ZFIN Person: Varshney, Gaurav

ZFIN ID: ZDB-PERS-140303-1

ZFIN ID: ZDB-PERS-140303-1

Varshney, Gaurav

Email:	Gaurav-varshney@omrf.org
URL:	http://varshneylab.omrf.org
Affiliation:	Varshney Lab
Address:	Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation 825 NE 13th Street, Oklahoma City, 73104
Country:
Phone:	405-271-2185
Fax:
ORCID ID:	0000-0002-0429-1904

BIOGRAPHY AND RESEARCH INTERESTS

Umea University, Sweden (Ph.D.)

National Human Genome Research Institute, NIH (Postdoc)

PUBLICATIONS

Lin, S.J., Vona, B., Lau, T., Huang, K., Zaki, M.S., Aldeen, H.S., Karimiani, E.G., Rocca, C., Noureldeen, M.M., Saad, A.K., Petree, C., Bartolomaeus, T., Abou Jamra, R., Zifarelli, G., Gotkhindikar, A., Wentzensen, I.M., Liao, M., Cork, E.E., Varshney, P., Hashemi, N., Mohammadi, M.H., Rad, A., Neira, J., Toosi, M.B., Knopp, C., Kurth, I., Challman, T.D., Smith, R., Abdalla, A., Haaf, T., Suri, M., Joshi, M., Chung, W.K., Moreno-De-Luca, A., Houlden, H., Maroofian, R., Varshney, G.K. (2023) Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15:102102

Accogli, A., Lin, S.J., Severino, M., Kim, S.H., Huang, K., Rocca, C., Landsverk, M., Zaki, M., Al-Maawali, A., Srinivasan, V.M., Al-Thihli, K., Schaefer, G.B., Davis, M., Tonduti, D., Doneda, C., Marten, L.M., Mühlhausen, C., Gomez, M., Lamantea, E., Mena, R., Nizon, M., Procaccio, V., Begtrup, A., Telegrafi, A., Cui, H., Schulz, H.L., Mohr, J., Biskup, S., Loos, M.A., Aráoz, H.V., Salpietro, V., Keppen, L.D., Chitre, M., Petree, C., Raymond, L., Vogt, J., Swayer, L.B., Basinger, A.A., Pedersen, S.V., Pearson, T.S., Grange, D.K., Lingapp, L., McDunnah, P., Horvath, R., Cogne, B., Isidor, B., Hahn, A., Gripp, K., Jafarnejad, S.M., Ostergaard, E., Prada, C.E., Ghezzi, D., Gowda, V.K., Taylor, R.W., Sonenberg, N., Houlden, H., Sissler, M., Varshney, G.K., Maroofian, R. (2023) Clinical, neuroradiological and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genetics in medicine : official journal of the American College of Medical Genetics. 25(11):100938

Calì, E., Lin, S.J., Rocca, C., Sahin, Y., Al Shamsi, A., El Chehadeh, S., Chaabouni, M., Mankad, K., Galanaki, E., Efthymiou, S., Sudhakar, S., Athanasiou-Fragkouli, A., Çelik, T., Narlı, N., Bianca, S., Murphy, D., De Carvalho Moreira, F.M., SYNaPS Study Group, Andrea Accogli, ., Petree, C., Huang, K., Monastiri, K., Edizadeh, M., Nardello, R., Ognibene, M., De Marco, P., Ruggieri, M., Zara, F., Striano, P., Şahin, Y., Al-Gazali, L., Abi Warde, M.T., Gerard, B., Zifarelli, G., Beetz, C., Fortuna, S., Soler, M., Valente, E.M., Varshney, G., Maroofian, R., Salpietro, V., Houlden, H. (2022) A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in medicine : official journal of the American College of Medical Genetics. 24(10):2194-2203

Lin, S.J., Vona, B., Porter, H.M., Izadi, M., Huang, K., Lacassie, Y., Rosenfeld, J.A., Khan, S., Petree, C., Ali, T.A., Muhammad, N., Khan, S.A., Muhammad, N., Liu, P., Haymon, M.L., Rüschendorf, F., Kong, I.K., Schnapp, L., Shur, N., Chorich, L., Layman, L., Haaf, T., Pourkarimi, E., Kim, H.G., Varshney, G.K. (2022) Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. 43(10):1472-1489

Bögershausen, N., Krawczyk, H.E., Jamra, R.A., Lin, S.J., Yigit, G., Hüning, I., Polo, A.M., Vona, B., Huang, K., Schmidt, J., Altmüller, J., Luppe, J., Platzer, K., Dörgeloh, B.B., Busche, A., Biskup, S., Mendes, M.I., Smith, D.E.C., Salomons, G.S., Zibat, A., Bültmann, E., Nürnberg, P., Spielmann, M., Lemke, J.R., Li, Y., Zenker, M., Varshney, G.K., Hillen, H.S., Kratz, C.P., Wollnik, B. (2022) WARS1 and SARS1: two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 43(10):1454-1471

Habicher, J., Varshney, G.K., Waldmann, L., Snitting, D., Allalou, A., Zhang, H., Ghanem, A., Öhman Mägi, C., Dierker, T., Kjellén, L., Burgess, S.M., Ledin, J. (2022) Chondroitin/dermatan sulfate glycosyltransferase genes are essential for craniofacial development. PLoS Genetics. 18:e1010067

Shin, U., Nakhro, K., Oh, C.K., Carrington, B., Song, H., Varshney, G.K., Kim, Y., Song, H., Jeon, S., Robbins, G., Kim, S., Yoon, S., Choi, Y.J., Kim, Y.J., Burgess, S., Kang, S., Sood, R., Lee, Y., Myung, K. (2021) Large-scale generation and phenotypic characterization of zebrafish CRISPR mutants of DNA repair genes. DNA repair. 107:103173

Lin, S.J., Vona, B., Barbalho, P.G., Kaiyrzhanov, R., Maroofian, R., Petree, C., Severino, M., Stanley, V., Varshney, P., Bahena, P., Alzahrani, F., Alhashem, A., Pagnamenta, A.T., Aubertin, G., Estrada-Veras, J.I., Hernández, H.A.D., Mazaheri, N., Oza, A., Thies, J., Renaud, D.L., Dugad, S., McEvoy, J., Sultan, T., Pais, L.S., Tabarki, B., Villalobos-Ramirez, D., Rad, A., Genomics England Research Consortium, Galehdari, H., Ashrafzadeh, F., Sahebzamani, A., Saeidi, K., Torti, E., Elloumi, H.Z., Mora, S., Palculict, T.B., Yang, H., Wren, J.D., Ben Fowler, ., Joshi, M., Behra, M., Burgess, S.M., Nath, S.K., Hanna, M.G., Kenna, M., Merritt, J.L., Houlden, H., Karimiani, E.G., Zaki, M.S., Haaf, T., Alkuraya, F.S., Gleeson, J.G., Varshney, G.K. (2021) Biallelic variants in KARS1 are associated with neurodevelopmental disorders and hearing loss recapitulated by the knockout zebrafish. Genetics in medicine : official journal of the American College of Medical Genetics. 23(10):1933-1943

Vona, B., Mazaheri, N., Lin, S.J., Dunbar, L.A., Maroofian, R., Azaiez, H., Booth, K.T., Vitry, S., Rad, A., Rüschendorf, F., Varshney, P., Fowler, B., Beetz, C., Alagramam, K.N., Murphy, D., Shariati, G., Sedaghat, A., Houlden, H., Petree, C., VijayKumar, S., Smith, R.J.H., Haaf, T., El-Amraoui, A., Bowl, M.R., Varshney, G.K., Galehdari, H. (2021) A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans. Human genetics. 140(6):915-931

Ichino, N., Serres, M.R., Urban, R.M., Urban, M.D., Treichel, A.J., Schaefbauer, K.J., Greif, L.E., Varshney, G.K., Skuster, K.J., McNulty, M.S., Daby, C.L., Wang, Y., Liao, H.K., El-Rass, S., Ding, Y., Liu, W., Anderson, J.L., Wishman, M.D., Sabharwal, A., Schimmenti, L.A., Sivasubbu, S., Balciunas, D., Hammerschmidt, M., Farber, S.A., Wen, X.Y., Xu, X., McGrail, M., Essner, J.J., Burgess, S.M., Clark, K.J., Ekker, S.C. (2020) Building the vertebrate codex using the gene breaking protein trap library. eLIFE. 9:

Rodríguez-Morales, R., Vélez-Negrón, V., Torrado-Tapias, A., Varshney, G., Behra, M. (2020) Expression patterns of activating transcription factor 5 (atf5a and atf5b) in zebrafish. Gene expression patterns : GEP. 37:119126

Banote, R.K., Chebli, J., Şatır, T.M., Varshney, G.K., Camacho, R., Ledin, J., Burgess, S.M., Abramsson, A., Zetterberg, H. (2020) Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish. Scientific Reports. 10:10127

Petree, C., Varshney, G.K. (2020) MultiFRAGing: Rapid and Simultaneous Genotyping of Multiple Alleles in a Single Reaction. Scientific Reports. 10:3172

Vona, B., Doll, J., Hofrichter, M.A.H., Haaf, T., Varshney, G.K. (2020) Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hearing Research. 397:107906

Acevedo-Canabal, A., Colón-Cruz, L., Rodriguez-Morales, R., Varshney, G.K., Burgess, S., González-Sepúlveda, L., Yudowski, G., Behra, M. (2019) Altered Swimming Behaviors in Zebrafish Larvae Lacking Cannabinoid Receptor 2. Cannabis and cannabinoid research. 4:88-101

Liu, K., Petree, C., Requena, T., Varshney, P., Varshney, G.K. (2019) Expanding the CRISPR Toolbox in Zebrafish for Studying Development and Disease. Frontiers in cell and developmental biology. 7:13

Pei, W., Xu, L., Huang, S.C., Pettie, K., Idol, J., Rissone, A., Jimenez, E., Sinclair, J.W., Slevin, C., Varshney, G.K., Jones, M., Carrington, B., Bishop, K., Huang, H., Sood, R., Lin, S., Burgess, S.M. (2018) Guided genetic screen to identify genes essential in the regeneration of hair cells and other tissues. NPJ Regenerative medicine. 3:11

Varshney, G.K., Carrington, B., Pei, W., Bishop, K., Chen, Z., Fan, C., Xu, L., Jones, M., LaFave, M.C., Ledin, J., Sood, R., Burgess, S.M. (2016) A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish. Nature Protocols. 11:2357-2375

Pei, W., Xu, L., Varshney, G.K., Carrington, B., Bishop, K., Jones, M., Huang, S.C., Idol, J., Pretorius, P.R., Beirl, A., Schimmenti, L.A., Kindt, K.S., Sood, R., Burgess, S.M. (2016) Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases. Scientific Reports. 6:29946

Vrljicak, P., Tao, S., Varshney, G.K., Quach, H.N., Joshi, A., LaFave, M.C., Burgess, S.M., Sampath, K. (2016) Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3 (Bethesda). 6(4):805-17

Varshney, G.K., Zhang, S., Pei, W., Adomako-Ankomah, A., Fohtung, J., Schaffer, K., Carrington, B., Maskeri, A., Slevin, C., Wolfsberg, T., Ledin, J., Sood, R., Burgess, S.M. (2016) CRISPRz: a database of zebrafish validated sgRNAs. Nucleic acids research. 44(D1):D822-6

Carrington, B., Varshney, G.K., Burgess, S.M., Sood, R. (2015) CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity. Nucleic acids research. 43(22):e157

Varshney, G.K., Zhang, S., Burgess, S.M., ZFIN Staff (2015) Automated Data Load From CRISPRz. ZFIN Direct Data Submission.

Marquart, G.D., Tabor, K.M., Brown, M., Strykowski, J.L., Varshney, G.K., LaFave, M.C., Mueller, T., Burgess, S.M., Higashijima, S., Burgess, H.A. (2015) A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies. Frontiers in neural circuits. 9:78

Marquart, G.D., Tabor, K.M., Brown, M., Strykowski, J.L., Varshney, G.K., LaFave, M.C., Mueller, T., Burgess, S.H., Higashijima, S., and Burgess, H.A. (2015) Enhancer Trap Transgenics. ZFIN Direct Data Submission.

Seiler, C., Gebhart, N., Zhang, Y., Shinton, S.A., Li, Y.S., Ross, N.L., Liu, X., Li, Q., Bilbee, A.N., Varshney, G.K., LaFave, M.C., Burgess, S.M., Balciuniene, J., Balciunas, D., Hardy, R.R., Kappes, D.J., Wiest, D.L., Rhodes, J. (2015) Mutagenesis Screen Identifies agtpbp1 and eps15L1 as Essential for T lymphocyte Development in Zebrafish. PLoS One. 10:e0131908

Varshney, G.K., Pei, W., LaFave, M.C., Idol, J., Xu, L., Gallardo, V., Carrington, B., Bishop, K., Jones, M., Li, M., Harper, U., Huang, S.C., Prakash, A., Chen, W., Sood, R., Ledin, J., Burgess, S.M. (2015) High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome research. 25(7):1030-42

Gallardo, V.E., Varshney, G.K., Lee, M., Bupp, S., Xu, L., Shinn, P., Crawford, N.P., Inglese, J., Burgess, S.M. (2015) Phenotype-driven chemical screening in zebrafish for collective cell migration inhibitors identifies multiple potential pathways for targeting metastasis. Disease models & mechanisms. 8(6):565-76

Yin, L., Maddison, L.A., Li, M., Kara, N., LaFave, M.C., Varshney, G.K., Burgess, S.M., Patton, J.G., Chen, W. (2015) Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Genetics. 200(2):431-41

Quach, H.N., Tao, S., Vrljicak, P., Joshi, A., Ruan, H., Sukumaran, R., Varshney, G.K., LaFave, M.C., Screen Team, T.D., Burgess, S.M., Winkler, C., Emelyanov, A., Parinov, S., Sampath, K. (2015) A Multifunctional Mutagenesis System for Analysis of Gene Function in Zebrafish. G3 (Bethesda). 5(6):1283-99

Varshney, G.K., Sood, R., Burgess, S.M. (2015) Understanding and Editing the Zebrafish Genome. Advances in genetics. 92:1-52

LaFave, M.C., Varshney, G.K., Vemulapalli, M., Mullikin, J.C., Burgess, S.M. (2014) A Defined Zebrafish Line for High-Throughput Genetics and Genomics: NHGRI-1. Genetics. 198(1):167-70

Varshney, G.K., Lu, J., Gildea, D., Huang, H., Pei, W., Yang, Z., Huang, S.C., Schoenfeld, D.S., Pho, N., Casero, D., Hirase, T., Mosbrook-Davis, D.M., Zhang, S., Jao, L.E., Zhang, B., Woods, I.G., Zimmerman, S., Schier, A.F., Wolfsberg, T., Pellegrini, M., Burgess, S.M., and Lin, S. (2013) A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome research. 23(4):727-735

NON-ZEBRAFISH PUBLICATIONS
LaFave MC, Varshney GK, Burgess SM. GeIST: a pipeline for mapping integrated DNA elements. Bioinformatics. 2015 Oct 1;31(19):3219-21. doi: 10.1093/bioinformatics/btv350. Epub 2015 Jun 6.

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. doi: 10.1172/JCI79213. Epub 2015 Jan 20.

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. Mol Ther. 2015 Mar;23(3):414-22. doi: 10.1038/mt.2014.240.

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 Jan 23. [Epub ahead of print] PubMed PMID: 24464997.

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. doi: 10.1186/1471-2407-13-93. PubMed PMID: 23442791; PubMed Central PMCID: PMC3598783.

Yamazaki Y, Schonherr C, Varshney GK, Dogru M, Hallberg B, Palmer RH. Goliath family E3 ligases regulate the recycling endosome pathway via VAMP3 ubiquitylation. EMBO J. 2013 Feb 20;32(4):524-37. doi: 10.1038/emboj.2013.1. Epub 2013 Jan 25. PubMed PMID: 23353890; PubMed Central PMCID: PMC3579141.

Eriksson T, Varshney G, Aspenstrom P, Palmer RH. Characterisation of the role of Vrp1 in cell fusion during the development of visceral muscle of Drosophila melanogaster. BMC Dev Biol. 2010 Aug 11;10:86. doi: 10.1186/1471-213X-10-86. PubMed PMID: 20701765; PubMed Central PMCID: PMC2931478.

Shirinian M, Popovic M, Grabbe C, Varshney G, Hugosson F, Bos H, Rehmann H, Palmer RH. The Rap1 guanine nucleotide exchange factor C3G is required for preservation of larval muscle integrity in Drosophila melanogaster. PLoS One. 2010 Mar 3;5(3):e9403. doi: 10.1371/journal.pone.0009403. Erratum in: PLoS One. 2010;5(3). doi: 10.1371/annotation/c3ebafa0-1531-4e9f-ab3a-660db7b8dcd2.

Shirinian M, Varshney G, Loren CE, Grabbe C, Palmer RH. Drosophila Anaplastic Lymphoma Kinase regulates Dpp signalling in the developing embryonic gut. Differentiation. 2007 Jun;75(5):418-26. Epub 2007 Feb 5. PubMed PMID: 17286600.

Varshney GK, Palmer RH. The bHLH transcription factor Hand is regulated by Alk in the Drosophila embryonic gut. Biochem Biophys Res Commun. 2006 Dec 29;351(4):839-46. Epub 2006 Oct 30. PubMed PMID: 17094947.

Varshney GK, Singh US, Mishra DP, Kumar A. Immuno-pathotyping of Karnal bunt (Tilletia indica) isolates of wheat using anti-mycelial antibodies. Indian J Exp Biol. 2003 Mar;41(3):255-61. PubMed PMID: 15267157.

Englund C, Loren CE, Grabbe C, Varshney GK, Deleuil F, Hallberg B, Palmer RH. Jeb signals through the Alk receptor tyrosine kinase to drive visceral muscle fusion. Nature. 2003 Oct 2;425(6957):512-6. PubMed PMID: 14523447.