The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
- E. Swart, J. Bracht, L. Landweber
- BiologyPLoS Biology
- 1 January 2013
With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantly…
Extrachromosomal circular DNA is common in yeast
- Henrik D. Møller, Lance L. Parsons, T. S. Jørgensen, D. Botstein, B. Regenberg
- BiologyProceedings of the National Academy of Sciences
- 2 June 2015
It is proposed that eccDNAs may be precursors to the copy number variation in eukaryotic genomes characteristic of both the evolutionary process and cancer progression, and that they might contribute substantially to genetic variation and evolution.
Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast
- G. I. Lang, Lance L. Parsons, A. Gammie
- BiologyG3: Genes, Genomes, Genetics
- 1 September 2013
A closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells is suggested.
C. elegans Positive Butanone Learning, Short-term, and Long-term Associative Memory Assays
- Amanda Kauffman, Lance L. Parsons, G. Stein, Airon A. Wills, Rachel Kaletsky, C. Murphy
- BiologyJournal of Visualized Experiments
- 11 March 2011
It is found that learning and short- and long-term memory can be distinguished, and that these processes share similar key molecules with higher organisms.
Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate
- S. Silverman, A. Petti, D. Botstein
- BiologyProceedings of the National Academy of Sciences
- 24 March 2010
The yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source.
Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster
- Bing He, A. Caudy, E. Wieschaus
- BiologyGenome Research
- 1 December 2012
This study developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions, and detects region-specific temporal patterns of transcription inheterochromatin during oogenesis and early embryonic development.
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.
- Henrik D. Møller, Rasmus K Bojsen, C. Tachibana, Lance L. Parsons, D. Botstein, B. Regenberg
- BiologyJournal of Visualized Experiments
- 4 April 2016
The Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae
- K. Matheson, Lance L. Parsons, A. Gammie
- Biology, EngineeringG3: Genes, Genomes, Genetics
- 5 June 2017
A high-quality, annotated genome sequence for W303 is provided for utilization in comparative analyses and genome-wide studies and variant mapping revealed more accurate identification of accumulated mutations in passaged mismatch repair-defective strains.
Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae
- R. McIsaac, S. Silverman, D. Botstein
- BiologyJournal of Visualized Experiments
- 14 June 2013
A protocol for using FISH to quantify the number of mRNAs in single yeast cells using multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes to detect nucleic acids in the native cellular environment is provided.
Bioconda: A sustainable and comprehensive software distribution for the life sciences
- Ryan K. Dale, B. Grüning, J. Köster
- Computer SciencebioRxiv
- 21 October 2017
The present Bioconda, a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda, improves analysis reproducibility by allowing users to define isolated environments with defined software versions.
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