Results 1 - 10 of 171

Ruler Arrays Detect Genomic

by Philip Alexander Rolfe, David K. Gifford, Philip Alexander Rolfe , 2009
"... A Ruler Array measures the distance between a set of microarray probes and a set of ex-perimentally defined locations in a nucleic acid, offering new possibilities for locating and characterizing changes in the nucleic acid sequence. Despite the known relevance of genomic changes to pathogens, cance ..."
Abstract - Add to MetaCart
, cancer, development, and evolution, many of these changes evade detection by existing high-throughput techniques. Since a microarray can interrogate thou-sands or millions of probes at once, Ruler Arrays can screen a small genome or part of a mammalian sized genome for insertions, deletions

Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

by David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-toh, Jill P. Mesirov, Michael C. Zody, Eric S. Lander
"... We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Thr ..."
Abstract - Cited by 68 (2 self) - Add to MetaCart
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes

1 SAIS-OPT: On the Characterization and Optimization of the SA-IS Algorithm for Suffix Array Construction

by Nataliya Timoshevskaya, Wu-chun Feng
"... Abstract—The suffix array and Burrows-Wheeler Transform are critical index structures in next generation sequence analysis. The construction of such index structures for mammalian-sized genomes can take thousands of seconds (i.e. tens of minutes). Its construction is complicated by computational ove ..."
Abstract - Add to MetaCart
Abstract—The suffix array and Burrows-Wheeler Transform are critical index structures in next generation sequence analysis. The construction of such index structures for mammalian-sized genomes can take thousands of seconds (i.e. tens of minutes). Its construction is complicated by computational

A Bioinformatics Approach for Determining Sample Identity from Different Lanes of High-Throughput Sequencing Data

by Rachel L. Goldfeder, Stephen C. J. Parker, Subramanian S. Ajay, Hatice Ozel Abaan, Elliott H , 2011
"... The ability to generate whole genome data is rapidly becoming commoditized. For example, a mammalian sized genome (,3Gb) can now be sequenced using approximately ten lanes on an Illumina HiSeq 2000. Since lanes from different runs are often combined, verifying that each lane in a genome’s build is f ..."
Abstract - Add to MetaCart
The ability to generate whole genome data is rapidly becoming commoditized. For example, a mammalian sized genome (,3Gb) can now be sequenced using approximately ten lanes on an Illumina HiSeq 2000. Since lanes from different runs are often combined, verifying that each lane in a genome’s build

The sequence and de novo assembly of the giant panda genome.

by Ruiqiang Li , Wei Fan , Geng Tian , Hongmei Zhu , Lin He , Jing Cai , Quanfei Huang , Qingle Cai , Bo Li , Yinqi Bai , Zhihe Zhang , Yaping Zhang , Wen Wang , Jun Li , Fuwen Wei , Heng Li , Min Jian , Jianwen Li , Zhaolei Zhang , Rasmus Nielsen , Dawei Li , Wanjun Gu , Zhentao Yang , Zhaoling Xuan , Oliver A Ryder , Chi-Ching Frederick , Leung , Yan Zhou , Jianjun Cao , Xiao Sun , Yonggui Fu , Xiaodong Fang , Xiaosen Guo , Bo Wang , Rong Hou , Fujun Shen , Bo Mu , Peixiang Ni , Runmao Lin , Wubin Qian , Guodong Wang , Chang Yu , Wenhui Nie , Jinhuan Wang , Zhigang Wu , Huiqing Liang , Jiumeng Min , Qi Wu , Shifeng Cheng , Jue Ruan , Mingwei Wang , Zhongbin Shi , Ming Wen , Binghang Liu , Xiaoli Ren , Huisong Zheng , Dong Dong , Kathleen Cook , Gao Shan , Hao Zhang , Carolin Kosiol , Xueying Xie , Zuhong Lu , Hancheng Zheng , Yingrui Li , Cynthia C Steiner , Tommy Tsan , Yuk Lam , Siyuan Lin , Qinghui Zhang , Guoqing Li , Jing Tian , Timing Gong , Hongde Liu , Dejin Zhang , Lin Fang , Chen Ye , Juanbin Zhang , Wenbo Hu , Anlong Xu , Yuanyuan Ren , Guojie Zhang , Michael W Bruford , Qibin Li , Lijia Ma , Yiran Guo , Na An , Yujie Hu , Yang Zheng , Yongyong Shi , Zhiqiang Li , Qing Liu , Yanling Chen , Jing Zhao , Ning Qu , Shancen Zhao , Feng Tian , Xiaoling Wang , Haiyin Wang , Lizhi Xu , Xiao Liu , Tomas Vinar , Yajun Wang , Tak-Wah Lam , Siu-Ming Yiu , Shiping Liu , Hemin Zhang , Desheng Li , Yan Huang , Xia Wang , Guohua Yang , Zhi Jiang , Junyi Wang , Nan Qin , Li Li , Jingxiang Li , Lars Bolund , Karsten Kristiansen , Ka-Shu Gane , Wong , Maynard Olson , Xiuqing Zhang , Songgang Li , Huanming Yang , Jian Wang , Jun Wang - Nature , 2010
"... Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific re ..."
Abstract - Cited by 116 (4 self) - Add to MetaCart
composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost

Conservation and Mammalian Brain Size Evolution

by Neurodevelopmental Lincrna Microsyteny, Eric Lewitus, B. Huttner
"... The mammalian neocortex has undergone repeated selection for increases and decreases in size and complexity, often over relatively short evolutionary time. But because probing developmental mechanisms across many species is experimentally unfeasible, it is unknown whether convergent morphologies in ..."
Abstract - Add to MetaCart
The mammalian neocortex has undergone repeated selection for increases and decreases in size and complexity, often over relatively short evolutionary time. But because probing developmental mechanisms across many species is experimentally unfeasible, it is unknown whether convergent morphologies

Stochastic mRNA synthesis in mammalian cells

by Arjun Raj, Charles S. Peskin, Daniel Tranchina, Diana Y. Vargas, Sanjay Tyagi - PLOS BIOL , 2006
"... Individual cells in genetically homogeneous populations have been found to express different numbers of molecules of specific proteins. We investigated the origins of these variations in mammalian cells by counting individual molecules of mRNA produced from a reporter gene that was stably integrated ..."
Abstract - Cited by 143 (15 self) - Add to MetaCart
of the bursts. The model showed that increasing the level of transcription factors increases the average size of the bursts rather than their frequency. These results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells

Larger Mammalian Body Size Leads to Lower Retroviral Activity

by Aris Katzourakis, Gkikas Magiorkinis, Aaron G. Lim, Sunetra Gupta, Robert Belshaw, Robert Gifford
"... Retroviruses have been infecting mammals for at least 100 million years, leaving descendants in host genomes known as endogenous retroviruses (ERVs). The abundance of ERVs is partly determined by their mode of replication, but it has also been suggested that host life history traits could enhance or ..."
Abstract - Add to MetaCart
or suppress their activity. We show that larger bodied species have lower levels of ERV activity by reconstructing the rate of ERV integration across 38 mammalian species. Body size explains 37 % of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding

Genomic Organization of

by Purinergic Px Receptors, Raúl Loera-valencia, Josué Obed Jaramillo-polanco, Andrómeda Linan-rico, María Guadalupe, Nieto Pescador, Juan Francisco, Jiménez Bremont, Carlos Barajas-lópez
"... Purinergic P2X receptors are a family of ligand-gated cationic channels activated by extracellular ATP. P2X subunit protein sequences are highly conserved between vertebrate species. However, they can generate a great diversity of coding splicing variants to fulfill several roles in mammalian physio ..."
Abstract - Add to MetaCart
. In order to obtain clues on mammalian P2X diversity, we have performed a bio-informatics analysis of the coding regions and introns of the seven P2X subunits present in human, simian, dog, mouse, rat and zebrafish. Here we report the arrangements of exon and intron se-quences, considering its number, size

Genome Sizes in Afrotheria, Xenarthra,

by C. A. Redi, H. Zacharias, S. Merani, M. Oliveira-miranda, M. Aguilera, M. Zuccotti, S. Garagna, E. Capanna
"... Topical literature and Web site databases provide genome sizes for;4,000 animal species, invertebrates and vertebrates, 330 of which are mammals. We provide the genome size for 67 mammalian species, including 51 never reported before. Knowledge of genome size facilitates sequencing projects. The dat ..."
Abstract - Add to MetaCart
Topical literature and Web site databases provide genome sizes for;4,000 animal species, invertebrates and vertebrates, 330 of which are mammals. We provide the genome size for 67 mammalian species, including 51 never reported before. Knowledge of genome size facilitates sequencing projects
Results 1 - 10 of 171