Coen Adema , PhD
Associate Research Professor
Department of Biology
University of New Mexico

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Research interests

Comparative immunobiology, molecular aspects and cell biology of parasite/invertebrate host compatibility, digenean/snail interactions, genomics of molluscs.

John "Joe" Alcock, MD
Assistant Professor
Department of Emergency Medicine
University of New Mexico School of Medicine

Research interests

My research investigates how tissue damage mediated by innate immune cells in reperfusion injury may have a survival benefit in infections. The antisepsis effect, termed "hemostatic containment," is triggered by signals that convey susceptibility to infection, such as poor blood flow and oxygenation. In active and incipient infections, the host accepts some sacrifice of body tissues while preventing pathogens from gaining access into sterile sites. This tradeoff prevents bacteremia and promotes survival in diseases such as abscesses. Other diseases mimic infection-prone states and elicit costly host injury that exceeds antibacterial benefits.

Michelle Baker , PhD
Research Assistant Professor
Department of Biology
University of New Mexico

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Research interests

The aims of my research are to examine the mechanisms that play a role in fetal maternal tolerance in marsupials, using the South American opossum (Monodelphis domestica) and the northern brown bandicoot (Isoodon macrourus) as model species. Mechanisms that have been identified as being important for the maintenance of pregnancy in eutherian mammals, including the expression of MHC, IL-10 and FasL as well as T cell and NK cell activity will be examined in these two species. A comparison between the opossum and the bandicoot, two species with similar gestation periods but different levels of placentation should provide some interesting insights into the maintenance of fetal maternal tolerance in mammals

Ulfar Bergthorsson , PhD
Assistant Professor
Department of Biology
University of New Mexico

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Research interests

Molecular evolution; evolution of bacterial and organellar genomes; horizontal gene transfer; evolution of RNA editing, gene duplication and evolution of novel gene function; evolution of mutation rate.

Sara Brant , PhD
Research Assistant Professor
Department of Biology
University of New Mexico

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Research interests

I study the evolution and global diversity of schistosomes, with a focus on avian schistosomes (Trichobilharzia) and the etiology and epidemiology of cercarial dermatitis in North America.

James Brown, PhD
Distinguished Professor
Department of Biology
University of New Mexico

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Research interests

Community ecology and biogeography, with special projects on granivory in desert ecosystems; biogeography of insular habitats; and structure of dynamics of geographic-scale assemblages of many species.

Charlie Cunningham, PhD
Assistant Professor
Department of Biology
University of New Mexico

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Research interests

Schistosomiasis is a disease caused by trematode flatworms of the genus Schistosoma and affects more than 200 million people worldwide. Although schistosomiasis is prevalent throughout the tropics, 85% of infected individuals live on the African continent. The estimated mortality owing to Schistosoma mansoni and S. haematobium in sub-Saharan Africa is 280,000 per year. Presently, the drug of choice for all forms of schistosomiasis is praziquantel but little is understood of its mode of action and indications of emerging drug resistance are becoming apparent.

The life cycles of schistosomes are complex, including both a vertebrate and invertebrate host. While developing within both hosts, they are exposed to hostile immune responses, and, during the transition between hosts, survive in an aquatic environment in which they may encounter pathogenic microorganisms. To withstand these immune and environmental challenges as well as treatment with praziquantel, it is likely that schistosomes differentially express genes that contribute to defense and stress responses.

We investigate the molecular pathways underpinning the schistosome response to stress encountered due to changes in environment (ie temperature shifts), exposure to potential pathogens (bacteria, virus) and chemicals (praziquantel). Understanding how schistosomes contend with these stressors may serve as a basis with which to enhance our knowledge of how they overcome the immune effector responses of their hosts and provide insight into new strategies for combating schistosome infection.

Harel Dahari , PhD
Research Associate
Los Alamos National Laboratory

Research interests

As a Research Associate at Los Alamos National Laboratories (LANL), I apply my interest on studying Hepatitis C virus kinetics during antiviral therapy. Recent work with my colleagues at LANL focused on leveraging recent advances in HCV cell culture replication to provide the quantitative data necessary for creating a computer model of the dynamic interplay between host and virus during replication of the virus in Huh-7 (human liver) cells.

Stephanie Forrest , PhD
Professor & Chair
Department of Computer Science
University of New Mexico

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Research interests

Biology and computation, including biologically inspired approaches to computer security, computational modeling of biological systems (immunology, cancer, and evolution), computer immunology, and evolutionary computation.

Philip Gerrish, PhD
Research Associate
Los Alamos National Laboratory

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Research interests

The central aims of my work to date have been: 1) to seek statistical properties of populations and evolutionary processes that are robust to the properties of their constituents, in the spirit of statistical mechanics, 2)to explore the effects of genetic linkage on these properties and on the evolution of mutation rates, and 3) to apply my findings in these areas to the ecology/evolution of infectious diseases under immune surveillance and the improvement of treatment strategies. Perhaps my main contribution has been to formalize the "clonal interference" phenomenon, evaluate its quantitative effects, and derive its statistical signature (a signature of asexuality).

William Hlavacek, PhD
Technical Staff Member, Theoretical Division
Los Alamos National Laboratory

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Research interests

Signal-transduction systems are key components of a cell's decision-making apparatus. I am interested in how to obtain a predictive understanding of these systems, particularly systems involved in innate and adaptive immunity. I believe mathematical models for the dynamics of protein interactions and structural models for protein complexes will be important tools for making accurate predictions about signal-transduction systems and I am pursuing such models for various systems as well as advanced methods for specifying, simulating, and analyzing these models. I am also interested in accurate large-scale reconstruction of genetic regulatory and metabolic networks, in part through analysis of high-throughput data, such as mRNA expression and metabolite profiles.

Terran Lane, PhD
Assistant Professor
Department of Computer Science
University of New Mexico

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Research interests

My primary research interest is in machine learning, with a focus on applications to hard, real-world data analysis and scientific discovery problems. Focusing on such problems is beneficial both to the target domain and to the study of machine learning itself. On the domain side, our advanced learning algorithms can identify novel and significant discoveries from scientific data. On the machine learning side, engaging with challenging real-world analysis problems almost invariably requires methods that go beyond current state of the art and require novel algorithm development. I have applied this approach to domains as diverse as computer security, user modeling, bioinformatics (analysis of RNA interference and microarray deconvolution), and neuroscience (discovery of brain activity networks from functional neuroimaging data).

Eric S Loker, PhD
Regents' Professor & Chair
Department of Biology
University of New Mexico

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Research interests

Comparative Immunology, with an emphasis on invertebrate models; schistosome evolutionary biology; trematode–snail interactions; biology of Biomphalaria and other freshwater snails, including genomics; host–parasite relationships.

Robert Miller , PhD
Professor
Department of Biology
University of New Mexico

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Research interests

Comparative Immunology; evolution of vertebrate antigen receptor genes; evolution of maternal/fetal interactions and immunity.

Melanie Moses , PhD
Assistant Professor
Department of Computer Science
University of New Mexico

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Research interests

I study the general principles that govern the behavior of complex systems. I examine a variety of systems that are composed of cooperating 'agents' whose collective behavior accomplishes some function for an organism or society. Examples of such systems are the adaptive immune system, ant colonies and human societies, and the agents are lymphocytes, ants or people. In studying these diverse systems, I ask one central question: is there an inherent tradeoff between the rate at which agents acquire energy and resources (which appears to decline as the number of agents in the system increases) and the rate at which agents acquire and communicate information (which appears to increase as the number of agents in the system increases). I use metabolic scaling theory and agent based simulations to answer this question. The immune system is a distributed system operating under the metabolic constraints of an organism; as such, it is an ideal system in which to study the energetic costs and benefits of information in an evolutionary context. My approach gives insights into evolutionary tradeoffs in immune investment across a range of species, and it also suggests improved ways to translate our knowledge from studies in vitrio and in small laboratory mammals to human immune function.

Alan Perelson , PhD
Senior Fellow, Theoretical Division
Los Alamos National Laboratory

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Research interests

I am interested in modeling the immune system and its response to viral and bacterial infections. Our group has focused heavily on modeling HIV and hepatitis B and C infection. We collaborate extensively with experimental groups throughout the world and build models to explain and add value to data. Our work on chronic viral infections has lead to profound increases in our understanding of many of the basic biological processes underlying disease pathogenesis, such as the rate of rate viral production in vivo, and the death rates of productive infected cells. We are involved with the analysis of data on primary HIV infection and are helping in the efforts to design an HIV vaccine. We also analyze labeling data obtained with CSFE, BrdU or deuterated glucose to gain insights into lymphocyte kinetics in health and disease. Recent work is leading us into the study of influenza and secondary bacterial pneumonia, as well as the study of the immune response to Listeria monocytogenes.

Ruy Ribeiro , PhD
Technical Staff Member, Theoretical Division
Los Alamos National Laboratory

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Research interests

I study the interaction of the immune system with pathogens. I am mainly interested in comparing the immune response to different viral infections, both acute and chronic. My research goals are to define the mechanisms and quantitative parameters of immunity in those cases, and I use the "natural tool" of diverse viral infections to explore the plasticity of the immune system. My approach is through theoretical and computational models closely grounded on biological principles and experimental data.

Helen Wearing , PhD
Assistant Professor
Departments of Biology and Mathematics
University of New Mexico

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Research interests

Research Interests: Theoretical biology and disease ecology; using mathematical and statistical approaches to understand the biological processes that shape population and community dynamics, with an emphasis on host-parasite interactions.

Christopher Witt, MD
Assistant Professor
Department of Biology
University of New Mexico

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Research interests

Avian systematics and molecular evolution; evolutionary inference using phylogenetic comparative methods; biogeography of the Neotropics; hummingbird evolution and comparative physiology; high-altitude adaptation; integrative ornithology.

Si-Ming Zhang, PhD
Research Associate Professor
Department of Biology
University of New Mexico

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Research interests

The freshwater snail Biomphalaria glabrata is an intermediate host that transmits a human blood fluke, Schistosoma mansoni, a causative agent of human schistosomiasis. It is estimated that more than 600 million people live in schistosomiasis-endemic areas and more than 200 million are infected. Although world-wide effort has been made to control schistosomiasis, it is still an important and highly prevalent health problem in many developing countries. Using the snail-parasite model system we are interested in addressing two general questions which are related to parasitology and evolutionary immunology.

1) Fundamental mechanisms of the snail internal defense: Much remains unknown regarding the molecular basis for the snail and parasite interactions. We have been applying different molecular approaches including RNAi, recombinant protein, proteomics, and biochemistry to investigate the role of putative anti-parasite molecules with focus on fibrinogen-related proteins (FREPs) in snail defense. Better understanding of the fundamental mechanisms of internal defense of the snail B. glabrata could provide a means towards control of transmission of schistosomiasis at the intranmolluscan stage.

2) Novel mechanism underlying the diversification of FREP genes: Our recent studies have shown that FREP genes encoding snail blood proteins can be extensively diversified by both mutational and recombinatorial processes, a capacity not previously recorded or anticipated from an invertebrate. The underlying mechanism for the generation of diversity and its biological rationale remain unclear. Similar phenomena however, have been uncovered gradually from other different invertebrates (e.g., sea urchins, fruit flies). These findings suggest that invertebrates are capable of generating an array of diverse molecules for defense. The FREP-model provides an ideal system to address the novel mechnaims of invertebrate immunity.