@unpublished{7950, abstract = {The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.}, author = {Biniaz, Ahmad and Jain, Kshitij and Lubiw, Anna and Masárová, Zuzana and Miltzow, Tillmann and Mondal, Debajyoti and Naredla, Anurag Murty and Tkadlec, Josef and Turcotte, Alexi}, booktitle = {arXiv}, title = {{Token swapping on trees}}, year = {2019}, } @article{6418, abstract = {Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.}, author = {Huylmans, Ann K and Toups, Melissa A and Macon, Ariana and Gammerdinger, William J and Vicoso, Beatriz}, issn = {1759-6653}, journal = {Genome biology and evolution}, number = {4}, pages = {1033--1044}, publisher = {Oxford University Press}, title = {{Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome}}, doi = {10.1093/gbe/evz053}, volume = {11}, year = {2019}, } @misc{7016, abstract = {Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.}, author = {Tomanek, Isabella}, keywords = {Escherichia coli, gene amplification, galactose, DOG, experimental evolution, Illumina sequence data, FACS data, microfluidics data}, publisher = {Institute of Science and Technology Austria}, title = {{Data for the paper "Gene amplification as a form of population-level gene expression regulation"}}, doi = {10.15479/AT:ISTA:7016}, year = {2019}, } @misc{7154, author = {Guseinov, Ruslan}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary data for "Programming temporal morphing of self-actuated shells"}}, doi = {10.15479/AT:ISTA:7154}, year = {2019}, } @misc{6060, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Supplementary data for "Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). }}, doi = {10.15479/AT:ISTA:6060}, year = {2019}, }