Publications
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  1. Lin SJ, Huang K, Petree C, Varshney P and Varshney GK^. Optimizing gRNA selection for High-Penetrance F0 CRISPR Screening for interrogating disease gene function. Nucleic Acids Research. 2025. doi: 1093/nar/gkaf180.
  1. Efthymiou, S., Leo, C.P., Deng, C., Zhang, K., Lin, S.-J., Maroofian, R., Kaiyrzhanov, R., Lin, R., Karagoz, I., Scardamaglia, A., Owrang, D., Turchetti, V., Jahnke, F., Huang K., Petree, C., Derrick, A.V., Rees, M.I., Alvi, J.R., Sultan, T., Li, C., Jacquemont, M.-L., Tran-Mau-Them, F., Valenzuela-Palafoll, M., Sidlow, R., Yoon, G., Morrow, M., Carere, A., O’Connor, M., Fleischer, J., Gerkes, E.H., Phornphutkul, C., Isidor, B., Rivier-Ringenbach, C., Philippe, C., Kurul, S.H., Soydemir, D., Kara, B., Sunnetci-Akkoyunlu, D., Bothe, V., Platzer, K., Wieczorek, D., Koch-Hogrebe, M., Rahner, N., Thuresson, A.-C., Matsson, H., Frykholm, C., Bozdoğan, S.T., Bişgin, A., Chatron, N., Lesca, G., Cabet, S., Tümer, Z., Hjortshøj, T.D., Rønde, G., Marquardt, T., Reunert, J., Afzal, E., Zamani, M., Azizimalamiri, R., Galehdari, H., Nourbakhshd, P., Chamanrou, N., Chung, S.-K., Suri, M., Benke, P.J., Zaki, M.S., Gleeson, J.G., Calame, D.G., Pehlivan, D., Yilmaz, H.I., Gezdirici, A., Rad, A., Abumansour, I.S., Oprea, G., Sidpra, J., Mankad, K., Vona, B., Fry, A.E., Varshney, G.K^., Houlden, H^., Fu, D^. 2024. Biallelic pathogenic variants in TRMT1 disrupt tRNA modification and induce a syndromic neurodevelopmental disorder. The American Journal of Human Genetics. 2025 doi: 1016/j.ajhg.2025.03.015. Apr 16. PMID: 40245862
  1. Scott A, Dugdale J, Koleilat A, Krauss A, Hernandez-Herrera GA, Wallace JG, Petree C, Varshney GK, Schimmenti LA. Vital Dyes YO-PRO-1 and DASPEI enter through the mechanotransduction channel of zebrafish hair cells. Journal of the Association for Research in Otolaryngology 2024 Oct 21. doi: 1007/s10162-024-00967-w PMID: 39433714
  1. Barish S, Lin SJ, Maroofian R, Gezdirici A, Alhebby H, Trimouille, Waberski MB, Tadahiro M, , Huber I, Tveten K, Holla Ø, Busk Ø, Houlden H, Karimiani EG, Toosi MB, Badv RS, Torbati PN, Eghbal F, Akhondian J, Safar AA, Alswaid A, Zifarelli G, Bauer P, Marafi D, Fatih JM, Huang K, Petree C, Calame DG, Lippe C, Alkuraya FS, Wali S, Lupski JR, Varshney GK^, Posey JE^, Pehlivan D^. Homozygous variants in WDR83OS lead to a neurodevelopmental disorder with hypercholanemia. The American Journal of Human Genetics 2024 doi: 1016/j.ajhg.2024.10.002
  1. Ree R^, Lin SJ, St Dahl L, Huang K, Petree C, Varshney GK^, and Arnesen T^. Naa80 is required for actin N-terminal acetylation and normal hearing in zebrafish. Life Science Alliance 2024 Oct 9;7(12):e202402795. doi: 26508/lsa.202402795. PMID: 39384430 (Cover Article)
  1. Zhang Y, Liu Y, Qin W, Zheng S, Xiao J, Xinxin X, Xuanyao Y, Jingjing Z, Shi Y, Ma H, , Varshney GK^, Fei JF^, Liu Y^. Cytosine Base Editors with Increased PAM and 2 Deaminase Motif Flexibility for Gene Editing in Zebrafish. Nature Communications 15, 9526 (2024). 1038/s41467-024-53735-y
  1. Banks E, Francis V, Lin SJ, Kharfallah F, Fonov V, Levesque M, Han C, Kulasekaran G, Tuznik M, Bayati A, Al-Khater R, Alkuraya FS, Argyriou L, Babaei M, Bahlo M, Bakhshoodeh B, Barr E, Bartik L, Bassiony M, Bertrand M, Braun D, Buchert R, Budetta M, Cadieux-Dion M, Calame D, Cope H, Cushing D, Efthymiou S, Elmaksoud MA, El Said HG, Froukh T, Gill HK, Gleeson JG, Gogoll L, Goh ES, Gowda VK, Haack TB, Hashem MO, Hauser S, Hoffman TL, Hogue JS, Hosokawa A, Houlden H, Huang K, Huynh S, Karimiani EG, Kaulfuß S, Korenke GC, Kritzer A, Lee H, Lupski JR, Marco EJ, McWalter K, Minassian A, Minassian BA, Murphy D, Neira-Fresneda J, Northrup H, Nyaga D, Oehl-Jaschkowitz B, Osmond M, Person R, Pehlivan D, Petree C, Sadleir LG, Saunders C, Schoels L, Shashi V, Spillman RC, Srinivasan VM, Torbati PN, Tos T; Undiagnosed Diseases Network; Zaki MS, Zhou D, Zweier C, Trempe JF, Durcan TM, Gan-Or Z, Avoli M, Alves C, Varshney GK, Maroofian R, Rudko DA, McPherson PS. Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy. Nature Communications 2024 Aug 22;15(1):7239. doi: 1038/s41467-024-51310-z.
  1. Qin W, Liang D, Lin SJ, Petree C, Huang K, Zhang Y, Li L, Varshney P, Mourrain P, Liu YM^, and Varshney GK^. ABE-Ultramax for high-efficiency biallelic adenine base editing in zebrafish. Nature Communications. 2024 Jul 4;15(1):5613. doi: 1038/s41467-024-49943-1.
  1. Kaiyrzhanov R, Rad A, Lin SJ, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M Severino M, Guille M, Tate EW, Varshney GK^, Houlden H, Maroofian R^. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. 2024 Apr 4;147(4):1436-1456. doi: 10.1093/brain/awad380. PMID: 37951597.
  1. Lin SJ, Vona B, Lau T, Huang K, Shujaa H, Zaki M, Aldeen H, , Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Jamra RA, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M,  Cork EE, Varshney P,  Hashemian N, Mohammadi MH, Aboulfazl Rad, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Mohnish S, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian M^, Varshney GK^. Biallelic variants in OGDHL encoding Oxoglutarate Dehydrogenase L might be responsible for a highly variable clinical phenotype. Genome Medicine 2023 Nov 29;15(1):102. doi: 1186/s13073-023-01258-4.
  1. Accogli A, Lin SJ, Severino M, Kim SH, Huang K, Rocca C, Landsverk M, Zaki M, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Swayer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingapp L, McDunnah P, Horvath R, Cogne B, Isidor B, Hahn A, Gripp K, Jafarnejad SM, Ostergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK^, Maroofian R^. Clinical, neuroradiological and molecular characterization of the TARS2-related disorder. Genetics in Medicine, 2023 Jul 13:100938. doi: 1016/j.gim.2023.100938.
  1. Jackson A, Lin SJ, Jones EA, Chandler KE, Orr D, Moss C, Haider Z, Ryan G, Holden S, Harrison M, Burrows N, Jones WD, Loveless M, Petree C, Stewart H, Low K, Donnelly D, Lovell S, Drosou K; Genomics England Research Consortium; Solve-RD consortium; Varshney GK^, Banka S. Clinical, genetic, epidemiologic and functional delineation of TSPEAR-related Autosomal Recessive Ectodermal Dysplasia 14. HGG Advances. 2023 Mar 3;4(2):100186. doi: 1016/j.xhgg.2023.100186. PMCID: PMC10064225
  1. Varshney P, and Varshney GK^. Expanded precision genome-editing toolbox for human disease modeling in zebrafish. Lab Animal (NY). 2022 Nov;51(11):287-289. doi:1038/s41684-022-01076-y. (Invited & Cover article)
  1. Calì E, Lin SJ, 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 FM; 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 MT, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 2022 Oct;24(10):2194-2203. doi: 1016/j.gim.2022.07.013. Epub 2022 Aug 24. PMID: 36001086.
  1. Lin SJ*, Vona B*^, Porter HM, Izadi M, Huang K, Lacassie Y, Rosenfeld JA, Khan S, Petree C, Ali TA, Muhammad N, Khan SA, Muhammad N, Liu P, Haymon ML, Rüschendorf F, Kong IK, Schnapp L, Shur N, Chorich L, Layman L, Haaf T, Pourkarimi E, Kim HG, Varshney GK^. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. 2022 Jul 11. doi: 1002/humu.24435. (Editor’s choice and Cover article)
  1. Bögershausen N, Krawczyk HE, Jamra RA, Lin SJ, Yigit G, Hüning I, Polo AM, Vona B, Huang K, Schmidt J, Altmüller J, Luppe J, Platzer K, Dörgeloh BB, Busche A, Biskup S, Mendes MI, Smith DEC, Salomons GS, Zibat A, Bültmann E, Nürnberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 2022 Jul 5. doi: 1002/humu.24430.
  1. 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. 2022 Feb 22;18(2):e1010067. doi: 1371/journal.pgen.1010067. eCollection 2022 Feb. PMID: 35192612. PMCID: PMC8896900
  1. 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: 1016/j.dnarep.2021.103173.
  1. 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. Genetics in Medicine 2021 Jun 25. doi: 1038/s41436-021-012391-1. PMCID: PMC8956360
  1. 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 Rheumatology. 2021 May 13. doi: 1002/art.41799. PMCID: PMC8589926
  1. 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. Human Genetics, 2021 Jun;140(6):915-931. doi: 1007/s00439-020-02254-z. PMCID: PMC8099798
  1. 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. Frontiers Molecular Neuroscience. 2021 Apr 20;14:624265. doi: 3389/fnmol.2021.624265 . 624265. PMCID: PMC8093779
  1. 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: 7554/eLife.54572. PMCID: PMC7486118
  1. 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. Scientific Reports. 2020 Sep 11;10(1):14954. doi: 1038/s41598-020-70890-6. PMCID: PMC7486895
  1. 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 Expression Patterns. 2020 Sep; 37:119126. doi: 1016/j.gep.2020.119126. PMCID: PMC8312729
  1. 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. Scientific Reports. 2020 Jun 23;10(1):10127. doi: 1038/s41598-020-66584-8. PMCID: PMC7311384
  1. Petree C, Varshney GK^. MultiFRAGing: Rapid and Simultaneous Genotyping of Multiple Alleles in a Single Reaction. Scientific Reports. 2020 Feb 21;10(1):3172. doi: 1038/s41598-020-59986-1. PMCID: PMC7035419
  1. Vona B, Doll J, Hofrichter MAH, Haaf T, Varshney GK^. Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hearing Research, 2020 Nov; 397:107906. doi: 1016/j.heares.2020.107906. PMCID: PMC7415493
  1. 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. The Anatomical Record (Hoboken). 2019 Dec 28. doi: 1002/ar.24331. PMCID: PMC8108486
  1. 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: 1242/dev.184218. PMCID: PMC6857586
  1. Acevedo-Canabal A, Colon-Cruz L, Rodriguez-Morales R, Varshney GK, Burgess 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. DOI: 1089/can.2018.0025
  2. 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. DOI: 3389/fcell.2019.00013
  3. 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. DOI: 1038/s41536-018-0050-7
  4. Mendoza-Garcia P, Hugosson F, Fallah M, Higgins ML, Iwasaki Y, Pfeifer K, Wolfstetter G, Varshney G, Popichenko D, Gergen JP, Hens K, Deplancke B, Palmer RH. The Zic family homologue Odd-paired regulates Alk expression in Drosophila. PLOS Genetics. April 3, 2017; 13(4): e1006617. PMCID: PMC5393633. DOI: 1371/journal.pgen.1006617
  5. 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. February 9, 2017; 7(2):719-722. PMCID: PMC5295614. DOI: 1534/g3.116.038091
  1. Varshney GK, Carrington B, Pei W, Bishop K, Chen Z, Xu L, Fan C, LaFave M, Ledin J, Sood R, Burgess SM. A High-Throughput functional workflow on CRISPR/Cas9 mediated targeted mutagenesis in zebrafish. Nature Protocols. December 2016; 11(12): 2357-2375. PMCID: PMC5630457. DOI: 1038/nprot.2016.141
  1. Varshney GK and Burgess SM. DNA-guided genome editing using structure-guided endonucleases. Genome Biology. September 15, 2016;17(1):187. PMCID: PMC5025577. DOI: 1186/s13059-016-1055-4
  1. Pei W, Xu L, Varshney GK, Carrington B, Bishop K, Jones MP, Huang SC, Idol J, Pretorius PR, Beirl A, Schimmenti L, Kindt K, Sood R, Burgess SM. Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases. Scientific Reports. July 18, 2016;6:29946. PMCID: PMC4947902. DOI: 1038/srep29946
  1. Vrljicak P*, Tao S*, Varshney GK*, Quach HN*, Joshi A, LaFave MC, Burgess SM, Sampath K. Genome-wide analysis of transposon and retroviral insertions reveals structural features in vertebrate genomes. G3: Genes Genomics Genetics. April 7, 2016;6(4):805-17. PMCID: PMC4825651. DOI: 1534/g3.115.026849
  1. 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. February 2016;24(2):198-201. PMCID: PMC4817827. DOI: 1038/mt.2016.17
  1. 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 sgRNA’s. Nucleic Acids Research. January 4, 2016;44(D1): D866-6. PMCID: PMC4702947. DOI: 1093/nar/gkv998
  1. 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. PMCID: PMC5605149. DOI: 10.1038/npjregenmed.2016.13
  1. 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 Research. December 15, 2015;43(22): e157. PMCID: PMC4678847. DOI: 1093/nar/gkv802
  1. Marquart GD, Tabor KM, Brown MR, Strykowski JL, Varshney GK, LaFave MC, Mueller T, Burgess SM, Higashijima Shin-ichi, Burgess HA. A 3D-searchable database of transgenic zebrafish Gal4 and Cre lines for functional neuroanatomy studies. Frontiers Neural Circuits. November 24, 2015;9:78. PMCID: PMC4656851. DOI: 3389/fncir.2015.00078
  1. LaFave MC, Varshney GK and Burgess SM. GeIST: a pipeline for mapping integrated DNA elements. October 1, 2015,31(19):3219-21. PMCID: PMC4592334. DOI: 10.1093/bioinformatics/btv350
  1. Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, Carrington B, Bishop K, Jones M, Li M, Harper U, Huang SC, Chen W, Sood R, Ledin J, Burgess SM. High-Throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Research. July 2015(7):1030-42. PMCID: PMC4484386. DOI: 1101/gr.186379.114
  1. Seiler C, Gebhart N, Zhang Y, Shinton S, Li Y, Ross N, Liu X, Bilbee A, Varshney GK, Lafave M, Burgess SM, Balciuniene J, Balciunas D, Hardy R, Kappes D, Wiest D, Rhodes J. Mutagenesis screen identifies agtpbp1 and eps15L1 as essential for T lymphocyte development in zebrafish. PLOS Genetics. July 10, 2015;10(7): e0131908. PMCID: PMC4498767 DOI: 1371/journal.pone.0131908
  1. 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. June 2015;200(2):431-41. PMCID: PMC4492370. DOI: 1534/genetics.115.176917
  1. Varshney GK, Sood R, Burgess SM. Understanding and editing the zebrafish genome. Advances in Genetics. 2015; 92:1-52. PMID: 26639914. DOI: 1016/bs.adgen.2015.09.002

50.  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. Disease Model Mechanisms. June 2015;8(6):565-76. PMCID: PMC4457032. DOI: 10.1242/dmm.018689

51.  Quach HN, Tao S, Vrljicak P, Joshi A, Ruan H, Sukumaran R, Varshney GK, LaFave MC, Screen Team TD, 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. April 2, 2015;5(6):1283-99. PMCID: PMC4478556. DOI: 10.1534/g3.114.015842

  1. 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. March 2015;23(3):414-22. PMCID: PMC4351464. DOI: 1038/mt.2014.240
  1. 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. Journal of Clinical Investigation. February 2015;125(2):870-80. PMCID: PMC4319425. DOI: 1172/JCI79213
  1. Lafave MC, Varshney GK, Vemulapalli M, Mullikin JC and Burgess SM. A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1. Genetics. September 2014;198(1):167-70. PMCID: PMC4174928. DOI: 1534/genetics.114.166769
  1. 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 Research. April 2014; 42(7):4257-69. PMCID: PMC3985626. DOI: 1093/nar/gkt1399
  1. Varshney GK and Burgess S.M. Mutagenesis and phenotyping resources in zebrafish for studying development and human disease. Briefings in Functional Genomics. March 2014;13(2):82-94. PMCID: PMC3954039. DOI: 1093/bfgp/elt042
  1. 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 Research. April 2013;23(4):727-35. PMCID: PMC3613589. DOI: 1101/gr.151464.112
  1. 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. February 27, 2013; 13:93. PMCID: PMC3598783. DOI: 1186/1471-2407-13-93
  1. Yamazaki Y, Schonherr C, Varshney GK, Dogru M, Hallberg B and Palmer RH. Goliath family E3 ligases regulate the recycling endosome pathway via VAMP3 ubiquitylation. EMBO J. February 20, 2013;32(4):524-37. PMCID: PMC3579141. DOI: 1038/emboj.2013.1
  1. Varshney GK, Huang H, Zhang S, Lu J, Gildea DE, Yang Z, Wolfsberg TG, Lin S, SM. The zebrafish insertion collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion. Nucleic Acids Research. January 2013;41. PMCID: PMC3531054. DOI: 1093/nar/gks946
  1. Amsterdam A, Varshney GK, Burgess SM. Retroviral-mediated insertional mutagenesis in zebrafish. Methods in Cell Biology. 2011; 104:59-82. PMCID: PMC3373308. DOI: 1016/B978-0-12-374814-0.00004-5
  1. Eriksson T, Varshney G, Aspenstrom P, Palmer RH. Characterization of the role of Vrp1 in cell fusion during the development of visceral muscle of Drosophila melanogaster. BMC Developmental Biology. August 11, 2010;10:86. PMCID: PMC2931478. DOI: 1186/1471-213X-10-86
  1. Shirinian M, Grabbe C, Popovic M, 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. March 3, 2010;5(3): e9403. PMCID: PMC2831063. DOI: 1371/journal.pone.0009403
  1. Shirinian M, Varshney G, Loren CE, Grabbe C, Palmer RH. Drosophila anaplastic lymphoma kinase regulates Dpp signalling in the developing embryonic gut. Differentiation. June 2007; 75(5):418-26. PMID: 17286600. DOI: 1016/j.bbrc.2006.10.117
  1. Varshney GK, Palmer RH. The bHLH transcription factor Hand is regulated by Alk in the Drosophila embryonic gut. Biochemical and Biophysical Research Communications. December 29, 2006;351(4):839-46. PMID: 17094947. DOI: 1016/j.bbrc.2006.10.117
  1. 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. October 2, 2003; 425(6957): 512-6. PMID: 14523447. DOI: 1038/nature01950