List of publications
[For a full list of publications on Google Scholar, click here]
 | Huang B, Orosco C, Stewart E, Balaraju M, Elhabashy YB, and Jain PK* Guide RNA binding induces reverse transcription bias during RT-qPCR analysis of RNA-targeting CRISPR/Cas systems. bioRxiv. 2026 Aug 17:2026.08.16.745121. [View] [*Corresponding author] |
| Rananaware SR, Shoemaker GM, Pizzano BLM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Flannery SJ, Lange IH, Pedada D, Fang A, Antal SG, Aguilar D, Rakestraw NR, Karalkar VN, Meister KS, Nguyen LT, and Jain PK* Novel CRISPR/Cas systems engineering and discovery. bioRxiv. 2026 Aug 11:2026.08.11.744272. [View] [*Corresponding author] |
 | Orosco C, Huang B, Rananaware SR, Bodin AP, Browning I, Fang A, Baugh MP, Lange IH, Elhabashy YB, Balaraju M, Lewis JG, Shah NH, Hanna MP, Flannery SJ, Meister KS, Karalkar V, and Jain PK* Structure of DNA-guided Cas12. Nature Structural & Molecular Biology. 2026 Aug. [View bioRxiv] [*Corresponding author] [Accepted in principle] |
| Madhavan R, Rananaware SR, Rakestraw NR, Nguyen LT, Maden M, and Jain PK‡ Acomys senescence profiling. bioRxiv. 2026 Jul 07:2026.07.07.737114. [View] [‡Senior author] [Submitted to Cell Reports] |
  | Iyyappan R§, Niu Y§, Li Y, Ming H, Pajdzik K, Rakestraw NR, Jain PK, He C, Zong C*, and Jiang Z* Single-nucleotide RNA m6A mapping in bovine preimplantation development reveals site-specific regulation of RPL12 at zygotic genome activation. Cell Reports. 2026 Jul 6; 45, 117635. [View] [Preprint Listing] [§Equal contributions][*Corresponding authors][‡Senior author] |
  | Rananaware SR, Narisetty KV, Shah RA, and Jain PK* CRISPR-based ex vivo gene editing of donor organs. Nature Reviews Bioengineering. 2026 Jun 29; doi:10.1038/s44222-026-00462-2. [View] [*Corresponding author] |
| Karalkar VN, Rananaware SR, Pedada D, Lewis JG, Bodin AP, and Jain PK* TAMIPAMI: A computational pipeline and software tool for CRISPR PAM and target discovery. bioRxiv. 2026 May 15:2026.05.15.725432. [View] [*Corresponding author] [Submitted to The CRISPR Journal] |
  | Orosco C§, Huang B§, Rananaware SR§, Bodin AP, Browning I, Fang A, Baugh MP, Lange IH, Elhabashy YB, Balaraju M, Lewis JG, Shah NH, Hanna MP, Flannery SJ, Meister KS, Karalkar V, and Jain PK* DNA-guided CRISPR–Cas12 for cellular RNA targeting. Nature Biotechnology. 2026 May 15; doi:10.1038/s41587-026-03129-w. [View] [Preprint Listing] [§Equal contributions][*Corresponding author] |
  | Nguyen LT§, Rakestraw NR§, Pizzano BLM, Iyyappan R, Young CB, Huang Y, Beerensson KT, Fang A, Antal SG, Anamisis KV, Peggs CMD, Yan J, Jing Y, Lewis JG, Burdine RD, Adamson B, Jiang Z, Toettcher JE, Myhrvold C*, and Jain PK* Efficient genome editing with chimeric oligonucleotide-directed editing. Nature Communications. 2026 Apr 13; 17, 71624. [View] [Preprint Listing] [§Equal contributions][*Corresponding authors] |
  | Jia Y, Horvath K, Rananaware SR, Jain PK‡, and Sampath J* Exploring the temperature stability of CRISPR-Cas12b using molecular dynamics simulations. Molecular Systems Design & Engineering. 2026 Feb; 11, 195–204. [View] [Preprint Listing] [‡Senior author] |
  | Rananaware SR, Shoemaker GM, Pizzano BLM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Flannery SJ, Lange IH, Pedada D, Fang A, Antal SG, Aguilar D, Rakestraw NR, Karalkar VN, Meister KS, Nguyen LT, and Jain PK* AsCas12a tolerates insertions in target DNA. Nucleic Acids Res. 2025 Sep 23;53(17). [View] [*Corresponding author] |
| Iyyappan R§, Niu Y§, Hao M, Pajdzik K, Rakestraw NR, Jain PK, He C, Zong C*, and Jiang Z* Single-nucleotide resolution epitranscriptomic profiling uncovers dynamic m6A regulation in bovine preimplantation development. bioRxiv. 2025 Jul 10:2025-07. [View] [§Equal contributions][*Corresponding authors] |
 | Orosco C§, Rananaware SR§, Huang B, Hanna MP, Ahmadimashhadi MR, Lewis JG, Baugh MP, Bodin AP, Flannery SJ, Lange IH, Fang ZR, Karalkar VN, Meister KS, and Jain PK* DNA-guided CRISPR/Cas12 for RNA targeting. medRxiv. 2024 Nov 21:2024-11. [View] [§Equal contributions][*Corresponding author] |
 | Jia Y, Horvath K, Rananaware SR, Jain PK, and Sampath J Exploring the thermostability of CRISPR–Cas12b using molecular dynamics simulations. arXiv. 2024 Aug 20:2408.11149v1. [View] |
 | Nguyen LT§, Rakestraw NR§, Pizzano BL, Young CB, Huang Y, Beerensson KT, Fang A, Antal SG, Anamiss KV, Peggs CM, Yan J, Jing Y, Burdine RD, Adamson B, Toettcher JE, Myhrvold C*, and Jain PK* Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing. bioRxiv. 2024 Jul 10:2024-07. [View] [§Equal contributions][*Corresponding authors] |
 | Rananaware SR, Meister KS, Shoemaker GM, Vesco EK, Sandoval LS, Lewis JG, Bodin AP, Karalkar VN, Lange IH, Pizzano BL, Chang M, M. Reza Ahmadimashhadi MR, Flannery SJ, Nguyen LT, Wang GP, and Jain PK* PAM-free diagnostics with diverse type V CRISPR-Cas systems. medRxiv. 2024:2024-05. [View] [*Corresponding author] |
| Xun G, Zhu Z, Lu J, Singh N, Jain PK‡, and Zhao H* Harnessing Noncanonical crRNA for Highly Efficient Genome Editing. Nature Communications, 2024, 15, 3823 (2024). https://doi.org/10.1038/s41467-024-48012-x [View]. [‡Senior author] |
 | Nguyen LT, Macaluso NC, Rakestraw NR, Carman DR, Pizzano BLM, Hautamaki RC, and Jain PK* Harnessing Non-canonical crRNAs to Improve Functionality of Cas12a Orthologs. Cell Reports, 2024, 43 (2), doi.org/10.1016/j.celrep.2024.113777. [View] [SSRN-2023][medRxiv-2021] [*Corresponding author] |
 | Rananaware SR, Vesco EK, Shoemaker GM, Anekar SS, Sandoval LSW, Meister KS, Macaluso NC, Nguyen LT, and Jain, PK*, Programmable RNA detection with CRISPR-Cas12a. Nature Communications, 2023, 14 (5409), doi.org/10.1038/s41467-023-41006-1. [View] [Research Square, 2023] [bioRxiv, 2023] [*Corresponding author] |
 | Shashank PR, Parker BM§, Rananaware SR§, Plotkin D, Couch C, Yang LG, Nguyen LT, Prasannakumar NR, Braswell WE, Jain PK‡, and Kawahara AY*, CRISPR-based diagnostics detects invasive insect pest.s Molecular Ecology Resources, 2023, 00, 1–15, doi.org/10.1111/1755-0998.13881. [View] [bioRxiv, 2023][§Equal contributions][‡Senior author] |
  | Nguyen LT§, Rananaware SR§, Yang LG§, Macaluso NC§, Ocana-Ortiz JE, Meister KS, Pizzano BLM, Sandoval LSW, Hautamaki RC, Fang ZR, Joseph SM, Shoemaker GM, Carman DR, Chang L, Rakestraw NR, Zachary JF, Guerra S, Perez A, Jain PK*, Engineering Highly Thermostable Cas12b via De Novo Structural Analyses for One-Pot Detection of Nucleic Acids Cell Reports Medicine, 2023, 4(5), 101037 https://doi.org/10.1016/j.xcrm.2023.101037 [View] [Highlighted on the cover] [medRxiv, 2022] [SSRN, 2023] [*Corresponding author][§Equal contributions] |
  | Shen Y, Khatri B, Rananaware S, Li D, Ostrov DA, Jain PK‡, Lessard CJ, and Nguyen CQ* Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population PLOS One, 2023, https://doi.org/10.1371/journal.pone.0276700 [‡Senior author] [Download pdf] [View] [bioRxiv version-2022] |
 | Wei X, Wang X, Zhang Z, Luo Y, Wang Z, Xiong W, Jain PK‡, Monnier JR, Wang H, Hu TY, Tang C, Albrecht H, and Liu C* A Click Chemistry Amplified Nanopore (CAN) Assay for Ultrasensitive Quantification of HIV p24 Antigen in Clinical Samples Nature Communications, 2022, 13, 6852 https://doi.org/10.1038/s41467-022-34273-x [‡Senior author] |
  | Nguyen, LT, Macaluso N, Pizzano B, Cash M, Spacek J, Karasek J, Miller MR, Lednicky JA, Dinglasan RD, Salemi M, and Jain PK* A Thermostable Cas12b from Brevibacillus Leverages One-pot Discrimination of SARS-CoV-2 Variants of Concern eBioMedicine- THE LANCET, 2022, https://doi.org/10.1016/j.ebiom.2022.103926 [*Corresponding author] [medRxiv] [Preprints with THE LANCET] [Download pdf] [View] |
  | Nguyen, LT, Rananaware SR, Pizzano BLM, Brandon ST, and Jain PK* Clinical validation of engineered CRISPR/Cas12a for rapid SARS-CoV-2 detection. Communications Medicine- Nature, 2022, https://doi.org/10.1038/s43856-021-00066-4 [*Corresponding author] [Download pdf] [View] |
  | Chiu CW, Xian M, Stephany JL, Xia X, Chiang CC, Ren F, Tsai CT, Shan SS, Liao YT, Esquivel-Upshaw JF, Rananaware SR, Nguyen LT, Macaluso NC, Jain PK‡, Cash MN, Mavian CN, Salemi M, Leon ME, Chang CW, Lin J, and Pearton SJ* Rapid SARS-CoV-2 Diagnosis Using Disposable Strips and a Metal-oxide-semiconductor Field-effect Transistor Platform, Journal of Vacuum Science & Technology B, 2022, doi.org/10.1116/6.0001615, 40, 023204. [‡Senior author] [View] [News] |
  | Nguyen LT, Gurijala, J, Rananaware SR, Pizzano BLM, Brandon ST, and Jain PK* CRISPR-ENHANCE: An enhanced nucleic acid detection platform using Cas12a. Methods, 2022, 10.1016/j.ymeth.2021.02.001 [*Corresponding author] [View] |
 | Shen Y, Ostrov DA, Santosh Rananaware SR, Jain PK‡, Nguyen CQ* Identification of risk and protective human leukocyte antigens in COVID-19 using genotyping and structural modeling medRxiv, 2021, https://doi.org/10.1101/2021.05.04.21256636 [‡Senior author] [Download pdf] [View] |
 | Nguyen LT, Smith,BM, Jain PK* Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection Nature Communications, 2020, 11, 4906 [*Corresponding author] [Download pdf] [View] [BioRxiv version] |
| Downing M and Jain PK*, Mesoporous silica nanoparticles: synthesis, properties, and biomedical applications. Nanoparticles for Biomedical Applications, 2019; 267-281, Book Chapter. [*Corresponding author] [View] | |
  | Jain PK*, Lo JH, Rananaware S, Downing M, Panda A, Tai M, Raghavan S, Fleming HE and Bhatia SN*. Non-viral delivery of CRISPR/Cas9 complex using CRISPR-GPS nanocomplexes. Nanoscale, 2019; 11, 21317-21323 [*Co-corresponding author] [Download pdf] [View] |
  | Jain PK, and Friedman SH*. A universal photo-cleavable clickable reagent for the reversible end labeling of any nucleic acid. ChemBioChem, 2018; 19, 1264. [Download pdf] [View] [F1000Prime recommendation] [Very Important Paper][ChemistryViews][Cover] |
 | Jain PK, Ramanan V, Schepers AG, Dalvie N, Panda A, Fleming HE and Bhatia SN*. Development of light-activated CRISPR using photocleavable protectors of guide RNAs. Angewandte Chemie International Edition, 2016; 55, 12440. [Download pdf] [View] [News articles] [Altmetrics] |
  | Sarode BR, Jain PK and Friedman SH*. Polymerizing Insulin with Photocleavable Linkers to Make Light-Sensitive Macropolymer Depot Materials. Macromolecular Bioscience, 2016; 16 (8): 1138-1146. [Download pdf] [View] [Featured on the cover] |
  | Dudani JS, Jain PK, Kwong GA, Stevens KR and Bhatia SN*. Photoactivated Spatiotemporally-Responsive Nanosensors of in Vivo Protease Activity. ACS Nano, 2015; 9(12), 11708-11717. [Download pdf] [View] |
 | Kala A, Jain PK and Friedman SH*. Patterning of cells through patterning of biology. Molecular BioSystems, 2014;10, 1689-1692. [Download pdf] [View] |
  | Kala A, Jain PK, Karunakaran D, Shah S and Friedman SH*. The synthesis of tetra-modified RNA for the multidimensional control of gene expression via light-activated RNA interference. Nature protocols, 2014; 9(1), 11-20. [Download pdf] [View] |
 | Jain PK, Karunakaran D and Friedman SH*. Construction of a Photoactivated Insulin Depot. Angewandte Chemie International Edition, 2013; 52, 1404-1409. [Download pdf] [View] [Featured on the frontispiece] [News articles] |
  | Jain PK, Shah S and Friedman SH*. Patterning of gene expression using new photolabile groups applied to light activated RNAi. Journal of the American Chemical Society, 2011; 133(3), 440-446. [Download pdf] [View] |
| Shah S, Jain PK, Kala A, Karunakaran D and Friedman SH*. Light-activated RNA interference using double-stranded siRNA precursors modified using a remarkable regiospecificity of diazo-based photolabile groups. Nucleic Acids Research, 2009; 37(13), 4508-4517. [Download pdf] [View] [Featured on the cover] |
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