New York University School of Medicine
Brianna Alvarez
New York, NY 10016
https://med.nyu.edu/research/scientific-cores-shared-resources/genome-technology-center
RRID: RRID:SCR_017929
DNA Analysis
Genomics
Microarray
Sequencing - DNA Sequencing
Sequencing - Next Generation Sequencing (NGS)
1.) Wiggins JM, Zhang Q, Zhang Y, Vand-Rajabpour F, Hanniford D, He L, Lu Y, Kenney JM, Sadeghi KD, Argibay D, Orlow I, Busam KJ, Lezcano C, Lee TK, Luo L, Gorlov IP, Amos C, Ernstoff MS, Seshan VE, Cust AE, Wilmott J, Scolyer RA, Mann GJ, Reiner A, Kostrzewa CE, Nagore E, Funchain P, Ko J, Edmiston SN, Conway K, Googe PB, Ollila DW, Lee JE, Rees JR, Thompson CL, Gerstenblith M, Bosenberg M, Gould Rothberg BE, Osman I, Saenger Y, Reynolds AZ, Boyce T, Holmen S, Yan S, Brunsgaard E, Bogner P, Kuan PF (2025 Oct 20). Tumor microRNA signatures associate with stage II/III melanoma patient outcomes Clinical cancer research : an official journal of the American Association for Cancer Research, (), 10.1158/1078-0432.CCR-24-3785. . PMCID: 12588674.
2.) Pucella JN, Maqueda-Alfaro RA, Ni H, Bandeira Sulczewski F, Eichinger A, Esteva E, Ra AC, Das A, Perez OA, Feng J, Stoeckius M, Smibert P, Khodadadi-Jamayran A, Dolgalev I, Ivanova E, Sota S, Cadwell K, Koralov SB, Zhong J, Soni C, Stetson DB, Weisberg SP, Farber DL, Idoyaga J, Reizis B (2025 Oct 14). Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells Nature Immunology, 26(11), 1946-1961. . PMCID: 12662804.
3.) Park SY, Sun H (2025 Oct). Transcriptomic analysis of Cr(VI)-induced changes in C2C12 cells during myogenic differentiation. Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS), 91(), 127714. . PMID: 40803287.
4.) Ibrahim M, Illa-Bochaca I, Jour G, Vega-Saenz de Miera E, Fracasso J, Ruggles K, Osman I, Schober M (2025 Sep 2). NF1 Loss Promotes EGFR Activation and Confers Sensitivity to EGFR Inhibition in NF1-Mutant Melanoma. Cancer research, 85(17), 3348-3364. . PMID: 40494652.
5.) Krishna Prasad GVR, Grigsby SJ, Erkenswick GA, Portal-Celhay C, Mittal E, Yang G, Fallon SM, Chen F, Klevorn T, Jain N, Li Y, Mitreva M, Martinot AJ, Ernst JD, Philips JA (2025 Jul 23). Macrophage-T cell interactions promote SLAMF1 expression for enhanced TB defense. Nature communications, 16(1), 6794. . PMID: 40701970.
6.) Wang L, Noyer L, Jishage M, Wang YH, Tao AY, McDermott M, Gando I, Sidhu I, Hu K, Zhong L, Sun K, Drmic D, Kaufmann U, Feske S (2025 Jun 20). CLNS1A regulates genome stability and cell cycle progression to control CD4 T cell function and autoimmunity. Science immunology, 10(108), eadq8860. . PMID: 40540585.
7.) Fu L, Upadhyay R, Pokrovskii M, Chen FM, Romero-Meza G, Griesemer A, Littman DR (2025 Jun). PRDM16-dependent antigen-presenting cells induce tolerance to gut antigens. Nature, 642(8068), 756-765. . PMID: 40228524.
8.) Laue HE, Willis AD, Wang F, MacDougall MC, Xu Y, Karagas MR, Madan JC, Fleisch AF, Lanphear BP, Cecil KM, Yolton K, Chen A, Buckley JP, Braun JM (2025 May 8). Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study. Genome medicine, 17(1), 50. . PMID: 40340756.
9.) Fathi F, Suek N, Vermette B, Breen K, Saad YS, Bay C, Parks CA, Stern J, Khalil K, Kim J, Jaffe IS, Aljabban I, Novikova E, Severa E, Herati RS, Burdorf L, Griesemer AD, Montgomery RA, Sykes M (2025 Apr 22). Donor-reactive T cells and innate immune cells promote pig-to-human decedent xenograft rejection. Research square, (), . . PMID: 40313748.
10.) Dannebaum R, Mikhaylichenko O, Siegel D, Li C, Hall E, Margeridon S, Herrera M, Loomis K, Riel T, Ramesh M, Gencoglu M, Hendel N, Henriquez A, Dzvova N, Abayan RJ, Lin X, Chavez M, Hanna N (2025 Apr). Digital PCR Assay Utilizing In-Droplet Methylation-Sensitive Digestion for Estimation of Fetal cfDNA From Plasma. Prenatal diagnosis, 45(4), 500-509. . PMID: 40090860.
11.) Santarossa CC, Li Y, Yousef S, Hasdemir HS, Rodriguez CC, Haase MB, Baek M, Coudray N, Pavek JG, Focke KN, Silverberg AL, Bautista C, Yeh J, Marty MT, Baker D, Tajkhorshid E, Ekiert DC, Bhabha G (2025 Mar 22). LetA defines a structurally distinct transporter family involved in lipid trafficking. bioRxiv : the preprint server for biology, (), . . PMID: 40166208.
12.) Zhong L, Wang YH, Kahlfuss S, Jishage M, McDermott M, Yang J, Tao AY, Hu K, Noyer L, Raphael D, Patel D, Knight TE, Chitlur M, Machaca K, Feske S (2025 Mar). STIM1-mediated NFAT signaling synergizes with STAT1 to control T-bet expression and T(H)1 differentiation. Nature immunology, 26(3), 484-496. . PMID: 39984734.
13.) Ghamlouch H, Gagler DC, Blaney P, Boyle EM, Wang Y, Avigan J, Choi J, Landgren O, Tsirigos A, Maura F, Morgan GJ, Davies FE (2025 Feb 26). A proinflammatory response and polarized differentiation of stromal elements characterizes the murine myeloma bone marrow niche. Experimental hematology & oncology, 14(1), 22. . PMID: 40011943.
14.) Gökbuget D, Goehring L, Boileau RM, Lenshoek K, Huang TT, Blelloch R (2025 Feb 25). KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition. Cell reports, 44(2), 115272. . PMID: 39908143.
15.) Son GY, Zou A, Wahl A, Huang KT, Zorgit S, Vinu M, Zhou F, Wagner L, Idaghdour Y, Yule DI, Feske S, Lacruz RS (2025 Feb 12). Loss of STIM1 and STIM2 in Salivary Glands Disrupts ANO1 Function but Does Not Induce Sjogren's Disease. Function (Oxford, England), 6(1), . . PMID: 39479800.
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17.) 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.
18.) 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.
19.) 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.
20.) 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.
21.) 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.
22.) 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.
23.) 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.
24.) 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.
25.) 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.
26.) 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.
27.) 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.
28.) 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.
29.) 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.
30.) 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.
31.) 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.
32.) 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.
33.) 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.
34.) 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.
35.) 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.
36.) 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.
37.) 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.
38.) 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.
39.) 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.
40.) 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.
41.) 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.
42.) 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.
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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
