Scientific Commons: 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...

Meta-analysis of genome scans of age-related macular degeneration (2005)

Fisher, Sheila A., Abecasis, Goncalo R., Yashar, Beverly M., Zareparsi, Sepideh, Swaroop, Anand, Iyengar, Sudha K., ...

A genetic contribution to the development of age-related macular degeneration (AMD) is well established. Several genome-wide linkage studies have identified a number of putative susceptibility loci...

Network constrained clustering for gene microarray data (2005)

Zhu, Dongxiao, Hero, Alfred O., Cheng, Hong, Khanna, Ritu, Swaroop, Anand

Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective. Directly inspired by metabolic network structural studies, we propose an improved gene clustering...

Network constrained clustering for gene microarray data (2005)

Zhu, Dongxiao, Hero, Alfred O, Cheng, Hong, Khanna, Ritu, Swaroop, Anand

Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective. Directly inspired by metabolic network structural studies, we propose an improved gene clustering...

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, ...