Selected Publications

  • Hawkins S, Mondaini A, Namboori SC, Nguyen GG, Yeo GW, Javed A, Bhinge A. “ePRINT: exonuclease assisted mapping of protein-RNA interactions.” Genome Biology, 25, 140, May 2024. DOI: https://doi.org/10.1186/s13059-024-03271-1

  • Ganssauge J, Hawkins S, Namboori SC, Leung SK, Mill J, Bhinge A. “Rapid and Inducible Mislocalization of Endogenous TDP43 in a Novel Human Model of Amyotrophic Lateral Sclerosis.” eLife, 2024. DOI: https://doi.org/10.7554/eLife.95062.1

  • Hawkins S, Namboori SC, Tariq A, Blaker C, Flaxman C, Dey NS, Henley P, Randall A, Rosa A, Stanton LW, Bhinge A. “Upregulation of β-catenin due to loss of miR-139 contributes to motor neuron death in Amyotrophic Lateral Sclerosis.” Stem Cell Reports, July 2022. DOI:https://doi.org/10.1016/j.stemcr.2022.05.019

  • Namboori SC, Thomas P, Ames R, Hawkins S, Garrett LO, Willis CRG, Stanton LW, Bhinge A. “Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons.” Stem Cell Reports, 16(12): 3020-3035, Dec 2021. DOI:https://doi.org/10.1016/j.stemcr.2021.10.010

  • Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW. “Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons.” Genome Research. 27(11):1783-1794, Nov 2017. DOI: 10.1101/gr.223313.117

  • *Bhinge, A., Namboori, S. C., Zhang, X., VanDongen, A. M. J.,*Stanton, L. W., “Genetic Correction of SOD1 Mutant iPSCs Reveals ERK and JNK Activated AP1 as a Driver of Neurodegeneration in Amyotrophic Lateral Sclerosis.” Stem cell reports 8, 856-869 (2017).(*co-corresponding author) DOI:https://doi.org/10.1016/j.stemcr.2017.02.019

  • Bhinge, A., Namboori, S. C., Bithell, A., Soldati, C., Buckley, N. J., Stanton, L. W. “MiR-375 is Essential for Human Spinal Motor Neuron Development and May Be Involved in Motor Neuron Degeneration.” Stem cells 34, 124-134 (2016). https://doi.org/10.1002/stem.2233

  • Bhinge, A., Poschmann, J., Namboori, S. C., Tian, X., Jia Hui Loh, S., Traczyk, A., Prabhakar, S., Stanton, L. W. “MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-beta/BMP signaling.” The EMBO journal 33, 1271-1283 (2014). https://doi.org/10.1002/embj.201387215

  • *Polioudakis, D., *Bhinge, A. A., Killion, P. J., Lee, B. K., Abell, N. S., Iyer, V. R.“A Myc-microRNA network promotes exit from quiescence by suppressing the interferon response and cell-cycle arrest genes.” Nucleic acids research 41, 2239-2254 (2013). (*co-first author) https://doi.org/10.1093/nar/gks1452

  • Lee, B. K., Bhinge, A. A., Battenhouse, A., McDaniell, R. M., Liu, Z., Song, L., Ni, Y., Birney, E., Lieb, J. D., Furey, T. S. et al.“Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.” Genome research 22, 9-24 (2012). doi:10.1101/gr.127597.111

  • ENCODE Consortium Project, “An integrated encyclopedia of DNA elements in the human genome.” Nature 489, 57-74 (2012). https://doi.org/10.1038/nature11247

  • Lee, B. K., Bhinge, A. A., Iyer, V. R.“Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis.” Nucleic acids research 39, 3558-3573 (2011). https://doi.org/10.1093/nar/gkq1313

  • ENCODE Consortium Project, “A user's guide to the encyclopedia of DNA elements (ENCODE).” PLoS biology 9, e1001046 (2011). https://doi.org/10.1371/journal.pbio.1001046

  • *Shivaswamy, S., *Bhinge, A., Zhao, Y., Jones, S., Hirst, M., Iyer, V. R., “Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.” PLoS biology 6, e65 (2008). (*co-first author, Selected as a Faculty of 1000 (Biology) article.) https://doi.org/10.1371/journal.pbio.0060065

  • ENCODE Consortium Project, “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.” Nature 447, 799-816 (2007). https://doi.org/10.1038/nature05874

  • Bhinge, A. A., Kim, J., Euskirchen, G. M., Snyder, M., Iyer, V. R., “Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).” Genome research 17, 910-916 (2007). doi:10.1101/gr.5574907

  • Kim, J., Bhinge, A. A., Morgan, X. C., Iyer, V. R., “Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.” Nature methods 2, 47-53 (2005). https://doi.org/10.1038/nmeth726