COVID19

• A metabolic handbook for the COVID-19 pandemic paper
• A time-resolved proteomic and prognostic map of COVID-19 | Cell Systems, 2021 | paper

RNA biolgoy

• [review] RNA-based recognition and targeting: sowing the seeds of specificity | Nature reviews
• [review] A tale of non- canonical tails: gene regulation by post-transcriptional RNA tailing

General Cancer Biology

• [Review] The Effects of Conjugated Linoleic Acids on Cancer
• Recent advances in the molecular mechanism of sex disparity in hepatocellular carcinoma (Review)
• Glutathione Depletion Induced by c-Myc Downregulation Triggers Apoptosis on Treatment with Alkylating Agents1
• Testis-specific protein, Y-linked 1 activates PI3K/AKT and RAS signaling pathways through suppressing IGFBP3 expression during tumor progression
• Elevated expression and potential roles of human Sp5, a member of Sp transcription factor family, in human cancers
• A Systems Biology Approach to Investigating the Interaction between Serotonin Synthesis by Tryptophan Hydroxylase and the Metabolic Homeostasis
• Cancer Evolution | Nature collection | 2017 | link

liver cancer

• 2018 간세포종 진료 가이드라인 (대한간암학회, 국립암센터)

prostate cancer

normal prostate epithelium : basal cell, luminal cell, neuroendocrine cell Cell types can determine cancer type

• Hormone sensitive
  • hormone therapy
• castration-resistant prostate cancer different cancer subtypes have distinct histological profiles:
  • prostate adenocarcinoma
  • small cell prostate caner

Molecular Biology

• Deep computational analysis details dysregulation of eukaryotic translation initiation complex eIF4F in human cancers | Cell Systems, 2021 | paper

Cell Metabolism

• review Glutamine reliance in cell metabolism | Experimental & Molecular Medicine volume 52, pages1496–1516 (2020)
• review Fructose and Mannose in Inborn Errors of Metabolism and Cancer
• paper Metabolic Heterogeneity in Human Lung Tumors | Cell
• Small Molecule Inhibition of CPS1 Activity through an Allosteric Pocke
• an application of S1P, lung cancer cell cancer target
• Analyzing Tumor Metabolism In Vivo

Evolutionary Biology

• Sequencing the chimpanzee genome: insights into human evolution and disease | Nature Review Genetics
• Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution
• Evolution of DNA methylation in the human brain | Nature Communications, 2021
  • cell-type DNA methylation difference can extend to whole gene
  • species- and cell-type specific DNA methylation changes
  • Human specific DMRs are enriched in genic regions and enhancers
  • Cell-type differentially methylated regions are enriched in GWAS variants for neuropsychiatric disorders

Aging (장영목 교수 (Georgia tech))

• review The Hallmarks of Agin | Cell, 2013
• Sarcopenia :
• epigenetic regulation == memory in cell ??
• aging in MT
  • oxidative stress (mitochondrial) theyory of aging
  • Artificial Mitochondria Transfer: Current Challenges, Advances, and Future Applications | 2017
• Rejuvenation of aged progenitor cells by exposure to a young systemic environment | Nature
  • Parabiosis
  • youthful factors in bolld
  • human parabiosis-on-a-chip
    • review Organoids-on-a-chip | Science, 2019

Drug discovery (윤태영 대표, Oscotec)

• reductionism in science to technology
  • observations --> (deconstruct) principles --> (reconstruct) applications
  • plants --> chemistry (extract chemicals) --> drug
• post-modern drug discovery
  • gene : gene therapy (antisense, RNAi, mRNA, CRISPR, etc)
  • protein : biologics (proteins, antibodies, etc), small molecules
  • cell/gene therapies : stem cells, CART-T, mRNA, small molecules, etc
  • Tissue/organ : regenerative medicine, tissue engineering, etc
• Drug Discovery is Target validation
  • hypothesis : The disease is caused by gene and its target .
  • drug : hit the drug target

OMICS Bioinformatics

• Model-based assessment of mammalian cell Metabolic functionalities using omics data
• Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis
• Characterizing and measuring bias in sequence data
• Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
  • iHepatocytes2322
• protocol MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
• In silico learning of tumor evolution through mutational time series | PNAX, 2019 | paper | code
• A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data ##sequencing
• whole genome sequencing vs exon sequencing
  • Whole Genome Sequencing sequences the complete DNA of an organism. In the case of a human this corresponds to about three billion base pairs of DNA. Whole genome sequencing entails sequencing all coding (exons) and noncoding (intron) nuclear DNA as well as mitochondrial DNA. This allows researchers to generate large quantities of data, which can then be analyzed.
  • The exome makes up only 1.5% of the whole human genome, however ALL protein coding genes are found in the exome. Since most genetic disorders are correlated with mutations in protein coding genes, most physicians and scientists who use sequencing technologies for diagnostic purposes start with an analysis of the exome. Exome sequencing and analysis typically takes less time than whole genome sequencing at less than half the cost.

single cell omics

• Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing | Cell, 2019 | paper
• Clonal fitness inferred from time-series modelling of single-cell cancer genomes | Nature, 2021 | paper | Data
• chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
• https://satijalab.org/signac/articles/overview.html
• Comprehensive Integration of Single-Cell Data
• A comparison of automatic cell identification methods for single-cell RNA sequencing data
• https://github.com/lwtan90/scATACseq_wilsontan
• https://satijalab.org/signac/0.2/articles/pbmc_vignette.html

chromosome sturcutre interaction

• Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

tool

• Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
• edgeR
• DESeq2
• TCGAbiolinks
• A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

Database

• NCBI
• ENSEMBL
• UCSC
• TCGA
  • GDC Data User's Guide
  • Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data
• cBioPortal
• ENCODE
• GENCODE
• KEGG
• COSMIC homepage
• Drug Repurposing Hub | BROAD Institute | homepage
• Human Gene Mutation Database (HGMD)
• Human Protein Atlas (HPA)

medical bioinformatics

• Phenotypic signatures in clinical data enable systematic identification of patients for genetic testing
• A longitudinal big data apporach for precision health | 2019 Nature medicine