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Your search keyword '"Ramrattan, Girish"' showing total 16 results
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16 results on '"Ramrattan, Girish"'

1. A retrospective multi-site examination of chronic kidney disease using longitudinal laboratory results and metadata to identify clinical and financial risk

Author

Fung, Mark, Haghamad, Aya, Montgomery, Elizabeth, Swanson, Kathleen, Wilkerson, Myra L., Stathakos, Kimon, VanNess, Richard, Nowak, Sarah A., Wilburn, Clayton, Kavus, Haluk, Swid, Mohammed Amer, Okoye, Nkemakonam, Ziemba, Yonah C., Ramrattan, Girish, Macy, Jonathan, McConnell, John, Lewis, Mary Jane, Bailey, Beth, Shotorbani, Khosrow, and Crawford, James M.

Published
2024
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5. Rapid Emergence of SARS-CoV-2 in the Greater New York Metropolitan Area: Geolocation, Demographics, Positivity Rates, and Hospitalization for 46 793 Persons Tested by Northwell Health.

Author

Reichberg, Samuel B, Mitra, Partha P, Haghamad, Aya, Ramrattan, Girish, Crawford, James M, Consortium, Northwell COVID-19 Research, Berry, Gregory J, Davidson, Karina W, Drach, Alex, Duong, Scott, Juretschko, Stefan, Maria, Naomi I, Yang, Yihe, and Ziemba, Yonah C

Subjects
AGE distribution, HOSPITAL care, INCOME, COVID-19 testing, METROPOLITAN areas, POLYMERASE chain reaction, POPULATION geography, RACE, SEX distribution, DISEASE incidence, REVERSE transcriptase polymerase chain reaction, DESCRIPTIVE statistics, COVID-19
Abstract

Background In March 2020, the greater New York metropolitan area became an epicenter for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The initial evolution of case incidence has not been well characterized. Methods Northwell Health Laboratories tested 46 793 persons for SARS-CoV-2 from 4 March through 10 April. The primary outcome measure was a positive reverse transcription–polymerase chain reaction test for SARS-CoV-2. The secondary outcomes included patient age, sex, and race, if stated; dates the specimen was obtained and the test result; clinical practice site sources; geolocation of patient residence; and hospitalization. Results From 8 March through 10 April, a total of 26 735 of 46 793 persons (57.1%) tested positive for SARS-CoV-2. Males of each race were disproportionally more affected than females above age 25, with a progressive male predominance as age increased. Of the positive persons, 7292 were hospitalized directly upon presentation; an additional 882 persons tested positive in an ambulatory setting before subsequent hospitalization, a median of 4.8 days later. Total hospitalization rate was thus 8174 persons (30.6% of positive persons). There was a broad range (>10-fold) in the cumulative number of positive cases across individual zip codes following documented first caseincidence. Test positivity was greater for persons living in zip codes with lower annual household income. Conclusions Our data reveal that SARS-CoV-2 incidence emerged rapidly and almost simultaneously across a broad demographic population in the region. These findings support the premise that SARS-CoV-2 infection was widely distributed prior to virus testing availability. [ABSTRACT FROM AUTHOR]

Published
2020
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7. Gastric Carcinomas With Lymphoid Stroma

Author

Hissong, Erika, primary, Ramrattan, Girish, additional, Zhang, Pan, additional, Zhou, Xi Kathy, additional, Young, Gloria, additional, Klimstra, David S., additional, Shia, Jinru, additional, Fernandes, Helen, additional, and Yantiss, Rhonda K., additional

Published
2018
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8. BpWrapper:BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

Author

Hernandez, Yozen, Bernstein, Rocky, Pagan, Pedro, Vargas, Levy, McCaig, William, Ramrattan, Girish, Akther, Saymon, Larracuente, Amanda, Di, Lia, Vieira, Filipe Jorge Garrett, Qiu, Wei-Gang, Hernandez, Yozen, Bernstein, Rocky, Pagan, Pedro, Vargas, Levy, McCaig, William, Ramrattan, Girish, Akther, Saymon, Larracuente, Amanda, Di, Lia, Vieira, Filipe Jorge Garrett, and Qiu, Wei-Gang

Published
2018

11. Erratum for Martin et al., Phylogenomic Identification of Regulatory Sequences in Bacteria: an Analysis of Statistical Power and an Application to Borrelia burgdorferi Sensu Lato

Author

Martin, Che L., primary, Sukarna, Tika Y., additional, Akther, Saymon, additional, Ramrattan, Girish, additional, Pagan, Pedro, additional, Di, Lia, additional, Mongodin, Emmanuel F., additional, Fraser, Claire M., additional, Schutzer, Steven E., additional, Luft, Benjamin J., additional, Casjens, Sherwood R., additional, and Qiu, Wei-Gang, additional

Published
2015
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13. Phylogenomic Identification of Regulatory Sequences in Bacteria: an Analysis of Statistical Power and an Application to Borrelia burgdorferi Sensu Lato

Author

Martin, Che I., primary, Sukarna, Tika Y., additional, Akther, Saymon, additional, Ramrattan, Girish, additional, Pagan, Pedro, additional, Di, Lia, additional, Mongodin, Emmanuel F., additional, Fraser, Claire M., additional, Schutzer, Steven E., additional, Luft, Benjamin J., additional, Casjens, Sherwood R., additional, and Qiu, Wei-Gang, additional

Published
2015
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14. BorreliaBase: a phylogeny-centered browser of Borrelia genomes

Author

Di, Lia, primary, Pagan, Pedro E, additional, Packer, Daniel, additional, Martin, Che L, additional, Akther, Saymon, additional, Ramrattan, Girish, additional, Mongodin, Emmanuel F, additional, Fraser, Claire M, additional, Schutzer, Steven E, additional, Luft, Benjamin J, additional, Casjens, Sherwood R, additional, and Qiu, Wei-Gang, additional

Published
2014
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16. Phylogenomic Identification of Regulatory Sequences in Bacteria: an Analysis of Statistical Power and an Application to Borrelia burgdorferiSensu Lato

Author

Martin, Che I., Sukarna, Tika Y., Akther, Saymon, Ramrattan, Girish, Pagan, Pedro, Di, Lia, Mongodin, Emmanuel F., Fraser, Claire M., Schutzer, Steven E., Luft, Benjamin J., Casjens, Sherwood R., and Qiu, Wei-Gang

Abstract

ABSTRACTPhylogenomic footprinting is an approach for ab initioidentification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical significance of conserved intergenic spacer (IGS) sequences. Simulations show that the binomial model is robust to variations in the value of evolutionary parameters, including base frequencies and the transition-to-transversion ratio. We used the model to search for regulatory sequences in the Lyme disease species group (Borrelia burgdorferisensu lato) using 23 genomes. The model indicates that the currently available set of Borreliagenomes would not yield regulatory sequences shorter than five bases, suggesting that genome sequences of additional B. burgdorferi sensu latospecies are needed. Nevertheless, we show that previously known regulatory elements are indeed strongly conserved in sequence or structure across these Borreliaspecies. Further, we predict with sufficient confidence two new RpoS binding sites, 39 promoters, 19 transcription terminators, 28 noncoding RNAs, and four sets of coregulated genes. These putative cis- and trans-regulatory elements suggest novel, Borrelia-specific mechanisms regulating the transition between the tick and host environments, a key adaptation and virulence mechanism of B. burgdorferi. Alignments of IGS sequences are available on BorreliaBase.org, an online database of orthologous open reading frame (ORF) and IGS sequences in Borrelia.IMPORTANCEWhile bacterial genomes contain mostly protein-coding genes, they also house DNA sequences regulating the expression of these genes. Gene regulatory sequences tend to be conserved during evolution. By sequencing and comparing related genomes, one can therefore identify regulatory sequences in bacteria based on sequence conservation. Here, we describe a statistical framework by which one may determine how many genomes need to be sequenced and at what level of evolutionary relatedness in order to achieve a high level of statistical significance. We applied the framework to Borrelia burgdorferi, the Lyme disease agent, and identified a large number of candidate regulatory sequences, many of which are known to be involved in regulating the phase transition between the tick vector and mammalian hosts.

Published
2015
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