Habicher H, Varshney GK, Waldman L, Snitting D, Allalou A, Zhang H, Ghanem A, Ohman C, Tabea D, Kjell L, Burgess SM, Ledin J, Chondroitin/dermatan sulfate glycosyltransferase genes 1 are essential for craniofacial development. PLoS Genetics (In press)
Shin U, Nakhro K, Oh CK, Carrington B, Song H, Varshney GK, Kim Y, Song H, Jeon S, Robbins G, Kim S, Yoon S, Choi YJ, Kim YJ, Burgess S, Kang S, Sood R, Lee Y, Myung K. Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes. DNA Repair (Amst). 2021 Jul 8;107:103173. doi: 10.1016/j.dnarep.2021.103173.
Lin SJ, Vona B, Barbalho PG, Kaiyrzhanov R, Maroofian R, Petree C, Severino M, Stanley V, Varshney P, Bahena P, Alzahrani F, Alhashem A, Pagnamenta AT, Aubertin G, Estrada-Veras JI, Hernández HAD, Mazaheri N, Oza A, Thies J, Renaud DL, Dugad S, McEvoy J, Sultan T, Pais LS, Tabarki B, Villalobos-Ramirez D, Rad A; Genomics England Research Consortium, Galehdari H, Ashrafzadeh F, Sahebzamani A, Saeidi K, Torti E, Elloumi HZ, Mora S, Palculict TB, Yang H, Wren JD, Ben Fowler, Joshi M, Behra M, Burgess SM, Nath SK, Hanna MG, Kenna M, Merritt JL 2nd, Houlden H, Karimiani EG, Zaki MS, Haaf T, Alkuraya FS, Gleeson JG, Varshney GK#. Biallelic variants in KARS1 are associated with neurodevelopmental disorders and hearing loss recapitulated by the knockout zebrafish. Genet Med. 2021 Jun 25. doi: 10.1038/s41436-021-012391.
Singh B, Maiti GP, Zhou X, Fazel-Najafabadi M, Bae SC, Sun C, Terao C, Okada Y, Chua KH, Kochi Y, Guthridge JM, Zhang H, Weirauch M, James JA, Harley JB, Varshney GK, Looger LL, Nath SK. Lupus susceptibility region containing CDKN1B rs34330 mechanistically influences expression and function of multiple target genes, also linked to proliferation and apoptosis. Arthritis Rheumatol. 2021 May 13. doi: 10.1002/art.41799.
Vona B#, Mazaheri N, Lin SJ, Dunbar LA, Maroofian R, Azaiez H, Booth KT, Vitry S, Rad A, Rüschendorf F, Varshney P, Fowler B, Beetz C, Alagramam KN, Murphy D, Shariati G, Sedaghat A, Houlden H, Petree C, VijayKumar S, Smith RJH, Haaf T, El-Amraoui A, Bowl MR#, Varshney GK#, Galehdari H#. A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans. Hum Genet. 2021 Jun;140(6):915-931. doi: 10.1007/s00439-020-02254-z.
Colón-Cruz L, Rodriguez-Morales R, Santana-Cruz A, Cantres-Velez J, Torrado-Tapias A, Lin SJ, Yudowski G, Kensler R, Marie B, Burgess SM, Renaud O, Varshney GK, Behra M. Cnr2 Is Important for Ribbon Synapse Maturation and Function in Hair Cells and Photoreceptors. Front Mol Neurosci. 2021 Apr 20;14:624265. doi:10.3389/ fnmol.2021. 624265.
Ichino N, Serres MR, Urban RM, Urban MD, Treichel AJ, Schaefbauer KJ, Greif LE, Varshney GK, Skuster KJ, McNulty MS, Daby CL, Wang Y, Liao HK, El-Rass S, Ding Y, Liu W, Anderson JL, Wishman MD, Sabharwal A, Schimmenti LA, Sivasubbu S, Balciunas, D, Hammerschmidt M, Farber SA, Wen XY, Xu X, McGrail M, Essner JJ, Burgess SM, Clark KJ, Ekker SC. Building the vertebrate codex using the gene breaking protein trap library. Elife. 2020 Aug 11;9:e54572. doi: 10.7554/eLife.54572.
Wolfstetter G, Pfeifer K, Backman M, Masudi TA, Mendoza-García P, Chen S, Sonnenberg H, Sukumar SK, Uçkun E, Varshney GK, Uv A, Palmer RH. Identification of the Wallenda JNKKK as an Alk suppressor reveals increased competitiveness of Alk-expressing cells. Sci Rep. 2020 Sep 11;10(1):14954. doi: 10.1038/s41598-020-70890-6.
Rodríguez-Morales R, Vélez-Negrón V, Torrado-Tapias A, Varshney G, Behra M. Expression patterns of activating transcription factor 5 (atf5a and atf5b) in zebrafish. Gene Expr Patterns. 2020 Sep; 37:119126. doi: 10.1016/j.gep.2020.119126.
Banote RK, Chebli J, Şatır TM, Varshney GK, Camacho R, Ledin J, Burgess SM, Abramsson A, Zetterberg H. Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish. Sci Rep. 2020 Jun 23;10(1):10127. doi: 10.1038/s41598-020-66584-8.
Petree C, and Varshney GK#. MultiFRAGing: Rapid and Simultaneous Genotyping of Multiple Alleles in a Single Reaction, 2020. Scientific Reports.
Vona B, Doll J, Hofrichter MAH, Haff T, Varshney GK#. Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. 2020. Hearing Research
Yao Q, Wang L, Mittal R, Yan D, Richmond MT, Denyer S, Requena T, Liu K, Varshney GK, Lu Z, Liu X. Transcriptomic Analyses of Inner Ear Sensory Epithelia in Zebrafish. Anat Rec (Hoboken). 2019 Dec 28. doi: 10.1002/ar.24331.
Mahamud MR, Geng X, Ho YC, Cha B, Kim Y, Ma J, Chen L, Myers G, Camper S, Mustacich D, Witte M, Choi D, Hong YK, Chen H, Varshney G, Engel JD, Wang S, Kim TH, Lim KC, Srinivasan RS. GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126. Development. 2019 Oct 3. pii: dev.184218. doi: 10.1242/dev.184218.
Acevedo-Canabal A, Colon-Cruz L, Rodriguez-Morales R, Varshney GK, Burges S, Gonzalez-Sepulveda L, Yukowski G, Behra M. Altered swimming behaviors in zebrafish larvae lacking cannabinoid receptor 2. Cannabis Cannabinoid Research. June 14, 2019;4(2):88-101. PMCID: PMC6590727.
Lui K, Petree C, Requena T, Varshney P, Varshney GK#. Expanding the CRISPR toolbox in zebrafish for studying development and disease. Frontiers in Cell and Developmental Biology. March 4, 2019;7-13. PMCID: PMC6409501.
Pei W, Xu L, Huang SC, Pettie K, Idol J, Rissone A, Jimenez E, Sinclair JW, Slevin C, Varshney GK, Jones M, Carrington B, Bishop K, Huang H, Sood R, Lin S, Burgess SM. Guided genetic screen to identify genes essential in the regeneration of hair cells and other tissues. npj Regenerative Medicine. June 4, 2018;3:11. PMCID: PMC5986822.
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: Genes Genomics Genetics . 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: Genes Genomics Genetics. 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.
# corresponding author
*indicates equal contribution