Recent Work

Lee HH, Kalhor R, Goela N, Bolot J, Church GM. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat Commun. 2019. (on Pubmed; PDF download)

Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM. Developmental barcoding of whole mouse via homing CRISPR. Science. 2018. (on Pubmed; PDF download)

Kalhor R, Mali P, Church GM. Rapidly evolving homing CRISPR barcodes. Nat Methods. 2017. (on Pubmed; PDF download)

Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014. (on Pubmed; PDF download)

Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2012. (on Pubmed; PDF download)

All Papers & Proceedings

2019

  1. Bhan, N., Strutz, J., Kalhor, R., Glaser, J., Kording, K., Church, G., & Tyo, K. (2019). Storing temporal data with minutes resolution into DNA. Abstracts of Papers of the American Chemical Society, 257. American Chemical Society.
  2. Tyo, K., Bhan, N., Strutz, J., Kalhor, R., Glaser, J., Boyden, E., … Church, G. (2019). Recording temporal data with minutes resolution into DNA. Biochemical and Molecular Engineering XXI. [URL]
  3. Lee, H. H., Kalhor, R., Goela, N., Bolot, J., & Church, G. M. (2019). Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nature Communications, 10(1), 1–12. 10.1038/s41467-019-10258-1

2018

  1. Kalhor, R., Kalhor, K., Mejia, L., Leeper, K., Graveline, A., Mali, P., & Church, G. M. (2018). Developmental barcoding of whole mouse via homing CRISPR. Science, 361(6405). 10.1126/science.aat9804
  2. Lee, H. H., Kalhor, R., Goela, N., Bolot, J., & Church, G. M. (2018). Enzymatic DNA synthesis for digital information storage. BioRxiv, 348987. 10.1101/348987

2017

  1. Ostrow, A. Z., Kalhor, R., Gan, Y., Villwock, S. K., Linke, C., Barberis, M., … Aparicio, O. M. (2017). Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae. Proceedings of the National Academy of Sciences, 114(12), E2411–E2419. 10.1073/pnas.1612422114
  2. Kalhor, R., Mali, P., & Church, G. M. (2017). Rapidly evolving homing CRISPR barcodes. Nature Methods, 14(2), 195–200. 10.1038/nmeth.4108

2016

  1. Tjong, H., Li, W., Kalhor, R., Dai, C., Hao, S., Gong, K., … Alber, F. (2016). Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proceedings of the National Academy of Sciences, 113(12), E1663–E1672. 10.1073/pnas.1512577113

2015

  1. Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Ferrante, T. C., Terry, R., … Church, G. M. (2015). Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nature Protocols, 10(3), 442–458. 10.1038/nprot.2014.191

2014

  1. Marblestone, A. H., Daugharthy, E. R., Kalhor, R., Peikon, I. D., Kebschull, J. M., Shipman, S. L., … others. (2014). Rosetta brains: A strategy for molecularly-annotated connectomics. ArXiv Preprint ArXiv:1404.5103.
  2. Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., … Church, G. M. (2014). Highly Multiplexed Subcellular RNA Sequencing in Situ. Science, 343(6177), 1360–1363. 10.1126/science.1250212

2013

  1. Marblestone, A. H., Daugharthy, E. R., Kalhor, R., Peikon, I. D., Kebschull, J. M., Shipman, S. L., … Church, G. M. (2013). Conneconomics: The Economics of Large-Scale Neural Connectomics. BioRxiv, 001214. 10.1101/001214
  2. Marblestone*, A. H., Zamft*, B. M., Maguire, Y. G., Shapiro, M. G., Cybulski, T. R., Glaser, J. I., … Kording**, K. P. (2013). Physical principles for scalable neural recording. Frontiers in Computational Neuroscience, 7. 10.3389/fncom.2013.00137

2012

  1. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2012). Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nature Biotechnology, 30(1), 90–98. 10.1038/nbt.2057

2011

  1. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2011). Solid-phase chromosome conformation capture for structural characterization of genome architectures. Nature Biotechnology, 30(1), 90–98. 10.1038/nbt.2057

2008

  1. Shojaee, S., Sina, F., Banihosseini, S. S., Kazemi, M. H., Kalhor, R., Shahidi, G.-A., … Elahi, E. (2008). Genome-wide Linkage Analysis of a Parkinsonian-Pyramidal Syndrome Pedigree by 500 K SNP Arrays. The American Journal of Human Genetics, 82(6), 1375–1384. 10.1016/j.ajhg.2008.05.005

2006

  1. Elahi, E., Kalhor, R., Banihosseini, S. S., Torabi, N., Pour-Jafari, H., Houshmand, M., … Loeys, B. (2006). Homozygous Missense Mutation in Fibulin-5 in an Iranian Autosomal Recessive Cutis Laxa Pedigree and Associated Haplotype. Journal of Investigative Dermatology, 126(7), 1506–1509. 10.1038/sj.jid.5700247

Patents

2019

  1. Lee, H. H.-yi, Church, G. M., & Kalhor, R. (2019). Enzymatic Nucleic Acid Synthesis. [URL]
  2. Church, G. M., Kalhor, R., & Mali, P. G. (2019). Self-Targeting Guide RNAs in CRISPR System. [URL]
  3. Kalhor, R., Juarez, J. F., Lee, H. H.-yi, & Church, G. M. (2019). Frequency-Based Modulation of Diverse Species in a Nucleic Acid Library. [URL]
  4. Church, G. M., Kalhor, R., & Mali, P. G. (2019). Engineered Guide RNA Sequences for In Situ Detection and Sequencing. [URL]

2014

  1. Wu, C.-ting, & Kalhor, R. (2014). Methods of Hybridizing Probes to Genomic DNA. [URL]

2011

  1. Chen, L., & Kalhor, R. (2011). Genome-wide chromosome conformation capture. [URL]
  2. Chen, L., & Kalhor, R. (2011). Tethered Conformation Capture. [URL]