Genome Research

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Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
Genome Research - Tập 21 Số 12 - Trang 2004-2013 - 2011
Andreas Schlattl, Simon Anders, Sebastian M. Waszak, Wolfgang Huber, Jan O. Korbel
Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have ev...... hiện toàn bộ
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
Genome Research - Tập 21 Số 6 - Trang 974-984 - 2011
Alexej Abyzov, Alexander E. Urban, M Snyder, Mark Gerstein
Copy number variation (CNV) in the genome is a complex phenomenon, and not completely understood. We have developed a method, CNVnator, for CNV discovery and genotyping from read-depth (RD) analysis of personal genome sequencing. Our method is based on combining the established mean-shift approach with additional refinements (multiple-bandwidth partitioning and GC correction) to broaden th...... hiện toàn bộ
Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
Genome Research - Tập 18 Số 3 - Trang 343-358 - 2008
Victoria P. Belancio, Dale J. Hedges, Prescott L. Deininger
Transposable elements (TEs) have shared an exceptionally long coexistence with their host organisms and have come to occupy a significant fraction of eukaryotic genomes. The bulk of the expansion occurring within mammalian genomes has arisen from the activity of type I retrotransposons, which amplify in a “copy-and-paste” fashion through an RNA intermediate. For better or worse, the sequen...... hiện toàn bộ
Improving gene annotation using peptide mass spectrometry
Genome Research - Tập 17 Số 2 - Trang 231-239 - 2007
Stephen Tanner, Zhouxin Shen, John N. Ng, Liliana Florea, Roderic Guigó, Steven P. Briggs, Vineet Bafna
Annotation of protein-coding genes is a key goal of genome sequencing projects. In spite of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to constr...... hiện toàn bộ
Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
Genome Research - Tập 17 Số 9 - Trang 1362-1377 - 2007
Nitin Gupta, Stephen Tanner, Navdeep Jaitly, Joshua Adkins, Mary Lipton, Robert A. Edwards, Margaret F. Romine, Andrei L. Osterman, Vineet Bafna, Richard Smith, Pavel A. Pevzner
While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let ...... hiện toàn bộ
Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane
Genome Research - Tập 13 Số 12 - Trang 2725-2735 - 2003
André L. Vettore
On the origin of prokaryotic species
Genome Research - Tập 19 Số 5 - Trang 744-756 - 2009
W. Ford Doolittle, Olga Zhaxybayeva
The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call “species” is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept—by which is meant a genetic and ecological theory of speciation—might best expla...... hiện toàn bộ
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
Genome Research - Tập 18 Số 4 - Trang 610-621 - 2008
Ryan D. Morin, Michael D. O’Connor, Malachi Griffith, Florian Kuchenbauer, Allen Delaney, Anna‐Liisa Prabhu, Yongjun Zhao, Helen McDonald, Thomas Zeng, Martin Hirst, Connie J. Eaves, Marco A. Marra
MicroRNAs (miRNAs) are emerging as important, albeit poorly characterized, regulators of biological processes. Key to further elucidation of their roles is the generation of more complete lists of their numbers and expression changes in different cell states. Here, we report a new method for surveying the expression of small RNAs, including microRNAs, using Illumina sequencing technology. ...... hiện toàn bộ
The Relative Power of Family-Based and Case-Control Designs for Linkage Disequilibrium Studies of Complex Human Diseases I. DNA Pooling
Genome Research - Tập 8 Số 12 - Trang 1273-1288 - 1998
Neil Risch, Jun Teng
We consider statistics for analyzing a variety of family-based and nonfamily-based designs for detecting linkage disequilibrium of a marker with a disease susceptibility locus. These designs include sibships with parents, sibships without parents, and use of unrelated controls. We also provide formulas for and evaluate the relative power of different study designs using these statistics. I...... hiện toàn bộ
Altered adenosine-to-inosine RNA editing in human cancer
Genome Research - Tập 17 Số 11 - Trang 1586-1595 - 2007
Nurit Paz, Erez Y. Levanon, Ninette Amariglio, Amy B. Heimberger, Zvi Ram, Shlomi Constantini, Zohar Barbash, Konstantin Adamsky, Michal Safran, Avi Hirschberg, Meir Krupsky, Issachar Ben-Dov, Simona Cazacu, Tom Mikkelsen, Chaya Brodie, Eli Eisenberg, Gideon Rechavi
Adenosine-to-inosine (A-to-I) RNA editing was recently shown to be abundant in the human transcriptome, affecting thousands of genes. Employing a bioinformatic approach, we identified significant global hypoediting of Alu repetitive elements in brain, prostate, lung, kidney, and testis tumors. Experimental validation confirmed this finding, showing significantly ...... hiện toàn bộ
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