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DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to(More)
TET2 is a close relative of TET1, an enzyme that converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. The gene encoding TET2 resides at chromosome 4q24, in a region showing recurrent microdeletions and copy-neutral loss of heterozygosity (CN-LOH) in patients with diverse myeloid malignancies. Somatic TET2 mutations are frequently(More)
TET family enzymes convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. Here, we show that Tet1 and Tet2 are Oct4-regulated enzymes that together sustain 5hmC in mouse embryonic stem cells (ESCs) and are induced concomitantly with 5hmC during reprogramming of fibroblasts to induced pluripotent stem cells. ESCs depleted of Tet1 by RNAi(More)
ii c 2000 Ali Jadbabaie All Rights Reserved iii To Nikroo iv Acknowledgements I would like to express my gratitude to the people who have made this thesis possible. First, I am obliged to my advisor, professor John Doyle, for taking the risk of accepting me as his student in the middle of the academic year. John has taught me to think independently, while(More)
Multiword expressions (MWEs) have been proved useful for many natural language processing tasks. However, how to use them to improve performance of statistical machine translation (SMT) is not well studied. This paper presents a simple yet effective strategy to extract domain bilingual multiword expressions. In addition, we implement three methods to(More)
A forward genetic screen of mice treated with the mutagen ENU identified a mutant mouse with chronic motor incoordination. This mutant, named Pingu (Pgu), carries a missense mutation, an I402T substitution in the S6 segment of the voltage-gated potassium channel Kcna2. The gene Kcna2 encodes the voltage-gated potassium channel α-subunit Kv1.2, which is(More)
This paper explores the feasibility of a graph-based approach to model student knowledge in the domain of programming. The key idea of this approach is that programming concepts are truly learned not in isolation, but rather in combination with other concepts. Following this idea, we represent a student model as a graph where links are gradually added when(More)
Integral feedback control is a basic engineering strategy for ensuring that the output of a system robustly tracks its desired value independent of noise or variations in system parameters. In biological systems, it is common for the response to an extracellular stimulus to return to its prestimulus value even in the continued presence of the signal-a(More)
BACKGROUND We recently showed that enzymes of the TET family convert 5-mC to 5-hydroxymethylcytosine (5-hmC) in DNA. 5-hmC is present at high levels in embryonic stem cells and Purkinje neurons. The methylation status of cytosines is typically assessed by reaction with sodium bisulfite followed by PCR amplification. Reaction with sodium bisulfite promotes(More)