Grant Application Research

The Center for Comparative Medicine and Surgery (CCMS)

The Center for Comparative Medicine and Surgery (CCMS) is a centralized, shared resource supporting animal research via veterinary, husbandry care, and research collaboration with the faculty at Icahn School of Medicine at Mount Sinai. The program has been fully accredited by the Association for Assessment & Accreditation of Laboratory Animal Care, International (AAALAC - #00002), since 1967. The center also provides assistance with research protocol design, clinical and anatomic pathology, and training of research personnel in the care and use of laboratory animals. There are four primary sites of operation, with the central administration located in the Annenberg Research Building, 26th Floor. The other major housing areas are the Icahn Medical Institute (IMI); the Hess Center for Science and Medicine (HCSM) and the Atran Research building.

Annenberg Research Building

The largest variety of species is housed in this building. Administrative offices, large animal surgical support (one operating room and two catheterization labs), and a veterinary diagnostic laboratory are located here.

Icahn Medical Institute

This state-of-the-art rodent barrier facility offers fully automated rodent housing (ventilated caging and automatic watering), necropsy suite, and Animal Biosafety Laboratory (ABSL3) capability. Also located within this vivarium are the Mouse Genetics Shared Research Facility, Metabolic monitoring facility, and Gnotobiotic rodent facility.

Atran Research Building

This small facility provides overflow support for the Annenberg and IMI, respectively. Animals housed in this area reflect the general health profiles of the major support areas.

Hess Center for Science and Medicine

The HCMS vivarium is the newest and largest vivarium on campus. Designed to specifically support Imaging, Neuroscience behavioral studies, and Cancer research, the vivarium is adjacent to the Translational and Molecular Imaging Institute’s small animal imaging suites and large animal imaging capability. Fully automated, robotics, cage wash support and state-of-the-art environmental monitoring systems are additional key features of this facility.

The faculty of the CCMS consists of five full time veterinarians: (Director, DVM/MS/DACLAM; Associate Director, Head of Veterinary Translational Medicine and Director of Behavioral Management Program, DVM/MPH/DACLAM; Head, Comparative Surgery Facility, DVM; Head of Small Animal Medicine, BVetMed (Hons) MRCVS; and Veterinary Pathologist, DVM). The Husbandry operation is managed by Assistant Director of Husbandry Operations, CMAR, three full time husbandry supervisors and three husbandry assistant supervisors. All supervisors are certified at the Laboratory Animal Technologist level LATg) by the American Association of Laboratory Animal Science (AALAS). An ongoing in-house training program is in place and conducted by two full time Training Coordinators (MLAS, MBA). The institution also supports a weekly AALAS certification training program for all husbandry and research personnel interested in certification.

Visit the Center for Comparative Medicine and Surgery or email Jonathan A. Cohen for more information.

Last Update: February 2023

The Clinical Research Unit (CRU) is the hub for conducting clinical and translational research at the Icahn School of Medicine at Mount Sinai. There are more than 100 protocols being performed from a wide variety of specialties and subspecialties involving research participants of all ages. The staff includes nurse practitioners who can perform physical examinations, monitor participants, and perform infusions, and medical assistants who perform phlebotomy, electrocardiograms and process samples. The reception area, located on the ground floor of the Annenberg Building (adjacent to the elevator bank), includes exam rooms for brief visits and minor procedures. The Ross Park CRU Annex is equipped with rooms for day-long procedures and interventions such as infusions and PK sampling. Resources are available for specimen processing as well. The CRU is open Monday - Friday from 8:00 AM - 5:30 PM. Walk-in phlebotomy services are available weekdays 9:00 AM to 4:30 PM.

Visit the Clinical Research Unit or email Kaitlyn Ennis for more information.

Last Updated: March 2023

The Icahn School of Medicine at Mount Sinai (the “School”) has established the Dean's CoREs and Shared Research Resources Program to provide substantial support for innovative, state-of-the-art technologies, and technical assistance essential to our research programs in Translational and Basic Sciences. The compact size of Mount Sinai makes it possible for all investigators to have essentially unlimited and easy access to these resources.

Support for the CoREs by The School, described below, totals approximately $1.5 million per year, of which user fee charges to investigators recovers 70% of direct costs. The School subsidizes the remaining 30 percent. This makes it possible to charge investigators reduced fees, which promotes increased use of the facilities, and to prevent duplication of these technologies in individual departments or laboratories. An important ancillary result is that the CoREs enhance the potential for collaboration in multidisciplinary research programs, since CoRE directors can bring together investigators working in similar research areas. This also facilitates the adoption of new experimental approaches by PI’s, especially in situations where crossover requiring basic science data is needed to underpin and to test clinical hypotheses. Thus, Icahn School of Medicine views its commitment to the CoREs as a significant part of its cost sharing.

A website was developed that is linked to individual CoREs. On the individual websites, there is information about the services, fees, protocols for preparations and where appropriate, the opportunity to sign up for usage on a web-based calendar.

Structure and Governance of the Dean's CoREs and Shared Research Resources Program

The Program reports to the Dean for Research Operations and Infrastructure, Reginald W. Miller, DVM, DACLAM. The program is administered through the Dean's Office by the CoRE Administration, Veronica Moses (Financial Director), Shekhar Patil, PhD (Administrative Director). Operational oversight is through a dual, peer review mechanism. Each CoRE has a dedicated Scientific Advisory Committee chosen from its user group. CoREs are reviewed on a two to five-year cycle, External Reviews. The external review criteria include publication credits, technology, and personnel expertise. These reviews assist the institution in determining the need for continued support, emerging trends in technology, and obsolescence of technology. Fiscal oversight and administrative support for the CoREs is provided through the office of the Senior Vice President for Finance, Mr. Stephen Harvey via Mrs. Veronica Moses. Dr. Miller works closely with this group to monitor the finances of the CoREs. Each CoRE is directed by a Scientific Director and Staff who provides research services, educates investigators on the use of the technology, and helps them develop studies using new technologies in support of their research projects. A senior member of the veterinary staff also serves as ex-officio on all the advisory committees of animal-based CoREs. Advisory committees meet quarterly to evaluate and recommend improvements and updates to CoRE technology and services.

Instrument capital costs are not recovered through user fees but rather through instrumentation grants, Dean’s funds or Departmental contributions with matching funds from the Dean.

 Flow Cytometry

The Flow Cytometry CoRE provides instrumentation and expertise for automated cytofluorimetric analysis and the high-speed sorting of specific cell populations. The equipment of this facility is state-of-the art consisting of multiple high-speed cell sorters and analytical flow cytometers with the capacity to analyze up to 45 simultaneous fluorescent colors in real time with data rates exceeding 20,000 per second.

All instruments are available for staff assisted operation, or autonomous operation with training provided. Analytical cytometers include the Cytek Biosciences Aurora, the ThermoFisher Attune, Amis ImageStream ISX-MkII, and the BD CantoII and X-20. Cell sorters include five BD FACSAriaII SORP high-speed cell sorters, two Miltenyi Tyto microfluidic cell sorters, and a Nanocellect microfluidic cell sorter with multiwall plate deposition. Four of the BD FACSAriaII cell sorters and the Miltenyi Tyto sorters reside within Class II biosafety cabinets, allowing for isolation of unfixed human samples, including samples from HIV patients. The Nanocellect Wolf resides within a laminar flow tissue culture hood and provides true sterile sorting in conjunction with the disposable sorting chip. The need for contained sorting of live human cells is increasing rapidly along with the emphasis on translational research. Sorting of human samples on cell sorters in conventional rooms is widely deemed unsafe because the sorting process generates an aerosol, and carries the risk of the transmission of pathogens to users and operators. The BSL2 cell sorting facility was completely funded by the institution ($1.8M) and is absolutely critical to the efforts of the institution in translational research, in particular in the areas of stem cell biology, immunology, cancer, and infectious diseases.

Please visit the website or email Jordi Ochando for more information.

Biorepository and Pathology

The facility provides a consultative service to determine investigator requirements for human tissue and fluid biospecimens in translational research, and then arranges procurement as feasible. After meeting with the investigators about their respective research needs, CoRE personnel determine the best mechanism to obtain samples and implement the collection. This is made possible by the physical location of this Dean's CoRE in the Icahn School of Medicine Department of Pathology, and the ability to collect both deidentified and consented 'waste' biospecimens not required for clinical diagnosis. If the requested specimens are not feasible through the Mount Sinai health care system alternative sources will be explored.

The facility also offers basic histology services with the capability to process, embed and section fixed and frozen tissues for the Mount Sinai research community. We also prepare unstained slides suitable for a variety of applications such as histochemistry, immunohistochemistry, immunofluorescence, in situ hybridization as well as hematoxylin and eosin (H&E) stained sections and basic histochemical stains for routine light microscopic evaluation. The CoRE has the requisite equipment for a fully operational translational research laboratory including tissue processor, embedding station, microtome, cryostat, automated immunostainer, complete digital scanning system, image analysis software, and a semi-automated tissue micro-arrayer. The CoRE is also able to provide DNA / RNA extractions from all tissue types as well as blood samples and has the capabilities to routinely isolate circulating tumor cells, cell-free DNA as well as serum / plasma.

PDFs provided on the CoREs website instruct and guide users on "Human Tissue and Fluids Handling Risks and Safety Precautions", "Human Specimen Single User Agreement" and "Commercial Use Policy and Disclosure". The CoRE serves to educate investigators about the appropriate human subjects considerations when requests for human materials are made, thus assuring that all human biospecimen applications are in full compliance with HIPAA and IRB regulations.

Please visit the website or email Rachel Brody for more information.

Irradiator

The use of gamma irradiation to the whole body in animals (rodents) and/or cells has been a major research model for many years. The Mount Sinai Medical center hosts one Precision X-ray X-RAD320 machine in support of this research. A dedicated technician has been hired and trained to oversee the equipment, but more importantly to assist researchers with their studies. Rather than training new post-docs and students on the use of the machine(s), the technician performs all exposures. The result has been greater consistency and reduced down time for the machines. This machine is housed within the central vivarium due to the proximity of the animals used in the various studies. A separate entrance has been designed such that non-animal users are not required to enter the main animal barriers. Please visit the website or email Kevin Kelley for more information.

Please visit the website or email Kevin Kelley for more information.

Stem Cell Engineering

The Stem Cell Engineering CoRE (SCEC) brings state-of-the-art, crucial instrumentation and methodologies for modern stem cell and gene editing research within reach of all School’s investigators. The mission of the SCEC is to support the researchers in their work to describe the pluripotent stem cells (PSC) function, harness stem cells to repair tissues, model human diseases, and bring new therapies to patients. The SCEC is centrally located in the Black Family Stem Cell Institute (BFSCI), making it convenient for researchers to stop by to follow their stem cell experiments or pick up reagents while staying within reach of their laboratories. The SCEC maintains and provides well-characterized PSC lines and provides the physical space, validated reagents, and hands-on training for scientists to use these stem cells for their research goals. The SCEC is staffed by experts who provide research services and offer PSC culture techniques and differentiation training. Central services of the SCEC are the derivation of induced pluripotent stem cells (iPSC) from patient samples and PSC genome editing using CRISPR-Cas9 technologies to create or repair putative disease DNA mutations. Other services include consulting, PSC characterization and differentiation, PSC reagent validation, training courses, and other custom services. The SCEC is well equipped to perform all offered services; its facilities include a tissue culture facility with a dedicated Bsl2+ space for working with viral vectors, the microelectrode array (MEA) system from Axion Biosystems available to users to functional characterize PSC-derived neurons and cardiomyocytes, digital PCR and PSC Colony-picking setup.

Please visit the website or email Samuele Marro for more information.

Microscopy

The Microscopy and Advanced Bioimaging CoRE provides access to high-end instrumentation for light and electron microscopy and to computer workstations for image processing, image deconvolution, and image analysis. CoRE scientists provide expertise, hands on training, full-service electron microscopy preparation, and free consultation services in support of studies using fixed and living preparations. CoRE scientists can also be engaged collaboratively to carry out broader experimental initiatives and novel lines of investigation. Instrumentation includes three conventional laser scanning confocal microscopes (Zeiss LSM780 and Leica TCS SP5 and SP8 microscopes) and two with super-resolution capabilities (Leica TCS SP8 3X STED and Zeiss LSM 880 with Airyscan); one Yokogawa CSU-XI spinning disk microscope; two electron microscopes (Hitachi 7000 and Hitachi 7700); one Olympus FV1000 MPE (with Coherent Chameleon Vision II) and one Olympus FVMPE-RS 9 multiphoton microscope (with Spectra Physics Insight X3 Dual laser) equipped for in vivo imaging; a LaVision UltraMicroscope II light sheet microscope; five widefield systems differentially equipped for tiled acquisition, structured illumination, time lapse imaging and/or polarized light imaging (two Zeiss AxioImagers.Z2 with ApoTome2; one AxioObserver.Z1, one Olympus IX70, one Zeiss Axioplan2); one high content Cellinsight CX7 LZR platform, and one macroscope equipped for brightfield and fluorescence acquisition (Olympus MVX10). Automated long term, multi-field time lapse recording of living cells can be accomplished on several systems equipped with motorized stages, autofocus, filters, shutters, fluorescence and brightfield optics, and stage-top incubators. An anesthesia delivery system is available for intravital imaging. Image analysis workstations are equipped with Imaris, Arivis Vision4D and MetaMorph. AutoQuant X3, Huygens Professional and Leica Lightening are all available for image deconvolution. All microscopes and workstations interface with Acquifer HIVE which provides centralized data storage and high-end image processing. All instruments and workstations are accessible to trained users 24/7.

Please visit our website for more information. Or email Deanna Benson for more information.

Hess Freezer Farm

The Freezer Farm Dean’s CoRE at the Icahn School of Medicine is a secure, safe, state of the facility located in the Hess Building, which is fully equipped to meet scientific and research requirements. In the event of limited laboratory space, researchers have the option to relocate their valuable short term sample inventory to the Hess Freezer Farm. In order to ensure the safety and preservation of the materials stored, the Hess Freezer Farm offers a variety of support systems and services including but not limited to emergency electrical back-up system, 24/7 temperature monitoring with on-and off-site call out system and emergency transport, available temperature recordings on all systems, freezer maintenance as necessary, access to dry ice and shipping materials, week-day access with support staff ready to assist, bar-code inventory services and specimen aliquoting services are also available as needed.

Please visit our website or email Rachel Brody for more information.

Mouse Genetics and Gene Targeting

The institutional Mouse Genetics and Gene Targeting (MGGT) CoRE has been established to provide the Mount Sinai research community with access to state-of-the-art facilities for the production of transgenic and gene targeted mice, as well as related rodent embryology techniques, on a fee-for-service basis. The MGGT CoRE can produce transgenic mice by injection of DNA fragments of varying length (including bacterial artificial chromosomes) into pronuclear stage single-cell mouse embryos. The facility uses CRISPR technology to do genome editing in vivo to create various gene-targeted mouse models, such as knock-outs or knock-ins. The facility can also assist laboratories with the production of targeted mutant lines of mice through the use of mouse embryonic stem (ES) cells. Targeted clones are used to create novel lines of mice by injection of ES cells into blastocysts to create chimeric mice which are mated with wild-type mice to establish germline transmission of the targeted gene.    In addition to the creation of novel transgenic and targeted mutation lines, the MGGT CoRE can assist laboratories with the maintenance of existing lines through the cryopreservation of sperm. Cryopreservation of mouse sperm allows investigators to successfully bank lines that are not in active use. Shipment of cryopreserved sperm can also serve as an alternative method for transferring lines to collaborators at other institutions. Through collaboration with the Center for Comparative Medicine and Surgery (CCMS), the MGGT CoRE also provides investigators with the means to import novel lines from other institutions by recovering mice from cryopreserved embryos or sperm, live embryos, or through the use of IVF rederivation of individual males that are shipped to Mount Sinai. This service is an excellent alternative to the importation of rodents via live animal quarantine. The staff of the MGGT CoRE is also available to assist investigators with other rodent surgical techniques, such as vasectomies, ovariectomies, ovary transplants, etc.   

Please visit the website or email Kevin Kelley for more information.

Irradiator

The use of gamma irradiation to the whole body in animals (rodents) and/or cells has been a major research model for many years. The Mount Sinai Medical center hosts one Precision X-ray X-RAD320 machine in support of this research. A dedicated technician has been hired and trained to oversee the equipment, but more importantly to assist researchers with their studies. Rather than training new post-docs and students on the use of the machine(s), the technician performs all exposures. The result has been greater consistency and reduced down time for the machines. This machine is housed within the central vivarium due to the proximity of the animals used in the various studies. A separate entrance has been designed such that non-animal users are not required to enter the main animal barriers.    Please visit the website or email Kevin Kelley for more information.

Please visit the website or email Kevin Kelley for more information.

Neuropathology Brain Bank & Research CoRE

This new research laboratory was launched in response to the Mount Sinai Strategic Plan in 2018.  The goal of the CoRE is to provide infrastructure to extend Mount Sinai’s leadership in neuropathology-focused research.  The new CoRE, with consists of approximately 1000 ft² is equipped with a broad range of instrumentation for automated processing and staining of human brain tissues. The NBBRC is also equipped to process animal model and cell culture tissues related to neuropathology research. The CoRE is staffed with a team of expert neuropathologists and histotechnologists paired with state-of-the-art techniques and methodology. The facility performs routine histology and special stains (e.g., immunofluorescence and immunohistochemistry). The CoRE also provides high-throughput DNA/RNA extraction from fluid and tissue specimens.  In addition, the division of neuropathology maintains a collection of well-characterized and carefully curated brain tissues for research. Tissues include a range of normal human and age-related diseases, including neurodegenerative diseases. Neuropathology CoRE services include:

• Tissue trimming, cassetting, processing, and embedding
• Cutting and routine staining of paraffin-embedded and frozen OCT sections
• Large format tissue processing
• Immunohistochemistry for both routine and novel markers on our BenchMark XT system (Ventana)
• Immunofluorescent staining
• In situ hybridization
• Routine stains (e.g., H&E, LFB, silver, trichrome, etc.)
• DNA/RNA isolation on our King Fisher Flex Purification System (Fisher Scientific)

Please visit the website or email John Crary for more information. 

Last Update: June 2021

The Icahn School of Medicine at Mount Sinai (ISMMS) ranks 14th on NIH Reporter among the nation's 150 ranked medical schools in receipt of research support from NIH and administers more than 711 NIH grants, contracts and other transactions awarded to 447 Principal Investigators. The National Institutes of Health (NIH) funding to ISMMS totaled $462 million in Fiscal Year 2022, an increase of 4.5 percent from the previous year and 141.3 percent in funding since 2012.

Visit the Research page or contact Jessica Moise for more information.

Last Update: February 2023

The Department of Pharmacy maintains an Investigational Drug Service (IDS) to support research activities at Icahn School of Medicine. The IDS is a research pharmacy charged with maintaining the control and accountability of investigational agents (FDA approved and non-approved) in compliance with Good Clinical Practices (GCPs), Good Manufacturing Practices (GMPs) and other regulations and laws as appropriate. The IDS provides dedicated research support including protocol review, storage, preparation, dispensing and education to groups and investigators engaged in research.

The IDS sets up specific procedures and systems for each clinical trial to assure maximum benefit and safety for patients enrolled in studies. The clinical coordinators are available to consult with any investigator or sponsor to discuss the logistics of conducting their trial at Mount Sinai. All human subject trials requiring the use of medications must get authorization from the IDS prior to Program for the Protection of Human Subjects (PPHS) final approval (IDS and PPHS reviews occur concurrently).

Visit Investigational Drug Services or email Ivy Cohen for more information.

Last Updated: November 2023

The Mount Sinai Data Warehouse (MSDW) provides data access for planning and executing clinical and translational research as well as for quality of care and process improvement initiatives. MSDW collects and organizes clinical and operational data derived from patient care processes across the Mount Sinai Health System, which is composed of 7 inpatient facilities. MSDW contains data on over 11 million patients and over 80 million patient encounters. The MSDW is compliant with New York State and HIPAA regulations and with Mount Sinai PPHS and IRB policies regarding protection of human subjects and participation in research.

The Scientific Computing and Data team has selected and prioritized data elements for inclusion in MSDW based on two main criteria: (1) the data elements required to produce a reasonably complete OMOP data repository, as specified by OHDSI's OMOP Common Data Model, and (2) those data elements judged by the MSDW Steering Committee as having the greatest value to Mount Sinai researchers. The MSDW includes all patients with a record in Mount Sinai's instance of the Epic EHR. Until a hospital or physician practice has migrated to the Epic EHR, the MSDW will contain only the registration information for the patients seen at those sites, unless those patients have also been seen elsewhere in the Mount Sinai Health System.

A project is currently underway to link the Mount Sinai Image Research Warehouse to the MSDW so that electronic health record data can easily be joined with imaging data. Additionally, there are plans to incorporate the metadata from PowerPath into MSDW on a weekly basis. This integration would allow researchers to easily link anatomical pathology data with electronic health record data.

Epic's Clarity reporting database is loaded from the Epic application's Chronicles database once per day overnight, thereby introducing a 1-day lag in the data. Epic's Caboodle data warehouse is loaded from the Clarity reporting database once per day overnight, thereby introducing a second 1-day lag. The data extracted and loaded to MSDW from Epic Caboodle once per day will therefore represent a lag of approximately 60 hours.

The MSDW supports the research community by: providing de-identified and identified data access for IRB approved studies; identifying cohorts and providing daily/weekly/monthly reports for these study population; providing upcoming appointment details for potential study recruits to aid in study enrollment; providing customized data marts for complex multi-dimensional studies. Researchers planning new studies or grant applications can search the MSDW2 to identify eligible cohorts by using one of our de-identified self-service query tools: Leaf, ATLAS, or TriNetX.

MSDW is situated on the Minerva High-Performance Computing (HPC) cluster, rather than on its own hardware, to lower operating costs and to facilitate links to other research data sets (imaging, genomics, pathology, etc.) already housed on Minerva. Minerva has over 2,000 applications available to enable multi-scale studies and data science.

We monitor, collect and analyze operational metrics for continuous quality improvement of our informatics ecosystem. We have developed tools that automatically collect system and user-related metrics for the MSDW, TriNetX, REDCap and other essential IT services. Relevant metrics include system uptime, number of users supported, number of self-service queries, databases, data marts and custom queries and the number of known data quality issues. Once a month we review operational metrics, to see if there are any processes that we could improve for better researcher and clinician productivity. We will also develop and refine metrics to track our effectiveness as informatics catalyzers at Sinai and in the broader CTSA/CD2H community. Our initial scientific impact metrics include the number and type of collaborations and support we provide, the number of training sessions and students attending, the number of data sets and code that we share, the number of publications and grants that we assist with. We will also track our activities and contributions to the CTSA/CD2H community through the sharing and adopting of best practices.

We are committed to partnering not only with our local researchers and clinicians, but with others nationally. We participate in the monthly iDTF (Informatics Domain Task Force) meetings and CD2H webinars to learn best practices from other sites, and have participated in iDTF face to face meetings at American Medical Informatics Association (AMIA). We also learned from participating in other calls and meetings, including the Healthcare Data Warehouse Association (HDWA), HIMSS and BioIT World. The Mount Sinai Data Warehouse team also manages the NYC CDRN including participating in monthly meetings, which is part of PCORNet. We also have worked closely with the iDTF, CD2H and groups over the past year to develop a survey around data quality and reproducibility for both researchers and data warehouse leads. The survey will be issued soon throughout the iDTF. We have developed online training modules for i2b2, and have worked with researchers 1:1 to enable use. We have deployed TriNetX. We have a team of four people to assist with research queries and a person dedicated to improving data quality and ensuring compliance and a clinical informaticist to bridge between the data analysts and the researchers/clinicians.

We also stay up-to-date on the implementation of NIH’s Strategic Plan for Data Science [and the NIH Data Commons, which may include opportunities to link our data into a broader FAIR-compliant ecosystem with other NCATS and NIH datasets. We will also track the progress with the STRIDES program to integrate and leverage NIH cloud-based efforts. We have been exploring options for migrating appropriate applications and data to the cloud, and will continue with our planned proof-of-concept to determine the best paths forward. We actively track technical advances in the international community through conferences and workshops and monitor the uptime and usage metrics for all of our services to explore opportunities to continually improve our partnership and improve the research productivity of the Mount Sinai and broader CTSA/CD2H communities.

Visit the Mount Sinai Data Warehouse for more information.

Last Updated: March 2023

Office of Research Services – Developed in response to the needs of the Mount Sinai Health System’s (MSHS) expansion and the parallel evolving complexity of research regulations, policies and processes, the Office of Research Services (ORS) was established to facilitate the conduct of translational and clinical research through a centralized infrastructure supported by ConduITS’ Administrative Core and the Office of the Dean of Icahn School of Medicine at Mount Sinai. The ORS provides oversight of program organization, evaluation, continuous improvement, quality, efficiency, safety and communications allowing ConduITS to continually identify barriers, gaps and unmet needs of the MSHS research community and to implement integrated solutions that impact the scope of Mount Sinai’s learning healthcare system. 

The ORS is staffed with 15 FTEs who provide researchers throughout the MSHS with the following services:

• Navigation of the internal research infrastructure which includes:
• Required training for the conduct of research
• Lifecycle of research management
• Clinical Trials Management System (CTMS)
• The ISMMS Offices of Research Administration
• Human Subjects Protections Program
• Grants and Contracts Office
• Investigational Drug Services
• Research Compliance
• Research Financial Conflicts of Interest
• Financial Administration of Clinical Trials

• Regulatory Coordination:
• Centralized ClinicalTrials.gov registration, updates and reporting
• Investigational New Drug Application and Investigational Device Exemption (IND/IDE) submissions & progress reports to the FDA
• Pre-protocol development
• Research recruitment strategies
• Consultations and  Services:
• Clinical Research Portal Maintenance
• Clinical Trial Feasibility Guidance
• Grant Application Resource Center Maintenance
• Multi-Site Study Support
• Spanish Translations for NIH Funded Studies
• Training, Education & Communications:
• Clinical Research Orientation
• Custom Training and Education
• Research Listserv

Given the increasing need for innovative informatics solutions to manage the workflow for translational sciences across the MSHS, the ORS has developed e-tools to assist researchers find answers to questions and provide navigation of the MSHS research infrastructure. These platforms also collect metrics about utilization, issues, and customer satisfaction to assist in the continuous improvement of the services provided by the ORS. In 2018, the ORS launched the health system’s global research help desk, Research 411, which replies to over 1,000 inquiries annually. The ConduITS Research Roadmap (RRM) was implemented in Q2 2019. The RRM is a web-based, interactive, real-time tool that provides MSHS researchers with navigation of the health system’s research operations, workflows, resources, and it embeds real-time and evolving regulatory guidance and best practices to provide the highest quality conduct of research at the MSHS. The RRM also provides a centralized, dedicated environment for ConduITS to communicate advances to the network of CTSA hubs across the nation. The ORS is leading the implementation of the institution’s system-wide clinical trials management system which further streamlines research study conduct, oversight and efficiency locally and remotely across an ever-expanding health system and collaborating institutions.

Research 411 e-Portal – Research 411 is a centralized, electronic portal for general research help desk questions, information, request for services and consultations and the collection of metrics for program evaluation of quality and efficiency system-wide. It is built with JIRA software which allows the ORS team to track communications in centrally accessible message threads for continual cross-coverage of issues, increasing productivity and eliminating down-time. The program is customizable to allow for the creation of on-demand tickets for emerging topics. Additionally, the program provides information about the volume of incoming tickets in a specific area or topic. This information is then used by the ORS team to identify where there is a gap, bottleneck and/or need for education and training and provides the ability to spotlight issues and locate solutions (see Research Roadmap below). Since its inaugural year, Research 411 has processed over 5288 inquiries, in the areas of IRB, GCO, IND/IDE support, Clinicaltrials.gov, OnCore, Research Orientation, and for case-by-case queries requiring tailored support and guidance.

Regulatory Support Knowledge Base (RSKB) – (self-serve support function) a feature of Research 411 is the ability to develop an organized repository of the solutions developed through the Research 411 portal. In essence, this becomes a Frequently Asked Questions (FAQ) self-help function of the ORS where research teams can access “articles” based on targeted solutions to issues local to MSHS, general best practices and knowledge gained from the questions and solutions provided through Research 411. Articles will be organized under categories and subcategories ensuring ease of use and search capability. The RSKB will improve efficiency and investigator productivity by eliminating the need to respond to redundant issues and providing instant access to solutions. The number of ORS developed RSKB articles, the volume of users accessing them and automated customer satisfaction surveys will be used as key performance measure when evaluating RSKB.

Research Roadmap (RRM) – The Research Roadmap is a robust and comprehensive web-based, centralized tool developed by the ORS. The RRM, visually designed to function like an interactive subway map, has been developed to provide system-wide navigation of the many “pathways” of the MSHS research infrastructure and provides a “line” to the CTSA national network of resources. It is an interactive, dynamic, easy-to-use tool that provides the most current, streamlined, and efficient access to administrative processes, external regulatory requirements, internal policies, most current news, education, and training opportunities toward the conduct of the highest quality research. The RRM increases efficiency by providing information for parallel processing, monitoring of timelines, and review processes. Locally designed and built, the RRM is complementary to the Research 411 portal as a tangible, immediately accessible, and continuously available web-based tool and platform for the dissemination of the “tips” and “best practices” learned through the Research 411 portal. The RRM increases productivity time by reducing the discovery time for research teams to understand research methods and processes. Controlled by the ORS, the team can real-time post the newest modifications and news for the system. Dissemination of RRM improvements is provided by the ORS managed research listserv, and availability of local hub innovations and tools is provided through a dedicated “line” for the CTSA national network of hubs and the CTSA program. The location of solutions that are developed for gaps and bottlenecks in research systems is more efficiently pinpointed and communicated on the RRM.

Clinical Trials Management System (OnCore) – ConduITS the Clinical & Translational Science Award at Mount Sinai received an administrative supplement from NCATS the NIH center that funds the CTSA program in August of 2018 to implement a system-wide Clinical Trials Management System (CTMS) “OnCore”. The Office of Research Services (ORS) within ConduITS is managing and supporting the expanded use of the CTMS. OnCore will allow institution-wide reporting of clinical research metrics, compliant oversight in research regulatory and billing compliance, and centralize access to the ISMMS research portfolio conducted at the Mount Sinai Health System. The CTMS impacts rapid activation of clinical trials by enhanced protocol and informed consent life cycle management improving IRB approval duration and continuing renewal. Additionally, the CTMS’ reporting capabilities allow for the analysis of slow or non-recruiting studies for evaluation and improvement of initial recruitment plans or study closure. The CTMS can improve regulatory compliance with clinical research billing and Clinicaltrials.gov registration and reporting.

ORS continues to collaborate and help lead in research innovation by implementing a new interface between the institution’s electronic IRB with OnCore. Next on the agenda is working towards integration the Electronic Health Record (Epic) with OnCore to send protocols with hospital billable services to Epic and the automatic flagging of patients as research participants for billing review and patient safety.

If you have any questions or want to read about updates to the OnCore role out contact Research411 or go to The Research Roadmap.

Last Update: March 2023

For more information visit our Website or submit a Research 411 request to contact us directly.

The Program for the Protection of Human Subjects (PPHS)

With full accreditation from the Association for the Accreditation of Human Research Protection Programs the Mount Sinai Health System's Human Research Protection Program is a comprehensive program to ensure the protection of the rights and welfare of subjects in Human Research. The Program for the Protection of Human Subjects (PPHS) is a key component of the overall HRPP.

The PPHS supports researchers throughout the Mount Sinai Health System in assuring the ethical conduct of research and compliance with federal, state and institutional regulations and provides a professional office staff to assist investigators, participants, and Institutional Review Boards (IRBs). In addition, the overall HRPP includes organizational, administrative, and investigator components, and is based on all individuals fulfilling their roles and responsibilities. Essential aspects of the overall mission of human subjects protection are provided by the organized interaction of the PPHS with the Financial Conflict of Interest Committee, the Financial Administration of Clinical Trials Office, Investigational Drug Services, The Office of Research Compliance, the Biosafety Program and the Radiation Safety Committee and CyberSecurity.

The PPHS is a signatory to the CTSA sponsored SMART IRB platform and uses it extensively when providing single IRB functions to investigators. The PPHS is posed to provide support whether we are the IRB of record or are a relying institution. 

The PPHS office offers support to investigators and their research teams through one-on-one scheduled meetings with IRB analysts to review individual applications and answer questions. The office also offers short presentations to groups, departments, or divisions on the human subjects research submission process by experienced IRB analysts. The PPHS office also offers assistance to researchers during business hours by phone, or through the general email address which is answered daily.

Visit or email the Protection of Human Subjects for more information.

Last Update: February 2023

eRAP

The eRAP Rapid Database Generator (eRAP RDG) is a 21CFR Part11 compliant web-based interactive tool for data entry and reporting. We rapidly develop custom databases for longitudinal single and multi-site studies. Features include reporting tools, a randomization engine, data and file upload. eRAP is also integrated with other Mount Sinai Health System clinical systems such as Epic, the Mount Sinai Data Warehouse, the Specimen Management Systems (Freezerworks and IPM LIMS) and SCC Labs, enabling making data sharing between systems. eRAP is developed using standard collaborative best practices, following the Software Development Life Cycle and Agile processes. Bitbucket is utilized as our repository and tickets are tracked with Jira. In addition, we support calendaring services for Mount Sinai’s Shared Research Facilities and other labs throughout Sinai. We have designed instrumentation-specific calendaring systems to ensure efficient scheduling.

Visit eRAP for more information.

REDCap

REDCap (Research Electronic Data Capture) is supported through the Icahn School of Medicine at Mount Sinai (ISMMS). Mount Sinai has over 2,000 active users. REDCap is a secure web-based application designed to support electronic data capture for research studies. REDCap provides a simple point-and-click interface to create web-based data entry and case report forms with the ability to customize real-time data entry validation (e.g., for data types and range checks), maintain project audit trails, export project data to advanced statistical software packages, and assign different levels of data access for each member of the research team. REDCap supports cross-sectional and longitudinal research designs. REDCap was designed in a manner that is consistent with all federal and local regulatory policies and procedures. REDCap allows the host institution to define REDCap data security policies, data backup schedules, data retention plans, and involvement of necessary departments (e.g., Institutional Review Board) in the REDCap project creation process. The web, application and database servers are housed in Mount Sinai’s secure data center and are subject to institutional policies on security, backup, recovery and control. Data collection tools developed within REDCap can be customized by the research team, with guidance from REDCap support staff at Mount Sinai supported in part through our CTSA. Data are captured by user-defined web-based forms and stored in dynamically maintained data tables. Fields can be added to the forms and to the tables using as the project progresses. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. More recently we have implemented REDCap plugins (Twilio and MyCap) for mobile based diary assessments and other survey administration.

Visit REDCap for more information.

Last Updated: March 2023

Responsible Conduct of Research

All pre- and postdoctoral trainees of the Graduate School of Biomedical Sciences are required to complete training in Responsible Conduct of Research (Course Code: BSR1021).

Format: BSR1021 classes consist of highly interactive lectures that present the subject material, augmented with case studies and videos provided by the NIH that form the basis for further discussion. In addition, one class on responsible publication, authorship and peer review is taught in the format of a panel discussion with Journal Editors and Study Section chairs.

Subject Matter: The subject matter is divided into 8 classes with the following topics: 1) Introduction to RCR; research misconduct and policies for handling misconduct, and safe laboratory practices; 2) mentor/mentee responsibilities and relationships; 3) Laboratory Notebooks and Data Management; 4) responsible authorship, publication and peer review; 5) policies regarding human subjects, and live vertebrate animal subjects in research; 6) Contemporary Issues in Research Ethics; 7) collaborative research including collaborations with industry; conflict of interest – personal, professional, and financial; and 8) The research misconduct review process. Starting August 2022, the following topics were added in response to NOT-OD-22-055: safe research environments (e.g., those that promote inclusion and are free of sexual, racial, ethnic, disability and other forms of discriminatory harassment); Collaboration with investigators in other countries; data analysis, image generation, electronic lab notebooks; secure and ethical data use and confidentiality.

Faculty Participation: Each class is team taught by faculty with expertise in the relevant topics. The faculty deliver the lecture materials and lead the discussions. Each class is followed by a short quiz. The faculty include Drs: Paul Cummins (Bioethicist); George Huntley (Ombuds, safe environments); Matthew O’Connell (Senior Assoc Dean for PhD programs, scientific misconduct, mentoring, plagiarism; course director); Eric Sobie (Data Recording, archiving, electronic and conventional notebooks, public databases ); Martin Walsh, Robert Krauss, Patrick Hof and James Manfredi, Erin Rich, Daniella Schiller - (responsible and confidential publication/authorship/peer review); Paul Kenny (collaborations and conflicts, inc with Industry and foreign laboratories); Jonathan Cohen  (Vertebrate Animal Studies); and Theodore Bania (IRB and Human research); Reginald Miller (ISMMS RIO). Additional faculty will be recruited as needed to accommodate the new topics

Duration: The course runs for a total of 8 hours over 4 weeks in the Fall semester, though will be extended with the addition of new topics. Attendance is mandatory. All trainees must retake the complete training after 4 years – (RCR Refresher, Course Code: BSR1023).

Frequency: Twice per week (Monday and Wednesday)

In addition, these trainees are required to take a sister course, Rigor and Reproducibility (course code BSR 1022). This course has the same format as BSR1021, but runs in the Spring Semester.

Format: Same as BSR1021

Subject Matter: The course is split into three areas: 1) R&R at the bench (Experimental Design; The scientific premise; use of controls; hypothesis testing; biological vs technical replicates; parallel and complementary approaches); 2) Human and animal experimental design and statistical analysis (IACUC and IRB requirements; power calculations; sex as a variable; other variables including genetics; design of clinical trials; statistical testing of hypotheses and reporting of methods); 3) Digital and Quantitative Data (Data management; big data issues; storage and back-up, use of public databases, metadata, digital image production, promoting reproduction by others).

Faculty Participation: Again, team teaching for the three areas: 1) Matthew O’Connell and David Dominguez Sola; 2) Amaia Lujambio and Tom Marron; 3) Eric Sobie, and Evren U. Azeloglu.

Duration: The course runs for a total of 8 hours over 4 weeks in the Fall semester. Attendance is mandatory. Refresher after 4 years.

Frequency: Twice per week (Monday and Wednesday)

For more information please email: registrar@mssm.edu

Last Updated: April 2023

Mount Sinai has invested over $200 million to its scientific computational, informatics and data infrastructure, tools and human expertise. This substantial commitment by Mount Sinai demonstrates, in a very tangible manner, the understanding that a well-designed and managed infrastructure empowers its scientists and researchers to be more productive and effective. Furthermore, this substantial investment is a holistic one that includes a professional operational and experienced Ph.D. scientific computing staff along with the hardware, software and new computational and data facilities optimized for our scientific workload. Scientific Computing consists of High Performance Computing, the Mount Sinai Data Warehouse, and Research Data Services.

Mount Sinai also has significantly invested in supercomputer resources available to researchers using high dimensional datasets. This supercomputer allows the efficient management of multiscale -omic databases and will unlock the intricate mechanisms that lead to human diseases, and hasten the discovery of treatments for them. Our scalable supercomputer resources are used for advanced quantitative analysis of massive and varied datasets to create predictive models of disease with over 2.0 petaflops of computational power (nearly 25,000 Intel compute cores and 100 NVIDIA GPUs and 32 petabytes of storage) available.

Minerva, created in 2012 and upgraded several times, most recently in January 2022, utilizes 24,214 Intel Platinum in three generations including 8358 2.6 GHz, 8268 2.9 GHz and 8168 2.7GHz compute cores (48 cores or 64 cores per node with two sockets in each node), 92 nodes with 1.5TB of memory per node, 353 nodes with 192 GB of memory per node, 48 V100 GPUs, 40 A100 GPUs, 210 terabytes of total memory 350 terabytes of solid-state storage, 32 petabytes of spinning storage accessed via IBM’s Spectrum Scale/General Parallel File System (GPFS) for a total of 2 petaflops of compute power. All of the nodes are connected via a Mellanox Extended Data Rate (EDR) Infiniband fat tree fabric (100 Gb/s). Minerva ranks among the largest in academic medicine in the U.S. All nodes are scheduled with IBM’s LSF. Minerva services include the MATLAB Distributed Computing Server, and web and database services. An archival storage system (IBM’s Tivoli Storage Manager) encrypts and saves copies of data on tape to two geographically disparate locations. Over 2,000 applications are supported. We have served over 2,000 users at Mount Sinai and 700 external users including many from CTSA organizations and support many large consoritia. The high-performance computing team has enabled over 1,400 publications that utilized the Minerva ecosystem over the last 10 years.

A dedicated Scientific Computing staff also aids and educates the user community on a regular basis. Mount Sinai also employs a team of domain-specific Ph.D. computational scientists with interdisciplinary expertise to assist researchers to make efficient and effective use of our computing and data resources. These scientists lead basic and advanced training and accelerate the scientific discovery process by assisting with code development, optimization and troubleshooting. They also conduct yearly surveys and actively solicit and respond to feedback. We are also guided by the Scientific Computing Advisory Board, comprised of early career and senior leadership at Mount Sinai.

Big Omics Data Engine (BODE), BODE2 and CATS supercomputers

In July 2014, the NIH awarded $2M to Patricia Kovatch to build and deploy the Big Omics Data Engine (BODE) (1S10OD018522-01) for NIH-funded genomics-based researchers. This machine, deployed on scope, schedule and budget is over 95 teraflops with 2,484 2.4 Ghz Intel Haswell cores in 207 Cray CS300AC nodes, 13 terabytes of memory (64 GB of memory/node), 5 petabytes of DDN SFA12KE storage connected via Infiniband. The machine entered production on February 1, 2015. BODE was decommissioned in June 2019, and a new NIH award for a BODE2 (1S10OD026880-01) entered production in November 2020. BODE2 has a peak speed of 355 teraflops with 3,840 cores in 80 nodes with 15 terabytes of memory collectively. It is connected with EDR Infiniband and have 14 petabytes of raw storage. The COVID and Translational Science supercomputer (CATS) was awarded in 2021 (1S10OD030463-01) to enable new kinds of scientific discovery and translation related to the newly emerged COVID-19 pandemic. CATS entered production in 1Q22 with 3,520 Intel cores, 82 TB of memory and 16 petabytes of storage. The enhanced capabilities of CATS will shorten the time to solution and enable more complex biomedical analyses.

Data Ark Data Commons

The Data Ark is a data commons resource based on the principles of making data findable, accessible, interoperable and reusable (FAIR). The Dark Ark includes both public and Sinai-generated data (both restricted and unrestricted), and aims to make it easy for researchers to manage, process and combine data in new ways to optimize the accuracy, power and generalizability of our science. The Data Ark team downloads, organizes and performs data quality assurance and quality control for a variety of data. The team also manages the data access process, answers user questions, and ensures that the latest versions of these data sets are available.

The initial data sets include the 1,000 Genomes Project, GTEx, GWAS Summary Stats, UK Biobank, and Mount Sinai COVID Electronic Health Record data set, and the STOP COVID NYC Cohort. Since 2022, the available data sets have expanded to include The Cancer Genome Atlas (TCGA), eTQLGen, UKBB-LD, LDSCORE, BLAST, Reference Genome, The Living Brain Brokect, and IBM® MarketScan®.

The Data Ark provides opportunities for researchers to share their data, work on data contributed by others, and save time otherwise spent locating, processing and correcting data. This data repository enables researchers to easily access far richer, larger and higher quality data than possible otherwise. It will also makes testing the generalizability of findings straightforward. Diverse research projects performed across Mount Sinai on exactly the same large data resource lends itself particularly well to collaboration and has the potential to dramatically increase the pace of our scientific advances.

BioMe Biobank

The BioMe Biobank Platform is an ongoing, prospective, hospital-based population research study that aims to enroll over 100,000 participants (currently >45,000 adult/pediatric samples). BioMe is a prototype example of an Electronic Medical Records (EMR)-linked Biobank that integrates a patient’s clinical care information and research data, as envisioned in the recently published National Research Council Report ‘Towards Precision Medicine.’ The Biobank has a large collection of DNA and plasma samples and large-scale genomic data that are stored in a way that protects patients' privacy while allowing research to be performed on de-identified clinical information from Mount Sinai's data warehouse system. Those consenting can be re-contacted for future work; We have exome SNP genotypes on approximately 40,000 of these and can perform a Genome Wide Association Study on demand for just about any phenotype in the EMR in this cohort. Please see BioMe Platform for more information.

INSIGHT, formerly NYC-CDRN (Clinical Data Research Network)

The INSIGHT Clinical Research Network (CRN) is an infrastructural initiative that offers users access to a centralized, accessible, robust database with 11 years of longitudinal high-quality research-ready data on 12 million unique patients eligible for trial enrollment. The INSIGHT Network also provides important research services, such as patient recruitment and a centralized IRB, to advance and streamline research. The INSIGHT Network is a unique partnership of more than 5 highly ranked academic medical centers and collaborators: Funded by the People Centered Research Foundation (PCRF), the INSIGHT CRN offers innovative services and data to support both observational and interventional research. A unique feature of the INSIGHT network is its secure, limited central data repository. Current available data includes administrative, clinical, and access to Medicare and Medicaid claims data, commercial claims data, and social determinants of health data. INSIGHT has been a leader in efforts to standardize data linkage across disparate sources: We have 1.4 million Medicaid beneficiaries (up to 2016)

• We have linked nearly 1 million Medicare beneficiaries to clinical data and social determinant data*
• We have linked 200,000 Medicaid beneficiaries clinical, claims and social determinant data*
• We are in the process of integrating patient reported outcomes (PROs) and registry data

The INSIGHT CRN also provides the infrastructure to carry out multi-site clinical trials using standardized and expedited administrative, contracting and regulatory processes. We are committed to engaging patients and clinicians to participate in clinical trials and to identify ways to widely disseminate research results.

The Insight CRN is characterized by a large, diverse patient population, reflecting the racial, ethnic and socio- economic diversity of New York City’s population as well as the extensive set of health care services offered by hospitals across a fragmented healthcare landscape. NYC patients seek care from multiple institutions, requiring unique informatics solutions that includes a centralized process for advanced patient identity management to link individual patient records across sites.

The INSIGHT Clinical Research network has successfully de-duplicated patient records across institutions and standardized data linkages across disparate data sources to provide a broad, unique, and complete view into a patient’s pattern of care. We have also implemented a high functioning governance structure that engages health system leaders, patients and clinicians across the spectrum of research development and implementation activities. INSIGHT’s streamlined services contributes the effectiveness and efficiency of multi- site research and has generated $100 million in research funding for our member institutions. Finally, INSIGHT Network sites have standardized data according to the PCORnet Common Data Model, which maximizes its capability to support pragmatic clinical trials

• Broad range of data uses and users
• Health systems and payers often use INSIGHT’s data to conduct further research into the cost and quality of care, especially as they relate to population health, quality improvement, and related healthcare delivery programs.
• Investigators use INSIGHT’s data to make prep-to-research queries, conduct observational and comparative effectiveness studies, and identify subjects to participate in clinical trials

Imaging Research Warehouse (IRW)

The IRW is directed by Dr. David Mendelson, and contains over 200,000 images in many modalities. All MSH and MS Queens imaging exams associated with an EPIC record and order, are de-identified daily (approximately 1000 exams/day). Ultrasounds are currently excluded, but also separately archived ready for pixel level de-identification on demand. This service (de-identification) is provided to any imaging source within the institution, including those outside of Radiology, as long as they agree to assign an accession number to an exam. Outside exams can be imported via PACS as long as an accession number is assigned. It has been live since Spring 2017. IRW resources include: (1) 250 Terabytes of archive; (2) Vioarchive de-identification engine (VNA); (3) 3 software engineers. Ongoing tasks include: (1) Support  the current mirror of PACS without PHI and a new second state with PHI for AI research (with IRB approval to include PHI); (2) Extend the IRW to Continuum sites as they are added to EPIC; (3) Add reports in a de-identified state with medical concepts extracted and used to label the images/imaging exams with NLP; (4) Tight integration with the MSDW; (5) Direct integration of DICOM Metadata; (6) Increase storage for all data types; (7) Collaboration with external sites; (8) Archive labelled data; (9) AI imaging-based research.

Mount Sinai Hospital Big Data Program

The Clinical Data Science Team is led by David L. Reich, MD, President, The Mount Sinai Hospital & Mount Sinai Queens. This unique translational program is focused on innovation within the clinical environment in the form of predictive analytics and decision-support tools. The existing data science team has created a unified data pipeline and computational cluster that supports a system-wide streaming clinical data platform. Our vision is to improve patient care using this platform to run validated algorithms that provide real time decision support at the point of care and in the community. Mount Sinai is uniquely positioned to leverage the era of big data, machine learning, and data science to promote translation of clinical innovation into routine healthcare delivery. Enabling factors include the unified EHR, the explosion of “-omic” data (DNA, RNA, protein), and the ability to obtain, store, and analyze high resolution physiologic data in clinical and population health settings There are currently several pilot efforts underway within the Mount Sinai Health System to utilize these data, many within the research setting.

Last Updated: March 2023