Anand Swaroop

NEW DEVELOPMENTS Seeing the Unseen: Microarray-Based Gene Expression Profiling in Vision (2008)

Sepideh Zareparsi, Alfred Hero, Donald J. Zack, Robert W. Williams, Anand Swaroop

Completion of genome sequencing efforts of humans and model organisms 1–3 have provided exciting opportunities for vision research. Questions that were hard to envisage, let alone resolve, suddenly...

Genetic susceptibility to age-related macular degeneration: a paradigm for dissecting complex disease traits (2007)

Swaroop, Anand, Branham, Kari EH, Chen, Wei, Abecasis, Goncalo

Age-related macular degeneration (AMD) is a progressive neurodegenerative disease, which affects quality of life for millions of elderly individuals worldwide. AMD is associated with a diverse...

Madeline 2.0 PDE: a new program for local and web-based pedigree drawing (2007)

Trager, Edward H., Khanna, Ritu, Marrs, Adrian, Siden, Lawrence, Branham, Kari E.H., Swaroop, Anand, ...

Summary: The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program for use in linkage and family-based association studies. The program is designed to handle large and complex...

In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development (2006)

Cheng, Hong, Aleman, Tomas S., Cideciyan, Artur V., Khanna, Ritu, Jacobson, Samuel G., Swaroop, Anand

Rod and cone photoreceptors in mammalian retina are generated from common pool(s) of neuroepithelial progenitors. NRL, CRX and NR2E3 are key transcriptional regulators that control photoreceptor...

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 (2006)

Chang, Bo, Khanna, Hemant, Hawes, Norman, Jimeno, David, He, Shirley, Lillo, Concepcion, ...

Centrosome- and cilia-associated proteins play crucial roles in establishing polarity and regulating intracellular transport in post-mitotic cells. Using genetic mapping and positional candidate...

In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development (2006)

Cheng, Hong, Aleman, Tomas S., Cideciyan, Artur V., Khanna, Ritu, Jacobson, Samuel G., Swaroop, Anand

Rod and cone photoreceptors in mammalian retina are generated from common pool(s) of neuroepithelial progenitors. NRL, CRX and NR2E3 are key transcriptional regulators that control photoreceptor...

High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS) (2005)

Zhu, Dongxiao, Hero, Alfred O, Qin, Zhaohui S, Swaroop, Anand

Many exploratory microarray data analysis tools such as gene clustering and relevance networks rely on detecting pairwise gene co-expression. Traditional screening of pairwise co-expression either...

Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin (2005)

Otto, Edgar A, Loeys, Bart, Khanna, Hemant, Hellemans, Jan, Sudbrak, Ralf, Fan, Shuling, ...

Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children1, 2, 3. Identification of four genes mutated in NPHP subtypes 1−4 (refs. 4−9) has linked the...

Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin (2005)

Otto, Edgar A, Loeys, Bart, Khanna, Hemant, Hellemans, Jan, Sudbrak, Ralf, Fan, Shuling, ...

Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children1, 2, 3. Identification of four genes mutated in NPHP subtypes 1−4 (refs. 4−9) has linked the...

Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degeneration (2005)

Zareparsi, Sepideh, Buraczynska, Monika, Branham, Kari E.H., Shah, Sapna, Eng, Donna, Li, Mingyao, ...

Age-related macular degeneration (AMD) is a genetically heterogeneous disease that leads to progressive and irreversible vision loss among the elderly. Inflammation, oxidative damage, cholesterol...

Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays (2004)

Alfred O. Hero, Gilles Fleury, Alan J. Mears, Anand Swaroop

This paper introduces a statistical methodology for the identification of differentially expressed genes in DNA microarray experiments based on multiple criteria. These criteria are false discovery...

Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays (2004)

Anand Swaroop, Alan J. Mears, Gilles Fleury, Alfred O. Hero

This paper introduces a statistical methodology for the identification of differentially expressed genes in DNA microarray experiments based on multiple criteria. These criteria are false discovery...

Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays (2004)

Alfred O. Hero, Gilles Fleury, Alan J. Mears, Anand Swaroop

This paper introduces a statistical methodology for the identification of differentially expressed genes in DNA microarray experiments based on multiple criteria. These criteria are false discovery...

QRX, a Novel Homeobox Gene, Modulates Photoreceptor Gene Expression (2004)

Wang, Qing-liang, Chen, Shiming, Esumi, Noriko, Swain, Prabodh K., Haines, Heidi S., Peng, Guanghua, ...

A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially...

Expression profiling of the developing and mature Nrl-/- mouse retina: Identification of retinal disease candidates and transcriptional regulatory targets of Nrl (2004)

Yoshida, Shigeo, Mears, Alan J., Friedman, James S., Carter, Todd, He, Shirley, Oh, Edwin, ...

The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account...

Photoreceptor specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptors (2004)

Cheng, Hong, Khanna, Hemant, Oh, Edwin C. T., Hicks, David, Mitton, Kenneth P., Swaroop, Anand

NR2E3, a photoreceptor-specific orphan nuclear receptor, is believed to play a pivotal role in the differentiation of photoreceptors. Mutations in the human NR2E3 gene and its mouse ortholog are...

Nuclear receptor NR2E3 gene mutations distort human retinal laminar architecture and cause an unusual degeneration (2004)

Jacobson, Samuel G., Sumaroka, Alexander, Aleman, Tomas S., Cideciyan, Artur V., Schwartz, Sharon B., Roman, Alejandro J., ...

Mutations in the nuclear receptor gene, NR2E3, cause a disorder of human retinal photoreceptor development characterized by hyperfunction and excess of the minority S (short wavelength or blue) cone...

QRX, a novel homeobox gene, modulates photoreceptor gene expression (2004)

Wang, Qing-liang, Chen, Shiming, Esumi, Noriko, Swain, Prabodh K., Haines, Heidi S., Peng, Guanghua, ...

A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially...

Nuclear receptor NR2E3 gene mutations distort human retinal laminar architecture and cause an unusual degeneration (2004)

Jacobson, Samuel G., Sumaroka, Alexander, Aleman, Tomas S., Cideciyan, Artur V., Schwartz, Sharon B., Roman, Alejandro J., ...

Mutations in the nuclear receptor gene, NR2E3, cause a disorder of human retinal photoreceptor development characterized by hyperfunction and excess of the minority S (short wavelength or blue) cone...

Photoreceptor-specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptors (2004)

Cheng, Hong, Khanna, Hemant, Oh, Edwin C.T., Hicks, David, Mitton, Kenneth P., Swaroop, Anand

NR2E3, a photoreceptor-specific orphan nuclear receptor, is believed to play a pivotal role in the differentiation of photoreceptors. Mutations in the human NR2E3 gene and its mouse ortholog are...

Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl (2004)

Yoshida, Shigeo, Mears, Alan J., Friedman, James S., Carter, Todd, He, Shirley, Oh, Edwin, ...

The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account...

QRX, a Novel Homeobox Gene, Modulates Photoreceptor Gene Expression (2004)

Wang, Qing-liang, Chen, Shiming, Esumi, Noriko, Swain, Prabodh K., Haines, Heidi S., Peng, Guanghua, ...

A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially...

Expression profiling of the developing and mature Nrl-/- mouse retina: Identification of retinal disease candidates and transcriptional regulatory targets of Nrl (2004)

Yoshida, Shigeo, Mears, Alan J., Friedman, James S., Carter, Todd, He, Shirley, Oh, Edwin, ...

The rod photoreceptor-specific neural retina leucine zipper protein Nrl is essential for rod differentiation and plays a critical role in regulating gene expression. In the mouse retina, rods account...

Photoreceptor specific nuclear receptor NR2E3 functions as a transcriptional activator in rod photoreceptors (2004)

Cheng, Hong, Khanna, Hemant, Oh, Edwin C. T., Hicks, David, Mitton, Kenneth P., Swaroop, Anand

NR2E3, a photoreceptor-specific orphan nuclear receptor, is believed to play a pivotal role in the differentiation of photoreceptors. Mutations in the human NR2E3 gene and its mouse ortholog are...

Nuclear receptor NR2E3 gene mutations distort human retinal laminar architecture and cause an unusual degeneration (2004)

Jacobson, Samuel G., Sumaroka, Alexander, Aleman, Tomas S., Cideciyan, Artur V., Schwartz, Sharon B., Roman, Alejandro J., ...

Mutations in the nuclear receptor gene, NR2E3, cause a disorder of human retinal photoreceptor development characterized by hyperfunction and excess of the minority S (short wavelength or blue) cone...

Mutation in a short-chain collagen gene, CTRP5, results in extracellular deposit formation in late-onset retinal degeneration - a genetic model for age-related macular degeneration (2003)

Hayward, Caroline, Shu, Xinhua, Cideciyan, Artur V, Lennon, Alan, Barran, Perdita, Zareparsi, Sepideh, ...

A primary feature of age-related macular degeneration (AMD) is the presence of extracellular deposits between the retinal pigment epithelium (RPE) and underlying Bruch's membrane, leading to RPE...

Mutation in a short-chain collagen gene, CTRP5, results in extracellular deposit formation in late-onset retinal degeneration - a genetic model for age-related macular degeneration (2003)

Hayward, Caroline, Shu, Xinhua, Cideciyan, Artur V, Lennon, Alan, Barran, Perdita, Zareparsi, Sepideh, ...

A primary feature of age-related macular degeneration (AMD) is the presence of extracellular deposits between the retinal pigment epithelium (RPE) and underlying Bruch's membrane, leading to RPE...

Interaction of retinal bZIP transcription factor NRL with Flt3-interacting zinc-finger protein Fiz1: possible role of Fiz1 as a transcriptional repressor (2003)

Mitton, Kenneth P., Swain, Prabodh K., Khanna, Hemant, Dowd, Mary, Apel, Ingrid J., Swaroop, Anand

NRL (neural retina leucine zipper) is a basic motif leucine zipper transcription factor of the Maf-subfamily. Multiple phosphorylated isoforms of NRL are detected specifically in rod photoreceptors....

Mutation in a short-chain collagen gene, CTRP5, results in extracellular deposit formation in late-onset retinal degeneration - a genetic model for age-related macular degeneration (2003)

Hayward, Caroline, Shu, Xinhua, Cideciyan, Artur V, Lennon, Alan, Barran, Perdita, Zareparsi, Sepideh, ...

A primary feature of age-related macular degeneration (AMD) is the presence of extracellular deposits between the retinal pigment epithelium (RPE) and underlying Bruch's membrane, leading to RPE...

Mutation in a short-chain collagen gene, CTRP5, results in extracellular deposit formation in late-onset retinal degeneration - a genetic model for age-related macular degeneration (2003)

Hayward, Caroline, Shu, Xinhua, Cideciyan, Artur V, Lennon, Alan, Barran, Perdita, Zareparsi, Sepideh, ...

A primary feature of age-related macular degeneration (AMD) is the presence of extracellular deposits between the retinal pigment epithelium (RPE) and underlying Bruch's membrane, leading to RPE...

Five novel RPGR mutations in families with X-linked retinitis pigmentosa Communicated by Mark H. Paalman Online Citation: Human Mutation , Mutation in Brief #396 (2000) Online http://journals.wiley.com/1059-7794/pdf/mutation/396.pdf (2001)

Guevara-Fujita, Maria, Fahrner, Stacey, Buraczynska, Kinga, Cook, Jason, Wheaton, Dianna, Cortes, Fanny, ...

X-linked forms of retinitis pigmentosa (XLRP) are among the most severe because of their early onset, often leading to significant visual impairment before the fourth decade. RP3, genetically...

Dinucleotide polymorphism at the DXS1178 locus is tightly linked to PGK1 at Xq13 (1995)

Swaroop, Anand, Yang-Feng, Teresa L., Fujita, Ricardo, Pakstis, Andrew J., Skolnick, Craig

A polymorphic CA repeat (locus name DXS1178 ) was isolated from a 1-megabase YAC (OTCC) containing the OTC gene, located at Xp21.1. However, amplification in human-rodent hybrid cells and segregation...

Localization of the Gene for Pigment Epithelium-Derived Factor (PEDF) to Chromosome 17p13.1 and Expression in Cultured Human Retinoblastoma Cells (1994)

Tombran-Tink, Joyce, Pawar, Hemant, Swaroop, Anand, Rodriguez, Ignacio, Chader, Gerald J.

The gene for pigment epithelium-derived factor (PEDF) was localized to chromosome 17 by the analysis of three independent somatic cell hybrid panels. Fluorescence in situ hybridization shows a...

Nucleotide sequence of a cDNA for the [beta]2 subunit isoform of Na+, K+-ATPase from human retina (1994)

Hernando, N., Martin-Vasallo, P., Ghosh, S., Ghosh, P. K., Swaroop, Anand, Coca-Prados, M.

Using as probe the entire human liver cDNA clone coding for the the [beta]2 subunit isoform of the Na+,K+-ATPase, which lacks the initiation codon ATG, and the entire 5'-untranslated region...

Molecular characterization of a novel human gene, SEC13R, related to the yeast secretory pathway gene SEC13, and mapping to a conserved linkage group on human chromosome 3p24-p25 and mouse chromosome 6 (1994)

Swaroop, Anand, Yang-Feng, Teresa L., Liu, Wanguo, Gieser, Linn, Barrow, Lon L., Chen, Kuang-Chao, ...

We previously described sequence tags from 58 novel dlrectionally cloned human cDNAs from an enriched retinal pigment epithelial cell line library (Gleser and Swaroop, 1992). The nucleotlde sequence...

Molecular Characterization of the Murine Neural Retina Leucine Zipper Gene, Nrl (1993)

Farjo, Qais, Jackson, Anne U., Xu, Junzhe, Gryzenia, Michele, Skolnick, Craig, Agarwal, Neeraj, ...

The NRL gene (D14S46E) is expressed in cells of human retina and encodes a putative DNA-binding protein of the leucine zipper family. Here we describe the analysis of the murine homolog of the NRL...

Mapping of the neural retina leucine zipper gene, Nrl , to mouse Chromosome 14 (1993)

Burmeister, Margit L., Jackson, Anne U., Meisler, Miriam H., Farjo, Qais, Swaroop, Anand, Mortlock, Douglas P., ...

Peer Reviewed

Neural retina-specific leucine zipper gene NRL (D14S46E) maps to human chromosome 14q11.1-q11.2 (1992)

Yang-Feng, Teresa L., Swaroop, Anand

The product of a neural retina-specific gene, NRL, belongs to the "leucine zipper" family of DNA-binding proteins and has a strong similarity to the v-maf oncogene product. The NRL gene maps to human...

Expressed sequence tags and chromosomal localization of cDNA clones from a subtracted retinal pigment epithelium library (1992)

Gieser, Linn, Swaroop, Anand

Expressed sequence tags (ESTs) provide useful molecular landmarks for physical mapping and identify the position of an expressed region in the genome. The use of subtracted cDNA libraries enriched...

A simple and efficient cDNA library subtraction procedure: isolation of human retina-specific cDNA clones (1991)

Swaroop, Anand, Xu, Junzhe, Agarwal, Neeraj, Weissman, Sherman M.

Differential expression of novel Gs{alpha} signal transduction protein cDNA species (1991)

Swaroop, Anand, Agarwal, Neeraj, Gruen, Jeffrey R., Bick, David, Weissman, Sherman M.

The Gsα guanine nucleotide-binding signal transduction protein is part of a heterotrimeric complex that is involved in the stimulation of adenylate cyclase upon activation of membrane receptors. We...

The mRNA of a human class I gene HLA G/HLA 6.0 exhibits a restricted pattern of expression (1990)

Shukla, Hridayabhiranjan, Swaroop, Anand, Srivastava, Rakesh, Weissman, Sherman M.

Charon BS (+) and (-), versatile {lambda} phage vectors for constructing directional cDNA libraries and their efficient transfer to plasmids (1988)

Swaroop, Anand, Weissman, Sherman M.

Noradrenaline treatment of rats stimulates $H_2O_2$ generation in liver mitochondria. (1983)

Swaroop, Anand, Patole, Milind S, Puranam, Ram S, Ramasarma, T

Treatment of rats with noradrenaline stimulated $H_20_2$ generation in liver mitochondria using succinate, choline or glycerol 1-phosphate as substrate. The dehydrogenase activity with either...

Noradrenaline treatment of rats stimulates $H_2O_2$ generation in liver mitochondria. (1983)

Swaroop, Anand, Patole, Milind S, Puranam, Ram S, Ramasarma, T

Treatment of rats with noradrenaline stimulated $H_20_2$ generation in liver mitochondria using succinate, choline or glycerol 1-phosphate as substrate. The dehydrogenase activity with either...

Generation of hydrogen peroxide on oxidation of NADH by hepatic plasma membranes (1981)

Ramasarma, T, Swaroop, Anand, MacKellar, W, Crane, FL

The oxidation of NADH by mouse liver plasma membranes was shown to be accompanied by the formation of H2O2. The rate of H2O2 formation was less than one-tenth the rate of oxygen uptake and much...

Retinopathy mutations in the bZIP protein NRL alter phosphorylation and transcriptional activity This article is a US Government work, and, as such, is in the public domain in the United States of America. Communicated by Peter Humphries

Kanda, Atsuhiro, Friedman, James S., Nishiguchi, Koji M., Swaroop, Anand

The transcription factor neural retina leucine zipper (NRL) is required for rod photoreceptor differentiation during mammalian retinal development. NRL interacts with CRX, NR2E3, and other...

Centrosomal-ciliary gene CEP290/NPHP6 mutations result in blindness with unexpected sparing of photoreceptors and visual brain: implications for therapy of Leber congenital amaurosis Communicated by Andrew Wilkie This article is a US Government work and, as such, is in the public domain in the United States of America.

Cideciyan, Artur V., Aleman, Tomas S., Jacobson, Samuel G., Khanna, Hemant, Sumaroka, Alexander, Aguirre, Geoffrey K., ...

Mutations in the centrosomal-ciliary gene CEP290/NPHP6 are associated with Joubert syndrome and are the most common cause of the childhood recessive blindness known as Leber congenital amaurosis...