Search Results - "Eberhardt, Ruth"

The Pfam protein families database: towards a more sustainable future by Finn, Robert D, Coggill, Penelope, Eberhardt, Ruth Y, Eddy, Sean R, Mistry, Jaina, Mitchell, Alex L, Potter, Simon C, Punta, Marco, Qureshi, Matloob, Sangrador-Vegas, Amaia, Salazar, Gustavo A, Tate, John, Bateman, Alex

“…In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release,…”
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Pfam: the protein families database by Finn, Robert D, Bateman, Alex, Clements, Jody, Coggill, Penelope, Eberhardt, Ruth Y, Eddy, Sean R, Heger, Andreas, Hetherington, Kirstie, Holm, Liisa, Mistry, Jaina, Sonnhammer, Erik L L, Tate, John, Punta, Marco

“…Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families,…”
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Rfam 12.0: updates to the RNA families database by Nawrocki, Eric P, Burge, Sarah W, Bateman, Alex, Daub, Jennifer, Eberhardt, Ruth Y, Eddy, Sean R, Floden, Evan W, Gardner, Paul P, Jones, Thomas A, Tate, John, Finn, Robert D

“…The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus…”
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Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland by Wright, Caroline F., Campbell, Patrick, Eberhardt, Ruth Y., Aitken, Stuart, Perrett, Daniel, Brent, Simon, Danecek, Petr, Gardner, Eugene J., Chundru, V. Kartik, Lindsay, Sarah J., Andrews, Katrina, Hampstead, Juliet, Kaplanis, Joanna, Samocha, Kaitlin E., Middleton, Anna, Foreman, Julia, Hobson, Rachel J., Parker, Michael J., Martin, Hilary C., FitzPatrick, David R., Hurles, Matthew E., Firth, Helen V.

“…The DDD study recruited more than 13,500 families with probands with severe, probably monogenic disorders in the United Kingdom and Ireland and obtained a…”
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The Pfam protein families database by Punta, Marco, Coggill, Penny C., Eberhardt, Ruth Y., Mistry, Jaina, Tate, John, Boursnell, Chris, Pang, Ningze, Forslund, Kristoffer, Ceric, Goran, Clements, Jody, Heger, Andreas, Holm, Liisa, Sonnhammer, Erik L. L., Eddy, Sean R., Bateman, Alex, Finn, Robert D.

“…Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is…”
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Filling out the structural map of the NTF2-like superfamily by Eberhardt, Ruth Y, Chang, Yuanyuan, Bateman, Alex, Murzin, Alexey G, Axelrod, Herbert L, Hwang, William C, Aravind, L

“…The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no…”
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Evaluating variants classified as pathogenic in ClinVar in the DDD Study by Wright, Caroline F., Eberhardt, Ruth Y., Constantinou, Panayiotis, Hurles, Matthew E., FitzPatrick, David R., Firth, Helen V.

“…Purpose Automated variant filtering is an essential part of diagnostic genome-wide sequencing but may generate false negative results. We sought to investigate…”
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Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders by Wigdor, Emilie M., Samocha, Kaitlin E., Eberhardt, Ruth Y., Chundru, V. Kartik, Firth, Helen V., Wright, Caroline F., Hurles, Matthew E., Martin, Hilary C.

“…Recent work has revealed an important role for rare, incompletely penetrant inherited coding variants in neurodevelopmental disorders (NDDs). Additionally, we…”
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Molecular autopsy by trio exome sequencing (ES) and postmortem examination in fetuses and neonates with prenatally identified structural anomalies by Quinlan-Jones, Elizabeth, Lord, Jenny, Williams, Denise, Hamilton, Sue, Marton, Tamas, Eberhardt, Ruth Y., Rinck, Gabriele, Prigmore, Elena, Keelagher, Rebecca, McMullan, Dominic J., Maher, Eamonn R., Hurles, Matthew E., Kilby, Mark D.

“…Purpose To determine the diagnostic yield of combined exome sequencing (ES) and autopsy in fetuses/neonates with prenatally identified structural anomalies…”
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Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms by Wright, Caroline F., Quaife, Nicholas M., Ramos-Hernández, Laura, Danecek, Petr, Ferla, Matteo P., Samocha, Kaitlin E., Kaplanis, Joanna, Gardner, Eugene J., Eberhardt, Ruth Y., Chao, Katherine R., Karczewski, Konrad J., Morales, Joannella, Gallone, Giuseppe, Balasubramanian, Meena, Banka, Siddharth, Gompertz, Lianne, Kerr, Bronwyn, Kirby, Amelia, Lynch, Sally A., Morton, Jenny E.V., Pinz, Hailey, Sansbury, Francis H., Stewart, Helen, Zuccarelli, Britton D., Cook, Stuart A., Taylor, Jenny C., Juusola, Jane, Retterer, Kyle, Firth, Helen V., Hurles, Matthew E., Lara-Pezzi, Enrique, Barton, Paul J.R., Whiffin, Nicola

“…Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The…”
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Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders by Gardner, Eugene J., Sifrim, Alejandro, Lindsay, Sarah J., Prigmore, Elena, Rajan, Diana, Danecek, Petr, Gallone, Giuseppe, Eberhardt, Ruth Y., Martin, Hilary C., Wright, Caroline F., FitzPatrick, David R., Firth, Helen V., Hurles, Matthew E.

“…Structural variation (SV) describes a broad class of genetic variation greater than 50 bp in size. SVs can cause a wide range of genetic diseases and are…”
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Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations by Chundru, V. Kartik, Zhang, Zhancheng, Walter, Klaudia, Lindsay, Sarah J., Danecek, Petr, Eberhardt, Ruth Y., Gardner, Eugene J., Malawsky, Daniel S., Wigdor, Emilie M., Torene, Rebecca, Retterer, Kyle, Wright, Caroline F., Ólafsdóttir, Hildur, Guillen Sacoto, Maria J., Ayaz, Akif, Akbeyaz, Ismail Hakki, Türkdoğan, Dilşad, Al Balushi, Aaisha Ibrahim, Bertoli-Avella, Aida, Bauer, Peter, Szenker-Ravi, Emmanuelle, Reversade, Bruno, McWalter, Kirsty, Sheridan, Eamonn, Firth, Helen V., Hurles, Matthew E., Samocha, Kaitlin E., Ustach, Vincent D., Martin, Hilary C.

“…Autosomal recessive coding variants are well-known causes of rare disorders. We quantified the contribution of these variants to developmental disorders in a…”
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Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase by Sheydina, Anna, Eberhardt, Ruth Y, Rigden, Daniel J, Chang, Yuanyuan, Li, Zhanwen, Zmasek, Christian C, Axelrod, Herbert L, Godzik, Adam

“…Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the…”
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The SHOCT domain: a widespread domain under-represented in model organisms by Eberhardt, Ruth Y, Bartholdson, S Josefin, Punta, Marco, Bateman, Alex

“…We have identified a new protein domain, which we have named the SHOCT domain (Short C-terminal domain). This domain is widespread in bacteria with over a…”
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Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase by Rigden, Daniel J, Eberhardt, Ruth Y, Gilbert, Harry J, Xu, Qingping, Chang, Yuanyuan, Godzik, Adam

“…Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP…”
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Detection of mosaic chromosomal alterations in children with severe developmental disorders recruited to the DDD study by Eberhardt, Ruth Y, Wright, Caroline F, FitzPatrick, David R, Hurles, Matthew E, Firth, Helen V

“…Structural mosaicism has been previously implicated in developmental disorders. We aimed to identify rare mosaic chromosomal alterations (MCAs) in probands…”
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New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily by Trame, Christine B, Chang, Yuanyuan, Axelrod, Herbert L, Eberhardt, Ruth Y, Coggill, Penelope, Punta, Marco, Rawlings, Neil D

“…The Acel_2062 protein from Acidothermus cellulolyticus is a protein of unknown function. Initial sequence analysis predicted that it was a metallopeptidase…”
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LUD, a new protein domain associated with lactate utilization by Hwang, William C, Bakolitsa, Constantina, Punta, Marco, Coggill, Penelope C, Bateman, Alex, Axelrod, Herbert L, Rawlings, Neil D, Sedova, Mayya, Peterson, Scott N, Eberhardt, Ruth Y, Aravind, L, Pascual, Jaime, Godzik, Adam

“…A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved…”
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Rfam: annotating families of non-coding RNA sequences by Daub, Jennifer, Eberhardt, Ruth Y, Tate, John G, Burge, Sarah W

“…The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the…”
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Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila by Coggill, Penelope, Eberhardt, Ruth Y, Finn, Robert D, Chang, Yuanyuan, Jaroszewski, Lukasz, Godzik, Adam, Das, Debanu, Xu, Qingping, Axelrod, Herbert L, Aravind, L, Murzin, Alexey G, Bateman, Alex

“…Every genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall…”
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