Search Results - "Rohl, Carol"

A quantitative atlas of polyadenylation in five mammals by Derti, Adnan, Garrett-Engele, Philip, Macisaac, Kenzie D, Stevens, Richard C, Sriram, Shreedharan, Chen, Ronghua, Rohl, Carol A, Johnson, Jason M, Babak, Tomas

“…We developed PolyA-seq, a strand-specific and quantitative method for high-throughput sequencing of 3' ends of polyadenylated transcripts, and used it to…”
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Definition, conservation and epigenetics of housekeeping and tissue-enriched genes by She, Xinwei, Rohl, Carol A, Castle, John C, Kulkarni, Amit V, Johnson, Jason M, Chen, Ronghua

“…Housekeeping genes (HKG) are constitutively expressed in all tissues while tissue-enriched genes (TEG) are expressed at a much higher level in a single tissue…”
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Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification by Castle, John C, Armour, Christopher D, Löwer, Martin, Haynor, David, Biery, Matthew, Bouzek, Heather, Chen, Ronghua, Jackson, Stuart, Johnson, Jason M, Rohl, Carol A, Raymond, Christopher K

“…Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of…”
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Digital transcriptome profiling using selective hexamer priming for cDNA synthesis by Armour, Christopher D, Castle, John C, Chen, Ronghua, Babak, Tomas, Loerch, Patrick, Jackson, Stuart, Shah, Jyoti K, Dey, John, Rohl, Carol A, Johnson, Jason M, Raymond, Christopher K

“…We developed a procedure for the preparation of whole transcriptome cDNA libraries depleted of ribosomal RNA from only 1 μg of total RNA. The method relies on…”
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Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations by Gray, Jeffrey J., Moughon, Stewart, Wang, Chu, Schueler-Furman, Ora, Kuhlman, Brian, Rohl, Carol A., Baker, David

“…Protein–protein docking algorithms provide a means to elucidate structural details for presently unknown complexes. Here, we present and evaluate a new method…”
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Modeling structurally variable regions in homologous proteins with rosetta by Rohl, Carol A., Strauss, Charlie E.M., Chivian, Dylan, Baker, David

“…A major limitation of current comparative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known…”
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DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing by Castle, John C, Biery, Matthew, Bouzek, Heather, Xie, Tao, Chen, Ronghua, Misura, Kira, Jackson, Stuart, Armour, Christopher D, Johnson, Jason M, Rohl, Carol A, Raymond, Christopher K

“…DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient,…”
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Physically Realistic Homology Models Built with ROSETTA Can Be More Accurate than Their Templates by Misura, Kira M. S., Chivian, Dylan, Rohl, Carol A., Kim, David E., Baker, David

“…We have developed a method that combines the ROSETTA de novo protein folding and refinement protocol with distance constraints derived from homologous…”
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De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta by Rohl, Carol A, Baker, David

“…As genome-sequencing projects rapidly increase the database of protein sequences, the gap between known sequences and known structures continues to grow…”
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De Novo Prediction of Three-dimensional Structures for Major Protein Families by Bonneau, Richard, Strauss, Charlie E.M, Rohl, Carol A, Chivian, Dylan, Bradley, Phillip, Malmström, Lars, Robertson, Tim, Baker, David

“…We use the Rosetta de novo structure prediction method to produce three-dimensional structure models for all Pfam-A sequence families with average length under…”
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Automated prediction of CASP-5 structures using the Robetta server by Chivian, Dylan, Kim, David E., Malmström, Lars, Bradley, Philip, Robertson, Timothy, Murphy, Paul, Strauss, Charles E.M., Bonneau, Richard, Rohl, Carol A., Baker, David

“…Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment‐insertion method. It combines template‐based and de novo…”
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Pokefind: a novel topological filter for use with protein structure prediction by Khatib, Firas, Rohl, Carol A., Karplus, Kevin

“…Motivation: Our focus has been on detecting topological properties that are rare in real proteins, but occur more frequently in models generated by protein…”
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Prediction of CASP6 structures using automated robetta protocols by Chivian, Dylan, Kim, David E., Malmström, Lars, Schonbrun, Jack, Rohl, Carol A., Baker, David

“…The Robetta server and revised automatic protocols were used to predict structures for CASP6 targets. Robetta is a publicly available protein structure…”
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Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation by Babak, Tomas, Garrett-Engele, Philip, Armour, Christopher D, Raymond, Christopher K, Keller, Mark P, Chen, Ronghua, Rohl, Carol A, Johnson, Jason M, Attie, Alan D, Fraser, Hunter B, Schadt, Eric E

“…Identifying associations between genotypes and gene expression levels using microarrays has enabled systematic interrogation of regulatory variation underlying…”
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An improved protein decoy set for testing energy functions for protein structure prediction by Tsai, Jerry, Bonneau, Richard, Morozov, Alexandre V., Kuhlman, Brian, Rohl, Carol A., Baker, David

“…We have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on…”
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Mapping the genetic architecture of gene expression in human liver by Schadt, Eric E, Molony, Cliona, Chudin, Eugene, Hao, Ke, Yang, Xia, Lum, Pek Y, Kasarskis, Andrew, Zhang, Bin, Wang, Susanna, Suver, Christine, Zhu, Jun, Millstein, Joshua, Sieberts, Solveig, Lamb, John, GuhaThakurta, Debraj, Derry, Jonathan, Storey, John D, Avila-Campillo, Iliana, Kruger, Mark J, Johnson, Jason M, Rohl, Carol A, van Nas, Atila, Mehrabian, Margarete, Drake, Thomas A, Lusis, Aldons J, Smith, Ryan C, Guengerich, F Peter, Strom, Stephen C, Schuetz, Erin, Rushmore, Thomas H, Ulrich, Roger

“…Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in…”
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Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation by Bradley, Philip, Chivian, Dylan, Meiler, Jens, Misura, Kira M.S., Rohl, Carol A., Schief, William R., Wedemeyer, William J., Schueler-Furman, Ora, Murphy, Paul, Schonbrun, Jack, Strauss, Charles E.M., Baker, David

“…We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target…”
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Circular Dichroism Spectra of Short, Fixed-Nucleus Alanine Helices by Chin, Der-Hang, Woody, Robert W., Rohl, Carol A., Baldwin, Robert L.

“…Very short alanine peptide helices can be studied in a fixed-nucleus, helix-forming system [Siedlicka, M., Goch, G., Ejchart, A., Sticht, H. & Bierzynski, A…”
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Rapid knot detection and application to protein structure prediction by Khatib, Firas, Weirauch, Matthew T., Rohl, Carol A.

“…Motivation: Knots in polypeptide chains have been found in very few proteins, and consequently should be generally avoided in protein structure prediction…”
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Protein structure estimation from minimal restraints using Rosetta by Rohl, Carol A

“…RosettaNMR combines the Rosetta de novo structure prediction method with limited NMR experimental data for rapid estimation of protein structure. The de novo…”
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