Publications
Each of these publications is in pdf format.
- High-Resolution Imaging with Adaptive Optics in Patients with Inherited Retinal Degeneration
Jacque L. Duncan, Yuhua Zhang, Jarel Gandhi, Chiaki Nakanishi, Mohammad Othman, Kari E. H. Branham, Anand Swaroop, and Austin Roorda. Investigative Ophthalmology and Visual Science. 2007;48:3283-3291. - Centrosomal-ciliary gene CEP290/NPHP6 mutations result in blindness with unexpected sparing of photoreceptors and visual brain: Implications for therapy of Leber congenital amaurosis
Artur V. Cideciyan, Tomas S. Aleman, Samuel G. Jacobson, Hemant Khanna, Alexander Sumaroka, Geoffrey K. Aguirre, Sharon B. Schwartz, Elizabeth A.M. Windsor, Shirley He, Bo Chang, Edwin M. Stone, Anand Swaroop. Human Mutation doi:10.1002/humu.20565, 2007. - Retinopathy mutations in the bZIP protein NRL alter phosphorylation and transcriptional activity
Atsuhiro Kanda, James S. Friedman, Koji M. Nishiguchi, Anand Swaroop. Human Mutation 28(6):589-598, 2007. - Madeline 2.0 PDE: A new program for local and web-based pedigree drawing
Edward H. Trager, Ritu Khanna, Adrian Marrs, Lawrence Sidden, Kari E.H. Branham, Anand Swaroop, Julia E. Richards. Bioinformatics doi:10.1093, 2007. 
Transformation of cone precursors to functional rod photoreceptors by bZIP transcription factor NRL
Edwin C. T. Oh, Naheed Khan, Elena Novelli, Hemant Khanna, Enrica Strettoi and Anand Swaroopdoi: 10.1073, 2007
Retinal repair by transplantation of photoreceptor precursors
R. E. MacLaren,R. A. Pearson, A. MacNeil,R. H. Douglas, T. E. Salt, M. Akimoto, A. Swaroop, J. C. Sowden and R. R. Ali Nature doi:10.1038, 2006
- Premature Truncation of a Novel Protein, RD3, Exhibiting Subnuclear Localization Is Associated with Retinal Degeneration
James S. Friedman, Bo Chang, Chira Kannabiran, Christina Chakarova, Hardeep P. Singh, Subhadra Jalali, Norman L. Hawes, Kari Branham, Mohammad Othman, Elena Filippova, Debra A. Thompson, Andrew R. Webster, Sten Andreasson, Samuel G. Jacobson, Shomi S. Bhattacharya, John R. Heckenlively and Anand Swaroop AJHG 79: 1059-1070, 2006 - Retinoic Acid Regulates the Expression of Photoreceptor Transcription Factor NRL
Hemant Khanna, Masayuki Akimoto, Sandrine Siffroi-Fernandez, James Friedman, David Hicks and Anand Swaroop JBC 281: 27327-27334, 2006 - In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development
Hong Cheng, Tomas S. Aleman, Artur V. Cideciyan, Ritu Khanna, Samuel G. Jacobson and Anand Swaroop HMG 15: 2588-2602, 2006 - An in-frame deletion in a novel centrosomal/ciliary protein CEP290/NPHP6 perturbs its interaction with RPGR and results in early-onset retinal degeneration in the rd16 mouse
Bo Chang, Hemant Khanna, Norman Hawes, David Jimeno, Shirley He, Concepcion Lillo, Sunil K. Parapuram, Hong Cheng, Alison Scott, Ron E. Hurd, John A. Sayer, Edgar A. Otto, Massimo Attanasio, John F. O'Toole, Genglin Jin, Chengchao Shou, Friedhelm Hildebrandt, David S. Williams, John R. Heckenlively, and Anand Swaroop HMG 15:1847-1857, 2006 - A novel centrosomal protein that activates transcription factor ATF4/CREB2 is mutated in cystic kidney disease with blindness and cerebellar defects.
Sayer, JA, Otto EA, O'Toole JF, Nurnberg G, Kennedy MA, Becker C, Hennies HC, Helou J, Attanasio M, Fausett BV, Utsch B, Khanna H, Liu Y, Drummond I, Kawakami I, Kusakabe T, Tsuda M, Ma L, Lee H, Larson RG, Allen SJ, Wilkinson CJ, Nigg EA, Shou C, Lillo C, Williams D, Hoppe B, Kemper M, Neuhaus T, Petry M, Kispert A, Zou Y, Gloy J, Ganner A, Walz G, Zhu X, Goldman D, Nurnberg P, Swaroop A, Leroux MR, Hildebrandt F Nat Genet. In Press. - Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors.
Akimoto M, Cheng H, Zhu D, Brzezinski JA, Khanna R, Filippova E, Oh EC, Jing Y, Linares JL, Brooks M, Zareparsi S, Mears AJ, Hero A, Glaser T, Swaroop A PNAS 103:3890-3895, 2006. - Activation of signaling pathways and stress response genes in an experimental model of retinal detachment.
Zacks DN, Han Y, Zeng Y, Swaroop A Invest Ophthalmol Vis Sci. 47:1691-1695, 2006. - Gene expression signatures and biomarkers of noninvasive and invasive breast cancer cells: comprehensive profiles by representational difference analysis, microarrays and proteomics.
Nagaraja GM, Othman M, Fox BP, Alsaber R, Pellegrino CM, Zeng Y, Khanna R, Tamburini P, Swaroop A, Kandpal RP Oncogene 2005, Nov 28PMID: 16314837 - Biomarkers of Cardiovascular Disease as Risk Factors for Age-Related Macular Degeneration.
Vine AK, Stader J, Branham K, Musch DC, Swaroop A Ophthalmology112:2076-2080, 2005 - Network constrained clustering for gene microarray data.
Zhu D, Hero AO, Cheng H, Khanna R, Swaroop A Bioinformatics21:4014-4020, 2005 - Mechanisms of aging in senescence-accelerated mice
Carter TA, Greenhall JA, Yoshida S, Fuchs S, Helton R, Swaroop A, Lockhart DJ, Barlow C Genome Biol. 6:R48, 2005 - High throughput screening of co-expressed gene pairs with controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS)
Zhu D, Hero AO, Qin ZS, Swaroop A - J Comput Biol. 12:1029-1045, 2005. - Cone-like morphological, molecular, and electrophysiological features of the photoreceptors of the Nrl knockout mouse
Daniele LL, Lillo C, Lyubarsky A, Philp N, Mears A, Swaroop A, Williams D, Pugh EN Jr - Invest Ophthalmol Vis Sci 46:2156-2167, 2005. - RPGR-ORF15, which is mutated in retinitis pigmentosa, associates with SMC1, SMC3, and microtubule transport proteins
Khanna H, Hurd TW, Lillo C, Shu X, Parapuram SK, He S, Akimoto M, Wright AF, Margolis B, Williams DS, Swaroop A - JBC 280:3358033587, 2005. - Strong Association of the Y402H Variant in Complement Factor H at 1q32 with Susceptibility to Age-Related Macular Degeneration
Zareparsi S, Branham KEH, Li M, Shah S, Klein RJ, Ott J, Hoh J , Abecasis GR, Swaroop A - Am. J. Hum. Genet 77:149-153, 2005. - Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degeneration
Zareparsi S, Buraczynska M, Branham KEH, Shah S, Eng D, Li M, Pawar H, Yashar BM, Moroi SE, Lichter PR, Petty HR, Richards JE, Abecasis GR, Elner VM, Swaroop A - Hum Mol Genet 1449-1455, 2005. - RPGR ORF15 isoform co-localizes with RPGRIP1 at centrioles and basal bodies and interacts with nucleophosmin
Shu X, Fry AM, Tulloch B, Manson FDC, Crabb JW, Khanna H, Faragher AJ, Lennon A, He S, Trojan P, Giessl A, Wolfrum U, Vervoort R, Swaroop A, Wright AF - Hum Mol Genet 10.1093,1183-1197, 2005. - Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin
Otto EA, Loeys B, Khanna H, Hellemans J, Sudbrak R, Fan S, Muerb U, O Toole JF, Helou J, Attanasio M, Utsch B, Sayer JA, Lillo C, Jimeno D, Coucke P, Paepe AD, Reinhardt R, Klages S, Tsuda M, Kawakami I, Kusakabe T, Omran H, Imm A, Tippens M, Raymond PA, Hill J, Beales P, He S, Kispert A, Margolis B, Williams DS, Swaroop A, Hildebrandt F - Nature Genetics 37, 282 - 288, 2005. - Recessive NRL mutations in patients with clumped pigmentary retinal degeneration and relative preservation of blue cone function
Nishiguchi KM, Friedman JS, Sandberg MA, Swaroop A, Berson EL, Dryja TP - Proc Natl Acad Sci USA. 101:17819-17824, 2004. - The minimal transactivation domain of the basic motif-leucine zipper transcription factor NRL interacts with TATA-binding protein
Friedman JS, Khanna H, Swain PK, DeNicola R, Cheng H, Mitton KP, Weber CH, Hicks D, Swaroop A - J Biol Chem. 279:47233-47241, 2004. - Altered expression of genes of the Bmp/Smad and Wnt/Calcium signaling pathways in the cone-only Nrl-knockout mouse retina, revealed by gene profiling using custom cDNA microarrays
Yu J, He S, Friedman JS, Ghosh D, Mears AJ, Hicks D, Swaroop A - J Biol Chem 2004 October;279:42211-42220. - Recruitment of the rod pathway by cones in the absence of rods
Strettoi E, Mears AJ and Swaroop A - J. Neurosci. 24:7576-7582,2004. - Mutation analysis of NR2E3 and NRL genes in enhanced S-cone syndrome
Wright AF, Reddick AC, Schwartz SB, Ferguson JS, Aleman TS, Kellner U, Jurklies B, Schuster A, Zrenner E, Wissinger B, Lennon A, Shu X, Cideciyan AV, Stone EM, Jacobson SG, Swaroop A - Hum Mutat. 24:439, 2004. - Nuclear receptor NR2E3 gene mutations distort human retina laminar architecture and cause an unusual degeneration
Jacobson SG, Sumaroka A, Aleman TS, Cideciyan AV, Schwartz SB, Roman AJ, McInnes RR, Sheffield VC, Stone EM, Swaroop A and Wright AF - Hum Mol Genet 13:1893-1902, 2004 - Expression of photoreceptor-specific nuclear receptor NR2E3 in rod photoreceptors of fetal human retina
Bumsted O Brien KM, Cheng H, Jiang Y, Schulte D, Swaroop A, Hendrickson AE - Invest Ophthalmol Vis Sci. 45:2807-2812, 2004. - Seeing the unseen: Microarray-based gene expression profiling in vision
Zareparsi S, Hero A, Zack DJ, Williams RW, Swaroop A - Invest Ophthalmol Vis Sci. 45:2457-2462, 2004. - Photoreceptor specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptors
Cheng H, Khanna H, Oh ECT, Hicks D, Mitton KP, Swaroop A - Hum Mol Genet. 13:1563-1575, 2004. - Expression profiling of the developing and mature Nrl-/- mouse retina: Identification of retinal disease candidates and transcriptional regulatory targets of Nrl
Yoshida S, Mears AJ, Friedman JS, Carter T, He S, Oh E, Jing Y, Farjo R, Fleury G, Barlow C, Hero AO, Swaroop A - Hum Mol Genet. 13:1487-1503, 2004 - QRX, a novel homeobox gene, modulates photoreceptor gene expression
Wang QL, Chen S, Esumi N, Swain PK, Haines HS, Peng G, Melia MB, Mcintosh I, Heckenlively JR, Jacobson SG, Stone EM, Swaroop A, Zack DJ - Hum Mol Genet. 2004 May;13:1025-1040. - Association of Apolipoprotein E alleles with susceptibility to age-related macular degeneration in a large cohort from a single center
Zareparsi S, Reddick AC, Branham KEH, Moore KB, Jessup L, Thoms S, Smith-Wheelock M, Yashar BM, Swaroop A - Invest Ophthalmol Vis Sci. 2004;45:1306-1310. - Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays
Hero AO, Fleury G, Mears A, Swaroop A - EURASIP Journal of Applied Signal Processing(EURASIP JASP). 2004:43-52; - From Disease Genes to Cellular Pathways: A Progress Report
Yu J, Mears AJ, Yoshida S, Farjo R, Carter TA, Ghosh D, Hero A, Barlow C, Swaroop A - Novartis Found Symp. 2004;255:147-60. - Age-related macular degeneration: a high-resolution genome scan for susceptibility Loci in a population enriched for late-stage disease
Abecasis GR, Yashar BM, Zhao Y, Ghiasvand NM, Zareparsi S, Branham KEH, Reddick AC, Trager EH, Yoshida S, Bahling J, Filippova E, Elner S, Johnson MW, Vine AK, Sieving PA, Jacobson SG, Richards JE, Swaroop A. - Am. J. Hum. Genet. 2004 Mar;74:482-494. - Transgenic mice expressing Cre-recombinase specifically in M- or S-cone photoreceptors
Akimoto M, Filippova E, Gage PJ, Zhu X, Craft CM, Swaroop A - Invest Ophthalmol Vis Sci. 2004 Jan;45:42-47. - Functional analysis of the rod photoreceptor cGMP phosphodiesterase alpha-subunit gene promoter: Nrl and Crx are required for full transcriptional activity
Pittler SJ, Zhang Y, Chen S, Mears AJ, Zack DJ, Ren Z, Swain PK, Yao S, Swaroop A, White JB - J. Biol. Chem. 2004 May;279:19800-19807. - Increasing evidence for syndromic phenotypes associated with RPGR mutations
Iannaccone A, Wang XF, Jablonski MM, Kuo SF, Baldi A, Cosgrove D, Morton CC, Swaroop A - Am J Ophthalmol. 2004;137:785-786. - Characterization of new transcripts enriched in the mouse retina and identification of candidate retinal disease genes
Lord-Grignon J, Mears AJ, Swaroop A, Bernier G - Invest Ophthalmol Vis Sci. 45(9):3313-9, 2004 - Gene discovery using Pareto depth sampling distributions
Fleury G, Hero A, Zareparsi S, Swaroop A - Special Issue on Genomics, Signal Processing and Statistics, Journal of Franklin Institute 2004;341:55-75. - Pareto depth sampling distributions for gene ranking
Fleury G, Hero A, Zareparsi S, Swaroop A - IEEE International Symposium on Biomedical Imaging, 2004. - Connexin 36 in photoreceptor cells: studies on transgenic rod-less and cone-less mouse retinas
Dang L, Pulukuri S, Mears AJ, Swaroop A, Reese BE, Sitaramayya A - Mol Vis. 2004 May;10:323-327. - Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina
Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, Swaroop A - Genome Biol. 2003 Sep 22;4:R65.1-17. - A comprehensive analysis of the expression of crystallins in mouse retina
Xi J, Farjo R, Yoshida S, Kern TS, Swaroop A, Andley UP - Mol Vis. 2003 Aug 28;9:410-9. 
GRK-1 Dependent Phosphorylation of S and M Opsins and their Binding to Cone Arrestin during Cone Phototransduction in the Mouse Retina
Zhu X, Brown B, Li A, Mears AJ, Swaroop A, Craft CM - J Neurosci. 2003 Jul 9;23(14):6152-60.
Interaction of retinal bZIP transcription factor NRL with Flt3-interacting zinc-finger protein Fiz1: possible role of Fiz1 as a transcriptional repressor
Mitton KP, Swain PK, Khanna H, Dowd M, Apel IJ, Swaroop A - Hum Mol Genet. 2003 Feb 15;12(4):365-73.
- Mutation screening of patients with Leber congenital amaurosis or the enhanced S-cone syndrome reveals a lack of sequence variations in the NRL gene
Acar C, Mears AJ, Yashar BM, Maheshwary AS, Andreasson S, Baldi A, Sieving PA, Iannaccone A, Musarella MA, Jacobson SG, Swaroop A - Mol Vis. 2003 Jan 24;9:14-7. - Microarray Analysis of Gene Expression in the Aging Human Retina
Yoshida S, Yashar BM, Hiriyanna S, Swaroop A - Invest Ophthalmol Vis Sci. 2002 Aug;43(8):2554-60. - Transcriptome analysis of the retina
Swaroop A, Zack DJ - Genome Biology. 2002, Jul 30; 3(8). - A Comprehensive Mutation Analysis of RP2 and RPGR in a North American Cohort of Families with X-linked Retinitis Pigmentosa
Breuer DK, Yashar BM, Filippova E, Hiriyanna S, Lyons RH, Mears AJ, Asaye B, Acar C, Vervoort R, Wright AF, Musarella MA, Wheeler P, MacDonald I, Iannaccone A, Birch D, Hoffman DR, Fishman GA, Heckenlively JR, Jacobson SG, Sieving PA, Swaroop A - Am J Hum Genet. 2002 Jun;70(6):1545-54. - Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays
Yu J, Othman MI, Farjo R, Zareparsi S, MacNee SP, Yoshida S, Swaroop A - Mol Vis. 2002 Apr 26;8:130-7. - Gene expression profile of native human retinal pigment epithelium
Buraczynska M, Mears AJ, Zareparsi S, Farjo R, Filippova E, Yuan Y, MacNee SP, Hughes B, Swaroop A - Invest Ophthalmol Vis Sci. 2002 Mar;43(3):603-7. - Mouse eye gene microarrays for investigating ocular development and disease
Farjo R, Yu J, Othman MI, Yoshida S, Sheth S, Glaser T, Baehr W, Swaroop A - Vision Res. 2002 Feb;42(4):463-70. - Nrl is required for rod photoreceptor development
Mears AJ, Kondo M, Swain PK, Takada Y, Bush RA, Saunders TL, Sieving PA, Swaroop A - Nat Genet. 2001 Dec;29(4):447-52. 
Multiple phosphorylated isoforms of NRL are expressed in rod photoreceptors
Swain PK, Hicks D, Mears AJ, Apel IJ, Smith JE, John SK, Hendrickson A, Milam AH, Swaroop A - J Biol Chem. 2001 Sep 28;276(39):36824-30.
- Remapping of the RP15 Locus for X-Linked Cone-Rod Degeneration to Xp11.4-p21.1, and Identification of a De Novo Insertion in the RPGR Exon ORF15
Mears AJ, Hiriyanna S, Vervoort R, Yashar B, Gieser L, Fahrner S, Daiger SP, Heckenlively JR, Sieving PA, Wright AF, Swaroop A - Am J Hum Genet. 2000 Oct;67(4):1000-3 - The Leucine Zipper of NRL Interacts with the CRX Homeodomain. A possible mechanism of transcriptional synergy in rhodopsin regulation
Mitton KP, Swain PK, Chen S, Xu S, Zack DJ, Swaroop A - J Biol Chem. 2000 Sep 22;275(38):29794-9.