CCMB Affiliated Faculty

His research interests include parsing, corpora, statistical methods, documentation of endangered languages, human sentence processing, machine learning and language acquisition, information extraction, question answering, spoken dialogue systems, syntax, prosody, and semantics.

Our laboratory applies solution state NMR spectroscopy to investigate the molecular basis of RNA function in processes ranging from gene expression (e.g. transcriptional activation and translation) to virion functioning (e.g. genome packaging and reverse transcription). We make extensive use of new NMR techniques involving measurements of residual dipolar couplings in determining global...

The central theme of my research is Monte Carlo methods; particularly methodological and theoretical aspects of Markov Chain Monte Carlo (MCMC). I'm also genuinely interested in statistical modeling (particularly form a Bayesian perspective). I have some applied ongoing projects in social science and biology

The effects of sensory experience and sleep on neural circuits, mechanisms underlying nervous system plasticity and memory formation.

Numerical analysis and interpretation of digital histological (whole-slide) data sets in tandem with expression data and other high-order data, Vector Quantization (VQ) tools and Gallois Fields, design of support vector engines for automated region-of-interest based image repository query.

Research: My main research interest is in the old-fashioned goal of Artificial Intelligence (AI), that of building autonomous agents that can learn to be broadly competent in complex, dynamic, and uncertain environments. The field of reinforcement learning (RL) has focused on this goal and accordingly my deepest contributions are in RL. More recently, I have been taking seriously the challenge...

Statistical design and analysis of human gene mapping studies of common multifactorial diseases. Genome-wide association and sequencing studies.
Application to type 2 diabetes and related traits, and bipolar disorder.

Research in the group of Charles L. Brooks III in the Department of Chemistry and Biophysics Program at the University of Michigan is focused on the application of statistical mechanics, quantum chemistry and computational methods to chemically and physically oriented problems in biology.

This laboratory's research is aimed at finding genes involved in behavioral and neurological and psychiatric diseases, especially related to depression and drug abuse. With the Human Genome sequenced, unprecedented numbers of genetic variants identified, untangling these risk factors is now possible and has started in my laboratory. This includes work on the phenotypes, on novel techniques to...

Camper lab focuses on development and function of the neuroendocrine system using transgenic mice, gene targeting, and molecular genetics analysis of mouse mutations. Bioinformatics projects ongoing in the lab include cross species DNA sequence comparisons to identify regulatory elements and analysis of 30,000 embryonic pituitary cDNA sequences in our database

Dr. Cavalcoli has broad research experience beginning with his PhD and post-doctoral research in molecular biology and virology. He received his PhD in 1993 from LSU, Baton Rouge in Virology and did a post-doc at University of Pittsburgh. In 1996, he made a transition to bioinformatics during a second post-doc at Parke-Davis in Ann Arbor. He has 12 years of experience with development and...

Dr. Andrew C Chang is currently working in collaboration with Dr. David Beer studying the pathogenesis of esophageal cancer. His particular interests include studying mechanisms of esophageal adenocarcinoma treatment resistance and chemoprevention.

Clinical projects under development include studies aimed at assessing outcomes after thoracic surgery among elderly patients and devising...

Dr. de Wet received a Ph.D. in Biology from the University of California, San Diego. He headed a molecular biology lab at Pfizer Inc in Groton, CT that initially worked on cloning and expressing mammalian genes and later specialized in central nervous system molecular biology. In 1998, Dr. de Wet moved to the bioinformatics group at Pfizer and worked on projects to identify genes from genome...

Our laboratory applies genomic and metagenomic analyses of microorganisms to problems in environmental and geological science. Applications in bioinformatics focus on comparative genomics and 'binning', whereby fragmentary metagenomic sequences of unknown origin are assigned to organisms on the basis of genome signatures. Of particular interest in this area are self-organizing maps of...

Dr. Duhaime uses (meta)genomic tools to investigate two realms of marine microbiology: (1) ocean plastic-microbe associations and the role of microbes in the fate of marine plastics, and (2) the evolution and ecology of ocean viruses and their microbial hosts, at both the community and single isolate level. Bioinformatic applications include developing strategies to manage large amounts of...

Dr. Feldman's laboratory focuses on the role of growth factors in neuronal growth and neuroprotection. The lab is specifically interested in the neurotrophic properties of the insulin-like growth factors I and II (IGF-I, IGF-II). They use molecular biology, gene therapy and protein biochemistry in their research. The lab primarily studies Amyotrophic Lateral Sclerosis (ALS) and Diabetic...

My research is devoted to understanding biological clocks. I use techniques from many fields, including computer simulation, detailed mathematical modeling and mathematical analysis, to understand biological timekeeping. My research aims to generate predictions that can be experimentally verified.

Assembly of nanoscale systems; supercooled and metastable liquids and complex fluids, colloids, and complex fluids; biomimetic materials design; computer simulation.

Our research involves the use of computational approaches, based on both biophysics and bioinformatics, to study the structure, function and evolution of biological macromolecules.

We are particularly interested in nature’s nanomachines: molecular motors and switches, which lie at the heart of biological processes, from the division and growth of cells...

The Gumucio laboratory works on endoderm/mesoderm cross-talk during organogenesis of the small intestine. An important signaling molecule is hedgehog, which is secreted by the endoderm and acts on several different cell types in the mesoderm. We are developing mouse models to explore this signaling and we are investigating in silico tools for the identification of hedgehog target genes and...

The Hanlon laboratory work is on combinatorics and new facets of the Macdonald Conjectures.

Network topology discovery, statistical pattern recognition, multimodality information integration, spatio-temporal modeling and analysis.

Early Post-Implantation Mammalian Body Patterning

Post-implantation development requires precisely coordinated cellular movements in preparation for gastrulation. We have characterized and genetically mapped a spontaneous X-linked mouse mutant, Polypodia (Ppd), which we discovered and established as a mutant line using in vitro fertilization and genetic crosses to explore early post-...

Prof. Jagadish studies the integration of data from multiple sources, and the usability, by non-technical users, of complex databases. Some questions he asks are: What happens when you can connect many different databases that are autonomously organized and managed? How can you query and integrate and analyze all the information that you potentially have access to? How can one represent, and...

My research interests include investigating the role of cell-type-specific genes in kidney disease initiation and progression, and applying systems biology approach to develop non-invasive molecular markers that can predict disease progression at early stage using large multi-center study cohorts.

His research interests lie in areas of medical genetics and population genetics, including the analysis of next-generation sequencing data, genetic association mapping of rare variants, genetics of polygenic traits, genetics-driven approach to drug discovery, association studies with unstratified population, confounding-conscious analysis of high-throughput biological data, fine-scale...

My research interests involve the analysis of high throughout omics data, focusing primarily on metabolomics, and the development of computational methods and tools for the analysis and integration of metabolomics data with other types of genomic data. I am also interested in biomedical ontologies and one of my current projects involves the development of Informed Consent Ontology.

My...

We study the mechanisms of small RNA function in C. elegans and mammalian systems using traditional and high-throughput methods, including massively-parallel sequencing, genome tiling microarrays, large-scale proteomics, and genome-wide RNAi screens. These projects provide great bioinformatic challenges to integrate diverse data and design computational predictions derived from these analyses...

Alexey Kondrashov is working on a variety of subjects in evolutionary genetics. His laboratory is trying to measure the rate of spontaneous mutation in Drosophila melanogaster, using several phenotype-based approaches. Also, he studies selection at the sequence level and parallelism in protein evolution using a comparative genomics approach.

Systems biology of renal diseases, including nephrotic syndrome, diabetes, hypertension and autoimmune diseases of the kidney. Coordination of NIH ORDR rare disease Nephrotic Syndrome Study Network for multi scalar analysis of glomerular disease: Anaylsis of genome wide expression data sets for molecular marker identification, transcriptional pathway mapping, promoter modeling and systems...

Our lab's research interests are in biopolymer dynamics, including dynamics of DNA, and DNA/protein interactions. We also use molecular dynamics methods to simulate lipid membranes, and interactions between lipid membranes and proteins, peptides, or nanoparticles. We also use microfluidic devices to study DNA/protein interactions or for genomic applications.

Genetic and genomic analyses of complex phenotypes, including bipolar disorder, cancer, blood clotting disease, and traits involving animal models and human microbiomes. Our approach emphasizes statistical analysis of genome-scale datasets (e.g, gene expression and genotyping data, results from next-generation sequencing), evolutionary history, bioinformatics, and pattern recognition.

The research goal of our lab is to unearth fundamental mechanisms underlying the diverse and complex functions of biological systems, and to engineer them for the development of beneficial biotechnologies, through a multidisciplinary approach integrating mathematical modeling, computer simulation and wet-lab experiments. More specifically, one part of our lab focuses on the quantitative...

Dr. Ljungman works on mechanisms of p53 activation and cellular responses to DNA-damaging agents.

The Lubman Research Lab is involved in developing novel biotechnologies to solve difficult biological problems. The focus of the work has been in the field of Proteomics and Cancer Research. Proteomics involves the study of the protein expression of a cell, where proteins are the entities that perform the functions of the cell. Dr. David M. Lubman's work has involved developing methods to...

Our group aims to explore the function and physiological role of novel enzymes and lipids involved in the development of neurological diseases and cancer. To achieve these goals, we propose to bridge chemical, analytical, and biological approaches to identify novel disease targets and develop chemical approaches for therapeutic intervention. Our expertise in cell and molecular biology,...

Genetics of bipolar disorder, genetics of major depression, longitudinal outcomes and translational research in mood disorders. Dr. McInnis directs a large clinical research enterprise focused on bipolar disorder genetics and longitudinal outcomes. Patients are cared for in a large clinic with 4 nurse practitioners, 2 social workers, 3 residents, and 3 attending psychiatrists. We are have an...

Proteomic data analyses especially in identification and characterization of known and novel alternative splice variants in cancer. Interaction network and pathway analyses of the splice variants expressed in cancer, structural comparisons between splice variants.

Dr. Michailidis works on computational problems in genomics and proteomics, modeling of biological networks, machine learning, applied probability, stochastic processing networks, and network tomography.

Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested in analyzing complex regions of the genome that are not easily resolved through modern sequencing approaches and which may exhibit interesting...

Dr. Nesvizhskii's research interest is in the field of quantitative proteomics, with a focus on the development of computational methods for processing and extracting biological information from complex proteomic datasets. Similar to other global high throughput technologies such as microarray gene expression analysis, proteomics is extremely dependent on the ability to quickly and reliably...

Medical informatics, decision analysis.

Professor Orr’s research centers on systems where the properties are controlled by the characteristics of surfaces or interfaces. As designed structures become ever smaller, their surface characteristics begin to influence, or even control, their behavior. Often the research involves scanning probe microscopies such as STM and AFM. Specific examples of research interests include: studies of...

I am a theoretical ecologist interested in population and community dynamics. My research areas encompass: (1) The spatio-temporal dynamics of nonlinear ecological systems for antagonistic interactions (predator-prey, host-parasite, and disturbance-recovery), particularly approaches to scale-up systems from small, individual, levels to more aggregated, population, levels, and approaches to...

Dr. Pienta's laboratory focuses on defining cancer as a complex adaptive system, with a special emphasis on understanding the biology of prostate cancer metastasis. The laboratory defines metastasis as a set of defined steps encompassing emigration, migration, and immigration of the cancer cells. Within each of these steps there exist Boolean network nodes that can be identified and targeted...

Dr. Radev's research interests include graph algorithms, semi-supervised machine learning, natural language processing, information retrieval, lexical networks, and applications to bioinformatics, political science, and webometrics.

We are interested in understanding mechanisms of chemically induced neurological and vascular diseases, and developing biomarkers of exposure and disease. In our lab and through collaborations, we study interactions of small molecules with target proteins using computational molecular modeling, kinetics, optical and fluorescence spectroscopy, protein mass spectrometry, quantitative structure-...

Dr. Rosania's laboratory studies the mechanism of action of emerging chemotherapeutic agents for treating cancer and degenerative diseases. Dr. Rosania's research is providing a fresh, new approach to the development of novel chemotherapeutic strategies, by combining knowledge of the mechanism of action of small molecules together with mechanistic insights into molecular process of fundamental...

Numerical and experimental work in disordered materials systems, including biological tissues and energetic materials. Design of batteries, including engineered and bioengineered constructs, and optimization of power supplies.

Dr. Schloss's research looks at resistance of the gut microbiota to perturbations such as colonization by exogenous pathogens and to mutations in host genes that give rise to tumors. To address these biological questions we develop computer software to process and analyze next generation sequencing data.

Dr. Schwartz's research interests include regulation of gene expression by growth factors, including: induction of expression of early response proto-oncogenes - molecular mechanisms by which transcription is stimulated, synergism among growth factors in such induction, consequences of altered expression of oncogenes on cell function.

Identification of genetic variants for type II diabetes and bipolar disease: My primary research interest is the identification of genetic variants that increase the risks of common diseases. For type II diabetes, as part of the Finland-United States Investigation of NIDDM genetics (FUSION) study, and for bipolar disease, as part of the Pritzker Neuropsychiatric Disorders Research Consortium,...

Research in the Sept lab covers four primary areas. The first focuses on the molecular interactions underlying cell migration, a process central to many aspects of development, differentiation and the cellular response to diseases such as cancer. Related to this is work characterizing and developing drugs that target sub-cellular filaments to treat parasitic diseases like toxoplasmosis,...

My research efforts over the past decade have evolved into several programs that are distinct in focus, yet coalesce into an overriding theme that include molecular genetic, biochemical and bioorganic chemical studies of microbial natural product biosynthesis. Metabolic engineering and combinatorial biosynthesis are powerful approaches for harnessing the tremendous metabolic capabilities of...

I have deep roots in biology and computer science. My primary research focuses on phylogenetic dataset construction, rates of evolution (molecular and character), and large- and small-scale biogeographic evolution.

There are more than 130 different therapeutic proteins or peptides that are used to treat a broad range of illnesses. One of these proteins, tissue plasminogen activator (tPA), has been used to treat myocardial infarction and stroke. Dr. Stringer's laboratory has determined that in addition to its proteolytic function, tPA has anti-inflammatory activity. The combination of these two...

Longitudinal and survival analysis, cure models, missing data, Box-Cox transformations, statistical methods for bioinformatics, surrogate and auxiliary variables, statistical modelling of biomedical data.

Multiscale simulations of complex systems, nanoscience, interactions of nanoparticles with biomolecular assembly, nanoparticle growth and self-assembly.

Dr. Wang's focus is on the development of new computational methods for drug design and discovery, chemo-informatics and bioinformatics, and protein folding. He works on discovery, design, synthesis, and development of new small molecule therapeutics for treatment of cancer and neurological diseases by targeting crucial regulators of apoptosis, signal transduction molecules and dopamine...

Emotional regulation of complex behaviors such as reinforcement, feeding, and stress are central to proper functioning of both animals and humans. This laboratory focuses on CNS circuits and cellular systems that participate and regulate these states and related pathological conditions. Using a variety of molecular, anatomical, behavioral and pharmacological approaches, it is possible to focus...

I'm interested in studying complex genetic diseases, particularly the genetics of quantitative traits such as lipid levels and human obesity. I've also been recently working on imputation of ungenotyped markers, population genetics, bioinformatics, and understanding the function behind genetic associations.

Evolutionary genetics and genomics, evolution of development

We study the pathophysiology of and investigate new treatments for acute lung injury and acute respiratory failure. Particular interests include the mechanisms leading to lung edema and functional failure and laboratory techniques that can be used to quantify such changes. We are particularly interested in the role of complement activation in the development of injury and interactions between...

Emergence and maintenance of infectious diseases and antibiotic resistance, integrated approach to study bacterial pathogens using epidemiologic, genomic, and informatic tools, and mechanisms of microbial pathogenesis.

Information systems, health informatics, technology adoption and acceptance, evaluation of impact of technologies, human factors and HCI issues.

The research done in our laboratory focuses on understanding the dynamical underpinnings of neural activity that is underlying brain cognitive function as well as its pathologies. That is, we would like to understand generic principles of the formation of spatiotemporal patterns in coupled dynamical systems that mediate neuronal communication and facilitate formation of different cognitive and...