100 years, the fruit fly
We discuss the identification of features that are associated with an outcome in RNA-Sequencing (RNA-Seq) and other sequencing-based comparative genomic experiments. RNA-Seq data takes form counts, so models based on normal distribution generally unsuitable. The problem is especially challenging because different sequencing experiments may generate quite total numbers reads, or ‘sequencing depths’. Existing methods for this Poisson negative binomial models: they useful but can be heavily...
We discuss the identification of genes that are associated with an outcome in RNA sequencing and other sequence-based comparative genomic experiments. RNA-sequencing data take form counts, so models based on Gaussian distribution unsuitable. Moreover, normalization is challenging because different experiments may generate quite total numbers reads. To overcome these difficulties, we use a log-linear model new approach to normalization. derive novel procedure estimate false discovery rate...
Highlights•MYC paralogs are significantly amplified (28% of all samples)•MYC antagonists mutated (MGA, 4% samples) or deleted (MNT, 10% alterations mutually exclusive with PIK3CA, PTEN, APC, BRAF alterations•Expression analysis reveals pan-cancer and tumor-specific MYC-associated pathwaysSummaryAlthough the MYC oncogene has been implicated in cancer, a systematic assessment MYC, related transcription factors, co-regulatory proteins, forming proximal network (PMN), across human cancers is...
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful known to play pathophysiological roles cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, microRNAs 5,185 TCGA tumors 1,019 ENCODE assays. Our predictions included hundreds candidate onco- tumor-suppressor lncRNAs) whose somatic alterations account for...
In this work, we find that CD8
Abstract Summary To construct gene co-expression networks based on single-cell RNA-Sequencing data, we present an algorithm called LEAP, which utilizes the estimated pseudotime of cells to find that involves time delay. Availability and Implementation R package LEAP available CRAN Supplementary information data are at Bioinformatics online.
T cells are a critical component of the response to SARS-CoV-2, but their kinetics after infection and vaccination insufficiently understood. Using "spheromer" peptide-MHC multimer reagents, we analyzed healthy subjects receiving two doses Pfizer/BioNTech BNT162b2 vaccine. Vaccination resulted in robust spike-specific cell responses for dominant CD4
Hirschsprung disease and Waardenburg syndrome are human genetic diseases characterized by distinct neural crest defects. Patients with suffer from gastrointestinal motility disorders, whereas consists of defective melanocyte function, deafness, craniofacial abnormalities. Mutations responsible for have been identified, some patients described characteristics both disorders. Here, we demonstrate that PAX3, which is often mutated in syndrome, required normal enteric ganglia formation. Pax3 can...
Abstract After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit poorly. We suggest using variable for different positions, and propose two models to predict these based on local sequences. These explain more than 50% the variations lead improved estimates gene isoform expressions both Illumina Applied Biosystems data.
Precision oncology uses genomic evidence to match patients with treatment but often fails identify all who may respond. The transcriptome of these "hidden responders" reveal responsive molecular states. We describe and evaluate a machine-learning approach classify aberrant pathway activity in tumors, which aid hidden responder identification. algorithm integrates RNA-seq, copy number, mutations from 33 different cancer types across Cancer Genome Atlas (TCGA) PanCanAtlas project predict...
Abstract Bone is one of the most common sites for metastasis across cancers. Cancer cells that travel through vasculature and invade new tissues can remain in a non-proliferative dormant state years before colonizing metastatic site. Switching from dormancy to colonization rate-limiting step bone metastasis. Here we develop an ex vivo co-culture method grow cancer mouse bones assess cell proliferation using healthy or cancer-primed bones. Profiling soluble factors conditioned media...
Synonymous rare codons are considered to be sub-optimal for gene expression because they translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous Rare at the 5' terminus have been shown increase translational efficiency. Although a general functional role farther within has not yet established, several recent reports identified rare-to-common codon substitutions that impair folding encoded protein. Here we test hypothesis...