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Simulating Genome Evolution, Made Easier

Jonathan Eisen likes a paper on new software for simulating genome evolution. The paper, published in Genome Biology, comes out of Ian Holmes' lab at Berkeley. His team has written three new open-source programs that address inherent problems in current programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features), and SIMGENOME (for syntenic genome blocks). "Each offers algorithms for parameter measurement and reconstruction of ancestral sequence," says the abstract, and all three perform better than the leading neutral DNA simulator (DAWG) in benchmarks. You can download the programs at BioWiki.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.