Search Results - "Palidwor, Gareth A"

A general model of codon bias due to GC mutational bias by Palidwor, Gareth A, Perkins, Theodore J, Xia, Xuhua

“…In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been…”
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Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs by Soleimani, Vahab D., Punch, Vincent G., Kawabe, Yoh-ichi, Jones, Andrew E., Palidwor, Gareth A., Porter, Christopher J., Cross, Joe W., Carvajal, Jaime J., Kockx, Christel E.M., van IJcken, Wilfred F.J., Perkins, Theodore J., Rigby, Peter W.J., Grosveld, Frank, Rudnicki, Michael A.

“…Pax3 and Pax7 regulate stem cell function in skeletal myogenesis. However, molecular insight into their distinct roles has remained elusive. Using gene…”
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Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data by Karimnezhad, Ali, Palidwor, Gareth A, Thavorn, Kednapa, Stewart, David J, Campbell, Pearl A, Lo, Bryan, Perkins, Theodore J

“…Treating cancer depends in part on identifying the mutations driving each patient's disease. Many clinical laboratories are adopting high-throughput sequencing…”
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MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data by Ramachandran, Parameswaran, Palidwor, Gareth A, Porter, Christopher J, Perkins, Theodore J

“…Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis…”
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Functional and genomic analyses of alpha-solenoid proteins by Fournier, David, Palidwor, Gareth A, Shcherbinin, Sergey, Szengel, Angelika, Schaefer, Martin H, Perez-Iratxeta, Carol, Andrade-Navarro, Miguel A

“…Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology…”
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Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis by Rothberg, Janet L. Manias, Maganti, Harinad B., Jrade, Hani, Porter, Christopher J., Palidwor, Gareth A., Cafariello, Christopher, Battaion, Hannah L., Khan, Safwat T., Perkins, Theodore J., Paulson, Robert F., Ito, Caryn Y., Stanford, William L.

“…Polycomb repressive complex 2 (PRC2) accessory proteins play substoichiometric, tissue-specific roles to recruit PRC2 to specific genomic loci or increase…”
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Detection of alpha-rod protein repeats using a neural network and application to huntingtin by Palidwor, Gareth A, Shcherbinin, Sergey, Huska, Matthew R, Rasko, Tamas, Stelzl, Ulrich, Arumughan, Anup, Foulle, Raphaele, Porras, Pablo, Sanchez-Pulido, Luis, Wanker, Erich E, Andrade-Navarro, Miguel A

“…A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel…”
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Cis-regulatory determinants of MyoD function by Soleimani, Vahab D, Nguyen, Duy, Ramachandran, Parameswaran, Palidwor, Gareth A, Porter, Christopher J, Yin, Hang, Perkins, Theodore J, Rudnicki, Michael A

“…Abstract Muscle-specific transcription factor MyoD orchestrates the myogenic gene expression program by binding to short DNA motifs called E-boxes within…”
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Peer2ref: a peer-reviewer finding web tool that uses author disambiguation by Andrade-Navarro, Miguel A, Palidwor, Gareth A, Perez-Iratxeta, Carol

“…Reviewer and editor selection for peer review is getting harder for authors and publishers due to the specialization onto narrower areas of research carried by…”
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Recent developments in StemBase: a tool to study gene expression in human and murine stem cells by Sandie, Reatha, Palidwor, Gareth A, Huska, Matthew R, Porter, Christopher J, Krzyzanowski, Paul M, Muro, Enrique M, Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A

“…Currently one of the largest online repositories for human and mouse stem cell gene expression data, StemBase was first designed as a simple web-interface to…”
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BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates by Ramachandran, Parameswaran, Palidwor, Gareth A, Perkins, Theodore J

“…Unraveling transcriptional regulatory networks is a central problem in molecular biology and, in this quest, chromatin immunoprecipitation and sequencing…”
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Chromatin tandem affinity purification sequencing by Soleimani, Vahab D, Palidwor, Gareth A, Ramachandran, Parameswaran, Perkins, Theodore J, Rudnicki, Michael A

“…Chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq) is a widely used method for mapping the interactions of proteins with…”
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Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing by Scimè, Anthony, Desrosiers, Justine, Trensz, Frédéric, Palidwor, Gareth A., Caron, Annabelle Z., Andrade-Navarro, Miguel A., Grenier, Guillaume

“…Skeletal muscle ageing is characterized by faulty degenerative/regenerative processes that promote the decline of its mass, strength, and endurance. In this…”
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StemBase: a resource for the analysis of stem cell gene expression data by Porter, Christopher J, Palidwor, Gareth A, Sandie, Reatha, Krzyzanowski, Paul M, Muro, Enrique M, Perez-Iratxeta, Carolina, Andrade-Navarro, Miguel A

“…StemBase is a database of gene expression data obtained from stem cells and derivatives mainly from mouse and human using DNA microarrays and Serial Analysis…”
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MLTrends: Graphing MEDLINE term usage over time by Palidwor, Gareth A, Andrade-Navarro, Miguel A

“…The MEDLINE database of medical literature is routinely used by researchers and doctors to find articles pertaining to their area of interest. Insight into…”
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Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin: e1000304 by Palidwor, Gareth A, Shcherbinin, Sergey, Huska, Matthew R, Rasko, Tamas, Stelzl, Ulrich, Arumughan, Anup, Foulle, Raphaele, Porras, Pablo, Sanchez-Pulido, Luis, Wanker, Erich E, Andrade-Navarro, Miguel A

“…A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel…”
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Tissue-specific codon usage in mouse by Palidwor, Gareth A

“…Codon usage bias is due to a combination of biased mutation and selection effects. Isochore-related GC mutational bias has been shown to be the dominant cause…”
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