TASK DEFINITION: Given a context passage, generate a question from the passage such that its answer is shortest continous span from the passage.
PROBLEM: Although peak finding in next-generation sequencing (NGS) datasets has been addressed extensively, there is no consensus on how to analyze and process biological replicates. Furthermore, most peak finders do not focus on accurate determination of enrichment site widths and are not widely applicable to different types of datasets. We developed JAMM (Joint Analysis of NGS replicates via Mixture Model clustering): a peak finder that can integrate information from biological replicates, determine enrichment site widths accurately and resolve neighboring narrow peaks. JAMM is a universal peak finder that is applicable to different types of datasets. We show that JAMM is among the best performing peak finders in terms of site detection accuracy and in terms of accurate determination of enrichment sites widths. In addition, JAMM's replicate integration improves peak spatial resolution, sorting and peak finding accuracy. JAMM is available for free and can run on Linux machines through the command line: [Link]

SOLUTION: Which peak calling algorithm employs mixture model clustering under the hood?

PROBLEM: Imatinib is one of the most recent medications used for the treatment of chronic myeloid leukemia (CML) and gastrointestinal stromal tumor (GIST). It is an orally administered protein-tyrosine kinase inhibitor, an enzyme which is produced by BCR-ABL fusion which results from translocation of 9:22 chromosome (Philadelphia chromosome). Imatinib blocks proliferation and induces apoptosis of BCR-ABL-expression in CML. Many side effects produced by imatinib have been documented but its induction of hepatotoxcity has been rarely reported. Only a few cases so far have been reported in the literature and almost all were in females. We describe another case of hepatotoxicity due to imatinib in a 17-year old female with clinical, laboratory and histopathological changes. The case described here suggests that imatinib may also induce immune hepatitis, in some patients.

SOLUTION: What tyrosine kinase, involved in a Philadelphia- chromosome positive chronic myelogenous leukemia, is the target of Imatinib (Gleevec)?

PROBLEM: During brain development, excess neurons that are formed die by apoptosis. cln3 was recently identified as the gene defective in juvenile Batten disease, an inherited neurodegenerative disease of childhood. In this disease, neurons die by apoptosis. Overexpression of this gene increases survival of human NT2 neuronal precursor cells. We, therefore, hypothesized that cln3 may be present in developing neurons and may play an important role in regulating the developmental process. NT2 neuronal cells were induced to develop into mature neurons. We evaluated cln3 expression by reverse transcription PCR and immunohistochemistry over a 7-wk period of differentiation. Also, cln3 expression was characterized in neonatal rat brain during the first week of life (P-1, P0, P4, and P8) and at P30. cln3 was differentially expressed during neuronal development into nondividing post-mitotic neurons. The greatest expression was noted during wk 6 and then dropped to predifferentiation levels during wk 7. cln3 expression was detected in all the rat brain developmental stages evaluated. The greatest expression was seen at P0 and was double compared with the other stages. We conclude that cln3 is present during critical periods of neuronal cell differentiation and brain development. As cln3 is antiapoptotic, we hypothesize that cln3 plays an important role in regulating brain development. These findings may have implications for identifying strategies aimed at neuroprotection and neuronal survival during development.

SOLUTION:
What is the effect of a defective CLN3 gene?