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.
The Arnhold Institute for Global Health
The Arnhold Institute for Global Health believes that global health is local health. They envision a world where vulnerable people in every community have access to health care. The Arnhold Institute develops and evaluates global health solutions which can be replicated at scale.
The Arnhold Institute specializes in global health systems and implementation research. Their global partners are based in Kenya, Nepal, Ghana and Queens, New York. The global research programs generate evidence about how to build and sustain better health care systems. For example, current work includes programs to enable hospitals and community health networks in Nepal to keep newborns alive and to build supportive, lifelong HIV treatment programs for children and adolescents in Kenya.
They partner with academic institutions, health systems, government partners, and leading community-based organizations to maximize the impact at scale. The institute is committed to applying global lessons from developing country contexts to low-resource settings in the United States.
Visit the Arnhold Institute for Global Health for more information.
Last updated: March 2021
Researchers at the Black Family Stem Cell Institute advance stem cell biology by harnessing the potential of both embryonic and adult stem cells. This promising field presents tremendous opportunities for scientific breakthroughs that translate into medical treatments capable of replacing damaged or malignant cells with healthy stem cells, differentiated cell derivatives, or bioengineered tissues. These advances are essential for providing the foundation for regenerative therapies in diseases such as blood and cardiovascular diseases, diabetes, eye, skin and liver-related diseases, Parkinson’s and neurodegenerative diseases, and certain cancers.
The Promise of Stem Cell Research
We investigate how stem cells form tissues during embryonic development and maintain organs throughout life. We ask fundamental questions about stem cell behavior, exploring how stem cells self-renew, communicate with their microenvironment, and “decide” their eventual functions. We are developing therapies that utilize tissue stem cells. In addition, we reprogram adult cells into pluripotent stem cells that can give rise to any tissue type. Growing and differentiating these cells in a controlled way will eventually allow us to replace degenerated cells and develop treatments for many diseases at their earliest stages. Our ultimate goal is to understand the mechanisms that direct stem cells to adopt specific fates so that we can develop novel, targeted therapies, and accomplish cell and tissue regeneration.
Our Collaborative Approach
The Black Family Stem Cell Institute pursues interdisciplinary research and fosters collaborations between basic and clinician scientists to ensure effective translation of discoveries from the lab bench to the clinic. Our investigators are producing reprogrammed stem cells to model human disease, test new therapies, and regenerate blood, immune cells, and tissues.
Visit us at https://icahn.mssm.edu/research/black-family-stem-cell/about or contact Nyomi Cepeda (firstname.lastname@example.org) for more information.
Last Update: February 2023
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.
Visit the Blavatnik Women's Health Research Institute for more information.
Last update: May 2023
The BioMedical Engineering and Imaging Institute (BMEII) focuses on biomedical engineering research and development in multimodality imaging, nanomedicine, artificial intelligence, sensor technologies, next generation medical devices, robotics and computer vision.
BMEII 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. BMEII 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, BMEII educates researchers, postdoctoral fellows, students, and technicians about biomedical imaging advances and options.
BMEII is responsible for coordinating and executing all in vivo imaging research at Mount Sinai. Currently, BMEII has over 65 members with expertise in all aspects of translational imaging research, from image acquisition to image analysis. Mount Sinai and BMEII 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 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 Prisma - whole body, high gradient scanner for highest resolution
- 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, BMEII has access to a variety of Siemens systems that are managed by the Department of Radiology at Mount Sinai but accessible for research through BMEII, including a 1.5T MR Aera scanner, 2 Vision PET/CT, and a multidetector CT Somatom Definition Flash.
BMEII 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 w/ sub-half mm3 PET volumetric resolution
All of these imaging systems are equipped with a variety of peripherals for physiological monitoring, physiological gating, fMRI experiments, drug infusion and anesthesia delivery.
BMEII XNAT serves as the central point for research data transfer, archive, and sharing. BMEII XNAT is built upon a secure database, supports automated pipelines for processing managed data, and provides tools for exploring the data. Currently, BMEII XNAT runs on two mirrored Linux servers with 60TB storage space on each. It can host more than 15,000 image sessions with backups.
BMEII leverages the data center at MSHS to host our computational and DGX servers. The computational cluster is used primarily for image retrieval and image clean up, while also housing SAPIENT (BMEII's image analysis pipeline tool). Our DGX cluster enables researchers to complete their AI/ML analyses.
In addition, BMEII 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: March 2023
Mount Sinai’s strategic plan provides a road map for major investments in research and infrastructure to establish a series of Institutes, including The Charles Bronfman Institute for Personalized Medicine (CBIPM). Headed by Alexander Charney, MD, PhD and Girish Nadkarni, MD, MPH, CBIPM brings together experts in clinical and biological data sciences to explore the nature of human disease. Institute faculty generate innovations and new paradigms in mapping of complex traits in diverse populations, clinical knowledge representation and phenomics, and personalized medicine clinical decision support.
CBIPM 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.
CBIPM’s laboratory and procedures are accredited by the College of American Pathologists (CAP) and approved by New York State/Clinical Laboratory Improvement Amendments (CLIA).
Bio Me Biobank Program
The Bio Me BioBank Program 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.
From September 2007, over 65,000 Mount Sinai Health System patients have enrolled in the Electronic Medical Record-linked Bio Me Biobank Program. The program is designed to generate a large collection of DNA and plasma samples, phenotypic (questionnaire-based and EMR-linked) and genomic data, that are stored in a way that protects the patient’s privacy. The three major self-reported racial/ethnic populations include 33% EA (European Ancestry), 22% AA (African Ancestry, 35% HA (Hispanic Ancestry). The biobank enables research to be performed on de-identified, comprehensive, electronic clinical information extracted from the Mount Sinai Data Warehouse (MSDW).
More than 31,900 of the BioMe participants have genotype data available for genetic analyses. Data include whole exome sequencing, genome-wide genotyping array (GSA), and for a subset of participants (N~12,000) whole genome sequencing data is available.
The Bio Me Biobank Program contributes under collaborative agreements with international research consortia and collaborations.
Mount Sinai Million Health Discoveries Program
The Mount Sinai Million Health Discoveries Program (MSMHDP) is focused on building genetics into the real world of clinical care by linking genetic data with electronic health record data. Started in August 2022, MSMHDP aims to recruit one million Mount Sinai participants from diverse ancestries characterized by a broad spectrum of longitudinal biomedical traits. High coverage exome sequencing, genotyping, and a subset of whole genome sequencing will be carried out by the Regeneron Genetics Center and will be made broadly available for academic and research purposes.
Enrolled participants in MSMHDP consent to be followed throughout their clinical care (past, present, and future) at Mount Sinai in real-time, integrating their genomic information with their electronic health records for discovery research. This clinical information can be complemented by detailed information as participants can choose to answer additional questionnaires on ancestry, residence history, familial medical history, education, socio-economic status, physical activity, smoking, alcohol use, and weight history. Recontacting of participants is permitted by consent, enabling a broad range of additional studies including in-depth clinical and deep phenotyping, mobile health applications, recruitment for prospective studies/trials, and return-of-results clinical care implementation projects.
Precision Clinical Research Unit
The Precision Clinical Research Unit (PCRU) within The Charles Bronfman Institute for Personalized Medicine, aims to bridge the gap between genetics and patient phenotype by conducting a milieu of clinical testing to better define patient characteristics in patients with specific genotypes. The PCRU performs medical tests, such as blood and cardiac testing, that aid in the diagnosis or detection of diseases and measure the progress of the disease. The unit serves as a catalyst to empower translational science, generate resources for internal and external investigators and engender profitable interactions with industry partners.
Rapid Randomized Trial Unit
The Rapid Randomized Trial Unit (RRTU) within The Charles Bronfman Institute for Personalized Medicine aims to deploy predictive models and other analytic tools into the clinical care setting using randomized and advanced-prospective trial designs. The RRTU brings together Mount Sinai’s world class technical expertise in machine learning and operational expertise in clinical trials to bring big data to the forefront of modern clinical medicine.
The technical foundation of the RRTU is the Mount Sinai Clinical Data Science group that maintains a real-time data feed of all data in the electronic medical record and the infrastructure to run machine learning models in real time and deploy the output of these models into clinical care both inside and alongside the EHR. The team has successfully deployed more than a dozen models into clinical care to facilitate patient risk stratification and ensure optimal care delivery.
Center for Genomic Data Analytics (CGDA)
The Center for Genomic Data Analytics (CGDA) within The Charles Bronfman Institute for Personalized Medicine at Mount Sinai aims to advance innovative medical research that will enhance genomic, biological and clinical understandings of human health and disease by maximizing the use of large-scale multi-modal datasets. CGDA provides analytical expertise in developing and applying tools and methods to examine genotyping and sequencing data, along with other multi-modal data including metabolomics, proteomics and clinical data in large-scale electronic health record-based biobanks. Some areas of focus include rare and common variant association testing, Mendelian randomization, genetic risk prediction, and electronic health record-based data mining. CGDA is committed to developing and utilizing cutting-edge methodological approaches in human genetics, statistical genetics, population genetics and data science. Furthermore, CGDA provides a hub for interdisciplinary collaboration among faculty, clinicians, and scientists, both within the ISSMS and beyond.
NIH Funded Programs
The Charles Bronfman Institute for Personalized Medicine represents Mount Sinai as a member site to several large NIH-funded research networks, including the Implementing Genomics In Practice (IGNITE) Network, Population Architecture Using Genomics and Epidemiology (PAGE) Network, the TOPMED (NHLBI Trans-omics for Precision Medicine) Program, GSP (NHGRI Genome Sequencing Program), All of Us Research Program, Researching COVID to Enhance Recovery (RECOVER), Psychiatric Genomics Consortium (PGC), and Kidney Precision Medicine Program, among others.
Visit The Charles Bronfman Institute for Personalized Medicine website for more information.
Last update: March 2023
Since its establishment in 2009, ConduITS, the Institute for Clinical and Translational Sciences, has worked hand in hand with Icahn School of Medicine at Mount Sinai (ISMMS) and health system leadership to foster foundational cultural changes facilitating transformative clinical and translational research and training needed to nimbly respond to emerging challenges and opportunities in Clinical Translational Science (CTS). ISMMS is one of over 50 CTSA-funded hubs across the country.
ConduITS’ mission is to advance health by transforming the MSHS into a translational research laboratory embracing a precision public health framework, creating a LHS with enhanced partnering with our patient population, community physicians and advocacy groups, scientists, and entrepreneurs, as well as other CTSA Hubs to ensure the highest quality research, promotion of team science, and development of innovative resources that will better harness big data and catalyze the translation of biomedical discoveries into better health across the lifespan. This will be accomplished through the following strategic aims.
- Workforce Development. Evolve learning opportunities promoting transdisciplinary clinical data science and entrepreneurial activities across the translational research spectrum.
- Diversity. Advance justice, equity, diversity, inclusion, and an antiracist mindset as core tenets of socially responsible clinical translational research and training, promote activity that drives sustainable change, and accelerate diversification across all leadership ranks in ConduITS.
- Collaboration and Engagement. Engage diverse stakeholders in all phases of translational research through accelerator models constituted to address priority community concerns and apply an environmental justice, life course, and data science framework to drive community-centered strategies and solutions using data science innovations to catalyze research, training, and engagement.
- Informatics. Leveraging informatics advances from our current cycle to better coordinate health care delivery with translational research by integrating secure electronic health records (EHRs), patient reported outcomes, remote monitoring technologies, clinical trials management systems, and institutional biobanks and data repositories, better connecting patients and clinicians with clinical trials and community engaged research.
- Methods and Processes. Innovate and streamline research administrative oversight and processes to minimize roadblocks, ensure quality and integrity, monitor outcomes and garner feedback from stakeholders to facilitate and enhance participation in clinical translational research.
- Integration. Incorporate translational research across the lifespan, with particular focus on perinatal and pediatric research, geriatric populations, and populations impacted by health disparities; accelerate inclusion of environment in life course precision medicine via our innovative Exposomics optional function.
ConduITS is currently focused on harnessing technological innovations for translational research and community engagement, decentralizing study activities, measuring environment on a scale parallel to genomics, and developing the workforce of tomorrow with the necessary data science competencies needed to respond to increasingly complex problems such as recalcitrant health disparities.
Any use of CTSA-supported resources requires citation of grant number UL1TR004419 awarded to ISMMS in the acknowledgment section of every publication resulting from this support. Adherence to the NIH Public Access Policy is also required.
Updated: March 2023
The mission of the Icahn School of Medicine Mount Sinai Diabetes, Obesity and Metabolism Institute (DOMI) is to develop better diagnostic, therapeutic and prevention strategies for Types 1 and 2 diabetes, obesity, diabetes, and the metabolic syndrome through basic and clinical research.
Ten areas form the core missions of the Metabolism Institute's research enterprise:
- Drug Discovery to Enhance Pancreatic Beta Cell Regeneration and Replacement for Types 1 and 2 diabetes.
- Reversing the Immunopatholobiology of Types 1 and Type 2 Diabetes, in collaboration with the Precision Immunology Institute.
- Understanding the Genetics, Epigenetics and Genomics of Diabetes and Beta Cell Regeneration, in collaboration with the Institute for Genomics and Multiscale Biology.
- Enhancing Understanding of Intermediary Metabolism and Signal Transduction in skeletal muscle, liver, the pancreatic beta cell and the adipocyte.
- Defining CNS Control of Metabolism in the adipocyte, liver and beta cell via the sympathetic and parasympathetic nervous system.
- Addressing the Vascular, Renal, and Neuropathic Complications of Diabetes.
- Performing and supporting Clinical Research in Type 1 Diabetes, Type 2 Diabetes, Obesity and Bariatric Surgery in collaboration with clinical researchers at Mount Sinai’s CTSA.
- Supporting The Artificial Pancreas program, the first and largest in New York City.
- Elucidating the metabolic interfaces between normal beta cell regeneration, and malignant cellular growth.
- Supporting Community Based Prevention, Diabetes Research and Epidemiology.
Research Cores available to the Diabetes, Obesity and Metabolism Institute include mouse metabolic and histopathologic phenotyping, Seahorse metabolic evaluation, high-throughput drug discovery, human and animal metabolomics, calorimetry, advanced cell biological imaging, proteomics, next-gen sequencing, epigenomics, bioinformatics, monoclonal antibody generation, microsurgery, among many others.
Finally, we share an NIH/NIDDK-supported joint P-30 Diabetes Research Center with Albert Einstein College of Medicine and Mount Sinai, the ES-DRC, with multiple cores, including a Human Islet and Adenoviral Core (HIAC) based at Mount Sinai.
Visit the Diabetes, Obesity and Metabolism Institute for more information.
Last Update: March 2021
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. 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 antibody-humanized mice from Regeneron Pharmaceuticals and Harbour BioMed
- Purification of antibodies
- Sequencing, chimerization, and recombinant production 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 by specialized robotics 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.
Sequencing and recombinant production
Antibody variable genes from the heavy and light chains are sequenced from the corresponding hybridoma cells using in house methodologies. Sequencing allows further insight into the structure of the antibodies and also provides another selection step to identify unique antibody clones. Heavy and light variable sequences are then DNA-synthesized and cloned into DNA expression vectors containing heavy and light constant regions, respectively. Antibodies at this stage can further be chimerized onto a variety of different constant (Fc) regions by cloning, thus allowing study of different Fc effector functions or allowing for other benefits assigned to a particular Fc (such as improved purification or other benefits). Vectors containing full heavy and light chains are then transfected into a mammalian expression system such as the Expi293 or CHO systems and purified from supernatant.
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.
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, including exclusive licensures for CTAD/Mount Sinai derived therapeutic antibody portfolios. 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 or Harbour human mice. Many of these projects are funded and the monoclonal antibodies produced are in various stages of licensing.
Last Update: April 2023
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 fully equipped 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 capability in the DeVita Lab and characterize compounds in investigator’s lab assays or from those that are commercially available. 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 – Small molecules hits identified from a screening exercise will be triaged to eliminate false positives or artifacts: compound purity from the active hits will be assessed, and material re-synthesized, scaled-up and purified. Hit compounds may then be interrogated in detail in the screening assay (8-point titration) or other follow-up assays as appropriate to confirm useful levels of biological 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 scaffold 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 computational methods. 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, as jumping off points for further optimization and provide preliminary data for grant applications.
- Lead Optimization – A promising lead series based on an assessment of biochemical potency, cell based activity, overall physicochemical profile and input from computational models 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 appropriate contract research organizations (CROs). 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 related 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 projects progress. The DDI and Medicinal Chemistry Team has been successful in gaining multiple PI NIH grants to support many of these activities with like-minded collaborators in a variety of therapeutics areas of interest to Mt Sinai Biology Labs.
Last Update: April 2023
Assay Development and Screening
The Assay Development and Screening Core can provide assay development and medium throughput screening service to all investigators at Icahn School of Medicines and outside collaborators.
Our core can also provide extensive consultation and technical assistance for user-initiated and executed projects, including support for assay design and data analysis.
Some of our integrated resources include:
- 50,000 newly invested small, diversified compounds from Life Chemicals
- 100,000 Diver-Set and CNS-Set small compounds from ChemBridge.
- More than 8.000 macrocycles from ChemBridge.
- Both human and mouse Mission shRNA libraries from Sigma-Aldrich.
- Liquid handling system: HpD300 Dispenser, which is able to handle samples from milliliters to picolitres.
- Two plate readers, FLIPR tetra plus with 384-channel head and Envision with whole sets of filters for reading different plates.
Our core is also able to screen small molecule in both cell-based and cell-free formats. Targets could be GPCRs, ion channels, enzymes and others. Besides primary screening, we can also support early hit cytotoxic studies.
Last Update: April 2023
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’s work is truly transformative: neural injury and repair, cognition, and neuropsychiatry. The Institute’s success is measured by advancing brain repair, developing new ways to advance cognition, and improving the treatment of neuropsychiatric disorders.
The Brain Institute's work spans molecular, cellular, synaptic, circuit, and behavioral studies of nervous system disorders, from animal models to investigations of human populations in the clinic. New knowledge from animal studies drive clinical investigations, while new insight from clinical studies 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: March 2023
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, SARS-CoV-2 and related coronaviruses, HIV, dengue and Ebola viruses, as well as on paramyxoviruses, hantaviruses, Zika, chikungunya, and monkeypox viruses.
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 particularly 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 Updated: February 2023
Science and technology have created tremendous opportunities to improve and extend our lives. At the Hasso Plattner Institute for Digital Health at Mount Sinai, we use the tools of data science, biomedical and digital engineering, and medical expertise to advance health care. The institute is a collaboration between the Hasso Plattner Institute for Digital Engineering in Potsdam, Germany, and the Mount Sinai Health System. Our goal is to develop innovations to revolutionize how people think about their personal health and health systems and have a tangible impact on patients’ lives.
The institute strives to develop research projects and artificial intelligence technologies to improve our ability to diagnose and treat patients. The Hasso Plattner Institute for Digital Health at Mount Sinai receives generous support from the Hasso Plattner Foundation. Below, we outline our research projects and machine learning efforts.
At the institute, we performresearch that combines biomedical and data sciences to develop digital health solutions for both patients and researchers. Our research projects include:
Digital Discovery Program: The Digital Discovery Program (DDP) is a comprehensive program of patient-centric health studies and clinical tools utilizing wearable, mobile and sensor technologies to generate and integrate multi-modal data to better understand these complex diseases which impact millions of individuals, lead to loss of life and health and costs billions each year.
- AI Ready Mount Sinai Platform: This multi-modal health data platform links patient data generated from different clinical departments to mitigate siloing and accelerate the advancement of health-care-driven, artificial intelligence (AI)-based solutions.
Machine Learning Efforts
Machine learning is a type of artificial intelligence research that enables a computer to use learning algorithms to draw inferences from data and “learn” new skills. These projects are intended to improve our provision of health care diagnostics and treatments. Projects include:
FlexIBle EHR Retrieval (FIBER): Using clinical data from a series of electronic libraries, this project streamlines the clinical modeling process.
Natural-Language Processing on Clinical Notes for Phenotyping Depression: This software application provides insights into patients’ underlying biological or neurological mechanisms that can inform and improve treatment decisions.
Prediction of Hypertension Onset by Leveraging EHR Data with Machine Learning: This system uses several machine learning approaches to help predict whether a patient will develop hypertension, facilitating early intervention.
Process Mining in Personalized Medicine: This technology analyzes real-world business process management problems to improve data flow and patient outcomes.
Updated: August 2023
The Institute for Exposomic Research envisions a world where we prevent disease with environmental origins and improve health outcomes for all, from the earliest stages of child development to later stages of adulthood. Our mission is to understand how environmental exposures affect health, disease, and development and to translate that knowledge into new strategies for prevention and treatment. Our approach is holistic, encompassing the chemical, nutritional, and social environments and the interrelationships among them. We aim to cultivate the public consciousness necessary to make meaningful changes in policies and practices to protect health and build healthier and more just communities where we live, play, and work. We strive to accomplish this mission while training the next generation of health professionals across multiple disciplines and in collaboration with practitioners from across the Mount Sinai Health System and beyond.
Last Updated: July 2023
Institute for Medical Education
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 Institute is committed to developing, mentoring, and retaining the best educators for learners and faculty throughout the Mount Sinai Health System. Fostering the success of our educators includes acknowledging or spotlighting those who display dedication and excellence in their work, supporting and facilitating innovative program development and dissemination of scholarship, and providing guidance and mentorship for career advancement and promotion. 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: February 2023
Working in conjunction with ConduITS, the newly constituted Institute for Transformative Clinical Trials (ITCT) has as its mission the design, conduct, and analysis of innovative clinical trials that span the spectrum from early phase to confirmatory to large-scale pragmatic trials.
What ITCT offers:
Expertise in the design and analysis of clinical trials
ITCT offers expertise in novel trial designs, including Bayesian and adaptive designs, bucket and platform trials, novel pragmatic and point-of-care trials, registry-based trials, and EHR-based trials, among others. Institute faculty have designed trials with a broad array of outcomes and data types that encompass imaging data, genomic and biomarker data, and health economic data, in addition to the traditional morbidity and mortality data. The Institute has extensive experience with patient-centered outcomes, such as return to independent living at home, cognitive status, quality of life and frailty.
In terms of analytical expertise, the Institute is experienced in conducting survival analysis, hierarchical modelling, cost-effectiveness modelling, longitudinal methods for analyzing quality of life and neuro-cognition, decision analysis, and predictive modelling using “big data”.
Expertise in the Coordination of Clinical Trials and Regulatory Compliance
ITCT offers coordinating center expertise, especially in the coordination of multi-site clinical trials. The regulatory group assists in obtaining approvals for clinical trials from the FDA, Health Canada and European regulatory authorities, as well as from central and local IRBs. It does the annual reporting to regulatory agencies. The Institute has managed Event Adjudication Committees and DSMBs for an array of device, biological and procedural trials.
One area of specialization is the application of novel approaches to recruit and retain patients, and strategies to ensure the involvement of diverse and vulnerable populations.
Expertise in Data Collection for Multicenter Trials
ITCT has faculty with long-standing knowledge in the design of electronic data capture systems that are 21CFR part 11 compliant, include drug and device tracking, upload features for imaging data, and EAC modules. It also has a wealth of expertise in REDCap programming.
The Institute also collaborates with others Institutes at Sinai, offering expertise in digital health tools for collecting patient-derived outcomes and bio-wearables to collect data directly from patients.
Last Updated: February 2023
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 are built 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 are a 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. The Center for Cancer and Aging was established in collaboration with the Department of Geriatrics to advance knowledge in the field of cancer prevention, screening, diagnosis, care, and management to improve the lives of older adults with cancer and their families.
The Center for Disaster Health, Trauma & Resilience was established to aid in individual and community-level prevention and resilience building and quicker, more effective response and intervention during and immediately after disasters and other traumatic experiences.
In addition, training and education is part of the research portfolio through student mentorships and a unique variety of short courses and workshops taught by our faculty and staff.
Last Update: March 2023
Recanati/Miller Transplantation Institute
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 10,000 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. RMTI is one of the UNOS approved transplant centers to provide the opportunity for HIV+ recipients (liver and kidney) to receive HIV+ organs, allowing these HIV+ recipients the opportunity to receive a life-saving transplant in a much shorter period of time.
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: February 2023
At the Institute for Equity and Justice in Health Sciences Education, we aim to teach health sciences educators, across disciplines and health professions, to dismantle and disrupt racism, bias, and oppression. Our Institute provides learning opportunities to accelerate anti-racist and anti-biased transformational change in educational programs through systems change, strategic planning, and priority setting.
We hope to measure the impact of racism, oppression, and bias on biomedical and health professions education by establishing inclusive and equitable learning and teaching environments grounded in anti-racist and anti-biased pedagogy.
We also provide opportunities and support for our students, staff, and faculty to do this important work and investigate its impact.
Our findings will be disseminated via scholarship and external consultation. We look forward to cultivating relationships with philanthropists and foundations, as well as federal, state, and local government agencies.
The Mindich Child Health and Development Institute (MCHDI)
The Mindich Child Health and Development Institute (MCHDI) is a translational research enterprise with the mission of advancing knowledge and therapies for diseases affecting infants, children, and adolescents.
Led by Bruce D. Gelb, MD, the MCHDI assembles 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. We currently have over 65 faculty members who specialize in allergy & asthma, cardiovascular disease, neurodevelopmental disorders, obesity & diabetes, and more.
Faculty at the MCHDI work in a multidisciplinary manner with researchers and physicians in various departments and institutes at Mount Sinai. Together, we strive toward the objectives of developing robust paradigms for understanding the effects of genetics and environment on the health of infants, children and adolescents, and personalizing pediatric medicine through genetics and genomics. In addition, we have taken substantial steps in expanding our reach in three exciting strategic areas: pediatric precision medicine, pediatric clinical trials, and inborn errors of immunity.
Last Update: February 2023
The Marc and Jennifer Lipschultz Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai (PrIISM) is an entity that encompasses and integrates disease-focused immunological research programs and cutting-edge technology centers. PrIISM is working to better understand the fundamental mechanisms used by immune cells to promote disease progression and response to treatment, developing and implementing novel technologies to better diagnose and guide treatment of disease, and generating new therapies to modulate the immune system in a broad spectrum of diseases, including cancer, inflammatory, cardiovascular, and neurological diseases. Technology available includes the Human Immune Monitoring Center and the Microbiome Translational Center.
The Graduate School of Biomedical Sciences at Icahn School of Medicine is ranked among the very best in the world for academic training and the Marc and Jennifer Lipschultz Precision Immunology Institute at Icahn School of Medicine at Mount Sinai (PrIISM) is dedicated to establishing a world-class immunology graduate program. The goal of the Immunology Training Area is to provide students interested in immunology with a rigorous and flexible program. Students will be given the individual intellectual and technical skills required to become outstanding scientists in the field of immunology. Students benefit from the multidisciplinary nature of our graduate program and take additional credits that could be in any area of interest to them and may include topics in microbiology, cancer, genetics, system biology, and genomic sciences among others. In addition, graduate students will also participate in an Immunology Journal Club, Work in Progress, and Seminar Series. Laboratory rotations and research training allows students to rotate and select any of the multiple laboratories that are currently working in immunology.
The Human Immune Monitoring Center
HIMC provides comprehensive immune monitoring services for clinical and translational studies based on the highest standard operating systems. It has a team of 25+ highly skilled and trained laboratory scientists specialized in immune profiling and biomarker discovery for the treatment and research of various diseases by performing a wide spectrum of innovative and standardized immune assays, with a strong focus on optimizing and standardizing protocols and operating procedures to ensure data quality and reproducibility. HIMC also has a quality assurance specialist that oversees equipment maintenance and protocol compliance. The standardized immune assays available in HIMC include: flow cytometry (Aurora), CyTOF mass cytometry, single cell RNA sequencing including TCR and BCR sequencing, single cell ATACseq, spatial transcriptomics, immune phenotyping, multiplex immunohistochemistry, antigen specific T cell assays, seromics and antibody profiling, Luminex multiplex assay, Olink assay, and an automated ELLA system, all provided in a cost-effective manner. HIMC also provides complete and streamlined sample processing of patient specimens (peripheral blood, bone marrow, CSF, urine, saliva, biopsies) and biobanking using a Laboratory Information Management System (LIMS).
Good Laboratory Practice facility
This state-of-the-art facility offers patient specimen processing and storage using electronic sample management and tracking systems. HIMC is currently operating with SOPs to ensure the uniformity, consistency, reliability, reproducibility, quality, and integrity of laboratory procedures. Equipment and facilities are appropriate for the procedures being performed, with all equipment maintained, operated, and calibrated at regular intervals according to written SOPs. Personnel receive training in all procedures performed, which are documented in their individual training records and repeated as needed. All procedures have written SOPs that are strictly adhered to with any deviations and corrective actions taken properly documented. Procedure worksheets capture all critical information including signature or initials of the person performing the procedure. The electronic worksheets are maintained in a centralized database and reviewed by QA and archived in designated folders in a secured server. All of these requirements will ensure the reliability of the results generated by the HIMC and provide all the resources necessary for the completion of this project.
The HIMC can handle very large numbers of samples and studies thanks to the implementation of robust SOPs for every aspect of operations, under a Laboratory Integration Management Systems (LIMS: FreezerWorks, iLab, RedCap). To illustrate capacity, in 2023, there are over 60 active clinical trials or studies, representing a monthly average of 470 patient specimen collection visits, generating an average of 5,000 monthly bio-specimen aliquots tracked by barcode for storage and downstream immune focused analysis. These samples were analyzed for a monthly average of 80 multiplex and ELISA, 528 Olink, 24 seromics or grand serology, 36 ELISPOT, 90 (spectral) flow cytometry, 510 CYTOF, 65 scRNAseq, 15 spatial transcriptomics, and 30 multiplex IHC assays. Samples include cells and serum or plasma from peripheral blood, bone marrow, tissue suspensions from multiple tissues sites (healthy tissues and tumor lesions), purified DNA/RNA/protein material, and tissue slides for spatial biology analysis. HIMC follows Good Laboratory Practices (GLP) as well as Good Documentation Practices (GDP).
The HIMC laboratory consists of about 2,500 sq. ft. of space located on the 5th and 6th floors of the Hess building at ISMMS. HIMC is equipped with three third generation HELIOS mass cytometry analyzers from Fluidigm (Standard Bio Tools) equipped with a SuperSampler fluidics system to facilitate large volume sample acquisitions of millions of cells; an Aurora Spectral Flow capable of high throughput single cell analysis of up to 40 parameters in a single sample, and a LSRFortessa BD special order analytical flow cytometer (5 lasers) with high throughput capability (96 well format) to support large clinical study analyses; RoboSep for magnetic bead based cell separation/isolation; two Olink Signature Q100 instruments, one Fluidigm Biomark HD and a Juno universal integrated fluidic circuit controller which enables the high throughput and accurate quantification of up to 1611 clinically relevant protein biomarkers using 1 µL of biological sample per panel via Olink Target 96, Target 48 or customizable Olink Flex; ELLA automated immunoassay system for real-time cytokine assay, Luminex 200, and the high-throughput xMAP Intelliflex, for multiplex microbead-based soluble protein analysis detecting up to 500 analytes per sample; Miltenyi GentleMacs tissue dissociator; 10X Genomics Chromium, Chromium X Controller System to encapsulate single cells and generate scRNAseq data after library preparation, QuBit, TapeStation 4200, 10X Visium system and CytAssist for spatial transcriptomics with fresh frozen or FFPE tissue, microtome, Cryostat; a QiaCube and a Qia Symphony machine for mid- and HTP-automated nucleic acid isolation, three tissue culture rooms dedicated for patient sample processing and to perform immune functional assays, 4 laminar hoods, 4 tissue culture incubators, centrifuges (six Eppendorf 5425R and 5810R), and a sample bar coding facility and sample management/tracking via a server maintained by Mount Sinai Freezerworks is utilized for storing, tracking, annotating and managing all tissue-fluid specimens including their derivatives (e.g. slides, DNA, RNA); Leica Bond Rx Research Stainer, AT2 Aperio slide auto scanner, and a Hamamatsu NanoZoomer S60 slide scanner, for high-dimensional multiplexed chromogenic IHC assay with consecutive staining on a single slide (MICSSS). Specimens are stored in fifteen -80 0C REVCO freezers both with emergency back-up systems. HIMC also has access to Axon Autoloader 4200AL microarray scanners with GenePix Pro software (Molecular Devices) for seromics assays, Opentrons OT-2 and 8-channel liquid handlers, a Biotek ELx405 Microplate Washer fitted with a Biostack Multiplate Stacker for washing steps of ELISA and ELISPOT, a Biotek Synergy L Microplate Fluorescence Reader also fitted with a Biostack Multiplate Stacker for ELISA, and a 4-color FACSCalibur™ (BD Biosciences) flow cytometer for real time flow cytometry analysis. Immune profiling analysis software includes Astrolabe and Cytobank.
HIMC meets weekly on Tuesday morning with all staff for work-in-progress discussions, introduction of new technology platforms and review of new data analysis. In addition, HIMC holds multiple internal project-specific meetings each week to review data and update the HIMC in-house designed pre-analysis bioinformatic pipelines. Furthermore, HIMC members meet with PIs to review study protocols or data analysis as needed.
Data QC/QA, Analysis and Storage
NGS Data generated at HIMC is subject to quality control (QC) to ensure that the data is reliable and accurate before end user delivery. Below are some of the procedures we regularly perform:
- Data cleaning: Removal of low-quality reads, adapter sequences, and other artifacts that can arise during sequencing.
- Quality assessment: Calculating various quality metrics such as per-base sequence quality, per-sequence quality scores, and GC content.
- Sequence alignment: This involves mapping sequence reads to a reference genome or transcriptome to identify and remove any reads that do not align well to the reference.
- Variant calling: This involves identifying differences (e.g., single nucleotide polymorphisms, insertions, deletions) between the sample being analyzed and the reference genome or transcriptome.
- Gene expression analysis: This involves quantifying the expression levels of genes in the sample being analyzed and normalizing the expression data to account for technical and batch variation.
- Statistical analysis: This involves performing statistical tests to identify differentially expressed genes, variants, or other features of interest. QC is performed using a variety of bioinformatics tools and software, such as FastQC, Trimmomatic, STAR, GATK, and DESeq2. The specific QC steps and tools used will depend on the type of data being analyzed, the experimental design, and the research question being addressed. HIMC has shared access to Mount Sinai’s HPC Cluster Minerva which consists of 2 petaflops of compute power, ~24,000 compute cores, 210 terabytes of memory, 20 GPU nodes and 32 petabytes of storage. As a distributed file system, large amounts of data can be stored, analyzed and accessed in parallel as the file systems span multiple machines. Minerva is fully HIPAA-compliant and allows PHI data to be stored and processed. All data housed by HIMC may be subject to deletion after 3 months of inactivity and if no services are needed in the foreseeable future. Every attempt will be made to contact and warn users before any data is deleted. Data can be transferred using secure web links or high-speed network transfers (Globus). All transfers include raw data, processed data and software code. All sequencing data is regularly backed up to the cloud using Amazon S3 and Amazon Glacier. HIMC has the expertise and knowledge to assist with the following assays and services: experimental design, NGS technologies (single cell, spatial transcriptomics, bulk seq, whole exome sequencing), CyTOF, Olink, statistical analysis, database design, app development.
Microbiome Translational Center
The Microbiome Translational Center (MTC) in the Marc and Jennifer Precision Immunology Institute of the Icahn School of Medicine at Mount Sinai (PrIISM) serves as a central resource hub for basic and translational microbiome research. The MTC compromises a team of experts in microbiology, gnotobiotics and microbiome research including computational analysis and provides expert advice on experimental design and innovative approaches to microbiome research. The MTC is directed by the facility director Dr. Bongers and its two faculty directors, Drs. Faith and Clemente. The MTC operates with a five-member technical staff with a combined experience of >30 years. The center facilitates translational microbiome discoveries by providing investigators with appropriate sample collection SOPs, digitized sample biobanking, and various downstream microbiome assays including: high-throughput microbial nucleotide isolation, preparation of 16S amplicon and shotgun metagenomics libraries using a Beckman liquid handling robotic, Illumina MiSeq/HiSeq sequencing, and computational analysis. The MTC also houses a state-of-the-art automated anaerobic culture facility for rapid isolation of microbes that includes quick strain identification using a MALDI Biotyper. We also maintain a biorepository of >1000 human microbiome samples and a bank of longitudinal reference microbiome material that are used to validate if assays are within set operational compliance criteria and all experiments are recorded into an electronic LabArchives Research notebook. The gnotobiotic mouse facility of the MTC accommodates up to 10 large gnotobiotic breeding isolators (210 cages) and maintains a daily census of approximately 600 animals. In addition, it can support up to 12 smaller experimental gnotobiotic isolators for individual experiments including those with defined consortia of bacteria and custom diets. Additionally, 144 positive pressure cages and up to 150 outside-the-isolator cages can be used to screen gnotobiotic mice with different community compositions. The gnotobiotic facility maintains a colony of vasectomized Swiss-Webster males for rederivation of new germ-free lines by embryo transfer in collaboration with the Mouse Genetics and Gene Targeting core at Mount Sinai, and over half of the lines maintained in our facility were rederived in-house with the remainder coming from existing gnotobiotic facilities across the United States. Mouse colonies are tracked in our custom web-based mouse tracking software and database. All germ-free quality control metrics are stored in a web-based digital platform available to the facility operators and maintained in perpetuity. Recently, the MTC has expanded its capabilities to include the generation of clinical grade bacterial strains for Live Biotherapeutic Products (LBPs). For this purpose, the center has dedicated space in a separate building to physically isolate the bacterial manufacturing processes from the research culturing operations of the facility. All of the equipment (anaerobic Coy chambers, 4°C refrigerator, -20°C freezer, and –80°C freezers) are used solely for the production and storage of clinical grade LBPs. The anaerobic chambers were designed to be easily sterilized between bacterial cultures and between the production of different LBPs. In addition, the facility can generate complex microbiome therapeutics for fecal microbiota transplantation.
Visit the Marc and Jennifer Lipschultz Precision Immunology Institute at the Icahn School of Medicine at Mount Sinai (PrIISM) or contact Miriam Merad, MD, PhD for more information.
Last Updated: May 2023
The Tisch Cancer Institute (TCI) was awarded National Cancer Institute (NCI) designation in 2015. The mission of the TCI, under the leadership of Ramon Parsons, MD, PhD is to advance basic, clinical and population health cancer research, in order to prevent cancer in healthy individuals and improve the lives of cancer patients and their families in our diverse communities.
To accomplish this mission, the TCI has four collaborative research programs:
- Cancer Immunology—identifying the mechanisms underlying the suppression of anti-tumor immunity in order to inform development of effective immunotherapies
- Cancer Mechanisms— understanding the biology of cancer cell development and proliferation, and identifying candidate therapeutics that target biological pathways
- Cancer Prevention and Control—reducing the burden of cancer incidence, mortality, and disparities in cancer risks and outcomes
- Cancer Clinical Investigation – developing new treatment approaches to cancer by translating discoveries into therapeutic trials.
TCI members span across multiple departments and institutes and work collaboratively within and across these multidisciplinary research programs. In 2022, cancer grant awards exceeded $32 million in direct costs.
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 Research Support Unit. In 2022, 302 therapeutic clinical trials were available, offering innovative cancer treatment to over 497 patients.
The Institute supports five shared resources to facilitate research: Flow Cytometry, Mouse Genetics, Microscopy, Biostatistics, and the Human Immune Monitoring Center. The TCI is also enhancing resources related to tissue biorepositories, bioinformatics, and analysis of biomedical data.
Through its educational seminars, pilot awards and strategic planning committees, The Tisch Cancer Institute develops and fosters a dynamic team of cancer researchers and clinical investigators, provides the research infrastructure needed to spur new cancer discoveries and translate those discoveries into new therapies. The Institute’s Community Outreach and Engagement Program works with community stakeholders to address cancer disparities and promote equity in cancer care access and treatment throughout New York City and beyond.
Updated: March 2023