Search Results - "Hendrix, David"

A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION by Danaee, Padideh, Ghaeini, Reza, Hendrix, David A

“…Cancer detection from gene expression data continues to pose a challenge due to the high dimensionality and complexity of these data. After decades of research…”
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LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search by Huang, Liang, Zhang, He, Deng, Dezhong, Zhao, Kai, Liu, Kaibo, Hendrix, David A, Mathews, David H

“…Abstract Motivation Predicting the secondary structure of an ribonucleic acid (RNA) sequence is useful in many applications. Existing algorithms [based on…”
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bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures by Lasher, Brittany, Hendrix, David A

“…Ribonucleic acid (RNA) is a polymeric molecule that is fundamental to biological processes, with structure being more highly conserved than primary sequence…”
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Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task by Valencia, Joseph D, Hendrix, David A

“…Ribosomes are information-processing macromolecular machines that integrate complex sequence patterns in messenger RNA (mRNA) transcripts to synthesize…”
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bpRNA: large-scale automated annotation and analysis of RNA secondary structure by Danaee, Padideh, Rouches, Mason, Wiley, Michelle, Deng, Dezhong, Huang, Liang, Hendrix, David

“…Abstract While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the…”
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A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential by Hill, Steven T, Kuintzle, Rachael, Teegarden, Amy, Merrill, Erich, Danaee, Padideh, Hendrix, David A

“…Abstract The current deluge of newly identified RNA transcripts presents a singular opportunity for improved assessment of coding potential, a cornerstone of…”
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The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development by Ritter, Nicole, Ali, Tamer, Kopitchinski, Nina, Schuster, Peggy, Beisaw, Arica, Hendrix, David A., Schulz, Marcel H., Müller-McNicoll, Michaela, Dimmeler, Stefanie, Grote, Phillip

“…Precisely controlled gene regulatory networks are required during embryonic development to give rise to various structures, including those of the…”
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Shadow Enhancers as a Source of Evolutionary Novelty by Hong, Joung-Woo, Hendrix, David A, Levine, Michael S

“…Some developmentally important genes can be regulated via two enhancers, one located nearby and the other, a "shadow" enhancer, 10 to 20 kilobases away…”
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Crowdsourcing to predict RNA degradation and secondary structure by Hendrix, David A.

“…Predicting RNA degradation is a fundamental task in designing RNA-based therapeutic agents. Dual crowdsourcing efforts for dataset creation and machine…”
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Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging by Kuintzle, Rachael C., Chow, Eileen S., Westby, Tara N., Gvakharia, Barbara O., Giebultowicz, Jadwiga M., Hendrix, David A

“…Disruption of the circadian clock, which directs rhythmic expression of numerous output genes, accelerates aging. To enquire how the circadian system protects…”
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MicroRNA and gene expression changes in unruptured human cerebral aneurysms by Bekelis, Kimon, Kerley-Hamilton, Joanna S, Teegarden, Amy, Tomlinson, Craig R, Kuintzle, Rachael, Simmons, Nathan, Singer, Robert J, Roberts, David W, Kellis, Manolis, Hendrix, David A

“…OBJECTIVE The molecular mechanisms behind cerebral aneurysm formation and rupture remain poorly understood. In the past decade, microRNAs (miRNAs) have been…”
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A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate by Shi, Weiyang, Levine, Mike, Haley, Benjamin, Hendrix, David

“…Small RNAs are involved in the regulation of gene expression. During a hunt for microRNAs in the simple chordate Ciona intestinalis , a distinct class of small…”
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miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data by Hendrix, David, Levine, Michael, Shi, Weiyang

“…MicroRNAs (miRs) have been broadly implicated in animal development and disease. We developed a novel computational strategy for the systematic, whole-genome…”
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In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression by Garcia, Gloria R, Goodale, Britton C, Wiley, Michelle W, La Du, Jane K, Hendrix, David A, Tanguay, Robert L

“…Xenobiotic activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzo- -dioxin (TCDD) prevents the proper formation of craniofacial…”
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Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development by Li, Shan, Teegarden, Amy, Bauer, Emily M., Choi, Jaewoo, Messaddeq, Nadia, Hendrix, David A., Ganguli-Indra, Gitali, Leid, Mark, Indra, Arup K.

“…The epidermal permeability barrier (EPB) prevents organisms from dehydration and infection. The transcriptional regulation of EPB development is poorly…”
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DELAY OF GERMINATION 1‐LIKE 4 acts as an inducer of seed reserve accumulation by Sall, Khadidiatou, Dekkers, Bas J. W., Nonogaki, Mariko, Katsuragawa, Yoshihiko, Koyari, Ryosuke, Hendrix, David, Willems, Leo A. J., Bentsink, Leónie, Nonogaki, Hiroyuki

“…Summary More than 70% of global food supply depends on seeds. The major seed reserves, such as proteins, lipids, and polysaccharides, are produced during seed…”
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Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer by Beaver, Laura M., Kuintzle, Rachael, Buchanan, Alex, Wiley, Michelle W., Glasser, Sarah T., Wong, Carmen P., Johnson, Gavin S., Chang, Jeff H., Löhr, Christiane V., Williams, David E., Dashwood, Roderick H., Hendrix, David A., Ho, Emily

“…Long noncoding RNAs (lncRNAs) have emerged as important in cancer development and progression. The impact of diet on lncRNA expression is largely unknown…”
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Lactate dehydrogenase expression modulates longevity and neurodegeneration in Drosophila melanogaster by Long, Dani M, Frame, Ariel K, Reardon, Patrick N, Cumming, Robert C, Hendrix, David A, Kretzschmar, Doris, Giebultowicz, Jadwiga M

“…Lactate dehydrogenase (LDH) catalyzes the conversion of glycolysis-derived pyruvate to lactate. Lactate has been shown to play key roles in brain energetics…”
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Sulforaphane Bioavailability and Chemopreventive Activity in Men Presenting for Biopsy of the Prostate Gland: A Randomized Controlled Trial by Zhang, Zhenzhen, Garzotto, Mark, Davis, Edward W., Mori, Motomi, Stoller, Wesley A., Farris, Paige E., Wong, Carmen P., Beaver, Laura M., Thomas, George V., Williams, David E., Dashwood, Roderick H., Hendrix, David A., Ho, Emily, Shannon, Jackilen

“…Previous studies suggest compounds such as sulforaphane (SFN) derived from cruciferous vegetables may prevent prostate cancer development and progression. This…”
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Neural-specific elongation of 3' UTRs during Drosophila development by Hilgers, Valérie, Perry, Michael W, Hendrix, David, Stark, Alexander, Levine, Michael, Haley, Benjamin

“…The 3' termini of eukaryotic mRNAs influence transcript stability, translation efficiency, and subcellular localization. Here we report that a subset of…”
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