Institution
Genome Institute of Singapore
Facility•Singapore, Singapore•
About: Genome Institute of Singapore is a facility organization based out in Singapore, Singapore. It is known for research contribution in the topics: Population & Gene. The organization has 1417 authors who have published 2061 publications receiving 142029 citations.
Papers published on a yearly basis
Papers
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TL;DR: A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality.
Abstract: Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.
12,489 citations
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Cold Spring Harbor Laboratory1, University of California, Irvine2, California Institute of Technology3, Florida State University College of Arts and Sciences4, Yale University5, Wellcome Trust Sanger Institute6, Norwegian University of Science and Technology7, Affymetrix8, University of North Carolina at Chapel Hill9, University of Lausanne10, University of Geneva11, Genome Institute of Singapore12, Stanford University13, Pompeu Fabra University14
TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
Abstract: Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
4,450 citations
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TL;DR: This study uses chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing to map the locations of TF-binding sites and identifies important features of the transcriptional regulatory networks that define ES-cell identity.
2,519 citations
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TL;DR: By integrating RNA interference–mediated depletion of Oct4 and Nanog with microarray expression profiling, it is demonstrated that these factors can activate or suppress transcription, and it is shown that common core downstream targets are important to keep ES cells from differentiating.
Abstract: Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. Using the chromatin immunoprecipitation paired-end ditags method, we mapped the binding sites of these factors in the mouse ES cell genome. We identified 1,083 and 3,006 high-confidence binding sites for Oct4 and Nanog, respectively. Comparative location analyses indicated that Oct4 and Nanog overlap substantially in their targets, and they are bound to genes in different configurations. Using de novo motif discovery algorithms, we defined the cis-acting elements mediating their respective binding to genomic sites. By integrating RNA interference-mediated depletion of Oct4 and Nanog with microarray expression profiling, we demonstrated that these factors can activate or suppress transcription. We further showed that common core downstream targets are important to keep ES cells from differentiating. The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination.
2,489 citations
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TL;DR: Rna22 as discussed by the authors identifies microRNA binding sites and their corresponding heteroduplexes, and then identifies the targeting microRNAs by finding putative microRN binding sites in the sequence of interest.
1,888 citations
Authors
Showing all 1421 results
Name | H-index | Papers | Citations |
---|---|---|---|
Alan Ashworth | 134 | 578 | 72089 |
Zhen Li | 127 | 1712 | 71351 |
Jianjun Liu | 112 | 1040 | 71032 |
Per Hall | 101 | 574 | 60629 |
Jun Liu | 100 | 1165 | 73692 |
Sanjay Gupta | 99 | 902 | 35039 |
Patrick Tan | 85 | 361 | 24370 |
Guoliang Li | 84 | 795 | 31122 |
Frank McKeon | 74 | 151 | 30024 |
Edison T. Liu | 74 | 240 | 27912 |
Kamila Czene | 73 | 404 | 22218 |
Bing Lim | 70 | 157 | 23132 |
Yik Ying Teo | 69 | 246 | 31107 |
Martin L. Hibberd | 69 | 247 | 17482 |
Yijun Ruan | 68 | 171 | 47506 |