MSTP trainers directory

Research Interests:

I relate human perception to the structure and function of the visual pathway. We make use of quantitative modeling of retinal and brain imaging, with applications to ophthalmologic  and neurologic disease.

Research Interests:

The Ahrens-Nicklas lab works to develop better treatments for patients with rare, inherited biochemical disorders of the brain.  We utilize genetic, biochemical and electrophysiologic techniques to both elucidate disease mechanisms and guide development of novel therapies.  

Research Interests:

1.  CAR T Cells Targeting Fibroblast Activation Protein
2.  Augmentation of CAR T cells Targeting Mesothelin
3.  Development of an augmented "off the shelf" NK Cell CAR Line
4.  Development of human-based models of immunotherapy (pleural effusions, tissue slices)
5.  Generating predictors of response to checkpoint therapy in Lung Cancer 
6.  Immunobiology of Mesothelioma and Lung 

Research Interests:

Our main focus is the neurobiological underpinnings of schizophrenia, autism, and epilepsy. We study these underpinnings using mouse models of brain development as well as human stem cell derived excitatory and inhibitory neurons, astrocytes, microglia, and blood brain barrier-like cells. Recently, we have been study the role of mitochondrial energetics in variable penetrance for schizophrenia in the 22q11.2 deletion syndrome. We also have numerous collaborations, including sodium channel mutation related epilepsy, energetics of synaptic vesicle cycling in human neurons, interneuron-cell based therapy for glioblastoma, role of blood brain barrier in neuropsychiatric illness, and the interaction of cannabinoids with HIV in human stem cell derived microglia.

Research Interests:

Epigenetics, X-Chromosome Inactivation, Xist RNA, female-biased autoimmunity, epigenetic analyses using female lymphocytes, allele-specific analyses, RNA/DNA FISH, microscopy, long noncoding RNAs

Research Interests:

The Arany lab focuses on cardiovascular metabolism. Such unfocused focus has led us to study a wide range of projects in the heart, liver, fat, and many other tissues, and has led us to use all techniques we can get out hands on, including human genetics, genetically engineered mouse models, cell culture, metabolomics, in vivo isotope metabolic tracing, and many more. In essence, the lab aims to ask fundamental questions within the (wide) space of cardiovascular metabolism, and leverages all available state-of-the-art approaches to do so.

Research Interests:

The Atchison laboratory studies the molecular mechanisms responsible for transcriptional regulation, epigenetic processes, and the control of B and T cell lineage development.

Research Interests:

The Precision Immunology and Microbiome Medicine laboratory delves into the intricate realms of Human Immunology, Microbiome dynamics, Autoimmunity, and Cancer Immunotherapy. Utilizing advanced Computational Immunology and Systems biology approaches, we decipher the dialogue between the immune system and and the microbiome. Our mission extends to the forefront of Precision Medicine, where we aim to tailor treatments to individual patients' unique profiles. Through groundbreaking research in Microbiome Medicine, we explore the symbiotic relationship between our bodies and the trillions of microbes inhabiting us, unlocking new avenues for therapeutic intervention.

Research Interests:

The Bailis lab aims aims to understand how metabolism underlies immunology and disease, by controlling the biochemistry of cells and tissues. We do so using in vitro and in vivo CRISPR engineering of primary human and mouse immune cells. Together with next generation sequencing and metabolomics, this permits us to fully interrogate how metabolic networks control immune cell function. The long term goal of our work is to develop diet and metabolite based therapies.

Research Interests:

Cellular immunology
Immune regulation
Immune neural and immune glial interactions
Immune therapies 
Biomarker development 

Research Interests:

The lab develops machine learning algorithms that integrate high-throughput data (RNASeq, CLIPSeq , WGS, etc.) to infer RNA biogenesis and function as these relate to human disease, followed by experimental verifications of inferred mechanisms. Research projects in the lab involve a mix of comp methods development, Genomics analysis, new assay tech development, and biochemical wet lab experiments.

Research Interests:

The Bartman lab studies how metabolic fluxes change in inflamed tissues and in tumors, using in vivo isotope tracing and mass spec metabolomics. We try to identify fluxes altered in disease, and then target those fluxes using genetic or pharmacologic approaches to test possible therapeutic approaches.

Research Interests:

The research in my laboratory focuses on the study of genomic imprinting and X inactivation in mice.

Research Interests:

Cognitive Neuroscience
Computational Modeling
Control of Action
Decision Processes
Memory and Learning

Research Interests:

The Bates lab is interested in the interactions between viruses and their host cells. We use a combination of molecular, cell biological, and genetic tools to understand how viruses invade host cells and evade host defenses with emphasis on emerging viral pathogens. We also use technologies such as modified mRNA and recombinant viruses to generate vaccines for highly pathogenic viruses.

Research Interests:

The Beatty Laboratory incorporates both basic science research and clinical investigation to define strategies for leveraging the immune system for the treatment of cancer. Our mission is to define mechanisms of resistance and response to immunotherapy in an effort to design effective strategies to condition tumors and patients for enhanced therapeutic responsiveness.

Research Interests:

The Behrens Laboratory is mainly focused on the understanding the pathogenesis of Cytokine Storm Syndrome, a common pathologic endpoint of a heterogeneous group of initiating diseases. Cytokine Storm Syndrome results in multi-organ failure and a stereotypical immune response including increased serum ferritin and Interferon gamma that leads to the organ failure itself. The lab is interested in dissecting the initiating, propagating, and regulatory factors that determine the pace and outcome of cytokine storm. This is done using a number of different murine models including perforin deficient mice, repeated TLR9 agonist injections, and other murine systems of systemic inflammation. The ultimate goal of these investigations is to improve the lives of patients that suffer from cytokine storm syndromes by developing strategies for treatment and prevention.

Research Interests:

The Belle lab studies the molecular pathways that facilitate cross talk between intestinal epithelial cells and immune cells in order to modulate the outcomes of infections, inflammatory processes and cancer. We use genetic mouse models, organoids and in vitro modeling to address the following broad questions:

1. How does the intestinal epithelial layer repair itself after injury?
2. How do epithelial cells prevent deleterious changes that lead to tumorigenesis in the face of chronic inflammation? 
3. How do epithelial cells influence the immune landscape?

Research Interests:

Epigenetics and chromatin structure/function in genomic regulation; Post-translational modifications of histones and transcription factors; Biological problems: chromatin regulation of transcription; neuroepigenetics and behavioral epigenetics (human, mouse, ant); chromatin regulation in disease including cancer, senescence and aging, and neurodegeneration (cell models, mouse, human).

Research Interests:

Breast and ovarian cancer can be caused by a combination of our environmental exposures as well as our genetic make-up. Family history of breast and ovarian cancer can be used to predict whether or not an individual needs additional screening or testing. Our research focuses on proteins that contribute to breast and ovarian cancer development and studies how accurate repair of DNA double-strand breaks is regulated using the budding yeast and mammalian systems. We have been focusing on the DNA repair genes, the RAD51 paralogs, which when mutated lead to increased breast and ovarian cancer risk using genetic, biochemical, and cell biological approaches. By understanding RAD51 paralog molecular function, the our lab aims to determine individuals who are at risk for cancer development and how cancer risk is compounded upon exposure to environmental toxicants that damage DNA.

My lab studies mechanisms of cancer development and how misregulation of DNA repair genes contributes to genetic instability and tumorigenesis. Part of my lab uses mammalian cells to study the RAD51 paralogs, genes that are mutated in hereditary breast and ovarian cancer, to determine their molecular function and to analyze patient derived mutations for DNA repair defects using genetics, molecular biology, and cell biology techniques. The other part of my laboratory uses the budding yeast system to dissect RAD51 paralog molecular function using genetic, biochemical, and molecular biology techniques. 

Research Interests:

Our lab works in translational genetics to improve diagnosis and treatment through the discovery, mechanistic understanding, and targeted treatment of novel human syndromes.

Research Interests:

The longest standing goal of my lab has been to understand how particular proteins direct accurate chromosome segregation at mitosis and meiosis. In humans, the chromosomal element-the centromere-that directs this process is not defined by a particular DNA sequence. Rather, the location of the centromere is dictated by an epigenetic mark generated by one or more resident proteins. These centromeric proteins interact directly with the DNA to create a specialized chromatin compartment that is distinct from any other part of the chromosome. By taking biophysical, biochemical, genetic, epigenomic, and cell biological approaches, our work is to define the composition and physical characteristics of the protein and protein/DNA complexes that epigenetically mark the location of the centromere on the chromosome. This work involves building centromeric chromatin from its component parts for analysis of its physical characteristics, developing biochemical assays to reconstitute steps in the process of establishing and maintaining the epigenetic mark, exploiting emerging genomic and epigenomic technologies to investigate the structure of centromeric chromatin, and using cell and organismal approaches to study the behavior of proteins involved in centromere inheritance and other essential aspects related to chromosome segregation at cell division. We are using the understanding gained from this work to advance technologies for building synthetic chromosomes for applications in research and medicine. An exciting area of interest for my group to emerge in the last several years has been with the enzyme PARP-1: a key component for signaling DNA damage and an important clinical target for small molecule inhibition. Our work with PARP-1 has defined the allosteric network that potently activates the enzyme upon binding to a DNA break. Most recently, we have discovered that clinical PARP inhibitor (PARPi) compounds fall into three distinct types, depending on their allosteric modulation of DNA binding affinity. Our collaborative team is using this understanding to develop 'designer' PARPi compounds where the allosteric effects they confer are tuned for either strong DNA retention (i.e. potent for cancer cell killing) or strong DNA release (i.e. for inhibiting PARP-1 activity in neuroinflammatory and cardiovascular disease where preserving cell viability is the goal). 

Research Interests:

Higher order chromatin structure, gene expression, epigenetics, globin genes, sickle cell disease, therapeutics

Research Interests:

Molecular genetics of neurodegenerative disease and brain aging; molecular mechanisms of risk factors for neurodegenerative disease

Research Interests:

We are interested in studying the evolution of cancer development from pre-malignancy through transformation.  Hematologic malignancies are an ideal disease model to study classical questions in cancer biology, given sample access and extensive description of the normal hematopoietic differentiation cascade. Genetic studies in acute myeloid leukemia (AML) have revealed a hierarchical arrangement of mutations such that certain mutations are postulated to be acquired either early or late in disease progression. This stepwise acquisition of mutations results in a genetically heterogeneous collection of clones contributing to disease development. Through the progression from pre-malignancy to leukemic transformation,  we study the following broad questions:

1) What are the necessary steps for a mutant cell to transform to leukemia?

2) After transformation, how do leukemic cells affect normal non-mutated cells? 

3) How can we revert or halt transformed cells early in disease development to prevent disease development?

We approach these questions through an intersection of genomic profiling of patient samples and synthetic biology approaches for modeling disease in mice.

Research Interests:

The research interests of our laboratory lie at the intersection of cancer biology, signal transduction, and metal homeostasis.

Research Interests:

Mechanisms of hemostasis and thrombosis.

Research Interests:

Bacterial pathogens, Bacteriology, Infectious Disease, Inflammasome, Innate Immune Defense, Immunology.

The Brodsky lab values diversity in all its forms. We seek to provide a rigorous and supportive training environment that enables individuals from all backgrounds to pursue their love of discovery and advancement of biomedical knowledge while being their authentic selves.

Research Interests:

SARS-CoV-2, HIV, human microbiome and virome, human gene therapy.

Research Interests:

My laboratory investigates how our immune system has adapted to the diverse microbial agents we encounter in our lifetime. We address this question by focusing on the gastrointestinal tract where a single layer epithelium separates our body from pathogens and microbial colonizers belonging to the microbiota. Through taking a comparative infection biology approach, our research has identified cellular mechanisms underlying the balanced immune response that is necessary for responding to life-threatening infections while avoiding chronic illnesses like inflammatory bowel disease. Ongoing projects include elucidating how symbiotic intestinal viruses, fungi, and parasites contribute to local and extraintestinal disease susceptibility, defining how the cellular pathway of autophagy mediates resilience towards infectious threats, and understanding how polymicrobial exposure in the natural environment contributes to the developmental maturation of the immune system. Through these projects, we hope to gain further insight into how microbial diversity in the intestinal ecosystem shapes host physiology and pave the way for therapies that restore balanced host-microbe relationships.

Research Interests:

The Cajigas lab is a translational neurosurgery research laboratory interested in addressing clinical knowledge and treatment gaps in the fields of movement disorders, epilepsy, and pain. The lab utilizes computational, engineering, and statistical methods to analyze electrophysiological data to assist with surgical planning, develop novel neurologic targets for neuromodulation, and understand the neural control of movement with the goals of restoring function after neurologic injury.

Research Interests:

B lymphocyte development, selection, and homeostasis; immunobiology of aging.

Research Interests:

Epithelial tissues rely on a highly coordinated balance between self-renewal, proliferation, and differentiation. Epigenetic mechanisms provide this precise control through the regulation of gene expression in order to establish and maintain cell fate and identity. Disruption of these pathways can disrupt diverse cellular processes including both metabolism and immunity, and ultimately drive diseases such as cancer. 

Research Interests:

I study the eco-epidemiology of tropical diseases. My current research uses canine rabies as a model system to understand how the social and spatial features of urban areas influence the emergence and persistence of infectious diseases.

Research Interests:

To understand disease-causing mechanisms through cellular structural imaging at the highest-possible resolution by cutting-edge cryo-electron tomography

Research Interests:

The over-arching goal of our research is to better understand the mechanisms of neurodegenerative disease in order to intervene in these disease processes.

Our general approach is to use unbiased genomic- or proteomic-scale screens in human-derived materials to generate leads, which are then followed mechanistically in relevant systems including neuronal culture and in vivo animal models. The pace of technology development is allowing us to acquire more data, faster, than ever before, but this does not always translate into biological understanding. We believe that to unlock the true potential of leads generated in this way, computational methods must work hand-in-hand with bench-based manipulative experiments. We are looking for new ways to do this all the time. 

Research Interests:

Genetic and mechanistic studies of viral-host interactions.

Research Interests:

The Chodosh laboratory uses genetically engineered mouse models, patient samples and bioinformatics to understand the mechanisms by which cancers develop, progress to more aggressive states, and ultimately contribute to cancer mortality. A broad array of basic and translational research approaches are used to address problems of fundamental clinical importance to cancer patients by elucidating pathways and principles common to human cancers. These approaches encompass genetics, genomics, molecular biology, biochemistry, cell biology, computational biology, functional imaging, animal studies, preclinical trials and clinical investigation. Particular areas of interest include: pathways regulating cancer development, metastasis, tumor dormancy and recurrence; the use of genomics and computational approaches to understand genetic programs in cancer; the impact of obesity on cancer recurrence; the mechanisms by which pregnancy protects against breast cancer; and the use of non-invasive imaging approaches to study tumor biology.

Research Interests:

Our laboratory is interested in the genetics of cancer and in particular, how genetic alterations affecting processes such as RNA splicing drive cancer and expose potential therapeutic vulnerabilities. 

Links: 
Choi Laboratory 
Penn Faculty Page

Research Interests:

The Chow Laboratory invents optical technologies to manipulate and monitor cellular physiology, and applies them to understanding how cells make decisions in response to external cues.

Research Interests:

Representation of information in thalamocortical networks. Epilepsy.

Research Interests:

Stem cells; hair follicle; wounding; aging skin.

Research Interests:

Epilepsy, neuronal excitability, CNS rhythm generation, circuit imaging, GABA receptors, development of neurotransmitter receptors and ion channels, synaptic function

Research Interests:

Evaluating glaucoma pathogenesis to identify effective treatments for a neurodegenerative disease affecting the retina and the optic nerve.

Dr. Cui can be found on Twitter @CuiLab. 

Research Interests:

Research in the Davidson Laboratory is focused on inherited genetic diseases that cause central nervous system dysfunction, with a focus on: i) recessive, childhood onset neurodegenerative disease, such as the lysosomal storage diseases mucopolysaccharidoses and Battens disease; ii) dominant genetic diseases, specifically the CAG repeat disorders, Huntington's disease and Spinocerebellar ataxia; iii) understanding how changes in the transcriptome impact neural development and neurodegenerative disease processes.

Research Interests:

Dr. Davis' research centers around utilizing both the advancing fields of invasive neurophysiology and neuroimaging to better localize epileptic networks in medication refractory epilepsy patients. She hopes that improving localization will enable epileptologists to better localize epileptic networks and assign individual patients to the most efficacious therapy, for example, seizure control devices, resective surgery, or continued medical management.

Research Interests:

The Day lab is interested in genetic heart muscle diseases. Our research program integrates translational and clinical science, with a primary focus on hypertrophic cardiomyopathy. We want to understand the full spectrum of disease evolution and progression, from the primary effects of sarcomere gene mutations in cardiac muscle cells to the phenotypic expression and predictors of adverse outcomes in patients.

Research Interests:

My lab's goal is to combine the power of machines and biology to understand, prevent, and treat infectious diseases.

Research Interests:

[1] Endothelial Cell Adhesion and Motility
[2] Angiogenesis
[3] Tumor Metastasis
[4] Pulmonary Hypertension

Research Interests:

My laboratory studies the proteins that control the actin cytoskeleton and cytoskeleton-membrane connections, as well as the signaling pathways that regulate their activities. We use interdisciplinary approaches, spanning structural biology, biochemistry and cell biology, allowing us to correlate the functional mechanisms of proteins to their cellular activities

Research Interests:

We study the pathogenesis of age-related macular degeneration of the retina, focusing on oxidative stress and inflammation. More broadly, we are interested in mechanisms of aging and therapeutic approaches to prevent age-related diseases. One therapy currently showing promise is oral administration of an oxidation-resistant fatty acid. We are also testing iron-specific chelation and antioxidant gene therapy in mouse models of macular degeneration. Multimodal in vivo retinal imaging in mice and functional testing with electroretinography greatly accelerate discovery.

Research Interests:

We use model systems (primary cells, iPSCs, mouse) of rare genetic neurodevelopmental disorders that disrupt glycosylation (known as Congenital Disorders of Glycosylation, or CDG) and glycoproteomics to study glycosylation in the brain.

Research Interests:

Dr. Eisenlohr studies the fundamental aspects of host defense, primarily against virus infections such as influenza and HIV.

Research Interests:

Dr. Elovitz brings the clinical and research world together to advance pregnancy health.  She has been actively involved in translational and clinical research for the over 20 years. Her research is or has been funded by the March of Dimes, Burroughs Wellcome Fund, National Institute of Child Health and Development, National Institute for Nursing Research, the National Institute of Mental Health and the National Institute for Allergy and Infectious Diseases. Dr. Elovitz supports, fosters, participates and advocates for collaborative research, from the bench to the bedside, to advance the mission of improving health outcomes for women and their children.  She has been very successful at growing a multidisciplinary research team that will undoubtedly push forward the needle on women's health. Her own research program has focused on understanding the mechanisms and consequences of adverse pregnancy outcomes both for the pregnancy of interest and for implications for the long-term health of the mother and child. Her research integrating immunology and microbiology into pregnancy health has led to novel discoveries in preterm birth. Dr. Elovitz is unique in that her research expertise spans the bench to the bedside. She has developed mouse models relevant to human pregnancy conditions, create unique in vitro systems and has implemented translational research that has created large biobanks of specimens with rigorous clinical metadata.

Research Interests:

Epigenetic regulation of stem cell biology, developmental biology, nuclear architecture and cardiovascular medicine.  We also have an interest in the use of mRNA and lipid nanoparticles to create CART cells to treat fibrosis.

Research Interests:

1) Elucidating the etiology, dysregulated cell types, signaling pathways, and effector cytokines in idiopathic multicentric Castleman disease (iMCD) and related cytokine storm disorders
iMCD is a poorly-understood and deadly hematologic disorder. A proinflammatory cytokine storm and reactive lymphoproliferation occur for an unknown etiology. The poor understanding of etiology and pathogenesis has limited the development of effective treatments and contributed to the significant morbidity and mortality associated with iMCD (55-77% 5-year overall survival). Currently, we leverage a variety of techniques to study the etiology and pathogenesis of iMCD. In addition, we leverage a biobank (CastleBank) to collect samples to fuel our translational research.

2) Identifying effective treatments for iMCD patients
The poor understanding of iMCD pathogenesis has slowed the development of treatment approaches. Currently, there is only one FDA-approved treatment for iMCD, which is effective in approximately one-third or patients. We run an international Natural History Study of Castleman Disease (ACCELERATE) to collect in-depth data on patients around the world to identify effective treatment approaches currently being used off-label.

3) PI3K/Akt/mTOR signaling in iMCD
Proteomic, flow cytometric, and immunostaining studies revealed upregulation of Vascular Endothelial Growth Factor (VEGF), activated CD8+ T cells, and uncontrolled PI3K/Akt/mTOR signaling in iMCD. Whole genome sequencing of an iMCD patient and both parents revealed rare compound heterozygous missense mutations in both alleles of a negative regulator of T cell activation and a candidate etiological mechanism. These novel findings led to the first-ever use of sirolimus in iMCD and a prolonged remission for a refractory patient (manuscript in submission). Drawing upon the world's largest collection of iMCD patients and their biospecimens in ACCELERATE, we are employing whole genome sequencing, transcriptomics, proteomics, flow cytometry and phospho-flow, and cellular signaling assays to continue to elucidate the role of PI3K/Akt/mTOR signaling in iMCD. As there are no animal models, we are also performing extensive correlative studies to quantify changes in VEGF, T cell activation, PI3K/Akt/mTOR signaling, and other immunological markers following in vivo sirolimus administration to patients and documenting treatment efficacy.

4) Investigating the role of stromal cells and chemokines in iMCD
Quantification of 1,129 plasma proteins in iMCD revealed highly up-regulated acute phase reactants and chemokines. The chemokines that were most upregulated are essential for normal lymph node morphology/function and typically produced by lymph node stromal cells. The most up-regulated chemokine, CXCL13, is responsible for homing B cells into the germinal center. This is interesting, because the pathological hallmark of iMCD is dysmorphic lymph node germinal centers with either too few (atrophic) or too many B cells (hyperplastic). Immunohistochemistry confirmed significantly increased germinal center expression of CXCL13. We are exploring the mechanisms of lymph node stromal cell activation and chemokine signaling.

5) Methods for accelerating drug development and drug repurposing

I am looking for motivated MD, PhD, and MD/PhD students to join my lab to help advance understanding of mechanisms involved in hyperinflammation/cytokine storm and translate these findings into novel treatment approaches for cytokine storm disorders.

 

Research Interests:

Calcium, Calcium channels, Calcium Signaling, Signal transduction in lymphocytes and macrophages, calcium dependent mechanisms of viral entry and egress in cells. Calcium regulation of gene expression in lymphocytes

Research Interests:

The synaptic and circuit mechanisms of behavioral control.

Research Interests:

Our research leverages genetic and genomic tools to identify the underlying biological mechanisms and novel therapeutic targets for neurodevelopmental and psychiatric disorders, including autism, ADHD, bipolar disorder, and schizophrenia. Our current work focuses on translating the ever-expanding results from large-scale genetic association studies (GWAS) of neuropsychiatric disorders into tractable biological mechanisms and testable hypotheses. To accomplish this, we are currently working to: 1) Perform population-level genetic and multi-OMIC profiling of the developing and adult human brain; 2) Develop and apply integrative functional genomic methods to identify the target genes and proximal mechanisms within genetic loci associated with psychiatric disorders; 3) Leverage systems biology to identify pathways of convergence among multiple distinct genetic risk factors, at both a population level and within an individual; 4) Characterize the brain-level molecular pathology of major neuropsychiatric disorders, through gene and network-level inference

Research Interests:

Dr. Gee's research interests are broadly in the field of biological and medical image analysis and computing. Toward this end, the group he directs, the Penn Image Computing and Science Laboratory (PICSL), conducts basic and applied research in mathematical, computational and statistical methods for extracting, analyzing and integrating information from imaging and ancillary data. Of particular interest to the lab are methods for detecting, quantifying and modeling the ways in which anatomy and physiology can vary in nature, over time, or as a consequence of disease or therapy. PICSL is well known internationally for its long track record of methodological innovation in nearly every area of the field, and for its commitment to translating research accomplishments into highly acclaimed open-source software that directly underpin hundreds of published imaging studies across the world every year. The group's large portfolio of interdisciplinary collaborations spans different model systems and the major modalities in biological and medical imaging of various organ systems in health and disease.

Research Interests:

Dr. Geffen is a leader in the field of auditory neuroscience. She is interested in the way the brain encodes information about the world and how our perception is shaped by our emotional state and experience. She combines computational and biological approaches to study the mechanisms behind dynamic auditory perception, memory and learning.

Dr. Geffen first became interested in systems neuroscience through her undergraduate thesis under mentorship of John Hopfield at Princeton University, in which she explored the mechanics of whisking in rats. She studied texture encoding in the somatosensory system with Christopher Moore at MIT during her first two years of graduate school at Harvard. She completed her Ph.D. in the laboratory of Markus Meister at Harvard University, where she discovered a novel retinal circuit for processing moving images. After her Ph.D., she was a fellow at the Center for Physics and Biology at Rockefeller University, where she worked under mentorship of Dr. Marcelo Magnasco, exploring the dynamics of natural sounds.

Dr. Geffen has been directing the Laboratory for Auditory Coding at the University of Pennsylvania since 2010. She was promoted to Associate Professor in 2018. Dr. Geffen's recent discoveries include: identifying a novel cell type that supports hearing of unexpected sounds; establishing the connection between emotional learning and sound perceptual acuity; and elucidating the neuronal code for representation of communication signals in the brain. Her scientific results are regularly published in well-recognized journals, including Nature Neuroscience, eLife and PLoS Biology. Her research accomplishments have been recognized with prestigious awards, including the Burroughs Wellcome Career Award at the Scientific Interface, the Klingenstein Foundation Award in Neurosciences, the Human Frontiers in Science Foundation Young Investigator Award, the Auditory Neurophysiology Young Investigator Spotlight Award and the Kaufman Foundation New Initiative Grant. Her research is supported by multiple grants from the NIH, including NIDCD and the BRAIN Initiative, as well as by private and international foundations. She serves as a permanent member on an NIH review panel, and has served as the general chair and workshop director for multiple national and international meetings. She currently serves as a co-director of the Cajal Course in Computational Neuroscience, and an organizer of the E.A.R.S. seminar series. Dr. Geffen is a dedicated mentor and her trainees have won the Brain Research Foundation Young Investigator Award, multiple Ruth L. Kirschstein National Research Service Awards from the NIH and the Saul Winegrad Award for Outstanding Dissertation.

Research Interests:

The current focus of the my lab is to merge mechanistic studies aimed at understanding the regulation of factor VIII cofactor function with translational efforts in hemophilia A gene therapy.

Research Interests:

Tumor Immunology; Chimeric Antigen Receptor T cells; Mouse Models of Human Leukemia; Murine Xenografts; Adoptive Cellular Therapy; Genetic Engineering of T cells; Genetic engineering of hematopoietic stem cells.

Research Interests:

The lab studies mechanisms of cerebral cortex circuit function and circuit dysfunction in neurodevelopmental disorders towards the development of mechanistically-informed, targeted therapies.

CHOP Directory Page

Research Interests:

This laboratory is devoted to understanding basic mechanisms of DNA repair and their impact on genome integrity, cancer etiology and response to targeted therapies. To investigate these interrelationships, we are devoted to elucidating BRCA1- and BRCA2- dependent homologous recombination mechanisms in breast and ovarian cancer, telomere length maintenance mechanisms that rely on a specialized form of homologous recombination, and DNA damage induced activation of immune responses to cancer. We utilize a myriad of approaches to investigate these areas, which include biochemistry, structural biology, cell biology, and genetically engineered mouse models.

Research Interests:

Genomic and metagenomic approaches to understand cutaneous host-microbe interactions in health and disease.

Research Interests:

The gut epithelium acts as an arbiter between harmful substances in the external environment and the human body. Our laboratory specializes in understanding mechanisms regulating the gut epithelium in health and disease. We use in vivo models and mouse/human 3D enteroid and colonoid (organoid) lines to understand the molecular basis of intestinal regeneration and inflammatory bowel disease (IBD). Within these contexts, we are interested in how RNA binding proteins impart global, post-transcriptional regulation of key pathways in normal physiology and pathophysiology.

Research Interests:

My research focus is on the characteristics and limits of functional neuroplasticity in the adult human brain. I investigate how the brain reorganizes itself in response to injury, and whether or not it is possible to enhance the brain's potential for reorganization in order to speed rehabilitation using noninvasive electrical or magnetic brain stimulation. A second area of interest for me is on the use of noninvasive brain stimulation to elucidate and enhance mechanisms of cognition in healthy individuals, and the biological, social, and ethical implications of neural enhancement.

The Laboratory for Cognition and Neural Stimulation (LCNS)

Research Interests:

Antiviral immune responses, Ebola, Marburg, Rabies, VSV, Lassa Fever, Junin, Innate immunity, Innate Immune Defense, Virus-host interaction, Zoonotic diseases, Antiviral therapeutics

Research Interests:

Human Immunology; Immune Dysregulation; Mouse models of disease; Primary Immune Deficiency; Asthma; Obesity.

Research Interests:

Influenza virus; SARS-CoV-2; antibodies; antigenic drift; vaccines.

Research Interests:

Regulatory networks, Immunity, Inflammation, Tissue repair, Mucosal interface, Helminth infection, Lung and intestinal injury, Transgenic mice.

Research Interests:

We are interested in developing new ways to diagnose, treat and cure bowel motility disorders. Bowel motility is controlled by a complex nervous system within the bowel wall called the "enteric nervous system" (ENS), by pacemaker cells and by bowel smooth muscle among other cell types. Our work is a mixture of developmental biology, genetics, cell biology, biochemistry, stem cell biology, imaging, and includes translational studies focused on the ENS and smooth muscle. These reviews written by MSTP students in my lab are a good introduction to the field:

Hashmi SK, Ceron RH, Heuckeroth RO. (2021) Visceral myopathy: clinical syndromes, genetics, pathophysiology, and fall of the cytoskeleton. Am J Physiol Gastrointest Liver Physiol. 2021 Jun 1;320(6):G919-G935. doi: 10.1152/ajpgi.00066.2021. Epub 2021 Mar 17.
Schneider S, Wright CM, Heuckeroth RO. (2019) Unexpected Roles for the Second Brain: Enteric Nervous System as Master Regulator of Bowel Function. Annu Rev Physiol. 2019 Feb 10;81:235-259. doi: 10.1146/annurev-physiol-021317-121515. Epub 2018 Oct 31.

Research Interests:

The Hill Lab studies how diet and metabolism influence immune health and inflammatory disease. Our goal is to make impactful discoveries that aid in the prevention, diagnosis, or treatment of food allergy, asthma, and obesity-associated inflammation, among other conditions. We use clinical and epidemiological information to guide basic and translational research aimed at understanding the genetic, molecular, and immunologic basis of immune disease. By studying disease mechanisms in our lab, we are poised to lead the development of new preventative and therapeutic approaches for these important conditions.

Research Interests:

My work has focused on using biomedical informatics approaches to study asthma and other pulmonary diseases. I began asthma genetics and pharmacogenetics research by participating in genome-wide association studies (GWAS) as a lead investigator and as part of large collaborations. Although promising loci were identified via these studies, I realized that translation of findings into insights that would have an impact on understanding disease pathophysiology was a difficult challenge that required novel research strategies. I have addressed this challenge by leveraging my background in biomedical informatics to generate novel genome-scale datasets and to integrate novel and publicly available datasets using creative approaches. Specifically, my lab has studied asthma and response to β2-agonists and glucocorticoids, commonly used asthma drugs, by obtaining and integrating omics-level data corresponding to in vitro and human studies. My lab also uses Electronic Health Record (EHR)-derived data to understand characteristics of real life populations with asthma and COPD, incorporating social, economic and environmental factor data obtained from secondary sources, and leveraging Biobank cohorts to perform genomics studies. I am the Director of the Exposure Biology Informatics Core of the Center of Excellence in Environmental Toxicology (CEET), where I lead efforts to analyze data and create informatics tools related to our environmental health studies.

Research Interests:

Medical informatics; data mining; evolutionary computation; machine learning; artificial intelligence; database design and implementation for clinical research; medical decision making.

Research Interests:

Our lab studies the dynamics of organelle motility along the cellular cytoskeleton, driven by the microtubule motors cytoplasmic dynein and kinesin. We are interested in the mechanisms leading to coordinated motor activity, required  to drive organelle transport over distance of up to 1 meter in neuronal axons. We also investigate the cellular mechanisms leading to neurodegeneration, including the dynamics of autophagy and mitophagy in neurons. Our work was the first to identify a key role for optineurin in the clearance of damaged mitochondria via mitophagy, downstream of PINK1 kinase and the E3 ubiquitin ligase parkin. As mutations in optineurin and the associated kinase TBK1 cause familial ALS, and mutations in PINK1 and parkin cause familial Parkinson's disease, this discovery demonstrates that the failure to clear damaged mitochondria is likely to contribute to the pathogenesis observed in multiple forms of neurodegeneration, a hypothesis currently under investigation in our lab. Together, we have developed a significant record of contributions to neuronal cell biology, focusing on the cellular and biophysical analysis of molecular motors, the mechanistic analysis of organelle trafficking, the elucidation of pathways for autophagy and mitophagy in neurons, and an improved understanding of pathogenic mechanisms leading to neurodegenerative disease.

Research Interests:

Our lab works to bring developmental processes that operate in vertebrate embryos and regenerating organs under an engineering control framework, so that we can build better tissues. We study how cells conspire to create complex structures, so that we can build models of human disease, reconstituted tissues for regenerative medicine, and new types of biological machines.

Research Interests:

Infectious Disease, Toxoplasma gondii, Zoonotic diseases, Host-pathogen interactions, Immunology, Parasites, Parasitology, Transgenic parasites, Inflammatory responses.

Research Interests:

Our lab combines microelectronics, microfluidics, nanomaterials, and machine learning to solve big problems in healthcare. We create miniaturized platforms for the diagnosis of disease, we develop new platforms to manufacture micro and nanomaterials, and we dip our toes into an assortment of other areas where we can leverage our engineering training to improve healthcare. This work requires an interdisciplinary approach in which engineers, scientists, and physicians work together to solve high impact problems in healthcare. 

Research Interests:

We are interested in how genome organization shapes organogenesis.

Research Interests:

Molecular biology of aging, cell senescence, telomeres, dyskeratosis congenita, pulmonary fibrosis, colon cancer, neurodegeneration, transplantation.

Research Interests:

My research is mainly in the area of robot-mediated rehabilitation. I am focused on the investigation and rehabilitation of dysfunction due to aging, neural disease, and neural injury. I am particularly interested in 1) exploring the relationships between brain plasticity and behavioral/motor control using robotics; 2) quantifying motor/cognitive impairment effects on motor control of the upper limb in real world tasks; 3) defining methods to maintain therapeutic effectiveness while administering local and remote, robot-mediated interventions in high and low resource settings; 4) global and affordable technology-mediated interventions after brain injury.

GRASP Lab Faculty Page

Research Interests:

My reseearch interests focus on the development and evaluation of clinical information systems that improve patient safety and compliance with practice guidelines. 

Currently, my lab is exploring how artificial intelligence can reinvent clinical encounters and the work resulting from those interactions. 

I lead a project called REDUCE, which uses video and audio recordings of clinical visits to gain necessary insights to improve patient-provider interactions on both sides. The goal is to remove clinicians from the secretary position that EHRs have put them in, reduce the burnout caused by the burden of documentation, and restore a more connected patient encounter. While the visit is being recorded, AI will summarize the appointment qualitatively, quantitatively, and equitably, and provide assessment based on symptoms shared verbally as well as those captured visibly by the technology. The long-term goal is to provide real-time automated guidance.
 
I'm also passionate about educating lay audiences about informatics. My podcast, Informatics in the Round, features lively, non-technical conversations on hot-button cultural issues from an informatics perspective. I'm co-author and co-editor of the Who Me? children's book series featuring scientists from marginalized groups, encouraging young children to consider careers in STEMM. I also produced and directed the documentary No Matter Where about the challenges of sharing information across the healthcare system, how these communication failures impact patients and providers, and the changes that must occur to create a safer world.
 
I'm curious, but also a "completer." I enjoy working with smart, hardworking, and fun people, and consider mentoring a vital part of what I do. I love working with teams, and look forward having MSTP trainees on mine! 

Research Interests:

The Joyce lab studies how chromosomes are functionally organized and folded in 3-D space and time. Our primary goal is to understand how the structure and position of chromosomes within the nucleus is established and inherited across cell divisions, and how dysfunctional organization contributes to genome instability. To this end, we develop and utilize technologies to visualize chromosomes and subchromosomal regions at single-cell resolution and in a high-throughput fashion. Our research takes advantage of both Drosophila and mammalian systems as models for chromosome function, which allows us to directly address the conservation and health relatedness of the mechanisms we discover.

Research Interests:

Our research group focuses on delineating disease pathogenesis of emerging viruses in order to uncover mechanisms of immune control. We primarily focus on emerging viral pathogens that present with unknown mechanisms of disease in the nervous system or placenta. Both regions of infection have interfaces (maternal-fetal and blood-brain) that provide extra protection to an essential organ or allogenic fetus. These interfaces necessitate a delicate balance of initiating an effective antiviral response while also ensuring that there is limited damage and tolerance is maintained. In order to achieve this balance, immune responses in these regions have evolved intricate layers of distinct control which are only now beginning to be fully appreciated.

Research Interests:

Memory, learning, neuromodulation.

Research Interests:

The Kahn Lab investigates signaling pathways in endothelial cells and other cell types in the cardiovascular system. We investigate mechanisms of disease related to both the blood and lymphatic vascular networks as well as those connecting vascular biology and thrombosis.

Research Interests:

Regulation of T cell responses; regulatory T cell expansion and homeostasis; Regulation of skin barrier function; cell signaling.

Research Interests:

We study how neural circuits give rise to complex behaviors, and how dysfunction of neural processes can cause mental illness. Our particular focus is in understanding how sleep -- a highly conserved behavior whose core function remains a mystery -- contributes to sculpting brain circuits during development and in other times of life.

Research Interests:

Molecular Mechanisms of Anesthetic Action; Neurobiology of Sleep; Wake Regulation; Mouse Genetics; Anesthetic pharmacology; Hibernation and Hypometabolic states; Disorders of Consciousness.

Research Interests:

We study Wnt signaling in normal and malignant hematopoietic stem cells. We investigate how Wnt signaling regulates chromatin structure and in hematopoietic stem cells and in early vertebrate embryos. We also study the pharmacology of litihum action in bipolar disorder with a focus on glycogen synthase kinase-3 (GSK-3). Recent work investigates the regulation of mRNA splicing by GSK-3 in leukemic cells. 

Research Interests:

Our laboratory focuses on the DNA modifying enzymes that provide an added layer of complexity to the genome. These enzymes can be involved in the purposeful introduction of mutations or in the chemical modification of nucleobases, making DNA a remarkably dynamic entity. Many of these processes are at the heart of the battle between the immune system and pathogens or are central to epigenetics.    

Our research program aims to understand diversity generating enzymes and pathways in vitro, to perturb their function in physiological settings, and to harness the biotechnological potential of these diversity-generating pathways.

Research Interests:

Epigenomic regulation of transcription and metabolism by nuclear receptors; mechanism of obesity-associated insulin resistance and diabetes; circadian regulation of metabolism.

Research Interests:

Alzheimer's disease, Frontotemporal lobar degeneration, Amyotrophic lateral sclerosis

Research Interests:

Intestinal epithelial stem cell biology and tissue regeneration, Colorectal cancer initiation, progression, and metastasis, organoid models of human telomere disorders, genetic tool development (evolving barcode systems, CRISPR-Cas9 forward genetic screening, mouse genetic models).

Research Interests:

I study insects and human health.

Research Interests:

Identification of disease genes for human diseases; Development of statistical and computational methods for genomics data

Research Interests:

We are interested in the basic emrbyology and tissue morphogenesis and how these fundamenatal ingishts will advance care of congenital anomalies in children. We are investigating molecular control of embryonic epithelium and cranial neural crest cells. Key molecular levers of regulation of these cells that are coordinated during craniofacial development include the IRF6 gene regulatory network and ESRP1/2 alternative splicing of genes important in epithelial-mesenchymal transition.  

Research Interests:

Epilepsy, EEG, Clinical Neurophysiology, Epilepsy Surgery, Brain Stimulation, Implantable devices, network neuroscience, deep brain stimulation, functional imaging, neuroengineering, Biomedical engineering, computational neuroscience.

Research Interests:

• Hepatic and non-hepatic outcomes of chronic hepatitis B and C, particularly among patients with HIV infection
• Adherence to hepatitis C virus therapy
• Hepatotoxicity of medications
• Evaluation of clinical outcomes
• Population-based and administrative databases 

 

Research Interests:

The Logsdon laboratory uses long-read sequencing, innovative computational methods, and synthetic biology approaches to investigate the sequence and structure of regions of the human genome that have remained unresolved for the past two decades. We are particularly interested in the centromeres, which comprise over half of the previously unresolved sequences and are among the most dynamic and rapidly evolving regions in the human genome. Ongoing projects include centromere variation among the human population in both health and disease, centromere evolution over time, and the design and engineering of new centromeres on human artificial chromosomes.

Research Interests:

The long-standing interest of our group is to understand how membrane and cytoskeleton adaptors modulate cellular processes to maintain homeostasis and how their dysregulation leads to disease. We are particularly interested in the role of these adaptors in brain development and bioenergetic regulation. Our research sits at the interface of human genetics, animal physiology, cell biology, and biochemistry. We use mouse, fly, and differentiated human iPSC models to decode the cellular and molecular mechanisms of protein adaptors in normal states and how they are functionally disrupted by pathogenic human variants. Our goal is to translate genetic information into pathophysiologic mechanisms that inform diagnosis and therapeutic approaches. Some of the techniques routinely used by our team include live and high-resolution microscopy, biochemistry, cellular assays, and proteomics, combined with advanced molecular methods, multiple imaging and behavioral modalities, and gene profiling in animal models of disease.

Research Interests:

Development and Function of Mammalian somatosensory system, pathological pain and itch conditions

Research Interests:

We are interested in how the brain perceives external sensory information and responds appropriately using the mouse olfactory system as a model. Rodents primarily use olfactory cues to guide their behaviors (e.g., locating food, communicating with conspecifics, and avoiding danger). Odor detection relies on a large family (~1200 in mice) of G-protein coupled odorant receptors (ORs) expressed in olfactory sensory neurons (OSNs) in the nose. OSNs transmit sensory information to the olfactory bulb, which relays the information to several olfactory cortical and subcortical regions. Some OSNs serve dual functions as odor detectors and mechanical sensors, thus the olfactory system carries both odor and nasal breathing signals into the brain. Our current investigation focuses on how the olfactory system interacts with non-olfactory regions (e.g., the prefrontal cortex and striatum) to influence the brain activity and behavioral output. Since olfactory dysfunction is manifested in neuropsychiatric and neurodegenerative disorders, we are also interested in analyzing the olfactory system and related circuits in diseased states.

Research Interests:

My laboratory investigates the regulation of normal and malignant hematopoiesis, bone marrow transplantation and T cell alloimmunity. A central focus of our studies is the role of Notch signaling in T cell development, differentiation and function, as well as in other aspects of hematopoiesis and lymphoid homeostasis. Using mouse models of bone marrow transplantation, we discovered essential functions for Notch receptors and ligands in graft-versus-host disease with a high fundamental and translational impact. We also identified specialized stromal niches that represent the critical sources of Notch ligands in secondary lymphoid organs. 

Research Interests:

Chimeric Antigen Receptor T cells, Chimeric Auto-Antigen Receptor T cells, Adoptive Cell Therapies, Listeria based vaccines, Canine hematopoietic cancers, Canine osteosarcoma, Canine Urothelial Carcinoma, Canine Soft Tissue Sarcomas.

Research Interests:

The goals of our research program in soft tissue mechanobiology and tissue engineering are to understand the physiologic and patho-physiologic processes that regulate the formation, maturation, and adult function of soft connective tissues.  We believe that such an understanding will better direct our efforts to generate functional tissue replacements and regenerative strategies, with a particular focus on articular cartilage and the knee meniscus. Our program utilizes various mechanical and biological testing modalities, scaffold fabrication techniques, and bioreactor culture conditions to explore these issues in both animal and human model systems.

Research Interests:

I am a Medical Oncologist with postdoctoral training in Cancer Genetics and PhD training in molecular and cellular biology. My research interests are in the genetics of human cancer, particularly the mechanisms of breast and prostate tumor formation in patients with inherited mutations in DNA repair genes. 

We have two main interests:
1) We leverage my clinical expertise in Li Fraumeni Syndrome to study p53-related breast and prostate cancer development, and to study specific hypomorphic TP53 mutations.  
2) I am the Director of the Basser Center for BRCA Men and BRCA Program and Director of the Cancer Genetics Clinic at the Philadelphia VAMC, and we leverage this clinical role to study BRCA-related prostate cancer and to identify novel prostate cancer genes.

Our studies span clinically oriented translational projects to basic science, in genetics, genomics, bioinformatics and cell biology.

Research Interests:

NF-kB signaling in immunity and inflammation with a primary focus on the role of this pathway in controlling the phenotype and function of vascular and lymphatic endothelial cells. 

Research Interests:

Research in my laboratory is focused on T cell biology and applications of genetically-engineered T cells to the treatment of disease.

Research Interests:

The Miner laboratory studies the intersection of autoimmunity and antiviral immunity. This includes studies of rare rheumatic diseases caused by mutations in genes that regulate immune responses to viruses, such as the TREX1, cGAS, STING, RIG-I, and STAT1 genes. The Miner laboratory is also developing novel therapeutics for rare diseases, and is conducting whole-genome CRISPR/Cas9 screens to discover novel regulators of these pathways.

Research Interests:

Neurobiology of mental disorders Neural development human induced pluripotent stem cells cell signalling cell and molecular biology.

Research Interests:

I am interested in quantifying and manipulating the dynamics of nuclear organization and gene expression during development and in disease. To do so my lab builds and applies advanced light microscopy technologies alongside computational analysis, biophysical modelling, optogenetics, gene editing, and  genomics.  

Research Interests:

The Morrisey Lab is comprised of a group of researchers dedicated to investigating cell fate decisions that occur in the lung during development, tissue homeostasis, and regeneration. We utilize cutting edge technologies including sing cell -omics, novel transgenic mouse models, advanced imaging techniques, and custom bioinformatics platforms to expand our understanding of how the respiratory system responds to acute and chronic disease and injury.

Our lab is composed of a highly collaborative team of graduate students, postdocs, physician-scientists, technicians, staff scientists, and a bioinformatics team.  Former Morrisey lab trainees are emerging as the next generation of leaders in pulmonary research and medicine. We invite you to view our webpage and learn more about us.

Research Interests:

Development of new PET radiotracers for neurodegenerative disease and neuroinflammation.
Application of quantitative neuroimaging and pattern analysis/machine learning methods to multi site neuroimaging studies to understand mechanisms and phenotypes of brain aging and neurodegenerative disease.
 

Research Interests:

Dr. John studies the malaria parasite, Plasmodium falciparum, to understand its basic molecular and cellular biology and functions of its specific metabolic pathways--what the parasite needs to make and why it needs to make it--to identify new antimalarial drug targets and develop new diagnostics. More recently, our work has expanded into new "breathalyzer" diagnostics for pediatric SARS-CoV-2 and the post-coronavirus syndrome MIS-C.

Research Interests:

Our focus is on defining new mechanisms that regulate immune cell activation and protective immune responses. Our goal is to use this information to design therapies with which to treat the immune-mediated pathologies found in autoimmune and allergic disease. 

Research Interests:

The Orthmann-Murphy laboratory studies the dynamic role of glial cells in acquired and inherited demyelinating disease.

Research Interests:

The Ortiz-Gonzalez lab is interested in pediatric neurodegenerative disorders and how these rare genetic disorders inform our knowledge of neurobiology and pathways critical for maintaining brain health. We focus on the role mitochondrial dysfunction in neurodegenerative phenotypes.

Research Interests:

The Paralkar Lab seeks to understand how the interplay of transcription factors and chromatin complexes regulates normal and malignant hematopoiesis, specifically hematopoietic stem cells self-renewal, myeloid differentiation, and myeloid leukemogenesis. A particular focus of our group is the regulation of ribosomal RNA and ribosome biogenesis.

Our work spans the spectrum from human patient sample studies and mouse models to cutting-edge molecular biology tools, high-throughput sequencing approaches, and novel computational algorithms.

Research Interests:

Transcriptional programs that regulate cardiovascular development.

Research Interests:

Precision cellular immunotherapies for B cell-mediated autoimmune diseases, canine cellular immunotherapy

Research Interests:

Adriana Petryna is Professor in Anthropology at the University of Pennsylvania. She directs the MD-PhD program in Anthropology and the undergraduate concentration in Medical Anthropology and Global Health. In her ethnographic studies in Eastern Europe and the United States, she probes the socio-political nature of science, how populations are enrolled in experimental knowledge-production, and what becomes of citizenship and ethics in that process. She is the author of the award-winning books, including Life Exposed: Biological Citizens after Chernobyl and When Experiments Travel: Clinical Trials and the Global Search for Human Subjects, and is co-editor of Global Pharmaceuticals: Ethics, Markets, Practices and When People Come First: Critical Studies in Global Health. A recently named Guggenheim Fellow, Petryna's research has been supported by the National Science Foundation, the National Endowment for the Humanities, the Wenner-Gren Foundation, the Social Science Research Council, and the School for Advanced Research. She was a Member of the School of Social Science at the Institute for Advanced Study and a Faculty Fellow at Princeton University's Center for Human Values. 

Research Interests:

The Cremins Lab focuses on higher-order genome folding and how classic epigenetic modifications work through long-range, spatial mechanisms to govern synaptic plasticity in healthy and diseased neural circuits. Much is already known regarding how transcription factors work in the context of the linear genome to regulate brain development. Yet, severe limitations exist in our ability to engineer chromatin in neural circuits to correct synaptic defects in vivo. At the lab's inception, it remained unclear whether and how genome folding could functionally influence cell type-specific gene expression. We have developed and applied new molecular and computational technologies to discover that nested subTADs and long-range loops undergo marked reconfiguration during neural lineage commitment, somatic cell reprogramming, neuronal activity stimulation, and in repeat expansion disorders. We demonstrated that loops induced by neural circuit activation, engineered through synthetic architectural proteins, and miswired in fragile X syndrome were tightly connected to transcription, thus providing early insight into the genome's structure-function relationship. We will now focus on a fundamental mystery in neuroscience: how memory is encoded over decades despite rapid turnover of synaptic proteins/RNAs. We hypothesize that the 3D genome integrates molecular traces of synaptic plasticity written on chromatin to store long-term memory in neural circuits. We will employ single-cell genomics and imaging technologies to dissect how individual synaptic inputs create 3D epigenetic traces. We will perform genome-wide CRISPR screens to identify specific loops and epigenetic modifications important for synaptic plasticity. We will also re-direct technologies used for genome architecture mapping to create molecular activity-dependent neural connectome maps. Finally, we will study how, when, and why pathologic genome misfolding leads to synaptic dysfunction. Addressing this knowledge gap will provide an essential foundation for our long-term goal to engineer the 3D genome to reverse pathologic synaptic defects in debilitating neurological diseases.

Research Interests:

Dr. Planet's research program focuses on the evolution and ecology of infectious disease. His current interests include the evolution and spread of antibiotic resistant strains, particularly community acquired MRSA, and the impact of the pulmonary microbiome in cystic fibrosis. Other organisms studied in teh Planet lab include nontuberculous mycobacteria and Prevotella melaninogenica. Dr. Planet's laboratory uses whole genome phylogenetics, high-throughput sequencing, and bioinformatics to generate hypotheses that are then tested with bench-based microbiology and molecular techniques.

Research Interests:

Host-pathogen interactions, Vector biology, Malaria, Complement, Innate immunity, Filariasis, Parasite adhesion, Kinetoplastid development

Research Interests:

The lab is broadly interested in understanding the role of the cardiac cytoskeleton as a novel target for the treatment of heart disease. A second arm of the lab, inspired by Dr. Prosser's daughter, is focused on genetic neurodevelopmental disorders, and designing RNA-based therapeutics for their treatment.  

Research Interests:

Our laboratory is focused on: 1) human genetics to identify novel genes and pathways involved in cardiometabolic diseases and traits; 2) experimental approaches to understanding the mechanisms by which these genes and pathways influence these phenotypes; 3) translational therapeutics for cardio metabolic diseases; 4) implementation science regarding the application of genomic medicine approaches in clinical practice. A variety of computational genomics methods, basic cell and molecular laboratory techniques, mouse models, and translational research approaches are used in addressing these questions.

Research Interests:

(1) The regulation and function of sleep
(2) Mechanism of fatigue during sickness

Research Interests:

Single cell, systems biology, cancer, development.

Research Interests:

His research focuses on: a) developing effective strategies to increase access to kidney transplantation, b) improving the process of selecting and caring for live kidney donors, c) determining outcomes of health policies on vulnerable populations with renal disease, including the elderly, and d) testing strategies to improve important health behaviors such as medication adherence.

Research Interests:

Computational Genomics; Bioinformatics; Epistasis; Pharmacogenomics; Big Data; Evolutionary Computation; Genetic Epidemiology; Statistical Genetics; Systems Genomics; Computational Biology; Translational Informatics; Cardiovascular Disease

Research Interests:

Mechanisms of Viral Associated Cancers.

Research Interests:

My research uses multi-modal neuroimaging to describe both normal and abnormal patterns of brain development, in order to better understand the origins of neuropsychiatric illness. To do this, we use large-scale neuroimaging datasets, with an emphasis on neuroinformatics, network science, and machine learning.  

Research Interests:

My research focuses on understanding the stimuli and clinical consequences of innate immune system activation in knee osteoarthritis (OA). We have taken a bedside-to bench approach to focus our preclinical work on mechanisms relevant to human disease. Our lab has identified several inflammatory pathways and mediators associated with synovial pathology, macrophage activation, and pain in patients with early-stage OA, including chemokine and Toll-like receptor mediated pathways. We now explore a functional role for these pathways on structural and symptomatic outcomes in pre-clinical models, employing behavioral measures of joint pain and function in preclinical models of joint injury and arthritis. I anticipate that these investigations will be applicable not only to OA, but to a broad range of musculoskeletal disorders characterized by tissue injury, chronic inflammation and pain, allowing us to develop novel targeted anti-inflammatory arthritis therapies.  

Research Interests:

My research focuses on the application of innovative imaging approaches to cancer diagnosis and treatment.  My specific expertise is in the development of now approaches to MRI signal acquisition and analysis. 

Research Interests:

1. Obesity pathogenesis, including insulin resistance and susceptibility to type 2 diabetes.
2. Adipose (fat) tissue biology
3. Adipocyte development
4. Mesenchymal stem cells and fibrosis responses.

Research Interests:

Molecular basis of behavior.

Research Interests:

Molecular Imaging; Chemical Biology; Synthetic Biology; Radiology; Nuclear Imaging and Therapy

Research Interests:

Our lab is interested in functional genomics, approaches that are aimed at understanding gene function by following the effects of direct perturbations at a large scale, we are developing novel perturbation and functional genomics approaches and applying them together with additional genomics approaches to study a range of human diseases including early and late onset neurodegenerative diseases.

Research Interests:

We have a wide range of interests, but we primarily focus on the molecular biology of cancer using CRISPR gene editing technology. 

Research Interests:

Our research is focused on understanding mechanisms of immune defense against bacterial pathogens, including Legionella pneumophila, Coxiella burnetii, Salmonella Typhimurium, and Yersinia spp., and in turn, how these pathogens subvert host immunity. 

Research Interests:

The Silverman Lab aims to understand the mechanisms of immune system variation and to discover novel approaches to predict and prevent immune-mediated diseases, specifically the microbial and developmental factors that lead to T1D. Current research studies in the lab involve the genetic and microbiota impacts on T1D; pediatric gnotobiotic mouse model; and selective IgA deficiency (SIgAD).

Specifically, transgenic expression of the MHCII E molecule in NOD mice (Eα16/NOD)completely prevents T1D, mirroring dominant HLA protection from T1D in humans. Using these Eα16/NOD mice as a model of dominant genetic protection from T1D, the Silverman Lab demonstrated that protection from autoimmunity operates by the immune system shaping the early-life commensal microbiota. The lab's ongoing project in this area aims to discover the mechanisms by which the host immune system impacts the development of commensal microbiota, and further, how commensal microbes educate the immune system to prevent autoimmunity. Modeling of HLA class II dominant protection from T1D supports the lab's long-term goal of developing early-life microbiota-based therapies to prevent T1D in humans

The Silverman Lab has collaborated with Paul Planet, MD, PhD, attending physician in the Division of Infectious Diseases at CHOP, to generate the first gnotobiotic mouse model of the pediatric microbiome, which we call Pediatric Community or "PedsCom." PedsCom is a consortium of 8 bacterial strains isolated from the intestine of pre-weaning diabetes-protected Eα16/NOD mice. These mice are unique and powerful tools to define the "rules of engagement" between the host and their commensal microbes.

Finally, the lab has recently defined the microbiome from pediatric patents lacking IgA. The team's ongoing research aims to determine the mechanism for the increased incidence of autoimmune disease in patients with SIgAD.  The lab developed a technique (mFLOW-SEQ) to tag microbes with a patient's own serum IgG antibodies followed by metagenomic sequencing to define those microbes which activate, and in some cases, over-activate their immune systems.

Research Interests:

Our laboratory studies cancer cell metabolism, tumor immunology, metastasis, and cellular responses to oxygen deprivation.

Research Interests:

Research in Dr. Hongjun Song's laboratory focuses on three core topics: (1) neural stem cell regulation and neurogenesis in the developing and adult mammalian brain and how these processes affect neural function; (2) epigenetic and epitranscriptomic mechanisms and their functions in the mammalian nervous system; (3) Biology and potential treatment of glioblastoma using a patient-derived tumor organoid model. The lab is also interested in addressing how dysfunction of these mechanisms may be involved in brain disorders. We are using both mouse model in vivo and patient iPSC-derived 2D cultures and 3D brain organoids for our studies.  

Research Interests:

Orthopaedic research, orthopaedic biomechanics and tissue engineering, tendons and ligaments, shoulder and elbow

Research Interests:

Hematopoietic stem cells and leukemia using mouse models.

Research Interests:

Metastasis, Pancreatic Cancer, Tumor Immunology, Cell Plasticity.

Research Interests:

We study the cell and molecular biology of parasites and how they interact with their mammalian host.
In recent years we have focused on the apicomplexan Cryptosporidium, a distant cousin to the parasite that cause malaria. Cryptosporidium is an important pathogen for which neither prophylaxis nor effective treatment are available. Cryptosporidium was first recognized in the 1980s as an AIDS-defining opportunistic infection, however, immunocompetent individuals are susceptible, and today Cryptosporidium accounts for 50% of all U.S. waterborne disease outbreaks.
Most recently, Cryptosporidium was identified as a leading cause of diarrheal disease and death in infants. Beyond acute disease, asymptomatic cryptosporidiosis causes stunting and environmental enteropathy with lasting impact on the development and health of children. Malnutrition and cryptosporidiosis are intimately linked. Cryptosporidium has long been difficult to study, but a series of recent advances has made the organism and the disease tractable. We developed genetic manipulation of the parasite and mouse infection models which has opened this important pathogen to sophisticated mechanistic studies.
Currently our research is exploring three areas of Cryptosporidium biology: 1) how does the parasite invade and manipulate the intestinal epithelial cells in which it develops, 2) how does the sexual part of the parasite’s lifecycle unfold and 3) how does the host immune system recognize and restrict Cryptosporidium infection?
Trainees in the lab use a broad range of modern approaches including single cell sequencing, super-resolution and live-cell microscopy, genetic engineering, flow cytometry, cryo-electron tomography and a variety of cell, organoid and animal model systems.

Research Interests:

Gene regulation plays a fundamental role in cellular development and cancer. Our lab uses genomics and systems biology approaches to understand the gene regulatory factors underlying cellular processes. We take snapshots of the regulatory systems using bulk and single-cell omics and imaging assays, and develop computational algorithms to integrate data and generate testable models of gene regulatory pathways in model systems.

Research Interests:

We study the impact of environmental factors (the "exposome") on human disease, including inflammatory, metabolic, and neurological diseases.

Research Interests:

Political Anthropology; Sovereignty; Violence; The Afterlives of Imperialism; Transnationalism and Diaspora; Race and Gender; Performance and Popular Culture; Culture and Political Economy; Popular Culture; the Caribbean.

Research Interests:

The Titchenell lab is focused on understanding how hormones and nutrients regulate metabolism with the goal of identifying new therapeutic targets and approaches to treat metabolic diseases such as diabetes, obesity and cancer. Specifically, my laboratory focuses on insulin action and the molecular mechanisms of insulin resistance with a particular focus on liver, adipose and skeletal muscle metabolism. We employ a host of cutting-edge technologies in biochemistry, molecular biology and organismal physiology to address these fundamental questions in biology.

Research Interests:

Developing targeted imaging and therapeutic agents designed to improve the detection and treatment of cancer. Specific research interests include (i) developing new nanoformulations that are capable of carrying extremely high payloads of drugs, radiosensitizing agents, and/or contrast agents; (ii) investigating new targeting strategies that maximize specificity and sensitivity; and (iii) developing new bioconjugation techniques that enable the highly efficient, site-specific labeling of antibodies and other targeting ligands.

Research Interests:

We are interested in understanding on a structural and biochemical level how DNA and RNA molecules are maintained and processed by living cells. In addition to the mechanisms and regulation of genome replication and transcription, this includes processes such as DNA repair, site-specific and homologous recombination, transposition, condensation of chromosomes, chromosome pairing and segregation, and RNA trafficking and splicing. Our approach is to establish three-dimensional models of macromolecular assemblies relating to a particular biological question using X-ray diffraction methods and to then develop mechanistic and functional models that can be tested experimentally.

Research Interests:

The goals of the Volk laboratory are to understand regulatory mechanisms governing dynamic interactions between cells and their surrounding extracellular matrix in the wound healing-fibrosis-cancer progression triad and to apply this knowledge to develop innovative regenerative and oncologic therapies for veterinary and human patients.

Research Interests:

The Vonderheide laboratory combines efforts in both basic research and clinical investigation to advance the understanding of tumor immunology and to develop novel immunotherapies for cancer. The chief hypothesis is that successful approaches in tumor immunotherapy will need to (a) optimize target antigens with regard to clinical applicability and risk of antigen loss, (b) repair host immuno-incompetence in antigen presentation and T cell function, and (c) circumvent immuno-suppressive factors of the tumor and tumor microenvironment.

Research Interests:

The role of mtDNA and nDNA mitochondrial genetic variation in all aspects of human biology including clinical genetics,  neuropsychiatric disoreders, SARS-CoV-2 pathophysiology, cancer, immunology, population biology, animal models, and genetic and metabolic therapeutics.

Research Interests:

The Warren lab studies normal and malignant hematopoiesis, with a special interest in granulopoiesis. The lab's research aims to understand the pathogenesis of severe congenital neutropenia and other marrow failure syndromes, as well as associated\ risk for malignant transformation. 

Research Interests:

Quantitative imaging approaches using MRI.

Research Interests:

DNA vaccines for infectious diseases or cancers, T cell immunity, Active immunization. Development of novel strategies for invivo biologic production, Self assembly invivo of designed vaccine antigens. 

Research Interests:

Pathogenesis of human coronaviruses including MERS-CoV, SARS-CoV-2 and nonlethal "seasonal" human respiratory viruses; Infection of primary nasal epithelium with translational applications; Murine coronavirus pathogenesis, central nervous system, liver and lung;  Viral innate immune antagonist;  Activation and antagonism of the OAS-RNase L pathway- Viral and cellular phosphodiesterases that antagonize RNase L; Zika virus pathogenesis; Endogenous dsRNA induced pathogenesis

Research Interests:

Our lab aims to understand cellular host responses to virus infection, and the environment encountered and manipulated by viruses. We study multiple viruses in an integrated experimental approach that combines biochemistry, molecular biology, genetics and cell biology. We have chosen viral models that provide tractable systems to investigate the dynamic interplay between viral genetic material and host defense strategies. The pathways illuminated are key to fighting diseases of both viral infection and genome instability, and our studies have significant implications for the development of efficient viral vectors for gene therapy.

Research Interests:

My lab is studying cellular metabolism, including mechanisms of metabolic adaptation to nutrient availability and mechanisms of metabolic regulation of gene expression in cancer and metabolic disease.

Research Interests:

T Cell Exhaustion, Immunotherapy, T Cell Memory, Viral Immunity, Immune Oncology, Immune Health.

Research Interests:

Dr. Wilson's laboratory focuses on the development of gene transfer vectors and their application in the treatment of inherited and acquired diseases. Characterization of these novel viral isolates has yielded important insights into basic virology. More importantly, recombinant versions of these viruses have proven to be useful as improved gene transfer vehicles to a variety of targets such as the liver, cardiac and skeletal muscle, and the brain.

Research Interests:

The research focus of the Advanced Cardiovascular Imaging Lab is the development of next generation imaging technologies for cardiovascular disease. As an interdisciplinary team of Radiologists, Physicists, Computational Scientists, and Engineers, we solve complex problems and develop new tools, to improve our scientific understanding of cardiovascular disease and clinical care of patients.

Research Interests:

Episodic Memory, neuroimaging, MRI, PET imaging, Alzheimer's Disease, Dementia, Memory Disorders, Cognitive Neurology, Aging.

Penn Memory Center 

Research Interests:

Steerable needles.

Research Interests:

I am a computational biomedical image analysis scientist whose program combines theoretical work on image segmentation, registration, and statistical morphometry with applied and translational research, primarily in the area of brain MRI analysis.  I lead a research program focused on using detailed imaging and image analysis of the medial temporal lobe (MTL) to derive effective and informative biomarkers for neurodegenerative diseases. My group is widely recognized one of the leaders in the detailed MTL neuroimaging field, particularly, as the main provider of advanced computational algorithms. Our major research products include the first ex vivo 3D computational atlas of the human hippocampus that combined ex vivo MRI and histology; the best-performing software for hippocampal subfield and MTL subregion segmentation in in vivo MRI (ASHS, in use by ADNI3); winning performance in general image segmentation challenges at MICCAI 2012 and 2013; and the demonstration of the efficacy of MTL subregional measures in detecting granular changes associated with early AD. My group is also heavily invested into open-source software development, including our flagship tool ITK-SNAP, which has tens of thousands of users.

Research Interests:

Genomics, change-point methods, empirical bayes estimation, model and variable selection, scan statistics, statistical modeling.

Research Interests:

Genetics and Epigenetic Control of Genome Function in Brain Development and Disease.