Rapid progress in high-throughput sequencing (HTS) has enabled the molecular characterization of mutational landscapes in heterogeneous populations and has improved our understanding of clonal evolution processes. Analyzing the sensitivity of detecting genomic mutations in HTS requires comprehensive profiling of sequencing artifacts. To this end, we introduce MERIT, designed for in-depth quanti...

Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome-scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we show that transcription factor (TF) dynamics and regulatory network organization are tightly linked. By cl...

Genome instability is regarded as a hallmark of cancer. Human tumors frequently carry clonally expanded mutations in their mitochondrial DNA (mtDNA), some of which may drive cancer progression and metastasis. The high prevalence of clonal mutations in tumor mtDNA has commonly led to the assumption that the mitochondrial genome in cancer is genetically unstable, yet this hypothesis has not been ...

The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerate...

The concept of lineage fidelity in acute leukemia has recently been challenged by the finding of rearrangements of the immunoglobulin heavy chain genes in a leukemic cell line and in a small number of sporadic cases of acute nonlymphocytic leukemia with a monocytic phenotype. We therefore screened leukemic blood or bone marrow samples of 33 adult patients with acute nonlymphocytic leukemia of F...

March, 2000 AFRICA N John Cohen was a product of the democratic frontier ethos of the American West. A rigorous stickler for accuracy of detail and fidelity to the facts, he was at the same time an unwavering optimist. His writing and teaching was infused with a moral vision––that ordinary men and women are endowed with the innate capacity to solve their common problems, to learn from mistakes ...

Recombination is a powerful policing mechanism to control intragenomic cheats. The "parliament of the genes" can often rapidly block driving genes from cheating during meiosis. But what if the genome parliament is reduced to only two members, or supergenes? Using a series of simple game-theoretic models inspired by the peculiar genetics of Oenothera sp., we illustrate that a two supergene genom...

A PCR strategy is described for global amplification of DNA from a single eukaryotic cell that enables the comprehensive analysis of the whole genome. By comparative genomic hybridization, not only gross DNA copy number variations, such as monosomic X and trisomic 21 in single male cells and cells from Down's syndrome patients, respectively, but multiple deletions and amplifications characteris...