-Omics

Research interests:

• AI and Machine Learning with particular emphasis on: Deep Learning, Neural Networks, Reinforcement Learning, and their Theoretical Foundations and Applications.
• Applications, particularly in the Natural Sciences:
  • Physics (High-Energy Physics, Cosmology, Quantum Mechanics);
  • Chemistry (Prediction of Molecular Properties, Prediction of Chemical Reactions, Drug Discovery, Chemoinformatics);
  • Biology (Neuroscience, Circadian Rhythms, Gene Regulation, Omic Sciences, Protein Structure Prediction, Bioinformatics, Systems Biology).

The Dai lab studies the intrinsic and extrinsic control of stem/progenitor cells in normal and diseased epithelial tissues. Skin – largest organ in the human body, is our major tissue of interest. Skin provides an essential physical and immunological barrier for organismal survival and health, and is a leading model for tissue stem cell research. The skin research field is populated by exceptional scientists and high-quality scientific literature, providing an intellectually stimulating ground for scientific interrogation.

The Hertel Lab focuses on understanding the mechanisms that allow for the generation of alternative splicing patterns. Their long-term goals are to understand how these processes are regulated, to relate the basic mechanisms of splice-site recognition to biological processes and to identify strategies to manipulate the expression of splicing isoforms in disease genes. To achieve these goals, they use a wide variety of approaches that include biochemistry, genetics, deep sequencing and bioinformatics.

The Lee Lab studies how transposons, widespread genomic parasites, influence genome function and evolution through epigenetic mechanisms, both in cis along linear chromosomes and in 3D nuclear space. They aim to identify genetic and dietary causes shaping variation in these transposon-mediated epigenetic effects and decipher the consequences on cellular functions that drive genome evolution within and between species.

The Liu Lab engineers specialized genetic systems that go beyond what nature’s genetic systems can do. They are especially interested in creating systems that dramatically accelerate the speed of biomolecular evolution, that reinterpret the genetic code, and that can record transient information as heritable genetic mutations. These systems are applied to the discovery of useful biomolecules, biopolymers, and therapeutics; the study of molecular evolution; cell and developmental biology; and the creation and evolution of synthetic life. The Liu Lab’s research spans the fields of genetic engineering, synthetic biology, chemical biology, cell biology, and directed evolution.

Key questions that guide the Liu Lab’s research include: What does the map between macromolecular sequence and function look like? How are nearly-infinite high dimensional sequence spaces, such as those defining RNA and protein function, productively searched? How does a gene’s evolutionary past shape its future? How does a cell’s past experiences influence its developmental future?

The Mortazavi Lab combines experimental work and computational analysis primarily in hematopoietic, skeletal muscle, and embryonic stem cells in human, mouse and other mammals to understand which regulatory elements are conserved, which elements are not conserved but functional, and which elements regulates what genes using a combination of ChIP-seq, DNA methylation, ATAC-seq and RNA-seq starting from ever low amounts as small as single cells and nuclei when practical.

The Ng Lab strives to characterize disease processes and how their molecular features evolve over time, with the ultimate goal of translating insights gained into novel diagnostic tools and therapeutic strategies to improve human health. Their experimental approach is to start with spatial omics analyses to characterize driver clones at the root of diseases throughout progression and treatment. They will then determine whether driver clone molecular risk and treatment response markers identified in primary tissues can be detected in biofluids. They will develop tools for tracking and forecasting driver clone dynamics by generating time-series omics data using disease models in mice, then implement and test rapid low cost diagnostic tests that assay for molecular risk and treatment response markers.

The Nie Lab works on computational systems biology, cell fates, multiscale biology, and tools for analyzing single-cell RNA-seq data, scientific computing, and computational mathematics. Topics of research interest include:

• Computational and Systems Biology
• Machine Learning
• Developmental Biology
• Stochastic Dynamics
• Scientific Computing
• Numerical Analysis

The Sandmeyer Lab studies retroviruslike elements using the budding yeast (Saccharomyces cerevisiae) retrotransposon Ty3. Retrotransposons make up almost half of the human genome but their regulation and impact on genomic function is not yet well understood; they study Ty3 as a model for understanding both retrotransposons and also retroviruses. Ty3 studies have elucidated the roles of virus structural protein in capsid assembly, roles of nucleoporins in nuclear entry and roles of transcription factors in integration specificity. They are currently focused on how RNA processing proteins help to localize and package the genomic RNA into particles. In addition, the laboratory is working to elucidate the genomic features which affect integration into chromosomal target sites. The laboratory uses a combination of molecular genetics, biochemistry and next generation sequencing to address these questions.

The lab is using nonconventional yeast to bioengineer metabolism to allow the biosustainable production of high-value chemicals. They developed a unique series of plasmids to allow combinatorial expression of genes for pathway engineering in Saccharomyces cerevisiae. However, S. cerevisiae is fermentative which restricts some of the metabolic studies that it supports. The lab therefore also studies a yeast, Yarrowia lipolytica, which has aerobic metabolism more similar to that of humans than that of S. cerevisiae. Y lipolytica stores excess carbon as lipid rather than polysaccharide. They sequenced, assembled and annotated a reference genome for the industrial CLIB89 strain of this yeast. Recently they completed transposon saturation mutagenesis of this strain in order to identify essential genes and to enable screening for conditionally essential genes. This approach is generally applicable to the development of new fungal systems in order to exploit their diverse metabolism for production of important chemicals.

The human genome contains less than 25,000 genes. However, the vast majority of our genes can produce multiple RNAs that encode different proteins and/or harbor different regulatory sequences. This is achieved largely by alternative mRNA splicing and polyadenylation. When, where, and how much is a specific RNA expressed?  How are these processes regulated? How does the mis-regulation of these processes contribute to human diseases? The Shi Lab is devoted to answering these questions. They combine biochemical, structural, and high throughput sequencing-based global analyses in their research.