Publications

We greatly appreciate acknowledgement of the Genomics Core Facility and/or personnel in publications and grant applications, specifically if any equipment, services, expertise, and/or data were used or generated by the Core. We are always thrilled to be co-authors too if Core personnel were considered to have been involved significantly in experimental design, data analysis and interpretation, or during manuscript writing.

Acknowledge the facility as: “NYU Center for Genomics and Systems Biology Genomics Core”

Once published, please send us a PDF or link to the paper for our records

2019

Jackson, C. A., Castro, D. M., Saldi, G. A., Bonneau, R., & Gresham, D. (2019). Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. BioRxiv, 581678.

2018

Hackley, C. R., Mazzoni, E. O., & Blau, J. (2018). cAMPr: A single-wavelength fluorescent sensor for cyclic AMP. Sci. Signal., 11(520), eaah3738.
Miller, D., Brandt, N., & Gresham, D. (2018). Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen .PLoS genetics, 14(5), e1007406.
Wang, W., Racioppi, C., Gravez, B., & Christiaen, L. (2018). Purification of fluorescent labeled cells from dissociated ciona embryos. In Transgenic Ascidians (pp. 101-107). Springer, Singapore.
Hong, J., Brandt, N., Abdul-Rahman, F., Yang, A., Hughes, T., & Gresham, D. (2018). An incoherent feedforward loop facilitates adaptive tuning of gene expression. Elife, 7, e32323.

2017

Hong, J., & Gresham, D. (2017). Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing. BioTechniques, 63(5), 221-226.
Gandhi, S., Haeussler, M., Razy-Krajka, F., Christiaen, L., & Stolfi, A. (2017). Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. Developmental biology, 425(1), 8-20.
Velasco, S., Ibrahim, M. M., Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M. A., … & Mahony, S. (2017). A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells. Cell Stem Cell, 20(2), 205-217.
Ziv, N., Shuster, B. M., Siegal, M. L., & Gresham, D. (2017). Resolving the complex genetic basis of phenotypic variation and variability of cellular growth. Genetics, 206(3), 1645-1657.

2016

Bik, H. M., Maritz, J. M., Luong, A., Shin, H., Dominguez-Bello, M. G., & Carlton, J. M. (2016). Microbial community patterns associated with automated teller machine keypads in New York City. mSphere, 1(6), e00226-16.
Efroni, I., Mello, A., Nawy, T., Ip, P. L., Rahni, R., DelRose, N., … & Birnbaum, K. D. (2016). Root regeneration triggers an embryo-like sequence guided by hormonal interactions. Cell, 165(7), 1721-1733.
Rao, P. N., Uplekar, S., Kayal, S., Mallick, P. K., Bandyopadhyay, N., Kale, S., … & Carlton, J. M. (2016). A method for amplicon deep sequencing of drug resistance genes in Plasmodium falciparum clinical isolates from India. Journal of clinical microbiology, 54(6), 1500-1511.
Gandhi, S., Christiaen, L., & Stolfi, A. (2016). Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona. bioRxiv, 041632.

2015

Sun, X., Huang, L., Markowitz, T. E., Blitzblau, H. G., Chen, D., Klein, F., & Hochwagen, A. (2015). Transcription dynamically patterns the meiotic chromosome-axis interface. Elife, 4, e07424.
Narendra, V., Rocha, P. P., An, D., Raviram, R., Skok, J. A., Mazzoni, E. O., & Reinberg, D. (2015). CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science, 347(6225), 1017-1021.
Kramer, M., Kranz, A. L., Su, A., Winterkorn, L. H., Albritton, S. E., & Ercan, S. (2015). Developmental dynamics of X-chromosome dosage compensation by the DCC and H4K20me1 in C. elegans. PLoS genetics, 11(12), e1005698.
Albritton, S. E., Kranz, A. L., Rao, P., Kramer, M., Dieterich, C., & Ercan, S. (2014). Sex-biased gene expression and evolution of the X chromosome in nematodes. Genetics, 197(3), 865-883.

2014

Stolfi, A., Lowe, E. K., Racioppi, C., Ristoratore, F., Brown, C. T., Swalla, B. J., & Christiaen, L. (2014). Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians. Elife, 3, e03728.
Xu, Z., Chen, H., Ling, J., Yu, D., Struffi, P., & Small, S. (2014). Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila. Genes & development, 28(6), 608-621.

2013

Kranz, A. L., Jiao, C. Y., Winterkorn, L. H., Albritton, S. E., Kramer, M., & Ercan, S. (2013). Genome-wide analysis of condensin binding in Caenorhabditis elegans. Genome biology, 14(10), R112.