Projects per year
Organization profile
The rapid pace of technological advancement in genome sequencing has created endless opportunity for novel discoveries across basic and translational sciences. To pioneer this data transformation, the Center for Advanced Genomics Technology at the Icahn School of Medicine at Mount Sinai has built an extensive technology toolbox with unprecedented access to and application of novel and existing methods in a multitude of genomics technologies. These capabilities span bulk, single-cell, spatial, and in situ genomic sequencing methods, all of which are leveraged to generate complementary cross-platform, orthogonally validated datasets to foster novel discovery and advance clinical applicability using human cohorts and model systems.
Technologies include novel molecular methods for extremely low-input library preparation methods; targeting genes of interest in both DNA and RNA profiling applications as well as amplification-free Cas9-based enrichment strategies; and a wide range of sequencing platforms, spanning the current and future state of the art for short-read, high-throughput, and long-read single molecule and nanopore sequencing methods from bulk tissue to single cells. Complementary use of these integrated technologies to approach critical open research questions creates the opportunity to accelerate discovery and characterization of previously unknown genetic structure, variation, and function across collaborative research at Icahn Mount Sinai and beyond.
The Center for Advanced Genomics Technology (CAGT) applies innovative, multi-omic technologies to accelerate biomedical and translational research studies within the Mount Sinai community. Advanced integrative approaches are critically important for generating diverse, high-resolution, multi-omics data for comprehensively characterizing the molecular underpinnings of health and disease.
The CAGT includes an expanded focus on faculty-driven research in the development and application of advanced genomic technology. Working synergistically since 2013 at the interface of molecular and computational biology, a team of more than 30 expert faculty and staff members with backgrounds in academia, industry, and clinical science has built and maintained an advanced technology facility that is recognized as one of the most reputable, certified, single-molecule and single-cell multi-omics facilities in the world. These advanced technologies, together with conventional next-generation sequencing methods, leverage technology-driven approaches to characterize and discover mechanisms associated with cancer, Mendelian disease, developmental disorders, and infectious disease, among others.
Fingerprint
Network
Profiles
Projects
- 1 Finished
-
The environmental REsistome: confluence of Human and Animal Biota in antibiotic resistance spread (REHAB)
Crook, D. D., Stoesser, N. N., Sheppard, A. A., Peto, T. E. T. E., Wilson, D. J. D. J., De Maio, N. N., Walker, A. S. A. S. & Sebra, R.
Natural Environment Research Council
1/06/16 → 31/05/20
Project: Research
Research output
-
The Breast Cancer Single-Cell Atlas: Defining cellular heterogeneity within model cell lines and primary tumors to inform disease subtype, stemness, and treatment options
Dave, A., Charytonowicz, D., Francoeur, N. J., Beaumont, M., Beaumont, K., Schmidt, H., Zeleke, T., Silva, J. & Sebra, R., 2023, (Accepted/In press) In: Cellular oncology (Dordrecht).Research output: Contribution to journal › Article › peer-review
Open Access -
Using EGFR amplification to stratify recurrent glioblastoma treated with immune checkpoint inhibitors
Friedman, J. S., Jun, T., Rashidipour, O., Huang, K. L., Ellis, E., Kadaba, P., Belani, P., Nael, K., Tsankova, N. M., Sebra, R. & Hormigo, A., 2023, (Accepted/In press) In: Cancer Immunology, Immunotherapy.Research output: Contribution to journal › Article › peer-review
-
An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics
Ramos, S. I., Mussa, Z. M., Falk, E. N., Pai, B., Giotti, B., Allette, K., Cai, P., Dekio, F., Sebra, R., Beaumont, K. G., Tsankov, A. M. & Tsankova, N. M., Dec 2022, In: Nature Communications. 13, 1, 7671.Research output: Contribution to journal › Article › peer-review
Open Access -
ARID1A mutation associated with recurrence and shorter progression-free survival in atypical meningiomas
Chaluts, D., Dullea, J. T., Ali, M., Vasan, V., Devarajan, A., Rutland, J. W., Gill, C. M., Ellis, E., Kinoshita, Y., McBride, R. B., Bederson, J., Donovan, M., Sebra, R., Umphlett, M. & Shrivastava, R. K., 2022, (Accepted/In press) In: Journal of Cancer Research and Clinical Oncology.Research output: Contribution to journal › Article › peer-review
-
A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants
Mount Sinai PSP Study Group, Sep 2022, In: Microbiology spectrum. 10, 5Research output: Contribution to journal › Article › peer-review
Open Access -
Association of mutations in DNA polymerase epsilon with increased CD8+ cell infiltration and prolonged progression-free survival in patients with meningiomas
Rutland, J. W., Dullea, J. T., Gill, C. M., Chaluts, D., Ranti, D., Ellis, E., Arrighi-Allisan, A., Kinoshita, Y., McBride, R. B., Bederson, J., Donovan, M., Sebra, R., Fowkes, M., Umphlett, M. & Shrivastava, R. K., Feb 2022, In: Neurosurgical Focus. 52, 2, E7.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation
Gibson, W. S., Rodriguez, O. L., Shields, K., Silver, C. A., Dorgham, A., Emery, M., Deikus, G., Sebra, R., Eichler, E. E., Bashir, A., Smith, M. L. & Watson, C. T., 2022, (Accepted/In press) In: Genes and Immunity.Research output: Contribution to journal › Article › peer-review
-
Correction: High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy (Acta Neuropathologica Communications, (2022), 10, 1, (149), 10.1186/s40478-022-01453-1)
Pai, B., Tome‑Garcia, J., Cheng, W. S., Nudelman, G., Beaumont, K. G., Ghatan, S., Panov, F., Caballero, E., Sarpong, K., Marcuse, L., Yoo, J., Jiang, Y., Schaefer, A., Akbarian, S., Sebra, R., Pinto, D., Zaslavsky, E. & Tsankova, N. M., Dec 2022, In: Acta neuropathologica communications. 10, 1, 171.Research output: Contribution to journal › Comment/debate
Open Access -
Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution
Kong, Y., Cao, L., Deikus, G., Fan, Y., Mead, E. A., Lai, W., Zhang, Y., Yong, R., Sebra, R., Wang, H., Zhang, X. S. & Fang, G., 4 Feb 2022, In: Science. 375, 6580, p. 515-522 8 p., A26.Research output: Contribution to journal › Article › peer-review
17 Scopus citations -
Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Zhang, Y., Blomquist, T. M., Kusko, R., Stetson, D., Zhang, Z., Yin, L., Sebra, R., Gong, B., Lococo, J. S., Mittal, V. K., Novoradovskaya, N., Yeo, J. Y., Dominiak, N., Hipp, J., Raymond, A., Qiu, F., Arib, H., Smith, M. L., Brock, J. E., Farkas, D. H., & 15 others , Dec 2022, In: Genome Biology. 23, 1, 141.Research output: Contribution to journal › Article › peer-review
Open Access -
Dissecting mechanisms of chamber-specific cardiac differentiation and its perturbation following retinoic acid exposure
Gonzalez, D. M., Schrode, N., Ebrahim, T. A. M., Broguiere, N., Rossi, G., Drakhlis, L., Zweigerdt, R., Lutolf, M. P., Beaumont, K. G., Sebra, R. & Dubois, N. C., 1 Jul 2022, In: Development (Cambridge). 149, 13Research output: Contribution to journal › Article › peer-review
Open Access -
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative
Butler-Laporte, G., Povysil, G., Kosmicki, J. A., Cirulli, E. T., Drivas, T., Furini, S., Saad, C., Schmidt, A., Olszewski, P., Korotko, U., Quinodoz, M., Çelik, E., Kundu, K., Walter, K., Jung, J., Stockwell, A. D., Sloofman, L. G., Jordan, D. M., Thompson, R. C., Del Valle, D., & 139 others , 3 Nov 2022, In: PLoS Genetics. 18, 11, e1010367.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations
Press / Media
-
Oncoscience | Association between tumor mutations and meningioma recurrence in Grade I/II disease
Corey Gill, Daniel Ranti, Michael Donovan, Raj Shrivastava,, Robert Sebra, Joshua Bederson & Yayoi Kinoshita
17/01/23 → 18/01/23
2 items of Media coverage
Press/Media
-
Researchers from Icahn School of Medicine at Mount Sinai Describe Findings in Meningeal Neoplasms (Nf2 Mutations Are Associated With Resistance To Radiation Therapy for Grade 2 and Grade 3 Recurrent Meningiomas)
Corey Gill, Michael Donovan, Raj Shrivastava,, Robert Sebra, Joshua Bederson & Yayoi Kinoshita
30/12/22
1 item of Media coverage
Press/Media
-
Molecular Changes Linked to Long COVID a Year After Hospitalization
Noam Beckmann, Aviva Goel, Lauren Lepow, Kai Nie, Seunghee Kim-Schulze, Girish Nadkarni, Eric Schadt, Robert Sebra, Panagiotis Roussos, Benjamin Glicksberg, Laura Huckins, Alexander Charney, Sacha Gnjatic & Gabriel Hoffman
23/12/22
1 item of Media coverage
Press/Media
-
Investigators at Icahn School of Medicine at Mount Sinai Report Findings in Meningeal Neoplasms (Arid1a Mutation Associated With Recurrence and Shorter Progression-free Survival In Atypical Meningiomas)
Corey Gill, Michael Donovan, Raj Shrivastava,, Robert Sebra, Joshua Bederson & Yayoi Kinoshita
13/12/22
1 item of Media coverage
Press/Media
-
Data on Chronic Obstructive Pulmonary Disease Detailed by a Researcher at Icahn School of Medicine at Mount Sinai (Hedgehog-interacting protein acts in the habenula to regulate nicotine intake)
Mary Heyer, ALEXANDER SMITH , Alexandra DiFeliceantonio, Purva Bali, Paul Kenny, Robert Sebra & Jessica Ables
29/11/22
1 item of Media coverage
Press/Media
-
Report Summarizes Temporal Lobe Epilepsy Study Findings from Icahn School of Medicine at Mount Sinai (High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy)
Fedor Panov, , Robert Sebra, Schahram Akbarian, Elena Zaslavsky, Anne Schaefer, Dalila Pinto, Lara Marcuse, Nadejda Tsankova & Saadi Ghatan,
11/11/22
1 item of Media coverage
Press/Media
-
PacBio Launches Single-Cell Transcriptome Solution Ushering in a New Era of RNA Discovery28 October 2022
28/10/22
1 item of Media coverage
Press/Media
-
Pacbio Launches Single-Cell Transcriptome Solution Ushering In A New Era Of RNA Discovery'
20/10/22
121 items of Media coverage
Press/Media
-
A first update on mapping the human genetic architecture of COVID-19 - Nature
Noam Beckmann, Daniel M. Jordan, Kumardeep Chaudhary, Michael Preuß, Pamela Sklar, Girish Nadkarni, Eimear Kenny, Robert Sebra, Ron Do, Laura Huckins, Noura Abul-Husn, Alexander Charney, Yuval Itan, Joseph Buxbaum, Paul O'Reilly & Clive Hoggart
3/08/22
1 item of Media coverage
Press/Media
-
Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR - Nature Biotechnology
Jocelyn Harris, William Marsiglia, Manishkumar Patel, Kai Nie, Seunghee Kim-Schulze, Robert Sebra, Florian Krammer,, Jordi Ochando, Sacha Gnjatic, Ivan Marazzi,, Ernesto Guccione, Arvin Dar, Megan Schwarz & Denis Torre
6/07/22
1 item of Media coverage
Press/Media
-
Are Scientists Being Fooled by Bacteria?
Gang Fang, Yimeng Kong, Yizhou Zhang,, Robert Sebra, Raymund Yong, & Gintaras Deikus
3/02/22 → 4/02/22
10 items of Media coverage
Press/Media
-
Cutting-edge molecular tools reveal potential COVID-19 diagnostic and therapeutic targets
Elisabet Pujadas, Nadine Schrode & Robert Sebra
11/11/21 → 17/11/21
6 items of Media coverage
Press/Media