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Regression based predictor for p53 transactivation

Sivakumar Gowrisankar, Anil G Jegga
2009 BMC Bioinformatics  
This study is a partial fulfillment of Sivakumar Gowrisankar's requirements toward his Ph.D. thesis at the University of Cincinnati, Cincinnati, USA. Special thanks to Dr.  ... 
doi:10.1186/1471-2105-10-215 pmid:19602281 pmcid:PMC2719629 fatcat:o2szxlg6pzabdhox4cizcgvkoa

Mast cell transcriptional networks

Clifford M. Takemoto, Youl-Nam Lee, Anil G. Jegga, Daniella Zablocki, Stephanie Brandal, Amir Shahlaee, Suming Huang, Ying Ye, Sivakumar Gowrisankar, Jimmy Huynh, Michael A. McDevitt
2008 Blood Cells, Molecules & Diseases  
Unregulated activation of mast cells can contribute to the pathogenesis of inflammatory and allergic diseases, including asthma, rheumatoid arthritis, inflammatory bowel disease, and multiple sclerosis (1;2). Absence of mast cells in animal models can lead to impairment in the innate immune response to parasites and bacterial infections(3-5). Aberrant clonal accumulation and proliferation of mast cells can result in a variety of diseases ranging from benign cutaneous mastocytosis to systemic
more » ... tocytosis or mast cell leukemia(6). Understanding mast cell differentiation provides important insights into mechanisms of lineage selection during hematopoiesis and can provide targets for new drug development to treat mast cell disorders,. In this review, we discuss controversies related to development, sites of origin" and the transcriptional program of mast cells.
doi:10.1016/j.bcmd.2008.02.005 pmid:18406636 pmcid:PMC2478671 fatcat:myxu5o6w55eftmnr3npuza4k2m

Cognitive Decline in Alzheimer's Disease: Limited Clinical Utility for GWAS or Polygenic Risk Scores in a Clinical Trial Setting

Jack Euesden, Sivakumar Gowrisankar, Angela Xiaoyan Qu, Pamela St. Jean, Arlene R. Hughes, David J. Pulford
2020 Genes  
Alzheimer's disease (AD) is a progressive and irreversible neurological disease. The genetics and molecular mechanisms underpinning differential cognitive decline in AD are not well understood; the genetics of AD risk have been studied far more assiduously. Materials and Methods: Two phase III clinical trials measuring cognitive decline over 48 weeks using Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-cog, n = 2060) and Clinical Dementia Rating-Sum of Boxes (CDR-SB, n = 1996)
more » ... e retrospectively genotyped. A Genome-Wide Association Study (GWAS) was performed to identify and replicate genetic variants associated with cognitive decline. The relationship between polygenic risk score (PRS) and cognitive decline was tested to investigate the predictive power of aggregating many variants of individually small effect. Results: No loci met candidate gene or genome-wide significance. PRS explained a very small percentage of variance in rates of cognitive decline (ADAS-cog: 0.54%). Conclusions: These results suggest that incorporating genetic information in the prediction of cognitive decline in AD currently appears to have limited utility in clinical trials, consistent with small effect sizes estimated elsewhere. If AD progression is more heritable soon after disease onset, genetics may have more clinical utility.
doi:10.3390/genes11050501 pmid:32370229 pmcid:PMC7290959 fatcat:bk3gmcywffdvji6474e65d65fi

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data

Trevor J. Pugh, Sami S. Amr, Mark J. Bowser, Sivakumar Gowrisankar, Elizabeth Hynes, Lisa M. Mahanta, Heidi L. Rehm, Birgit Funke, Matthew S. Lebo
2015 Genetics in Medicine  
Purpose: To develop and validate VisCap, a software program targeted to clinical laboratories for inference and visualization of germ-line copy-number variants (CNVs) from targeted nextgeneration sequencing data. Methods: VisCap calculates the fraction of overall sequence coverage assigned to genomic intervals and computes log2 ratios of these values to the median of reference samples profiled using the same test configuration. Candidate CNVs are called when log2 ratios exceed user-defined
more » ... holds. Results: We optimized VisCap using 14 cases with known CNVs, followed by prospective analysis of 1,104 cases referred for diagnostic DNA sequencing. To verify calls in the prospective cohort, we used droplet digital polymerase chain reaction (PCR) to confirm 10/27 candidate CNVs and 72/72 copy-neutral genomic regions scored by VisCap. We also used a genome-wide bead array to confirm the absence of CNV calls across panels applied to 10 cases. To improve specificity, we instituted a visual scoring system that enabled experienced reviewers to differentiate true-positive from false-positive calls with minimal impact on laboratory workflow. Conclusions: VisCap is a sensitive method for inferring CNVs from targeted sequence data from targeted gene panels. Visual scoring of data underlying CNV calls is a critical step to reduce false-positive calls for follow-up testing. Genet Med advance online publication 17 December 2015
doi:10.1038/gim.2015.156 pmid:26681316 pmcid:PMC4940431 fatcat:4xhpvy452vefzhvrujp7un5o7m

Ultrasonic Studies on Molecular Interactions in Binary Mixtures of N-Methyl Aniline with Methyl Isobutylketone, +3-Pentanone, and +Cycloalkanones at 303.15 K

M. Gowrisankar, P. Venkateswarlu, K. Sivakumar, S. Sivarambabu
2013 Journal of Solution Chemistry  
Densities, q, viscosities, g, and ultrasonic sound velocities u of pure methyl isobutylketone, diethylketone, cyclopentanone, cyclohexanone, 2-methyl cyclohexanone and those of their binary mixtures with N-methyl aniline were measured at 303.15 K over the entire composition range. These experimental data have been used to calculate the excess volume (V E ), deviation in ultrasonic sound velocity (Du), isentropic compressibility
doi:10.1007/s10953-013-0003-0 pmid:23761942 pmcid:PMC3676644 fatcat:fdr56scppfh4zlzoqguqqmpqa4

Evaluation of Second-Generation Sequencing of 19 Dilated Cardiomyopathy Genes for Clinical Applications

Sivakumar Gowrisankar, Jordan P. Lerner-Ellis, Stephanie Cox, Emily T. White, Megan Manion, Kevin LeVan, Jonathan Liu, Lisa M. Farwell, Oleg Iartchouk, Heidi L. Rehm, Birgit H. Funke
2010 Journal of Molecular Diagnostics  
Gowrisankar et al JMD November 2010, Vol. 12, No. 6 Gowrisankar et al JMD November 2010, Vol. 12, No. 6 Gowrisankar et al JMD November 2010, Vol. 12, No. 6  ... 
doi:10.2353/jmoldx.2010.100014 pmid:20864638 pmcid:PMC2963910 fatcat:uueyvitoszgc5nptmjjjpomnlm

A rare penetrant mutation in CFH confers high risk of age-related macular degeneration

Soumya Raychaudhuri, Oleg Iartchouk, Kimberly Chin, Perciliz L Tan, Albert K Tai, Stephan Ripke, Sivakumar Gowrisankar, Soumya Vemuri, Kate Montgomery, Yi Yu, Robyn Reynolds, Donald J Zack (+5 others)
2011 Nature Genetics  
Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms Correspondence to: Johanna M. Seddon. CONTRIBUTIONS Raychaudhuri, JMS, NK, and MJD conceptualized this study, wrote the initial manuscript, and interpreted all results. Raychaudhuri oversaw the statistical analyses and coordinated collaborative
more » ... al efforts. JMS and MJD oversaw genome-wide genotyping of Boston-phased. Ripke analyzed the genome-wide Boston-phased genotype data to assess population stratification and recent ancestry. JMS, KC, RR, and YY organized the Boston clinical cohort. BC, PC, and DZ organized the Baltimore clinical cohort. PT and NK genotyped Baltimore samples. AT genotyped Boston samples. OI, SG, SV, and KM sequenced the CFH gene.
doi:10.1038/ng.976 pmid:22019782 pmcid:PMC3225644 fatcat:7mu6bbhew5drthtbmvh2u32ppy

The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing

Trevor J. Pugh, Melissa A. Kelly, Sivakumar Gowrisankar, Elizabeth Hynes, Michael A. Seidman, Samantha M. Baxter, Mark Bowser, Bryan Harrison, Daniel Aaron, Lisa M. Mahanta, Neal K. Lakdawala, Gregory McDermott (+4 others)
2014 Genetics in Medicine  
doi:10.1038/gim.2013.204 pmid:24503780 fatcat:5lfimcj7qrbxdhko3bmcupwtde

Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration

Johanna M Seddon, Yi Yu, Elizabeth C Miller, Robyn Reynolds, Perciliz L Tan, Sivakumar Gowrisankar, Jacqueline I Goldstein, Michael Triebwasser, Holly E Anderson, Jennyfer Zerbib, David Kavanagh, Eric Souied (+4 others)
2013 Nature Genetics  
To define the role of rare variants in advanced age-related macular degeneration (AMD) risk, we sequenced the exons of 681 genes within AMD-associated loci and pathways in 2,493 cases and controls. We first tested each gene for increased or decreased burden of rare variants in cases compared to controls. We found that 7.8% of AMD cases compared to 2.3% of controls are carriers of rare missense CFI variants (OR=3.6, p=2×10 −8 ). There was a predominance of dysfunctional variants in cases
more » ... to controls. We then tested individual variants for association to disease. We observed significant association with rare missense alleles outside CFI. Genotyping in 5,115 independent samples confirmed associations to AMD with a K155Q allele in C3 (replication p=3.5×10 −5 , OR=2.8; joint p=5.2×10 −9 , OR=3.8) and a P167S allele in C9 (replication p=2.4×10 −5 , OR=2.2; joint p=6.5×10 −7 , OR=2.2). Finally, we show that the 155Q allele in C3 results in resistance to proteolytic inactivation by CFH and CFI. These results implicate loss of C3 protein regulation and excessive alternative complement activation in AMD pathogenesis, thus informing both the direction of effect and mechanistic underpinnings of this disorder.
doi:10.1038/ng.2741 pmid:24036952 pmcid:PMC3902040 fatcat:2cxnoxijqjevncgintfuahcpsq

Thermodynamics of amine + ketone mixtures: Volumetric, speed of sound data and viscosity at 303.15 K and 308.15 K for the binary mixtures of N , N -diethylaniline + aliphatic ketones (C 3 –C 5 ) + 4-methyl-2-pentanone

Manukonda Gowrisankar, Ponneri Venkateswarlu, Kasibhatta Sivakumar, Sakamuri Sivarambabu
2017 Arabian Journal of Chemistry  
Acknowledgments The author M .Gowrisankar is highly thankful to University Grants Commission (UGC), New Delhi, India, for providing a Teacher Fellowship and expresses gratitude to the Management of J.K.C  ...  The present study is a continuation of our earlier research (Gowrisankar et al., 2012a (Gowrisankar et al., ,b, 2013a,b) ,b) on the thermodynamic properties of binary liquid mixtures.  ...  E /cm 3 mol À1 À2.385 0.1882 0.0884 0.001 Du/m s À1 51.256 À6.522 3.3786 0.049 Dj s /TPa À1 À24.422 7.217 À2.2429 0.015 Dg/mPa s 1.177 À0.161 À0.2723 0.001 Please cite this article in press as: Gowrisankar  ... 
doi:10.1016/j.arabjc.2013.09.042 fatcat:ge2mzj4lcvhtxpwlyjt2xvzdoy

DENSITIES, ULTRASONIC SOUND SPEED (u) AND VISCOSITY DATA (η) OF BINARY LIQUID MIXTURES OF ETHYLBENZOATE WITH KETONES AT VARIOUS TEMPERATURES

D Vijayalakshmi, M Gowrisankar, K Sivakumar, & Venkateswarlu
2014 International Journal of Physics and Research (IJPR)   unpublished
Gowrisankar, K. Sivakumar & P.  ...  Gowrisankar, K. Sivakumar & P. Venkateswarlu compressibility have been calculated and correlated by a Redlich-Kister type polynomial equation to derive the coefficients and standard deviation.  ... 
fatcat:7452f37dpbethctyztc2yr3l4i

Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine

Ellen Tsai, Rimma Shakbatyan, Jason Evans, Peter Rossetti, Chet Graham, Himanshu Sharma, Chiao-Feng Lin, Matthew Lebo
2016 Journal of Personalized Medicine  
Acknowledgments: We would like to thank Sivakumar Gowrisankar, Ignaty Leshchiner, Netsanet Gebremedhin, Eugene Clark, and Heidi Rehm for their contributions setting up the initial pipeline.  ... 
doi:10.3390/jpm6010012 pmid:26927186 pmcid:PMC4810391 fatcat:63hmafphhbgyhnm7h5ehkvltfm

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies [article]

Li Tai Fang, Bin Zhu, Yongmei Zhao, Wanqiu Chen, Zhaowei Yang, Liz Kerrigan, Kurt Langenbach, Maryellen de Mars, Charles Lu, Kenneth Idler, Howard Jacob, Ying Yu (+53 others)
2019 bioRxiv   pre-print
Gowrisankar of Novartis, Susan Chacko of the Center 475 for Information Technology, the National Institute of Health for their assistance with data 476 transfer; Dr.  ...  as a genomic background for other reference Acknowledgements 473 We thank Justin Zook of the National Institute of Standard Technology for advice in establishing 474 reference samples and truth set; Sivakumar  ... 
doi:10.1101/625624 fatcat:dkkd4s2k3jefhbuveyiny3zpte

Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing [article]

Wenming Xiao
2019 bioRxiv   pre-print
Acknowledgements We thank Sivakumar Gowrisankar of Novartis, Susan Chacko of the Center for Information Technology, the National Institute of Health for their assistance with data transfer, Dr.  ... 
doi:10.1101/626440 fatcat:sxskeoedlbbgblt6xjdjcmo4bm

Bisphenol A and its analogues disrupt centrosome cycle and microtubule dynamics in prostate cancer

Shuk-Mei Ho, Rahul Rao, Sarah To, Emma Schoch, Pheruza Tarapore
2017 Endocrine-Related Cancer  
Jegga, Anil G; Chen, Jing; Gowrisankar, Sivakumar; Deshmukh, Mrunal A; Gudivada, RangaChandra; ...  ...  Jegga, Anil G; Gupta, Ashima; Gowrisankar, Sivakumar; Deshmukh, Mrunal A; Connolly, Steven; Fin ...  ... 
doi:10.1530/erc-16-0175 pmid:27998958 pmcid:PMC5226663 fatcat:wjarbt6chrgxzbcnd7s6hgifry
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