ZFIN ID: ZDB-LAB-170214-4
Varshney Lab
PI/Director: Varshney, Gaurav
Contact Person: Varshney, Gaurav
Email: Gaurav-varshney@omrf.org
URL: http://varshneylab.omrf.org
Address: Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation 825 NE 13th Street, Oklahoma City, 73104
Country: United States
Phone: 405-271-2185
Fax:
Line Designation: omf


GENOMIC FEATURES ORIGINATING FROM THIS LAB
Show all 8 genomic features


STATEMENT OF RESEARCH INTERESTS


LAB MEMBERS
Lin, Sheng-Jia Post-Doc


ZEBRAFISH PUBLICATIONS OF LAB MEMBERS
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
Lin, S.J., Huang, Y.C., Chen, H.Y., Fang, J.Y., Hsu, S.Y., Shih, H.Y., Liu, Y.C., Cheng, Y.C. (2021) RGS2 Suppresses Melanoma Growth via Inhibiting MAPK and AKT Signaling Pathways. Anticancer research. 41:6135-6145
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
Yeh, T.H., Liu, H.F., Li, Y.W., Lu, C.S., Shih, H.Y., Chiu, C.C., Lin, S.J., Huang, Y.C., Cheng, Y.C. (2018) C9orf72 is essential for neurodevelopment and motility mediated by cyclin G1. Experimental neurology. 304:114-124
Huang, Y.C., Lin, S.J., Shih, H.Y., Chou, C.H., Chu, H.H., Chiu, C.C., Yuh, C.H., Yeh, T.H., Cheng, Y.C. (2017) Epigenetic regulation of NOTCH1 and NOTCH3 by KMT2A inhibits glioma proliferation. Oncotarget. 8:63110-63120
Lin, S.J., Chiang, M.C., Shih, H.Y., Chiang, K.C., Cheng, Y.C. (2017) Spatiotemporal expression of foxo4, foxo6a, and foxo6b in the developing brain and retina are transcriptionally regulated by PI3K signaling in zebrafish. Development genes and evolution. 227(3):219-230
Shih, H.Y., Hsu, S.Y., Ouyang, P., Lin, S.J., Chou, T.Y., Chiang, M.C., Cheng, Y.C. (2017) Bmp5 Regulates Neural Crest Cell Survival and Proliferation Via Two Different Signaling Pathways. Stem cells (Dayton, Ohio). 35(4):1003-1014
Lin, S.J., Chiang, M.C., Shih, H.Y., Hsu, L.S., Yeh, T.H., Huang, Y.C., Lin, C.Y., Cheng, Y.C. (2017) Regulator of G protein signaling 2 (Rgs2) regulates neural crest development through Pparδ-Sox10 cascade. Biochimica et biophysica acta. 1864(3):463-474
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
Chiang, K.C., Hsu, S.Y., Lin, S.J., Yeh, C.N., Pang, J.H., Wang, S.Y., Hsu, J.T., Yeh, T.S., Chen, L.W., Kuo, S.F., Cheng, Y.C., Juang, H.H. (2016) PTEN Insufficiency Increases Breast Cancer Cell Metastasis In Vitro and In Vivo in a Xenograft Zebrafish Model. Anticancer research. 36:3997-4005
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
Cheng, Y.C., Huang, Y.C., Yeh, T.H., Shih, H.Y., Lin, C.Y., Lin, S.J., Chiu, C.C., Huang, C.W., Jiang, Y.J. (2015) Deltex1 is inhibited by the Notch-Hairy/E(Spl) signaling pathway and induces neuronal and glial differentiation. Neural Development. 10:28
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
Huang, Y.C., Shih, H.Y., Lin, S.J., Chiu, C.C., Ma, T.L., Yeh, T.H., Cheng, Y.C. (2015) The epigenetic factor Kmt2a/Mll1 regulates neural progenitor proliferation and neuronal and glial differentiation. Developmental Neurobiology. 75(5):452-62
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
Cheng, Y.C., Chiang, M.C., Shih, H.Y., Ma, T.L., Yeh, T.H., Huang, Y.C., Lin, C.Y., Lin, S.J. (2015) The transcription factor hairy/E(spl)-related 2 induces proliferation of neural progenitors and regulates neurogenesis and gliogenesis. Developmental Biology. 397(1):116-28
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
Chen, S.Y., Shih, H.Y., Lin, S.J., Hsiao, C.D., Li, Z.C., and Cheng, Y.C. (2013) Etv5a regulates the proliferation of ventral mesoderm cells and the formation of hemato-vascular derivatives. Journal of Cell Science. 126(Pt 24):5626-34
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
Cheng, Y.C., Scotting, P.J., Hsu, L.S., Lin, S.J., Shih, H.Y., Hsieh, F.Y., Wu, H.L., Tsao, C.L., and Shen, C.J. (2013) Zebrafish rgs4 is essential for motility and axonogenesis mediated by Akt signaling. Cellular and molecular life sciences : CMLS. 70(5):935-950
Hsieh, F.Y., Ma, T.L., Shih, H.Y., Lin, S.J., Huang, C.W., Wang, H.Y., and Cheng, Y.C. (2013) Dner inhibits neural progenitor proliferation and induces neuronal and glial differentiation in zebrafish. Developmental Biology. 375(1):1-12
Cheng, Y.C., Hsieh, F.Y., Chiang, M.C., Scotting, P.J., Shih, H.Y., Lin, S.J., Wu, H.L., and Lee, H.T. (2013) Akt1 Mediates Neuronal Differentiation in Zebrafish via a Reciprocal Interaction with Notch Signaling. PLoS One. 8(1):e54262