Watkins-Chow D*, Varshney GK*, Garret L, Chen Z, Jimenez E, Rivas C, Bishop K, Sood R, Harper U, Pavan WJ and Burgess SM, Highly-efficient Cpf1-mediated gene targeting in mice following high concentration pronuclear injection. G3: Genes Genomics Genetics, 2016 * Joint first authors
Pei W, Tanaka K, Huang SC, Xu L, Liu B, Sinclair JW, Idol J, Varshney GK, Huang H, Lin S, Nusssenblatt RB, Mori R, Burgess SM, Extracellular Hsp60 triggers tissue regeneration and wound healing by regulating inflammation and cell proliferation, npj Regenerative Medicine, Article number 16013 (2016). doi:10.1038/npjregenmed.2016.13
Varshney GK*, Carrington B*, Pei W, Bishop K, Chen Z, Xu L, Fan C, Xu L, Jones MP, LaFave M, Ledin J, Sood R, Burgess SM. A High-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish. Nature Protocols 11 2357-2375 (2016)
Varshney GK, Burgess SM. DNA-guided genome editing using structure-guided endonucleases. Genome Biol. 2016 Sep 15;17(1):187. doi:10.1186/s13059-016-1055-4.
Pei W, Xu L, Varshney GK, Carrington B, Bishop K, Jones M, Huang SC, Idol J, Pretorius PR, Beirl A, Schimmenti LA, Kindt KS, Sood R, Burgess SM. Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases. Sci Rep. 2016 Jul 18;6:29946. doi: 10.1038/srep29946.
Varshney GK*, Pei W*, Burgess SM. Using Zebrafish to Study Human Deafness and Hearing Regeneration. Genetics of Deafness. Monograph in Human Genetics. Basel, Karger, 2016, vol 20, pp 110-131
Chandler RJ, LaFave MC, Varshney GK, Burgess SM, Venditti CP. Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy? Molecular Therapy 2016 Feb;24(2):198-201.
Vrljicak P*, Tao S*, Varshney GK*, Quach HN, Joshi A, LaFave MC, Burgess SM, Sampath K6. Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3 (Bethesda). 2016 Jan 27.
Varshney GK, Sood R, Burgess SM. Understanding and Editing the Zebrafish Genome. Advances in Genetics 2015;92:1-52.
Marquart GD, Tabor KM, Brown M, Strykowski JL, Varshney GK, LaFave MC, Mueller T, Burgess SM, Higashijima S, Burgess HA. A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies. Frontiers in Neural Circuits. 2015 Nov 24;9:78.
Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016 Jan 4;44(D1):D822-6.
Carrington B, Varshney GK, Burgess SM, Sood R. CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic Acids Res. 2015 Dec 15;43(22):e157.
Seiler C, Gebhart N, Zhang Y, Shinton SA, Li YS, Ross NL, Liu X, Li Q, Bilbee AN, Varshney GK, LaFave MC, Burgess SM, Balciuniene J, Balciunas D, Hardy RR, Kappes DJ, Wiest DL, Rhodes J. Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Zebrafish. PLoS One. 2015 Jul 10;10(7):e0131908.
LaFave MC, Varshney GK, Burgess SM. GeIST: a pipeline for mapping integrated DNA elements. Bioinformatics. 2015 Oct 1;31(19):3219-21.
Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, Carrington B, Bishop K, Jones M, Li M, Harper U, Huang SC, Prakash A, Chen W, Sood R, Ledin J, Burgess SM1. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 2015 Jul;25(7):1030-42.
Yin L, Maddison LA, Li M, Kara N, LaFave MC, Varshney GK, Burgess SM, Patton JG, Chen W. Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Genetics. 2015 Jun;200(2):431-41.
Quach HN, Tao S, Vrljicak P, Joshi A, Ruan H, Sukumaran R, Varshney GK, LaFave MC; Ds Screen Team, Burgess SM, Winkler C, Emelyanov A, Parinov S, Sampath K. A Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish. G3 (Bethesda). 2015 Apr 2;5(6):1283-99.
Gallardo VE, Varshney GK, Lee M, Bupp S, Xu L, Shinn P, Crawford NP, Inglese J, Burgess SM. Phenotype-driven chemical screening in zebrafish for compounds that inhibit collective cell migration identifies multiple pathways potentially involved in metastatic invasion. Dis Model Mech. 2015 Jun;8(6):565-76.
Chandler RJ, LaFave MC, Varshney GK, Trivedi NS, Carrillo-Carrasco N, Senac JS, Wu W, Hoffmann V, Elkahloun AG, Burgess SM, Venditti CP. Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy. J Clin Invest. 2015 Feb;125(2):870-80.
Walia JS, Altaleb N, Bello A, Kruck C, LaFave MC, Varshney GK, Burgess SM, Chowdhury B, Hurlbut D, Hemming R, Kobinger GP, Triggs-Raine B. Long-term correction of Sandhoff disease following intravenous delivery of rAAV9 to mouse neonates. Molecular Therapy 2015 Mar;23(3):414-22.
LaFave MC, Varshney GK, Vemulapalli M, Mullikin JC, Burgess SM. A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1. Genetics. 2014 Sep;198(1):167-70.
LaFave MC*, Varshney GK*, Gildea DE, Wolfsberg TG, Baxevanis AD, Burgess SM. MLV integration site selection is driven by strong enhancers and active promoters. Nucleic Acids Res. 2014 Apr;42(7):4257-69.
Varshney GK, Burgess SM. Mutagenesis and phenotyping resources in zebrafish for studying development and human disease. Brief Funct Genomics. 2014 Mar;13(2):82-94.
Chen L, Stuart L, Ohsumi TK, Burgess S, Varshney GK, Dastur A, Borowsky M, Benes C, Lacy-Hulbert A, Schmidt EV. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics. BMC Cancer. 2013 Feb 27;13:93.
Varshney GK*, Lu J*, Gildea DE, Huang H, Pei W, Yang Z, Huang SC, Schoenfeld D, Pho NH, Casero D, Hirase T, Mosbrook-Davis D, Zhang S, Jao LE, Zhang B, Woods IG, Zimmerman S, Schier AF, Wolfsberg TG, Pellegrini M, Burgess SM, Lin S. A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome Res. 2013 Apr;23(4):727-35.
Varshney GK, Huang H, Zhang S, Lu J, Gildea DE, Yang Z, Wolfsberg TG, Lin S, Burgess SM. The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion. Nucleic Acids Res. 2013 Jan;41(Database issue):D861-4.
Amsterdam A, Varshney GK, Burgess SM. Retroviral-mediated Insertional Mutagenesis in Zebrafish. Methods Cell Biol. 2011;104:59-82.
*indicates equal contribution