Taejeong Bae
A5078372676- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Evolution and Genetic Dynamics
- Gene expression and cancer classification
- Pluripotent Stem Cells Research
- Genetic factors in colorectal cancer
- Computational Drug Discovery Methods
- Renal and related cancers
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Prenatal Screening and Diagnostics
- Microtubule and mitosis dynamics
- Colorectal Cancer Treatments and Studies
- Colorectal Cancer Screening and Detection
- Chromosomal and Genetic Variations
- Insect symbiosis and bacterial influences
- Genetics, Bioinformatics, and Biomedical Research
- 14-3-3 protein interactions
- Genomics and Chromatin Dynamics
- Gene Regulatory Network Analysis
Mayo Clinic
2015-2025
Mayo Clinic in Florida
2015-2024
WinnMed
2024
Mayo Clinic in Arizona
2021-2023
Gumi University
2020
Seoul National University
2010-2013
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set eight structural variant classes comprising both balanced unbalanced variants, which constructed using short-read DNA sequencing data statistically phased onto haplotype blocks 26 populations. Analysing this set, identify gene-intersecting exhibiting population stratification naturally occurring homozygous gene knockouts that suggest...
Somatic mosaicism in the human brain may alter function of individual neurons. We analyzed genomes single cells from forebrains three fetuses (15 to 21 weeks postconception) using clonal cell populations. detected 200 400 single-nucleotide variations (SNVs) per cell. SNV patterns resembled those found cancer genomes, indicating a role background mutagenesis cancer. SNVs with frequency >2% were also present spleen, revealing pregastrulation origin. reconstructed lineages for first five...
Mutations provide an enduring record Somatic mutations pepper our cells with change, but because they are not in the germline, do propagate to next generation. Bizzotto et al. leveraged data on distribution of somatic adults take a backward look at earliest moments human development. Calculation cellular lineages basis shared shows number from which body will develop when embryo gastrulates. The lineage for forebrain is identifiable, as asymmetrical fates spun out many gastrula cells....
Mosaic mutations can be used to track cell lineages in humans. We cloning analyze embryonic two living individuals and a postmortem human specimen. Of 10 reconstructed postzygotic divisions, none resulted balanced contributions of daughter tissues. In both individuals, one from the first cleavage was dominant across tissues, with 90% frequency blood. propose that efficiency DNA repair contributes lineage imbalance. Allocation brain correlated anterior-posterior axis, associating history fate...
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 schizophrenia, and 59 autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, had 20 60 detectable single-nucleotide mutations, but ~6% harbored hundreds mutations. Hypermutability was associated age damaging in genes implicated cancers and, some brains, reflected vivo clonal expansions. Somatic duplications, likely arising during development, were found ~5% normal...
Since detergent-resistant lipid rafts are involved in pathogen invasion, cholesterol homeostasis, angiogenesis, neurodegenerative diseases and signal transduction, protein identification the could provide important information to study their function. Here, we analyzed raft proteins isolated from rat liver by capillary liquid chromatography-tandem mass spectrometry. Out of 196 identified, 32% belonged or plasma membrane, 24% mitochondrial, 20% microsomal, 7% miscellaneous, 17% unknown...
The process of drug discovery and development is time-consuming costly, the probability success low. Therefore, there rising interest in repositioning existing drugs for new medical indications. When successful, this reduces risk failure costs associated with de novo development. However, many cases, indications have been found serendipitously. Thus a clear need establishment rational methods repositioning.In study, we established database call "PharmDB" which integrates data disease...
Abstract Background Post-zygotic mutations incurred during DNA replication, repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in from non-cancerous tissues poses significant challenges, particularly if the only are present a small fraction cells. Results Here, Brain Mosaicism Network conducts coordinated, multi-institutional study examine ability existing methods...
Background Anticancer therapies that target single signal transduction pathways often fail to prevent proliferation of cancer cells because overlapping functions and cross-talk between different signaling pathways. Recent research has identified balanced multi-component might be more efficacious than highly specific component in certain cases. Ideally, synergistic combinations can provide 1) increased efficacy the therapeutic effect 2) reduced toxicity as a result decreased dosage providing...
Abstract When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant that evade surveillance can lead to cancer. Neurons with karyotypes arise during neurotypical brain development, but neurons almost never origin of cancers. Instead, mutations in bring about neurodevelopmental disorders, and contribute polygenic landscape neuropsychiatric neurodegenerative disease. A subset human harbors idiosyncratic copy number variants (CNVs, “CNV neurons”),...
Abstract The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. molecular determinants that distinguish benign malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Free (CFP) patients. CAPs had tissues the residual polyp origin contiguous cancer; CFPs matched to based on size, histology dysplasia. determine whether features CFPs, conducted Whole Genome Sequencing, RNA-seq, RRBS over 90 31...
Epithelial ovarian cancer (EOC) commonly acquires resistance to chemotherapy, and this is the major obstacle better prognosis. Elucidating molecular targets altered by chemotherapy critically required understand overcome drug resistance. As a combination including paclitaxel prevalent prescription for treatment of EOC, uncover gene expression in paclitaxel-resistant we analyzed multidirectional microarray profiles both EOC cell lines patients with Cyclin-dependent kinase 1 (CDK1) was found...
Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon human brain cells, with potential functional consequences. Using clonal approach, we previously detected 200-400 mosaic SNVs per cell three fetal brains (15-21 wk postconception). However, variation has not yet been investigated. Here, discover validate four (SVs) same resolve their precise breakpoints. The SVs were of kilobase scale...
The CRISPR-Cas9 system has enabled researchers to precisely modify/edit the sequence of a genome. A typical editing experiment consists two steps: (1) cultured cells; (2) cell cloning and selection clones with without intended edit, presumed be isogenic. application may result in off-target edits, whereas will reveal culture-acquired mutations. We analyzed extent former latter by whole genome sequencing three experiments involving separate genomic loci conducted independent laboratories. In...
// Yi Rang Kim 1,* , Mi Sung Park 2,* Ki Hwan Eum 3 Juhee Jeong Won Lee 4 Taejeong Bae 5 Dae Ho 6 and Jin Woo Choi 3,7 1 Department of Hemato-Oncology, Yuseong Sun Hospital, Daejeon, Republic Korea 2 Institute for Metabolic Disease, School Medicine, Wonkwang University, Iksan, Jeonbuk, Interfused Biomedical Science Dental Research Institute, Dentistry, Chonbuk, Obstetrics Gynecology, Samsung Medical Center Sungkyunkwan University Seoul, Division Statistics Informatics, Health Sciences...
Abstract Background Gene set analysis is a powerful method of deducing biological meaning for an priori defined genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways gene ontology (GO) terms. Major difficulties towards interpretation are integrating diverse types annotation categories and exploring the relationships between terms similar information. Results GARNET (Gene Annotation Relationship NEtwork Tools) integrative platform with many...
Abstract Background Gene expression signatures have been commonly used as diagnostic and prognostic markers for cancer subtyping. However, frequently include many passengers , which are not directly related to progression. Their upstream regulators such transcription factors (TFs) may take a more critical role drivers or master provide better clues on the underlying regulatory mechanisms therapeutic applications. Results In order identify regulators, we took known 85 signature genes...