New York University School of Medicine

Contact Info:

Brianna Alvarez

New York, NY 10016

https://med.nyu.edu/research/scientific-cores-shared-resources/genome-technology-center

Grants and Identifiers:

RRID: RRID:SCR_017929

Instrumentation:

Services Provided:

DNA Analysis

Genomics

Microarray

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Relevant Publications:

1.) Assis BA, Sullivan AP, Marciniak S, Bergey CM, Garcia V, Szpiech ZA, Langkilde T, Perry GH (2025 Jan 2). Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants. Nature communications, 16(1), 89. . PMID: 39746982.

2.) Barcia Durán JG, Das D, Gildea M, Amadori L, Gourvest M, Kaur R, Eberhardt N, Smyrnis P, Cilhoroz B, Sajja S, Rahman K, Fernandez DM, Faries P, Narula N, Vanguri R, Goldberg IJ, Fisher EA, Berger JS, Moore KJ, Giannarelli C (2024 Dec). Immune checkpoint landscape of human atherosclerosis and influence of cardiometabolic factors. Nature cardiovascular research, 3(12), 1482-1502. . PMID: 39613875.

3.) Goldberg GW, Kogenaru M, Keegan S, Haase MAB, Kagermazova L, Arias MA, Onyebeke K, Adams S, Beyer DK, Fenyö D, Noyes MB, Boeke JD (2024 Nov 27). Engineered transcription-associated Cas9 targeting in eukaryotic cells. Nature communications, 15(1), 10287. . PMID: 39604381.

4.) Marsman G, Zheng X, Čerina D, Lacey KA, Liu M, Humme D, Goosmann C, Brinkmann V, Harbort CJ, Torres VJ, Zychlinsky A (2024 Nov 26). Histone H1 kills MRSA. Cell reports, 43(11), 114969. doi: 10.1016/j.celrep.2024.114969. PMID: 39546397.

5.) Mankiewicz Ledins P, Lin EZ, Bhattacharya C, Pollitt KJG, Dyson AH, Hénaff EM (2024 Oct 11). A deployable film method to enable replicable sampling of low-abundance environmental microbiomes. Scientific reports, 14(1), 23857. . PMID: 39394219.

6.) Mays JC, Mei S, Kogenaru M, Quysbertf HM, Bosco N, Zhao X, Bianchi JJ, Goldberg A, Kidiyoor GR, Holt LJ, Fenyö D, Davoli T (2024 Sep 29). KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells. bioRxiv : the preprint server for biology, (), . . PMID: 39386620.

7.) Chang SH, Mezzano-Robinson V, Zhou H, Moreira A, Pillai R, Ramaswami S, Loomis C, Heguy A, Tsirigos A, Pass HI (2024 Sep). Digital spatial profiling to predict recurrence in grade 3 stage I lung adenocarcinoma. The Journal of thoracic and cardiovascular surgery, 168(3), 648-657.e8. doi: 10.1016/j.jtcvs.2023.10.047. PMID: 37890657.

8.) Molenaars M, Mir H, Alvarez SW, Arivazhagan L, Rosselot C, Zhan D, Park CY, Garcia-Ocana A, Schmidt AM, Possemato R (2024 Aug 19). Acute inhibition of iron-sulfur cluster biosynthesis disrupts metabolic flexibility in mice. bioRxiv : the preprint server for biology, (), . . PMID: 39229169.

9.) Wang H, Bollepogu Raja KK, Yeung K, Morrison CA, Terrizzano A, Khodadadi-Jamayran A, Chen P, Jordan A, Fritsch C, Sprecher SG, Mardon G, Treisman JE (2024 Aug 17). Synergistic activation by Glass and Pointed promotes neuronal identity in the Drosophila eye disc. Nature communications, 15(1), 7091. . PMID: 39154080.

10.) Samper N, Harðardóttir L, Depierreux DM, Song SC, Nakazawa A, Gando I, Nakamura TY, Sharkey AM, Nowosad CR, Feske S, Colucci F, Coetzee WA (2024 Aug 14). Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development. bioRxiv : the preprint server for biology, (), . . PMID: 39211194.

11.) Fu L, Upadhyay R, Pokrovskii M, Romero-Meza G, Griesemer A, Littman DR (2024 Jul 25). RORγt-dependent antigen-presenting cells direct regulatory T cell-mediated tolerance to food antigen. bioRxiv : the preprint server for biology, (), . . PMID: 39091750.

12.) Wilson ML, Romano SN, Khatri N, Aharon D, Liu Y, Kaufman OH, Draper BW, Marlow FL (2024 Jun 19). Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios. Nature communications, 15(1), 5248. . PMID: 38898112.

13.) Goehring L, Keegan S, Lahiri S, Xia W, Kong M, Jimenez-Sainz J, Gupta D, Drapkin R, Jensen RB, Smith DJ, Rothenberg E, Fenyö D, Huang TT (2024 Jun 3). Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency. Nature communications, 15(1), 4716. . PMID: 38830843.

14.) Blum JE, Kong R, Schulman EA, Chen FM, Upadhyay R, Romero-Meza G, Littman DR, Fischbach MA, Nagashima K, Sattely ES (2024 May 29). Discovery and characterization of dietary antigens in oral tolerance bioRxiv, (), 2024.05.26.593976. . PMCID: 11160622.

15.) Zhou C, Pawline MB, Pironti A, Morales SM, Perault AI, Ulrich RJ, Podkowik M, Lejeune A, DuMont A, Stubbe FX, Korman A, Jones DR, Schluter J, Richardson AR, Fey PD, Drlica K, Cadwell K, Torres VJ, Shopsin B (2024 May 11). Microbiota and metabolic adaptation shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization. bioRxiv : the preprint server for biology, (), . . PMID: 38766195.

16.) Ulrich RJ, Podkowik M, Tierce R, Irnov I, Putzel G, Samhadaneh N, Lacey KA, Boff D, Morales SM, Makita S, Karagounis TK, Zwack EE, Zhou C, Kim R, Drlica K, Pironti A, van Bakel H, Torres VJ, Shopsin B (2024 Apr 17). Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus bioRxiv, (), 2024.04.17.589803. . PMCID: 11042277.

17.) Li AH, Park SY, Li P, Zhou C, Kluz T, Li J, Costa M, Sun H (2024 Feb 1). Transcriptome Analysis Reveals Anti-Cancer Effects of Isorhapontigenin (ISO) on Highly Invasive Human T24 Bladder Cancer Cells. International journal of molecular sciences, 25(3), . . PMID: 38339062.

18.) Calderon A, Mestvirishvili T, Boccalatte F, Ruggles KV, David G (2024 Jan 23). Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells. Epigenetics & chromatin, 17(1), 2. . PMID: 38254205.

19.) Martin MF, Bonaventure B, McCray NE, Peersen OB, Rozen-Gagnon K, Stapleford KA (2024 Jan 15). Distinct chikungunya virus polymerase palm subdomains contribute to virus replication and virion assembly. bioRxiv : the preprint server for biology, (), . . PMID: 38293111.

20.) Zhang W, Golynker I, Brosh R, Fajardo A, Zhu Y, Wudzinska AM, Ordoñez R, Ribeiro-Dos-Santos AM, Carrau L, Damani-Yokota P, Yeung ST, Khairallah C, Vela Gartner A, Chalhoub N, Huang E, Ashe HJ, Khanna KM, Maurano MT, Kim SY, tenOever BR, Boeke JD (2023 Nov). Mouse genome rewriting and tailoring of three important disease loci. Nature, 623(7986), 423-431. . PMID: 37914927.

21.) Mitra A, Thompson B, Strange A, Amato CM, Vassallo M, Dolgalev I, Hester-McCullough J, Muramatsu T, Kimono D, Puranik AS, Weber JS, Woods D (2023 Oct 13). A Population of Tumor-Infiltrating CD4+ T Cells Co-Expressing CD38 and CD39 Is Associated with Checkpoint Inhibitor Resistance. Clinical cancer research : an official journal of the American Association for Cancer Research, 29(20), 4242-4255. . PMID: 37505479.

22.) Noval MG, Spector SN, Bartnicki E, Izzo F, Narula N, Yeung ST, Damani-Yokota P, Dewan MZ, Mezzano V, Rodriguez-Rodriguez BA, Loomis C, Khanna KM, Stapleford KA (2023 Aug 3). MAVS signaling is required for preventing persistent chikungunya heart infection and chronic vascular tissue inflammation. Nature communications, 14(1), 4668. . PMID: 37537212.

23.) Frazel PW, Fricano-Kugler K, May-Zhang AA, O'Dea MR, Prakash P, Desmet NM, Lee H, Meltzer RH, Fontanez KM, Hettige P, Agam Y, Lithwick-Yanai G, Lipson D, Luikart BW, Dasen JD, Liddelow SA (2023 Jul 18). Single-cell analysis of the nervous system at small and large scales with instant partitions. bioRxiv : the preprint server for biology, (), . . PMID: 37503160.

24.) Glytsou C, Chen X, Zacharioudakis E, Al-Santli W, Zhou H, Nadorp B, Lee S, Lasry A, Sun Z, Papaioannou D, Cammer M, Wang K, Zal T, Zal MA, Carter BZ, Ishizawa J, Tibes R, Tsirigos A, Andreeff M, Gavathiotis E, Aifantis I (2023 Jul 7). Mitophagy Promotes Resistance to BH3 Mimetics in Acute Myeloid Leukemia. Cancer discovery, 13(7), 1656-1677. . PMID: 37088914.

25.) Tu NH, Inoue K, Lewis PK, Khan A, Hwang JH, Chokshi V, Dabovic BB, Selvaraj S, Bhattacharya A, Dubeykovskaya Z, Pinkerton NM, Bunnett NW, Loomis CA, Albertson DG, Schmidt BL (2023 Jun 21). Calcitonin Related Polypeptide Alpha Mediates Oral Cancer Pain Cells, 12(13), 1675. . PMCID: 10341289.

26.) MacRae MR, Puvanendran D, Haase MAB, Coudray N, Kolich L, Lam C, Baek M, Bhabha G, Ekiert DC (2023 Jun). Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning. The Journal of biological chemistry, 299(6), 104744. . PMID: 37100290.

27.) Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, Rodriguez Hernaez J, Lee S, Cervantes KS, Hinkley MM, Ntatsoulis K, Cesarano A, Hockemeyer K, Haining WN, Witkowski MT, Qi J, Tsirigos A, Perna F, Aifantis I, Kadoch C (2023 Apr 20). Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion. Molecular cell, 83(8), 1216-1236.e12. . PMID: 36944333.

28.) Steele MM, Jaiswal A, Delclaux I, Dryg ID, Murugan D, Femel J, Son S, du Bois H, Hill C, Leachman SA, Chang YH, Coussens LM, Anandasabapathy N, Lund AW (2023 Apr). T cell egress via lymphatic vessels is tuned by antigen encounter and limits tumor control. Nature immunology, 24(4), 664-675. . PMID: 36849745.

29.) Calderon A, Mestvirishvili T, Boccalatte F, Ruggles K, David G (2023 Mar 18). The Sin3B chromatin modifier restricts cell cycle progression to dictate hematopoietic stem cell differentiation. bioRxiv : the preprint server for biology, (), . . PMID: 36747851.

30.) Heim TA, Lin Z, Steele MM, Mudianto T, Lund AW (2023 Feb 15). CXCR6 promotes dermal CD8(+) T cell survival and transition to long-term tissue residence. bioRxiv : the preprint server for biology, (), . . PMID: 36824892.

31.) Dutheil S, Watson LS, Davis RE, Snyder GL (2023 Feb 1). Lumateperone Normalizes Pathological Levels of Acute Inflammation through Important Pathways Known to Be Involved in Mood Regulation. The Journal of neuroscience : the official journal of the Society for Neuroscience, 43(5), 863-877. . PMID: 36549907.

32.) Oluwadare J, Cabodevilla AG, Son NH, Hu Y, Mullick AE, Verano M, Alemán JO, Ramasamy R, Goldberg IJ (2022 Nov). Blocking Lipid Uptake Pathways Does not Prevent Toxicity in Adipose Triglyceride Lipase (ATGL) Deficiency. Journal of lipid research, 63(11), 100274. . PMID: 36115595.

33.) Wang YH, Noyer L, Kahlfuss S, Raphael D, Tao AY, Kaufmann U, Zhu J, Mitchell-Flack M, Sidhu I, Zhou F, Vaeth M, Thomas PG, Saunders SP, Stauderman K, Curotto de Lafaille MA, Feske S (2022 Oct 7). Distinct roles of ORAI1 in T cell-mediated allergic airway inflammation and immunity to influenza A virus infection. Science advances, 8(40), eabn6552. . PMID: 36206339.

34.) Cheng P, Zhao X, Katsnelson L, Camacho-Hernandez EM, Mermerian A, Mays JC, Lippman SM, Rosales-Alvarez RE, Moya R, Shwetar J, Grun D, Fenyo D, Davoli T (2022 Sep 21). Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways eLife, 11(), e75227. . PMCID: 9491860.

35.) Coleman KE, Yin Y, Lui SKL, Keegan S, Fenyo D, Smith DJ, Rothenberg E, Huang TT (2022 Apr 1). USP1-trapping lesions as a source of DNA replication stress and genomic instability. Nature communications, 13(1), 1740. doi: 10.1038/s41467-022-29369-3. PMID: 35365626.

36.) Hu HL, Srinivas KP, Wang S, Chao MV, Lionnet T, Mohr I, Wilson AC, Depledge DP, Huang TT (2022 Feb 3). Single-cell transcriptomics identifies Gadd45b as a regulator of herpesvirus-reactivating neurons. EMBO reports, 23(2), e53543. doi: 10.15252/embr.202153543. PMID: 34842321.

37.) Huang HW, Ryoo HD (2021 Oct). Drosophila fabp is required for light-dependent Rhodopsin-1 clearance and photoreceptor survival. PLoS genetics, 17(10), e1009551. doi: 10.1371/journal.pgen.1009551. PMID: 34714826.

38.) Pankiewicz JE, Lizińczyk AM, Franco LA, Diaz JR, Martá-Ariza M, Sadowski MJ (2021 Sep 26). Absence of Apolipoprotein E is associated with exacerbation of prion pathology and promotes microglial neurodegenerative phenotype. Acta neuropathologica communications, 9(1), 157. doi: 10.1186/s40478-021-01261-z. PMID: 34565486.

39.) Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I (2021 Jul 1). Targeting the m⁶A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes & development, 35(13), 1005-1019. . PMID: 34168039.

40.) Rubio RM, Depledge DP, Bianco C, Thompson L, Mohr I (2018 Dec 1). RNA m⁶ A modification enzymes shape innate responses to DNA by regulating interferon β. Genes & development, 32(23), 1472-1484. . PMID: 30463905.

Description:

NYULMC's Genome Technology Center provides an environment that facilitates crosstalk between researchers from different fields such as biology, chemistry and bioinformatics. The NYULMC Genome Technology Center provides access to highly specialized equipment and unique expertise, including: 1. high-throughput genomic and computational methodologies, such as gene and microRNA expression profiling and functional genomics experiments (protein:chromatin DNA interactions) 2. genome-wide array- and quantitative PCR-based expression profiling 3. high-capacity chromatin structure studies (ChIP-on-chip) 4. DNA analyses (whole genome SNP genotyping, high-resolution chromosome copy number analysis, high-capacity quantitative PCR and pyrosequencing) 5. consultations and 1-on-1 assistance with issues of experimental design 6. storage, annotation, processing, and analysis of data 7. educational activities to assist the user community with various aspects of genomics, bioinformatics and other fields of modern biology