Search Results - "Howard, Brian E."

SWIFT-Active Screener: Accelerated document screening through active learning and integrated recall estimation by Howard, Brian E., Phillips, Jason, Tandon, Arpit, Maharana, Adyasha, Elmore, Rebecca, Mav, Deepak, Sedykh, Alex, Thayer, Kristina, Merrick, B. Alex, Walker, Vickie, Rooney, Andrew, Shah, Ruchir R.

“…•Machine learning tools can reduce screening burden in systematic reviews.•SWIFT-Active Screener is a machine learning web app for document screening.•It uses…”
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A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics by Mav, Deepak, Shah, Ruchir R, Howard, Brian E, Auerbach, Scott S, Bushel, Pierre R, Collins, Jennifer B, Gerhold, David L, Judson, Richard S, Karmaus, Agnes L, Maull, Elizabeth A, Mendrick, Donna L, Merrick, B Alex, Sipes, Nisha S, Svoboda, Daniel, Paules, Richard S

“…Changes in gene expression can help reveal the mechanisms of disease processes and the mode of action for toxicities and adverse effects on cellular responses…”
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High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants by Howard, Brian E, Hu, Qiwen, Babaoglu, Ahmet Can, Chandra, Manan, Borghi, Monica, Tan, Xiaoping, He, Luyan, Winter-Sederoff, Heike, Gassmann, Walter, Veronese, Paola, Heber, Steffen

“…We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time…”
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Low-calorie sweeteners and health outcomes: A demonstration of rapid evidence mapping (rEM) by Lam, Juleen, Howard, Brian E., Thayer, Kristina, Shah, Ruchir R.

“…“Evidence Mapping” is an emerging tool that is increasingly being used to systematically identify, review, organize, quantify, and summarize the literature. It…”
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A Tissue-Specific and Toxicology-Focused Knowledge Graph by Tripodi, Ignacio J., Schmidt, Lena, Howard, Brian E., Mav, Deepak, Shah, Ruchir

“…Molecular biology-focused knowledge graphs (KGs) are directed graphs that integrate information from heterogeneous sources of biological and biomedical data,…”
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Risk and Protective Factors in the COVID-19 Pandemic: A Rapid Evidence Map by Elmore, Rebecca, Schmidt, Lena, Lam, Juleen, Howard, Brian E, Tandon, Arpit, Norman, Christopher, Phillips, Jason, Shah, Mihir, Patel, Shyam, Albert, Tyler, Taxman, Debra J, Shah, Ruchir R

“…Given the worldwide spread of the 2019 Novel Coronavirus (COVID-19), there is an urgent need to identify risk and protective factors and expose areas of…”
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Unsupervised assessment of microarray data quality using a Gaussian mixture model by Howard, Brian E, Sick, Beate, Heber, Steffen

“…Quality assessment of microarray data is an important and often challenging aspect of gene expression analysis. This task frequently involves the examination…”
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SWIFT-Review: a text-mining workbench for systematic review by Howard, Brian E, Phillips, Jason, Miller, Kyle, Tandon, Arpit, Mav, Deepak, Shah, Mihir R, Holmgren, Stephanie, Pelch, Katherine E, Walker, Vickie, Rooney, Andrew A, Macleod, Malcolm, Shah, Ruchir R, Thayer, Kristina

“…There is growing interest in using machine learning approaches to priority rank studies and reduce human burden in screening literature when conducting…”
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Towards reliable isoform quantification using RNA-SEQ data by Howard, Brian E, Heber, Steffen

“…In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here we explore the use of RNA sequencing (RNA-Seq) datasets…”
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Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry by Frahm, Jennifer L., Howard, Brian E., Heber, Steffen, Muddiman, David C.

“…The number and wide dynamic range of components found in biological matrixes present several challenges for global proteomics. In this perspective, we will…”
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Towards reliable isoform quantification using RNA-SEQ data by Howard, Brian E, Heber, Steffen

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High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants: e74183 by Howard, Brian E, Hu, Qiwen, Babaoglu, Ahmet Can, Chandra, Manan, Borghi, Monica, Tan, Xiaoping, He, Luyan, Winter-Sederoff, Heike, Gassmann, Walter, Veronese, Paola

“…We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time…”
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Unsupervised Data Augmentation with Naive Augmentation and without Unlabeled Data by Lowell, David, Howard, Brian E, Lipton, Zachary C, Wallace, Byron C

“…Unsupervised Data Augmentation (UDA) is a semi-supervised technique that applies a consistency loss to penalize differences between a model's predictions on…”
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Improved RNA-Seq Partitions in Linear Models for Isoform Quantification by Howard, Brian E., Veronese, Paola, Heber, Steffen

“…Here, we present an extension of our isoform quantification method that accommodates paired end RNA Sequencing data. We explore several alternate methods of…”
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Towards Reliable Isoform Quantification Using RNA-Seq Data by Howard, B.E., Heber, S.

“…In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here we explore the use of RNA sequencing (RNA-Seq) datasets…”
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Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier by Howard, B.E., Sick, B., Perera, I., Yang Ju Im, Winter-Sederoff, H., Heber, S.

“…Recent research has demonstrated the utility of using supervised classification systems for automatic identification of low quality microarray data. However,…”
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Learning about clinical trials: the Western multicentre,randomized,double-blind, placebo-controlled clinical trial on the effect of caffeine on alertness and cardiovascular parameters by OSTBYE CHERYL PAUSE ORTRUN MEISSNER, TRULS

“…SUMMARY With an increased emphasis on evidence-based medicine, teaching epidemiology and biostatistics to medical students is becoming increasingly important…”
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