Search Results - "Sepulveda, Jorge L."

Using R and Bioconductor in Clinical Genomics and Transcriptomics by Sepulveda, Jorge L.

“…Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing (NGS). Recent guidelines…”
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Molecular and histologic considerations in the assessment of serrated polyps by Yang, Hui-Min, Mitchell, James M, Sepulveda, Jorge L, Sepulveda, Antonia R

“…CONTEXT : Colorectal cancer is a heterogeneous disease resulting from different molecular pathways of carcinogenesis. Recent data evaluating the histologic…”
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Changes in SARS-CoV-2 viral load and mortality during the initial wave of the pandemic in New York City by Satlin, Michael J, Zucker, Jason, Baer, Benjamin R, Rajan, Mangala, Hupert, Nathaniel, Schang, Luis M, Pinheiro, Laura C, Shen, Yanhan, Sobieszczyk, Magdalena E, Westblade, Lars F, Goyal, Parag, Wells, Martin T, Sepulveda, Jorge L, Safford, Monika M

“…Public health interventions such as social distancing and mask wearing decrease the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)…”
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When to re-order laboratory tests? Learning laboratory test shelf-life by Levy-Fix, Gal, Gorman, Sharon Lipsky, Sepulveda, Jorge L., Elhadad, Noémie

“…[Display omitted] •Order logs of laboratory tests can indicate when to re-test laboratory tests.•Methods from anomaly detection are a powerful way to capture…”
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Pretest Symptom Duration and Cycle Threshold Values for Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-Transcription Polymerase Chain Reaction Predict Coronavirus Disease 2019 Mortality by Miller, Emily Happy, Zucker, Jason, Castor, Delivette, Annavajhala, Medini K, Sepulveda, Jorge L, Green, Daniel A, Whittier, Susan, Scherer, Matthew, Medrano, Nicola, Sobieszczyk, Magdalena E, Yin, Michael T, Kuhn, Louise, Uhlemann, Anne-Catrin

“…Abstract Background The relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and patient symptom duration in both in-…”
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Evaluation of Mutational Testing of Preneoplastic Barrett's Mucosa by Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Endoscopic Samples for Detection of Concurrent Dysplasia and Adenocarcinoma in Barrett's Esophagus by Del Portillo, Armando, Lagana, Stephen M, Yao, Yuan, Uehara, Takeshi, Jhala, Nirag, Ganguly, Tapan, Nagy, Peter, Gutierrez, Jorge, Luna, Aesis, Abrams, Julian, Liu, Yang, Brand, Randall, Sepulveda, Jorge L, Falk, Gary W, Sepulveda, Antonia R

“…Barrett's intestinal metaplasia (BIM) may harbor genomic mutations before the histologic appearance of dysplasia and cancer and requires frequent surveillance…”
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SARS-CoV-2 Viral Load Predicts Mortality in Patients with and without Cancer Who Are Hospitalized with COVID-19 by Westblade, Lars F., Brar, Gagandeep, Pinheiro, Laura C., Paidoussis, Demetrios, Rajan, Mangala, Martin, Peter, Goyal, Parag, Sepulveda, Jorge L., Zhang, Lisa, George, Gary, Liu, Dakai, Whittier, Susan, Plate, Markus, Small, Catherine B., Rand, Jacob H., Cushing, Melissa M., Walsh, Thomas J., Cooke, Joseph, Safford, Monika M., Loda, Massimo, Satlin, Michael J.

“…Patients with cancer may be at increased risk of severe coronavirus disease 2019 (COVID-19), but the role of viral load on this risk is unknown. We measured…”
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Machine Learning Highlights Downtrending of COVID-19 Patients with a Distinct Laboratory Profile by Yang, He S., Hou, Yu, Zhang, Hao, Chadburn, Amy, Westblade, Lars F., Fedeli, Richard, Steel, Peter A. D., Racine-Brzostek, Sabrina E., Velu, Priya, Sepulveda, Jorge L., Satlin, Michael J., Cushing, Melissa M., Kaushal, Rainu, Zhao, Zhen, Wang, Fei

“…Background . New York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2-confirmed cases in 2020. A change in the pattern…”
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Combinatorial Expression of GATA4, Nkx2-5, and Serum Response Factor Directs Early Cardiac Gene Activity by Sepulveda, Jorge L., Vlahopoulos, Spiros, Iyer, Dinakar, Belaguli, Narasimhaswamy, Schwartz, Robert J.

“…Herein, the restricted expression of serum response factors (SRF) closely overlapped withNkx2-5 and GATA4 transcripts in early chick embryos coinciding with…”
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Cardiomyogenic differentiation potential of human adipose precursor cells by Lee, Wen-Chi C, Sepulveda, Jorge L, Rubin, J. Peter, Marra, Kacey G

“…Abstract DNA demethylation agent 5-azacytidine has been widely described in literature as an effective chemical stimulus used to promote cardiomyogenic…”
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Clinical Performance of SARS-CoV-2 Molecular Tests by Green, Daniel A, Zucker, Jason, Westblade, Lars F, Whittier, Susan, Rennert, Hanna, Velu, Priya, Craney, Arryn, Cushing, Melissa, Liu, Dakai, Sobieszczyk, Magdalena E, Boehme, Amelia K, Sepulveda, Jorge L

“…Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19),…”
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Demonstration and Characterization of Mutations Induced by Helicobacter pylori Organisms in Gastric Epithelial Cells by Yao, Yuan, Tao, Hong, Park, Dong Il, Sepulveda, Jorge L., Sepulveda, Antonia R.

“…Background:  Helicobacter pylori gastritis increases gastric cancer risk. Microsatellite instability‐type mutations are secondary to deficient DNA mismatch…”
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The ideal laboratory information system by Sepulveda, Jorge L, Young, Donald S

“…Laboratory information systems (LIS) are critical components of the operation of clinical laboratories. However, the functionalities of LIS have lagged…”
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Development of an Accessible and Scalable Quantitative Polymerase Chain Reaction Assay for Monkeypox Virus Detection by Porzucek, Abigail J, Proctor, Abigale M, Klinkhammer, Katharina E, Tritsch, Sarah R, Robertson, Molly A, Bashor, Jonathan P, Villani, Jack, Sepulveda, Jorge L, Mores, Christopher N

“…Abstract During the 2022 monkeypox (MPX) outbreak, testing has been limited and results delayed, allowing ongoing transmission. Gold-standard quantitative…”
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Temporal trends of hemoglobin A1c testing by Pivovarov, Rimma, Albers, David J, Hripcsak, George, Sepulveda, Jorge L, Elhadad, Noémie

“…The study of utilization patterns can quantify potential overuse of laboratory tests and find new ways to reduce healthcare costs. We demonstrate the use of…”
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Blood component utilization in COVID‐19 patients in New York City: Transfusions do not follow the curve by DeSimone, Robert A., Costa, Victoria A., Kane, Kathleen, Sepulveda, Jorge L., Ellsworth, Grant B., Gulick, Roy M., Zucker, Jason, Sobieszcyk, Magdalena E, Schwartz, Joseph, Cushing, Melissa M.

“…Background Blood suppliers and transfusion services have worked diligently to maintain an adequate blood supply during the COVID‐19 pandemic. Our experience…”
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Performance of the Abbott ID NOW rapid SARS-CoV-2 amplification assay in relation to nasopharyngeal viral RNA loads by Sepulveda, Jorge L., Abdulbaki, Rami, Sands, Zachary, Codoy, Maria, Mendoza, Salome, Isaacson, Nancy, Kochar, Olga, Keiser, John, Haile-Mariam, Tenagne, Meltzer, Andrew C., Mores, Christopher N., Sepulveda, Antonia R.

“…•Calibration of the Xpert with viral stock dilutions was linear and reproducible.•Overall Xpert/ID-NOW positive agreement = 70% and negative…”
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Racial Differences in the Association Between Luminal Master Regulator Gene Expression Levels and Breast Cancer Survival by Byun, Jung S, Singhal, Sandeep K, Park, Samson, Yi, Dae Ik, Yan, Tingfen, Caban, Ambar, Jones, Alana, Mukhopadhyay, Partha, Gil, Sara M, Hewitt, Stephen M, Newman, Lisa, Davis, Melissa B, Jenkins, Brittany D, Sepulveda, Jorge L, De Siervi, Adriana, Nápoles, Anna María, Vohra, Nasreen A, Gardner, Kevin

“…Compared with their European American (EA) counterparts, African American (AA) women are more likely to die from breast cancer in the United States. This…”
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High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing by Sepulveda, Jorge L, Gutierrez-Pajares, Jorge L, Luna, Aesis, Yao, Yuan, Tobias, John W, Thomas, Steven, Woo, Yanghee, Giorgi, Federico, Komissarova, Elena V, Califano, Andrea, Wang, Timothy C, Sepulveda, Antonia R

“…Gastric cancers are the most frequent gastric malignancy and usually arise in the sequence of Helicobacter pylori -associated chronic gastritis. CpG…”
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High‐resolution genomic alterations in Barrett's metaplasia of patients who progress to esophageal dysplasia and adenocarcinoma by Sepulveda, Jorge L., Komissarova, Elena V., Kongkarnka, Sarawut, Friedman, Richard A., Davison, Jon M., Levy, Brynn, Bryk, Diana, Jobanputra, Vaidehi, Del Portillo, Armando, Falk, Gary W., Sonett, Joshua R., Lightdale, Charles J., Abrams, Julian A., Wang, Timothy C., Sepulveda, Antonia R.

“…The main risk factor for esophageal dysplasia and adenocarcinoma (DAC) is Barrett's esophagus (BE), characterized by intestinal metaplasia. The critical…”
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