Search Results - "Clark, Wyatt"

Information-theoretic evaluation of predicted ontological annotations by Clark, Wyatt T, Radivojac, Predrag

“…The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, with protein function…”
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Analysis of protein function and its prediction from amino acid sequence by Clark, Wyatt T., Radivojac, Predrag

“…Understanding protein function is one of the keys to understanding life at the molecular level. It is also important in the context of human disease because…”
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Testing the ortholog conjecture with comparative functional genomic data from mammals by Nehrt, Nathan L, Clark, Wyatt T, Radivojac, Predrag, Hahn, Matthew W

“…A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the "ortholog conjecture")…”
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Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix by Trinidad, Marena, Hong, Xinying, Froelich, Steven, Daiker, Jessica, Sacco, James, Nguyen, Hong Phuc, Campagna, Madelynn, Suhr, Dean, Suhr, Teryn, LeBowitz, Jonathan H, Gelb, Michael H, Clark, Wyatt T

“…Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by mutations in the arylsulfatase A gene (ARSA) and categorized into three subtypes…”
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Utilizing ExAC to assess the hidden contribution of variants of unknown significance to Sanfilippo Type B incidence by Clark, Wyatt T, Yu, G Karen, Aoyagi-Scharber, Mika, LeBowitz, Jonathan H

“…Given the large and expanding quantity of publicly available sequencing data, it should be possible to extract incidence information for monogenic diseases…”
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The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective by Jiang, Yuxiang, Clark, Wyatt T, Friedberg, Iddo, Radivojac, Predrag

“…The automated functional annotation of biological macromolecules is a problem of computational assignment of biological concepts or ontological terms to genes…”
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Identifying therapeutic drug targets using bidirectional effect genes by Estrada, Karol, Froelich, Steven, Wuster, Arthur, Bauer, Christopher R., Sterling, Teague, Clark, Wyatt T., Ru, Yuanbin, Trinidad, Marena, Nguyen, Hong Phuc, Luu, Amanda R., Wendt, Daniel J., Yogalingam, Gouri, Yu, Guoying Karen, LeBowitz, Jonathan H., Cardon, Lon R.

“…Prioritizing genes for translation to therapeutics for common diseases has been challenging. Here, we propose an approach to identify drug targets with high…”
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An integrated approach to inferring gene-disease associations in humans by Radivojac, Predrag, Peng, Kang, Clark, Wyatt T., Peters, Brandon J., Mohan, Amrita, Boyle, Sean M., Mooney, Sean D.

“…One of the most important tasks of modern bioinformatics is the development of computational tools that can be used to understand and treat human disease. To…”
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Comparative analysis of pseudogenes across three phyla by Sisu, Cristina, Pei, Baikang, Leng, Jing, Frankish, Adam, Zhang, Yan, Balasubramanian, Suganthi, Harte, Rachel, Wang, Daifeng, Rutenberg-Schoenberg, Michael, Clark, Wyatt, Diekhans, Mark, Rozowsky, Joel, Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark B.

“…Significance Pseudogenes have long been considered nonfunctional elements. However, recent studies have shown they can potentially regulate the expression of…”
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Vector quantization kernels for the classification of protein sequences and structures by Clark, Wyatt T, Radivojac, Predrag

“…We propose a new kernel-based method for the classification of protein sequences and structures. We first represent each protein as a set of time series data…”
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Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms by Abyzov, Alexej, Li, Shantao, Kim, Daniel Rhee, Mohiyuddin, Marghoob, Stütz, Adrian M., Parrish, Nicholas F., Mu, Xinmeng Jasmine, Clark, Wyatt, Chen, Ken, Hurles, Matthew, Korbel, Jan O., Lam, Hugo Y. K., Lee, Charles, Gerstein, Mark B.

“…Investigating genomic structural variants at basepair resolution is crucial for understanding their formation mechanisms. We identify and analyse 8,943…”
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The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice by Ismail, Ashrafali Mohamed, Witt, Evan, Bouwman, Taren, Clark, Wyatt, Yates, Bridget, Franco, Matteo, Fong, Sylvia

“…Adeno-associated virus (AAV)-based vectors are used clinically for gene transfer and persist as extrachromosomal episomes. A small fraction of vector genomes…”
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Assessment of predicted enzymatic activity of α‐N‐acetylglucosaminidase variants of unknown significance for CAGI 2016 by Clark, Wyatt T., Kasak, Laura, Bakolitsa, Constantina, Hu, Zhiqiang, Andreoletti, Gaia, Babbi, Giulia, Bromberg, Yana, Casadio, Rita, Dunbrack, Roland, Folkman, Lukas, Ford, Colby T., Jones, David, Katsonis, Panagiotis, Kundu, Kunal, Lichtarge, Olivier, Martelli, Pier L., Mooney, Sean D., Nodzak, Conor, Pal, Lipika R., Radivojac, Predrag, Savojardo, Castrense, Shi, Xinghua, Zhou, Yaoqi, Uppal, Aneeta, Xu, Qifang, Yin, Yizhou, Pejaver, Vikas, Wang, Meng, Wei, Liping, Moult, John, Yu, Guoying Karen, Brenner, Steven E., LeBowitz, Jonathan H.

“…The NAGLU challenge of the fourth edition of the Critical Assessment of Genome Interpretation experiment (CAGI4) in 2016, invited participants to predict the…”
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Characterization of glycan substrates accumulating in GM1 Gangliosidosis by Lawrence, Roger, Van Vleet, Jeremy L., Mangini, Linley, Harris, Adam, Martin, Nathan, Clark, Wyatt, Chandriani, Sanjay, LeBowitz, Jonathan H., Giugliani, Roberto, d'Azzo, Alessandra, Yogalingam, Gouri, Crawford, Brett E.

“…GM1 gangliosidosis is a rare autosomal recessive genetic disorder caused by the disruption of the GLB1 gene that encodes β-galactosidase, a lysosomal hydrolase…”
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Prediction of functional regulatory SNPs in monogenic and complex disease by Zhao, Yiqiang, Clark, Wyatt T., Mort, Matthew, Cooper, David N., Radivojac, Predrag, Mooney, Sean D.

“…Next‐generation sequencing (NGS) technologies are yielding ever higher volumes of human genome sequence data. Given this large amount of data, it has become…”
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From protein-disease associations to disease informatics by Dalkilic, Mehmet M, Costello, James C, Clark, Wyatt T, Radivojac, Predrag

“…Advancements in high-throughput technology and computational power have brought about significant progress in our understanding of cellular processes,…”
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Utilizing activity assays and population-wide allele frequencies to assess the contribution of novel mutations in NAGLU to MPS IIIB incidence by LeBowitz, Jonathan H., Clark, Wyatt T., Karen Yu, G., Aoyagi-Scharber, Mika

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Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms by Abyzov, Alexej, Li, Shantao, Kim, Daniel Rhee, Mohiyuddin, Marghoob, Stütz, Adrian M., Parrish, Nicholas F., Mu, Xinmeng Jasmine, Clark, Wyatt, Chen, Ken, Hurles, Matthew, Korbel, Jan O., Lam, Hugo Y. K., Lee, Charles, Gerstein, Mark B.

“…Nature Communications 6: Article number: 7256 (2015); Published 1 June 2015; Updated 8 September 2015 The affiliation details for Alexej Abyzov are incorrect…”
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Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals: e1002073 by Nehrt, Nathan L, Clark, Wyatt T, Radivojac, Predrag, Hahn, Matthew W

“…A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the "ortholog conjecture")…”
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Understanding protein function through statistical inference and evolutionary analysis by Clark, Wyatt Travis

“…The ability to characterize the functional behavior of an individual protein in a variety of different contexts is one of the cornerstones of carrying out…”
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