WorldCat Identities

Sirota, Marina

Overview
Works: 24 works in 28 publications in 1 language and 230 library holdings
Genres: Academic theses 
Roles: Editor, Other, Author, Contributor
Publication Timeline
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Most widely held works by Marina Sirota
A bioinformatics guide for molecular biologists by Marina Sirota( Book )

5 editions published between 2013 and 2014 in English and held by 194 WorldCat member libraries worldwide

Informatics can vastly assist progress in research and development in cell and molecular biology and biomedicine. However, many investigators are either unaware of the ways in which informatics can improve their research or find it inaccessible due to a feeling of "informatics anxiety." This sense of apprehension results from improper communication of the principles behind these approaches and of the value of the many tools available. In fact, many researchers are inherently distrustful of these tools. A more complete understanding of bioinformatics offered in A Bioinformatics Guide for Molecular Biologists will allow the reader to become comfortable with these techniques, encouraging their use - thus helping to make sense of the vast accumulation of data. To make these concepts more accessible, the editors approach the field of bioinformatics from the viewpoint of a molecular biologist, (1) arming the biologist with a basic understanding of the fundamental concepts in the field, (2) presenting approaches for using the tools from the standpoint of the data for which they are created, and (3) showing how the field of informatics is quickly adapting to the advancements in biology and biomedical technologies. All concepts are paired with recommendations for the appropriate programming environment and tools best suited to solve the particular problem at hand. It is a must-read for those interested in learning informatics techniques required for successful research and development in the laboratory. -- from back cover
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novogene prediction by Samuel S Gross( )

1 edition published in 2007 in English and held by 2 WorldCat member libraries worldwide

Environmental pollution and social factors as contributors to preterm birth in Fresno County by Amy M Padula( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks by Joel T Dudley( )

1 edition published in 2010 in English and held by 2 WorldCat member libraries worldwide

Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety by Milena A Gianfrancesco( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Correction to: Hydroxychloroquine dosing in immune-mediated diseases: implications for patient safety by Milena A Gianfrancesco( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research by March of Dimes Prematurity Research Centers( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing by Silvia Pineda( )

1 edition published in 2019 in English and held by 2 WorldCat member libraries worldwide

Developing and applying integrative computational methods to study autoimmune disease by Marina Sirota( )

1 edition published in 2010 in English and held by 2 WorldCat member libraries worldwide

Autoimmune diseases are painful and debilitating conditions which affect millions of people in the United States and all over the world. At present such conditions are often difficult to diagnose and many have no satisfactory treatment. Given the wealth and availability of genomic data such as genetic variation and gene expression, computational integrative methods provide a powerful opportunity to improve human health by refining the current knowledge about diagnostics, therapeutics and disease mechanism. For instance numerous genome-wide association studies (GWAS) performed across autoimmune diseases, provide a great opportunity to study disease relationships based on genetic variation. Comparing such profiles allows us to quantify allele-specific pair-wise relationships between these diseases to find two broad clusters of autoimmune disease. We furthermore find that certain polymorphisms, toggle SNPs, predispose individuals to one class of autoimmune disease but are protective against the other class. While studying allelic differences between diseases may point to key novel disease-specific genes and pathways, studying similarities across diseases might lead to discovery of common therapeutic options as well as common disease mechanisms. In particular we integrate genetic variation data across several studies to discover the role of a complement factor in Rheumatoid Arthritis and Multiple Sclerosis. Gene expression microarrays are also often used to study human diseases as well as the perturbation of biological systems by drug compounds providing an opportunity to discover novel relationships between diseases and drugs. We present a systematic computational method to predict novel therapeutic indications based on gene expression. We tested our top prediction for Crohn's disease (CD) using the rat model of inflammatory bowel disease (IBD), and successfully demonstrated the predicted efficacy of an anti-seizure drug in treating disease. In this work, we have showed that integrative computational tools can be used to improve diagnostics, learn more about disease mechanism and discover novel therapeutics for autoimmune disease
Cumulative Risk and Impact Modeling on Environmental Chemical and Social Stressors by Hongtai Huang( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth by Nadav Rappoport( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Comprehensive analysis of normal adjacent to tumor transcriptomes by Dvir Aran( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research by Bin Chen( )

1 edition published in 2015 in English and held by 2 WorldCat member libraries worldwide

Are minor alleles more likely to be risk alleles? by Takashi Kido( )

1 edition published in 2018 in English and held by 2 WorldCat member libraries worldwide

Effect of genome and environment on metabolic and inflammatory profiles by Marina Sirota( )

1 edition published in 2015 in Undetermined and held by 1 WorldCat member library worldwide

Twin and family studies have established the contribution of genetic factors to variation in metabolic, hematologic and immunological parameters. The majority of these studies analyzed single or combined traits into pre-defined syndromes. In the present study, we explore an alternative multivariate approach in which a broad range of metabolic, hematologic, and immunological traits are analyzed simultaneously to determine the resemblance of monozygotic (MZ) twin pairs, twin-spouse pairs and unrelated, non-cohabiting individuals. A total of 517 participants from the Netherlands Twin Register, including 210 MZ twin pairs and 64 twin-spouse pairs, took part in the study. Data were collected on body composition, blood pressure, heart rate, and multiple biomarkers assessed in fasting blood samples, including lipid levels, glucose, insulin, liver enzymes, hematological measurements and cytokine levels. For all 51 measured traits, pair-wise Pearson correlations, correcting for family relatedness, were calculated across all the individuals in the cohort. Hierarchical clustering techniques were applied to group the measured traits into sub-clusters based on similarity. Sub-clusters were observed among metabolic traits and among inflammatory markers. We defined a phenotypic profile as the collection of all the traits measured for a given individual. Average within-pair similarity of phenotypic profiles was determined for the groups of MZ twin pairs, spouse pairs and pairs of unrelated individuals. The average similarity across the full phenotypic profile was higher for MZ twin pairs than for spouse pairs, and lowest for pairs of unrelated individuals. Cohabiting MZ twins were more similar in their phenotypic profile compared to MZ twins who no longer lived together. The correspondence in the phenotypic profile is therefore determined to a large degree by familial, mostly genetic, factors, while household factors contribute to a lesser degree to profile similarity
Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research by Marina Sirota( )

1 edition published in 2018 in Undetermined and held by 1 WorldCat member library worldwide

The original version of the Data Descriptor contained errors in the author list and affiliations. Rita Leite's first name was misspelled as "Rite" and affiliations 4 and 5 were incorrectly swapped. In addition, members of the March of Dimes Prematurity Research Center consortium were not listed in the agreed positions within the author list. These errors have now been corrected in the HTML and PDF versions
Using health-system-wide data to understand hepatitis B virus prophylaxis and reactivation outcomes in patients receiving rituximab( )

1 edition published in 2017 in English and held by 1 WorldCat member library worldwide

Abstract : Abstract: Hepatitis B virus (HBV) reactivation in the setting of rituximab use is a potentially fatal but preventable safety event. The rate of HBV screening and proportion of patients at risk who receive antiviral prophylaxis in patients initiating rituximab is unknown. We analyzed electronic health record (EHR) data from 2 health systems, a university center and a safety net health system, including diagnosis grouper codes, problem lists, medications, laboratory results, procedures codes, clinical encounter notes, and scanned documents. We identified all patients who received rituximab between 6/1/2012 and 1/1/2016. We calculated the proportion of rituximab users with inadequate screening for HBV according to the Centers for Disease Control guidelines for detecting latent HBV infection before their first rituximab infusion during the study period. We also assessed the proportion of patients with positive hepatitis B screening tests who were prescribed antiviral prophylaxis. Finally, we characterized safety failures and adverse events. We included 926 patients from the university and 132 patients from the safety net health system. Sixty-one percent of patients from the university had adequate screening for HBV compared with 90% from the safety net. Among patients at risk for reactivation based on results of HBV testing, 66% and 92% received antiviral prophylaxis at the university and safety net, respectively. We found wide variations in hepatitis B screening practices among patients receiving rituximab, resulting in unnecessary risks to patients. Interventions should be developed to improve patient safety procedures in this high-risk patient population. Abstract : Supplemental Digital Content is available in the text
Enabling precision medicine in neonatology, an integrated repository for preterm birth research by Marina Sirota( )

1 edition published in 2018 in Undetermined and held by 1 WorldCat member library worldwide

Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes' Database for Preterm Birth Research (http://www.immport.org/resources/mod), a unique resource that contains a variety of 'omics' datasets related to preterm birth. The database is open publicly, and as of January 2018, links 13 molecular studies with data across tens of thousands of patients from 6 measurement modalities. The data in the repository are highly diverse and include genomic, transcriptomic, immunological, and microbiome data. Relevant datasets are augmented with additional molecular characterizations of almost 25,000 biological samples from public databases. We believe our data-sharing efforts will lead to enhanced research collaborations and coordination accelerating the overall pace of discovery in preterm birth research
Enabling precision medicine in neonatology, an integrated repository for preterm birth research by Marina Sirota( )

1 edition published in 2018 in Undetermined and held by 1 WorldCat member library worldwide

Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes' Database for Preterm Birth Research (http://www.immport.org/resources/mod), a unique resource that contains a variety of 'omics' datasets related to preterm birth. The database is open publicly, and as of January 2018, links 13 molecular studies with data across tens of thousands of patients from 6 measurement modalities. The data in the repository are highly diverse and include genomic, transcriptomic, immunological, and microbiome data. Relevant datasets are augmented with additional molecular characterizations of almost 25,000 biological samples from public databases. We believe our data-sharing efforts will lead to enhanced research collaborations and coordination accelerating the overall pace of discovery in preterm birth research
Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research by Marina Sirota( )

1 edition published in 2018 in Undetermined and held by 1 WorldCat member library worldwide

The original version of the Data Descriptor contained errors in the author list and affiliations. Rita Leite's first name was misspelled as "Rite" and affiliations 4 and 5 were incorrectly swapped. In addition, members of the March of Dimes Prematurity Research Center consortium were not listed in the agreed positions within the author list. These errors have now been corrected in the HTML and PDF versions
 
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A bioinformatics guide for molecular biologists
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