The Grant Application Resource Center (GARC) provides standardized language and links to information to support the development of grant applications. Use this page to obtain information about the Institutes at the Icahn School of Medicine at Mount Sinai (ISMMS) to include in your proposals.
For inquiries about research collaboration please contact James Faghmous, PhD.
Mount Sinai’s strategic plan provides a road map for major investments in research and infrastructure to establish a series of new Institutes, including The Charles Bronfman Institute for Personalized Medicine (IPM).
The Institute is dedicated to advancing personalized health and health care with three core objectives:
- Provide clinical and translational investigators with greater and easier access to high quality, standardized biospecimen collections, linked with full clinical information.
- Provide an academic research home and technology support for discovering clinically important genotype-phenotype associations through interdisciplinary, translational genomics programs.
- Facilitate clinical development of gene-based diagnostics and risk assessment algorithms and evaluate their impact on health care delivery at the patient and population level.
IPM is home to research faculty pursuing studies in the clinical areas of pharmacogenomics, obesity and metabolic traits, cardiovascular and kidney disease. Institute faculty generates innovations and new paradigms in mapping of complex traits in diverse populations, clinical knowledge representation and phenomics, and personalized medicine clinical decision support.
Headed by Judy Cho,MD, IPM provides full and sole support for the IPM BioMe Biobank Program including the Biobank Informatics and Genomic Data Analysis Services Center (BIGDASC).
BioMe™ Biobank Program
To discover better treatments, researchers are seeking to unravel the complexity of disease at the most basic level through “molecular” studies. The donation of samples from many thousands of individuals is essential to such studies. BioMe is a biobank program of the Charles Bronfman Institute for Personalized Medicine at Mount Sinai. BioMe is dedicated to advancing the application of human blood-derived biospecimen and clinical data to life science research to accelerate the development of personalized healthcare and medical solutions.
Since September 2007, over 38,000 Mount Sinai Health System patients have enrolled in the Electronic Medical Record-linked BioMe Biobank Program. It is designed to generate a large collection of DNA and plasma samples, and phenotypic (questionnaire-based and EMR-linked) and genomic data, that are stored in a way that protects patient’s privacy. The three major self-reported racial/ethnic populations include 32% EA (European Ancestry), 24% AA (African Ancestry, 35% HA (Hispanic Ancestry). At the same time, it enables research to be performed on de-identified, comprehensive, electronic clinical information extracted from the Mount Sinai Data Warehouse (MSDW).
IPM represents Mount Sinai as a member site to several large NIH-funded research networks, including the IGNITE Implementing GeNomics In pracTicE Network, Population Architecture Using Genomics and Epidemiology (PAGE), Phase II, eMERGE II Network (electronic medical records and genomics), the eMERGE-Pharmacogenetics Research Network (PGRN) research partnership, the CKD Biomarker Consortium, among others.
The BioMe Biobank Program contributes under collaborative agreements with international research consortia and collaborations, including:
- GIANT (Genetic Investigation of Anthropometric Traits) – GWAS data contributed for discovery analysis for anthropometric traits from all BioMe™ participants and workgroup participation
- COGENT BP (Continental Origins and Genetic Epidemiology Network) – GWAS data for BP from African American BioMe™ participants contributed for discovery analysis
- GHBP (Genomics in Hispanics for Blood Pressure) – GWAS data for BP from Hispanics contributed for discovery analysis
- Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory (John Guttag): Predictive Modelling and Personalized Health Decision Support Tools
- Genetics of Obesity and related traits in African Americans – GWAS data of BMI from African Americans BioMe™ participants contributed for discovery and follow up analysis and workgroup participation
- African American Type 2 Diabetes Genetics Consortium – GWAS data of T2D from African American BioMe™ participants contributed for analysis
- CHARGE (Cohorts for Heart and Aging Research In Genomic Epidemiology) – Exome chip date contributed for analysis of BP from all BioMe™ participants
- CKDGen (CKD Genetics Consortium) – GWAS data contributed for discovery analysis and workgroup participation
- CKDGen (CKD Genetics Consortium) – Exome chip data contributed for analysis of BP from all BioMe™ participants
- GLGC (Global Lipids Genetics Consortium) – Exome chip data contributed for discovery analysis of all lipids from all BioMe™ participants
- GLGC (Global Lipids Genetics Consortium) – Exome chip data contributed for follow-up analysis of CAD from all African American BioMe™ participants
- ESP-LDL (Exome Sequencing Projects LDL Cholesterol) – Exome chip data contributed for follow-up analysis of LDL from all BioMe™ participants
- MAGIC (Meta-Analyses of Glucose and Insulin-related traits Consortium) – Exome chip data contributed for discovery analysis of HbA1c from all BioMe™ participants
- CHARGE (Cohorts for Heart and Aging Research In Genomic Epidemiology) – Exome chip data contributed for discovery analysis of Glycaemic traits from all BioMe™ participants
- CHARGE (Cohorts for Heart and Aging Research In Genomic Epidemiology) – Exome chip data contributed for follow-up analysis of Amyloidoses from all BioMe™ participants
- MEDIA MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium – GWAS data contributed for discovery analysis of T2D from African American BioMe™ participants.
- TranscenD (TRANS-ethnic Evaluation of vitamin D) – GWAS data contributed for discovery analysis of Vitamin D from all BioMe™ participants.
- Lipids in HA – GWAS data contributed for discovery analysis of Lipids from all Hispanic American BioMe™ participants.
- AAGILE (African American Glucose and Insulin Genetic Epidemiology (AAGILE) Consortium) – GWAS data contributed for discovery analysis of HbA1c and glucose from all African American BioMe™ participants.
- DIAGRAM+ and GOT2D (Genetics of Type 2 Diabetes) – GWAS data contributed for follow-up analysis of T2D from all BioMe™ participants.
- BP in HA GWAS data contributed for discovery analysis of BP from all Hispanic American BioMe™ participants.
- ICBP (International Consortium for Blood Pressure) – GWAS data contributed for discovery analysis of BP from all European American BioMe™ participants.
- Anthropometric Traits in HA – GWAS data contributed for discovery analysis of Anthropometric Traits from all Hispanic American BioMe™ participants.
- T2D Genes – Targeted sequencing for follow-up analysis of T2D from all European American BioMe™ participants.
Visit the Charles Bronfman Institute for Personalized Medicine or email the Charles Bronfman Institute for Personalized Medicine for more information.
Last Updated: June 27, 2017
The mission of the Mindich Child Health and Development Institute (MCHDI) is to enable translational research of diseases affecting infants, children and adolescents by assembling outstanding physician-scientists and scientists in an intellectually rich and supportive environment, which fosters collaborative scientific investigation as well as the training of the next generation of scientific leaders for pediatric medicine.
The MCHDI is dedicated to translational research to better understand the pathogenesis of prevalent pediatric conditions and diseases in order to then develop and implement new treatment strategies. Leveraging Mount Sinai's leadership in genetics and genomics sciences, as well as environmental medicine, the MCHDI has focused on the following areas of research emphasis to maximize its impact on new discoveries:
- Asthma and Allergy
- Cardiovascular Diseases
- Neurodevelopmental Disorders
- Obesity and Diabetes
- Other Childhood Diseases
Last Update: June 1, 2017
The purpose of the Blavatnik Family Women’s Health Research Institute is to optimize quality of care for women across the life span and to narrow gaps in treatment and outcomes in underserved populations.
As a research Institute, our focus will be to transform women’s health by advancing science, training the next generation of scientific leaders in women’s health, and promoting breakthroughs in clinical care.
Women make up more than half of the population in the United States. They use health care services more frequently than men do. And, women make most of the health care decisions for their families. However, while women live longer, they experience poorer health than men on a variety of outcomes. To date, too few institutions have established interdisciplinary research institutes dedicated to advancing science in the field of women’s health.
With the Blavatnik Family Women’s Health Research Institute, Mount Sinai is filling that gap and taking a leadership role by leveraging existing faculty in several departments and institutes with overlapping research interests.
The Blavatnik Family Women’s Health Research Institute aims to build and expand a research portfolio in key areas in women’s health, including:
- Mental health and depression
- Disparities and health equity research
- Maternal and infant morbidity and mortality
- Quality of care
- Gynecological cancer
- Reproductive endocrinology and infertility
- LGBT health
- Global health
The Blavatnik Family Women’s Health Research Institute will facilitate collaborations across existing departments and institutes of the Icahn School of Medicine at Mount Sinai, leveraging and building on the existing strengths of the Mount Sinai Health System.
Updated: April 4th , 2018
ConduITS the Institutes for Translational Sciences was established in 2009 when Mount Sinai received a prestigious Clinical and Translational Science Award (CTSA) from the National Institutes of Health. To read more, please visit ConduITS.
Center for Therapeutic Antibody Development
The mission of CTAD is to collaborate with researchers in the design and development of monoclonal antibodies (mAb) for research and commercialization. Because of their sensitivity and specificity, mAb are critical basic science research tools and are the core technology for many diagnostic tests such as those used to verify pregnancy or influenza infection. In the past decade they have become the most successful new drug classification with yearly sales exceeding fifty billion dollars. If monoclonal antibodies are needed for basic science studies/grant submission, therapeutic or diagnostics use CTAD is available for a consultation to determine the best approach to producing the antibody of interest. If the antibody target has therapeutic value it is possible that it can be made in a humanized mouse system through collaborations with industrial partners.
The Center for Therapeutic Antibody Development (CTAD) has been in existence since 1996 under the guidance of Dr. Thomas Moran. The facility assists in all aspects of the generation of mAb from expressing the target protein to screening and purifying the selected clones. Hundreds of antibodies have been successfully generated for scientists at Mount Sinai as well as for other institutions. To date, over 30 monoclonal antibodies generated in the facility have been commercialized for basic science use.
Areas of Expertise
CTAD can assist in or perform any or all of the steps needed to generate high quality monoclonal antibodies for research or therapeutic use including:
- Production of protein using various expression systems
- Purification of protein
- Immunization of appropriate host
- Fusion and immortalization of B cell clones
- Screening and selection of clones
- Production of human monoclonal antibodies using mice from Regeneron Pharmaceuticals
- Purification of antibodies
- Mycoplasma testing
Protein expression and purification
CTAD has expert assistance available to prepare, purify and express proteins using methods that maximize native protein folding and stability. In most instances proteins can be produced when given only the genetic sequence of the protein.
Immunization and fusion
The CTAD has IACUC approval for the generation of hybridomas in mice, hamster and rat. Immunization protocols are selected according to the target immunogen and intended use of the antibody by the investigator. After fusion of B cells to an appropriate immortalized cell line, clones are selected and grown in semi-solid media. Clones are picked and transferred to 96 well plates for screening and expansion of cells.
The selection of the screening method will be done through consultation with the investigator. Generally, the screening method is selected according to the assay of interest. If the priority for a successful antibody is use in flow cytometry, then flow is the most appropriate screening method. Other screens could include ELISA and functional screens. Screening can be done using a proxy antigen, which is a recombinant protein typically similar to the immunogen, or using the naturally expressed protein. All clones generated will be cryopreserved for storage for possible future applications.
Antibodies that pass the screening criteria are isotyped and may or may not go through a second type of screening. When the desired antibodies are identified, CTAD will expand the clone and purify the antibody preparations.
CTAD and Therapeutic monoclonal antibodies
Therapeutic monoclonal antibodies generated more than 50 billion dollars in sales last year. Six of the top 15 selling drugs in this country are monoclonal antibodies and Humera, a mAb specific for the cytokine TNF is now the largest seller at 9.5 billion. There are more that 250 candidates currently in various stages of development/testing. CTAD is committed to developing monoclonal antibodies with potential use as therapeutics. Currently a number of collaborations between CTAD/Mount Sinai investigators and pharmaceutical or biotech companies are in progress. Calls for targets that address unmet medical needs are released annually to encourage Mount Sinai investigators to work with CTAD to produce human antibodies with therapeutic potential using Regeneron human mice. Many of these projects are funded and the monoclonal antibodies produced are in various stages of licensing.
Last Update: June 1, 2017
Medicinal Chemistry Program
The Medicinal Chemistry Program of the Drug Discovery Institute is a resource available to basic and clinical research investigators at Mount Sinai who are interested in employing small molecule chemistry to furnish research probes or to develop new experimental small molecule therapeutics. Chemists in the Program operate in a newly renovated medicinal chemistry laboratory space located in the Icahn Medical Institute Building and in an environment conducive to interdisciplinary research, for example with biophysical (x-ray, NMR) and computational researchers; this capitalizes on existing strengths within Icahn School of Medicine.
To initiate the search for novel small molecule agents, research groups will run computational virtual screens in conjunction with the DDI’s Structure Based Drug Design Core and assay development with the Assay Development Core. Screening hits that are identified by the team will be available to work collaboratively with the research groups in three progressively more interdisciplinary phases:
- Hit confirmation and resupply - Data from a screening campaign will be triaged to eliminate false positives or artifacts: compound purity from the active wells will be assessed, and material re-synthesized, scaled-up and purified. Hit compounds may then be interrogated in detail in the screening assay or other follow-up assays as appropriate to confirm useful levels of activity.
- Hit to Lead Chemistry - Confirmed hits will then be assessed and ranked based on a number of factors in addition to potency, particularly chemical tractability. A chemically tractable lead will be of reasonably low molecular weight structure (<500 Da), which is amenable to rapid analog synthesis to facilitate exploration of structure activity relationships. Depending on the molecular type additional analogs may be available from commercial sources, or parallel libraries will be designed and synthesized to explore various sites for modification and improvement of the structure. A successful screening campaign will yield three or four tractable lead series suitable for this type for early exploration. Compound series where potency and selectivity can be usefully modulated will be characterized in more detail with respect to drug-like properties, and where appropriate with respect to predictive pharmacology models generated by the Systems Pharmacology Core (see the SPCC description for details). Medicinal chemists, together with biologists and pharmacologists will also work with Mount Sinai’s MSIP office to develop a strategy to define and protect intellectual property on novel composition of matter. In vitro leads of this type may serve as research tools for interrogation of novel disease targets or as jumping off points for further optimization.
- Lead Optimization - Based on an assessment of biochemical potency, cell based activity, overall physicochemical profile and input from models from the SPBCC, one series may be selected for further optimization. The objectives of the lead optimization are to increase potency in cell-based assays and to test molecules in more downstream in vitro and in vivo functional assays. In vitro ADME parameters such as microsomal stability and physical properties such as aqueous solubility will be monitored as leads progress by outsourcing to approapriate contract research organizations (CRO). When an adequate balance of in vitro potency and physicochemical properties is achieved, initial in vivo rodent PK (IV, ip and oral) will be obtained at CROs. At this stage in lead optimization broader pharmacological profiling of leads is appropriate: for example selectivity profiling versus panels of receptors and enzymes. Early in vitro safety parameters may also be assessed at external collaborators, for example hERG channel or CYP450 activity. These assays may identify additional parameters that require optimization or influence go/no decisions on continued optimization; they will also provide input for model development by the SBDD on novel experimental therapeutics discovered at the institute.
Optimized leads produced by the DDI will have in vivo efficacy in animal models (either disease or biomarker), at an acceptable dose and route of administration, with no obvious toxicity or metabolic liabilities. Medicinal chemistry is central to the design and synthesis of these leads, and chemists will interact with scientists in the TCBC, SPBCC and PPC of the ETI as projects progress.
Last Update: May 25, 2017
Molecular Informatics Core
The Molecular Informatics Core (MIC) facilitates sophisticated use of molecular structure information by providing access to databases, state-of-the-art software, and expert support for protein sequence and structure analysis, protein structure modeling, characterization of protein-ligand interactions, and virtual screening. The MIC staff assists researchers with the development and execution of computational strategies to address specific research questions. Working closely with other core facilities of the Experimental Therapeutics Institute (ETI) at Mount Sinai, in particular the Integrated Screening Core, the MIC will support target characterization, lead discovery, and lead optimization.
Target characterization services include: protein structure modeling for target proteins, identification and prioritization of ligand binding sites in protein structures, and modeling of protein-ligand complexes. In the area of lead discovery the MIC offers small-molecule virtual screening and docking, including high-throughput computational screening of small-molecule libraries, containing more than 4,000,000 compounds, against experimental and predicted target protein structures; construction of targeted libraries for HT chemical screening based on virtual screening results; targeted docking of selected compounds into experimental and predicted target protein structures. For lead optimization the MIC offers services to model and characterize protein-ligand interactions, identification of affinity and selectivity determining residues in the target protein, and support for structure-based refinement of protein-ligand interactions to enhance affinity and selectivity.
Last Update: March 22, 2012
Pluripotent Stem Cell (PSC) Core Facility
The study of human embryonic stem cells (hESCs) and Induced Pluripotent Stem Cells (iPSCs) collectively referred to as pluripotent stem cells and their differentiation into specific lineages provides an extraordinary opportunity to study the cellular / molecular mechanisms regulating pluripotency and differentiation. It also offers a potentially unlimited source of numerous cell types for drug screening and cell-based therapies. The Pluripotent Stem Cell Shared Resource Facility has been established to facilitate the transfer of this technology to the Mount Sinai community and other institutions. The objectives of this facility are:
- To generate induced pluripotent stem cells using the latest transgene-free Sendai virus and mRNA/micro RNA technology.
- To provide undifferentiated PSCs, mouse embryonic fibroblasts (MEFs) and/or hematopoietic, cardiac and endoderm progenitors.
- To train faculty, postdoctoral fellows and students in the maintenance and the differentiation of pluripotent stem cells.
- To provide tested media / reagents necessary for the maintenance as well as the differentiation of pluripotent stem cells at discounted prices.
- To karyotype and bank hESC and iPSC stocks.
- To generate gene targeted hESC lines and iPSC lines.
- To assist PIs with pilot projects.
Last Update: June 1, 2017
Systems Pharmacology-Bioinformatics and Computational Systems Biology Core
The Systems Pharmacology-Bioinformatics and Computational Systems Biology Core assists Mount Sinai investigators with analyzing their genomics and proteomics datasets such as those collected by RNA-seq, cDNA microarray, ChIP-seq, IP/MS proteomics, SILAC phosphoproteomics or exome sequencing. The Core has the capabilities of visualizing cellular networks from lists of differentially expressed genes/proteins identified experimentally or considered as disease gene lists using the tools developed in-house. The Systems Pharmacology-Bioinformatics and Computational Systems Biology Core also has the capabilities of performing gene-set enrichment analyses using data collected from ENCODE, the Epigenomics Roadmap, KEGG, BioCarta, WikiPathways, Reactome, The Gene Ontology, MGI Mammalian Phenotype Browser, LINCS Connectivity Map, OMIM, BioGPS, CCLE, PFAM and InterPro and more. Such analyses can be performed by the popular tools Enrichr, ChEA and KEA. In addition, the Core has the capabilities of building customized web-portals dedicated to specific projects for interactive data exploration and data analysis on the web.
Last Update: September 23, 2015
The Friedman Brain Institute is an interdisciplinary hub for defining the mechanisms underlying brain and nervous system diseases and for translating those findings into preventative or restorative interventions. The Institute is focused on three major areas of investigation where Mount Sinai can be truly transformative: neural injury and repair, cognition, and neuropsychiatry. The Institute will be judged by its success in advancing brain repair, developing new ways to advance cognition, and improving the treatment of neuropsychiatric disorders.
The Brain Institute's work spans basic molecular and genetic research of nervous system disorders, from animal models to investigations of human populations in the clinic. New knowledge from animal studies will drive clinical investigations, while new insight from clinical studies will help guide more basic exploration into the underlying mechanisms. This broad-based approach incorporates a wide range of state-of-the-art methodologies and coordinates efforts among numerous departments at the Icahn School of Medicine, including neuroscience, neurology, psychiatry, neurosurgery, pharmacology, geriatrics, ophthalmology, and rehabilitative medicine.
Mount Sinai has been recognized as a leader in brain research and treatment for over a century. It has been at the forefront of the rapidly evolving discipline of basic neuroscience, while its longstanding reputation for excellence in clinical neurology, neurosurgery, psychiatry, ophthalmology, and rehabilitative medicine has continued to grow.
Last Update: May 25, 2017
The Global Health and Emerging Pathogens Institute is the nucleus of Mount Sinai’s work on infectious diseases and the pathogens that cause them. The Institute, based in New York City, builds on Mount Sinai’s internationally recognized expertise in RNA virus research and encompasses ongoing research on the molecular pathogenesis of influenza, HIV, and dengue and Ebola viruses, as well as on hepatitis C and West Nile.
The innate component of the immune response is a rapid one, in which the body recognizes and fights off general classes of infectious agents. Mount Sinai has been at the forefront of current research, identifying viral factors that inhibit innate immune responses and showing how such factors contribute to the pathogenesis of the virus. Global Health and Emerging Pathogens Institute expertise in virology will prove invaluable as we work to develop robust vaccines and antiviral drugs that save people lives.
The Global Health and Emerging Pathogens Institute is focused on expanding Mount Sinai’s world-renowned programs in RNA viruses. Our strategy serves as a model for developing new programs to study other viruses, specially zoonotic and emerging viruses, including MERS and Zika viruses. These viruses blur the line between animal and human viruses and do not respect country borders, consistent with the concept “one world, one health, one medicine”, linking human, animal and environmental health. The Institute is also developing research programs driven by local and global public health needs. One emerging area of interest is the impact of host genetics and of the microbiome in virus disease.
Last Update: May 25, 2017
The Immunology Institute at Icahn School of Medicine brings together and fosters collaboration between faculty members in multiple disciplines and departments who conduct research in Basic Immunology, Oncology, Inflammation (with a focus on Inflammatory Bowel Diseases, Skin Inflammatory Diseases, Vascular Inflammation and Neuro-inflammation) as well as Allergy and Transplantation. The overall goal is to provide an institutional mechanism to enhance clinical translation of basic immunology research, exploring and dissecting the contribution of immune pathways to disease pathophysiology with the intention of developing novel therapeutic approaches and identifying novel biomarkers of disease course and response to treatment.
Last Update: May 31, 2017
The Institute for Genomics and Multiscale Biology at the Icahn School of Medicine is a "core technology institute", which enables Mount Sinai Researchers to carry out cutting-edge genomic-based basic and translational research that brings state of the art high throughput genomic technologies under one roof to provide a centralized resource to carry out large scale genomic studies. The Genomic institute has three core units: The Genomics Core, the Proteomics/Metabolomics Core, and the Computational Genomics Core. Each core has state-of-the-art equipment, technical and analytical infrastructure manned and run by highly skilled and knowledgeable technical and scientific staff to facilitate sophisticated genomic, proteomic and metabolomic research. Eric Schadt, PhD Chair of the Department of Genetics and Genomic Sciences, directs the Institute. Andrew Kasarskis, PhD is the Co-Director of the Institute.
The Genomics Core:
Apart from housing the standard Sanger Sequencing facility, the Genomics Core provides the latest next generation sequencing and microarray technologies. The Genomics Core currently operates multiple next generation sequencing platforms: 4 Illumina HiSeqs, one MiSeq, one Pac Bio RS system. Two Astro platforms that are the latest high tech models over the RS system will be commissioned by the end of 2012. The Genomics Core facility is directed by Milind Mahajan, PhD and has 12 full time staff including three PhD level staff appointments. The day-to-day production, R&D operation, and scientific and business oversight of Genomics Core are handled by Milind Mahajan, PhD and Andrew Kasarskis. All necessary infrastructures such as high performance computation and bioinformatics support are already in place. The types of high throughput sequencing projects that are being routinely carried out include preparation of Seq-libraries followed by sequencing for RNA-seq, CHIP-seq, and small RNA Seq, targeted gene selection sequencing and whole exome and genomic sequencing from variety of clinical and non-clinical samples from different biological sources.
Microarray Technology is offered for Genome Wide Association Studies, Pharmocogenetics, Genomics, Methylation, candidate gene, and genotyping analyses. The Core has extensive experience and expertise in genotyping and expression array analysis on Affymetrix and Illumina platforms. Currently, the Core uses the Illumina platform for genotyping employing the Golden Gate assay as well as OmniExpress, OmniQuad2.5, and Omni2.5-8 arrays. The Core has all the necessary liquid robotic automation systems, a HiScan and Bead Express system to carry out wide range of sample volumes. With the existing latest state of the art equipment and facilities, the current capacity is to process up to 600 samples per week.
Quantitative PCR analysis for small-scale gene expression quantitation and detection of single nucleotide polymorphisms is available using an Applied Biosystem 7900HT with associated robotics for accurate reaction set-up using a Biomek FX for automated liquid handeling. Automated, high throughput nucleic acid purification from blood, tissue or bacteria is performed in a 96 well format using a Qiagen Universal BioRobot. To assess the quality of nucleic acids, the Genomic Institute has an Agilent Bioanalyzer 2100.
The Genomic Institute has ample computing power, and software developed in-house that is described below and listed in the Major Equipment document. The data are processed on a 360-core compute cluster with 128GB of RAM available on each node (with ~50 cores per node). Additional servers, with large amounts of RAM, bring up the total amount of available RAM to 1.2 TB. A 400 TB networked storage device from Isilon provides ample storage for the sequencing data. The storage and computer clusters are connected to each other through a 10G interconnect. A special server from Avere provides tiered data access, with frequently used files being cached for rapid access. An externally accessible website is hosted on two mirrored servers, with load balancing controlled by an F5 load-balancer. Nodes on the compute cluster are pre-loaded with all of the necessary software to perform routine analysis of high-throughput sequencing data and are regularly updated with the latest public genomic data resources. Several tools, for analysis and data exploration, have been developed in-house. These are deployed as browser-based tools backed by distributed web-services that help maintain performance and availability. The servers are housed in two 42U racks with ample power and air-conditioning. Both power and air-conditioning have backup, ensuring 24/7 operation. A dedicated system administrator helps keep the software up to-date. In addition, two programmers/analysts develop software and analyze data.
Scientific Computing Infrastructure:
Mount Sinai has committed over $50M to its scientific computational and data cyberinfrastructure, recognizing that a well-designed and managed infrastructure empowers its scientists and researchers to be more productive and effective. This significant investment includes professional staff, expertise, hardware, software and a new computational and data facility dedicated to scientific computing. Mount Sinai closely collaborates and partners with other facilities and vendors, to keep its cyberinfrastructure and services state-of-the-art. The staff follows the communities’ best practices and procedures to ensure that the computing and data services are the most efficient and effective for the researchers.
Mount Sinai’s robust computing and data cyberinfrastructure has been designed for the rapid and accurate ingest of the sequencer output and high performance post-processing and analysis by the computational cluster and affiliated file systems and storage. The cyberinfrastructure resources have been tailored specifically to handle the computational and data workflow from the sequencer, including a high bandwidth network.
The computing and data center at Mount Sinai contains over 10,000 square-feet of space. It offers several complementary resources, including an SGI Altix 1300 cluster with 816 CPU cores, 64 Nehalem-class nodes with Quad Data Rate (QDR) Infiniband connectivity and 38 nodes with Double Data Rate (DDR) Infiniband. All of those nodes are attached to 65 Terabytes of Lustre-based high-speed shared storage. The software and programming environments are the best of breed, and include community standards such as Linux and MPI. The clusters also run resource managers and schedulers optimized for the job workload, optimized to process as many jobs as possible for the highest overall machine utilization, job throughput and job success rate. The clusters are operated with over 95% uptime, using scalable and reproducible configuration management techniques. The machines are also monitored for security.
High Performance Computing (HPC) Cluster:
The new High Performance Computing cluster and storage will be installed at the beginning of March 2012, and expect to open the cluster up for general access in mid-April 2012. The resource expansion is specifically designed for applications in learning and modeling biological networks, application of Bayesian analysis frameworks more generally, second and third-generation sequence analysis, modeling the kinetics of DNA synthesis to detect 6-methyladenosine, 4- and 5-methylcytosine, 8-oxoguanine and other modified nucleotides. The hardware accessible for analysis includes systems optimized for embarrassingly parallel jobs such as QTL analyses that are CPU bound as well as parallel jobs such as Bayesian network reconstruction that are memory bound. In addition, there is support for jobs requiring substantial shared memory, such as all-by-all comparisons or splice-form specific RNA-seq results to generate isoform-specific coexpression networks, an n2 problem with an estimated between 100,000 and 200,000 for most tissues. High-availability storage is provided to support both very large files and very large numbers of small files in these analyses. In summary, the compute infrastructure is designed to be flexible to allow both exact mathematical models of high complexity and heuristic machine learning approaches to be explored in addressing biological hypotheses in an iterative and complementary way.
Last Update: April 16, 2012
The Institute for Medical Education (IME) was established in 2001 to promote and advance innovative medical education and scholarship as well as recognize and reward our outstanding educators. The IME serves the vital need in our institution of creating, educating, mentoring, and retaining the best educators for our students, residents, and faculty. Fostering the success of our educators includes recognizing and rewarding those who display dedication and excellence in their work and providing programs that develop and reinforce their scholarship, teaching skills, and successful promotion. In doing so, we create a network of dedicated educators that contributes its knowledge and experience back to this community by serving as teachers and mentors. Our activities have positioned the Institute as a center for teaching and learning excellence across the Mount Sinai health system.
The scope of the IME goals encompasses promoting scholarship and dissemination of innovative medical education approaches, acknowledging and rewarding our accomplished educators, creating faculty development opportunities for all teaching faculty and supporting career advancement of medical educators in academia. Specifically, the IME aims to:
- Recognize and reward excellence in education and teaching
- Facilitate the academic promotion of educators
- Support skills development in teaching, learning and medical education research
- Promote the dissemination of innovative medical education scholarship
- Create an educational community whose members inform and support one another
Last Update: May 25, 2017
The Institute for Translational Epidemiology, headed by Emanuela Taioli, MD, PhD, takes advantage of Mount Sinai's extraordinary strengths in both research and clinical practice to establish a strong program in epidemiologic research that connects to clinical, basic, and applied research programs within the Mount Sinai Health System. Our vision is to advance interdisciplinary and patient-oriented research and to contribute to translational and integrative research at the School of Medicine. The Institute is committed to expanding the role of epidemiology in clinical research, and the presence of several world-class clinical and research programs makes ISMMS an ideal setting to establish a strong epidemiology research program to complement existing clinical and preventive activities. New concentration areas will build on existing clinical and research strengths in Chronic Disease Epidemiology, Infectious Disease Epidemiology, Mental Health, Occupational Epidemiology, Epidemiologic Methods, Life Course Epidemiology, and Molecular and Genetic Epidemiology. Training, education, and health inequalities will be part of the research portfolio.
Epidemiologic research has successfully identified the main lifestyle and environmental risk factors associated with chronic diseases. One important finding of epidemiologic research on chronic diseases is that many features are shared between different types of diseases. Risk factors such as tobacco use, obesity, and environmental pollutants contribute to the etiology of different groups of chronic diseases. But the main tools of epidemiologic research, such as prospective cohort studies, are also ideally suited to study several chronic outcomes in parallel. A major challenge of epidemiologic research rests in the elucidation of the separate and combined effects of genetic, biochemical, and lifestyle risk factors of chronic diseases and outcome determinants.
In recent years, the emphasis in epidemiologic research has shifted from etiologic to outcome research. With the introduction of novel, ground-breaking therapeutic approaches, based on recent discoveries in immunology and genetics, researchers are now well positioned to study the effect of these therapies on long-term survival and quality of life. It is also important to assess if appropriate treatment is equally administered to all the patients in need for such treatment, or if the same racial/ethnic disparities observed in disease prevention and early detection persist in disease treatment. In this way, epidemiologic research is addressing the growing interest in racial/ethnic/gender disparities in health and healthcare delivery.
Another key area of epidemiologic research is the comparative effectiveness of alternative treatments in real-life settings, where patients suitable for treatment belong to a variety of ages and races, have a spectrum of comorbidities, and differ in insurance coverage. Evaluating therapeutic approaches in such diverse segments of the population offers insights on the translation of new discovery science into clinical practice.
The Institute collaborates closely with the Department of Population Health Science and Policy and the Department of Preventive Medicine, as well as a variety of other Mount Sinai entities in building the research portfolio. In addition, training and education is part of the research portfolio.
Visit the Institute for Translational Epidemiology for more information.
Last Update: May 28, 2017
The mission of the Icahn School of Medicine Mount Sinai Diabetes, Obesity and Metabolism Institute is to develop better therapeutic and prevention strategies for types 1 and 2 diabetes, obesity, diabetes, and the metabolic syndrome through basic and clinical research.
Six areas form the core of the Metabolism Institute's research enterprise: (1) Pancreatic Beta Cell Regeneration and Replacement. (2) Type 1 Diabetes Immunopatholobiology Research Program, in collaboration with the Immunology Institute. (3) The Genetics and Genomics of Diabetes in collaboration with the Institute for Genomics and Multiscale Biology and the Charles Bronfman Institute for Personalized Medicine. (4) CNS Control of Metabolism. (5) Fuel Metabolism and Signal Transduction in skeletal muscle, liver, pancreatic beta cells and the adipocyte. (6) Complications of Diabetes: vascular, renal, and neuropathic. (7) Clinical Research in Type 1 Diabetes, Type 2 Diabetes, Obesity and Bariatric Surgery in collaboration with the Mount Sinai CTSA. (8) Community Based Prevention, Diabetes Research and Epidemiology. (9) Diabetes and Cancer research.
The Research Cores within and used by the Diabetes, Obesity and Metabolism Institute include mouse metabolic and histopathologic phenotyping, high-throughput screening and drug discovery, human and animal imaging, cell biological imaging, proteomics, next-gen sequencing, epigenomics, monoclonal antibody generation, microsurgery, among many others.
Finally, we share an NIH/NIDDK-supported joint Albert Einstein College of Medicine and Mount Sinai Diabetes Research Center (ES-DRC), with multiple cores, including a Human Islet and Adenoviral Core (HIAC) based at Mount Sinai. Complete information is available at Einstein-Mount Sinai Diabetes Research Center.
Last Update: September 23, 2015
As one of the largest and most comprehensive adult and pediatric abdominal transplantation centers in the world, the Recanati/Miller Transplantation Institute (RMTI) at The Mount Sinai Health System is committed to outstanding patient care, research, and educational programs. Our transplant services for adults and children include kidney, liver, pancreas, and intestinal organ transplant. In addition, RMTI has one of the largest living donor programs in the United States. Through our Zweig Family Center for Living Donation, we provide the best in medical, surgical, and psychological care to living organ donors. Additionally, we provide comprehensive, personalized treatment and compassionate care to people with a wide variety of liver/bile duct and pancreatic diseases, including cancers affecting these organs.
We bring together a distinguished team of surgeons, physicians, and other healthcare professionals to support patients with end stage disease in every step of their care up to and including transplantation. RMTI team members view transplantation as one step in the continuum of patient care. Our multidisciplinary approach ensures that patients benefit from the expertise of multiple specialists, who understand their unique needs.
Having performed more than 5,500 liver, kidney, pancreas, and intestinal transplants over 40 years, we have a rich history of innovation and excellence in the field of organ transplantation. One of the key factors in our success is close collaboration between our physicians and the scientists who conduct state-of-the-art research here. It enables us to provide leading-edge technologies and the most up-to-date therapies to our patients, including individuals with complex medical needs. For example, RMTI researchers working side-by-side with our clinical teams have made great strides in increasing the eligibility of patients previously denied kidney / pancreas transplants due to medical conditions, such as Hepatitis B, Hepatitis C, and HIV.
At RMTI, we offer a full spectrum of abdominal organ transplantation programs and services, including: adult and pediatric liver disease and transplantation, adult and pediatric kidney transplantation, adult pancreas transplantation and intestinal rehabilitation and transplantation.
Last update: July 5, 2017
Under the leadership of Steven Burakoff, MD the Tisch Cancer Institute (TCI) was awarded National Cancer Institute (NCI) designation in 2015. The mission of the TCI is to advance the field of cancer research, treatment and prevention and to facilitate the availability of these advancements to our communities so as to extend and improve the lives of cancer patients and their families.
To accomplish this mission, the TCI has four research programs: Cancer Immunology, which addresses anti-tumor immunity and fosters the development of cancer vaccines; Cancer Mechanisms, which seeks to understand the biology of cancer cell development; Liver Cancer, whose focus is to discover novel approaches to diagnose and treat liver cancer; and Cancer Prevention and Control, which addresses the important aspects of primary and secondary cancer prevention. Cancer Institute members span across multiple departments in the medical center and work collaboratively within and across these multidisciplinary research programs. As of March 2017, cancer grant awards exceeded $65 million in direct costs.
As part of its mission, the Tisch Cancer Institute supports several Shared Resources and Facilities that are critical to cancer research. These include Cancer Biostatistics, Flow Cytometry, Mouse Genetics and Microscopy, as well as important specialized facilities such as the Hematological Malignancies Tissue Bank, the Human Immune Monitoring Core, and the Vaccine and Cellular Therapy Lab.
To facilitate cancer clinical research, the Tisch Cancer Institute provides oversight of all cancer clinical trials through its Protocol Review and Monitoring Committee and its Cancer Clinical Trials Office. In 2016, there were 162 open therapeutic cancer clinical trials that enrolled a total of 361 new patients.
In addition, the TCI provides competitive Research Awards to basic, clinical, and population cancer scientists to facilitate new insights into cancer biology, prevention and treatment.
Last update: June 1, 2017
The Translational and Molecular Imaging Institute (TMII) serves as a research catalyst for a new generation of translational and molecular imaging methodologies. It offers researchers highly efficient, cost-effective services for commonly used imaging tests, without the usual institutional overhead. TMII provides expertise for developing and validating new procedures and encourages interdisciplinary collaborations that help close the gaps between clinical and preclinical studies. Through its targeted seminars, research fellowships, publications, and other training programs, TMII educates researchers, postdoctoral fellows, students, and technicians about biomedical imaging advances and options.
TMII is responsible for coordinating and executing all in vivo imaging research at Mount Sinai. Currently, TMII has over 50 members with expertise in all aspects of translational imaging research, from image acquisition to image analysis. Mount Sinai and TMII have entered into a strategic partnership with Siemens Medical Systems to support its effort in translational research. Housed in approximately 20,000 square feet in the new Hess Center for Science and Medicine, are state-of-the-art Siemens systems, including:
- 7T MRI - whole body, actively shielded human scanner
- PET/MR(3T) mMR system - fully integrated, simultaneous, multi-modal, whole body scanner
- 3T MRI Skyra - wide bore whole body scanner
- Somatom Force CT - dual-source for faster and lower dose imaging
These systems are available for human and large animal research. In addition, TMII has access to a variety of Siemens systems that are managed by the Department of Radiology at Mount Sinai but accessible for research thru TMII, including a 1.5T MR Aera scanner, a PET/CT(40) Biograph mCT, and a multidetector CT Somatom Definition Flash.
TMII also provides preclinical imaging services performed on a variety of small animal scanners including:
- 9.4T (89mm bore size) Bruker vertical bore scanner
- 7.0T (154mm bore size) Bruker horizontal bore scanner
- Biophotonic IVIS spectrum
- Micro ultrasound Vevo 2100 from VisualSonics
- Micro PET/CT (TBD)
All of these imaging systems are equipped with a variety of peripherals for physiological monitoring, physiological gating, fMRI experiments, drug infusion and anesthesia delivery.
TMII has a data center in the new Center for Science and Medicine that contains a dedicated server room hosting a larger Mac Server Cluster of 2 x 16TB of initial online storage with direct connectivity to all of the imaging modalities. TMII XNAT serves as the central point for research data transfer, archive, and sharing. TMII XNAT is built upon a secure database, supports automated pipelines for processing managed data, and provides tools for exploring the data. Currently TMII XNAT runs on two mirrored Linux servers with 60TB storage space on each. It can host more than 15,000 image sessions with backups. In addition, TMII offers an image analysis room equipped with a large viewing display and more than 15 high-performance workstations to facilitate learning and image analysis as well as a nanomedicine laboratory for the design, synthesis and evaluation of novel imaging probes and drug delivery systems.
Updated: May 25, 2017