Search Results - "Capra, A."

DNA Replication through G-Quadruplex Motifs Is Promoted by the Saccharomyces cerevisiae Pif1 DNA Helicase by Paeschke, Katrin, Capra, John A., Zakian, Virginia A.

“…G-quadruplex (G4) DNA structures are extremely stable four-stranded secondary structures held together by noncanonical G-G base pairs. Genome-wide chromatin…”
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Predicting functionally important residues from sequence conservation by Capra, John A., Singh, Mona

“…Motivation: All residues in a protein are not equally important. Some are essential for the proper structure and function of the protein, whereas others can be…”
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Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis by Marinko, Justin T, Huang, Hui, Penn, Wesley D, Capra, John A, Schlebach, Jonathan P, Sanders, Charles R

“…Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics…”
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Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage by Wamstad, Joseph A, Alexander, Jeffrey M, Truty, Rebecca M, Shrikumar, Avanti, Li, Fugen, Eilertson, Kirsten E, Ding, Huiming, Wylie, John N, Pico, Alexander R, Capra, John A, Erwin, Genevieve, Kattman, Steven J, Keller, Gordon M, Srivastava, Deepak, Levine, Stuart S, Pollard, Katherine S, Holloway, Alisha K, Boyer, Laurie A, Bruneau, Benoit G

“…Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation…”
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Quantifying the contribution of Neanderthal introgression to the heritability of complex traits by McArthur, Evonne, Rinker, David C., Capra, John A.

“…Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human…”
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Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks by Li, Bian, Yang, Yucheng T, Capra, John A, Gerstein, Mark B

“…Predicting mutation-induced changes in protein thermodynamic stability (ΔΔG) is of great interest in protein engineering, variant interpretation, and protein…”
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Learning and interpreting the gene regulatory grammar in a deep learning framework by Chen, Ling, Capra, John A

“…Deep neural networks (DNNs) have achieved state-of-the-art performance in identifying gene regulatory sequences, but they have provided limited insight into…”
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Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties by Chen, Ling, Fish, Alexandra E, Capra, John A

“…Genomic regions with gene regulatory enhancer activity turnover rapidly across mammals. In contrast, gene expression patterns and transcription factor binding…”
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The 3D mutational constraint on amino acid sites in the human proteome by Li, Bian, Roden, Dan M., Capra, John A.

“…Quantification of the tolerance of protein sites to genetic variation has become a cornerstone of variant interpretation. We hypothesize that the constraint on…”
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Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function by Benton, Mary Lauren, Talipineni, Sai Charan, Kostka, Dennis, Capra, John A

“…Non-coding gene regulatory enhancers are essential to transcription in mammalian cells. As a result, a large variety of experimental and computational…”
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High-Throughput Reclassification of SCN5A Variants by Glazer, Andrew M., Wada, Yuko, Li, Bian, Muhammad, Ayesha, Kalash, Olivia R., O’Neill, Matthew J., Shields, Tiffany, Hall, Lynn, Short, Laura, Blair, Marcia A., Kroncke, Brett M., Capra, John A., Roden, Dan M.

“…Partial or complete loss-of-function variants in SCN5A are the most common genetic cause of the arrhythmia disorder Brugada syndrome (BrS1). However, the…”
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The phenotypic legacy of admixture between modern humans and Neandertals by Simonti, Corinne N., Vernot, Benjamin, Bastarache, Lisa, Bottinger, Erwin, Carrell, David S., Chisholm, Rex L., Crosslin, David R., Hebbring, Scott J., Jarvik, Gail P., Kullo, Iftikhar J., Li, Rongling, Pathak, Jyotishman, Ritchie, Marylyn D., Roden, Dan M., Verma, Shefali S., Tromp, Gerard, Prato, Jeffrey D., Bush, William S., Akey, Joshua M., Denny, Joshua C., Capra, John A.

“…Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human…”
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Many human accelerated regions are developmental enhancers by Capra, John A., Erwin, Genevieve D., McKinsey, Gabriel, Rubenstein, John L. R., Pollard, Katherine S.

“…The genetic changes underlying the dramatic differences in form and function between humans and other primates are largely unknown, although it is clear that…”
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Lifetime of magnetically trapped antihydrogen in ALPHA by Capra, A.

“…How long antihydrogen atoms linger in the ALPHA magnetic trap is an important characteristic of the ALPHA apparatus. The initial trapping experiments in 2010…”
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Acetylation of RNA Polymerase II Regulates Growth-Factor-Induced Gene Transcription in Mammalian Cells by Schröder, Sebastian, Herker, Eva, Itzen, Friederike, He, Daniel, Thomas, Sean, Gilchrist, Daniel A, Kaehlcke, Katrin, Cho, Sungyoo, Pollard, Katherine S, Capra, John A, Schnölzer, Martina, Cole, Philip A, Geyer, Matthias, Bruneau, Benoit G, Adelman, Karen, Ott, Melanie

“…Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA…”
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G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae by Capra, John A, Paeschke, Katrin, Singh, Mona, Zakian, Virginia A

“…G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have…”
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Mosaic patterns of selection in genomic regions associated with diverse human traits by Abraham, Abin, LaBella, Abigail L, Capra, John A, Rokas, Antonis

“…Natural selection shapes the genetic architecture of many human traits. However, the prevalence of different modes of selection on genomic regions associated…”
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Integrating diverse datasets improves developmental enhancer prediction by Erwin, Genevieve D, Oksenberg, Nir, Truty, Rebecca M, Kostka, Dennis, Murphy, Karl K, Ahituv, Nadav, Pollard, Katherine S, Capra, John A

“…Gene-regulatory enhancers have been identified using various approaches, including evolutionary conservation, regulatory protein binding, chromatin…”
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Recycling of poor quality urban wastewater by drip irrigation systems by Capra, A., Scicolone, B.

“…Drip irrigation, combined with wastewater reuse, may offer the most effective and efficient way to cope with water shortage for crops and protect the…”
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Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features by Abraham, Abin, Kavoussi, Nicholas L, Sui, Wilson, Bejan, Cosmin, Capra, John A, Hsi, Ryan

“…To assess the accuracy of machine learning models in predicting kidney stone composition using variables extracted from the electronic health record (EHR). We…”
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