Publications

All publications, Patents

Select publications

Asami S, Yin C, Garza LA, Kalhor R† (2024). Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues. BioRxiv. 2024.09.24.614640 (PDF)

Handler JS†, Li Z, Dveirin RK, Lin JD, Fang W, Wu S, Forsmo JE, Goodarzi H, Fertig EJ, Kalhor R† (2025). A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception. Cell Reports 44(12):116701 (bioRxiv, PubMed, PDF)

Fang W, Bell CM, Sapirstein A, Asami S, Leeper K, Zack DJ, Ji H†, Kalhor R† (2022). Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. Cell 185(24):4604-4620.e32 (bioRxiv, PubMed, PDF)

Kalhor R†, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM (2018). Developmental barcoding of whole mouse via homing CRISPR. Science 361(6405):eaat9804 (bioRxiv, PubMed, PDF)

All publications

Bold: Kalhor Lab members ＊: Equal contribution †: Corresponding author

  1. Handler JS†, Li Z, Dveirin RK, Lin JD, Fang W, Wu S, Forsmo JE, Goodarzi H, Fertig EJ, Kalhor R† (2025). A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception. Cell Reports 44(12):116701 (bioRxiv, PubMed, PDF)
  2. Islam M, Yang Y, Simmons AJ, Shah VM, Musale KP, Xu Y, Tasneem N, Chen Z, Trinh LT, Molina P, Ramirez-Solano MA, Sadien ID, Dou J, Rolong A, Chen K, Magnuson MA, Rathmell JC, Macara IG, Winton DJ, Liu Q, Zafar H, Kalhor R, Church GM, Shrubsole MJ, Coffey RJ, Lau KS. Temporal recording of mammalian development and precancer. Nature 2024 Oct;634(8036):1187-1195 (bioRxiv, PubMed, PDF).
  3. Asami S, Yin C, Garza LA, Kalhor R† (2024). Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues. BioRxiv 2024.09.24.614640 (PDF)
  4. Lee SS, Sweren E, Dare E, Derr P, Derr K, Wang CC, Hardesty B, Willis AA, Chen J, Vuillier JK, Du J, Wool J, Ruci A, Wang VY, Lee C, Iyengar S, Asami S, Daskam M, Lee C, Lee JC, Cho D, Kim J, Martinez-Peña EG, Lee SM, He X, Wakeman M, Sicilia I, Dobbs DT, van Ee A, Li A, Xue Y, Williams KL, Kirby CS, Kim D, Kim S, Xu L, Wang R, Ferrer M, Chen Y, Kang JU, Kalhor R, Kang S, Garza LA (2024). The use of ectopic volar fibroblasts to modify skin identity. Science 2024 Sep 6;385(6713):eadi1650 (PubMed, PDF)
  5. Callisto A, Strutz J, Leeper K, Kalhor R, Church GM, Tyo KEJ, Bhan N (2024). Post-translation digital data encoding into the genomes of mammalian cell populations. BioRxiv 2024.05.12.591851 (PDF)
  6. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S (2023). Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell 3;83(15):2624-2640 (PubMed, PDF)
  7. Fang W, Bell CM, Sapirstein A, Asami S, Leeper K, Zack DJ, Ji H†, Kalhor R† (2022). Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. Cell 185(24):4604-4620.e32 (bioRxiv, PubMed, PDF)
  8. Zou RS＊, Marin-Gonzalez A＊, Liu Y, Liu HB, Shen L, Dveirin RK, Luo JXJ, Kalhor R, Ha T (2022). Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites Nature Cell Biology. 24(9):1433-1444 (bioRxiv, PubMed, PDF)
  9. Leeper K, Kalhor K, Vernet A, Graveline A, Church GM, Mali P, Kalhor R† (2021). Lineage barcoding in mice with homing CRISPR. Nature Protocols 16(4):2088-2108 (PubMed, PDF)
  10. Bhan N, Callisto A, Strutz J, Glaser J, Kalhor R, Boyden ES, Church G, Kording K, Tyo KEJ (2021). Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis. Journal of American Chemical Society 143(40):16630-16640 (bioRxiv, PubMed, PDF)
  11. Lee HH＊, Kalhor R＊, Goela N＊, Bolot J, Church GM (2019). Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nature Communications 10(1):2383 (bioRxiv, PubMed, PDF)
  12. Kalhor R†, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM (2018). Developmental barcoding of whole mouse via homing CRISPR. Science 361(6405):eaat9804 (bioRxiv, PubMed, PDF)
  13. Ostrow AZ, Kalhor R, Gan Y, Villwock SK, Linke C, Barberis M, Chen L, Aparicio OM (2017). Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae. Proc Natl Acad Sci U S A 114(12):E2411-E2419 (PubMed, PDF)
  14. Kalhor R, Mali P, Church, GM (2017). Rapidly evolving homing CRISPR barcodes. Nature Methods 14(2):195-200 (bioRxiv, PubMed, PDF)
  15. Tjong H, Li W, Kalhor R, Dai C, Hao S, Gong K, Zhou Y, Li H, Zhou XJ, Le Gros MA, Larabell CA, Chen L, Alber F (2016). Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A 113(12):E1663-72 (PubMed, PDF)
  16. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM (2015). Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nature Protocols 10(3):442-58 (PubMed, PDF)
  17. Marblestone AH, Daugharthy ER, Kalhor R, Peikon ID, Kebschull JM, Shipman SL, Mishchenko Y, Lee JH, Kording KP, Boyden ES, Zador AM, Church GM (2014) Rosetta brains: A strategy for molecularly-annotated connectomics. arXiv:1404.5103 (PDF)
  18. 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 (2014). Highly multiplexed subcellular RNA sequencing in situ. Science 343(6177):1360-3 (PubMed, PDF)
  19. Marblestone AH, Daugharthy ER, Kalhor R, Peikon ID, Kebschull JM, Shipman, SL, Mishchenko Y, Lee Jehyuk, Dalrymple DA, Zamft BM, Kording KP, Boyden ES, Zador AM, Church GM (2013). Conneconomics: The Economics of Large-Scale Neural Connectomics. bioRxiv 001214 (PDF)
  20. Marblestone AH, Zamft BM, Maguire YG, Shapiro MG, Cybulski TR, Glaser JI, Amodei D, Stranges PB, Kalhor R, Dalrymple DA, Seo D, Alon E, Maharbiz MM, Carmena JM, Rabaey JM, Boyden ES, Church GM, Kording KP (2013). Physical principles for scalable neural recording. Frontiers in Computational Neuroscience 7:137 (arXiv, PubMed, PDF)
  21. 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):90-8 (PubMed, PDF, Cover Story)
  22. Suri F＊, Kalhor R＊, Zargar SJ, Nilforooshan N, Yazdani S, Nezari H, Paylakhi SH, Narooie-Nejhad M, Bayat B, Sedaghati T, Ahmadian A, Elahi E (2008). Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol. Molecular Vision 14:2349-56 (PubMed, PDF)
  23. Shojaee S, Sina F, Banihosseini SS, Kazemi MH, Kalhor R, Shahidi GA, Fakhrai-Rad H, Ronaghi M, Elahi E (2008). Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays. American Journal of Human Genetics 82(6):1375-84 (PubMed, PDF)
  24. Bates DL, Barthel KK, Wu Y, Kalhor R, Stroud JC, Giffin MJ, Chen L (2008). Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element. Structure 16(5):684-94 (PubMed, PDF)
  25. Alavi A, Elahi E, Tehrani MH, Amoli FA, Javadi MA, Rafati N, Chiani M, Banihosseini SS, Bayat B, Kalhor R, Amini SS (2007). Four mutations (three novel, one founder) in TACSTD2 among Iranian GDLD patients. Invest Ophthalmol Vis Sci 48(10):4490-7 (PubMed, PDF)
  26. Elahi E, Kalhor R, Banihosseini SS, Torabi N, Pour-Jafari H, Houshmand M, Amini SS, Ramezani A, Loeys B (2006). Homozygous missense mutation in fibulin-5 in an Iranian autosomal recessive cutis laxa pedigree and associated haplotype. J Invest Dermatol 126(7):1506-9 (PubMed, PDF)

Patents

Inventors (priority date, publication date) Title (Assignee)

  1. Kalhor R, Jun J, Leeper K (2024, 2025) Methods for high-throughput identification of genomic harbors for transgene expression in biological samples (Johns Hopkins)
  2. Kalhor R, Asami S (2023, 2025) Methods for detecting dna sequence variation in thick tissue sections (Johns Hopkins)
  3. Kalhor R, Forsmo JE (2022, 2024) Methods for intron-driven gene editing and control (Johns Hopkins)
  4. Kalhor R, Asami S (2022, 2024) Methods for detecting rna and molecular analysis in thick tissue sections (Johns Hopkins)
  5. Kalhor R, Lee HH, Church GM (2017, 2020) Enzymatic DNA synthesis using the terminal transferase activity of template-dependent DNA polymerases (Harvard University)
  6. Lee HH, Kalhor R, Church GM (2017, 2019) Methods of encoding and high-throughput decoding of information stored in DNA (Harvard University)
  7. Church GM, Kalhor R, Mali PG (2016, 2019) Engineered guide RNA sequences for in situ detection and sequencing (Harvard University)
  8. Kalhor R, Fernandez Juarez J, Lee HH, Church GM (2016, 2019) Frequency-based modulation of diverse species in a nucleic acid library (Harvard University)
  9. Church GM, Kalhor R, Mali PG (2016, 2019) Self-targeting guide RNAs in CRISPR system (Harvard University)
  10. Kalhor R, Lee HH, Church GM (2016, 2019). Enzymatic nucleic acid synthesis (Harvard University)
  11. Lee HH, Kalhor R, Church GM (2016, 2017) Method of secure communication via nucleotide polymers (Harvard University)
  12. Lee HH, Church GM, Kalhor R (2016, 2017) Enzymatic nucleic acid synthesis (Harvard University)
  13. Wu CT, Kalhor R (2013, 2014) Methods of hybridizing probes to genomic DNA (Harvard University)
  14. Steemers FJ, Gunderson K, Royce T, Pignatelli N, Goryshin IY, Caruccio N, Maffitt M, Jendrisak J, Amini S, Kaper F, Turk C, Kalhor R (2010, 2013) Linking sequence reads using paired code tags (Illumina Inc)
  15. Chen L, Kalhor R (2010, 2011) Tethered conformation capture (University of Southern California)
  16. Chen L, Kalhor R (2008, 2010) Genome-wide chromosome conformation capture (University of Southern California)