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• Angela Brooks (BME) Transcriptome Analysis of RNA Splicing and Cancer
• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• Phil Crews (Chem) Marine Natural Products as Potent Agents Against Human Disease
• Camilla Forsberg (BME) How Stem Cell Fate Is Decided
• David Haussler (BME) Cancer Genomics
• Lindsay Hinck (MCD) Loss of Growth Control and Cancer
• Doug Kellogg (MCD) Control of Cell Growth and Size
• Juhee Lee (AMS) Applications of Bayesian Models to Bioinformatics Data
• Scott Lokey (Chem) A Small Molecule Approach for Studying Signaling Pathways Related to Cell Motility and Cancer
• Pradip Mascharak (Chem) Delivery of Small Messenger Molecules to Biological Targets
• Karen Ottemann (METX) Bacterial Pathogens Sense and Respond to Host Environments
• Carrie Partch (Chem) Exploring the Molecular Basis for Circadian Timekeeping in Mammals
• Jevgenij Raskatov (Chem) Disease-Oriented Chemical Biology
• Seth Rubin (Chem) Molecular Mechanisms of Cell Cycle Regulation and Cancer
• Jeremy Sanford (MCD) Post Transcriptional Control of Gene Expression
• Holger Schmidt (EE) Integrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip
• Michael Stone (Chem) Assembly, Structure, and Regulation of the Telomerase Ribonucleoprotein
• Josh Stuart (BME) Computational Functional Genomics, with Application to Integrative Analysis of Cancer
• Bill Sullivan (MCD) Cell Cycle, Cytoskeleton and Pathogenesis
• John Tamkun (MCD) Regulation of Chromatin Structure and Gene Expression
• Zhu Wang (MCD) Cellular Behaviors in Prostate Cancer Initiation
• Ali Yanik (EE) Development of Nano-fluidic Platforms for Cancer Diagnostics
• Jin Zhang (Chem) The Application of Molecular and Nanomaterial Systems to the Detection and Treatment of Cancer
• Martha Zúñiga (MCD) Cellular and Molecular Regulation of Antigen Presentation in Health and Disease

Prof. Angela BrooksTranscriptome Analysis of RNA Splicing and Cancer

Angela Brooks, Dept. of Biomolecular Engineering

The Brooks lab focuses on the study of somatic mutations that cause changes to the transcriptome, particularly through mRNA splicing. We aim to gain a better understanding of how alternative splicing is regulated and the functional consequences of splicing dysregulation through the study of these cancer genome alterations. We are developing computational approaches to analyze genome and transcriptome sequencing data and developing high-throughput experimental approaches to characterize the functional impact of cancer variants. [More]

Brooks' Publications Brooks' E-Mail

Prof Manel CampsUse of Random Mutagenesis for Studies of Evolution and for Therapy

Manel Camps, Microbiology and Environmental Toxicology

The Camps laboratory studies how random changes in genetic information (mutations) facilitate the acquisition of new biochemical activities. They couple the generation of random mutant libraries with specific selections or screens to study the functional impact of individual point mutations and to establish how genes evolve in response to selective pressure. As model systems they use extended-spectrum beta-lactamase resistance and the evolution of alterations in the substrate specificity of the demethylase ALKBH2. This work is combined (in a collaboration) with high-end computational approaches aimed at anticipating the effect of individual mutations, alone, or in combination. A separate application of random mutant library generation in vivo is the use of mutation footprints to dissect the role of individual players involved in DNA replication. Finally, the Camps laboratory is applying concepts of directed evolution to whole genomics analysis, with an emphasis on cancer. The goal of these studies is to help understand the contribution of DNA repair genes to resistance to chemotherapy and to oncogenesis. [More]

Camps' Publications Manel Camps' Email

Prof Phil CrewsMarine Natural Products as Potent Agents Against Human Disease

Phil Crews, Dept. of Chemistry and Biochemistry

A primary goal of Phillip Crews' marine natural products research is to understand the chemistry of tropical marine sponges. Using bioassay-guided isolation assists us in the discovery of natural products potent against human diseases, such as cancer or viruses. Their search for novel active compounds incorporates elements of structure elucidation, but there are other dimensions to this research, including questions in the areas of chemical ecology, marine natural products biosynthesis, and the relationship between secondary metabolite chemistry and taxonomy... [More]

Crews' Publications Phil Crews' E-Mail

Prof Camilla ForsgergHow Stem Cell Fate Is Decided

Camilla Forsberg, Dept. of Biomolecular Engineering

Camila Forsberg's research group focuses on stem cell fate decisions that give rise to variant blood cell types. Are such decisions made by the stem cell itself, by its descendant multipotent progenitors, or both? To answer such questions, Forsberg's group conducts molecular lineage tracing of HSC differentiation in vivo. In order to elucidate the mechanisms of fate decisions, they employ global analyses, such as genome-wide gene expression analysis and chromatin remodeling assays. The ultimate goal of this research is to facilitate our ability to direct specific fates and improve clinical applications of hematopoietic and non-hematopoietic stem cell therapy. [More]

Forsberg Publications Camilla Forsberg's Email

Prof. David HausslerCancer Genomics

David Haussler, Biomolecular Engineering

The Haussler lab's informatics and experimental work in the area of cancer genomics, including the Xena Cancer Browser, provides a complete analysis pipeline from raw DNA reads through the detection and interpretation of mutations and altered gene expression in tumor samples. Haussler's group collaborates with researchers at medical centers around the world. He built the CGHub database to hold NCI's cancer genome data, co-founded the Genome 10K project so science can learn from other vertebrate genomes, co-founded the Treehouse Childhood Cancer Project to enable international comparison of childhood cancer genomes, and is a co-founder of the Global Alliance for Genomics and Health (GA4GH), a coalition of the top research, health care, and disease advocacy organizations that have taken the first steps to standardize and enable secure sharing of genomic and clinical data. [More]

Haussler Publications David Haussler's E-Mail

Prof Lindsay HInckLoss of Growth Control and Cancer

Lindsay Hinck, MCD Biology

One in eight women in the United States will develop breast cancer in her lifetime. Only about 15% of these cancers have been linked to specific gene mutations; therefore a major challenge in breast cancer research is to identify the causes of the disease. We have identified Slits as breast tumor suppressors that regulate several critical pathways controlling cell proliferation and migration. Current research focuses on developing therapeutic strategies to target these pathways. [More]

Hinck Publications Lindsay Hinck's Email

Prof KelloggControl of Cell Growth and Size

Doug Kellogg, Dept. of MCD Biology

Cells show extraordinary diversity in size and shape.  The mechanisms by which cells control their growth and size are poorly understood and represent a fundamental unsolved problem in cell biology.  The goal of the Kellogg laboratory's work is to elucidate these mechanisms. Their approach is to use biochemistry, genetics, and mathematical modeling to understand signaling networks that are required for control of cell size and cell growth. [More]
Kellogg's Publications Doug Kellogg's E-Mail

Prof Joel KubbyApplications of Adaptive Optics for Biological Microscopy

Joel Kubby, Dept. of Electrical Engineering

Professor Joel Kubby is collaborating with engineers, physicists and biologists to utilize Adaptive Optics for the improvement of deep tissue imaging of living cells. Current biological microscopy is incapable of obtaining high quality live imaging in samples greater than 30 microns beneath the plasma membrane, where many critical cellular processes occur. Much of the degradation in image quality is the result of local differences in the refractive index, both within the sample and between the sample and the immersion lens. Adaptive optics was first used to correct for image aberrations in astronomical imaging. Kubby and his collaborators have shown that the same principles that improved resolution in telescopes can be adapted to improve wide-field, confocal, two-photon, super-resolution and spinning disk microscopy systems that are crucial for biological research. [More]
Kubby Publications Joel Kubby's Email

Applications of Bayesian Models to Bioinformatics DataProf. Juhee Lee

Juhee Lee, Dept. of Applied Math and Statistics

Juhee Lee's research interests include the development of Bayesian models (parametric and nonparametric) and their application of to bioinformatics data. Her work features allocation models (with applications to tumor heterogeneity), roobust statistical modeling with nonparametric Bayesian methods, and clinical trial design. [More]

Lee's Publications
Juhee Lee's E-mail

Prof Scott LokeyA Small Molecule Approach for Studying Signaling Pathways Related to Cell Motility and Cancer

Scott Lokey, Chemistry and Biochemistry

The laboratory of Scott Lokey uses a small molecule approach, called chemical genetics, to study signaling pathways related to cell cycle checkpoints and the actin cytoskeleton. In one study, Lokey and his co-workers are developing screens of natural compounds that can be used to examine how cells detect their own DNA damage. Studies such as these might lead to development of a new class of chemotherapeutic agents. [More]

Lokey Publications Lokey's E-Mail

xxxDelivery of Small Messenger Molecules to Biological Targets

Pradip Mascharak, Chemistry and Biochemistry

Dr. Pradip Mascharak’s bioinorganic chemistry laboratory conducts basic and applied research regarding metal-based, nitric oxide (NO) and carbon monoxide (CO) carriers that release NO (or CO) when activated by light. In cancer cells, NO induces apoptosis (programmed cell death), which is the primary cellular mechanism of tumor clearing in chemotherapeutic treatments. Unlike conventional chemotherapy where the drug is distributed systemically, Mascharak’s synthetic “NO donors” allow unique control over where, when, and how much NO is released. Various chemical principles guide the design of such nitrosyls (NO carriers) that deliver NO to biological targets under specific conditions. Results of parallel theoretical studies are also utilized to elucidate the electronic origin of the NO photolability. This “photodynamic” approach has intriguing implications for the development of drugs in treating skin and other cancers. Recently the group has turned their focus on CO, another surprising addition to the list of small signaling molecule in biology. Low doses of CO has been shown to provide cytoprotective action to oxidatively damaged tissues (such as during stroke and ischemia). Mascharak's group has initiated syntheses of designed metal-CO complexes (based on Smart Design principles) that readily deliver CO to damaged tissues and neoplastic sites. Attempts are also being made to attach these NO/CO donors on inert matrices and employ the composites in catheters, powders, or patches for delivery of these two gaseous "drugs" in hospital settings. [More]

Mascharak Publications Pradip Mascharak's Email

Prof Karen OttemannHow Bacterial Pathogens Sense and Respond to Host Environments

Karen Ottemann, Dept. of Microbiology and Environmental Toxicology

Professor Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their host environment into pathogenic outcomes. Mistakes in sensation and subsequent gene expression by bacteria may result in their elimination by the host immune response or peristaltic flow. Elucidation of such processes will hopefully lead to identification of anti-bacterial drug targets. Ottemann is particularly interested in the role of outer membrane proteins and chemotaxis associated with the bacterium Helicobacter pylori. This pathogen infects some 3 billion humans and can lead to serious disease, including ulcers and cancer. [More]

Ottemann Publications Karen Ottemann's Email

Prof Rubin Exploring the Molecular Basis for Circadian Timekeeping in Mammals

Carrie Partch , Chemistry and Biochemistry

Mammalian physiology is synchronized into 24-hour rhythms that coincide with the solar day by an intrinsic molecular clock. As a global regulator of homeostasis, disruption of the circadian clock has profound consequences on human health, leading to depression, metabolic syndromes, cancer, and premature aging. The Partch lab studies how the 24-hour periodicity of this molecular clock is generated and how it integrates with the cell cycle to limit proliferation using cell biology, biochemistry and biophysical techniques. They are also interested in chemical biology approaches to modulate clock timing with structurally informed in vitro and cell-based screening platforms. [More]

Partch Publications Carrie Partch's E-Mail


Prof. Jevgenij A. RaskatovDisease-Oriented Chemical Biology

Jevgenij A. Raskatov, Dept. of Chemistry and Biochemistry

Raskatov draws inspiration from aging-related medicinally challenging questions, which are becoming increasingly pressing as life expectancy continues to rise (the cancer/inflammation interface is of specific interest). Raskatov's lab identifies biomolecular signaling nodes that are sufficiently well-understood at the molecular level, so that a biology problem can be translated into a chemistry problem. As chemists, their goal is to synthesize molecules and study their properties by means of NMR spectroscopy (1), crystallography (2) and DFT computation (3). Molecular scaffolds that show initial promise are tested in relevant biological systems both in cell culture (4) and in vivo (5). [More]

Jevgenij Raskatov's Publications Jevgenij Raskatov's Email

Prof RubinMolecular Mechanisms of Cell Cycle Regulation and Cancer

Seth Rubin, Chemistry and Biochemistry

The Rubin laboratory uses a variety of structural and biochemical techniques to investigate the molecular mechanisms that control the eukaryotic cell cycle. The aim is to elucidate detailed molecular pictures of protein-protein interactions and how these interactions are regulated by structural and chemical modifications. Improper regulation of these protein interaction networks is commonly associated with aberrant cell proliferation and cancer. [More]

Rubin Publications Seth Rubin's E-Mail


Prof. Jeremy SanfordPost Transcriptional Control of Gene Expression

Jeremy Sanford , Dept. of MCD Biology

Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA processing reactions such as pre-mRNA splicing, mRNA export, translation and mRNA decay are influenced by the interplay of trans-acting proteins with their cognate cis-acting RNA elements. We think that by elucidating the cis-acting RNA elements recognized by specific RNA binding proteins it will be possible to gain a better understanding of both the physiological relevance and mechanisms of action for these critical regulators of gene expression. [More]

Jeremy Sanford's Publications Jeremy Sanford's Email

Prof Holger SchmidtIntegrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip

Holger Schmidt, Dept. of Electrical Engineering

Optofluidics describes the combination of optics and microfluidics and holds great promise for novel devices for biomedical instrumentation, analytical chemistry and other fields that deal with liquid analytes. A highly desirable extension of optofluidics is to use integrated optics to replace the bulky microscopy analysis that is still commonly in use. This would allow development of a fully planar, fully integrated lab on a chip. We are using optofluidic approaches for early infectious disease and cancer detection and genome analysis. [More]

Schmidt Publications Holger Schmidt's Email

Prof Michael StoneAssembly, Structure, and Regulation of the Telomerase Ribonucleoprotein

Michael Stone, Dept. of Chemistry and Biochemistry

The Stone Research Group combines the use of biochemical and structural methods with newly emerging single-molecule techniques to probe the dynamics of protein-nucleic acid interactions and the molecular mechanisms of biological motors.  Our current area of focus is the structure and function of the telomerase ribonucleoprotein, an RNA-dependent DNA polymerase that maintains genomic stability by synthesizing repetitive DNA sequences at chromosome termini.  These short DNA repeats provide the foundation for specialized chromatin structures, called telomeres, which prevent deleterious chromosome fusion events by differentiating chromosome ends from sites of DNA damage.  It has been shown that telomere length typically decreases with every round of cell division, leading to the so-called ‘molecular clock’ hypothesis, wherein telomere length serves as a signal to control cellular lifespan. This notion is consistent with the finding that active telomere DNA synthesis is normally restricted to rapidly dividing cell types such as stem cells and the majority of human cancers. Our research seeks to elucidate physical mechanisms governing telomere length regulation, and in turn establish a conceptual framework within which to develop novel diagnostic and therapeutic strategies for human disease. [More]

Stone Publications Michael Stone's Email

Prof Josh StuartComputational Functional Genomics, with Application to Integrative Analysis of Cancer

Josh Stuart, Dept. of Biomolecular Engineering

Josh Stuart's background is in machine-learning applied to high-throughput datasets and an expertise in developing computational models to integrate multiple sources of molecular biology information. His research focuses on discovering how gene networks program cellular responses and search engines to scan large collections of high-throughput results to predict how genes function. His labrecently developed the PARADIGM pathway-based models to integrate multiple sources of gene activity to predict alterations and clinical outcomes in tumor samples to decipher pathway alterations in many cancer cohorts. Stuart co-leads a Genome Data Analysis Center for the TCGA project, co-chairs the pan-cancer TCGA effort, is a member of the bioinformatics pathway’s group for the International Cancer Genome Consortium, and directs the computational pathway analysis for a Stand Up To Cancer Dream Team to identify therapies for resistant prostate cancer. [More]

Stuart Publications Josh Stuart's Email

Prof Bill SullivanCell Cycle, Cytoskeleton and Pathogenesis

Bill Sullivan, Dept. of MCD Biology

The Sullivan lab uses the Drosophila embryo as a model system to investigate the mechanisms that drive furrow invagination during cytokinesis. Through a combination of cellular and molecular genetic approaches, the Sullivan group has showed that furrow formation requires coordinated cell cycle regulated and endocytic-based vesicle recruitment. These studies have also identified a new role for cell cycle checkpoints in coordinating the nuclear cycle with cytokinesis. More recently, the lab has applied these approaches toward understanding the mechanisms by which the widespread intracellular insect pathogen, Wolbachia, influences host nuclear and cytoplasmic cell cycles. [More]

Sullivan's Publications Bill Sullivan's E-Mail

Prof John TamkunRegulation of Chromatin Structure and Gene Expression

John Tamkun, Dept. of MCD Biology

The Tamkun lab investigates regulation of chromatin's high order structure and its role in gene expression. Composed of DNA and proteins, chromatin's ability to fold enables the eukaryotic genome to be packaged into an extremely small space inside the nucleus of the cell. Proper transcription and replication of the genome also depend upon precise regulation of these dynamic structures, with defects in these processes believed to underly many human diseases. [More]

Tamkun Publications John Tamkun's E-Mail

Prof Zhu WangCellular Behaviors in Prostate Cancer Initiation

Zhu Wang, Dept. of MCD Biology

Prostate cancer is the second leading cause of cancer death in men in the United States. Recent cancer genomics studies have suggested a variety of genetic alterations that may play a role in cancer initiation. Yet in which cells these genetic alterations occur remains unknown. There has been evidence suggesting that tumors originating from different cell types could have distinct pathology and disease outcomes. We attempt to identify the cell of origin for prostate cancer and dissect the interactions of basal and luminal cells in cancer initiation using mouse models, with the goal of translating our findings to better therapeutics. [More]

Wang Publications Zhu Wang's E-Mail

Prof Alli YanikDevelopment of Nano-fluidic Platforms for Cancer Diagnostics

Ali Yanik, Dept. of Electrical Engineering

Ali Yanik's current research focuses on Circulating Tumor Cell (CTC) detection from human blood, using nano-fluidic platforms for cancer diagnostics. His research interests includes nanoplasmonic and metamaterial devices for ultrasensitive infrared/terahertz spectroscopy of biomolecules/chemicals and high-throughput, cost-effective BioNEMS technologies for life sciences and point-of-care diagnostics. His expertise is in high-end nanolithography and bio-patterning as well as theory and engineering of nanophotonic devices. [More]

Yanik Publications Ali Yanik's Email

Prof Jin ZhangThe Application of Molecular and Nanomaterial Systems to the Detection and Treatment of Cancer

Jin Zhang , Dept. of Chemistry and Biochemistry

The Zhang research group is interested in the application of molecular and nanomaterial systems in conjunction with optical spectroscopy and related techniques for biomedical detection and treatment, with emphasis on cancer therapies and cancer biomarker detection.  Specific projects include: 1) investigation of mechanisms of photodynamic therapy and catalytic therapy based on porphyrins, phthalocyanines, and related compounds; 2) detection of small molecule, protein, and DNA cancer biomarkers using fluorescence based on quantum dots (QDs) and surface-enhanced Raman scattering (SERS) based on metal nanostrutcures; and 3) photothermal imaging and therapy of cancer using unique metal nanostructures.  This research involves systematic study of the structural, optical, and photophysical as well as photochemical properties of the materials using a combination of microscopy, x-ray, spectroscopy, and electrochemistry techniques. [More]
Zhang Publications Jin Zhang's Email

Prof Martha ZunigaCellular and Molecular Regulation of Antigen Presentation in Health and Disease

Martha Zuñiga, Department of MCD Biology

The Zúñiga lab is interested in the regulation of immune responses in health and disease.  Major Histocompatibility Complex (MHC) molecules (called HLA molecules in humans) present self, tumor, and pathogen-derived antigens to the T cells.  The presentation of MHC molecules in different cellular contexts is of paramount importance in determining immune responsiveness versus tolerance. One major project in the lab focuses on mechanisms of immunological tolerance to cutaneous antigens. We have found that skin-derived regulatory T cells can induce ..... [More]

Martha Zuñiga's Publications Martha Zuñiga's Email
 

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