Publications

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2023
Qian X, Srinivasan T, He J, Lu J, Jin Y, Gu H, Chen R. Ceramide compensation by ceramide synthases preserves retinal function and structure in a retinal dystrophy mouse model. Dis Model Mech. 2023 ;16(7).
Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, Noafal MEl, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol. 2023 ;14:1188831.
Wong WJ, Emdin C, Bick AG, Zekavat SM, Niroula A, Pirruccello JP, Dichtel L, Griffin G, Uddin MMesbah, Gibson CJ, Kovalcik V, Lin AE, McConkey ME, Vromman A, Sellar RS, Kim PG, Agrawal M, Weinstock J, Long MT, Yu B, Banerjee R, Nicholls RC, Dennis A, Kelly M, Loh P-R, McCarroll S, Boerwinkle E, Vasan RS, Jaiswal S, Johnson AD, Chung RT, Corey K, Levy D, Ballantyne C, Ebert BL, Natarajan P. Clonal haematopoiesis and risk of chronic liver disease. Nature. 2023 ;616(7958):747-754.
Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol. 2023 ;40(12).
Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SAziz, Shah SFahim, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MCristina, Novelli A, Magliozzi M, Fadda MTeresa, Streff H, Machol K, Lewis RA, Zoete V, Squeo GMaria, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang Y-B, Antonarakis SE. FOXI3 pathogenic variants cause one form of craniofacial microsomia. Nat Commun. 2023 ;14(1):2026.
Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, Li Y, Gao N, Jung SYun, Creighton CJ, Li JJessica, Cui Y, Arimura S, Lei Y, Li W, Shen L. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res. 2023 ;42(1):113.
Lu J, Zheng KQ, Bertrand RElaine, Quinlan J, Ferdous S, Srinivasan T, Oh S, Wang K, Chen R. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res. 2023 ;234:109596.
Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras M-C, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KK-H, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science. 2023 ;380(6648):eabn8153.
Labbé F, Abdeladhim M, Abrudan J, Araki ASaori, Araujo RN, Arensburger P, Benoit JB, Brazil RPecanha, Bruno RV, Rivas GBueno da S, de Abreu VCarvalho, Charamis J, Coutinho-Abreu IV, da Costa-Latgé SG, Darby A, Dillon VM, Emrich SJ, Fernandez-Medina D, Gontijo NFigueiredo, Flanley CM, Gatherer D, Genta FA, Gesing S, Giraldo-Calderón GI, Gomes B, Aguiar ERoberto Gu, Hamilton JGC, Hamarsheh O, Hawksworth M, Hendershot JM, Hickner PV, Imler J-L, Ioannidis P, Jennings EC, Kamhawi S, Karageorgiou C, Kennedy RC, Krueger A, Latorre-Estivalis JM, Ligoxygakis P, Meireles-Filho ACarlos A, Minx P, Miranda JCarlos, Montague MJ, Nowling RJ, Oliveira F, Ortigão-Farias J, Pavan MG, Pereira MHoracio, Pitaluga ANobrega, Olmo RProveti, Ramalho-Ortigao M, Ribeiro JMC, Rosendale AJ, Sant'Anna MRV, Scherer SE, Secundino NFC, Shoue DA, Moraes Cda Silva, Gesto JSilveira M, Souza NAraujo, Syed Z, Tadros S, Teles-de-Freitas R, Telleria EL, Tomlinson C, Traub-Csekö YM, Marques JTrindade, Tu Z, Unger MF, Valenzuela J, Ferreira FV, de Oliveira KPV, Vigoder FM, Vontas J, Wang L, Weedall GD, Zhioua E, Richards S, Warren WC, Waterhouse RM, Dillon RJ, McDowell MAnn. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World. PLoS Negl Trop Dis. 2023 ;17(4):e0010862.
Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FEnnes, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MHeide, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKai-How, Bonet TMarques. A global catalog of whole-genome diversity from 233 primate species. Science. 2023 ;380(6648):906-913.
Chen Q, Sasikala-Appukuttan AKirshna, Husain Z, Shrivastava A, Spain M, Sendler ED, Daines B, Fischer S, Chen R, Cook TA, Friedrich M. Global Gene Expression Analysis Reveals Complex Cuticle Organization of the Tribolium Compound Eye. Genome Biol Evol. 2023 ;15(1).
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FEnnes, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Amaral JValsecchi, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CChuen, Lee J, Tan P, Lim WKhong, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MHeide, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKai-How. The landscape of tolerated genetic variation in humans and primates. Science. 2023 ;380(6648):eabn8153.
Santhanam A, Shihabeddin E, Wei H, Wu J, O'Brien J. Molecular basis of retinal remodeling in a zebrafish model of retinitis pigmentosa. Cell Mol Life Sci. 2023 ;80(12):362.
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, Kurolap A, Henig NZunz, Fatih JM, Herman I, Du H, Mitani T, Becker L, Rathkolb B, Gerlini R, Seisenberger C, Marschall S, Hunter JV, Gerard A, Heidlebaugh A, Challman T, Spillmann RC, Jhangiani SN, Coban-Akdemir Z, Lalani S, Liu L, Revah-Politi A, Iglesias A, Guzman E, Baugh E, Boddaert N, Rondeau S, Ormieres C, Barcia G, Tan QKG, Thiffault I, Pastinen T, Sheikh K, Biliciler S, Mei D, Melani F, Shashi V, Yaron Y, Steele M, Wakeling E, Østergaard E, Nazaryan-Petersen L, Millan F, Santiago-Sim T, Thevenon J, Bruel A-L, Thauvin-Robinet C, Popp D, Platzer K, Gawlinski P, Wiszniewski W, Marafi D, Pehlivan D, Posey JE, Gibbs RA, Gailus-Durner V, Guerrini R, Fuchs H, de Angelis MHrabě, Hölter SM, Cheung H-H, Gu S, Lupski JR. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet. 2023 ;110(8):1394-1413.
Shao Y, Zhou L, Li F, Zhao L, Zhang B-L, Shao F, Chen J-W, Chen C-Y, Bi X, Zhuang X-L, Zhu H-L, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang Y-M, Chen W, Li G, Lu H-M, Liu Y, Kuderna LFK, Farh KKai-How, Fan P-F, Yu L, Li M, Liu Z-J, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MHeide, Yao Y-G, Zhang Y-P, Wang W, Qi X-G, Zhang G, Wu D-D. Phylogenomic analyses provide insights into primate evolution. Science. 2023 ;380(6648):913-924.
Petit F, Longoni M, Wells J, Maser RS, Bogenschutz EL, Dysart MJ, Contreras HTM, Frénois F, Pober BR, Clark RD, Giampietro PF, Ropers HH, Hu H, Loscertales M, Wagner R, Ai X, Brand H, Jourdain A-S, Delrue M-A, Gilbert-Dussardier B, Devisme L, Keren B, McCulley DJ, Qiao L, Hernan R, Wynn J, Scott TM, Calame DG, Coban-Akdemir Z, Hernandez P, Hernandez-Garcia A, Yonath H, Lupski JR, Shen Y, Chung WK, Scott DA, Bult CJ, Donahoe PK, High FA. PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. Am J Hum Genet. 2023 ;110(10):1787-1803.
Raja KKumar Boll, Yeung K, Shim Y-K, Li Y, Chen R, Mardon G. A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines. Nat Commun. 2023 ;14(1):7205.
Paulin LF, Raveendran M, Harris RA, Rogers J, von Haeseler A, Sedlazeck FJ. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics. 2023 ;24(1):23.
Schlosser P, Zhang J, Liu H, Surapaneni AL, Rhee EP, Arking DE, Yu B, Boerwinkle E, Welling PA, Chatterjee N, Susztak K, Coresh J, Grams ME. Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage. Genome Biol. 2023 ;24(1):150.
Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S, Eichler EE, Levine JE, Rogers J. Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets (). Genes (Basel). 2023 ;14(12).
2022
Qian X, Liu H, Fu S, Lu J, Hung Y-T, Turner C, Gu H, Chen R. AAV8-Mediated Gene Therapy Rescues Retinal Degeneration Phenotype in a Tlcd3b Knockout Mouse Model. Invest Ophthalmol Vis Sci. 2022 ;63(3):11.
Khalaf-Nazzal R, Fasham J, Inskeep KA, Blizzard LE, Leslie JS, Wakeling MN, Ubeyratna N, Mitani T, Griffith JL, Baker W, Al-Hijawi F', Keough KC, Gezdirici A, Pena L, Spaeth CG, Turnpenny PD, Walsh JR, Ray R, Neilson A, Kouranova E, Cui X, Curiel DT, Pehlivan D, Akdemir ZCoban, Posey JE, Lupski JR, Dobyns WB, Stottmann RW, Crosby AH, Baple EL. Bi-allelic CAMSAP1 variants cause a clinically recognizable neuronal migration disorder. Am J Hum Genet. 2022 ;109(11):2068-2079.
M Casanova I, Chen R, Garzel LM, Olstad KJ, Kim S, Harris RA, Li Y, Raveendran M, Liang Q, Wang J, Yiu G, Stout JTimothy, Roberts JA, Rogers J, Moshiri A, Thomasy SM. Clinical presentation, treatment, and genetic and histopathological analysis of juvenile cataracts and secondary glaucoma in a rhesus macaque (Macaca mulatta). J Med Primatol. 2022 ;51(2):119-123.
Lermi NOzirmak, Gray SB, Bowen CM, Reyes-Uribe L, Dray BK, Deng N, Harris RA, Raveendran M, Benavides F, Hodo CL, Taggart MW, Maresso KColbert, Sinha KM, Rogers J, Vilar E. Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLoS Genet. 2022 ;18(4):e1010163.
Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny DM, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience. 2022 ;11.